Query         gi|254780289|ref|YP_003064702.1| RNA polymerase sigma factor RpoD [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 682
No_of_seqs    267 out of 2830
Neff          7.9 
Searched_HMMs 39220
Date          Sun May 29 16:46:22 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780289.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK05658 RNA polymerase sigma  100.0       0       0 1529.1  62.2  618   19-682     1-620 (620)
  2 PRK05901 RNA polymerase sigma  100.0       0       0  878.3  41.3  384   22-681    14-397 (398)
  3 PRK09210 RNA polymerase sigma  100.0       0       0  823.7  38.7  357   28-681    12-368 (368)
  4 TIGR02997 Sig70-cyanoRpoD RNA  100.0       0       0  821.6  31.0  246  415-668    90-336 (336)
  5 TIGR02393 RpoD_Cterm RNA polym 100.0       0       0  831.2  24.2  238  444-681     1-240 (240)
  6 PRK07598 RNA polymerase sigma  100.0       0       0  732.4  38.6  254  421-682   155-408 (410)
  7 PRK07406 RNA polymerase sigma  100.0       0       0  706.4  34.7  246  430-680   139-384 (385)
  8 PRK07921 RNA polymerase sigma  100.0       0       0  668.4  34.6  240  441-680    80-319 (320)
  9 COG0568 RpoD DNA-directed RNA  100.0       0       0  669.6  30.7  267  414-681    74-342 (342)
 10 PRK05949 RNA polymerase sigma  100.0       0       0  650.0  34.4  245  430-681    82-326 (327)
 11 PRK07405 RNA polymerase sigma  100.0       0       0  645.6  34.0  239  440-681    79-317 (318)
 12 PRK05657 RNA polymerase sigma  100.0       0       0  645.0  27.6  234  444-677    90-323 (328)
 13 TIGR02394 rpoS_proteo RNA poly 100.0       0       0  646.6  20.5  231  443-673    46-283 (292)
 14 PRK06596 RNA polymerase factor 100.0       0       0  510.8  27.9  226  443-673    48-282 (284)
 15 PRK07500 rpoH2 RNA polymerase  100.0       0       0  478.1  27.6  236  442-680    39-288 (289)
 16 PRK07122 RNA polymerase sigma  100.0       0       0  478.3  24.9  236  425-669    21-260 (263)
 17 PRK08583 RNA polymerase sigma  100.0       0       0  466.2  25.7  248  414-673     2-255 (257)
 18 PRK08215 sporulation sigma fac 100.0       0       0  459.2  26.9  240  417-669    14-255 (257)
 19 PRK07408 RNA polymerase sigma  100.0       0       0  455.4  25.1  234  428-670    12-250 (256)
 20 PRK05572 sporulation sigma fac 100.0       0       0  448.8  25.0  235  421-669    11-247 (251)
 21 PRK05911 RNA polymerase sigma  100.0       0       0  444.0  26.5  242  425-680     7-257 (257)
 22 PRK06288 RNA polymerase sigma  100.0       0       0  438.7  26.4  239  421-669     7-254 (261)
 23 PRK07670 RNA polymerase sigma  100.0       0       0  427.9  24.1  222  441-669    16-243 (250)
 24 PRK06986 fliA flagellar biosyn 100.0       0       0  417.4  25.5  221  439-669     4-229 (234)
 25 TIGR02392 rpoH_proteo alternat 100.0       0       0  419.0  21.2  252  414-669     8-275 (279)
 26 PRK05803 sporulation sigma fac 100.0       0       0  406.9  21.8  209  405-669    13-224 (228)
 27 PRK08301 sporulation sigma fac 100.0       0       0  403.0  20.5  192  422-669    39-233 (239)
 28 PRK12427 flagellar biosynthesi 100.0 1.4E-45       0  378.8  22.7  221  432-669     2-227 (229)
 29 TIGR02980 SigBFG RNA polymeras 100.0       0       0  387.1  13.1  219  442-669     2-226 (229)
 30 TIGR02885 spore_sigF RNA polym 100.0 2.4E-39   6E-44  329.6  12.7  220  440-669     8-229 (231)
 31 COG1191 FliA DNA-directed RNA  100.0 2.9E-36 7.4E-41  305.2  24.3  235  422-670     6-243 (247)
 32 TIGR02479 FliA_WhiG RNA polyme 100.0 4.5E-36 1.2E-40  303.7  18.1  215  448-669     1-224 (227)
 33 TIGR02850 spore_sigG RNA polym 100.0   4E-28   1E-32  241.0  21.5  235  422-669    16-252 (254)
 34 TIGR02846 spore_sigmaK RNA pol 100.0 2.1E-28 5.4E-33  243.1  12.1  192  422-669    30-225 (228)
 35 pfam04546 Sigma70_ner Sigma-70  99.9 2.4E-24 6.2E-29  211.1  20.2  209  160-417     1-210 (210)
 36 TIGR02941 Sigma_B RNA polymera  99.9 1.5E-25 3.7E-30  220.7  14.0  240  422-671    10-254 (256)
 37 TIGR02835 spore_sigmaE RNA pol  99.8 3.4E-20 8.5E-25  178.4  13.9  193  422-670    34-229 (234)
 38 PRK08295 RNA polymerase factor  99.8 6.7E-19 1.7E-23  168.2  19.1  194  422-670     6-201 (209)
 39 TIGR02937 sigma70-ECF RNA poly  99.8 1.9E-17 4.9E-22  156.7  14.8  159  444-669     2-160 (162)
 40 PRK06759 RNA polymerase factor  99.7 1.8E-15 4.6E-20  141.1  15.7  149  444-670     5-153 (154)
 41 pfam03979 Sigma70_r1_1 Sigma-7  99.5 3.4E-14 8.6E-19  131.1   7.2   63   24-86      2-64  (79)
 42 pfam04539 Sigma70_r3 Sigma-70   99.5 1.3E-13 3.3E-18  126.4   6.4   77  527-603     1-77  (78)
 43 PRK09652 RNA polymerase sigma   99.2 3.5E-09 8.8E-14   91.5  17.0  184  428-681     7-190 (192)
 44 PRK09641 RNA polymerase sigma   99.2 7.5E-09 1.9E-13   88.8  17.4  180  425-669     3-182 (187)
 45 PRK12519 RNA polymerase sigma   99.2 9.3E-09 2.4E-13   88.1  17.0  184  422-681    11-194 (194)
 46 PRK11923 algU RNA polymerase s  99.1 3.5E-08 8.9E-13   83.6  17.0  188  423-681     3-191 (193)
 47 PRK13919 putative RNA polymera  99.1 1.7E-08 4.3E-13   86.0  15.2  172  428-669    11-182 (187)
 48 PRK09648 RNA polymerase sigma   99.0 7.6E-08 1.9E-12   80.9  17.7  175  423-669     5-183 (187)
 49 PRK12513 RNA polymerase sigma   99.0 9.4E-08 2.4E-12   80.2  18.0  172  428-669    14-185 (194)
 50 PRK11922 RNA polymerase sigma   99.0   1E-07 2.7E-12   79.8  17.9  186  420-669    10-195 (231)
 51 PRK09646 RNA polymerase sigma   99.0 3.8E-08 9.6E-13   83.3  15.6  177  422-669    12-188 (194)
 52 PRK12543 RNA polymerase sigma   99.0 1.3E-07 3.2E-12   79.1  18.0  171  426-669     5-175 (190)
 53 PRK06811 RNA polymerase factor  99.0 1.3E-07 3.4E-12   79.0  17.5  168  428-669     4-174 (185)
 54 PRK12534 RNA polymerase sigma   99.0   2E-07 5.1E-12   77.5  17.3  177  421-669     6-183 (187)
 55 PRK05602 RNA polymerase sigma   98.9 2.2E-07 5.7E-12   77.2  16.9  168  427-669     7-174 (186)
 56 PRK11924 RNA polymerase sigma   98.9 2.8E-07 7.1E-12   76.5  16.3  170  429-669     2-171 (180)
 57 PRK12522 RNA polymerase sigma   98.9 3.3E-07 8.3E-12   75.9  16.4  172  441-681     1-172 (173)
 58 PRK12514 RNA polymerase sigma   98.9 3.6E-07 9.2E-12   75.5  16.2  174  423-669     2-175 (179)
 59 PRK12531 RNA polymerase sigma   98.9 5.1E-07 1.3E-11   74.4  16.9  178  423-669    10-187 (194)
 60 PRK12515 RNA polymerase sigma   98.9 4.7E-07 1.2E-11   74.7  16.6  169  427-669     9-177 (189)
 61 PRK12520 RNA polymerase sigma   98.9 2.2E-07 5.6E-12   77.3  14.7  171  448-669     7-177 (191)
 62 PRK12524 RNA polymerase sigma   98.9 8.4E-07 2.2E-11   72.6  17.2  169  428-669    14-182 (196)
 63 PRK09640 RNA polymerase sigma   98.8 7.2E-07 1.8E-11   73.2  16.2  177  428-681    11-187 (188)
 64 PRK09647 RNA polymerase sigma   98.8 6.4E-07 1.6E-11   73.6  15.7  171  429-669    33-203 (222)
 65 PRK12544 RNA polymerase sigma   98.8 8.4E-07 2.1E-11   72.7  16.2  170  447-669    23-195 (207)
 66 PRK12537 RNA polymerase sigma   98.8 5.9E-07 1.5E-11   73.9  15.3  176  423-669     6-181 (184)
 67 TIGR02394 rpoS_proteo RNA poly  98.8 3.6E-08 9.2E-13   83.5   8.8  124  115-238     9-144 (292)
 68 PRK09643 RNA polymerase sigma   98.8 9.1E-07 2.3E-11   72.4  15.9  170  427-677    14-183 (197)
 69 PRK12538 RNA polymerase sigma   98.8 2.4E-06 6.1E-11   69.1  17.7  171  425-670    48-218 (233)
 70 PRK09638 RNA polymerase sigma   98.8   1E-06 2.7E-11   71.9  15.7  168  427-669     6-173 (177)
 71 PRK12512 RNA polymerase sigma   98.8 6.2E-07 1.6E-11   73.7  14.4  169  423-669     5-177 (184)
 72 TIGR02859 spore_sigH RNA polym  98.8   2E-07 5.1E-12   77.6  11.9  182  428-668     7-190 (198)
 73 PRK12533 RNA polymerase sigma   98.8 1.7E-06 4.4E-11   70.2  16.4  164  442-669    20-183 (217)
 74 pfam00140 Sigma70_r1_2 Sigma-7  98.8 6.8E-09 1.7E-13   89.2   4.0   35  118-152     1-35  (37)
 75 PRK07500 rpoH2 RNA polymerase   98.7 2.6E-06 6.6E-11   68.8  16.4   84  117-200     4-97  (289)
 76 PRK12526 RNA polymerase sigma   98.7   2E-06   5E-11   69.8  14.9  174  428-669    26-199 (206)
 77 PRK12536 RNA polymerase sigma   98.7 2.7E-06 6.8E-11   68.7  15.5  170  424-669     2-172 (178)
 78 TIGR02984 Sig-70_plancto1 RNA   98.7 4.6E-07 1.2E-11   74.7  11.4  167  450-669    17-187 (190)
 79 PRK09415 RNA polymerase factor  98.7 4.7E-06 1.2E-10   66.7  16.4  159  442-669    15-173 (177)
 80 PRK12542 RNA polymerase sigma   98.7 3.4E-06 8.6E-11   67.9  15.5  162  442-670     8-169 (185)
 81 PRK09644 RNA polymerase sigma   98.7 2.7E-06 6.8E-11   68.7  14.8  152  446-670     4-155 (165)
 82 COG1595 RpoE DNA-directed RNA   98.7 5.3E-06 1.3E-10   66.4  16.3  164  439-670    11-174 (182)
 83 PRK12532 RNA polymerase sigma   98.7 4.5E-06 1.1E-10   66.9  15.9  172  447-669    10-182 (195)
 84 PRK12518 RNA polymerase sigma   98.6 3.8E-06 9.6E-11   67.5  14.5  165  431-669     2-166 (175)
 85 PRK12545 RNA polymerase sigma   98.6 7.7E-06   2E-10   65.1  16.0  176  447-671    12-187 (201)
 86 pfam07638 Sigma70_ECF ECF sigm  98.6 3.8E-06 9.7E-11   67.5  14.3  175  425-669     2-181 (185)
 87 PRK12539 RNA polymerase sigma   98.6 1.3E-05 3.3E-10   63.3  16.2  171  422-669     3-177 (184)
 88 PRK08311 putative RNA polymera  98.6 3.9E-07 9.8E-12   75.3   8.0   93  427-522     5-99  (237)
 89 pfam04542 Sigma70_r2 Sigma-70   98.5 2.1E-07 5.4E-12   77.4   6.4   71  448-518     1-71  (71)
 90 PRK09639 RNA polymerase sigma   98.5 1.4E-05 3.7E-10   62.9  15.2  157  441-669     1-157 (166)
 91 PRK09642 RNA polymerase sigma   98.5 1.3E-05 3.3E-10   63.3  15.0  148  453-669     5-152 (160)
 92 PRK12517 RNA polymerase sigma   98.5 2.7E-05 6.8E-10   60.8  16.5  155  440-669    20-174 (188)
 93 PRK12530 RNA polymerase sigma   98.5 1.9E-05 4.9E-10   61.9  15.7  160  455-669    21-182 (191)
 94 PRK09651 RNA polymerase sigma   98.5 2.2E-05 5.7E-10   61.4  15.0  156  442-668     9-164 (172)
 95 PRK09637 RNA polymerase sigma   98.5 1.6E-05 4.1E-10   62.6  14.2  149  446-669     4-152 (181)
 96 PRK09047 RNA polymerase factor  98.5 9.9E-06 2.5E-10   64.2  13.1   74  592-669    79-152 (161)
 97 PRK12541 RNA polymerase sigma   98.4 2.6E-05 6.7E-10   60.9  14.9  155  442-669     4-158 (161)
 98 PRK07037 extracytoplasmic-func  98.4 2.6E-05 6.6E-10   60.9  14.8  159  442-669    11-169 (183)
 99 pfam04545 Sigma70_r4 Sigma-70,  98.4 4.5E-07 1.2E-11   74.8   5.7   50  616-669     1-50  (50)
100 TIGR02948 SigW_bacill RNA poly  98.4 3.2E-06 8.3E-11   68.0   9.2  161  427-652     5-165 (187)
101 PRK12535 RNA polymerase sigma   98.4  0.0001 2.6E-09   56.2  16.6  170  423-669     9-178 (195)
102 PRK09645 RNA polymerase sigma   98.4 4.8E-05 1.2E-09   58.8  14.7  157  442-669     6-162 (171)
103 PRK12546 RNA polymerase sigma   98.3 5.8E-05 1.5E-09   58.1  14.7  153  442-669     7-159 (188)
104 PRK12547 RNA polymerase sigma   98.3 0.00011 2.9E-09   55.8  15.9  155  441-669     4-158 (164)
105 PRK12527 RNA polymerase sigma   98.3  0.0001 2.7E-09   56.1  14.7  154  454-682     6-159 (159)
106 PRK09649 RNA polymerase sigma   98.3 0.00011 2.9E-09   55.8  14.7  171  422-669     6-176 (185)
107 PRK12516 RNA polymerase sigma   98.3 0.00013 3.2E-09   55.5  14.8  155  441-669    11-165 (190)
108 PRK08241 RNA polymerase factor  98.2  0.0002   5E-09   53.9  14.6  186  429-669    11-202 (341)
109 PRK12523 RNA polymerase sigma   98.2 0.00017 4.4E-09   54.4  14.2  155  444-669    11-165 (172)
110 TIGR02952 Sig70_famx2 RNA poly  98.2 8.4E-05 2.1E-09   56.9  12.5  131  468-669    36-169 (171)
111 PRK12540 RNA polymerase sigma   98.1 0.00039 9.9E-09   51.6  15.3  155  443-671     5-159 (181)
112 cd06171 Sigma70_r4 Sigma70, re  98.1 1.5E-05 3.8E-10   62.8   6.7   55  610-668     1-55  (55)
113 PRK12511 RNA polymerase sigma   98.0 0.00036 9.2E-09   51.9  13.1  150  446-669     8-157 (182)
114 PRK12525 RNA polymerase sigma   97.9 0.00083 2.1E-08   49.0  14.0  152  446-668    12-163 (168)
115 PRK09636 RNA polymerase sigma   97.9  0.0011 2.7E-08   48.2  14.5  153  448-670     5-158 (289)
116 PRK05803 sporulation sigma fac  97.9 0.00012   3E-09   55.7   8.4   67  121-187    17-92  (228)
117 PRK12529 RNA polymerase sigma   97.8  0.0046 1.2E-07   43.2  15.4  155  444-666    14-170 (178)
118 PRK12528 RNA polymerase sigma   97.7  0.0049 1.2E-07   42.9  14.2  154  444-668    11-164 (167)
119 TIGR02985 Sig70_bacteroi1 RNA   97.6  0.0043 1.1E-07   43.4  13.6  164  444-669     2-165 (167)
120 PRK09635 sigI RNA polymerase s  97.5   0.014 3.6E-07   39.3  16.5  155  447-669     9-164 (290)
121 PRK06930 positive control sigm  97.4  0.0006 1.5E-08   50.1   7.1   61  605-669   100-160 (170)
122 TIGR03001 Sig-70_gmx1 RNA poly  97.4  0.0038 9.7E-08   43.8  11.0  143  498-656    37-199 (249)
123 PRK08301 sporulation sigma fac  97.4  0.0016   4E-08   46.8   8.8   56  132-187    37-101 (239)
124 COG0568 RpoD DNA-directed RNA   97.3  0.0031 7.9E-08   44.5   9.1   26  543-568   296-321 (342)
125 PRK05658 RNA polymerase sigma   97.1  0.0011 2.7E-08   48.1   5.3  229  314-574   344-609 (620)
126 pfam08281 Sigma70_r4_2 Sigma-7  96.8  0.0051 1.3E-07   42.8   6.6   53  611-667     2-54  (54)
127 TIGR02393 RpoD_Cterm RNA polym  96.7  0.0013 3.2E-08   47.6   2.8  190  161-358    15-224 (240)
128 TIGR02957 SigX4 RNA polymerase  96.6   0.014 3.6E-07   39.3   7.5   71  597-671    86-157 (287)
129 TIGR02983 SigE-fam_strep RNA p  96.5  0.0015 3.9E-08   46.9   2.3  150  447-670    10-160 (165)
130 TIGR02233 Myxo_sigma_rel Myxoc  96.5  0.0054 1.4E-07   42.6   5.0   59  603-665     8-70  (106)
131 PRK08215 sporulation sigma fac  96.3  0.0055 1.4E-07   42.5   4.3   62  128-189    13-83  (257)
132 pfam00196 GerE Bacterial regul  95.9   0.028 7.1E-07   37.0   6.3   56  617-677     1-56  (58)
133 PRK10360 DNA-binding transcrip  95.8   0.045 1.1E-06   35.4   7.0   60  618-682   136-195 (196)
134 PRK08583 RNA polymerase sigma   95.8  0.0099 2.5E-07   40.5   3.6   62  125-186     1-72  (257)
135 PRK03975 tfx putative transcri  95.8   0.029 7.5E-07   36.8   5.8   46  619-669     4-49  (139)
136 TIGR02392 rpoH_proteo alternat  95.7    0.11 2.9E-06   32.2   8.5   68  121-188     3-80  (279)
137 PRK00118 putative DNA-binding   95.6    0.04   1E-06   35.7   5.9   47  619-669    17-63  (105)
138 PRK10188 DNA-binding transcrip  95.5    0.06 1.5E-06   34.3   6.5   52  619-675   179-230 (240)
139 smart00421 HTH_LUXR helix_turn  95.5   0.055 1.4E-06   34.7   6.2   56  617-677     1-56  (58)
140 PRK09958 DNA-binding transcrip  95.4   0.065 1.7E-06   34.1   6.6   56  617-677   141-196 (204)
141 pfam04297 UPF0122 Putative hel  95.2   0.063 1.6E-06   34.2   5.9   47  619-669    17-63  (101)
142 PRK10403 transcriptional regul  95.1     0.1 2.6E-06   32.5   6.8   58  618-680   152-209 (215)
143 PRK09390 fixJ response regulat  95.0    0.19 4.7E-06   30.5   7.8   59  614-677   136-194 (202)
144 PRK09483 response regulator; P  95.0    0.11 2.8E-06   32.3   6.6   55  618-677   147-201 (216)
145 PRK10840 transcriptional regul  94.9    0.12   3E-06   32.1   6.6   54  619-677   150-203 (216)
146 PRK05572 sporulation sigma fac  94.9   0.031 7.9E-07   36.6   3.6   59  130-188     8-75  (251)
147 COG3413 Predicted DNA binding   94.8    0.11 2.9E-06   32.1   6.3   51  618-668   154-207 (215)
148 PRK05949 RNA polymerase sigma   94.7    0.41   1E-05   27.8   9.1   39  112-150    11-49  (327)
149 cd06170 LuxR_C_like C-terminal  94.6    0.15 3.9E-06   31.1   6.6   53  620-677     1-53  (57)
150 PRK07406 RNA polymerase sigma   94.5    0.44 1.1E-05   27.5   9.3   38  113-150    69-106 (385)
151 PRK11475 DNA-binding transcrip  94.3    0.19 4.9E-06   30.3   6.5   52  619-675   134-185 (205)
152 TIGR03020 EpsA transcriptional  94.2    0.51 1.3E-05   27.0  11.2   85  587-676   137-242 (247)
153 COG2771 CsgD DNA-binding HTH d  94.2    0.25 6.3E-06   29.5   6.9   58  618-680     3-60  (65)
154 PRK10651 transcriptional regul  94.2     0.2   5E-06   30.3   6.3   54  618-676   154-207 (216)
155 TIGR02939 RpoE_Sigma70 RNA pol  94.2    0.52 1.3E-05   27.0  12.5  159  428-651     9-168 (192)
156 PRK13870 transcriptional regul  94.1    0.53 1.4E-05   26.9  11.4   51  620-675   174-224 (234)
157 PRK09935 transcriptional regul  94.0    0.24 6.2E-06   29.5   6.6   54  619-677   149-202 (210)
158 PRK07405 RNA polymerase sigma   94.0    0.47 1.2E-05   27.3   7.9   37  115-151     5-41  (318)
159 TIGR03541 reg_near_HchA LuxR f  93.9    0.58 1.5E-05   26.6  11.5   53  618-675   170-222 (232)
160 pfam04967 HTH_10 HTH DNA bindi  93.7    0.28 7.2E-06   29.1   6.4   48  620-667     1-51  (53)
161 COG2197 CitB Response regulato  93.0    0.46 1.2E-05   27.3   6.6   56  618-678   147-202 (211)
162 COG4566 TtrR Response regulato  92.9     0.8   2E-05   25.5   8.6   68  608-680   131-198 (202)
163 TIGR02997 Sig70-cyanoRpoD RNA   92.8     0.6 1.5E-05   26.4   7.0   29  119-147     1-29  (336)
164 TIGR00721 tfx DNA-binding prot  92.7     0.2 5.1E-06   30.2   4.4   45  620-669     7-51  (142)
165 TIGR02989 Sig-70_gvs1 RNA poly  92.4    0.92 2.4E-05   25.0  16.0  135  467-667    25-159 (163)
166 TIGR02950 SigM_subfam RNA poly  92.0    0.62 1.6E-05   26.3   6.2   77  587-667    81-157 (162)
167 TIGR02895 spore_sigI RNA polym  91.2    0.69 1.7E-05   26.0   5.7   77  442-518     8-87  (225)
168 TIGR02960 SigX5 RNA polymerase  90.6     1.4 3.5E-05   23.6   8.2  155  465-663    27-183 (329)
169 TIGR02954 Sig70_famx3 RNA poly  90.4     1.4 3.6E-05   23.5  13.5  162  431-669     7-168 (173)
170 PRK10100 DNA-binding transcrip  90.1     1.5 3.7E-05   23.4   6.6   54  619-677   155-208 (216)
171 TIGR02999 Sig-70_X6 RNA polyme  88.7     1.9 4.8E-05   22.6  11.7  161  426-657     3-179 (194)
172 pfam01726 LexA_DNA_bind LexA D  88.0     1.7 4.4E-05   22.8   5.8   37  531-567    10-47  (65)
173 PRK12423 LexA repressor; Provi  87.6       1 2.6E-05   24.7   4.3   41  527-567     6-47  (202)
174 PRK04841 transcriptional regul  87.5     2.2 5.5E-05   22.0   6.4   54  619-677   838-891 (903)
175 COG1356 tfx Transcriptional re  86.5    0.49 1.3E-05   27.1   2.3   12  572-583    66-77  (143)
176 TIGR03209 P21_Cbot clostridium  86.3    0.33 8.4E-06   28.5   1.3   41  612-656   100-140 (142)
177 PRK00215 LexA repressor; Valid  85.7     2.4   6E-05   21.8   5.4   41  528-568     5-46  (204)
178 COG2739 Uncharacterized protei  84.2     2.6 6.6E-05   21.4   5.1   36  620-659    18-53  (105)
179 PRK10869 recombination and rep  84.0     3.1 7.9E-05   20.8  17.0  109  313-454   276-384 (553)
180 pfam02650 HTH_WhiA Sporulation  82.2     3.1 7.9E-05   20.8   4.8   42  617-661   141-188 (191)
181 COG1809 (2R)-phospho-3-sulfola  82.1     3.1 7.9E-05   20.8   4.8   24   56-79     55-78  (258)
182 PRK00286 xseA exodeoxyribonucl  81.8     3.7 9.5E-05   20.2   6.7   13   61-73    147-159 (443)
183 PRK09954 hypothetical protein;  80.4     4.1 0.00011   19.8   5.3   43   30-75      4-46  (362)
184 PRK13239 alkylmercury lyase; P  79.8     4.1 0.00011   19.8   4.8   28  543-570    33-60  (206)
185 COG1570 XseA Exonuclease VII,   79.6     4.3 0.00011   19.7   5.6   46  558-605   212-257 (440)
186 PRK09191 two-component respons  79.5     4.4 0.00011   19.6   5.0  124  448-574     6-132 (261)
187 pfam07374 DUF1492 Protein of u  77.7     4.9 0.00013   19.2   6.3   55  609-667    44-99  (100)
188 pfam04963 Sigma54_CBD Sigma-54  76.8     5.2 0.00013   19.1   7.8  129  507-668    16-148 (195)
189 PRK13558 bacterio-opsin activa  76.3     5.3 0.00014   19.0   6.9   55  613-667   610-667 (674)
190 COG4367 Uncharacterized protei  74.4     5.9 0.00015   18.6   5.3   39  535-573    10-50  (97)
191 TIGR02612 mob_myst_A mobile my  73.2     2.7   7E-05   21.3   2.4   41  618-662    21-61  (150)
192 PRK09247 ATP-dependent DNA lig  73.1     3.8 9.7E-05   20.1   3.1   27  623-649   507-533 (537)
193 COG1802 GntR Transcriptional r  72.3     5.2 0.00013   19.1   3.6   38  424-464   185-222 (230)
194 pfam05263 DUF722 Protein of un  71.5     6.8 0.00017   18.1   6.1   51  608-660    70-120 (130)
195 KOG0996 consensus               71.1     6.9 0.00018   18.1  16.5   54   26-79    139-224 (1293)
196 PRK13869 plasmid-partitioning   71.0       7 0.00018   18.1   4.2   13  470-482   155-167 (405)
197 COG1481 Uncharacterized protei  70.8       7 0.00018   18.0   5.3   45  617-664   251-301 (308)
198 pfam02601 Exonuc_VII_L Exonucl  70.1     7.3 0.00018   17.9   7.1   45   29-73     26-70  (295)
199 cd04981 IgV_H Immunoglobulin (  68.9    0.31 7.9E-06   28.7  -3.2   21  492-512    22-42  (117)
200 TIGR02168 SMC_prok_B chromosom  68.6     7.8  0.0002   17.7  18.3   28  427-454   468-495 (1191)
201 cd00228 eu-GS Eukaryotic Gluta  67.0     5.4 0.00014   18.9   2.8  128  484-632   257-398 (471)
202 PRK11414 putative DNA-binding   66.6     7.9  0.0002   17.6   3.6   16  446-461   129-144 (221)
203 cd00569 HTH_Hin_like Helix-tur  65.2     8.9 0.00023   17.2   4.3   35  619-657     5-39  (42)
204 pfam06971 Put_DNA-bind_N Putat  64.4     9.2 0.00023   17.1   4.2   47  520-566     1-47  (49)
205 PRK06266 transcription initiat  63.6     7.7  0.0002   17.7   3.0   24  545-568    35-58  (178)
206 PRK05932 RNA polymerase factor  63.6     9.5 0.00024   17.0   9.3   68  545-619   348-415 (461)
207 TIGR01637 phage_arpU phage tra  63.5     9.5 0.00024   17.0   7.5   56  611-668    75-130 (139)
208 pfam02001 DUF134 Protein of un  61.7      10 0.00026   16.7   5.6   46  619-668    36-81  (100)
209 pfam04748 Polysacc_deac_2 Dive  61.5      10 0.00026   16.7   3.4  141   17-180    62-204 (213)
210 TIGR02395 rpoN_sigma RNA polym  61.0      10 0.00027   16.7   3.4  267  315-618   134-431 (477)
211 COG2856 Predicted Zn peptidase  59.5      10 0.00026   16.7   3.1   16  359-374   112-127 (213)
212 TIGR02147 Fsuc_second hypothet  57.5      12  0.0003   16.2   6.2  118  536-662   132-260 (281)
213 COG3824 Predicted Zn-dependent  57.3     4.6 0.00012   19.5   1.0   27  637-663   108-135 (136)
214 KOG2727 consensus               57.0      12 0.00031   16.2   8.6   54  502-567   922-975 (1244)
215 pfam10078 DUF2316 Uncharacteri  57.0      12 0.00031   16.2   4.6   37  535-571    10-48  (89)
216 pfam12324 HTH_15 Helix-turn-he  56.8      12 0.00031   16.1   6.8   36  536-571    26-63  (77)
217 PRK09943 DNA-binding transcrip  56.7      12 0.00031   16.1   3.9   22  451-475    47-68  (185)
218 COG2186 FadR Transcriptional r  55.9      11 0.00029   16.3   2.8   19  446-464   145-163 (241)
219 pfam01698 FLO_LFY Floricaula /  55.8      12 0.00031   16.1   2.9   43   29-73     44-94  (382)
220 COG1476 Predicted transcriptio  55.4      13 0.00033   16.0   3.9   21  641-661    16-36  (68)
221 KOG2773 consensus               55.2      13 0.00033   16.0  12.5  171  345-551   193-367 (483)
222 pfam08279 HTH_11 HTH domain. T  53.9      13 0.00034   15.8   4.0   22  547-568    16-37  (55)
223 PRK11564 stationary phase indu  53.6      14 0.00034   15.8   4.6   48   32-79     19-68  (426)
224 TIGR01764 excise DNA binding d  53.3      14 0.00035   15.7   3.0   25  547-571     2-26  (49)
225 PRK07023 short chain dehydroge  53.3      14 0.00035   15.7   6.6   89  454-554   133-221 (243)
226 PRK04424 fatty acid biosynthes  52.9      14 0.00035   15.7   4.8   19  544-562    19-37  (185)
227 pfam02885 Glycos_trans_3N Glyc  52.6      14 0.00036   15.6   3.7   47   31-77      2-51  (66)
228 pfam06239 ECSIT Evolutionarily  52.0      14 0.00036   15.6   3.8   27  408-434   122-148 (229)
229 TIGR02607 antidote_HigA addict  52.0      13 0.00033   15.9   2.6   40  537-579    13-52  (81)
230 PRK02842 light-independent pro  51.7      11 0.00029   16.4   2.2   45  622-666   232-277 (425)
231 COG1510 Predicted transcriptio  51.6      12  0.0003   16.2   2.3   26  544-569    39-64  (177)
232 PRK01381 Trp operon repressor;  50.5      15 0.00038   15.4   4.3   42  612-653    24-69  (99)
233 PRK01388 arginine deiminase; P  50.3      12  0.0003   16.3   2.1   42   38-79     24-69  (410)
234 TIGR02865 spore_II_E stage II   50.0      15 0.00039   15.4   6.9   64  572-635   590-660 (794)
235 pfam10668 Phage_terminase Phag  50.0      15 0.00039   15.4   3.4   32  535-566    11-42  (60)
236 pfam11913 DUF3431 Protein of u  49.4     2.8   7E-05   21.2  -1.2   24  646-669   158-181 (222)
237 KOG3099 consensus               49.3      16  0.0004   15.3   3.0   11  375-385   109-119 (340)
238 pfam12128 DUF3584 Protein of u  48.5      16 0.00041   15.2  23.9   16  478-493   907-922 (1192)
239 pfam02682 AHS1 Allophanate hyd  48.3      16 0.00041   15.2   3.2   47  513-575    82-128 (202)
240 TIGR03338 phnR_burk phosphonat  48.0      16 0.00042   15.1   2.9   46   28-76     17-64  (212)
241 TIGR01026 fliI_yscN ATPase Fli  47.5      17 0.00042   15.1   3.9   41  506-549   253-293 (455)
242 TIGR02546 III_secr_ATP type II  47.5      17 0.00042   15.1   3.5   43  506-551   232-274 (430)
243 PRK05472 redox-sensing transcr  47.0      17 0.00043   15.0   5.4   24  473-496    89-112 (211)
244 pfam04760 IF2_N Translation in  46.2      17 0.00044   14.9   2.8   34  547-580     4-37  (52)
245 COG2316 Predicted hydrolase (H  45.0      14 0.00035   15.7   1.8   19  645-663   171-189 (212)
246 PRK04217 hypothetical protein;  44.6      18 0.00046   14.8   5.6   45  620-668    43-87  (110)
247 COG1342 Predicted DNA-binding   44.3      18 0.00047   14.7   5.2   45  619-667    33-77  (99)
248 PRK06704 RNA polymerase factor  44.2      18 0.00047   14.7   7.8   40  468-507    42-81  (228)
249 PRK09863 putative frv operon r  44.2      18 0.00047   14.7   4.0   49   28-79      3-54  (585)
250 TIGR01632 L11_bact ribosomal p  44.1      18 0.00047   14.7   2.6   38   42-79     99-144 (144)
251 pfam02638 DUF187 Uncharacteriz  44.0      13 0.00034   15.9   1.6   20   58-77     56-75  (394)
252 COG1654 BirA Biotin operon rep  44.0      19 0.00047   14.7   4.4   33  539-571    12-44  (79)
253 pfam01371 Trp_repressor Trp re  43.9      19 0.00047   14.7   3.4   44  613-656    19-66  (88)
254 pfam04931 DNA_pol_phi DNA poly  43.8      19 0.00048   14.7  11.5   16  604-619   699-714 (784)
255 TIGR00169 leuB 3-isopropylmala  43.7     8.2 0.00021   17.5   0.5   82  506-599   171-262 (370)
256 COG2188 PhnF Transcriptional r  43.4      19 0.00048   14.6   3.4   26  544-569    29-54  (236)
257 pfam11268 DUF3071 Protein of u  42.9      19 0.00049   14.6   3.4   67  492-566    22-88  (169)
258 COG2390 DeoR Transcriptional r  42.7      19 0.00049   14.6   4.8   25  636-660   255-279 (321)
259 pfam09339 HTH_IclR IclR helix-  42.6      19 0.00049   14.5   4.0   30  540-569    12-41  (52)
260 PRK04483 threonyl-tRNA synthet  42.3      11 0.00027   16.6   0.9   36  127-172    53-88  (634)
261 TIGR00373 TIGR00373 conserved   42.0      20  0.0005   14.5   2.6   46  546-591    30-75  (168)
262 TIGR02169 SMC_prok_A chromosom  41.7      20 0.00051   14.4  21.7   51  133-183   239-292 (1202)
263 PRK12444 threonyl-tRNA synthet  41.7      12  0.0003   16.3   1.0   22  493-514   265-286 (639)
264 TIGR03070 couple_hipB transcri  41.1      20 0.00052   14.4   3.4   23  640-662    16-38  (58)
265 TIGR02959 SigZ RNA polymerase   41.0      20 0.00052   14.4   3.9   43  606-652    87-129 (170)
266 PRK09392 ftrB transcriptional   40.5      21 0.00053   14.3   3.4   18  551-568   178-195 (236)
267 cd02758 MopB_Tetrathionate-Ra   40.2      21 0.00053   14.3   3.6   22  414-435   342-363 (735)
268 pfam11633 Nsp3 Replicase polyp  40.1      17 0.00045   14.9   1.7   39   16-54     10-53  (142)
269 COG0856 Orotate phosphoribosyl  40.0      21 0.00054   14.3   3.7   30  453-500    87-116 (203)
270 PRK04140 hypothetical protein;  40.0      21 0.00054   14.2   4.1   15   63-77      6-20  (319)
271 pfam09286 Pro-kuma_activ Pro-k  39.9      21 0.00054   14.2   4.3   37   41-80     45-81  (141)
272 smart00531 TFIIE Transcription  39.6      21 0.00054   14.2   2.9  100  546-652    15-121 (147)
273 COG2049 DUR1 Allophanate hydro  39.6      21 0.00054   14.2   2.4   42  517-574    84-125 (223)
274 TIGR01279 DPOR_bchN light-inde  39.4       6 0.00015   18.6  -0.7   58  612-669   242-305 (458)
275 TIGR00223 panD aspartate 1-dec  39.1     5.8 0.00015   18.7  -0.9   53  447-507    14-67  (127)
276 PRK10286 O-6-alkylguanine-DNA:  38.6      22 0.00056   14.1   6.2   78  502-581    60-140 (171)
277 cd06569 GH20_Sm-chitobiase-lik  38.6      22 0.00056   14.1   3.7   50   31-81     56-117 (445)
278 pfam01381 HTH_3 Helix-turn-hel  38.6      22 0.00056   14.1   2.8   23  640-662    10-32  (55)
279 pfam05049 IIGP Interferon-indu  38.5      22 0.00056   14.1   4.0   36  113-148    95-139 (375)
280 CHL00059 atpA ATP synthase CF1  38.1      22 0.00057   14.0   3.9   49  499-550   237-285 (501)
281 cd00092 HTH_CRP helix_turn_hel  37.8      23 0.00058   14.0   3.5   22  547-568    26-47  (67)
282 smart00787 Spc7 Spc7 kinetocho  37.7      23 0.00058   14.0  20.7   36  121-156    51-89  (312)
283 PRK11637 hypothetical protein;  37.7      23 0.00058   14.0  17.2   26  331-356    77-102 (404)
284 pfam00392 GntR Bacterial regul  37.7      23 0.00058   14.0   2.6   27  544-570    22-48  (64)
285 KOG0976 consensus               37.4      23 0.00058   14.0  17.7   55  403-457   374-428 (1265)
286 COG5174 TFA2 Transcription ini  37.4      23 0.00058   14.0   4.1   41  533-573    85-126 (285)
287 smart00796 AHS1 Allophanate hy  37.1      13 0.00034   15.9   0.7   48  511-574    81-128 (201)
288 PRK11920 rirA iron-responsive   37.0      23 0.00059   13.9   5.2   29  542-570    20-48  (153)
289 pfam06953 ArsD Arsenical resis  36.7      19 0.00049   14.6   1.5   21  542-562    84-104 (119)
290 TIGR02237 recomb_radB DNA repa  36.6      17 0.00044   14.9   1.3   22  442-463   127-148 (223)
291 PRK09990 DNA-binding transcrip  36.3      24 0.00061   13.8   3.3   56   21-79      6-64  (251)
292 PRK04184 DNA topoisomerase VI   36.2      24 0.00061   13.8   3.7   48  473-520   381-454 (533)
293 TIGR01436 glu_cys_lig_pln glut  35.6      24 0.00062   13.8   2.1   87  544-648   284-382 (446)
294 PRK10225 DNA-binding transcrip  35.4      24 0.00062   13.7   3.5   19  447-465   143-161 (257)
295 COG0853 PanD Aspartate 1-decar  35.3     4.9 0.00012   19.3  -1.7   50  448-505    14-63  (126)
296 PRK09526 lacI lac repressor; R  35.1      25 0.00063   13.7   2.8   29   47-75     20-49  (342)
297 PRK11886 biotin--protein ligas  35.0      25 0.00063   13.7   2.9   49   28-79      3-51  (319)
298 PRK10430 DNA-binding transcrip  34.9      25 0.00064   13.7   5.9   79  501-582   135-216 (239)
299 PRK11753 cAMP-regulatory prote  34.7      25 0.00064   13.7   3.4   26  639-668   168-193 (211)
300 pfam01325 Fe_dep_repress Iron   34.4      25 0.00065   13.6   3.0   29  542-570    16-44  (58)
301 cd07377 WHTH_GntR Winged helix  33.9      26 0.00066   13.6   3.2   26  545-570    24-49  (66)
302 PRK13752 putative transcriptio  33.8      22 0.00056   14.1   1.4   25  546-570     7-31  (144)
303 PRK13394 3-hydroxybutyrate deh  33.2      26 0.00067   13.5   4.1  110  439-556   121-237 (262)
304 TIGR02018 his_ut_repres histid  33.1      26 0.00068   13.5   5.1   68  503-600     5-75  (234)
305 COG1522 Lrp Transcriptional re  32.7      27 0.00068   13.4   4.2   36  532-568     9-44  (154)
306 cd06919 Asp_decarbox Aspartate  32.6     4.7 0.00012   19.4  -2.2   35  471-505    29-63  (111)
307 TIGR02513 type_III_yscB type I  32.3      10 0.00026   16.8  -0.5  103  537-652     5-117 (140)
308 TIGR02267 TIGR02267 Myxococcus  32.2      27  0.0007   13.4   2.6   24  427-450    62-85  (123)
309 cd01107 HTH_BmrR Helix-Turn-He  32.1      27  0.0007   13.3   2.2   23  548-570     2-24  (108)
310 pfam12129 Phtf-FEM1B_bdg Male   31.9      20  0.0005   14.5   0.9   57  442-512    42-98  (159)
311 pfam00325 Crp Bacterial regula  31.7      28 0.00071   13.3   2.4   21  548-568     4-24  (32)
312 PRK00876 nadE NAD synthetase;   31.7      28 0.00071   13.3   8.3   35  638-673   277-311 (325)
313 PRK03837 transcriptional regul  31.6      28 0.00071   13.3   3.0   51   23-76     15-68  (243)
314 COG1649 Uncharacterized protei  31.5      27 0.00069   13.4   1.6   23   55-77     58-80  (418)
315 COG1318 Predicted transcriptio  31.4      28 0.00072   13.3   2.8   22  547-568    62-83  (182)
316 pfam00382 TFIIB Transcription   31.2      28 0.00072   13.2   1.7   67  550-653     2-68  (71)
317 PRK00413 thrS threonyl-tRNA sy  31.1      19  0.0005   14.5   0.8   10  129-138    53-62  (639)
318 KOG1495 consensus               30.8      14 0.00036   15.6   0.0   62  443-505    79-151 (332)
319 COG4977 Transcriptional regula  30.8      29 0.00073   13.2   5.1   40  530-569   220-259 (328)
320 smart00345 HTH_GNTR helix_turn  30.6      29 0.00074   13.2   2.9   27  544-570    18-44  (60)
321 KOG4021 consensus               30.6      24 0.00062   13.8   1.2   13  492-504   176-188 (239)
322 smart00530 HTH_XRE Helix-turn-  30.3      29 0.00074   13.1   3.9   23  640-662    11-33  (56)
323 TIGR03337 phnR transcriptional  30.3      29 0.00074   13.1   3.4   45  418-468    19-63  (231)
324 PRK13890 conjugal transfer pro  30.2      29 0.00075   13.1   3.5   29  545-573    17-45  (119)
325 cd02986 DLP Dim1 family, Dim1-  30.0      28 0.00072   13.2   1.5   18  111-128    18-35  (114)
326 TIGR02404 trehalos_R_Bsub treh  30.0      30 0.00075   13.1   2.7   33  541-573    19-51  (236)
327 PRK09973 putative outer membra  29.7      30 0.00076   13.1   4.0   28  330-357    21-48  (85)
328 PRK12824 acetoacetyl-CoA reduc  29.6      30 0.00076   13.0   3.7   99  441-556   119-220 (245)
329 pfam02969 TAF TATA box binding  29.6      30 0.00076   13.0   2.7   46  626-674    10-55  (66)
330 KOG0697 consensus               29.6      30 0.00076   13.0   2.2   35   27-61     81-123 (379)
331 pfam05635 Ribosomal_S23p S23 r  29.6      30 0.00076   13.0   4.6   13  422-434    88-100 (110)
332 TIGR01942 pcnB poly(A) polymer  29.5      18 0.00047   14.7   0.4   12  493-504   392-403 (448)
333 PRK04406 hypothetical protein;  29.4      30 0.00077   13.0   7.6   52  313-364     5-56  (75)
334 PRK13209 L-xylulose 5-phosphat  29.1      31 0.00078   13.0   2.3   48   30-77     22-73  (283)
335 PRK05557 fabG 3-ketoacyl-(acyl  28.8      31 0.00079   12.9   3.2   97  441-556   122-223 (248)
336 pfam01710 Transposase_14 Trans  28.7      31 0.00079   12.9   4.8   23  546-568    18-40  (120)
337 pfam04100 Vps53_N Vps53-like,   28.3      31  0.0008   12.9  11.4   28   45-73      6-33  (375)
338 smart00346 HTH_ICLR helix_turn  28.3      31  0.0008   12.9   4.0   31  540-570    14-44  (91)
339 PRK09391 fixK transcriptional   28.2      32  0.0008   12.9   3.4   18  639-656   173-190 (224)
340 PRK10219 DNA-binding transcrip  28.1      32 0.00081   12.9   5.3   37  533-569     8-44  (107)
341 pfam02261 Asp_decarbox Asparta  28.1     6.4 0.00016   18.4  -2.1   35  472-506    31-65  (116)
342 PRK11161 fumarate/nitrate redu  28.0      32 0.00081   12.8   8.2   37  629-669   168-210 (235)
343 cd01667 TGS_ThrRS_N TGS _ThrRS  27.9     9.3 0.00024   17.1  -1.3   47  543-589    13-59  (61)
344 pfam09413 DUF2007 Protein of u  27.9      25 0.00064   13.6   0.9   11   67-77     16-26  (68)
345 COG3711 BglG Transcriptional a  27.8      32 0.00082   12.8   6.4   54   29-82      5-59  (491)
346 PRK05629 hypothetical protein;  27.6      32 0.00082   12.8   6.2   43  528-571   244-286 (331)
347 KOG2822 consensus               27.5      12 0.00031   16.2  -0.8   28  457-485   203-230 (407)
348 pfam02082 Rrf2 Transcriptional  27.5      32 0.00082   12.8   5.5   46  544-589    22-67  (82)
349 TIGR03324 alt_F1F0_F1_al alter  27.3      33 0.00083   12.8   3.9   50  499-551   236-285 (497)
350 cd00907 Bacterioferritin Bacte  27.2      33 0.00083   12.7   1.7   14  353-366    55-68  (153)
351 pfam02271 UCR_14kD Ubiquinol-c  27.1      33 0.00084   12.7   3.7   45  445-490     7-51  (105)
352 pfam03917 GSH_synth_ATP Eukary  26.9      33 0.00084   12.7   5.3  128  484-632   256-397 (469)
353 pfam03444 DUF293 Domain of unk  26.9      33 0.00084   12.7   6.5   43  529-571     6-48  (79)
354 PRK06200 2,3-dihydroxy-2,3-dih  26.8      33 0.00085   12.7   1.5   94  452-555   137-233 (263)
355 PRK02119 hypothetical protein;  26.7      33 0.00085   12.7   7.1   50  315-364     5-54  (73)
356 smart00491 HELICc2 helicase su  26.6      33 0.00085   12.7   1.4   48  467-514    77-126 (142)
357 TIGR02470 sucr_synth sucrose s  26.3      29 0.00074   13.2   1.0   62  514-575   343-432 (790)
358 COG3355 Predicted transcriptio  26.2      34 0.00087   12.6   6.5   26  543-568    39-64  (126)
359 TIGR01572 A_thl_para_3677 Arab  26.2     8.5 0.00022   17.4  -1.8   42  458-500    46-87  (290)
360 TIGR02944 suf_reg_Xantho FeS a  26.1      34 0.00087   12.6   2.5   52  538-589    17-68  (130)
361 PRK00901 methylated-DNA--prote  25.9      34 0.00088   12.6   5.0   75  505-581    48-124 (155)
362 TIGR01097 3A0109s02M phosphona  25.6      22 0.00056   14.1   0.3   12  501-512    37-48  (192)
363 PTZ00183 centrin; Provisional   25.6      35 0.00089   12.5   6.1   54   21-74     16-76  (168)
364 cd04781 HTH_MerR-like_sg6 Heli  25.5      33 0.00085   12.7   1.2   23  548-570     2-24  (120)
365 pfam08726 efhand_Ca_insen Ca2+  25.5      35 0.00089   12.5   2.3   27   28-57      9-35  (69)
366 pfam09184 PPP4R2 PPP4R2. PPP4R  25.2      35  0.0009   12.5   4.6   11  321-331    89-99  (285)
367 PRK09764 DNA-binding transcrip  25.0      35  0.0009   12.5   4.1   35  419-453    24-58  (239)
368 PRK12469 RNA polymerase factor  25.0      36 0.00091   12.5   6.8  110  533-651   347-466 (475)
369 TIGR01736 FGAM_synth_II phosph  25.0      36 0.00091   12.5   1.5   18  540-557    13-30  (763)
370 cd04782 HTH_BltR Helix-Turn-He  24.9      36 0.00091   12.4   2.1   23  548-570     2-24  (97)
371 TIGR00270 TIGR00270 conserved   24.8      36 0.00091   12.4   4.6   63  525-592    80-165 (169)
372 COG3904 Predicted periplasmic   24.7      25 0.00064   13.6   0.4   29  636-666   202-230 (245)
373 pfam10500 SR-25 Nuclear RNA-sp  24.7      36 0.00092   12.4   2.0   47  606-665    14-60  (74)
374 KOG4697 consensus               24.6      36 0.00092   12.4   2.0   26  489-514   107-132 (160)
375 PRK10857 DNA-binding transcrip  24.6      36 0.00092   12.4   5.1   22  547-568    26-47  (164)
376 PRK05449 aspartate alpha-decar  24.5     8.1 0.00021   17.5  -2.2   35  472-506    31-65  (126)
377 KOG3361 consensus               24.3      36 0.00093   12.4   2.3   80  452-565    39-132 (157)
378 PRK08643 acetoin reductase; Va  24.3      37 0.00093   12.4   4.4  107  441-556   118-231 (256)
379 smart00492 HELICc3 helicase su  24.2      35  0.0009   12.5   1.1   30  485-514    94-125 (141)
380 smart00342 HTH_ARAC helix_turn  24.1      37 0.00094   12.3   3.7   23  546-568     1-23  (84)
381 PRK10703 DNA-binding transcrip  24.0      37 0.00094   12.3   2.8   47  470-523   246-294 (335)
382 COG2344 AT-rich DNA-binding pr  23.9      37 0.00095   12.3   5.2   29  473-503    89-117 (211)
383 PRK09281 F0F1 ATP synthase sub  23.8      37 0.00095   12.3   4.2   45  501-548   238-282 (502)
384 PRK13805 bifunctional acetalde  23.6      38 0.00096   12.3  11.4  137  422-567   677-829 (862)
385 smart00419 HTH_CRP helix_turn_  23.6      38 0.00096   12.3   2.9   21  548-568    10-30  (48)
386 COG4477 EzrA Negative regulato  23.2      38 0.00097   12.2  16.2   22  467-488   440-463 (570)
387 PRK08219 short chain dehydroge  23.1      38 0.00098   12.2   3.5   81  453-555   123-203 (226)
388 TIGR01004 PulS_OutS lipoprotei  23.0      39 0.00098   12.2   3.4   61  460-552    56-116 (136)
389 PRK09464 pdhR transcriptional   23.0      39 0.00098   12.2   5.2   51   24-77     12-65  (254)
390 PRK12274 serine/threonine prot  22.9      39 0.00098   12.2   5.6   52  579-631   104-163 (198)
391 pfam10498 IFT57 Intra-flagella  22.9      39 0.00099   12.2  12.8   28  331-358   235-262 (355)
392 TIGR03103 trio_acet_GNAT GNAT-  22.8      31 0.00078   13.0   0.6   62  408-470   278-349 (547)
393 PRK00509 argininosuccinate syn  22.8      39 0.00099   12.1   3.9   33  113-145   117-161 (398)
394 pfam06056 Terminase_5 Putative  22.7      39 0.00099   12.1   1.7   30  534-566     4-33  (58)
395 COG4473 EcsB Predicted ABC-typ  22.7      39 0.00099   12.1   1.6   30  117-146    72-101 (379)
396 smart00803 TAF TATA box bindin  22.7      39 0.00099   12.1   2.7   21  653-673    33-53  (65)
397 KOG0464 consensus               22.7      33 0.00085   12.7   0.7   26   56-81     69-94  (753)
398 PRK02793 hypothetical protein;  22.7      39   0.001   12.1   7.1   49  316-364     5-53  (72)
399 TIGR02485 CobZ_N-term precorri  22.6      39   0.001   12.1   3.5   44  545-593   327-371 (467)
400 TIGR03653 arch_L6P archaeal ri  22.4      37 0.00094   12.3   0.9   32  649-682   133-164 (170)
401 pfam10566 Glyco_hydro_97 Glyco  22.4      39   0.001   12.1   2.7   40  443-482   402-453 (643)
402 pfam02002 TFIIE_alpha TFIIE al  22.4      40   0.001   12.1   2.8   27  545-571    26-52  (105)
403 PRK08359 transcription factor;  22.4      40   0.001   12.1   5.7   23  545-567    95-117 (175)
404 PRK08217 fabG 3-ketoacyl-(acyl  22.3      40   0.001   12.1   5.7   96  443-556   132-231 (253)
405 TIGR02617 tnaA_trp_ase tryptop  22.3      40   0.001   12.1   1.5   19  448-466   201-219 (468)
406 PRK03501 ppnK inorganic polyph  22.2      40   0.001   12.1   2.7   32   56-87     12-43  (264)
407 cd01109 HTH_YyaN Helix-Turn-He  22.2      40   0.001   12.1   2.3   23  548-570     2-24  (113)
408 pfam01418 HTH_6 Helix-turn-hel  22.2      40   0.001   12.1   3.4   18  548-565    36-53  (106)
409 pfam07455 Psu Phage polarity s  22.1      38 0.00096   12.3   0.9   73  501-582    60-139 (188)
410 pfam04433 SWIRM SWIRM domain.   22.0      40   0.001   12.0   3.8   33   40-75     49-81  (84)
411 PRK10014 DNA-binding transcrip  22.0      40   0.001   12.0   3.1   19  478-496   166-184 (342)
412 pfam04492 Phage_rep_O Bacterio  21.9      40   0.001   12.0   5.4   40  618-657    28-72  (100)
413 pfam08765 Mor Mor transcriptio  21.9      40   0.001   12.0   4.6   41  621-668    59-99  (107)
414 smart00344 HTH_ASNC helix_turn  21.8      40   0.001   12.0   4.2   37  533-570     5-41  (108)
415 cd02844 PAZ_CAF_like PAZ domai  21.3      41  0.0011   11.9   1.6   24  482-505    53-76  (135)
416 PRK12429 3-hydroxybutyrate deh  21.3      41  0.0011   11.9   2.7  106  442-556   121-233 (258)
417 TIGR00370 TIGR00370 conserved   21.1      38 0.00098   12.2   0.8   23  639-661   105-127 (217)
418 PRK07740 hypothetical protein;  21.1      25 0.00063   13.7  -0.2   14  640-653   185-198 (240)
419 COG0411 LivG ABC-type branched  21.1      23 0.00058   14.0  -0.4   60  417-479   175-234 (250)
420 TIGR02104 pulA_typeI pullulana  21.0      42  0.0011   11.9   1.7   20   67-86    188-207 (655)
421 PRK02234 recU Holliday junctio  21.0      42  0.0011   11.9   1.2   16  463-478    25-40  (199)
422 COG4809 Archaeal ADP-dependent  21.0      33 0.00084   12.7   0.4  116  412-562   288-403 (466)
423 COG1904 UxaC Glucuronate isome  20.9      42  0.0011   11.9   3.0   95  421-523   244-341 (463)
424 pfam11503 DUF3215 Protein of u  20.9      26 0.00067   13.5  -0.1   44   39-82      9-56  (77)
425 COG1675 TFA1 Transcription ini  20.9      42  0.0011   11.9   5.6   34  543-577    30-65  (176)
426 cd05133 RasGAP_IQGAP1 IQGAP1 i  20.7      42  0.0011   11.8   1.8   43  142-185    18-60  (360)
427 PRK09706 transcriptional repre  20.5      43  0.0011   11.8   4.1   24  545-568    17-40  (135)
428 pfam06970 RepA_N Replication i  20.5      43  0.0011   11.8   2.7   19  548-566    54-72  (76)
429 TIGR01752 flav_long flavodoxin  20.5      39   0.001   12.1   0.7   19  550-568    18-37  (176)
430 KOG1389 consensus               20.4      43  0.0011   11.8   1.6   25  554-582   358-382 (435)
431 TIGR00624 tag DNA-3-methyladen  20.3      43  0.0011   11.8   1.3   31  474-508   141-172 (185)
432 TIGR02881 spore_V_K stage V sp  20.1      44  0.0011   11.7   2.7   55  468-528   173-233 (261)
433 cd04770 HTH_HMRTR Helix-Turn-H  20.0      44  0.0011   11.7   1.8   23  548-570     2-24  (123)

No 1  
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=100.00  E-value=0  Score=1529.11  Aligned_cols=618  Identities=53%  Similarity=0.785  Sum_probs=564.3

Q ss_pred             CCCCCHHCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEEECCCCCCCCCCCCCCC-CCCH
Q ss_conf             554430202899999999787848867899975268435998889999999984797783278410000123643-2110
Q gi|254780289|r   19 DDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL-DLAS   97 (682)
Q Consensus        19 ~~~~~~d~~~~~ik~LI~~gke~GylTydeIn~~LP~d~~~~e~ie~i~~~L~~~GI~Vve~~~~~~~~~~~~~~-~~~~   97 (682)
                      +|+|++|.+++.||+||++||+||||||+|||++||++.++|||||+|+++|++|||+|+|++++++.....+.. ..++
T Consensus         1 ~~~~~~~~~~~~ik~LI~~GKe~GyLTy~EInd~LP~d~~~~eqId~ii~~L~~~GI~Vve~~~~~~~~~~~~~~~~~d~   80 (620)
T PRK05658          1 GDSPLLKNQQSALKLLIKRGKERGYLTYAELNDHLPEDIVDSEQIEDIISMINDMGIQVVESAPDADDLLLADNAAESDE   80 (620)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEEEECCCCCCHHCCCCCCCCCCH
T ss_conf             99525654789999999985416826599999768998999899999999999779737506864200001445443204


Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCC
Q ss_conf             11122334444200345777728999999856976889788999999999889999999872823899999999873117
Q gi|254780289|r   98 SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG  177 (682)
Q Consensus        98 ~~~~e~~~~~~~~~~e~~rtdDPVRMYLREMG~V~LLTREgEIeIAKRIE~G~~~i~~al~~~P~ti~~il~~~e~i~~g  177 (682)
                      +..+++..+++.+++++|||||||||||||||+||||||||||+||||||+|+++|+++||+||++++++++|++.|.+|
T Consensus        81 ~~~ee~~~~l~~~~~e~grTdDPVRMYLREMG~V~LLTREGEIeIAKRIE~G~~~~~~ai~~~P~~i~~il~~~e~l~~g  160 (620)
T PRK05658         81 EAEEEAAAALSSVESEIGRTDDPVRMYLREMGTVELLTREGEIEIAKRIEDGENIMIAALCESPLTIDAILEWYDRLENE  160 (620)
T ss_pred             HHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCC
T ss_conf             56655443102210125888980999999728876788074999999999999999999962969999999999999828


Q ss_pred             CHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCHHHHHH
Q ss_conf             10367876421013543333333433333211000111000100000000122100001111101356666530344310
Q gi|254780289|r  178 TTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN  257 (682)
Q Consensus       178 e~~LrdIIDld~t~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~e~~~e~~~~~~~~~~~~~~~~~~e~e~~~~~  257 (682)
                      +++++|||+.+.+......           .......                             ...........+..
T Consensus       161 e~rl~diIdg~~d~~~~~~-----------~~~~~~~-----------------------------~~~~~~~~~~~~~~  200 (620)
T PRK05658        161 EIRLRELIDGFVDPNAEEA-----------PTATHVG-----------------------------SELSEEDEDDDEEE  200 (620)
T ss_pred             CEEHHHHHHCCCCCCCCCC-----------CCCCCCC-----------------------------CCCCCCCCCCCCCC
T ss_conf             7139999842468432223-----------1101233-----------------------------33322221111112


Q ss_pred             HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             00222334555564442102347987668999999999999987521012000799999999999999862100577887
Q gi|254780289|r  258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDL  337 (682)
Q Consensus       258 ~e~e~de~~~sla~~e~eLk~~v~e~l~~i~~~~~kl~k~~~~~~~~~~~~~~~kk~~kl~~eL~e~~~~lkl~~k~iE~  337 (682)
                      .+.+.+....+++.+...+++.+.+.|..+.+.|.++.++..+...     ...+++.+++.+|.+.|..|+|++++|+.
T Consensus       201 ~~~~~d~~~~~~~~~~~~~~~~v~e~f~~i~k~~~k~~k~~~k~~~-----~~~k~~~k~~~~L~~~~~~lkl~~k~ie~  275 (620)
T PRK05658        201 DEEDDDEAAKSLAADEAILPEKVLEKFKALAKQYKKLRKAQKKKGR-----EQEKKYAKLREKLKEELKSLRLTSKQIEE  275 (620)
T ss_pred             CCCCCCCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCH-----HHHHHHHHHHHHHHHHHHHCCCCHHHHHH
T ss_conf             2222220003257660756899999999999999999999997332-----40499999999999999845898899999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH-HHHCCCHHHHHHHCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             89999999999999999999999-97125357777631677689899999861355106765543456776532233332
Q gi|254780289|r  338 LVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI  416 (682)
Q Consensus       338 L~~~l~~~~k~Ir~~Er~L~rl~-~k~~i~R~~Fi~~f~gnEt~~~wl~~~~~~~~~~~~~~l~~~~~eI~~~q~kL~~i  416 (682)
                      |++.++..+++|+.+|+.|+++| .++||||++|++.|++|++++.|+.+.... .+.|+.++.....+|..+|++|..+
T Consensus       276 L~~~l~~~~~~Ir~~Er~I~rl~v~~~~m~R~~Fi~~f~g~e~~~~W~~k~~~~-~k~~~~~l~~~~~~I~~~q~kL~~i  354 (620)
T PRK05658        276 LVDQMRDINKRVRTLERQILRLAVERCKMPRKDFLRLFPGNETDITWLEKEIAS-GKPWSEFLKRVYDEIQRLQQELEAI  354 (620)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCCCCHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999999999999871999999998732443435689999884-3436999998699999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEE
Q ss_conf             22221126889999998765332112468999875557899988752235677788754436799998874385457312
Q gi|254780289|r  417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF  496 (682)
Q Consensus       417 e~~~gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f  496 (682)
                      +..+|+++.+||+++++|++|++++++||++||+|||||||||||||+||||+|+|||||||||||||||||||+|||||
T Consensus       355 e~~~gl~i~elK~i~r~I~~Ge~~a~~AKkeMiEANLRLVISIAKKYtNRGLqFLDLIQEGNiGLMkAVdKFeyrrGyKF  434 (620)
T PRK05658        355 EEETGLTIEELKEINRQISKGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF  434 (620)
T ss_pred             HHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCHHHHHHHHHCCCCCCCCH
T ss_conf             99849799999999999999877789999999986189999999983148998789987440799999986284559713


Q ss_pred             EHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCC
Q ss_conf             01028989999999997228704614205889899999999987760889997899987099989999999860898755
Q gi|254780289|r  497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL  576 (682)
Q Consensus       497 ~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl  576 (682)
                      |||||||||||||||||||||||||||||+++|||++|++|++.|++||+|||+|||++||||++||+++|+++++||||
T Consensus       435 STYATWWIRQAITRaIaDqaRTIRiPVHmietinkl~r~~r~l~qe~Grept~eEia~~~~~~~~kvr~vlki~~epiSl  514 (620)
T PRK05658        435 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERLGMPEDKVRKVLKIAKEPISL  514 (620)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCC
T ss_conf             57799999999999998617740151889999999999999999982899999999989498999999999864898024


Q ss_pred             CCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHH
Q ss_conf             36358899860475623898899899999999999999997329988999999981879867468899989966789999
Q gi|254780289|r  577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI  656 (682)
Q Consensus       577 ~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~  656 (682)
                      +||||+++||+|||||+|+++.+|.+++...+|++++.+||++|+|||++||+||||||++++|||||||++|+||||||
T Consensus       515 e~pig~~~ds~lgdfied~~~~~p~~~~~~~~l~~~~~~vl~~Lt~rE~~vl~~RfGi~~~~~~TLeevg~~f~vtRERi  594 (620)
T PRK05658        515 ETPIGDDEDSHLGDFIEDKNAELPIDAATQESLREQTTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI  594 (620)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHH
T ss_conf             38878888764001016899998799999999999999998479999999999957999999678999998829768989


Q ss_pred             HHHHHHHHHHHCCHHHHHHHHHHHCC
Q ss_conf             99999999983296777875665179
Q gi|254780289|r  657 RQIEAKAIRKLKHPSRSKKLRSFLDG  682 (682)
Q Consensus       657 rqi~~~a~~~l~~~~~~~~l~~~~~~  682 (682)
                      ||||+|||||||||+|+++||+|||-
T Consensus       595 RQIEakalrklrhp~r~~~l~~fl~~  620 (620)
T PRK05658        595 RQIEAKALRKLRHPSRSRKLRSFLDD  620 (620)
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCC
T ss_conf             99999999985687257888876049


No 2  
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=100.00  E-value=0  Score=878.34  Aligned_cols=384  Identities=47%  Similarity=0.755  Sum_probs=343.8

Q ss_pred             CCHHCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEEECCCCCCCCCCCCCCCCCCHHHHH
Q ss_conf             43020289999999978784886789997526843599888999999998479778327841000012364321101112
Q gi|254780289|r   22 LVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASN  101 (682)
Q Consensus        22 ~~~d~~~~~ik~LI~~gke~GylTydeIn~~LP~d~~~~e~ie~i~~~L~~~GI~Vve~~~~~~~~~~~~~~~~~~~~~~  101 (682)
                      ......+..+|+||.+||++|||||+|||++||++.+++|+||+|+.+|++|||+|++..+............   ...+
T Consensus        14 ~~~~~~~~~lk~Li~~gKe~G~lTy~EIn~~Lp~~~~~~e~id~i~~~l~d~gi~v~~~~~~~~~~~~~~~~~---~~~~   90 (398)
T PRK05901         14 AAKKKKQKKAKELKALAKEDGDITYEEIDEDLDLDFDEDEDIDDVIIFLDDLDEDVENEADVDEDKEDDEDDE---IAEK   90 (398)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCCCCC---CCCC
T ss_conf             4057899999999998862798369999975898679989999999999977973046763111233343332---1210


Q ss_pred             HHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCHHH
Q ss_conf             23344442003457777289999998569768897889999999998899999998728238999999998731171036
Q gi|254780289|r  102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL  181 (682)
Q Consensus       102 e~~~~~~~~~~e~~rtdDPVRMYLREMG~V~LLTREgEIeIAKRIE~G~~~i~~al~~~P~ti~~il~~~e~i~~ge~~L  181 (682)
                      .........+++.++|||||||||||||+||||||++||+||||||+|...            .                
T Consensus        91 ~~~~~~~~~~~~~~~tdd~v~~yl~~~g~~~ll~~~~e~~~a~~~~~~~~~------------~----------------  142 (398)
T PRK05901         91 SEKDRQARKDAELTATADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYA------------E----------------  142 (398)
T ss_pred             HHHHHHHCCCCCCCCCCCCHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHH------------H----------------
T ss_conf             234444113333688897199999862755488879999999999840456------------7----------------


Q ss_pred             HHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCHHHHHHHHHH
Q ss_conf             78764210135433333334333332110001110001000000001221000011111013566665303443100022
Q gi|254780289|r  182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED  261 (682)
Q Consensus       182 rdIIDld~t~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~e~~~e~~~~~~~~~~~~~~~~~~e~e~~~~~~e~e  261 (682)
                       +                                                                              
T Consensus       143 -~------------------------------------------------------------------------------  143 (398)
T PRK05901        143 -E------------------------------------------------------------------------------  143 (398)
T ss_pred             -H------------------------------------------------------------------------------
T ss_conf             -6------------------------------------------------------------------------------


Q ss_pred             HHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             23345555644421023479876689999999999999875210120007999999999999998621005778878999
Q gi|254780289|r  262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ  341 (682)
Q Consensus       262 ~de~~~sla~~e~eLk~~v~e~l~~i~~~~~kl~k~~~~~~~~~~~~~~~kk~~kl~~eL~e~~~~lkl~~k~iE~L~~~  341 (682)
                                                                                .+              +     
T Consensus       144 ----------------------------------------------------------~~--------------~-----  146 (398)
T PRK05901        144 ----------------------------------------------------------LL--------------E-----  146 (398)
T ss_pred             ----------------------------------------------------------HH--------------H-----
T ss_conf             ----------------------------------------------------------67--------------6-----


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999712535777763167768989999986135510676554345677653223333222221
Q gi|254780289|r  342 LYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG  421 (682)
Q Consensus       342 l~~~~k~Ir~~Er~L~rl~~k~~i~R~~Fi~~f~gnEt~~~wl~~~~~~~~~~~~~~l~~~~~eI~~~q~kL~~ie~~~g  421 (682)
                                  +             .           ...|                                      
T Consensus       147 ------------~-------------~-----------~~~~--------------------------------------  152 (398)
T PRK05901        147 ------------K-------------R-----------DLRW--------------------------------------  152 (398)
T ss_pred             ------------H-------------H-----------HHHH--------------------------------------
T ss_conf             ------------7-------------7-----------7777--------------------------------------


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHH
Q ss_conf             12688999999876533211246899987555789998875223567778875443679999887438545731201028
Q gi|254780289|r  422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM  501 (682)
Q Consensus       422 l~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~  501 (682)
                                     ..+..++||++||+|||||||||||+|.|+|++|+|||||||+|||+||+||||.|||||||||+
T Consensus       153 ---------------~~~~~~~Ar~~Li~aNLRLVvsIAkkY~~~Gl~l~DLIQEGniGLirAvekFDp~rG~rFSTYA~  217 (398)
T PRK05901        153 ---------------IARDGKRAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYAT  217 (398)
T ss_pred             ---------------HHHCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHH
T ss_conf             ---------------53053999999999706999999976468998988999986899999999719777995421149


Q ss_pred             HHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             98999999999722870461420588989999999998776088999789998709998999999986089875536358
Q gi|254780289|r  502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG  581 (682)
Q Consensus       502 ~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~  581 (682)
                      |||||+|+|||++|+|+||+|+||.+++|++.++.+++.+++||+||++|||+.||+|+++|+.++++++.|+|||+|+|
T Consensus       218 wWIRqaI~rai~~~~r~IRiP~h~~e~~~k~~r~~~~l~~~~gr~Pt~eEiA~~lg~~~~~v~~~~~~~~~~~SLd~~vg  297 (398)
T PRK05901        218 WWIRQAITRAMADQARTIRIPVHMVETINKLGRIERELLQELGREPTPEELAEEMDFTPEKVREIQKYAREPISLDKTIG  297 (398)
T ss_pred             HHHHHHHHHHHHHCCCEEECCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCC
T ss_conf             99999999999966873523323999999999999999998489999999998819999999999997289855678778


Q ss_pred             CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             89986047562389889989999999999999999732998899999998187986746889998996678999999999
Q gi|254780289|r  582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA  661 (682)
Q Consensus       582 ~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~  661 (682)
                      ++++++|+|+++|.++.+|++.+....+++.|..+|.+|+|||+.||++||||+++.|+||+|||+.||||||||||||.
T Consensus       298 ~d~~~~l~d~i~D~~~~~p~~~~~~~~l~~~l~~~L~~L~~REr~Ii~~RyGL~~~~~~TL~eIg~~lgvSrERVRQIE~  377 (398)
T PRK05901        298 DEGDSQFGDFIEDSEAVSPVDAVSFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIES  377 (398)
T ss_pred             CCCCCCHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             99865186641699999999999999999999999838999999999997589998960399999897969999999999


Q ss_pred             HHHHHHCCHHHHHHHHHHHC
Q ss_conf             99998329677787566517
Q gi|254780289|r  662 KAIRKLKHPSRSKKLRSFLD  681 (682)
Q Consensus       662 ~a~~~l~~~~~~~~l~~~~~  681 (682)
                      +||+|||||+|+..|++|||
T Consensus       378 kAL~KLR~~~~~~~l~~~l~  397 (398)
T PRK05901        378 KTMRKLRHPSRSQVLRDFLD  397 (398)
T ss_pred             HHHHHHCCCHHHHHHHHHHC
T ss_conf             99999678378879999857


No 3  
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=100.00  E-value=0  Score=823.65  Aligned_cols=357  Identities=53%  Similarity=0.843  Sum_probs=328.4

Q ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             89999999978784886789997526843599888999999998479778327841000012364321101112233444
Q gi|254780289|r   28 DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQ  107 (682)
Q Consensus        28 ~~~ik~LI~~gke~GylTydeIn~~LP~d~~~~e~ie~i~~~L~~~GI~Vve~~~~~~~~~~~~~~~~~~~~~~e~~~~~  107 (682)
                      .+.++.||++||++|||||+||+++||+..++++++|.|+..|.+.||.|++..+..............+      ....
T Consensus        12 ~~~~~~l~~~~~~~g~~~~~ei~~~~~~~~~~~~~~~~~~~~l~~~~i~i~~~~~~~~~~~~~~~~~~~~------~~~~   85 (368)
T PRK09210         12 EVVVKELIEKGKKRGTLTYDEIAEKLQPFELDSDQIDDLYERLEDAGISIVDENGNPSSKALQEEKKEEE------LEDE   85 (368)
T ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEEECCCCCCCCCCCCCCCCCCC------HHHH
T ss_conf             9999999999987697559999987043489999999999999987898847877642100001111100------0000


Q ss_pred             HHHCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCHHHHHHHHH
Q ss_conf             42003457777289999998569768897889999999998899999998728238999999998731171036787642
Q gi|254780289|r  108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL  187 (682)
Q Consensus       108 ~~~~~e~~rtdDPVRMYLREMG~V~LLTREgEIeIAKRIE~G~~~i~~al~~~P~ti~~il~~~e~i~~ge~~LrdIIDl  187 (682)
                      .....+...++|||||||+|||++||||+|+|+++||||++|-                                     
T Consensus        86 ~~~~~~~~~~~d~v~~YL~eI~~~pLLt~eEE~~La~r~~~GD-------------------------------------  128 (368)
T PRK09210         86 DLSVPPGVKINDPVRMYLKEIGRVPLLTAEEEIELAKRIEEGD-------------------------------------  128 (368)
T ss_pred             CCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCC-------------------------------------
T ss_conf             0132114655858999999956788999999999999988157-------------------------------------


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             10135433333334333332110001110001000000001221000011111013566665303443100022233455
Q gi|254780289|r  188 EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH  267 (682)
Q Consensus       188 d~t~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~e~~~e~~~~~~~~~~~~~~~~~~e~e~~~~~~e~e~de~~~  267 (682)
                                                                                                      
T Consensus       129 --------------------------------------------------------------------------------  128 (368)
T PRK09210        129 --------------------------------------------------------------------------------  128 (368)
T ss_pred             --------------------------------------------------------------------------------
T ss_conf             --------------------------------------------------------------------------------


Q ss_pred             HHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             55644421023479876689999999999999875210120007999999999999998621005778878999999999
Q gi|254780289|r  268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK  347 (682)
Q Consensus       268 sla~~e~eLk~~v~e~l~~i~~~~~kl~k~~~~~~~~~~~~~~~kk~~kl~~eL~e~~~~lkl~~k~iE~L~~~l~~~~k  347 (682)
                                                                                                      
T Consensus       129 --------------------------------------------------------------------------------  128 (368)
T PRK09210        129 --------------------------------------------------------------------------------  128 (368)
T ss_pred             --------------------------------------------------------------------------------
T ss_conf             --------------------------------------------------------------------------------


Q ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999712535777763167768989999986135510676554345677653223333222221126889
Q gi|254780289|r  348 RIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF  427 (682)
Q Consensus       348 ~Ir~~Er~L~rl~~k~~i~R~~Fi~~f~gnEt~~~wl~~~~~~~~~~~~~~l~~~~~eI~~~q~kL~~ie~~~gl~i~El  427 (682)
                                                                                                      
T Consensus       129 --------------------------------------------------------------------------------  128 (368)
T PRK09210        129 --------------------------------------------------------------------------------  128 (368)
T ss_pred             --------------------------------------------------------------------------------
T ss_conf             --------------------------------------------------------------------------------


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHH
Q ss_conf             99999876533211246899987555789998875223567778875443679999887438545731201028989999
Q gi|254780289|r  428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA  507 (682)
Q Consensus       428 K~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~  507 (682)
                                    ..||++||+|||||||||||+|.|+|++|+|||||||+|||+||+||||+|||||||||+|||||+
T Consensus       129 --------------~~Ar~~Li~aNLRLVVsIAkkY~~~Gl~l~DLIQEGNiGLmkAVeKFDp~rG~RFSTYA~WWIRqa  194 (368)
T PRK09210        129 --------------EEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQA  194 (368)
T ss_pred             --------------HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHH
T ss_conf             --------------999999999838999999986668998989999986799999999729877995334669999999


Q ss_pred             HHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCE
Q ss_conf             99999722870461420588989999999998776088999789998709998999999986089875536358899860
Q gi|254780289|r  508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH  587 (682)
Q Consensus       508 i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~  587 (682)
                      |+|||++||||||+|+||.+++||+.++.+++.+++||+||++|||+.||+|+++|+.++++++.|+|||+|+|++++++
T Consensus       195 I~raI~~q~r~IRiPvh~~e~~~kl~r~~r~L~q~lGrePt~eEIA~~lgi~~e~V~~i~~~~~~~~SLd~pvg~e~~s~  274 (368)
T PRK09210        195 ITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGRDPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSH  274 (368)
T ss_pred             HHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCH
T ss_conf             99999982785135424999999999999999998389998899998949989999999985388856688678877552


Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf             47562389889989999999999999999732998899999998187986746889998996678999999999999983
Q gi|254780289|r  588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL  667 (682)
Q Consensus       588 ~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l  667 (682)
                      ++|+++|.++.+|.+.+....+++.|..+|.+|+|||+.||++||||+++.|+||+|||+.||||||||||||.+||+||
T Consensus       275 l~d~i~D~~~~~p~e~~~~~~l~~~l~~~L~~L~~REr~Il~~RfGL~~~~~~TLeEIg~~lgvSRERVRQIE~kAL~KL  354 (368)
T PRK09210        275 LGDFIEDQDATSPADHAAYELLKEQLEEVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL  354 (368)
T ss_pred             HHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             87552489999989999999999999999817999999999997599968961499999896979899999999999997


Q ss_pred             CCHHHHHHHHHHHC
Q ss_conf             29677787566517
Q gi|254780289|r  668 KHPSRSKKLRSFLD  681 (682)
Q Consensus       668 ~~~~~~~~l~~~~~  681 (682)
                      |||+|+++|++|||
T Consensus       355 R~~~~~~~l~~~l~  368 (368)
T PRK09210        355 RHPSRSKQLKDFLE  368 (368)
T ss_pred             CCCHHHHHHHHHHC
T ss_conf             67368789888739


No 4  
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family.
Probab=100.00  E-value=0  Score=821.59  Aligned_cols=246  Identities=48%  Similarity=0.826  Sum_probs=236.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             32222211268899999987653321124689998755578999887522356777887544367999988743854573
Q gi|254780289|r  415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY  494 (682)
Q Consensus       415 ~ie~~~gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~  494 (682)
                      ...+.+.++. ||+.+       .+..++||.+||+|||||||||||||.|||++|+||||||+|||.+||+||||.|||
T Consensus        90 aWA~~a~l~l-eLk~~-------~r~G~RAK~kMi~ANLRLVVSvAKKYq~RglElLDLIQEG~lGL~RAVEKFDPtrGY  161 (336)
T TIGR02997        90 AWAEAAQLEL-ELKLV-------LRQGQRAKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTRGY  161 (336)
T ss_pred             HHHHHHHHHH-HHHHH-------HHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf             8899842258-99999-------997899999998760226889999851368833568876343122112335777788


Q ss_pred             EEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCC
Q ss_conf             12010289899999999972287046142058898999999999877608899978999870999899999998608987
Q gi|254780289|r  495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI  574 (682)
Q Consensus       495 ~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  574 (682)
                      ||||||+|||||+||||||.||||||+|+||.|++||+.|++|++.|++||.||.+|||+.|+|++++|+.++..++.|+
T Consensus       162 KFSTYAYWWIRQ~ITRAIA~qSRTIRLPiH~~EKLnkiKK~qReL~q~lGR~Ps~~EiAe~lel~~~qvR~~l~~~~~p~  241 (336)
T TIGR02997       162 KFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLNKIKKVQRELSQKLGRRPSEAEIAEALELEPEQVRELLQRARQPV  241 (336)
T ss_pred             CCCCHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCC
T ss_conf             63301246875688999843688324741076666899899899999838897868999883889889999999707874


Q ss_pred             CCCCCC-CCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCH
Q ss_conf             553635-8899860475623898899899999999999999997329988999999981879867468899989966789
Q gi|254780289|r  575 SLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR  653 (682)
Q Consensus       575 sl~~~~-~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~  653 (682)
                      |||+|| |+++||.|||+|+|++..+|++.+.+.+|+..|..+|+.|+|||++||+|||||+++.++||.|||+.|||||
T Consensus       242 SLd~~VrG~e~dt~LgdLl~d~~~~~P~~~~~~~~l~~dL~~lL~~L~p~e~~VL~LRfGL~~~~~~TL~eiG~~l~lSR  321 (336)
T TIGR02997       242 SLDTRVRGDEEDTELGDLLEDEDGESPEEQVEQESLRQDLESLLAELTPRERQVLRLRFGLDDGEPLTLAEIGERLNLSR  321 (336)
T ss_pred             CCCCCCCCCCCCCHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCH
T ss_conf             45773268885422654326888998278999999999999988637988999999857899897532789998838836


Q ss_pred             HHHHHHHHHHHHHHC
Q ss_conf             999999999999832
Q gi|254780289|r  654 ERIRQIEAKAIRKLK  668 (682)
Q Consensus       654 er~rqi~~~a~~~l~  668 (682)
                      |||||||++||+|||
T Consensus       322 ERVRQiE~~AL~kLR  336 (336)
T TIGR02997       322 ERVRQIEAKALRKLR  336 (336)
T ss_pred             HHHHHHHHHHHHHCC
T ss_conf             888899999975349


No 5  
>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=100.00  E-value=0  Score=831.21  Aligned_cols=238  Identities=65%  Similarity=1.022  Sum_probs=236.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCC
Q ss_conf             68999875557899988752235677788754436799998874385457312010289899999999972287046142
Q gi|254780289|r  444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV  523 (682)
Q Consensus       444 AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~  523 (682)
                      ||++||+|||||||||||||.||||+|+|||||||+||||||+||||++|||||||||||||||||||||||||||||||
T Consensus         1 Ak~~l~~sNLRLVvSIAKkY~nRGL~F~DLIQEGn~GL~KAv~KFdy~kGyKFSTYATWWIRQAITRAIADQARtIRiPV   80 (240)
T TIGR02393         1 AKKKLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV   80 (240)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCH
T ss_conf             93568873014666676663047863343676523578988776213578865511578999999998875137201103


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHH
Q ss_conf             05889899999999987760889997899987099989999999860898755363588998604756238988998999
Q gi|254780289|r  524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS  603 (682)
Q Consensus       524 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~  603 (682)
                      ||+|||||+.++.|++.|++||+||+||||+.||++++||+.+.+++++|||||+|||+|+||.|+|||+|+++.+|.+.
T Consensus        81 Hm~ETINk~~~~~R~l~Q~~Gr~Pt~EelAe~~g~~~~Kv~~i~~~~~~PiSLe~piG~e~dS~l~DFi~D~~~~~P~~~  160 (240)
T TIGR02393        81 HMVETINKLIKAERKLLQELGREPTDEELAERMGLPVEKVREIKKIAQEPISLETPIGEEEDSSLGDFIEDESIESPEDA  160 (240)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHH
T ss_conf             26678889999989999872889987789987089989999999862488656667788777744265257444685899


Q ss_pred             HHHHHHHHHHHHHHH-CCCHHHHHHHHHHHCCCCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHC
Q ss_conf             999999999999973-2998899999998187986-74688999899667899999999999998329677787566517
Q gi|254780289|r  604 AIQANLRETTTRVLA-SLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD  681 (682)
Q Consensus       604 ~~~~~~~~~~~~~l~-~l~~re~~v~~~r~g~~~~-~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~~~~~  681 (682)
                      +....|+++|..||. +|++||+.||+|||||.++ +++||||||+.|+||||||||||+|||||||||+|++.||+|++
T Consensus       161 ~~~~~l~~~l~~vL~~~L~~rE~~Vl~~RyGL~d~~~~~TLEEVG~~f~VTRERIRQIE~KALRKLrhp~r~~~Lk~f~~  240 (240)
T TIGR02393       161 AAKELLREQLEEVLENTLTERERKVLRMRYGLLDGEKPKTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKDFLD  240 (240)
T ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHCC
T ss_conf             99999999999998601788899999874389988765337888765178711456888999885028436677776419


No 6  
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=100.00  E-value=0  Score=732.38  Aligned_cols=254  Identities=46%  Similarity=0.789  Sum_probs=241.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHH
Q ss_conf             11268899999987653321124689998755578999887522356777887544367999988743854573120102
Q gi|254780289|r  421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA  500 (682)
Q Consensus       421 gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya  500 (682)
                      +++..++..+   +    +..++||++||+|||||||||||+|.|+|++|+|||||||+|||+||+||||+|||||||||
T Consensus       155 ~~~~~el~~~---~----~~G~~Ar~kLI~aNLRLVVsIAkkY~~rGl~l~DLIQEGniGLirAVEKFDp~rG~RFSTYA  227 (410)
T PRK07598        155 KLTVEELEQI---Q----KQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYA  227 (410)
T ss_pred             CCCHHHHHHH---H----HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEE
T ss_conf             1469999999---9----99999999999998999999998657899898999987489999999970965597257621


Q ss_pred             HHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             89899999999972287046142058898999999999877608899978999870999899999998608987553635
Q gi|254780289|r  501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI  580 (682)
Q Consensus       501 ~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~  580 (682)
                      +|||||+|+|||++|+||||+|+|+.+.+||+.++.+++.+++||.||.+|||+.||+++++|+.++.....|+|||+|+
T Consensus       228 ~WWIRQaI~RaI~~~~r~IRlP~h~~e~l~ki~r~~r~L~q~lGR~Pt~eEIA~~lg~s~e~V~~~l~~~~~~vSLd~pv  307 (410)
T PRK07598        228 YWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETKV  307 (410)
T ss_pred             HHHHHHHHHHHHHHHCCEECCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCC
T ss_conf             89999999999998088020460299999999999999998759999799999880999999999998727885536788


Q ss_pred             CCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             88998604756238988998999999999999999973299889999999818798674688999899667899999999
Q gi|254780289|r  581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE  660 (682)
Q Consensus       581 ~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~  660 (682)
                      |+|++++++|+++|.+ .+|++.+....++..|..+|..|+|||+.||++||||+++.|+||+|||+.||||||||||||
T Consensus       308 g~d~d~~l~dll~~~~-~~pee~~~~~~l~~~L~~lL~~L~~REr~IL~lRfGL~dg~~~TL~EIG~~lgISRERVRQIE  386 (410)
T PRK07598        308 GKDKDTELGDLLETDD-VSPEEMLMRESLQRDLQQLLADLTSRERDVIRMRFGLADGRTYSLAEIGRALDLSRERVRQIE  386 (410)
T ss_pred             CCCCCCCHHHHHCCCC-CCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             8888641888744589-998999999999999999983699999999999648999796689999989796999999999


Q ss_pred             HHHHHHHCCHHHHHHHHHHHCC
Q ss_conf             9999983296777875665179
Q gi|254780289|r  661 AKAIRKLKHPSRSKKLRSFLDG  682 (682)
Q Consensus       661 ~~a~~~l~~~~~~~~l~~~~~~  682 (682)
                      .+||+|||||+|+..|++|||.
T Consensus       387 ~kAL~KLR~p~r~~~Lr~yl~~  408 (410)
T PRK07598        387 AKALQKLRQPKRRNRIRDYLEL  408 (410)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHH
T ss_conf             9999996773778999999872


No 7  
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=100.00  E-value=0  Score=706.36  Aligned_cols=246  Identities=54%  Similarity=0.874  Sum_probs=237.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHH
Q ss_conf             99987653321124689998755578999887522356777887544367999988743854573120102898999999
Q gi|254780289|r  430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT  509 (682)
Q Consensus       430 i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~  509 (682)
                      +.+.+..|    ++||++||+|||||||||||+|.|+|++|+|||||||+|||+||+||||.|||||||||+|||||+|+
T Consensus       139 l~~~~~~g----~~Ar~~LI~aNLRLVVsIAkkY~~rGl~l~DLIQEGniGLirAvEKFDp~rG~RFSTYA~WWIRqaI~  214 (385)
T PRK07406        139 FRRRLMLG----RRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAIT  214 (385)
T ss_pred             HHHHHHHH----HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEHHHHHHHHHHH
T ss_conf             99999879----99999999998999999998656899898899998589999999981965488221102999999999


Q ss_pred             HHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEE
Q ss_conf             99972287046142058898999999999877608899978999870999899999998608987553635889986047
Q gi|254780289|r  510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG  589 (682)
Q Consensus       510 ~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~  589 (682)
                      |||++|+|+||+|+|+.+.++++.++.+.+.+++||.||++|||+.+++++++|+.+++.++.|+|||+|+|++++++++
T Consensus       215 RaI~~~sr~IRlP~h~~e~l~ki~k~~~~L~~~lGr~Pt~eEIA~~l~i~~e~v~~~~~~~~~~vSLD~pvg~~~ds~l~  294 (385)
T PRK07406        215 RAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLG  294 (385)
T ss_pred             HHHHHCCCEECCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCHH
T ss_conf             99997386120208999999999999999998708998699999993999999999998548986545888876533188


Q ss_pred             EEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             56238988998999999999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       590 ~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      |++++ +..+|++.+....+++.|..+|++|+|||+.||++||||+++.|+||+|||+.||||||||||||.+||+||||
T Consensus       295 D~i~~-d~~~pe~~~~~~~lr~~L~~~L~~L~eREr~II~lRfGL~dg~~~TL~EIg~~lgISRERVRQIE~rAL~KLR~  373 (385)
T PRK07406        295 DFIEA-DGETPEDDVSKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRH  373 (385)
T ss_pred             HHHHC-CCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
T ss_conf             89863-59999999999999999999986499999999999758999996469999989795999999999999999677


Q ss_pred             HHHHHHHHHHH
Q ss_conf             67778756651
Q gi|254780289|r  670 PSRSKKLRSFL  680 (682)
Q Consensus       670 ~~~~~~l~~~~  680 (682)
                      |+|+..|+.||
T Consensus       374 p~r~~~L~~yl  384 (385)
T PRK07406        374 PNRNSVLKEYI  384 (385)
T ss_pred             CHHHHHHHHHH
T ss_conf             17789999974


No 8  
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=100.00  E-value=0  Score=668.40  Aligned_cols=240  Identities=47%  Similarity=0.854  Sum_probs=236.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEE
Q ss_conf             12468999875557899988752235677788754436799998874385457312010289899999999972287046
Q gi|254780289|r  441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR  520 (682)
Q Consensus       441 ~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r  520 (682)
                      ..+||++||+|||||||||||+|.|+|++|.|||||||||||+||+||||+|||||||||+|||||+|+|+|.+|+|+||
T Consensus        80 g~~A~~~lI~aNLRLVvsIAk~Y~~~Gl~~~DLIQEGniGLirAvekFDp~rG~rFSTYA~wWIRq~I~r~i~~~~r~IR  159 (320)
T PRK07921         80 GEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIR  159 (320)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             69999999998189999999856589999899999838999988851689999812877799999999999997086214


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCH
Q ss_conf             14205889899999999987760889997899987099989999999860898755363588998604756238988998
Q gi|254780289|r  521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP  600 (682)
Q Consensus       521 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~  600 (682)
                      +|+|+.+.++++.++.+++.+++||+||++|||+.+|+|+++|..++..++.|+|||.|+|+|++++++|+++|.+..+|
T Consensus       160 lP~~~~~~~~ki~~~~~~l~~~lGR~Pt~eEIA~~lgi~~~~v~~~l~~~~~~~SLD~~vg~d~~~~l~d~i~D~~~~~~  239 (320)
T PRK07921        160 LPVHLVEQVNKLARIKREMHQHLGREATDEELAEESGIPEEKINDLLEHSRDPVSLDMPVGSDEEAPLGDFIEDAEAMSA  239 (320)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCH
T ss_conf             71889999999999999999983899989999988199999999999972888366776688875303324405678998


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHH
Q ss_conf             99999999999999997329988999999981879867468899989966789999999999999832967778756651
Q gi|254780289|r  601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL  680 (682)
Q Consensus       601 ~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~~~~  680 (682)
                      ++.+....++..|..+|++|+|||+.||++||||+++.|+||+|||+.||||||||||||.+||+|||||.|+..|++|.
T Consensus       240 e~~~~~~~l~~~L~~~L~~L~eREr~IL~~RfGl~~~~~~TL~EIg~~lgvSrERVRQIE~~AL~KLR~~~~~~~L~~y~  319 (320)
T PRK07921        240 ENAVIAELLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRHGERADRLRSYA  319 (320)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHH
T ss_conf             99999999999999999759999999999974899989747999998979699999999999999970728888887542


No 9  
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=100.00  E-value=0  Score=669.59  Aligned_cols=267  Identities=56%  Similarity=0.881  Sum_probs=258.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             33222221126889999998765332112468999875557899988752235677788754436799998874385457
Q gi|254780289|r  414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG  493 (682)
Q Consensus       414 ~~ie~~~gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g  493 (682)
                      ..++....++..|.+.+...+..|++ ...||++||+|||||||||||+|.|+||+|+|||||||+||||||+||||.||
T Consensus        74 ~~~~~~~~l~~~Ee~~la~~~~~g~~-~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAVekFdp~rG  152 (342)
T COG0568          74 RAIEAAPLLTPEEEKALARRLKRGER-DLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKG  152 (342)
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHCCCHHHHHHHHHCCCCCC
T ss_conf             88764001597899999999985885-59999999999889999999986337986889885250999999996296668


Q ss_pred             CEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCC
Q ss_conf             31201028989999999997228704614205889899999999987760889997899987099989999999860898
Q gi|254780289|r  494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP  573 (682)
Q Consensus       494 ~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  573 (682)
                      |||||||||||||+|+|+|++||||||+|+||++++|++.|+.+++.|++||+|+++|||+.||++.++|+.+++.++.|
T Consensus       153 ~kFsTYA~wWIrqaI~raI~~q~rtIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~  232 (342)
T COG0568         153 FKFSTYATWWIRQAITRAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEP  232 (342)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCC
T ss_conf             72110999999999999999742346576999999999999999999984589979999999599999999999865367


Q ss_pred             CCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHC-CCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCC
Q ss_conf             7553635889986047562389889989999999999999999732-998899999998187986746889998996678
Q gi|254780289|r  574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT  652 (682)
Q Consensus       574 ~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~-l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~  652 (682)
                      +|||+|+|+|+|+.++||++|.+..+|++.+.+.++++.+..+|++ |+|||+.||++|||++++.|+||+|||+.||||
T Consensus       233 ~SLd~~ig~ded~~l~d~leD~~~~~p~~~~~~~~~~~~~~~~L~~~Lt~rE~~Vi~~R~gl~~~~~~TLeevg~~~~vs  312 (342)
T COG0568         233 ISLDTPIGDDEDSELGDFLEDDKSVSPEDAVERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEPKTLEELGEEFGIS  312 (342)
T ss_pred             CCCCCCCCCCCCCHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHCCC
T ss_conf             67678488885207888764268789899999888999999998715999999999999556799955199999895986


Q ss_pred             HHHHHHHHHHHHHHHC-CHHHHHHHHHHHC
Q ss_conf             9999999999999832-9677787566517
Q gi|254780289|r  653 RERIRQIEAKAIRKLK-HPSRSKKLRSFLD  681 (682)
Q Consensus       653 ~er~rqi~~~a~~~l~-~~~~~~~l~~~~~  681 (682)
                      ||||||||++||+||| ||.++..|++|++
T Consensus       313 rERvRQIE~kAl~KLr~~~~~~~~~~~~l~  342 (342)
T COG0568         313 RERVRQIEAKALRKLRRHPERSALLRSYLD  342 (342)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             999999999999999870632227777539


No 10 
>PRK05949 RNA polymerase sigma factor; Validated
Probab=100.00  E-value=0  Score=650.02  Aligned_cols=245  Identities=43%  Similarity=0.793  Sum_probs=235.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHH
Q ss_conf             99987653321124689998755578999887522356777887544367999988743854573120102898999999
Q gi|254780289|r  430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT  509 (682)
Q Consensus       430 i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~  509 (682)
                      +.+.+..|    ++||++||+|||||||||||+|.|+|++|.|||||||+|||+||+||||.|||||||||+|||||+|+
T Consensus        82 l~~~~~~g----~~A~~~LI~sNLRLVvsIAkrY~~~Gl~~~DLIQEGniGLirAvekFDp~rG~RFSTYA~wWIRq~I~  157 (327)
T PRK05949         82 LKQALKQG----KRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAIT  157 (327)
T ss_pred             HHHHHHHH----HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEHHHHHHHHHH
T ss_conf             99998758----99999999981999999998643699898999998589999999980965597134200999989999


Q ss_pred             HHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEE
Q ss_conf             99972287046142058898999999999877608899978999870999899999998608987553635889986047
Q gi|254780289|r  510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG  589 (682)
Q Consensus       510 ~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~  589 (682)
                      |||.+|+|+||+|+|+.+.++++.++.+++.+++||.||++|||+.||+++++|+.++.+++.|+|||.|+|++++++++
T Consensus       158 r~i~~~~r~IRlP~~~~~~~~ki~~~~~~l~~~lgr~pt~~EiA~~l~i~~~~v~~~l~~~~~~~SLD~~v~d~~~~~l~  237 (327)
T PRK05949        158 RAIAQQARTIRLPIHITEKLNKIKKTQRELSQKLGRSATPAEIAKALELEPSQIREYLSMARQPISLDVRVGDNQDTELS  237 (327)
T ss_pred             HHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHH
T ss_conf             99998288744637899999999999999999818899889999894999999999998418872236746999740266


Q ss_pred             EEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             56238988998999999999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       590 ~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      |+++|.+ .+|++.+....+++.+..+|+.|+|||+.||++||||+++.|+||+|||+.||||||||||||.+||+||||
T Consensus       238 dll~d~~-~~pe~~~~~~~lr~~l~~~L~~L~~REr~Ii~~RfGl~~~~~~TL~EIg~~lgiSrERVRQIE~rAL~KLR~  316 (327)
T PRK05949        238 ELLEDEG-VSPDQYITQELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGQRLNLSRERVRQLEHQALAHLRR  316 (327)
T ss_pred             HHHCCCC-CCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             6733688-999999999999999999985699999999999718999698579999999895999999999999999862


Q ss_pred             HHHHHHHHHHHC
Q ss_conf             677787566517
Q gi|254780289|r  670 PSRSKKLRSFLD  681 (682)
Q Consensus       670 ~~~~~~l~~~~~  681 (682)
                        |+..|+.||-
T Consensus       317 --~~~~l~~y~~  326 (327)
T PRK05949        317 --RRANVKEYIA  326 (327)
T ss_pred             --CHHHHHHHHC
T ss_conf             --5788899865


No 11 
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=100.00  E-value=0  Score=645.57  Aligned_cols=239  Identities=44%  Similarity=0.798  Sum_probs=232.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEE
Q ss_conf             11246899987555789998875223567778875443679999887438545731201028989999999997228704
Q gi|254780289|r  440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI  519 (682)
Q Consensus       440 e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~  519 (682)
                      ...+||.+||+|||||||||||+|.|+|++|.|||||||+|||+||+||||.|||||||||+|||||+|+|+|.+++|+|
T Consensus        79 ~g~~A~~~lv~~NLRLVv~iAk~y~~~gl~~~DLIQEGniGLi~AvekFDp~rG~rFSTYA~wWIrq~I~r~i~~~~r~I  158 (318)
T PRK07405         79 EGEAAKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTI  158 (318)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEHHHHHHHHHHHHHHHCCCCC
T ss_conf             27999999999819999999986657997988999986899999999709765980222009999999999999769851


Q ss_pred             ECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCC
Q ss_conf             61420588989999999998776088999789998709998999999986089875536358899860475623898899
Q gi|254780289|r  520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS  599 (682)
Q Consensus       520 r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~  599 (682)
                      |+|+|+.+.++++.++.+++.+++||+||++|||+.+|+++++|..++..++.|+|||.|+|++++++++|+++|.+ .+
T Consensus       159 RlP~~~~~~~~ki~~~~~~L~~~lGr~Pt~~EIAe~lgi~~e~V~~~l~~~~~~~SLD~~v~d~~~~~l~dll~D~~-~~  237 (318)
T PRK07405        159 RLPIHITEKLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDDG-AS  237 (318)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHCCCC-CC
T ss_conf             68778999999999999999987189864899998859999999999998078867688889998640566754788-98


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHHHH
Q ss_conf             89999999999999999732998899999998187986746889998996678999999999999983296777875665
Q gi|254780289|r  600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF  679 (682)
Q Consensus       600 ~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~~~  679 (682)
                      |++.+....++..+..+|+.|+|||+.||++||||+++.|+||+|||+.||||||||||||.+||.|||+  |+..|++|
T Consensus       238 pe~~~~~~~l~~~L~~~L~~L~eREr~II~lRfGl~~~~~~TL~EIg~~lgvSrERVRQIE~~AL~KLR~--~~~~l~~y  315 (318)
T PRK07405        238 PEDFATQSSLRRDLERLMADLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRK--RKANIQEY  315 (318)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH--HHHHHHHH
T ss_conf             7999999999999999996299989999999807789897479999989795999999999999999987--28888998


Q ss_pred             HC
Q ss_conf             17
Q gi|254780289|r  680 LD  681 (682)
Q Consensus       680 ~~  681 (682)
                      |-
T Consensus       316 l~  317 (318)
T PRK07405        316 LA  317 (318)
T ss_pred             HC
T ss_conf             63


No 12 
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=100.00  E-value=0  Score=645.02  Aligned_cols=234  Identities=41%  Similarity=0.739  Sum_probs=229.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCC
Q ss_conf             68999875557899988752235677788754436799998874385457312010289899999999972287046142
Q gi|254780289|r  444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV  523 (682)
Q Consensus       444 AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~  523 (682)
                      |+++||+|||||||||||+|.|+|++|.|||||||+|||+||+||||.|||||||||+|||||+|.|||.+|+|+||+|+
T Consensus        90 Ar~~LI~sNLRLVvsIAkkY~~~Gl~l~DLIQEGniGLikAveKFDp~rG~RFSTYA~WWIRq~I~raI~~~~r~IRlP~  169 (328)
T PRK05657         90 ARQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPV  169 (328)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             99999998189999999855689989899998868999999997197669984230099999999999996577777561


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHH
Q ss_conf             05889899999999987760889997899987099989999999860898755363588998604756238988998999
Q gi|254780289|r  524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS  603 (682)
Q Consensus       524 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~  603 (682)
                      |+.+.+|++.++.+++.+.+||+||++|||+.+|+++++|..++..++.++|||+|+|.|++.+++|+++|.+..+|++.
T Consensus       170 ~~~~~l~~i~ra~~~l~~~~gr~pt~eEIA~~lg~~~~~v~~~l~~~~~~~SLD~pv~~d~~~tl~d~l~D~~~~~pd~~  249 (328)
T PRK05657        170 HVVKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDAPLGGDPEKSLLDILADDQENGPEDT  249 (328)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCHHHH
T ss_conf             19999999999999999984899989999999695999999999745876344453589985117888627789999999


Q ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHH
Q ss_conf             99999999999997329988999999981879867468899989966789999999999999832967778756
Q gi|254780289|r  604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR  677 (682)
Q Consensus       604 ~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~  677 (682)
                      +....++..+..+|+.|+|||+.||++||||+++.|+||+|||+.||||||||||||.+||+|||++.++..|.
T Consensus       250 ~~~~~l~~~l~~~L~~L~~REr~II~~RfGL~~~e~~TL~EIg~~lgvSRERVRQIE~~AL~KLR~~l~~~~l~  323 (328)
T PRK05657        250 TQDDDLKQSIVKWLFELNDKQREVIERRFGLNGYEAATLEEVAREIGLTRERVRQIQVEALRRLREILQTQGLS  323 (328)
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             99999999999998069999999999980889989605999998969799999999999999987999986997


No 13 
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS; InterPro: IPR012761   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 RpoS (also called sigma-38, KatF, etc.), found only in proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second principal sigma factor at that time.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=100.00  E-value=0  Score=646.57  Aligned_cols=231  Identities=45%  Similarity=0.742  Sum_probs=226.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECC
Q ss_conf             46899987555789998875223567778875443679999887438545731201028989999999997228704614
Q gi|254780289|r  443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP  522 (682)
Q Consensus       443 ~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~  522 (682)
                      .||+.|||+||||||||||+|.|||+||+|||-|||+|||+||+||||.|||||||||||||||+|-|||-.||||||+|
T Consensus        46 eAR~~MIE~NLRLVV~IAk~Y~nRGlpLlDLIEEGNLGLm~AvEKFDPeRGFRFSTYATWWIRQtIERAIMNQaRTiRLP  125 (292)
T TIGR02394        46 EARKKMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLP  125 (292)
T ss_pred             HHHHHHHHHHCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEECC
T ss_conf             89888776401267678644047651457777653356654210458899984430111366532786531354411053


Q ss_pred             CHHHHHHHHHHHHHHHHHH---HCC---CCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCC-CCEEEEEECCC
Q ss_conf             2058898999999999877---608---8999789998709998999999986089875536358899-86047562389
Q gi|254780289|r  523 VHMRDKIHKVVRTARRMSN---KIK---REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED-TSHLGDFIEDK  595 (682)
Q Consensus       523 ~~~~~~~~~~~~~~~~~~~---~~~---~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~-~~~~~~~~~d~  595 (682)
                      ||++.-+|.+.|++|+|.+   ..|   ||||+||||+.++=|+++|.++|..+-.++|||+|++.|. ..+++|+|+|.
T Consensus       126 vHV~kELNv~LRa~r~L~~ns~~~~E~~~EpS~eeiA~~~~kpvedv~~~L~Lne~~~S~D~Pl~~D~n~~Sl~d~~ADe  205 (292)
T TIGR02394       126 VHVVKELNVYLRAARQLEKNSAKLDEEEREPSVEEIAELLDKPVEDVSKVLALNERIASLDAPLDEDSNSKSLLDTIADE  205 (292)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCEEEECCCCCCCCCHHHHHCCCCC
T ss_conf             14346777999988876556763373357788789998838988899999841799525305778774301210004788


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHH
Q ss_conf             889989999999999999999732998899999998187986746889998996678999999999999983296777
Q gi|254780289|r  596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS  673 (682)
Q Consensus       596 ~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~  673 (682)
                      +..+|+..+....|+..+...|+.|+.|++.||..||||.+.++.|||+||..+|+||||||||..-||.||||--..
T Consensus       206 ~~~~P~~~~~~~~l~~~~~~~L~~Lne~~R~V~~rRFGL~g~E~~TLE~va~~~gLTRERvRQIQ~eaL~~Lr~~L~~  283 (292)
T TIGR02394       206 QSIDPESLVQNDDLKQLIEAWLAELNERQREVLARRFGLRGYEKATLEEVAKELGLTRERVRQIQVEALKKLRRILER  283 (292)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHCHHHHEEHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             877807642189999999998861063211210100376654266699999872881047899889999999999986


No 14 
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=100.00  E-value=0  Score=510.83  Aligned_cols=226  Identities=32%  Similarity=0.506  Sum_probs=192.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECC
Q ss_conf             46899987555789998875223567778875443679999887438545731201028989999999997228704614
Q gi|254780289|r  443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP  522 (682)
Q Consensus       443 ~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~  522 (682)
                      .|+++||+|||||||||||+|.|+|+++.|||||||||||+||+||||+|||||||||+|||||+|+|+|.++||+||+|
T Consensus        48 ~A~~~Li~sNLRLVvsiAkky~~~gl~l~DLIQEGniGLikAvekFDp~kG~rFSTYA~wWIrq~I~r~i~~~~r~Vrip  127 (284)
T PRK06596         48 EAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVA  127 (284)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHH
T ss_conf             99999999867999999984678999989999998999999997058998998186799999999999998745613788


Q ss_pred             CHHHHHHHHHHHHHHHHHH--HCCCCCCHHHHHHHCCCCHHHHHHHH-HHHCCCCCCCCCCCCCCCC--EEEEEECCCCC
Q ss_conf             2058898999999999877--60889997899987099989999999-8608987553635889986--04756238988
Q gi|254780289|r  523 VHMRDKIHKVVRTARRMSN--KIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS--HLGDFIEDKNA  597 (682)
Q Consensus       523 ~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~sl~~~~~~~~~~--~~~~~~~d~~~  597 (682)
                      +|..+.  ++....++..+  ...++|+.++||+.||++.++|..+. +++..++|||+|++++++.  .+.|+++|.. 
T Consensus       128 ~~~~~r--kl~~~lr~~~~~~~~~~~~~~~eiA~~l~~~~~~v~~~~~~l~~~~~SLd~~~~~~~~~~~~~~d~l~d~~-  204 (284)
T PRK06596        128 TTKAQR--KLFFNLRKAKKRLGWLNPEEVEMIAEELGVSEEEVREMESRLSGQDASLDAPIDDDDGESGAPQDYLEDKS-  204 (284)
T ss_pred             HHHHHH--HHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHCCCC-
T ss_conf             899999--99999999999871459862999999979199999999998537982023788888777542466514678-


Q ss_pred             CCHHHHHHHH----HHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHH
Q ss_conf             9989999999----999999999732998899999998187986746889998996678999999999999983296777
Q gi|254780289|r  598 VSPLDSAIQA----NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS  673 (682)
Q Consensus       598 ~~~~~~~~~~----~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~  673 (682)
                      .+|++.+...    .++..|..+|+.|+|||+.||++|||.  +.|+||+|||+.||||||||||||.+||+|||+.-++
T Consensus       205 ~~~~~~~~~~~~~~~~~~~L~~al~~L~~REr~Il~~Ry~~--d~~~TL~EIg~~lgiSrERVRQIe~kAL~KLR~~L~~  282 (284)
T PRK06596        205 SDPAAVLEEDNWEDQRRELLADALETLDERSRDIIEARWLD--DDKSTLQELAAEYGVSAERIRQIEKNAMKKLKAAIEA  282 (284)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             98678999999999999999999860999999999997679--9994899999997979999999999999999999880


No 15 
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=100.00  E-value=0  Score=478.08  Aligned_cols=236  Identities=32%  Similarity=0.483  Sum_probs=202.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEEC
Q ss_conf             24689998755578999887522356777887544367999988743854573120102898999999999722870461
Q gi|254780289|r  442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI  521 (682)
Q Consensus       442 ~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~  521 (682)
                      ..|+++||++|||||+|||++|.|+|+++.|||||||+|||+||+||||+|||||||||+|||||+|.|+|.+++++||+
T Consensus        39 ~~Ar~~LI~~NLRLV~~iA~ry~~~g~~l~DLIQeG~iGLi~AvekFDp~rG~rFSTYA~wWIr~aI~r~i~~~~~~iR~  118 (289)
T PRK07500         39 EDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFDPDRDVRFSTYATWWIRASIQDYILRNWSIVRG  118 (289)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             99999999985899999998745899897899998699999999736988899721101999999998877736651000


Q ss_pred             CCHHHHHH--HHHHHHHHHH---HHHCCCCCCHHHHHHHCCCCHHHHHHHH-HHHCCCCCCCCCCCCCCCCE--EEEEEC
Q ss_conf             42058898--9999999998---7760889997899987099989999999-86089875536358899860--475623
Q gi|254780289|r  522 PVHMRDKI--HKVVRTARRM---SNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTSH--LGDFIE  593 (682)
Q Consensus       522 ~~~~~~~~--~~~~~~~~~~---~~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~sl~~~~~~~~~~~--~~~~~~  593 (682)
                      |+|..+..  .++.+...++   ...+++.|+.+|||+.||+|+++|..+. ++...++||+.|++++++.+  +.|++.
T Consensus       119 p~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~SL~~~~~~d~~~~~~~~d~l~  198 (289)
T PRK07500        119 GTSSAQKALFFNLRRLRARLAQSDEQLTKHEIHREIATALGVSLSDVEMMDARLSGPDSSLNAPQSEEDEGRSERMDFLV  198 (289)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHC
T ss_conf             03887899999999999999986154565543999998809999999999999737986666806787777401555404


Q ss_pred             CCCCCCHHHHHH----HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             898899899999----9999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  594 DKNAVSPLDSAI----QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       594 d~~~~~~~~~~~----~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      |.. +.|++.+.    ...++..|..+|+.|++||+.||++|||.  +.|.||.|||+.|||||||||||+.+||+|||+
T Consensus       199 d~~-~~p~~~~e~~~~~~~~~~~L~~~l~~L~eREr~Ii~~r~~~--~e~~TL~EIg~~lgvSreRVRQIe~kAL~KLR~  275 (289)
T PRK07500        199 DDS-PLPDEIVESSIDGERRRQWLTQALQTLNERELFIIRERRLR--EDGATLEALGEELGISKERVRQIEARALEKLRR  275 (289)
T ss_pred             CCC-CCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             688-98389999999999999999999854999999999997668--998589999999797999999999999999999


Q ss_pred             H--HHHHHHHHHH
Q ss_conf             6--7778756651
Q gi|254780289|r  670 P--SRSKKLRSFL  680 (682)
Q Consensus       670 ~--~~~~~l~~~~  680 (682)
                      .  +++.-++.|+
T Consensus       276 ~L~~~~~e~~~~~  288 (289)
T PRK07500        276 ALLSQSPEAAYFL  288 (289)
T ss_pred             HHHHHCHHHHHHH
T ss_conf             9998477988863


No 16 
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00  E-value=0  Score=478.33  Aligned_cols=236  Identities=24%  Similarity=0.382  Sum_probs=216.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHH
Q ss_conf             88999999876533211246899987555789998875223567778875443679999887438545731201028989
Q gi|254780289|r  425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV  504 (682)
Q Consensus       425 ~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i  504 (682)
                      ..|..-+..|-.|..+.++||++||++|||||++||++|.|+|+++.||||+||+|||+||+||||+|||||||||+|||
T Consensus        21 ~~~~~~~~~~~~~~~~~~~aR~~lI~~nLrLV~~iA~ry~~rGl~~~DLiQeG~iGLi~A~ekFDp~rG~rFsTYA~~wI  100 (263)
T PRK07122         21 PEMFRELAGLPAGSPEFQRQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVEAGSDFVSFAVPTI  100 (263)
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHH
T ss_conf             99999998568999899999999999909999999987216898888999999999999999719877998599999999


Q ss_pred             HHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHH--HCCCCCCCCCCCC
Q ss_conf             99999999722870461420588989999999998776088999789998709998999999986--0898755363588
Q gi|254780289|r  505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGD  582 (682)
Q Consensus       505 ~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~sl~~~~~~  582 (682)
                      ||+|.+++.+++|+||+|+|+.+...++.++..++.+++||+||++|||+.||++.++|..++..  ...|+|||.|+++
T Consensus       101 rgaI~r~lr~~~~~IRlP~~~~~~~~ki~~~~~~l~~~~gr~Pt~~EiA~~lg~~~~~v~~~l~~~~~~~~~SlD~~~~~  180 (263)
T PRK07122        101 MGEVRRHFRDNSWSVKVPRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSSYNTLSIDSGGGS  180 (263)
T ss_pred             HHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCC
T ss_conf             99999999982875465799999989999999999998688999999998969399999999987335898778788888


Q ss_pred             CCCC--EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             9986--04756238988998999999999999999973299889999999818798674688999899667899999999
Q gi|254780289|r  583 EDTS--HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE  660 (682)
Q Consensus       583 ~~~~--~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~  660 (682)
                      +++.  .+.|.+.|.+     ........++.+..+|+.|++||+.||++|||    .++||.|||+.||||+||||||+
T Consensus       181 ~~~~~~~l~d~~~d~~-----~~~e~~~~~~~L~~~l~~L~eREr~Vi~lry~----e~~Tl~EIa~~lGiSreRVrQIe  251 (263)
T PRK07122        181 GDDDARAIADTLGDVD-----AGLDHIENREALRPLLAALPERERTVLVLRFF----ESMTQTQIAERVGISQMHVSRLL  251 (263)
T ss_pred             CCCCCCHHHHHCCCCC-----HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHC----CCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             8865203546416976-----42899999999999997599999999999956----99989999999897999999999


Q ss_pred             HHHHHHHCC
Q ss_conf             999998329
Q gi|254780289|r  661 AKAIRKLKH  669 (682)
Q Consensus       661 ~~a~~~l~~  669 (682)
                      .+||.|||.
T Consensus       252 ~~AL~KLR~  260 (263)
T PRK07122        252 AKSLARLRD  260 (263)
T ss_pred             HHHHHHHHH
T ss_conf             999999999


No 17 
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=100.00  E-value=0  Score=466.21  Aligned_cols=248  Identities=21%  Similarity=0.398  Sum_probs=221.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             33222221126889999998765-33211246899987555789998875223567778875443679999887438545
Q gi|254780289|r  414 KSISVETGISISEFRHIVSMVRK-GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL  492 (682)
Q Consensus       414 ~~ie~~~gl~i~ElK~i~r~I~~-ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~  492 (682)
                      .++.+..-|+..|..++.++.+. |.   ..|+++||++|||||++||++|.++|+++.|||||||+|||+||+||||+|
T Consensus         2 ~~~~~~~~Lt~eee~~L~~~~~~~gd---~~Ar~~Li~~nlrLV~~iA~~y~~~g~~~~DLiQeG~iGLi~AiekFDp~r   78 (257)
T PRK08583          2 KESSQPTKLTKEDVNQWIAEYQENQD---EEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDYSF   78 (257)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHCCC---HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             86768999999999999999988199---999999999849999999998626898861799999999999987069865


Q ss_pred             CCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHC-
Q ss_conf             7312010289899999999972287046142058898999999999877608899978999870999899999998608-
Q gi|254780289|r  493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK-  571 (682)
Q Consensus       493 g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-  571 (682)
                      ||||||||+|||||+|.+++.+++|+||+|+|+.+.++++.++..++.+++||.||++|||+.||++.++|..++.... 
T Consensus        79 G~rFsTYA~~wIr~~I~~~lr~~~~~ir~P~~~~~~~~ki~~~~~~l~~~~~r~pt~~eiA~~l~~s~e~v~~~l~~~~~  158 (257)
T PRK08583         79 GRSFEAFAVPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELTDELQRSPKISEIADRLGVSEEEVLEAMEMGKS  158 (257)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCC
T ss_conf             88839878999999999999964871135499999988899999999998089987999998959599999999997516


Q ss_pred             -CCCCCCCCCCCCCCC---EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHH
Q ss_conf             -987553635889986---0475623898899899999999999999997329988999999981879867468899989
Q gi|254780289|r  572 -EPISLETPIGDEDTS---HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK  647 (682)
Q Consensus       572 -~~~sl~~~~~~~~~~---~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~  647 (682)
                       .++|||.|++++++.   ++.|.+.+     |++.......+..+..++..|++||+.||.+|||    .+.|+.|||+
T Consensus       159 ~~~~Sld~~~~~d~d~~~~~~~d~~~~-----~e~~~e~~e~~~~l~~~l~~L~erEr~Ii~lry~----~~~t~~eIa~  229 (257)
T PRK08583        159 YQALSVDHSIEADSDGSTVTLLDIVGQ-----QEDGYELTEQRMILEKILPVLSDREKSIIQCTFI----ENLSQKETGE  229 (257)
T ss_pred             CCCCCCCCCCCCCCCCCCCCHHHCCCC-----CCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHC----CCCCHHHHHH
T ss_conf             897027888877888771204330489-----6624789999999999995499999999999957----9999999999


Q ss_pred             HHCCCHHHHHHHHHHHHHHHCCHHHH
Q ss_conf             96678999999999999983296777
Q gi|254780289|r  648 QFCVTRERIRQIEAKAIRKLKHPSRS  673 (682)
Q Consensus       648 ~~~~~~er~rqi~~~a~~~l~~~~~~  673 (682)
                      .||||+||||||+.+||.|||++.+.
T Consensus       230 ~lGiS~eRVrQi~~~Al~kLR~~~~~  255 (257)
T PRK08583        230 RLGISQMHVSRLQRQAIKKLREAAFL  255 (257)
T ss_pred             HHCCCHHHHHHHHHHHHHHHHHHHCC
T ss_conf             98969999999999999998777505


No 18 
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=100.00  E-value=0  Score=459.20  Aligned_cols=240  Identities=30%  Similarity=0.456  Sum_probs=213.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEE
Q ss_conf             22221126889999998765332112468999875557899988752235677788754436799998874385457312
Q gi|254780289|r  417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF  496 (682)
Q Consensus       417 e~~~gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f  496 (682)
                      ...--|+..|.+++.++++.|.   ..|+++||++|||||+|||++|.|+|+++.|||||||+|||+||+||||.|||||
T Consensus        14 ~k~PlLt~EEe~~L~~~~~~gD---~~Ar~~LI~~nLrLV~~iA~ky~~~g~~~~DLiQeG~iGLi~AiekFDp~rG~rF   90 (257)
T PRK08215         14 SKLPVLKNEEMKELFRRMQNGD---TSAREKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKAIDNFDLSQNVKF   90 (257)
T ss_pred             CCCCCCCHHHHHHHHHHHHHCC---HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCE
T ss_conf             2489999999999999999388---9999999998789999999876589989889999879999999997097679954


Q ss_pred             EHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCC
Q ss_conf             01028989999999997228704614205889899999999987760889997899987099989999999860898755
Q gi|254780289|r  497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL  576 (682)
Q Consensus       497 ~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl  576 (682)
                      ||||+|||||+|.++|.++ ++||+|.|+....+++.+...++.+++||+||++|||+.||++.++|..++...+.|+||
T Consensus        91 sTYA~~wIr~~I~~~i~~~-~~irip~~~~~~~~k~~~~~~~l~~~~~r~pt~~eiA~~l~i~~~~v~~~l~~~~~~~SL  169 (257)
T PRK08215         91 STYAVPMIIGEIRRYLRDN-NPIRVSRSLRDIAYKALQVREKLIKENSKEPTVSEIAKELEVPREEVVFALDAIQDPVSL  169 (257)
T ss_pred             EEHHHHHHHHHHHHHHHHC-CCCEEEHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCC
T ss_conf             3211999999999999967-985100999999999999999999983899999999988098999999999863898667


Q ss_pred             CCCCCCCCCC--EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHH
Q ss_conf             3635889986--04756238988998999999999999999973299889999999818798674688999899667899
Q gi|254780289|r  577 ETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE  654 (682)
Q Consensus       577 ~~~~~~~~~~--~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~e  654 (682)
                      +.|+++|++.  ++.|.+.|..... ...+.    ...+.++|+.|+|||+.||++||+    .++|+.|||+.||||||
T Consensus       170 ~~~~~~d~~d~~~~~d~~~d~~~~~-~~~~~----~~~l~~~l~~L~~REr~Ii~~ry~----~~~Tl~eIa~~lGvSre  240 (257)
T PRK08215        170 FEPIYHDGGDPIFVMDQISDEKNKD-EQWLE----EIALKEAMKRLNDREKMILNLRFF----QGKTQMEVADEIGISQA  240 (257)
T ss_pred             CCCCCCCCCCCHHHHHCCCCCCCCC-HHHHH----HHHHHHHHHCCCHHHHHHHHHHHC----CCCCHHHHHHHHCCCHH
T ss_conf             6855578997104422147976550-89999----999999996499999999999947----99989999999896999


Q ss_pred             HHHHHHHHHHHHHCC
Q ss_conf             999999999998329
Q gi|254780289|r  655 RIRQIEAKAIRKLKH  669 (682)
Q Consensus       655 r~rqi~~~a~~~l~~  669 (682)
                      ||||||.+||.|||.
T Consensus       241 RVrQie~~AL~kLR~  255 (257)
T PRK08215        241 QVSRLEKAALKHMRK  255 (257)
T ss_pred             HHHHHHHHHHHHHHH
T ss_conf             999999999999985


No 19 
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00  E-value=0  Score=455.36  Aligned_cols=234  Identities=25%  Similarity=0.401  Sum_probs=205.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHH
Q ss_conf             999998765332112468999875557899988752235-6777887544367999988743854573120102898999
Q gi|254780289|r  428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR-GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ  506 (682)
Q Consensus       428 K~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~-~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~  506 (682)
                      .++.++.+.  ..-.+|+++||++|||||++||++|.++ |+++.||||+||+|||+||+||||.+||||||||+|||||
T Consensus        12 ~eL~~~y~~--~gd~~ar~~LI~~nlrLV~~iA~ry~~~~~~~~~DLiQeG~iGLi~AvekFDp~kG~rFsTYA~~wIr~   89 (256)
T PRK07408         12 MELLRAYQQ--TPSIALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLEQVGYLGLIRAIERFDPSKGHAFSSFAVPYIRG   89 (256)
T ss_pred             HHHHHHHHH--CCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHH
T ss_conf             999999988--499999999999809999999998615799987899999999999999973973389889999999999


Q ss_pred             HHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHH--HHCCCCCCCCCCCCCC
Q ss_conf             99999972287046142058898999999999877608899978999870999899999998--6089875536358899
Q gi|254780289|r  507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDED  584 (682)
Q Consensus       507 ~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~sl~~~~~~~~  584 (682)
                      +|.++|.+++|+||+|+|+.+..+++.++...+.+++||+||.+|||+.||+|+++|..++.  .+..|+|||.|+++++
T Consensus        90 ~I~~~lr~~~~~iRiP~~~~~~~~ki~~~~~~l~~~~gr~pt~~EiA~~l~is~~~v~~~~~~~~~~~~~SLd~~~~~~~  169 (256)
T PRK07408         90 EIQHYLRDKSPTVRIPRRWLELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRMPLSLDAPVSQDE  169 (256)
T ss_pred             HHHHHHHHHCCCEECCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCEECCCCCCCCC
T ss_conf             99999998089741369999999999999999999878999899999895969999999999872788730566477999


Q ss_pred             C--CEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             8--60475623898899899999999999999997329988999999981879867468899989966789999999999
Q gi|254780289|r  585 T--SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK  662 (682)
Q Consensus       585 ~--~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~  662 (682)
                      +  .+++|.++|++...+.....   .+..+.++|..|++||+.||++|||.+    .||.|||+.||||++|||||+.+
T Consensus       170 d~~~~l~d~l~d~~~~~~~~~~e---~~~~L~~~l~~L~eREr~Il~~ry~~~----~tl~EIa~~lgvS~~rVsqi~~~  242 (256)
T PRK07408        170 DGSTSLGDLLPDPRYRSFQLAQE---DRIRLQQALAQLEERTREVLEFVFLHD----LTQKEAAERLGISPVTVSRRVKK  242 (256)
T ss_pred             CCCCHHHHHCCCCCCCHHHHHHH---HHHHHHHHHHCCCHHHHHHHHHHHCCC----CCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             87611777558999753889999---999999998569999999999996379----98999998979899999999999


Q ss_pred             HHHHHCCH
Q ss_conf             99983296
Q gi|254780289|r  663 AIRKLKHP  670 (682)
Q Consensus       663 a~~~l~~~  670 (682)
                      ||.|||+-
T Consensus       243 AL~kLR~~  250 (256)
T PRK07408        243 GLQQLKKL  250 (256)
T ss_pred             HHHHHHHH
T ss_conf             99999997


No 20 
>PRK05572 sporulation sigma factor SigF; Validated
Probab=100.00  E-value=0  Score=448.79  Aligned_cols=235  Identities=29%  Similarity=0.452  Sum_probs=210.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHH
Q ss_conf             11268899999987653321124689998755578999887522356777887544367999988743854573120102
Q gi|254780289|r  421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA  500 (682)
Q Consensus       421 gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya  500 (682)
                      .|+..|-.++.++++.|..   +|+++||++|||||+|||++|.|+|+++.|||||||+|||+||+||||++||||||||
T Consensus        11 ~Ls~eee~~L~~~~~~Gd~---~Ar~~Li~~nlrLV~siA~ry~~~g~~~~DLiQeG~iGLi~A~ekFDp~~G~rFsTYA   87 (251)
T PRK05572         11 QLKDEENKELIKKAQDGDK---EARDKLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYA   87 (251)
T ss_pred             CCCHHHHHHHHHHHHCCCH---HHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHH
T ss_conf             9999999999999980799---9999999985999999998775899998899999999999996225989898402200


Q ss_pred             HHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             89899999999972287046142058898999999999877608899978999870999899999998608987553635
Q gi|254780289|r  501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI  580 (682)
Q Consensus       501 ~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~  580 (682)
                      +|||||+|.++|.+++ +||+|.|+.+..+++.++...+.+.+||.||.+|||+.+|++.++|..++.....+.|++.++
T Consensus        88 ~~wIr~~I~~~ir~~~-~irvp~~~~~~~~ki~~~~~~l~~~~~r~ps~~eia~~lg~~~~~v~~~~~~~~~~~sl~~~~  166 (251)
T PRK05572         88 VPMIIGEIQRFLRDDG-IIKVSRSLKELANKIRKDKEELSKELGRAPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETV  166 (251)
T ss_pred             HHHHHHHHHHHHHHCC-CCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCC
T ss_conf             9999999999998578-766868899999889999999999878899899999997939999999998817987534666


Q ss_pred             CCCCCC--EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             889986--047562389889989999999999999999732998899999998187986746889998996678999999
Q gi|254780289|r  581 GDEDTS--HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ  658 (682)
Q Consensus       581 ~~~~~~--~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rq  658 (682)
                      +++++.  ++.|.++|....  .....    +..+.++|..|++||+.||.+|||    .++||.|||+.||||+|||||
T Consensus       167 ~~~d~~~~~l~d~~~~~~~~--~~~~~----~~~L~~~l~~L~~rEr~Vi~~ry~----~~~tl~EIa~~lgiS~eRVrQ  236 (251)
T PRK05572        167 HENDGDPITLLDQIADQSEE--DDWFD----KIALKEAIRELDERERLIIYLRYF----KDKTQSEVAKRLGISQVQVSR  236 (251)
T ss_pred             CCCCCCHHHHHHHCCCCCHH--HHHHH----HHHHHHHHHCCCHHHHHHHHHHHC----CCCCHHHHHHHHCCCHHHHHH
T ss_conf             67899715665412687346--89999----999999997289999999999817----898899999997979999999


Q ss_pred             HHHHHHHHHCC
Q ss_conf             99999998329
Q gi|254780289|r  659 IEAKAIRKLKH  669 (682)
Q Consensus       659 i~~~a~~~l~~  669 (682)
                      |+.+||+|||.
T Consensus       237 I~~~Al~kLR~  247 (251)
T PRK05572        237 LEKKILKQMKE  247 (251)
T ss_pred             HHHHHHHHHHH
T ss_conf             99999999999


No 21 
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=100.00  E-value=0  Score=444.03  Aligned_cols=242  Identities=24%  Similarity=0.377  Sum_probs=213.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC---CCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHH
Q ss_conf             88999999876533211246899987555789998875223---567778875443679999887438545731201028
Q gi|254780289|r  425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM  501 (682)
Q Consensus       425 ~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~---~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~  501 (682)
                      .++.++.++-.  +..-..|+++||++|||||++||++|.+   .|+++.||||+||+|||+||+||||+|||||||||+
T Consensus         7 ~~~~~lw~~y~--~~~d~~ar~~LI~~nLrLV~~iA~r~~~~~p~~v~~~DLiQeG~iGLi~AiekFDp~kG~rFsTYA~   84 (257)
T PRK05911          7 QNIAETWQLYW--ETQEIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYAL   84 (257)
T ss_pred             HHHHHHHHHHH--HCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH
T ss_conf             78999999998--8399999999999839999999999864699999889999999999999998329866999488769


Q ss_pred             HHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCC--CCCCCCC
Q ss_conf             98999999999722870461420588989999999998776088999789998709998999999986089--8755363
Q gi|254780289|r  502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE--PISLETP  579 (682)
Q Consensus       502 ~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~--~~sl~~~  579 (682)
                      |||||+|.+++..+.|   +|+|+.+.++++.++.+.+.+++||+||.+|||+.||+++++|..++.....  .+||+.+
T Consensus        85 ~wIr~aI~~~lr~~~~---lpr~~~~~~~ki~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~sl~~~  161 (257)
T PRK05911         85 FLIKAAIIDDLRKQDW---VPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEE  161 (257)
T ss_pred             HHHHHHHHHHHHHCCC---CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCEECCCCC
T ss_conf             9989999999987162---5579999999999999999998688999999998839799999999985355222305788


Q ss_pred             CCC--CCC--CEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHH
Q ss_conf             588--998--6047562389889989999999999999999732998899999998187986746889998996678999
Q gi|254780289|r  580 IGD--EDT--SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER  655 (682)
Q Consensus       580 ~~~--~~~--~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er  655 (682)
                      .+.  |++  .++.|.++|+...+|.+.+....++..+.++|..|+|||+.||.+||    +.++||.|||+.|||||||
T Consensus       162 ~~~~~d~~~~~~l~d~i~d~~~~~~~~~~~~~~~~~~L~~al~~L~erEr~Ii~lry----~e~~Tl~EIg~~lgvS~eR  237 (257)
T PRK05911        162 FPSQSDDEAGLALEERIADERAETGYDVVDKKEFSSILANAILALEEKERKVMALYY----YEELVLKEIGKILGVSESR  237 (257)
T ss_pred             CCCCCCCCCCCCHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHC----CCCCCHHHHHHHHCCCHHH
T ss_conf             887888876530777467988899899999999999999998658999999999874----8987899999897988999


Q ss_pred             HHHHHHHHHHHHCCHHHHHHHHHHH
Q ss_conf             9999999999832967778756651
Q gi|254780289|r  656 IRQIEAKAIRKLKHPSRSKKLRSFL  680 (682)
Q Consensus       656 ~rqi~~~a~~~l~~~~~~~~l~~~~  680 (682)
                      ||||+.+||.|||.     .|.+|+
T Consensus       238 VrQi~~~AL~kLR~-----~L~a~~  257 (257)
T PRK05911        238 VSQIHSKALLKLRA-----ALSAFL  257 (257)
T ss_pred             HHHHHHHHHHHHHH-----HHHHCC
T ss_conf             99999999999999-----998609


No 22 
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=100.00  E-value=0  Score=438.67  Aligned_cols=239  Identities=28%  Similarity=0.401  Sum_probs=215.5

Q ss_pred             HHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHC---CCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEE
Q ss_conf             1126889999998765-3321124689998755578999887522---35677788754436799998874385457312
Q gi|254780289|r  421 GISISEFRHIVSMVRK-GECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF  496 (682)
Q Consensus       421 gl~i~ElK~i~r~I~~-ge~e~~~AK~~l~~anlr~v~~~~~~~~---~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f  496 (682)
                      .++..|-+++.++.+. |.   ..|+++||++|||||++||++|.   ++|+++.|||||||+|||+||+||||++||||
T Consensus         7 ~~s~eee~eL~~~~~~~gd---~~ar~~LI~~nlrLV~~iA~~~~~~~~~~~~~~DLiQeG~iGLi~AvekFDp~rG~rF   83 (261)
T PRK06288          7 KYAQQDETELWKSYKETGD---AKIREYLILKYSPLVKYVAGRVAVGMPQNVEFDDLVSYGVFGLLDAIEKFDPEREIKF   83 (261)
T ss_pred             CCCHHHHHHHHHHHHHCCC---HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             2386999999999988199---9999999998599999999998457999999999999999999999996599878883


Q ss_pred             EHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHH--HHCCCC
Q ss_conf             010289899999999972287046142058898999999999877608899978999870999899999998--608987
Q gi|254780289|r  497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPI  574 (682)
Q Consensus       497 ~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~  574 (682)
                      ||||+|||||+|..++....   ++|+|+.+..+++.++...+.+++||.||.+|||+.||+++++|..++.  ....++
T Consensus        84 sTYA~~wIr~aI~~~lR~~~---~~pr~~~~~~~ki~~~~~~l~~~~gr~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~  160 (261)
T PRK06288         84 ETYAITRIRGAIFDELRSID---WIPRSVRQKARQVERAIAMLEAKLGRTPTDDEIAKELGISLEEYHSLLSKVSGTSVV  160 (261)
T ss_pred             HHHHHHHHHHHHHHHHHHHH---HCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCC
T ss_conf             98799999999999999860---031999999999999999999986899987888878199999999999997269974


Q ss_pred             CCCCCCCC---CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCC
Q ss_conf             55363588---998604756238988998999999999999999973299889999999818798674688999899667
Q gi|254780289|r  575 SLETPIGD---EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV  651 (682)
Q Consensus       575 sl~~~~~~---~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~  651 (682)
                      |||.|+..   +++.+++|.++|+...+|+..+....++..+..+|..|++||+.||.+|||    .++||.|||+.|||
T Consensus       161 SLd~~~~~~~~~~~~~~~d~l~d~~~~~p~~~~e~~~~~~~l~~~l~~L~erEr~Il~lry~----e~~Tl~eIa~~lgi  236 (261)
T PRK06288        161 SLNDLLFLGDENDEVSLMDTLEDPAAMNPDEIIEKEEIKRVIVEAINTLPEREKKVITLYYY----EDLTLKEIGEVLGV  236 (261)
T ss_pred             CCCCCCCCCCCCCCCCHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCC----CCCCHHHHHHHHCC
T ss_conf             76777657999864308787058898999999999999999999987089999999999807----99889999999797


Q ss_pred             CHHHHHHHHHHHHHHHCC
Q ss_conf             899999999999998329
Q gi|254780289|r  652 TRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       652 ~~er~rqi~~~a~~~l~~  669 (682)
                      |+||||||+.+||.|||.
T Consensus       237 S~eRVrQie~~AL~kLR~  254 (261)
T PRK06288        237 TESRISQIHTKAVLQLRA  254 (261)
T ss_pred             CHHHHHHHHHHHHHHHHH
T ss_conf             899999999999999999


No 23 
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=100.00  E-value=0  Score=427.92  Aligned_cols=222  Identities=27%  Similarity=0.433  Sum_probs=207.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCC---CCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCC
Q ss_conf             1246899987555789998875223---5677788754436799998874385457312010289899999999972287
Q gi|254780289|r  441 ASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC  517 (682)
Q Consensus       441 ~~~AK~~l~~anlr~v~~~~~~~~~---~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~  517 (682)
                      -..|+++||++|||||++||++|.+   +|+++.||||+||+|||+||+||||++||||||||+|||||+|.+++.+++ 
T Consensus        16 D~~Ar~~LV~~nl~LV~~ia~r~~~~~~~~v~~eDLiQeG~iGLi~AiekFDp~~G~rFsTYA~~wIr~aI~~~lr~~~-   94 (250)
T PRK07670         16 DPEAADDLIRRYMPLVTYHVQRISAGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKED-   94 (250)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCC-
T ss_conf             9999999999819999999999970489999888999999999999999609866999077219999999999987425-


Q ss_pred             EEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHH--HHCCCCCCCCCCCCC-CCCEEEEEECC
Q ss_conf             046142058898999999999877608899978999870999899999998--608987553635889-98604756238
Q gi|254780289|r  518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDE-DTSHLGDFIED  594 (682)
Q Consensus       518 ~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~sl~~~~~~~-~~~~~~~~~~d  594 (682)
                        |+|+|+.+..+++.++..++.+++||.||++|||+.||+++++|..++.  ....++|||.+++++ ++.++.+.+.|
T Consensus        95 --~lpr~~~~~~~ki~~~~~~l~~~~gr~ps~~eia~~lg~s~~~v~~~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~~d  172 (250)
T PRK07670         95 --WLPRSSREKTKKVEAAIEKLEQRYMRNVTPSEVAAELGMSEEEVVTTMNEGFFANLLSIDEKLHDQDDGENVQVMIRD  172 (250)
T ss_pred             --CCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHC
T ss_conf             --400999999999999999999983899988899877199999999999987547980367777788885047788852


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             988998999999999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       595 ~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      +...+|++.+....++..|..+|+.|++||+.||.+||    +.++||.|||+.||||+||||||+.+||.|||.
T Consensus       173 ~~~~~pe~~~~~~~~~~~L~~~l~~L~~rEr~Vl~l~y----~e~~Tl~eIa~~lgvS~erVrQi~~~AL~kLr~  243 (250)
T PRK07670        173 DKAVTPEEKLVKEELIEQLAEKIKELNEKEQLVISLFY----KEELTLTEIGQVLNLSTSRISQIHSKALFKLKK  243 (250)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHC----CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             46799999999999999999998558999999999974----898689999999897999999999999999999


No 24 
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=100.00  E-value=0  Score=417.42  Aligned_cols=221  Identities=27%  Similarity=0.453  Sum_probs=198.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCC---CCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHC
Q ss_conf             2112468999875557899988752235---6777887544367999988743854573120102898999999999722
Q gi|254780289|r  439 CEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ  515 (682)
Q Consensus       439 ~e~~~AK~~l~~anlr~v~~~~~~~~~~---~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~  515 (682)
                      .+.++||++||++|||||++||++|.++   |+++.|||||||+|||+||+||||++||||||||+|||||+|..++...
T Consensus         4 ~~g~~Ar~~Lv~~nl~LV~~iA~r~~~r~~~~v~~~DLiQeG~iGLi~AvekFDp~~G~rFsTYA~~~Ir~aI~~~~r~~   83 (234)
T PRK06986          4 AQGKMSQDSLVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEASRRYDGEQGASFETYAGQRIRGAMLDELRSG   83 (234)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHC
T ss_conf             76899999999981999999999997338999988999999999999999981886699969999999999999999854


Q ss_pred             CCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHH--HCCCCCCCCCCCCCCCCEEEEEEC
Q ss_conf             870461420588989999999998776088999789998709998999999986--089875536358899860475623
Q gi|254780289|r  516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIE  593 (682)
Q Consensus       516 ~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~sl~~~~~~~~~~~~~~~~~  593 (682)
                      .+   +|.++.....++.++.+.+.+++||+||.+|||+.||+++++|..++..  ...++|+|.+..+++ + +.+. .
T Consensus        84 ~~---~~r~~~~~~~~i~~~~~~l~~~~~r~pt~~eia~~l~~s~e~v~~~~~~~~~~~~~sld~~~~~~~-~-~~~~-~  157 (234)
T PRK06986         84 DW---VPRSVRRNAREVADAIRELEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDDLGESGE-L-LTDE-D  157 (234)
T ss_pred             CC---CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC-C-CCCC-C
T ss_conf             56---649999999999999999999878799899999895949999999999850577868776776643-1-1122-2


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             8988998999999999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       594 d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      +....+|.+.+....++..|..+|+.|+|||+.||.+||    +.++||.|||+.|||||||||||+.+||.|||.
T Consensus       158 ~~~~~~~~~~~~~~~~~~~l~~~l~~L~~rEr~Ii~l~y----~~~~tl~eIa~~lgiS~eRVrQie~~AL~kLR~  229 (234)
T PRK06986        158 QSEHEDPLQQLEDEELREALVEAIEKLPEREQLVLSLYY----DEELNLKEIGAVLGVSESRVSQIHSQAIKRLRA  229 (234)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHC----CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             457899999999999999999999809999999999873----899899999999797899999999999999999


No 25 
>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=100.00  E-value=0  Score=418.99  Aligned_cols=252  Identities=28%  Similarity=0.429  Sum_probs=216.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             33222221126889999998765332112468999875557899988752235677788754436799998874385457
Q gi|254780289|r  414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG  493 (682)
Q Consensus       414 ~~ie~~~gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g  493 (682)
                      ..+...--|++.|-..+.++++....  ..|=++||-+||||||+||+.|.|+|||..||||||||||||||.||||.+|
T Consensus         8 ~~vn~~P~L~~EEE~~LA~r~r~~~D--l~AA~~Lv~SHLRfVv~iArgY~GYGL~~aDLIQEGNIGLMkAVkRFdP~~G   85 (279)
T TIGR02392         8 RAVNRIPMLTAEEEQELAKRLREEGD--LDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERG   85 (279)
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHCCC--HHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             99971789998899999998654237--7899987466247875532036777744244342222665533442178987


Q ss_pred             CEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHH-HHHHHHHHHC-CCCCCH---HHHHHHCCCCHHHHHHHH-
Q ss_conf             3120102898999999999722870461420588989999-9999987760-889997---899987099989999999-
Q gi|254780289|r  494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV-RTARRMSNKI-KREPTP---EEIAKKLAMPVEGVRKVL-  567 (682)
Q Consensus       494 ~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~-~~~~~~~~~~-~~~~~~---~~~a~~~~~~~~~~~~~~-  567 (682)
                      +|++|||+||||.+|+.||-.+||+|+|.+...|...+|+ |-.+...+.+ +.--++   +-||+.||++..+|..|- 
T Consensus        86 vRLvSfAvHWIkAeIHEyILrnWRlVKvATTkaQrKLFFNLRk~K~ki~~l~~gw~~~~e~~~~A~~L~V~~~eV~eMe~  165 (279)
T TIGR02392        86 VRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRKLFFNLRKMKKKITRLQDGWLNPEEVEAIAEELGVSEEEVLEMES  165 (279)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf             22047888999999866899755598885277678887658889998631015798989999999763898889988751


Q ss_pred             HHHCCCCCCCCCCCCCCCC-----EEEEEECCCCCCCHHHHHHHHH----HHHHHHHHHHCCCHHHHHHHHHHHCCCCCC
Q ss_conf             8608987553635889986-----0475623898899899999999----999999997329988999999981879867
Q gi|254780289|r  568 KITKEPISLETPIGDEDTS-----HLGDFIEDKNAVSPLDSAIQAN----LRETTTRVLASLTPREERVLRMRFGIGMNT  638 (682)
Q Consensus       568 ~~~~~~~sl~~~~~~~~~~-----~~~~~~~d~~~~~~~~~~~~~~----~~~~~~~~l~~l~~re~~v~~~r~g~~~~~  638 (682)
                      +++...+|||.|+.+++++     ...+++.|+...+|...+....    .+..|..+|.+|+.|++.||..|+  ..+.
T Consensus       166 RlsG~D~~L~~~~~~~~~~~~~~~~~~~yL~D~~~~~~~~~l~~~~~~~~~~~~L~~AL~~Ld~RsR~I~~~Rw--L~d~  243 (279)
T TIGR02392       166 RLSGRDISLNASIDDDEDDGGSDFAPIAYLADKATSDPEATLEEEQWEELQTQKLANALESLDARSRRIIEARW--LDDD  243 (279)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--CCCC
T ss_conf             45537733478876553456311457886304777788899999899999999999998852288799998730--2788


Q ss_pred             -CCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             -4688999899667899999999999998329
Q gi|254780289|r  639 -DHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       639 -~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                       |.||+++|..||||+|||||||+.|+.|||.
T Consensus       244 ~~~TL~~LA~eygvSaERiRQiE~~Am~K~k~  275 (279)
T TIGR02392       244 GKLTLHELAAEYGVSAERIRQIEKNAMKKLKA  275 (279)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             99647899988487466799999999999999


No 26 
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=100.00  E-value=0  Score=406.88  Aligned_cols=209  Identities=31%  Similarity=0.477  Sum_probs=180.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             77653223333222221126889999998765332112468999875557899988752235677788754436799998
Q gi|254780289|r  405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA  484 (682)
Q Consensus       405 eI~~~q~kL~~ie~~~gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a  484 (682)
                      ++.-++.-|.++....-|+..|-..+.++++.|.   ..|+++||+|||||||||||+|.|+|+++.|||||||+|||+|
T Consensus        13 ~~~~l~syl~~i~~~~~Ls~eEE~~La~~~~~GD---~~Ar~~LI~~NLRLVvsIAkky~~~g~~l~DLIQEGniGLi~A   89 (228)
T PRK05803         13 EVLFLVSYVKNNSFPQPLSEEEERKYLELMKQGD---EEARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKA   89 (228)
T ss_pred             HHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHCCC---HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             8999999997478899999999999999998468---9999999998779999999627799989899999999999999


Q ss_pred             HHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHH
Q ss_conf             87438545731201028989999999997228704614205889899999999987760889997899987099989999
Q gi|254780289|r  485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR  564 (682)
Q Consensus       485 ~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~  564 (682)
                      |+||||+|||||||||+||||++|.+++....                                                
T Consensus        90 vekFDp~rG~rFSTYA~~wIr~~I~~~lr~~k------------------------------------------------  121 (228)
T PRK05803         90 IDSFDAGKGTKLATYAARCIENEILMHLRNLK------------------------------------------------  121 (228)
T ss_pred             HHHHCCCCCCCCHHCCHHHHHHHHHHHHHHHH------------------------------------------------
T ss_conf             99848998997052009999999999999988------------------------------------------------


Q ss_pred             HHHHHHCCCCCCCCCCCCCCC---CEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCC
Q ss_conf             999860898755363588998---60475623898899899999999999999997329988999999981879867468
Q gi|254780289|r  565 KVLKITKEPISLETPIGDEDT---SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT  641 (682)
Q Consensus       565 ~~~~~~~~~~sl~~~~~~~~~---~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~t  641 (682)
                          ..+.++|++.|+|.|.+   .++.|++.+... ++.+.+........+..+|+.|+|||+.||++||||+++.|+|
T Consensus       122 ----k~~~~~sl~~~i~~d~e~~e~~l~d~l~~~~~-~~~e~~~~~~~~~~l~~~l~~L~~REr~II~~RfGL~~~~~~T  196 (228)
T PRK05803        122 ----KTKGEVSLQDPIGVDKEGNEISLIDILKSESD-DVIEMVELSMEVEKLYKKIDILDPREKEVIEMRYGLGDGKEKT  196 (228)
T ss_pred             ----HHCCCCCCCCCCCCCCCCCCCHHHHHCCCCCC-CHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCC
T ss_conf             ----75355012374466878983224343168899-8799999999899999998518988999999986478999715


Q ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             8999899667899999999999998329
Q gi|254780289|r  642 LEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       642 l~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      |+|||+.||||||||||||.+||.|||.
T Consensus       197 l~eIg~~lgiSrERVRQIe~~Al~KLrk  224 (228)
T PRK05803        197 QREIAKALGISRSYVSRIEKKALKKLFK  224 (228)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             9999999897999999999999999999


No 27 
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=100.00  E-value=0  Score=403.01  Aligned_cols=192  Identities=26%  Similarity=0.419  Sum_probs=164.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHH
Q ss_conf             12688999999876533211246899987555789998875223567778875443679999887438545731201028
Q gi|254780289|r  422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM  501 (682)
Q Consensus       422 l~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~  501 (682)
                      |+..|-.++.++++.|..   .|+++||+|||||||||||+|.|+|+++.|||||||+|||+||+||||.|||||||||+
T Consensus        39 Ls~eeE~~l~~~~~~GD~---~Ar~~LI~~NLRLVv~IAkky~~~G~~l~DLIqEGniGLikAvekFDp~kG~rFSTYA~  115 (239)
T PRK08301         39 LSKEEEEVLLNKLPKGDE---AVRSILIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYAS  115 (239)
T ss_pred             CCHHHHHHHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHH
T ss_conf             899999999999983469---99999999878999999975768997989999985899999999649888997163019


Q ss_pred             HHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             98999999999722870461420588989999999998776088999789998709998999999986089875536358
Q gi|254780289|r  502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG  581 (682)
Q Consensus       502 ~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~  581 (682)
                      |||+|+|.+++..+.++                                                    +.++|++.|++
T Consensus       116 ~~I~~eI~~~lr~~~~~----------------------------------------------------r~evsl~epl~  143 (239)
T PRK08301        116 RCIENEILMYLRRNNKV----------------------------------------------------RSEVSFDEPLN  143 (239)
T ss_pred             HHHHHHHHHHHHHHHHH----------------------------------------------------HCCCHHCCCCC
T ss_conf             99999999999970424----------------------------------------------------22400015368


Q ss_pred             CCCC---CEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             8998---6047562389889989999999999999999732998899999998187986746889998996678999999
Q gi|254780289|r  582 DEDT---SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ  658 (682)
Q Consensus       582 ~~~~---~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rq  658 (682)
                      -+.+   ..+.|++.+.+ ..+.+.......+..+..+|+.|+|||+.||++||||+++.|+||+|||+.||||||||||
T Consensus       144 ~d~d~~e~~l~D~l~~d~-d~~~~~~e~~~~~~~L~~al~~L~eREr~Ii~lRfGL~~~~~~Tl~EIa~~lgISrerVrQ  222 (239)
T PRK08301        144 IDWDGNELLLSDVLGTDN-DIIYKDIEDEVDKKLLLKALKKLNDREKQIMELRFGLAGGEEKTQKEVADMLGISQSYISR  222 (239)
T ss_pred             CCCCCCHHHHHHCCCCCC-CHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHH
T ss_conf             776656224301148987-5066789999999999999964899999999999578899840699999998978999999


Q ss_pred             HHHHHHHHHCC
Q ss_conf             99999998329
Q gi|254780289|r  659 IEAKAIRKLKH  669 (682)
Q Consensus       659 i~~~a~~~l~~  669 (682)
                      ||.+||+|||.
T Consensus       223 Ie~~AL~KLR~  233 (239)
T PRK08301        223 LEKRIIKRLKK  233 (239)
T ss_pred             HHHHHHHHHHH
T ss_conf             99999999999


No 28 
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=100.00  E-value=1.4e-45  Score=378.77  Aligned_cols=221  Identities=19%  Similarity=0.336  Sum_probs=193.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC---CCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHH
Q ss_conf             987653321124689998755578999887522356---77788754436799998874385457312010289899999
Q gi|254780289|r  432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG---LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI  508 (682)
Q Consensus       432 r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~---~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i  508 (682)
                      +++..+..-+.++|++||++||+||.+||++|.+++   +++.||+|+|++|||+|++|||+++| +|||||+|||||+|
T Consensus         2 ~~~~~~~~~~~~~k~~lV~~~L~LV~~ia~r~~~~~~~~vd~dDLiq~G~iGLi~Ai~rFD~~~g-~F~tYA~~rIrGaI   80 (229)
T PRK12427          2 REFEACLTLTAAEEGKYLNAYLPLVKRIVRQLSFQADSVIGKEDMQQIALMGLLEALRRYGHPDG-QFAAYAVHRIRGSI   80 (229)
T ss_pred             CCCHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCC-CHHHHHHHHHHHHH
T ss_conf             65220356899999999999599999999999742877798888999999999999984499898-85999999999999


Q ss_pred             HHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHH--HCCCCCCCCCCCCCCCC
Q ss_conf             9999722870461420588989999999998776088999789998709998999999986--08987553635889986
Q gi|254780289|r  509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTS  586 (682)
Q Consensus       509 ~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~sl~~~~~~~~~~  586 (682)
                      .+++.++.|   +|+++.+..+++..+.+++.+++||+||++|||+.||+++++|..++..  +..++|||.++++++..
T Consensus        81 ~d~lR~~~~---~pR~~r~~~~ki~~a~~~l~~~lgr~Pt~~EiA~~l~is~~~v~~~~~~~~~~~~~sld~~~~~e~~~  157 (229)
T PRK12427         81 LDQLREHDW---RPRRLRQKTHKTNEAIRQIAKRLGHEPNFEEISAELNLTADEYQEYLLLENAGAMESLDEILALEAHN  157 (229)
T ss_pred             HHHHHHHCC---CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCC
T ss_conf             999987213---75999999999999999999985889999999989199999999999987366875723344578876


Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             04756238988998999999999999999973299889999999818798674688999899667899999999999998
Q gi|254780289|r  587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK  666 (682)
Q Consensus       587 ~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~  666 (682)
                      .   .+.+   .++.   ....++..|..+|++|++||+.||.|||    ..+.||.|||+.||||++|||||+.+||.|
T Consensus       158 ~---~~~~---~~~~---e~~~~~~~L~~al~~L~erEr~Vi~l~y----~e~ltlkEIa~~LgvS~~RVsQi~~kal~k  224 (229)
T PRK12427        158 D---ILQS---RDLE---ENIIIEDNLKQAISQLDEREQMILHLYY----QQELSMKEIAQVLDLTEARICQLNKKLVQK  224 (229)
T ss_pred             C---CCCC---CCHH---HHHHHHHHHHHHHHHCCHHHHHHHHHHC----CCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf             5---4567---6646---7899999999999719999999999980----589989999999798899999999999999


Q ss_pred             HCC
Q ss_conf             329
Q gi|254780289|r  667 LKH  669 (682)
Q Consensus       667 l~~  669 (682)
                      ||.
T Consensus       225 LR~  227 (229)
T PRK12427        225 IKS  227 (229)
T ss_pred             HHH
T ss_conf             884


No 29 
>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=100.00  E-value=0  Score=387.09  Aligned_cols=219  Identities=31%  Similarity=0.507  Sum_probs=205.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEE
Q ss_conf             2468999875557899988752235677-788754436799998874385457312010289899999999972287046
Q gi|254780289|r  442 SIAKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR  520 (682)
Q Consensus       442 ~~AK~~l~~anlr~v~~~~~~~~~~~~~-~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r  520 (682)
                      .+|+.+||++||+||-|||+||.|||.+ +.||+|-|+|||||||||||+++|.+|||||+|.|.++|.||+.|++|+||
T Consensus         2 ~~~R~~Lv~~nlpLv~~~A~RF~~RGe~~~EDL~QVG~iGL~kAidrFD~~~g~~F~tyAVPtI~GEIkR~fRD~~W~vr   81 (229)
T TIGR02980         2 KEAREKLVELNLPLVESIARRFRSRGEPHLEDLVQVGTIGLVKAIDRFDPSYGVKFSTYAVPTIMGEIKRFFRDDTWAVR   81 (229)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCEEEEEEEEEECCCCEEE
T ss_conf             67889999961279999999851378874311578888888877753011116986641046023323133424873266


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCC--CCCCCCCCC-C-CCC-CEEEEEECCC
Q ss_conf             1420588989999999998776088999789998709998999999986089--875536358-8-998-6047562389
Q gi|254780289|r  521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE--PISLETPIG-D-EDT-SHLGDFIEDK  595 (682)
Q Consensus       521 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~--~~sl~~~~~-~-~~~-~~~~~~~~d~  595 (682)
                      ||....|.-++++++...|.+++||.||+.|||+.|++|.++|..+|.+.+.  |.|||+|++ + ||+ .+|+|.|.+.
T Consensus        82 VPRrlkEl~~~~~~a~eeL~~~lgR~Pt~~EiAe~L~~s~EEv~~aleA~~~Y~~~Sld~~~~a~~dg~~~~L~D~lG~~  161 (229)
T TIGR02980        82 VPRRLKELRLKINKATEELTQRLGRSPTVAEIAEELGVSEEEVVEALEAGNSYSALSLDATIEADDDGDPIALLDTLGDE  161 (229)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHCCC
T ss_conf             05138988999999999999982889887899988588999999999865417861120004558888424566444022


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             88998999999999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       596 ~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                           +.......-+.+|..+|+.|||||+.||.|||    -...|=.|||+++|||==-|=-|+++||.|||.
T Consensus       162 -----D~~~e~~~~~~aLk~~l~~LpeRER~il~lRF----f~~~TQ~eiA~~lGiSQMhVSRl~~~~L~~LR~  226 (229)
T TIGR02980       162 -----DDALETVEDRLALKPLLAALPERERRILLLRF----FEDKTQSEIAERLGISQMHVSRLLRRALKRLRE  226 (229)
T ss_pred             -----CCHHHHHHHHHHHHHHHHHCCHHHCEEEEEEE----ECCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHH
T ss_conf             -----43267899999999998507902707610001----069778999978184367889999999999998


No 30 
>TIGR02885 spore_sigF RNA polymerase sigma-F factor; InterPro: IPR014236   The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.   With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , .    Members of this entry represent RNA polymerase sigma factor F. Within the Firmicutes, Sigma-F is specifically, and universally, a component of the endospore formation program, and is expressed in the forespore to turn on the expression of dozens of genes. It is closely related to sigma-G, which is also expressed in the forespore.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=100.00  E-value=2.4e-39  Score=329.58  Aligned_cols=220  Identities=30%  Similarity=0.482  Sum_probs=200.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEE
Q ss_conf             11246899987555789998875223567778875443679999887438545731201028989999999997228704
Q gi|254780289|r  440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI  519 (682)
Q Consensus       440 e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~  519 (682)
                      -=..|.++||+.|+|||.||.+||.|||++..||+|-|||||+|||+|||-+...||||||+|.|.++|.|++.|. +.|
T Consensus         8 GDk~A~dkLi~~N~~LV~siv~rF~nRGYe~eDlFQIGciGLvKAidkFD~~y~VKFSTYAVPmI~GEIkRFLRDD-G~i   86 (231)
T TIGR02885         8 GDKEARDKLIEENLRLVSSIVKRFLNRGYEYEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDD-GII   86 (231)
T ss_pred             HHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHCCC-CCE
T ss_conf             0489999998723346899999852068870000222115566655421767770155212220221222310268-855


Q ss_pred             ECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC--EEEEEECCCCC
Q ss_conf             6142058898999999999877608899978999870999899999998608987553635889986--04756238988
Q gi|254780289|r  520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNA  597 (682)
Q Consensus       520 r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~--~~~~~~~d~~~  597 (682)
                      ||..++.++-+|+.+....|..++||+||++|||+.+|++.++|-.++..++.|-||-.-|++|++.  +|.|-|.|+..
T Consensus        87 kVSRSlK~la~k~~~~kE~L~~~l~R~PTi~Elae~lg~~~EEiv~A~Es~~~~~sly~tvh~dDGdPi~LlD~i~d~~~  166 (231)
T TIGR02885        87 KVSRSLKELARKIRYEKEELTKKLGREPTINELAEALGVSPEEIVMALESARSLQSLYDTVHEDDGDPILLLDQIADKGS  166 (231)
T ss_pred             EEEHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHCCEEECCCCCHHHHHHHHCCCCC
T ss_conf             75152789999998779999998389988899988758788786644202576101100114179464467665212577


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             998999999999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       598 ~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      .+ .+....-    +|.++|..|+|||+.||.+||    -.+.|=-|||..+|+|===|--||.|+|.++|.
T Consensus       167 ~~-~~~~~ki----~Lke~i~~Ld~rer~ii~LRY----FKDkTQ~eVA~~LGISQVQVSRlEkk~L~~~k~  229 (231)
T TIGR02885       167 ED-SDLLEKI----ALKEAISKLDERERQIIMLRY----FKDKTQTEVAKMLGISQVQVSRLEKKVLKKMKE  229 (231)
T ss_pred             CH-HHHHHHH----HHHHHHHHCCCCCCEEEEEEC----CCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHH
T ss_conf             13-6899989----999998612522678977410----140017999977185700122789999999874


No 31 
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=100.00  E-value=2.9e-36  Score=305.21  Aligned_cols=235  Identities=29%  Similarity=0.485  Sum_probs=210.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHH
Q ss_conf             12688999999876533211246899987555789998875223567-77887544367999988743854573120102
Q gi|254780289|r  422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA  500 (682)
Q Consensus       422 l~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~-~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya  500 (682)
                      ++-.++.......+.|.   ..|+ .+|+.||+||.+||.+|.|+|. .+.||||.|++||++||+|||+.+|.+|+|||
T Consensus         6 ~~~~e~~~~~~~~~~g~---~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA   81 (247)
T COG1191           6 LSKEEEEKLLEYYAEGD---EEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYA   81 (247)
T ss_pred             CCHHHHHHHHHHHHHCC---HHHH-HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHH
T ss_conf             24689999999998458---9999-9999978999999999980599854389997899999999974931286148889


Q ss_pred             HHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHC--CCCCCCC
Q ss_conf             89899999999972287046142058898999999999877608899978999870999899999998608--9875536
Q gi|254780289|r  501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLET  578 (682)
Q Consensus       501 ~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~--~~~sl~~  578 (682)
                      .+.|+++|.+++.++. +|++|+...+..+++..+..++.+++||+||.+|||+.||++.++|..++....  .++|++.
T Consensus        82 ~~~I~Gei~d~LR~~~-~v~vpR~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~  160 (247)
T COG1191          82 VRRIRGEILDYLRKND-SVKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDE  160 (247)
T ss_pred             HHHHHHHHHHHHHHCC-CCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCC
T ss_conf             9999999999998478-746768998887788999999999847998689999896989999999998730124541100


Q ss_pred             CCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             35889986047562389889989999999999999999732998899999998187986746889998996678999999
Q gi|254780289|r  579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ  658 (682)
Q Consensus       579 ~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rq  658 (682)
                      .+..++|..     .+....+|.+......+...+.+++..|++||+.|+.+||    ..+.|+-|||+.+|||.-||-|
T Consensus       161 ~~~~~~d~~-----~~~~~~~~~~~~~~~~~~~~l~~~i~~L~EREk~Vl~l~y----~eelt~kEI~~~LgISes~VSq  231 (247)
T COG1191         161 DVLKDDDDD-----VDDQIENPDDGVEKEELLEILKEAIEPLPEREKLVLVLRY----KEELTQKEIAEVLGISESRVSR  231 (247)
T ss_pred             CCCCCCCCC-----HHHCCCCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HHCCCHHHHHHHHCCCHHHHHH
T ss_conf             001356520-----2202356035778899999999998766899999999999----7015799999994914989999


Q ss_pred             HHHHHHHHHCCH
Q ss_conf             999999983296
Q gi|254780289|r  659 IEAKAIRKLKHP  670 (682)
Q Consensus       659 i~~~a~~~l~~~  670 (682)
                      |+.+||.|||+-
T Consensus       232 l~kkai~kLr~~  243 (247)
T COG1191         232 LHKKAIKKLRKE  243 (247)
T ss_pred             HHHHHHHHHHHH
T ss_conf             999999999998


No 32 
>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=100.00  E-value=4.5e-36  Score=303.68  Aligned_cols=215  Identities=30%  Similarity=0.514  Sum_probs=201.0

Q ss_pred             HHHHHHHHHHHHHHHHCCC---CCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCH
Q ss_conf             9875557899988752235---6777887544367999988743854573120102898999999999722870461420
Q gi|254780289|r  448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH  524 (682)
Q Consensus       448 l~~anlr~v~~~~~~~~~~---~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~  524 (682)
                      +|...+.||-.+|.+-..+   .+++.||||.|.+|||.|++|||+.+|.+|.|||+.|||+||--.....-|   +|..
T Consensus         1 l~~~Y~pLVk~~a~rl~~~~P~~v~~~DL~q~G~~GL~dA~~ryd~~~g~~F~TyA~~RIRGAmlDELR~~DW---~PRs   77 (227)
T TIGR02479         1 LIKKYLPLVKRIAGRLVVQLPSSVELDDLIQAGMIGLLDAIERYDPSKGVKFETYAVQRIRGAMLDELRKLDW---VPRS   77 (227)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHCCCCHHHHHHHHHHCCC---CCHH
T ss_conf             9001268999988664310488234875898889999999983188888944100011130205788753066---7836


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHH--HHCCCCCCCCCCCCCCCC----EEEEEECCCCCC
Q ss_conf             58898999999999877608899978999870999899999998--608987553635889986----047562389889
Q gi|254780289|r  525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTS----HLGDFIEDKNAV  598 (682)
Q Consensus       525 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~sl~~~~~~~~~~----~~~~~~~d~~~~  598 (682)
                      ..+..+++.++.+++.+.+||.||.+|||+.|||++++|+.++.  .+..-+|||.-.-+++++    ++.|.|.+++..
T Consensus        78 ~R~~~~~~~~a~~~Le~~LgR~P~~~EiA~~Lg~~~~e~~~~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~~~~~~~~~  157 (227)
T TIGR02479        78 LRQKARKLEEAIEELEARLGREPTEEEIAEELGMDLKEVRQALNEINAESLVSLDELLESGDDGGAEGSLIDLIEDDKSE  157 (227)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHEECCCCCC
T ss_conf             89998689999999999869898888999983999989999999988998764899984146322345323100143576


Q ss_pred             CHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             98999999999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       599 ~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      +|+..+.+..|+..|.++|.+||+||+-||.|+|    .++.||-|||..+|||--||.||+++|+.|||.
T Consensus       158 ~P~~~~~~~~L~~~l~~ai~~L~eRE~LVl~LYY----~eELnLKEIg~VL~lsESRvSQiHs~A~~~Lr~  224 (227)
T TIGR02479       158 DPEEELEREELREALAEAIEKLSEREKLVLSLYY----YEELNLKEIGEVLGLSESRVSQIHSQALKKLRA  224 (227)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             8135899999999999997406855788888864----127668899988378705799999999999987


No 33 
>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=99.97  E-value=4e-28  Score=240.97  Aligned_cols=235  Identities=31%  Similarity=0.499  Sum_probs=209.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHH
Q ss_conf             12688999999876533211246899987555789998875223567778875443679999887438545731201028
Q gi|254780289|r  422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM  501 (682)
Q Consensus       422 l~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~  501 (682)
                      +...+.+++..+++.|+.   .|+.++|.+|||||.||..+|.|||-...||+|-||+|||||+|-||.....||||||+
T Consensus        16 l~~~~~~~l~~~~~~G~~---~ar~~l~~~nlrlvlsviqrf~nrGe~~ddlfqvGCiGl~k~idnfdl~~nv~fstyav   92 (254)
T TIGR02850        16 LKNEEMRELFVRMKSGDK---SAREKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLIKSIDNFDLSQNVKFSTYAV   92 (254)
T ss_pred             CCHHHHHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHH
T ss_conf             354789999999851207---89999875226888888887511454034567632577777655310111320011346


Q ss_pred             HHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             98999999999722870461420588989999999998776088999789998709998999999986089875536358
Q gi|254780289|r  502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG  581 (682)
Q Consensus       502 ~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~  581 (682)
                      +.|-+.|.|++.|+ ..||+...+.+...+-......+..+..++||..+||..|++|.++|-.++...++||||=.|+.
T Consensus        93 PmiiGeirrylrdn-~~irvsrslrd~ay~alqvr~~l~~~~~~eP~~~~ia~~l~~~~~~~v~aldaiq~PvslfeP~y  171 (254)
T TIGR02850        93 PMIIGEIRRYLRDN-NPIRVSRSLRDIAYKALQVRDKLVSKNSKEPTVSEIAKELDVPKEEVVFALDAIQDPVSLFEPIY  171 (254)
T ss_pred             HHHHHHHHHHHHCC-CCEEEHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHH
T ss_conf             67889889985248-74130355889999999999999853125875889998734755787765664216423431001


Q ss_pred             CCCCC--EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             89986--0475623898899899999999999999997329988999999981879867468899989966789999999
Q gi|254780289|r  582 DEDTS--HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI  659 (682)
Q Consensus       582 ~~~~~--~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi  659 (682)
                      .|++.  ...|-+.|....   +...-..+  .+.++|..|+.||+-||.+||    -...|--||+...|+|.-.|-.+
T Consensus       172 ~d~Gd~i~vmdq~~d~~~~---d~~W~~~~--~l~~~~~~l~~re~~il~~rf----f~G~tqmeva~eiGisqaqvsrl  242 (254)
T TIGR02850       172 NDGGDPIYVMDQISDEKNK---DEQWLEEI--ALKEALKRLNEREKLILKLRF----FEGKTQMEVAEEIGISQAQVSRL  242 (254)
T ss_pred             CCCCCEEEEEECCCCHHHH---HHHHHHHH--HHHHHHHHHHHHHHHHHHHHH----HCCCHHHHHHHHHCCHHHHHHHH
T ss_conf             3799748874010020345---69999888--999999987667887777553----14631334565403016888888


Q ss_pred             HHHHHHHHCC
Q ss_conf             9999998329
Q gi|254780289|r  660 EAKAIRKLKH  669 (682)
Q Consensus       660 ~~~a~~~l~~  669 (682)
                      |..||..++.
T Consensus       243 ek~a~~~~~k  252 (254)
T TIGR02850       243 EKAALKHMRK  252 (254)
T ss_pred             HHHHHHHHHH
T ss_conf             8999999751


No 34 
>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=99.96  E-value=2.1e-28  Score=243.13  Aligned_cols=192  Identities=30%  Similarity=0.447  Sum_probs=166.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHH
Q ss_conf             12688999999876533211246899987555789998875223567778875443679999887438545731201028
Q gi|254780289|r  422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM  501 (682)
Q Consensus       422 l~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~  501 (682)
                      |+..|-+.-..+++.|..   .||+.|||.|||||-+|.|||.+.|-+..|||+-|+|||+||||.|++.+|.|++|||.
T Consensus        30 Ls~~eE~~YL~~l~~GD~---~Ar~~LiErNLRLVAHiVKKf~~~G~~~dDLISIGTiGLIKAidsf~~~KGt~LATYAA  106 (228)
T TIGR02846        30 LSEEEEKKYLERLKEGDE---EARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPEKGTRLATYAA  106 (228)
T ss_pred             CCHHHHHHHHHHHHHHHH---HHHHHHHHHCCCEEEEEEECCCCCCCCCCCHHCCCCHHEECCEECCCCCCCCHHHHHHH
T ss_conf             986689999999873159---99999776333000215651178874100001002201000110224787731566786


Q ss_pred             HHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             98999999999722870461420588989999999998776088999789998709998999999986089875536358
Q gi|254780289|r  502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG  581 (682)
Q Consensus       502 ~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~  581 (682)
                      --|-.+|.=++...                                                    +-++.-|||..|||
T Consensus       107 rCiENEILM~lR~~----------------------------------------------------KK~k~eV~L~DPIG  134 (228)
T TIGR02846       107 RCIENEILMHLRAL----------------------------------------------------KKTKGEVSLQDPIG  134 (228)
T ss_pred             HHHHHHHHHHHHHC----------------------------------------------------CCCCCCEEECCCCC
T ss_conf             65347899999743----------------------------------------------------67478332107888


Q ss_pred             CCCC---CEEEEEECCCCCCCHHHHHHHHHHHHHHHHHH-HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHH
Q ss_conf             8998---60475623898899899999999999999997-3299889999999818798674688999899667899999
Q gi|254780289|r  582 DEDT---SHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR  657 (682)
Q Consensus       582 ~~~~---~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l-~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~r  657 (682)
                      -|-+   -+|.|++...+-.-+ +.+....--..+..-| ..|.+||+.||.+||||.++.+.|=.|||+.+|+||-=|-
T Consensus       135 ~DKEGNEIsL~DiL~~~~d~v~-e~v~~~~~~~~l~~~~~~~L~~rE~~vi~~RyGL~~~~~~tQREIA~~LgISRSYVS  213 (228)
T TIGR02846       135 VDKEGNEISLIDILGSDEDSVI-EQVEKKLEIKKLYKKLNSVLKGREREVIEMRYGLKDGREKTQREIAKILGISRSYVS  213 (228)
T ss_pred             CCCCCCEEEEEECCCCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCCHHHH
T ss_conf             6767642300000168873168-888864459999999998740888999987436688895417899877086500454


Q ss_pred             HHHHHHHHHHCC
Q ss_conf             999999998329
Q gi|254780289|r  658 QIEAKAIRKLKH  669 (682)
Q Consensus       658 qi~~~a~~~l~~  669 (682)
                      -||.|||.||-|
T Consensus       214 RIEK~Al~Kl~~  225 (228)
T TIGR02846       214 RIEKKALKKLYK  225 (228)
T ss_pred             HHHHHHHHHHHH
T ss_conf             888999999986


No 35 
>pfam04546 Sigma70_ner Sigma-70, non-essential region. The domain is found in the primary vegetative sigma factor. The function of this domain is unclear and can be removed without loss of function.
Probab=99.94  E-value=2.4e-24  Score=211.13  Aligned_cols=209  Identities=17%  Similarity=0.252  Sum_probs=160.9

Q ss_pred             CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHH
Q ss_conf             82389999999987311710367876421013543333333433333211000111000100000000122100001111
Q gi|254780289|r  160 SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD  239 (682)
Q Consensus       160 ~P~ti~~il~~~e~i~~ge~~LrdIIDld~t~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~e~~~e~~~~~~~~  239 (682)
                      ||.++.+++.+|++|.+|+++|.|+|+++           .++.+..+..............+..               
T Consensus         1 yP~ti~~ll~~y~~v~~ge~rl~dli~Gf-----------~Dp~~~~~~~~~~~~~~~~~~~~~~---------------   54 (210)
T pfam04546         1 YPGAIAYLLEQYDRVEAGEGRLSDLISGF-----------IDPNADAAAATAPAIESELDEEDLE---------------   54 (210)
T ss_pred             CCHHHHHHHHHHHHHHCCCCCHHHHHHHC-----------CCCCCCCCCCCCCCCCCCCCCCCCC---------------
T ss_conf             97799999999999981886289998734-----------7987556655555544432111113---------------


Q ss_pred             HHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q ss_conf             10135666653034431000222334555564442102347987668999999999999987521012000799999999
Q gi|254780289|r  240 DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKE  319 (682)
Q Consensus       240 ~~~~~~~~~~e~e~~~~~~e~e~de~~~sla~~e~eLk~~v~e~l~~i~~~~~kl~k~~~~~~~~~~~~~~~kk~~kl~~  319 (682)
                                      .+.+.+.+.............++.+.++|..+.+.|.++.+...      ++|..++++.+.+.
T Consensus        55 ----------------~~~~~~~~~~~~~~~~d~gpdpeea~~rf~~l~~~~~~~~~a~~------k~G~~~~~~~k~~~  112 (210)
T pfam04546        55 ----------------DDDDDDDEDDDEEEEADLGPDPEEARERFAELREQYEKTRKAIE------KHGRGSKKAQKARE  112 (210)
T ss_pred             ----------------CCCCCCCCCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH------HCCCCHHHHHHHHH
T ss_conf             ----------------33334565542021665389999999999999999999999998------63987199999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHCCCHHHHHHHCCCCCCCHHHHHHHHHCCCCHHHHH
Q ss_conf             99999986210057788789999999999999999999999-97125357777631677689899999861355106765
Q gi|254780289|r  320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF  398 (682)
Q Consensus       320 eL~e~~~~lkl~~k~iE~L~~~l~~~~k~Ir~~Er~L~rl~-~k~~i~R~~Fi~~f~gnEt~~~wl~~~~~~~~~~~~~~  398 (682)
                      +|++.|+.|+|+|++|+.|++.++..+..||.+||.|+++| .++||||+.|++.|+|||||+.|++...+.+ +.|+..
T Consensus       113 ~l~e~f~~~Kl~pk~~d~L~~~lR~~v~~IR~~ER~I~~lcV~~a~MpRk~Fik~F~gnEtn~~W~~~~~k~~-k~~s~~  191 (210)
T pfam04546       113 ALAEEFKQFRLVPKQFDRLVDNLRGMVDRVRAQERQIMKLCVERAKMPRKDFIKSFPGNETNLDWLDELLAAK-KPYAEA  191 (210)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCCCCHHHHHHHHHCC-CHHHHH
T ss_conf             9999999861768999999999999999999999999999999818998999988678888889999998739-648999


Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q ss_conf             5434567765322333322
Q gi|254780289|r  399 VACEVDSILKIRNEIKSIS  417 (682)
Q Consensus       399 l~~~~~eI~~~q~kL~~ie  417 (682)
                      +..++++|.++|++|..|+
T Consensus       192 L~~~~~~I~~~Q~kL~~iE  210 (210)
T pfam04546       192 LERVKPDIQRAQQKLIDIE  210 (210)
T ss_pred             HHHHHHHHHHHHHHHHHCC
T ss_conf             9996999999999998619


No 36 
>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=99.94  E-value=1.5e-25  Score=220.74  Aligned_cols=240  Identities=22%  Similarity=0.422  Sum_probs=207.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHH
Q ss_conf             12688999999876533211246899987555789998875223567778875443679999887438545731201028
Q gi|254780289|r  422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM  501 (682)
Q Consensus       422 l~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~  501 (682)
                      ++..++-.+....+.-- ....|-.+||..-=.||-|||.||...+---.||||.|-+||+-||.||||+.|-+|-.||.
T Consensus        10 ~~~e~v~~wI~e~Q~nP-~n~eaQeklV~hY~~Lv~SiAykYSKg~~~HEDlvQVGM~GLlgAirRyD~s~g~~FE~Fai   88 (256)
T TIGR02941        10 LTKEDVIQWIKEFQKNP-KNEEAQEKLVKHYQDLVESIAYKYSKGSAIHEDLVQVGMVGLLGAIRRYDYSYGKAFEAFAI   88 (256)
T ss_pred             CCHHHHHHHHHHHCCCC-CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf             78878999999963699-83257899999998999988754048788333045676899999986511000456566236


Q ss_pred             HHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHC--CCCCCCCC
Q ss_conf             9899999999972287046142058898999999999877608899978999870999899999998608--98755363
Q gi|254780289|r  502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETP  579 (682)
Q Consensus       502 ~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~--~~~sl~~~  579 (682)
                      |.|-+.|.|+++|.+|-|+||....+.=.|+.++.-+|..++.|-|++.|||++||+|+++|..+|.+.+  ...|+|..
T Consensus        89 PTiiGEIKrylRDKTWsvHVPRRIKelGpkIkk~~dELT~~lqrSP~i~EIA~~lg~SEEEVLE~Me~g~sY~alSvD~~  168 (256)
T TIGR02941        89 PTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELTDELQRSPKIAEIADRLGVSEEEVLEIMEMGQSYKALSVDDK  168 (256)
T ss_pred             CCHHHHHHHHHCCCCCCCCCCCCHHCCCCCCHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHCCCCCCEEECCCC
T ss_conf             61001011211156430015741100377201455664444214870654641217748889877614777433322530


Q ss_pred             CCCCCC-CE--EEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHH
Q ss_conf             588998-60--475623898899899999999999999997329988999999981879867468899989966789999
Q gi|254780289|r  580 IGDEDT-SH--LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI  656 (682)
Q Consensus       580 ~~~~~~-~~--~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~  656 (682)
                      |=.|.| ||  +.|++...     ++......-|--|..+|..|++||+.||..-|    -...+=-|-|..+|+|-=-|
T Consensus       169 iEadsDGStVa~ld~vG~~-----edgYd~tE~Rm~LekIlpiLserE~~ii~c~f----~enlsQKeTGErlGiSQMHV  239 (256)
T TIGR02941       169 IEADSDGSTVALLDLVGEV-----EDGYDQTEKRMVLEKILPILSEREKEIIECTF----IENLSQKETGERLGISQMHV  239 (256)
T ss_pred             CCCCCCCCCCHHHHHHCCC-----CCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCCCHHHHHCCHHHHHH
T ss_conf             0036888511111121676-----66545788888888741000544567666553----14787300232224035567


Q ss_pred             HHHHHHHHHHHCCHH
Q ss_conf             999999999832967
Q gi|254780289|r  657 RQIEAKAIRKLKHPS  671 (682)
Q Consensus       657 rqi~~~a~~~l~~~~  671 (682)
                      --|..+||+|||...
T Consensus       240 SRl~R~ai~KL~eAa  254 (256)
T TIGR02941       240 SRLQRRAIKKLKEAA  254 (256)
T ss_pred             HHHHHHHHHHHHHHH
T ss_conf             788899999999972


No 37 
>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=99.85  E-value=3.4e-20  Score=178.43  Aligned_cols=193  Identities=26%  Similarity=0.440  Sum_probs=165.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHH
Q ss_conf             12688999999876533211246899987555789998875223567778875443679999887438545731201028
Q gi|254780289|r  422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM  501 (682)
Q Consensus       422 l~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~  501 (682)
                      ++..|-..+..++..|..   .+|.-||+-||||||.||+||-|.|+...|||+-|++||+|||.-|+|.+-.|++|||.
T Consensus        34 l~~eee~~l~~~l~~Gd~---~~~~~liernlrlvvyia~kf~ntG~~~edl~s~GtiGlikav~tf~P~k~iklatyas  110 (234)
T TIGR02835        34 LTKEEEEALLEKLEKGDE---AAKSILIERNLRLVVYIARKFENTGINIEDLVSIGTIGLIKAVNTFNPEKKIKLATYAS  110 (234)
T ss_pred             CCHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHCCCCCEEEHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf             871579999999875479---99999886222431121012202562110222221478887765227301103556776


Q ss_pred             HHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             98999999999722870461420588989999999998776088999789998709998999999986089875536358
Q gi|254780289|r  502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG  581 (682)
Q Consensus       502 ~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~  581 (682)
                      -.|-..|.-++..+.+                                                    .+.-||++.|+.
T Consensus       111 ~Cieneilmylrr~~~----------------------------------------------------~~~evsf~ePln  138 (234)
T TIGR02835       111 RCIENEILMYLRRNNK----------------------------------------------------IRSEVSFDEPLN  138 (234)
T ss_pred             HHHHHHHHHHHHHHCC----------------------------------------------------CCCEEEECCCCC
T ss_conf             7678889998875112----------------------------------------------------100000025546


Q ss_pred             CCCCCE---EEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             899860---47562389889989999999999999999732998899999998187986746889998996678999999
Q gi|254780289|r  582 DEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ  658 (682)
Q Consensus       582 ~~~~~~---~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rq  658 (682)
                      -|+|++   +.|++.-.+ ..-........-+..+..+|..|+.||++|+.+||||.++...|-.+|+..+|+|..-|-.
T Consensus       139 ~dW~Gnelllsd~lGt~~-~~~~~~~e~~v~~~ll~~al~~l~~re~~i~~lrfGl~~~~e~tqk~vad~lGisqsyisr  217 (234)
T TIGR02835       139 VDWDGNELLLSDVLGTDS-DIVYKVLEEEVDRELLKKALKKLNDREKKIMELRFGLAGGTEKTQKEVADLLGISQSYISR  217 (234)
T ss_pred             CCCCCCHHHHHHHHCCCH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             566762114344414742-6889999999999999999998767678766763043677214678889886246899999


Q ss_pred             HHHHHHHHHCCH
Q ss_conf             999999983296
Q gi|254780289|r  659 IEAKAIRKLKHP  670 (682)
Q Consensus       659 i~~~a~~~l~~~  670 (682)
                      +|.+-+++|+.-
T Consensus       218 lek~i~krl~ke  229 (234)
T TIGR02835       218 LEKRILKRLKKE  229 (234)
T ss_pred             HHHHHHHHHHHH
T ss_conf             999999999999


No 38 
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=99.84  E-value=6.7e-19  Score=168.17  Aligned_cols=194  Identities=24%  Similarity=0.320  Sum_probs=161.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHH
Q ss_conf             12688999999876533211246899987555789998875223567778875443679999887438545731201028
Q gi|254780289|r  422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM  501 (682)
Q Consensus       422 l~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~  501 (682)
                      +...+=.+++.+++.|..   .|...|+..+.++|.++|++|.+.+....||+|||.|++++|+++|++.+|.+|+||+.
T Consensus         6 ~~~~~d~~Li~~~~~GD~---~Af~~L~~~y~~~v~~~~~~~~~~~~d~EDlvQe~~i~l~kai~~f~~~k~~~F~t~~~   82 (209)
T PRK08295          6 LRDKEDEELVELAQSGDT---EALEYLIEKYKNFVRAKARSYFLIGAEREDIVQEGMIGLYKAIRDYDEDKLSSFKSFAE   82 (209)
T ss_pred             CCHHHHHHHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH
T ss_conf             872019999999991679---99999999989999999999828987799999999999999998568654872899999


Q ss_pred             HHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             98999999999722870461420588989999999998776088999789998709998999999986089875536358
Q gi|254780289|r  502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG  581 (682)
Q Consensus       502 ~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~  581 (682)
                      +||+..|..++....|--+.|.                                               ...+|||.|+.
T Consensus        83 ~~i~~~i~~~ir~~~r~k~~~~-----------------------------------------------~~~~sld~~~~  115 (209)
T PRK08295         83 LCITRQIITAIKTANRQKHIPL-----------------------------------------------NSYVSLDKPIY  115 (209)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCC-----------------------------------------------CHHHCCCCCCC
T ss_conf             9999999999999833045452-----------------------------------------------02414566645


Q ss_pred             CCC-CCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHH-HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             899-860475623898899899999999999999997-329988999999981879867468899989966789999999
Q gi|254780289|r  582 DED-TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI  659 (682)
Q Consensus       582 ~~~-~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l-~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi  659 (682)
                      +++ +.++.+++.+....+|++..........+.+.+ ..|+|+++.|+.++|     ..+|+.|||+.+|+|-..|+..
T Consensus       116 ~~~~~~~~~~~~~~~~~~~pe~~~~~~e~~~~i~~~i~~~l~~~e~~V~~~~~-----eg~s~~EIA~~l~is~~tV~~~  190 (209)
T PRK08295        116 DEESDRTLLDVISGAKVTDPEELIISKEELEIIEEKILELLSDLEKEVLELYL-----DGKSYQEIAEELNRHVKSIDNA  190 (209)
T ss_pred             CCCCHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHH
T ss_conf             55420356543046778999999999999999999998469189999999998-----6999999999989299999999


Q ss_pred             HHHHHHHHCCH
Q ss_conf             99999983296
Q gi|254780289|r  660 EAKAIRKLKHP  670 (682)
Q Consensus       660 ~~~a~~~l~~~  670 (682)
                      -.+|.+|||.-
T Consensus       191 l~RarkkLr~~  201 (209)
T PRK08295        191 LQRVKRKLEKY  201 (209)
T ss_pred             HHHHHHHHHHH
T ss_conf             99999999999


No 39 
>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=99.77  E-value=1.9e-17  Score=156.68  Aligned_cols=159  Identities=23%  Similarity=0.290  Sum_probs=135.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCC
Q ss_conf             68999875557899988752235677788754436799998874385457312010289899999999972287046142
Q gi|254780289|r  444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV  523 (682)
Q Consensus       444 AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~  523 (682)
                      |-.+++..|.++|.++|++|++.+.+..||+|||.++|++++++|++. |..|+||+.+|+|..|..++..+.+..+.+.
T Consensus         2 a~~~l~~~~~~~~~~~a~~~~~~~~~aeDl~Qe~~~~~~~~~~~~~~~-~~~f~~wl~~~~~n~~~d~~R~~~~~~~~~~   80 (162)
T TIGR02937         2 AFEELVERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE-GGSFKAWLFRIARNLILDYLRRKRRRVRRLR   80 (162)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             788999999999999999971787579999999999999878624878-7653899999999999999998664420014


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHH
Q ss_conf             05889899999999987760889997899987099989999999860898755363588998604756238988998999
Q gi|254780289|r  524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS  603 (682)
Q Consensus       524 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~  603 (682)
                      ......                                                     +.     ..-. . .++|++ 
T Consensus        81 ~~~~~~-----------------------------------------------------~~-----~~~~-~-~~~~~~-   99 (162)
T TIGR02937        81 VELDED-----------------------------------------------------DE-----LEEL-E-DPSPEE-   99 (162)
T ss_pred             HHHCCH-----------------------------------------------------HH-----HHHH-C-CCCHHH-
T ss_conf             541221-----------------------------------------------------34-----4321-3-578778-


Q ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             999999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       604 ~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      +. ......|.++|..|||+++.||.+||    ....|+.|||+.+|+|...|+++-.+|++||+.
T Consensus       100 ~~-~~~~~~l~~al~~Lp~~~r~~~~l~~----~~~~s~~eIA~~lg~s~~~v~~~~~ra~~~L~~  160 (162)
T TIGR02937       100 LE-EEEREALREALEKLPEREREVLVLRY----LEGLSYKEIAEILGISEGTVKSRLKRARKKLRE  160 (162)
T ss_pred             HH-HHHHHHHHHHHHHCCHHHHHHHHHHH----HHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             99-99999999998747998999999999----718998899998689999999999999999985


No 40 
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=99.70  E-value=1.8e-15  Score=141.11  Aligned_cols=149  Identities=22%  Similarity=0.271  Sum_probs=114.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCC
Q ss_conf             68999875557899988752235677788754436799998874385457312010289899999999972287046142
Q gi|254780289|r  444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV  523 (682)
Q Consensus       444 AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~  523 (682)
                      +-.++++..=.+|++++|+|.-. -.+.|++|+|.|||.+|+++||+.+| .|||||..+||..+...+..+.+.     
T Consensus         5 sFee~~~~Y~pmI~~~lkkl~i~-~d~dd~~Q~g~i~Lw~a~~~yd~~kg-~fstya~~~ir~~~ld~lrKe~~~-----   77 (154)
T PRK06759          5 TFTEAVVLYEGLIVNQIKKLGIY-QDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYILERLKKEFAV-----   77 (154)
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHHHHHCCCCCC-CHHHHHHHHHHHHHHHHHHHCCCC-----
T ss_conf             59999999878999999993673-33899999999999999997694347-669999999999999999863143-----


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHH
Q ss_conf             05889899999999987760889997899987099989999999860898755363588998604756238988998999
Q gi|254780289|r  524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS  603 (682)
Q Consensus       524 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~  603 (682)
                                                .+                      ..  .++++                 |++.
T Consensus        78 --------------------------~e----------------------~~--~~~~~-----------------~ed~   90 (154)
T PRK06759         78 --------------------------QE----------------------KC--VCVGE-----------------YEDH   90 (154)
T ss_pred             --------------------------CC----------------------CC--CCCCC-----------------CHHH
T ss_conf             --------------------------34----------------------33--35565-----------------2255


Q ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCH
Q ss_conf             9999999999999732998899999998187986746889998996678999999999999983296
Q gi|254780289|r  604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP  670 (682)
Q Consensus       604 ~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~  670 (682)
                      .........+.++|+.|+|||+.||.++|    -..+|..||+..+|||...|+++..+||.|||+.
T Consensus        91 ~~~~d~~~~l~~~l~~L~~re~~ii~~~~----~~g~t~~EIA~~~gis~~~Vk~~~r~Al~KLR~~  153 (154)
T PRK06759         91 FHFEDVEMKVKDFMSVLDEKEKYIIFERF----FVGKTMGEIALETEMTYYQVRWIYRQALEKMRNS  153 (154)
T ss_pred             HHHCHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHC
T ss_conf             51011889999999849999999999999----9699899999998989999999999999998733


No 41 
>pfam03979 Sigma70_r1_1 Sigma-70 factor, region 1.1. Region 1.1 modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase. Region 1.1 is also involved in promoter binding.
Probab=99.52  E-value=3.4e-14  Score=131.06  Aligned_cols=63  Identities=46%  Similarity=0.780  Sum_probs=58.3

Q ss_pred             HHCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEEECCCCCCCC
Q ss_conf             020289999999978784886789997526843599888999999998479778327841000
Q gi|254780289|r   24 FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE   86 (682)
Q Consensus        24 ~d~~~~~ik~LI~~gke~GylTydeIn~~LP~d~~~~e~ie~i~~~L~~~GI~Vve~~~~~~~   86 (682)
                      .|++++.||+||.+||+||||||++||++||++.++|++||+||++|++|||.|+++++..+.
T Consensus         2 ~d~~~~~ik~LI~~GK~~GylTy~eIn~~Lp~~~~~~d~ie~i~~~L~~~gI~Vve~~~~~e~   64 (79)
T pfam03979         2 EDLSQAQVKKLIEQGKKRGYLTYDEINEALPPDDVDSEQIDDIISMLEDMGIEVVEEADSEEL   64 (79)
T ss_pred             CHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEEEECCCCCCC
T ss_conf             304799999999987645836399999768876799999999999999889968527972212


No 42 
>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=99.46  E-value=1.3e-13  Score=126.44  Aligned_cols=77  Identities=44%  Similarity=0.821  Sum_probs=74.7

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHH
Q ss_conf             89899999999987760889997899987099989999999860898755363588998604756238988998999
Q gi|254780289|r  527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS  603 (682)
Q Consensus       527 ~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~  603 (682)
                      ++|||+.|+.++|.|++||+||.+|||+.||||+++|+.++..++.|+|||+|+|++++++|+||++|.+.++|++.
T Consensus         1 E~i~ki~ka~~~L~q~lgR~Pt~eEiA~~l~~s~~~v~~~~~~~~~~~SLd~p~~~~~~~~l~d~i~D~~~~~P~e~   77 (78)
T pfam04539         1 ELLNKIKRAQRELEQELGREPTPEEIAEELGISEEKVREVLEAAREPVSLDLPVGEEEDGELGDLLEDDDAESPEDA   77 (78)
T ss_pred             CHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCEEEECCCCCCCCCCHHHHCCCCCCCCHHHH
T ss_conf             97799999999999998889999999999694999999999875898661067688998628662059999881010


No 43 
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=99.21  E-value=3.5e-09  Score=91.50  Aligned_cols=184  Identities=20%  Similarity=0.235  Sum_probs=130.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHH
Q ss_conf             99999876533211246899987555789998875223567778875443679999887438545731201028989999
Q gi|254780289|r  428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA  507 (682)
Q Consensus       428 K~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~  507 (682)
                      .+++.+++.|...   |=..++..+..+|.++|.+|.+..-.-.|++|+.-+.|.+.+.+|++..  .|.+|...-.|..
T Consensus         7 ~~Li~~~~~Gd~~---A~~~L~~~y~~~l~~~~~~~~~~~~~aeDv~Qe~fl~l~~~~~~~~~~~--~~~~wL~~iarn~   81 (192)
T PRK09652          7 QELVERVQQGDRA---AFELLVRKYQPRLYRLLSRLVRDPADAEDLAQETFIKAYRALPSFRGGA--AFYTWLYRIAVNT   81 (192)
T ss_pred             HHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCH--HHHHHHHHHHHHH
T ss_conf             9999999838899---9999999999999999999969999999987599999887113457711--7999999999999


Q ss_pred             HHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCE
Q ss_conf             99999722870461420588989999999998776088999789998709998999999986089875536358899860
Q gi|254780289|r  508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH  587 (682)
Q Consensus       508 i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~  587 (682)
                      +                    ++.+.+..+        .+...                        +.+.+  ++....
T Consensus        82 ~--------------------~d~~r~~~r--------~~~~~------------------------~~~~~--~~~~~~  107 (192)
T PRK09652         82 A--------------------INYLRKQGR--------RPPES------------------------DLDAE--DAEYFE  107 (192)
T ss_pred             H--------------------HHHHHHHHC--------CCCCC------------------------CCCHH--HHHHHC
T ss_conf             9--------------------999999716--------56655------------------------40023--454300


Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf             47562389889989999999999999999732998899999998187986746889998996678999999999999983
Q gi|254780289|r  588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL  667 (682)
Q Consensus       588 ~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l  667 (682)
                      ..+.  .....+|++.+....+...|..+|..|||+++.|+.++|    -...|..|||..+|+|..-|++.=.+|+++|
T Consensus       108 ~~~~--~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~----~~~~s~~EIA~~lgis~~tVk~~l~Ra~~~L  181 (192)
T PRK09652        108 DADA--LREISSPEEELLSQELEQRVRRAIESLPEELRTAITLRE----IEGLSYEEIAEIMGCPIGTVRSRIFRAREAL  181 (192)
T ss_pred             CCCC--CCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             0003--555576799999999999999999839999998888999----7299999999998939999999999999999


Q ss_pred             CCHHHHHHHHHHHC
Q ss_conf             29677787566517
Q gi|254780289|r  668 KHPSRSKKLRSFLD  681 (682)
Q Consensus       668 ~~~~~~~~l~~~~~  681 (682)
                      |     +.|+.||+
T Consensus       182 r-----~~L~~~~~  190 (192)
T PRK09652        182 R-----AKLQPLLD  190 (192)
T ss_pred             H-----HHHHHHHH
T ss_conf             9-----99898771


No 44 
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=99.18  E-value=7.5e-09  Score=88.84  Aligned_cols=180  Identities=16%  Similarity=0.246  Sum_probs=131.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHH
Q ss_conf             88999999876533211246899987555789998875223567778875443679999887438545731201028989
Q gi|254780289|r  425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV  504 (682)
Q Consensus       425 ~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i  504 (682)
                      ..+++++++++.|..   .|-.++++..-..|..+|.+|++..-.-.|++|+.-+.+.+..++|++...  |+|   |-.
T Consensus         3 ~~i~~Li~~~~~GD~---~Af~~L~~~y~~~l~~~~~~~~~~~~~AeD~vQe~flk~~~~~~~~~~~~~--~~~---WL~   74 (187)
T PRK09641          3 TLIKKRIKQVKKGDQ---NAFADIVDLYKDKIYQLCYRMLGNRHEAEDIAQEAFIRAYVNIDSFDINRK--FST---WLY   74 (187)
T ss_pred             HHHHHHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCCC--HHH---HHH
T ss_conf             899999999993889---999999999999999999999099999999999999999984612574134--999---999


Q ss_pred             HHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             99999999722870461420588989999999998776088999789998709998999999986089875536358899
Q gi|254780289|r  505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED  584 (682)
Q Consensus       505 ~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~  584 (682)
                      +-+...++ |.                +.+..                                   ...+++.++...+
T Consensus        75 ~Ia~N~~~-d~----------------~Rk~~-----------------------------------~~~~~~~~~~~~~  102 (187)
T PRK09641         75 RIATNLTI-DR----------------LRKKK-----------------------------------PDYYLDAEVAGTE  102 (187)
T ss_pred             HHHHHHHH-HH----------------HHHHC-----------------------------------CCCCHHHHHCCCC
T ss_conf             99999999-99----------------99726-----------------------------------5343126540310


Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             86047562389889989999999999999999732998899999998187986746889998996678999999999999
Q gi|254780289|r  585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI  664 (682)
Q Consensus       585 ~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~  664 (682)
                      +..+.+.+.+ ...+|++.+....+...+..+|..|||+.+.|+.|||    -..+|..||+..+|+|-.-|+..=.+|+
T Consensus       103 ~~~~~~~~~~-~~~~~~~~~~~~e~~~~l~~al~~Lp~~~r~v~~L~~----~~~~s~~EIA~~l~is~~tVk~~l~RAr  177 (187)
T PRK09641        103 GLTMYSQLAA-DEALPEDQVESLELQETIQEEILQLPDKYRTVIVLKY----IEELSLKEISEILDLPVGTVKTRIHRGR  177 (187)
T ss_pred             CCHHHHHCCC-CCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             0004430356-6798478999999999999999828988889999999----8299899999998939999999999999


Q ss_pred             HHHCC
Q ss_conf             98329
Q gi|254780289|r  665 RKLKH  669 (682)
Q Consensus       665 ~~l~~  669 (682)
                      ++||.
T Consensus       178 ~~Lr~  182 (187)
T PRK09641        178 EALRK  182 (187)
T ss_pred             HHHHH
T ss_conf             99999


No 45 
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=99.15  E-value=9.3e-09  Score=88.11  Aligned_cols=184  Identities=18%  Similarity=0.276  Sum_probs=129.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHH
Q ss_conf             12688999999876533211246899987555789998875223567778875443679999887438545731201028
Q gi|254780289|r  422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM  501 (682)
Q Consensus       422 l~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~  501 (682)
                      |+...=.+++..++.|..   .|-.+|+...-+.|..+|.+|.+..-.-.|++|+.-+.+.+... |+..+| .|+||..
T Consensus        11 m~~~tD~eLi~~~~~GD~---~Af~~L~~ry~~~l~~~a~~~~~~~~~AeDlvQe~fl~~~~~~~-~~~~~~-~~~~wL~   85 (194)
T PRK12519         11 LSSRSDAELFSALKAGQS---AALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRKSS-YDPKRG-SLSSYLL   85 (194)
T ss_pred             CCCCCHHHHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH-CCCCCC-CHHHHHH
T ss_conf             999609999999993859---99999999999999999999939999999999999999998633-166624-2999999


Q ss_pred             HHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             98999999999722870461420588989999999998776088999789998709998999999986089875536358
Q gi|254780289|r  502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG  581 (682)
Q Consensus       502 ~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~  581 (682)
                      -..|..+...+..+.+..+                           ..+.                            .+
T Consensus        86 ~ia~n~~~d~~R~~~~~~~---------------------------~~~~----------------------------~~  110 (194)
T PRK12519         86 TLTRSRAIDRLRSRRSRQR---------------------------LLER----------------------------WQ  110 (194)
T ss_pred             HHHHHHHHHHHHHHHCCCC---------------------------HHHH----------------------------HH
T ss_conf             9999999999998632012---------------------------2444----------------------------44


Q ss_pred             CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             89986047562389889989999999999999999732998899999998187986746889998996678999999999
Q gi|254780289|r  582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA  661 (682)
Q Consensus       582 ~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~  661 (682)
                      .       +...+.....|.+.+........|..+|..|||+.+.|+.|||    -..+|..||++.+|+|.--|+.--.
T Consensus       111 ~-------~~~~~~~~~~~~~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~~----~eg~s~~EIA~~lgis~~tVk~rl~  179 (194)
T PRK12519        111 Q-------ELLGEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAY----YEGLSQSEIAKRLGIPLGTVKARAR  179 (194)
T ss_pred             H-------HHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             5-------4114677898588998999999999999819988756889999----8199999999998949999999999


Q ss_pred             HHHHHHCCHHHHHHHHHHHC
Q ss_conf             99998329677787566517
Q gi|254780289|r  662 KAIRKLKHPSRSKKLRSFLD  681 (682)
Q Consensus       662 ~a~~~l~~~~~~~~l~~~~~  681 (682)
                      +|+.+||     +.|+.|||
T Consensus       180 rA~~~Lr-----~~L~e~le  194 (194)
T PRK12519        180 QGLLKLR-----ELLQDLLE  194 (194)
T ss_pred             HHHHHHH-----HHHHHHHC
T ss_conf             9999999-----99898739


No 46 
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=99.07  E-value=3.5e-08  Score=83.56  Aligned_cols=188  Identities=19%  Similarity=0.271  Sum_probs=134.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHH
Q ss_conf             26889999998765332112468999875557899988752235677788754436799998874385457312010289
Q gi|254780289|r  423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW  502 (682)
Q Consensus       423 ~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~  502 (682)
                      +..+-.+++.+++.|...   |=..++...-+.|..+|.+|++..-.-.|++|+.-+.+.+..++|+...  .|.|   |
T Consensus         3 t~~~D~~Li~~~~~GD~~---Af~~L~~~y~~~l~~~~~~~~~d~~~AeDi~Qe~f~~~~~~~~~~~~~~--~f~~---W   74 (193)
T PRK11923          3 TQEEDQQLVERVQRGDKR---AFDLLVLKYQHKILGLIVRFVHDTHEAQDVAQEAFIKAYRALGNFRGDS--AFYT---W   74 (193)
T ss_pred             CCCCHHHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCCCH--HHHH---H
T ss_conf             871099999999948699---9999999999999999999909999999999999999986132126504--6899---9


Q ss_pred             HHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCC-CCCC
Q ss_conf             899999999972287046142058898999999999877608899978999870999899999998608987553-6358
Q gi|254780289|r  503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE-TPIG  581 (682)
Q Consensus       503 ~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~-~~~~  581 (682)
                      -.|-++..++                 +.+.+.        .|.+...+                      ++.+ .+..
T Consensus        75 L~~Ia~n~~~-----------------~~~~~~--------~rr~~~~~----------------------~~~~~~~~~  107 (193)
T PRK11923         75 LYRIAINTAK-----------------NHLVSR--------GRRPPDSD----------------------VSSEDAEFY  107 (193)
T ss_pred             HHHHHHHHHH-----------------HHHHHH--------HCCCCCCC----------------------CCHHHHHHC
T ss_conf             9999999999-----------------999998--------65575333----------------------453466522


Q ss_pred             CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             89986047562389889989999999999999999732998899999998187986746889998996678999999999
Q gi|254780289|r  582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA  661 (682)
Q Consensus       582 ~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~  661 (682)
                      +.+     +.+.  +..+|+..+....+...|..+|..|||+.+.|+.|||    -..+|..|||..+|+|-.-|+.-=.
T Consensus       108 ~~~-----~~~~--~~~~~e~~~~~~e~~~~i~~~l~~Lp~~~R~v~~L~~----~egls~~EIA~~l~is~~tVk~rl~  176 (193)
T PRK11923        108 DGD-----HALK--DIESPERALLRDEIEATVHRTIQQLPEDLRTALTLRE----FDGLSYEDIASVMQCPVGTVRSRIF  176 (193)
T ss_pred             CCC-----CCCC--CCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             554-----3223--4488889999999999999999817898999999999----9499999999998929999999999


Q ss_pred             HHHHHHCCHHHHHHHHHHHC
Q ss_conf             99998329677787566517
Q gi|254780289|r  662 KAIRKLKHPSRSKKLRSFLD  681 (682)
Q Consensus       662 ~a~~~l~~~~~~~~l~~~~~  681 (682)
                      +|..+||.     .|+.|+.
T Consensus       177 RAr~~Lr~-----~L~~ll~  191 (193)
T PRK11923        177 RAREAIDK-----ALQPLLQ  191 (193)
T ss_pred             HHHHHHHH-----HHHHHHH
T ss_conf             99999999-----9899873


No 47 
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=99.07  E-value=1.7e-08  Score=86.02  Aligned_cols=172  Identities=20%  Similarity=0.283  Sum_probs=117.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHH
Q ss_conf             99999876533211246899987555789998875223567778875443679999887438545731201028989999
Q gi|254780289|r  428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA  507 (682)
Q Consensus       428 K~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~  507 (682)
                      .+++.+++.|..   .|-..++.-.-..|.++|.+|++..-.-.|++||.-+.+.+..++|++.+| .|+||   -.+=+
T Consensus        11 ~eLi~~~~~GD~---~Af~~L~~ry~~~l~~~~~~~~~d~~~AEDivQe~flki~~~~~~~~~~~~-~~~~w---L~~ia   83 (187)
T PRK13919         11 EALLALVARGDE---EAFRALFRRYAGSFLALARRMGLDGAAAEDVVQEAMIRVWQKAKEFDPRRG-SARAF---LLTLG   83 (187)
T ss_pred             HHHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCC-CHHHH---HHHHH
T ss_conf             999999994779---999999999999999999999099999999999999999999987687646-49999---99999


Q ss_pred             HHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCE
Q ss_conf             99999722870461420588989999999998776088999789998709998999999986089875536358899860
Q gi|254780289|r  508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH  587 (682)
Q Consensus       508 i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~  587 (682)
                      ...++                 +.+.+                                  -.+.|++++.-.. ..+..
T Consensus        84 ~n~~~-----------------d~~Rk----------------------------------~~~~~~~~~~~~~-~~~~~  111 (187)
T PRK13919         84 HHAAV-----------------DEVRR----------------------------------RAARPLPLEPDPE-REEEA  111 (187)
T ss_pred             HHHHH-----------------HHHHH----------------------------------HHCCCCCCCCCCH-HHHHH
T ss_conf             99999-----------------99997----------------------------------6267787776610-11332


Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf             47562389889989999999999999999732998899999998187986746889998996678999999999999983
Q gi|254780289|r  588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL  667 (682)
Q Consensus       588 ~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l  667 (682)
                      + +      .+.|.........+..+..+|..|||+.+.|+.|+|    -..+|..||++.+|+|---|+..-.+|+++|
T Consensus       112 ~-~------~~~~~~~~e~~~~~~~l~~al~~L~~~~r~vi~L~~----~~g~s~~EIA~~L~is~~TVk~~l~rA~k~L  180 (187)
T PRK13919        112 F-D------LPGPGLDEEGHLDRTRLGRALKALSPEERRVIEVLY----YQGYTHREAARLLGLPLGTLKTWARRALSKL  180 (187)
T ss_pred             C-C------CCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             0-4------688640278789999999999849999999999999----8599999999998939999999999999999


Q ss_pred             CC
Q ss_conf             29
Q gi|254780289|r  668 KH  669 (682)
Q Consensus       668 ~~  669 (682)
                      |.
T Consensus       181 r~  182 (187)
T PRK13919        181 KE  182 (187)
T ss_pred             HH
T ss_conf             99


No 48 
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=99.04  E-value=7.6e-08  Score=80.91  Aligned_cols=175  Identities=19%  Similarity=0.263  Sum_probs=125.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC----CCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEH
Q ss_conf             26889999998765332112468999875557899988752235----67778875443679999887438545731201
Q gi|254780289|r  423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR----GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST  498 (682)
Q Consensus       423 ~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~----~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~t  498 (682)
                      ...++.+++.+...|...   |-.+|+...-..|...|.+..++    ...-.|++||.-+.+.+++.+|.. .|-.|+|
T Consensus         5 ~~~~l~~Li~~a~~GD~~---Af~~L~~~~~~~v~r~~~~~l~~~~~~~~dAeDl~Qe~fl~~~~~l~~f~~-~~~~f~~   80 (187)
T PRK09648          5 AGEELDALVAEAVAGDRR---ALREVLETIHPLVVRYCRARLGTVERSGLSADDVAQEVCLAVITALPRYRD-QGRPFLA   80 (187)
T ss_pred             CHHHHHHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCC-CCCCHHH
T ss_conf             217899999999845899---999999999999999999997144587643999999999999983766266-7784999


Q ss_pred             HHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCC
Q ss_conf             02898999999999722870461420588989999999998776088999789998709998999999986089875536
Q gi|254780289|r  499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET  578 (682)
Q Consensus       499 ya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~  578 (682)
                          |+. .|.+..               .++.+.+..        |.+.                       .      
T Consensus        81 ----Wl~-~Ia~n~---------------~~d~~R~~~--------r~~~-----------------------~------  103 (187)
T PRK09648         81 ----FVY-GIAAHK---------------VADAHRAAG--------RDKA-----------------------Y------  103 (187)
T ss_pred             ----HHH-HHHHHH---------------HHHHHHHHH--------CCCC-----------------------C------
T ss_conf             ----999-999999---------------999999874--------6764-----------------------3------


Q ss_pred             CCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             35889986047562389889989999999999999999732998899999998187986746889998996678999999
Q gi|254780289|r  579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ  658 (682)
Q Consensus       579 ~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rq  658 (682)
                      |..+     +.+..  ....+|++.+........+..+|+.|||+.+.||.|||    -..+|..|||+.+|+|---|+.
T Consensus       104 ~~~~-----~~~~~--~~~~~pe~~~~~~e~~~~l~~~l~~Lp~~~R~vl~L~~----~~g~s~~EIA~~lg~s~~tVk~  172 (187)
T PRK09648        104 PTEE-----VPERP--SDEAGPEQRALEAESSARMRELLEILPEKQREILILRV----VVGLSAEETAEAVGSTPGAVRV  172 (187)
T ss_pred             CCCC-----CCCCC--CCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHH
T ss_conf             2112-----33347--87788589999899999999999839999999999999----8499999999998939999999


Q ss_pred             HHHHHHHHHCC
Q ss_conf             99999998329
Q gi|254780289|r  659 IEAKAIRKLKH  669 (682)
Q Consensus       659 i~~~a~~~l~~  669 (682)
                      .-.+|+.+||.
T Consensus       173 ~l~RA~~~Lr~  183 (187)
T PRK09648        173 AQHRALSRLRA  183 (187)
T ss_pred             HHHHHHHHHHH
T ss_conf             99999999999


No 49 
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=99.04  E-value=9.4e-08  Score=80.16  Aligned_cols=172  Identities=15%  Similarity=0.205  Sum_probs=126.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHH
Q ss_conf             99999876533211246899987555789998875223567778875443679999887438545731201028989999
Q gi|254780289|r  428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA  507 (682)
Q Consensus       428 K~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~  507 (682)
                      .+++.+++.|...   |=.+++...-..|..++.+|++.--.-.|++|+.-+-+.+...+|++.  ..|.||...-.|..
T Consensus        14 ~eL~~~~~~GD~~---Af~~L~~~y~~~l~~~~~~~~~d~~~AeDl~Qevfl~~~~~~~~~~~~--~~~~~wL~~ia~n~   88 (194)
T PRK12513         14 EALMLRYRAGDAA---AFEALYARHRTGLYRFLLRLARDPALADDIFQETWLRVIRARSQWQPR--ARFRTWLYQIARNR   88 (194)
T ss_pred             HHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHH
T ss_conf             9999999946299---999999999999999999996999999999989999999887616975--45999999999999


Q ss_pred             HHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCE
Q ss_conf             99999722870461420588989999999998776088999789998709998999999986089875536358899860
Q gi|254780289|r  508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH  587 (682)
Q Consensus       508 i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~  587 (682)
                      +..++..+.+                    .       .+.                        +.+.+        . 
T Consensus        89 ~~~~~R~~~~--------------------~-------~~~------------------------~~~~~--------~-  108 (194)
T PRK12513         89 LIDHWRKHGA--------------------R-------QAP------------------------SLDAD--------E-  108 (194)
T ss_pred             HHHHHHHHHC--------------------C-------CCC------------------------CCCHH--------H-
T ss_conf             9999998744--------------------3-------775------------------------31103--------6-


Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf             47562389889989999999999999999732998899999998187986746889998996678999999999999983
Q gi|254780289|r  588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL  667 (682)
Q Consensus       588 ~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l  667 (682)
                      ...... ....+|+..+........|..+|+.|||+.+.|+.|||    -..+|..||+..+|+|--=|+..=.+|+++|
T Consensus       109 ~~~~~~-~~~~~~e~~~~~~e~~~~l~~~l~~Lp~~~r~il~L~~----~~g~s~~EIA~~l~is~~tVk~~l~rA~~~L  183 (194)
T PRK12513        109 LAHALA-DDGAGPEQQLSLFRDRRRLQAALETLPDEQREVFLLRE----HGDLSLEEIAQLTGVPLETVKSRLRYALQKL  183 (194)
T ss_pred             HHHCCC-CCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             650367-78899999999999999999999729989999999999----8499999999998949999999999999999


Q ss_pred             CC
Q ss_conf             29
Q gi|254780289|r  668 KH  669 (682)
Q Consensus       668 ~~  669 (682)
                      |.
T Consensus       184 r~  185 (194)
T PRK12513        184 RE  185 (194)
T ss_pred             HH
T ss_conf             99


No 50 
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=99.03  E-value=1e-07  Score=79.79  Aligned_cols=186  Identities=18%  Similarity=0.259  Sum_probs=136.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHH
Q ss_conf             21126889999998765332112468999875557899988752235677788754436799998874385457312010
Q gi|254780289|r  420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY  499 (682)
Q Consensus       420 ~gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~ty  499 (682)
                      ..++-.+-.+++.+++.|..   .|=..++...-+.|..+|.++++..-.-.|++|+--+-+.+..++|+....  |.  
T Consensus        10 ~~~~~~~D~eLi~~~~~GD~---~Af~~L~~ry~~~ly~~a~~~~~~~~dAEDlvQevFlk~~~~l~~f~~~~~--f~--   82 (231)
T PRK11922         10 TPLSAADDAELVARVLAGDE---AAFEQLMRRHNRRLYRLARAILRDDAEAEDVVQEAYLRAFRALARFRGDAS--LS--   82 (231)
T ss_pred             CCCCCCCHHHHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCCC--HH--
T ss_conf             99999759999999995659---999999999999999999999299999999999999999987530577565--99--


Q ss_pred             HHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCC
Q ss_conf             28989999999997228704614205889899999999987760889997899987099989999999860898755363
Q gi|254780289|r  500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP  579 (682)
Q Consensus       500 a~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~  579 (682)
                       +|-.+-+...++                 +.+.+..+..                                 ..+... 
T Consensus        83 -tWL~~Ia~N~~l-----------------d~lRk~~~~~---------------------------------~~~~~~-  110 (231)
T PRK11922         83 -TWLSRIVLNEAL-----------------GRLRRRRRDV---------------------------------IELRLA-  110 (231)
T ss_pred             -HHHHHHHHHHHH-----------------HHHHHHHCCC---------------------------------CCCCCC-
T ss_conf             -999999999999-----------------9999874122---------------------------------311000-


Q ss_pred             CCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             58899860475623898899899999999999999997329988999999981879867468899989966789999999
Q gi|254780289|r  580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI  659 (682)
Q Consensus       580 ~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi  659 (682)
                       ....+.....+..+....+|+.......+...+..+|+.|||+.+.|+.|||    -..+|..||++.+|+|---|+..
T Consensus       111 -~~~~~~~~~~~~~~~~~~~pe~~~~~~E~~~~l~~al~~Lp~~~R~v~~L~~----~eglS~~EIA~~Lgis~~TVKsr  185 (231)
T PRK11922        111 -TESEEGEEIEFPDADPAEDPEDAAARREIRALLERAIDALPDAFRAVFVLRV----VEELSVEETAQALGLPEETVKTR  185 (231)
T ss_pred             -CCCCCCHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             -1233210100233567899999999999999999999809999999999999----93999999999989399999999


Q ss_pred             HHHHHHHHCC
Q ss_conf             9999998329
Q gi|254780289|r  660 EAKAIRKLKH  669 (682)
Q Consensus       660 ~~~a~~~l~~  669 (682)
                      =.+|.++||.
T Consensus       186 L~RArk~LRe  195 (231)
T PRK11922        186 LHRARRLLRE  195 (231)
T ss_pred             HHHHHHHHHH
T ss_conf             9999999999


No 51 
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=99.03  E-value=3.8e-08  Score=83.29  Aligned_cols=177  Identities=16%  Similarity=0.237  Sum_probs=125.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHH
Q ss_conf             12688999999876533211246899987555789998875223567778875443679999887438545731201028
Q gi|254780289|r  422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM  501 (682)
Q Consensus       422 l~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~  501 (682)
                      .+..+..+++.+++.|...   |=.+|+...-+.|..+|.+|++.--.-.|++|+.-+-+.+...+|++.+| .|.   +
T Consensus        12 ~~~~d~~~Li~~~~~GD~~---Af~~Ly~~y~~~l~~~~~~~~~d~~~AeDivQevFl~~~~~~~~~~~~~~-~~~---~   84 (194)
T PRK09646         12 APSPDLDALLRRVARGDQD---AFAELYDRTASRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SAL---A   84 (194)
T ss_pred             CCCCCHHHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCC-CHH---H
T ss_conf             3796699999999936799---99999999999999999999299999999999999999997521475426-599---9


Q ss_pred             HHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             98999999999722870461420588989999999998776088999789998709998999999986089875536358
Q gi|254780289|r  502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG  581 (682)
Q Consensus       502 ~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~  581 (682)
                      |-.+-+..+++                 +.+.+.....    .+                               +...+
T Consensus        85 WL~~Ia~n~~~-----------------d~~R~~~~~~----~~-------------------------------~~~~~  112 (194)
T PRK09646         85 WLLTLAHRRAV-----------------DRVRSEQAAS----QR-------------------------------EVRYG  112 (194)
T ss_pred             HHHHHHHHHHH-----------------HHHHHHHHHH----HH-------------------------------HHHHC
T ss_conf             99999999999-----------------9999987413----24-------------------------------43200


Q ss_pred             CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             89986047562389889989999999999999999732998899999998187986746889998996678999999999
Q gi|254780289|r  582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA  661 (682)
Q Consensus       582 ~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~  661 (682)
                      ..+..        .....+.+.+........|..+|..|||+.+.||.|||    -..+|.+||++.+|+|-.-|+.-=.
T Consensus       113 ~~~~~--------~~~~~~~e~~~~~~~~~~l~~~l~~Lp~~~R~vi~L~~----~~g~s~~EIA~~Lgis~~TVk~rl~  180 (194)
T PRK09646        113 ARNVD--------PAFDQVAEEVEARLERERVRGCLDALTDTQREAITLAY----YGGLTYREVAERLAVPLGTVKTRMR  180 (194)
T ss_pred             CCCCC--------CCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             02368--------87553147899899999999999867815789999999----9399999999998919999999999


Q ss_pred             HHHHHHCC
Q ss_conf             99998329
Q gi|254780289|r  662 KAIRKLKH  669 (682)
Q Consensus       662 ~a~~~l~~  669 (682)
                      +|+++||.
T Consensus       181 rA~~~LR~  188 (194)
T PRK09646        181 DGLRRLRD  188 (194)
T ss_pred             HHHHHHHH
T ss_conf             99999999


No 52 
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=99.02  E-value=1.3e-07  Score=79.13  Aligned_cols=171  Identities=16%  Similarity=0.258  Sum_probs=125.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHH
Q ss_conf             89999998765332112468999875557899988752235677788754436799998874385457312010289899
Q gi|254780289|r  426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK  505 (682)
Q Consensus       426 ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~  505 (682)
                      ..++++.+++.|...   |=.++++..-+.|..+|.++++..-.-.|++||.-+-+.+...+|++...  |.|    |+.
T Consensus         5 d~~~Li~~~~~Gd~~---Af~~Ly~~y~~~l~~~~~~~~~d~~~AeD~vQe~Flk~~~~~~~~~~~~~--~~~----WL~   75 (190)
T PRK12543          5 DYKHLIQLTLSGNKE---AYSELYDVTIQEVYKTVHFLIEDKTDVDDVVQEVYIQLYESLRKYDSEKP--FRP----WLI   75 (190)
T ss_pred             CHHHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCC--HHH----HHH
T ss_conf             899999999956699---99999999999999999999099999999999999999999987188886--899----999


Q ss_pred             HHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf             99999997228704614205889899999999987760889997899987099989999999860898755363588998
Q gi|254780289|r  506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT  585 (682)
Q Consensus       506 ~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~  585 (682)
                      .-..+.+.+..|                +..+..                                  ..++.     . 
T Consensus        76 ~ia~n~~~~~~r----------------~~~~~~----------------------------------~~~~~-----~-   99 (190)
T PRK12543         76 GLVIKQIHSYRR----------------KRWMRL----------------------------------RIFKK-----A-   99 (190)
T ss_pred             HHHHHHHHHHHH----------------HHHHHC----------------------------------CCCCC-----H-
T ss_conf             999999999999----------------875003----------------------------------41220-----0-


Q ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             60475623898899899999999999999997329988999999981879867468899989966789999999999999
Q gi|254780289|r  586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR  665 (682)
Q Consensus       586 ~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~  665 (682)
                          +....+....|++.+........+..+|..|||+.+.|+.|||    -..+|..|||..+|+|-.-|+--=.+|++
T Consensus       100 ----~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~vi~L~~----~~g~s~~EIA~~l~is~~tVk~rl~rA~k  171 (190)
T PRK12543        100 ----EEQRKPVQIDFSNDLLSKISNQKLIELIHKLPYKLKQVIILRY----LHDYSQEEVAQILHIPIGTVKSRIHAALK  171 (190)
T ss_pred             ----HHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             ----1001555688268999999999999999849999999999999----85999999999989399999999999999


Q ss_pred             HHCC
Q ss_conf             8329
Q gi|254780289|r  666 KLKH  669 (682)
Q Consensus       666 ~l~~  669 (682)
                      +||.
T Consensus       172 ~LR~  175 (190)
T PRK12543        172 KLRQ  175 (190)
T ss_pred             HHHH
T ss_conf             9999


No 53 
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=99.00  E-value=1.3e-07  Score=78.96  Aligned_cols=168  Identities=15%  Similarity=0.216  Sum_probs=121.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC---HHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHH
Q ss_conf             999998765332112468999875557899988752235677---78875443679999887438545731201028989
Q gi|254780289|r  428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ---FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV  504 (682)
Q Consensus       428 K~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~---~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i  504 (682)
                      .+++.+++.|..   .|-.++++..-++|.+++.++.+....   -.|++|+.-+-+.+...+|++.+| +|+||   -.
T Consensus         4 ~~Li~~~~~GD~---~Af~~l~~~y~~~v~~~~~~~l~~~~~~~~aeD~vQevFi~~~~~~~~~~~~~~-~f~~W---L~   76 (185)
T PRK06811          4 DNFIKELKKKNE---KALEFIIDTYGNLIKKIVHKVLGTDQYKQLIEECVNDIFLSIWNNIDKFDEEKG-SFKNW---IA   76 (185)
T ss_pred             HHHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCHHCCCCCC-CHHHH---HH
T ss_conf             999999982789---999999999999999999999677688989999999999999983700388645-29999---99


Q ss_pred             HHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             99999999722870461420588989999999998776088999789998709998999999986089875536358899
Q gi|254780289|r  505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED  584 (682)
Q Consensus       505 ~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~  584 (682)
                      +=+..+++                 +.+.+..+        ..                         .++.+      +
T Consensus        77 ~Ia~n~~~-----------------d~~Rk~~r--------~~-------------------------~~~~~------~  100 (185)
T PRK06811         77 AISKYKAI-----------------DYKRKLTK--------NN-------------------------NIDSD------E  100 (185)
T ss_pred             HHHHHHHH-----------------HHHHHHCC--------CC-------------------------CCCHH------H
T ss_conf             99999999-----------------99997426--------56-------------------------66456------5


Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             86047562389889989999999999999999732998899999998187986746889998996678999999999999
Q gi|254780289|r  585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI  664 (682)
Q Consensus       585 ~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~  664 (682)
                             .......+|++.......+..+..+|..|||+.+.|+.|||    -..+|.+|||+.+|+|.--|+..=.+|+
T Consensus       101 -------~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~----~~~~s~~EIA~~l~is~~tVk~rl~Rar  169 (185)
T PRK06811        101 -------FILISEESIENEIILKENKEEIIKLINDLKKLDREIFIKRY----LLGESIEEIAKKLGLTRSAIDNRLSRGR  169 (185)
T ss_pred             -------HCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             -------21355588788999999999999998489999999999999----9499999999998929999999999999


Q ss_pred             HHHCC
Q ss_conf             98329
Q gi|254780289|r  665 RKLKH  669 (682)
Q Consensus       665 ~~l~~  669 (682)
                      ++||.
T Consensus       170 ~~Lr~  174 (185)
T PRK06811        170 KKLKN  174 (185)
T ss_pred             HHHHH
T ss_conf             99999


No 54 
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=98.96  E-value=2e-07  Score=77.55  Aligned_cols=177  Identities=18%  Similarity=0.255  Sum_probs=131.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHH
Q ss_conf             11268899999987653321124689998755578999887522356777887544367999988743854573120102
Q gi|254780289|r  421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA  500 (682)
Q Consensus       421 gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya  500 (682)
                      |.+-.+...++..++.|...   |=..|+...-+.|.+++.+|++..-.-.|++|+.-+-+.+..++|++.+|+-+    
T Consensus         6 ~~~~de~~~Li~~~~~GD~~---Af~~Ly~~y~~~l~~~~~~~~~~~~~AeDv~Qe~Fl~vw~~~~~~~~~~~~~~----   78 (187)
T PRK12534          6 GHDDDETGRLLTATAGGDRH---AFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRARGL----   78 (187)
T ss_pred             CCCCHHHHHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCHH----
T ss_conf             99962899999999936899---99999999999999999998699999999999999999987533687522189----


Q ss_pred             HHHHHH-HHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCC
Q ss_conf             898999-9999997228704614205889899999999987760889997899987099989999999860898755363
Q gi|254780289|r  501 MWWVKQ-AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP  579 (682)
Q Consensus       501 ~~~i~~-~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~  579 (682)
                       +|+.. +...|+ |..|                +..                                ..+..++++..
T Consensus        79 -tWl~~IarN~~~-d~lR----------------~~~--------------------------------~~~~~~~~~~~  108 (187)
T PRK12534         79 -TWLAMIARNKAI-DHLR----------------ANA--------------------------------PQRRNVALDDA  108 (187)
T ss_pred             -HHHHHHHHHHHH-HHHH----------------HCC--------------------------------CCCCCCCCCCC
T ss_conf             -999999999999-9999----------------624--------------------------------41357773411


Q ss_pred             CCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             58899860475623898899899999999999999997329988999999981879867468899989966789999999
Q gi|254780289|r  580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI  659 (682)
Q Consensus       580 ~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi  659 (682)
                            .   . +. ....+|.+.......+..|..+|..|+|..+.|+.++|    -..+|++||++.+|+|---|+.-
T Consensus       109 ------~---~-~~-~~~~~~~e~~~~~~~~~~l~~al~~L~~~~r~vi~l~~----~eg~s~~EIA~~l~i~~gTVksr  173 (187)
T PRK12534        109 ------G---E-LR-AADASPLERTERASTRRRIDHCLAELEPPRSELIRTAF----FEGITYEELAARTDTPIGTVKSW  173 (187)
T ss_pred             ------C---C-CC-CCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             ------0---0-13-56898277899999999999999868998999999999----84999999999989199999999


Q ss_pred             HHHHHHHHCC
Q ss_conf             9999998329
Q gi|254780289|r  660 EAKAIRKLKH  669 (682)
Q Consensus       660 ~~~a~~~l~~  669 (682)
                      =.+|+++||.
T Consensus       174 l~ra~~~Lr~  183 (187)
T PRK12534        174 IRRGLAKLKA  183 (187)
T ss_pred             HHHHHHHHHH
T ss_conf             9999999999


No 55 
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=98.94  E-value=2.2e-07  Score=77.22  Aligned_cols=168  Identities=17%  Similarity=0.265  Sum_probs=124.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHH
Q ss_conf             99999987653321124689998755578999887522356777887544367999988743854573120102898999
Q gi|254780289|r  427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ  506 (682)
Q Consensus       427 lK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~  506 (682)
                      =.+++..++.|...   |-.+|+...-..|.++|.++++..-.-.|++|+.-+.+.+...+|++..+ +|.|   |-.+-
T Consensus         7 D~eLi~~~~~Gd~~---Af~~L~~~y~~~l~~~~~~~~~d~~~AeDivQe~fl~~~~~~~~~~~~~~-~~~~---wL~~i   79 (186)
T PRK05602          7 DAELMARVGAGDAS---AFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWNQAPSWRPGEA-RFDT---WLHRV   79 (186)
T ss_pred             HHHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCCH-HHHH---HHHHH
T ss_conf             99999999928899---99999999999999999999299999999999999999987222588620-3999---99999


Q ss_pred             HHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             99999972287046142058898999999999877608899978999870999899999998608987553635889986
Q gi|254780289|r  507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS  586 (682)
Q Consensus       507 ~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~  586 (682)
                      +...++                 +.+.+ .+                                   .++++.+       
T Consensus        80 a~n~~~-----------------d~~Rk-~~-----------------------------------~~~~~~~-------   99 (186)
T PRK05602         80 VLNLCY-----------------DRLRR-RR-----------------------------------EVPVEDA-------   99 (186)
T ss_pred             HHHHHH-----------------HHHHH-HH-----------------------------------CCCCCCC-------
T ss_conf             999999-----------------99987-14-----------------------------------1573222-------


Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             04756238988998999999999999999973299889999999818798674688999899667899999999999998
Q gi|254780289|r  587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK  666 (682)
Q Consensus       587 ~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~  666 (682)
                        .+. .+ ...+|++..........+..+|..|||+.+.|+.|+|    -..+|..||+..+|+|---|+..=.+|+++
T Consensus       100 --~~~-~~-~~~~~~~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~~----~~g~s~~EIA~~l~is~~tVk~~l~RAr~~  171 (186)
T PRK05602        100 --PEV-PD-PAPGPDERLEARQRARRVEQALAALPERQREAIVLQY----YQGLSNIEAARVMGLSVDALESLLARARRA  171 (186)
T ss_pred             --CCC-CC-CCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf             --000-34-6898778999999999999999759987889999998----638999999999893999999999999999


Q ss_pred             HCC
Q ss_conf             329
Q gi|254780289|r  667 LKH  669 (682)
Q Consensus       667 l~~  669 (682)
                      ||.
T Consensus       172 Lr~  174 (186)
T PRK05602        172 LRA  174 (186)
T ss_pred             HHH
T ss_conf             999


No 56 
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=98.91  E-value=2.8e-07  Score=76.46  Aligned_cols=170  Identities=17%  Similarity=0.207  Sum_probs=122.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHH
Q ss_conf             99998765332112468999875557899988752235677788754436799998874385457312010289899999
Q gi|254780289|r  429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI  508 (682)
Q Consensus       429 ~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i  508 (682)
                      +++...+.|..   .|=.++....-.+|.++|.++++..-.-.|++|+.-+.+++..+.|+....++  +    |+..-.
T Consensus         2 ~l~~~a~~Gd~---~Af~~ly~~y~~~l~~~~~~~~~d~~~AeDi~Qe~fi~l~~~~~~~~~~~~~~--~----wL~~ia   72 (180)
T PRK11924          2 QLPAVAASGDK---EAFSELFLPHAPDLLRYARRQLGNRALAEDAVQEAFLRAWRKADLFNGKGSAR--T----WLLTIA   72 (180)
T ss_pred             HHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCHH--H----HHHHHH
T ss_conf             88899995599---99999999999999999999929999999999999999988632235434799--9----999999


Q ss_pred             HHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEE
Q ss_conf             99997228704614205889899999999987760889997899987099989999999860898755363588998604
Q gi|254780289|r  509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL  588 (682)
Q Consensus       509 ~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~  588 (682)
                      .+.+.+..|                +..+.                               ...+.+.+.+         
T Consensus        73 rn~~~d~~r----------------k~~~~-------------------------------~~~~~~~~~~---------   96 (180)
T PRK11924         73 RNKCYDMLR----------------RRRRE-------------------------------RKEAAEDEDL---------   96 (180)
T ss_pred             HHHHHHHHH----------------HHHHH-------------------------------CCCCCCHHHC---------
T ss_conf             999999999----------------97201-------------------------------0223311001---------


Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf             75623898899899999999999999997329988999999981879867468899989966789999999999999832
Q gi|254780289|r  589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK  668 (682)
Q Consensus       589 ~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~  668 (682)
                      .++  .....+|.+..........|..+|..|+|+++.|+.|+|    -..++++|||+.+|+|..-|++.=.+|.++||
T Consensus        97 ~~~--~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~----~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr  170 (180)
T PRK11924         97 APL--SAEFETPEAALLAKDDLARIDRCLDALPEKQREVFLLRY----VEGLSYQEIADQLGVPLGTVKSRLRRARQKLR  170 (180)
T ss_pred             CCC--CCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             333--446698589999999999999999859999999999999----96859999999989499999999999999999


Q ss_pred             C
Q ss_conf             9
Q gi|254780289|r  669 H  669 (682)
Q Consensus       669 ~  669 (682)
                      -
T Consensus       171 ~  171 (180)
T PRK11924        171 E  171 (180)
T ss_pred             H
T ss_conf             9


No 57 
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=98.90  E-value=3.3e-07  Score=75.90  Aligned_cols=172  Identities=15%  Similarity=0.200  Sum_probs=120.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEE
Q ss_conf             12468999875557899988752235677788754436799998874385457312010289899999999972287046
Q gi|254780289|r  441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR  520 (682)
Q Consensus       441 ~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r  520 (682)
                      +++|=.+|++..-+.|..+|.++++..-.-.|++|+.-+-+.+..++|+...  .|.   +|-.+=+...++ |      
T Consensus         1 ~Eeafe~L~~~y~~~l~~~~~~~~~~~~~AeDl~Qe~flk~~~~~~~~~~~~--~~~---~WL~~Ia~N~~~-d------   68 (173)
T PRK12522          1 MEEKVEELIDIYKDQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVE--NYK---KWITTICVRTFY-D------   68 (173)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCC--CHH---HHHHHHHHHHHH-H------
T ss_conf             9799999999999999999999919999999999999999999777668854--489---999999999999-9------


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCH
Q ss_conf             14205889899999999987760889997899987099989999999860898755363588998604756238988998
Q gi|254780289|r  521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP  600 (682)
Q Consensus       521 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~  600 (682)
                                .+.+..+..                                 ....+..  +..+   +..+..++..+|
T Consensus        69 ----------~~Rk~~r~~---------------------------------~~~~~~~--~~~~---~~~~~~~~~~~~  100 (173)
T PRK12522         69 ----------FYRKKKRWK---------------------------------DRILDLF--HKED---GGEIEFADDVNI  100 (173)
T ss_pred             ----------HHHHHCCCC---------------------------------CCCCCCC--CHHH---HHCCCCCCCCCC
T ss_conf             ----------999863412---------------------------------1110100--0100---001235677885


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHH
Q ss_conf             99999999999999997329988999999981879867468899989966789999999999999832967778756651
Q gi|254780289|r  601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL  680 (682)
Q Consensus       601 ~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~~~~  680 (682)
                      .+..........+..+|..|||+.+.|+.|+|    -...|..||++.+|+|---|+--=.+|.++||     ..|++|+
T Consensus       101 ~~~~~~~~~~~~l~~~l~~L~~~~R~vi~L~~----~~~~s~~EIA~~l~is~~tVksrl~rAr~~Lr-----~~Le~~~  171 (173)
T PRK12522        101 SEEFIQKVEAEMIREVIQLLNEKYKTVLVLYY----YEQYSYKEMSEILNIPIGTVKYRLNYAKKQMR-----EHLEGFV  171 (173)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH-----HHHHCCC
T ss_conf             29999999999999999819999999999999----83999999999989399999999999999999-----9875651


Q ss_pred             C
Q ss_conf             7
Q gi|254780289|r  681 D  681 (682)
Q Consensus       681 ~  681 (682)
                      .
T Consensus       172 ~  172 (173)
T PRK12522        172 H  172 (173)
T ss_pred             C
T ss_conf             3


No 58 
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=98.89  E-value=3.6e-07  Score=75.54  Aligned_cols=174  Identities=14%  Similarity=0.243  Sum_probs=127.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHH
Q ss_conf             26889999998765332112468999875557899988752235677788754436799998874385457312010289
Q gi|254780289|r  423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW  502 (682)
Q Consensus       423 ~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~  502 (682)
                      .+.+...++.+++.|...   |=..|+..+-+.|..+|.+|++..-.-.|++|+.-+-+.+..++|.... ..|+|   |
T Consensus         2 ~p~d~~~Li~~~~~GD~~---Af~~L~~~y~~~l~~~a~~~~~d~~~AeDi~Qe~fl~~~~~~~~~~~~~-~~~~~---w   74 (179)
T PRK12514          2 QPDDIEKLIVRVSLGDRD---AFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSG-LSPMT---W   74 (179)
T ss_pred             CCCCHHHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCC-CCHHH---H
T ss_conf             971099999999965899---9999999999999999999909999999999999999998875157665-53999---9


Q ss_pred             HHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             89999999997228704614205889899999999987760889997899987099989999999860898755363588
Q gi|254780289|r  503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD  582 (682)
Q Consensus       503 ~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~  582 (682)
                      -.+-+...++ |.                +.+          +.+.                        ...++.    
T Consensus        75 L~~iarN~~i-d~----------------~R~----------~~~~------------------------~~~~~~----   99 (179)
T PRK12514         75 LITIARNHAI-DR----------------LRA----------RKAV------------------------AVDIDE----   99 (179)
T ss_pred             HHHHHHHHHH-HH----------------HHH----------CCCC------------------------CCCHHH----
T ss_conf             9999999999-99----------------986----------3777------------------------787456----


Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             99860475623898899899999999999999997329988999999981879867468899989966789999999999
Q gi|254780289|r  583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK  662 (682)
Q Consensus       583 ~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~  662 (682)
                           ..++. + ..++|+..+........+..+|..|||+.+.|+.|+|    -..+|..||++.+|+|---|+.-=.+
T Consensus       100 -----~~~~~-~-~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~r~~~~l~~----~eg~s~~EIA~~l~is~~tVk~~l~r  168 (179)
T PRK12514        100 -----AHDLA-D-PSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAY----LEGLSYKELAERHDVPLNTMRTWLRR  168 (179)
T ss_pred             -----HHHHC-C-CCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             -----76512-4-6898699999889999999999875599999999996----06998999999889099999999999


Q ss_pred             HHHHHCC
Q ss_conf             9998329
Q gi|254780289|r  663 AIRKLKH  669 (682)
Q Consensus       663 a~~~l~~  669 (682)
                      |+++||.
T Consensus       169 A~~~Lr~  175 (179)
T PRK12514        169 SLLKLRE  175 (179)
T ss_pred             HHHHHHH
T ss_conf             9999999


No 59 
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=98.88  E-value=5.1e-07  Score=74.38  Aligned_cols=178  Identities=17%  Similarity=0.174  Sum_probs=122.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHH
Q ss_conf             26889999998765332112468999875557899988752235677788754436799998874385457312010289
Q gi|254780289|r  423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW  502 (682)
Q Consensus       423 ~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~  502 (682)
                      +-.+-.+++.+++.|..+   |=.+|++..-..|.+.|.++++..-.-.|++|+.-+.+.+....|++.++ .|+||..=
T Consensus        10 ~~~~~~eLi~r~~~GD~~---Af~~Ly~~y~~~l~~~~~~~~~d~~~AeDlvQe~Flk~~~~~~~~~~~~s-~f~tWl~~   85 (194)
T PRK12531         10 GRQEWLECMEKVKSRDKQ---AFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYT   85 (194)
T ss_pred             CCHHHHHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCC-CHHHHHHH
T ss_conf             516699999999958899---99999999999999999999399999999999999999998886676536-09999999


Q ss_pred             HHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             89999999997228704614205889899999999987760889997899987099989999999860898755363588
Q gi|254780289|r  503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD  582 (682)
Q Consensus       503 ~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~  582 (682)
                      -.+..+..++..+.                           ++..                         .++.+.... 
T Consensus        86 Ia~N~~~d~lRk~~---------------------------~~~~-------------------------~~~~~~~~~-  112 (194)
T PRK12531         86 IIRNLCFDLLRKQK---------------------------GKDL-------------------------HIHADDIWP-  112 (194)
T ss_pred             HHHHHHHHHHHHHC---------------------------CCCC-------------------------CCCHHHCCC-
T ss_conf             99999999999740---------------------------4343-------------------------432111142-


Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             99860475623898899899999999999999997329988999999981879867468899989966789999999999
Q gi|254780289|r  583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK  662 (682)
Q Consensus       583 ~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~  662 (682)
                      . +....+.+   +..+|+    ...+++++..+|..||++.+.|+.|+|    -..+|..||++.+|+|-.-|+--=.+
T Consensus       113 ~-~~~~~~~~---~~~~~e----~~~~~~~~~~~l~~Lp~~~R~vi~L~~----~e~~s~~EIAe~l~is~~TVKsrl~r  180 (194)
T PRK12531        113 S-DYYPPDLV---DHYSPE----QDMLKEQVMKFLDRLPKAQRDVLQAVY----LEELPHQQVAEMFDIPLGTVKSRLRL  180 (194)
T ss_pred             C-CCCCCCCC---CCCCHH----HHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             2-24783000---125879----999999999999869999999999998----86999999999989299999999999


Q ss_pred             HHHHHCC
Q ss_conf             9998329
Q gi|254780289|r  663 AIRKLKH  669 (682)
Q Consensus       663 a~~~l~~  669 (682)
                      |+++||.
T Consensus       181 A~k~LR~  187 (194)
T PRK12531        181 AVEKLRH  187 (194)
T ss_pred             HHHHHHH
T ss_conf             9999999


No 60 
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=98.88  E-value=4.7e-07  Score=74.68  Aligned_cols=169  Identities=18%  Similarity=0.261  Sum_probs=124.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHH
Q ss_conf             99999987653321124689998755578999887522356777887544367999988743854573120102898999
Q gi|254780289|r  427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ  506 (682)
Q Consensus       427 lK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~  506 (682)
                      =..++.+++.|..   .|=.+|+...-..|...|.+|++..-.-.|++|+.-+.+.+..++|++...  |.|   |-.+-
T Consensus         9 D~~Lv~~~~~gd~---~Af~~L~~ry~~~l~~~~~~~~~~~~~AeDivQe~Fl~~~~~~~~~~~~~~--~~~---WL~~I   80 (189)
T PRK12515          9 DEMLLARIAQGDR---TAMHTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGRSQ--VST---WLLSI   80 (189)
T ss_pred             HHHHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCH--HHH---HHHHH
T ss_conf             9999999993779---999999999999999999999299999999999999999986510253022--999---99999


Q ss_pred             HHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             99999972287046142058898999999999877608899978999870999899999998608987553635889986
Q gi|254780289|r  507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS  586 (682)
Q Consensus       507 ~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~  586 (682)
                      +..+++                 +.+.+..        +                          .++      ..++..
T Consensus        81 arn~~~-----------------~~~r~~~--------~--------------------------~~~------~~~~~~  103 (189)
T PRK12515         81 ARFKAL-----------------SALRQRK--------D--------------------------EEI------DDEAAA  103 (189)
T ss_pred             HHHHHH-----------------HHHHHCC--------C--------------------------CCC------CHHHHH
T ss_conf             999999-----------------9998513--------3--------------------------666------545676


Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             04756238988998999999999999999973299889999999818798674688999899667899999999999998
Q gi|254780289|r  587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK  666 (682)
Q Consensus       587 ~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~  666 (682)
                      .    +.| ...+|+...........+..+|..|||+.+.||.|||    -...|+.|||..+|+|---|+..=.+|+++
T Consensus       104 ~----~~~-~~~~~e~~~~~~~~~~~l~~~l~~L~~~~R~vi~l~~----~e~~s~~EIA~~lgis~~tV~~~l~RAr~~  174 (189)
T PRK12515        104 A----IED-GSDTPEVALQKKDTSAILRACIAKLSPAHREIIDLVY----YHEKSVEEVGEIVGIPESTVKTRMFYARKK  174 (189)
T ss_pred             H----CCC-CCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf             3----367-7899889998999999999998759999999999999----849999999999892999999999999999


Q ss_pred             HCC
Q ss_conf             329
Q gi|254780289|r  667 LKH  669 (682)
Q Consensus       667 l~~  669 (682)
                      ||-
T Consensus       175 Lr~  177 (189)
T PRK12515        175 LAE  177 (189)
T ss_pred             HHH
T ss_conf             999


No 61 
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=98.87  E-value=2.2e-07  Score=77.25  Aligned_cols=171  Identities=17%  Similarity=0.204  Sum_probs=117.8

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHH
Q ss_conf             98755578999887522356777887544367999988743854573120102898999999999722870461420588
Q gi|254780289|r  448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD  527 (682)
Q Consensus       448 l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~  527 (682)
                      .+++.=+.+...|.+|++..-.-.|++|+--+.++...++|...  .+|.||.+=-.|..+.-++..+.|..+++..   
T Consensus         7 ~le~~r~~L~r~A~~~v~d~~~AEDvvQetfl~~~~~~~~f~~~--~~~~tWL~~IarN~~id~lR~~~r~~~~~~~---   81 (191)
T PRK12520          7 QLEALRPYLLRFARLQLRDEAWAEDAVSETLLAALEKPERFAGQ--SQLKTYLVGILKHKIIDALRSGRREVRLSLD---   81 (191)
T ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHHHHHHHHHCCCCCCCCC---
T ss_conf             99999999999999994999999999999999999817642765--4559899999999999999983675555433---


Q ss_pred             HHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHH
Q ss_conf             98999999999877608899978999870999899999998608987553635889986047562389889989999999
Q gi|254780289|r  528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA  607 (682)
Q Consensus       528 ~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~  607 (682)
                                     .....+.+.+..           .+      .+        .+++..+.  .....+|+..+.+.
T Consensus        82 ---------------~~~~~~~~~~~~-----------~~------~~--------~~~~~~~~--p~~~~~Pe~~l~~~  119 (191)
T PRK12520         82 ---------------EGDEQSDDDLFD-----------AL------FT--------ADGHYREP--PSDWGDPEATLQRR  119 (191)
T ss_pred             ---------------CCCCCCHHHHHH-----------HH------HC--------CCCCCCCC--CCCCCCHHHHHHHH
T ss_conf             ---------------456554046777-----------76------22--------34432358--76659999999999


Q ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             99999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       608 ~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      .+...+..+|+.|||+.+.|+.|||    ....+..|||..+|+|..-|++.=.+|..+||-
T Consensus       120 e~~~~l~~aL~~Lp~~~R~v~~Lr~----~~~ls~~EIA~~l~~s~~tVk~~l~RAR~~Lr~  177 (191)
T PRK12520        120 QFFEVLQACVERLPARTGRVFMMRE----WLELETEEICKELQITATNLWVMLYRARLRLRE  177 (191)
T ss_pred             HHHHHHHHHHHHCCHHHHHHHHHHH----HHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             9999999999877499999999999----938999999999894999999999999999999


No 62 
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=98.85  E-value=8.4e-07  Score=72.64  Aligned_cols=169  Identities=16%  Similarity=0.235  Sum_probs=124.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHH
Q ss_conf             99999876533211246899987555789998875223567778875443679999887438545731201028989999
Q gi|254780289|r  428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA  507 (682)
Q Consensus       428 K~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~  507 (682)
                      .+++..++.|..   .|=.+|+...-+.|.++|.++.+.--.-.|++|+.-+-+.+....|...++ +|+|   |-.+-+
T Consensus        14 ~~Lv~~~~~GD~---~Af~~L~~ry~~~l~~~a~~~l~d~~~AEDlvQe~Fl~~~~~~~~~~~~~~-~~~t---WL~~Ia   86 (196)
T PRK12524         14 EALLVLFANGDP---AAARALTLRLAPRALAVATRVLGNRAEAEDVTQEAMLRLWRIAPDWRQGEA-RVST---WLYRVV   86 (196)
T ss_pred             HHHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCC-HHHH---HHHHHH
T ss_conf             999999992889---999999999999999999999199999999999999999997466156520-7999---999999


Q ss_pred             HHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCE
Q ss_conf             99999722870461420588989999999998776088999789998709998999999986089875536358899860
Q gi|254780289|r  508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH  587 (682)
Q Consensus       508 i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~  587 (682)
                      ...++.                 .+.+..        +                          ...+++      +...
T Consensus        87 ~N~~~d-----------------~~R~~~--------~--------------------------~~~~~~------~~~~  109 (196)
T PRK12524         87 CNLCTD-----------------RLRRQR--------R--------------------------ASVDLD------DAPE  109 (196)
T ss_pred             HHHHHH-----------------HHHHHH--------C--------------------------CCCCCC------CCCC
T ss_conf             999999-----------------999850--------5--------------------------677611------2433


Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf             47562389889989999999999999999732998899999998187986746889998996678999999999999983
Q gi|254780289|r  588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL  667 (682)
Q Consensus       588 ~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l  667 (682)
                          .. ...++|++.+........|..+|..|||+.+.|+.|||    -..+|..||+..+|+|-.-|+..=.+|+++|
T Consensus       110 ----~~-~~~~~~e~~~~~~~~~~~l~~al~~Lp~~~R~vi~L~~----~eg~s~~EIA~~lgis~~tVk~~l~Rark~L  180 (196)
T PRK12524        110 ----PA-DAAPGAEEALQEGDRMRALDAALAALPERQRQAVVLRH----IEGLSNPEIAEVMQIGVEAVESLTARGKRAL  180 (196)
T ss_pred             ----CC-CCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             ----24-56898879999899999999999859999999989999----8089999999998929999999999999999


Q ss_pred             CC
Q ss_conf             29
Q gi|254780289|r  668 KH  669 (682)
Q Consensus       668 ~~  669 (682)
                      |.
T Consensus       181 r~  182 (196)
T PRK12524        181 AA  182 (196)
T ss_pred             HH
T ss_conf             99


No 63 
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=98.83  E-value=7.2e-07  Score=73.17  Aligned_cols=177  Identities=18%  Similarity=0.287  Sum_probs=122.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHH
Q ss_conf             99999876533211246899987555789998875223567778875443679999887438545731201028989999
Q gi|254780289|r  428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA  507 (682)
Q Consensus       428 K~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~  507 (682)
                      .+++.+++.|..-=++|=.+++...-..|.+.+.++++.--.-.|++||.-+-+.+..++|+..  .+|.   +|-.+=+
T Consensus        11 ~eLv~~~~~g~~gD~~AF~~L~~~y~~~v~~~~~~~~~~~~dAEDl~Qe~flk~~~~l~~~~~~--~~f~---~WL~~Ia   85 (188)
T PRK09640         11 EELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGK--SKFK---TWLYSIT   85 (188)
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHH---HHHHHHH
T ss_conf             9999999827963899999999999999999999990999999999999999999988765898--8789---9999999


Q ss_pred             HHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCE
Q ss_conf             99999722870461420588989999999998776088999789998709998999999986089875536358899860
Q gi|254780289|r  508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH  587 (682)
Q Consensus       508 i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~  587 (682)
                      ...++.                 .+.+..        |.+..                     ....+++. +.+     
T Consensus        86 ~N~~~d-----------------~~Rk~~--------r~~~~---------------------~~~~~~~~-~~~-----  113 (188)
T PRK09640         86 YNECIT-----------------QYRKER--------RKRRL---------------------MDALSLDP-LEE-----  113 (188)
T ss_pred             HHHHHH-----------------HHHHHC--------CCCCC---------------------CCCCCCCC-CCC-----
T ss_conf             999999-----------------999861--------54555---------------------43000244-456-----


Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf             47562389889989999999999999999732998899999998187986746889998996678999999999999983
Q gi|254780289|r  588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL  667 (682)
Q Consensus       588 ~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l  667 (682)
                                 .+.+.......+..+..+|..|+|.++.|+.|||    -..+|..||+..+|+|---|+.-=.+|+.+|
T Consensus       114 -----------~~~~~~~~~e~~~~l~~~l~~L~~~~R~vl~L~~----~~~ls~~EIA~~l~is~~tVksrl~RAr~~L  178 (188)
T PRK09640        114 -----------ASEEKAPKPEERGGLDRWLVHVNPIDREILVLRF----VAELEFQEIADIMHMGLSATKMRYKRALDKL  178 (188)
T ss_pred             -----------CCCCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             -----------8631002489999999999848999999999999----9299999999998929999999999999999


Q ss_pred             CCHHHHHHHHHHHC
Q ss_conf             29677787566517
Q gi|254780289|r  668 KHPSRSKKLRSFLD  681 (682)
Q Consensus       668 ~~~~~~~~l~~~~~  681 (682)
                      |     +.|++|.|
T Consensus       179 r-----~~L~~~~e  187 (188)
T PRK09640        179 R-----EKFAGLAE  187 (188)
T ss_pred             H-----HHHHCCCC
T ss_conf             9-----98645146


No 64 
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=98.82  E-value=6.4e-07  Score=73.61  Aligned_cols=171  Identities=18%  Similarity=0.223  Sum_probs=126.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHH
Q ss_conf             99998765332112468999875557899988752235677788754436799998874385457312010289899999
Q gi|254780289|r  429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI  508 (682)
Q Consensus       429 ~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i  508 (682)
                      ...-..+.|.+.-..|-.+|++..-+.|...|.++++.--.-.||+||.-+-+.+..++|++  | .|+|   |-.|=+.
T Consensus        33 ~~~~~~~~~~~~d~~AF~eLv~rh~~~vy~~a~r~~gn~~dAEDlvQEtFlka~r~l~~f~~--~-sf~t---WL~rIA~  106 (222)
T PRK09647         33 GTAVFDATGDKATMPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEG---WLHRITT  106 (222)
T ss_pred             CHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCC--C-CHHH---HHHHHHH
T ss_conf             44888741452458999999999999999999998599989999999999999986222477--3-0899---9999999


Q ss_pred             HHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEE
Q ss_conf             99997228704614205889899999999987760889997899987099989999999860898755363588998604
Q gi|254780289|r  509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL  588 (682)
Q Consensus       509 ~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~  588 (682)
                      ..++. .                +.|..        |                            +..+ .+.++.    
T Consensus       107 N~~iD-~----------------~Rr~~--------r----------------------------~~~~-~~~e~~----  128 (222)
T PRK09647        107 NLFLD-M----------------VRRRQ--------R----------------------------IRME-ALPEDY----  128 (222)
T ss_pred             HHHHH-H----------------HHHCC--------C----------------------------CCCC-CCCCHH----
T ss_conf             99999-9----------------98112--------4----------------------------6655-561134----


Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf             75623898899899999999999999997329988999999981879867468899989966789999999999999832
Q gi|254780289|r  589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK  668 (682)
Q Consensus       589 ~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~  668 (682)
                       +.+.+ ..++|+..+....+...|..+|..|+|+.+.||.|||    -..+|.+||++.+|+|---|+.-=.+|+++||
T Consensus       129 -e~~~~-~~~~pe~~~~~~~~~~~L~~al~~Lp~~qR~vl~Lr~----~eglS~~EIAe~Lgis~gTVKsrl~RAr~~LR  202 (222)
T PRK09647        129 -DRVPA-DEPNPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCD----IEGLSYEEIAATLGVKLGTVRSRIHRGRQALR  202 (222)
T ss_pred             -HHCCC-CCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             -42566-7899789999999999999999829999988998799----63999999999989399999999999999999


Q ss_pred             C
Q ss_conf             9
Q gi|254780289|r  669 H  669 (682)
Q Consensus       669 ~  669 (682)
                      .
T Consensus       203 ~  203 (222)
T PRK09647        203 A  203 (222)
T ss_pred             H
T ss_conf             9


No 65 
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=98.82  E-value=8.4e-07  Score=72.67  Aligned_cols=170  Identities=16%  Similarity=0.153  Sum_probs=114.2

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHH---HHCCCEEECCC
Q ss_conf             998755578999887522356777887544367999988743854573120102898999999999---72287046142
Q gi|254780289|r  447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI---ADQSCTIRIPV  523 (682)
Q Consensus       447 ~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~---~~~~~~~r~~~  523 (682)
                      .||+..=+-.+..|.++.+.--.-.|++||.-+-..+..++|+.+.  +|+|   |-.|=+...++   ..+.|...++ 
T Consensus        23 ~l~e~y~~~L~r~A~r~l~d~~~AEDlvQEtFlka~~~l~~F~g~s--~f~t---WL~~Ia~N~~iD~lRk~~r~~~~~-   96 (207)
T PRK12544         23 VFLEDLRAQMLKFAKLQLRDNHLAEDAVQEALFSAYQNADSFAGRA--AFKT---WVFAILKNKIIDLLRQKKRHVSAS-   96 (207)
T ss_pred             HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCC--CHHH---HHHHHHHHHHHHHHHHHCCCCCCC-
T ss_conf             9999999999999999949999999999999999998177438888--6098---999999999999999851656521-


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHH
Q ss_conf             05889899999999987760889997899987099989999999860898755363588998604756238988998999
Q gi|254780289|r  524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS  603 (682)
Q Consensus       524 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~  603 (682)
                                        .+-..+...+                       .++ ++.+ +.+++...-.......|++.
T Consensus        97 ------------------~~~~~~~~~~-----------------------~~~-~~~d-~~g~~~~~e~p~~~~~pee~  133 (207)
T PRK12544         97 ------------------QLEDGDEGEA-----------------------LIE-ALFD-ESGHWQKDERPQKWDQPEEG  133 (207)
T ss_pred             ------------------CCCCCCCHHH-----------------------HHH-HHHC-CCCCCCCCCCCCCCCCHHHH
T ss_conf             ------------------0134541013-----------------------466-6511-12343333465333898999


Q ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             999999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       604 ~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      +....+...+..+|..|||+.+.|+.|||    -...+..||++.+|+|-.-|+..=.+|-.+||.
T Consensus       134 l~~~e~~~~l~~aL~~Lp~~~R~vl~Lr~----~eglS~~EIAe~Lgis~~tVks~L~RAR~~Lr~  195 (207)
T PRK12544        134 VEQEQFWRIFDACLDALPAKYARVFMMRE----FIELETPEICHNEDLTVSNLNVMLYRSRLRLRE  195 (207)
T ss_pred             HHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999839999999999999----819999999999797999999999999999999


No 66 
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=98.81  E-value=5.9e-07  Score=73.87  Aligned_cols=176  Identities=12%  Similarity=0.185  Sum_probs=119.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHH
Q ss_conf             26889999998765332112468999875557899988752235677788754436799998874385457312010289
Q gi|254780289|r  423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW  502 (682)
Q Consensus       423 ~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~  502 (682)
                      ++.+...+++.+++|..   .|-.+++...-..|..+|.+|++.--.-.|++|+.-+-+.+..++|++.+|. |.   + 
T Consensus         6 ~p~d~e~ll~~~~~GD~---~Af~~Ly~~y~~~l~~~~~~~~~d~~~AeDivQe~Fl~~~~~~~~~~~~~~~-~~---~-   77 (184)
T PRK12537          6 APFDYEACLQACARGER---RALQRLYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTKAASFDAARGS-AR---G-   77 (184)
T ss_pred             CCCCHHHHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCCCCCC-HH---H-
T ss_conf             99999999999995889---9999999999999999999992999999999999999999860416844263-99---9-


Q ss_pred             HHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             89999999997228704614205889899999999987760889997899987099989999999860898755363588
Q gi|254780289|r  503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD  582 (682)
Q Consensus       503 ~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~  582 (682)
                      |+..-..+..                +|.+.+..+.       .+..+...                  ...+.+     
T Consensus        78 WL~~Iarn~~----------------~~~lR~~~r~-------~~~~~~~~------------------~~~~~~-----  111 (184)
T PRK12537         78 WIYSVTRHLA----------------LNTLRDTRRE-------VVLDDDAS------------------EQATAQ-----  111 (184)
T ss_pred             HHHHHHHHHH----------------HHHHHHHCCC-------CCCCCHHH------------------HHCCCC-----
T ss_conf             9999999999----------------9999985065-------66651002------------------101346-----


Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             99860475623898899899999999999999997329988999999981879867468899989966789999999999
Q gi|254780289|r  583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK  662 (682)
Q Consensus       583 ~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~  662 (682)
                                ......+   ..........|..+|..|+|+.+.|+.++|    -..+|..||++.+|+|-.-|+..=.+
T Consensus       112 ----------~~~~~~~---~~~~~~~~~~l~~~l~~L~~~~r~~i~l~~----~eg~s~~EIA~~l~is~~TVk~rl~r  174 (184)
T PRK12537        112 ----------GWQEIID---DFDLWVNSGKIHRCLEQLEPARRNCILHAY----VDGCSHAEIAQRLGAPLGTVKAWIKR  174 (184)
T ss_pred             ----------CCCCCCC---HHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             ----------7777556---798999999999999809998999999988----43999999999989299999999999


Q ss_pred             HHHHHCC
Q ss_conf             9998329
Q gi|254780289|r  663 AIRKLKH  669 (682)
Q Consensus       663 a~~~l~~  669 (682)
                      |+.+||.
T Consensus       175 A~~~LR~  181 (184)
T PRK12537        175 SLKALRE  181 (184)
T ss_pred             HHHHHHH
T ss_conf             9999998


No 67 
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS; InterPro: IPR012761   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 RpoS (also called sigma-38, KatF, etc.), found only in proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second principal sigma factor at that time.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=98.80  E-value=3.6e-08  Score=83.47  Aligned_cols=124  Identities=21%  Similarity=0.154  Sum_probs=93.2

Q ss_pred             CCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHH------------HHHHHHHHHHCCHHHHHHHHHHHHHHCCCHHHH
Q ss_conf             77772899999985697688978899999999988------------999999987282389999999987311710367
Q gi|254780289|r  115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG------------RAMMMASLCESPLTFQALIIWRDELNDGTTLLR  182 (682)
Q Consensus       115 ~rtdDPVRMYLREMG~V~LLTREgEIeIAKRIE~G------------~~~i~~al~~~P~ti~~il~~~e~i~~ge~~Lr  182 (682)
                      ..+-||+.+||||+|.-||||.++|+.+|.|--+|            .+-|.++--+|-.-.-.++|+.++-+=|=|..-
T Consensus         9 ~~~~D~~Q~YL~eIg~~PLLt~~EE~~~Arra~~GD~eAR~~MIE~NLRLVV~IAk~Y~nRGlpLlDLIEEGNLGLm~Av   88 (292)
T TIGR02394         9 TRVADVTQLYLREIGFKPLLTAEEELAYARRALAGDFEARKKMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAV   88 (292)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             23302688878886015588988999998886507888988877640126767864404765145777765335665421


Q ss_pred             HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHH
Q ss_conf             87642101354333333343333321100011100010000000012210000111
Q gi|254780289|r  183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSK  238 (682)
Q Consensus       183 dIIDld~t~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~e~~~e~~~~~~~  238 (682)
                      +-+|-.-.|.+.++.+||..+..+-.-.++..+...+.+.+.+.+...........
T Consensus        89 EKFDPeRGFRFSTYATWWIRQtIERAIMNQaRTiRLPvHV~kELNv~LRa~r~L~~  144 (292)
T TIGR02394        89 EKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHVVKELNVYLRAARQLEK  144 (292)
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEECCHHHHHHHHHHHHHHHHHHH
T ss_conf             04588999844301113665327865313544110531434677799998887655


No 68 
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=98.80  E-value=9.1e-07  Score=72.38  Aligned_cols=170  Identities=14%  Similarity=0.165  Sum_probs=119.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHH
Q ss_conf             99999987653321124689998755578999887522356777887544367999988743854573120102898999
Q gi|254780289|r  427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ  506 (682)
Q Consensus       427 lK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~  506 (682)
                      =.+++.+++.|..   .|=.+|+...-..|..+|.++++..-.-.|++|+--+-+.+...+|+...  .|.   +|-.+=
T Consensus        14 D~eLi~~~~~GD~---~Af~~L~~ry~~~l~~~a~~~~~~~~~AeDvvQe~flk~~~~~~~~~~~~--~f~---~WL~~I   85 (197)
T PRK09643         14 DAELLAAHVAGDR---YAFGELFRRHHRQLWRLARRTSGTREDAADALQDAMLSAHRGAGSFRGDA--AVS---SWLHRI   85 (197)
T ss_pred             HHHHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCC--HHH---HHHHHH
T ss_conf             9999999992779---99999999999999999999919999999999999999999886338863--499---999999


Q ss_pred             HHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             99999972287046142058898999999999877608899978999870999899999998608987553635889986
Q gi|254780289|r  507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS  586 (682)
Q Consensus       507 ~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~  586 (682)
                      +...++                 +.+.+..        +.+                         .++++.    ..  
T Consensus        86 a~N~~~-----------------d~~Rk~~--------~~~-------------------------~~~~~~----~~--  109 (197)
T PRK09643         86 VVNACL-----------------DRLRRAK--------ARP-------------------------TVPLED----VY--  109 (197)
T ss_pred             HHHHHH-----------------HHHHHHC--------CCC-------------------------CCCCCC----CC--
T ss_conf             999999-----------------9999851--------467-------------------------788665----67--


Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             04756238988998999999999999999973299889999999818798674688999899667899999999999998
Q gi|254780289|r  587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK  666 (682)
Q Consensus       587 ~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~  666 (682)
                                 ..+.+..........+.++|..|||..+.||.|+|    -..+|+.||++.+|+|-.-|+..-.+|+.+
T Consensus       110 -----------~~~~~~~~~~e~~~~l~~al~~Lp~~~R~vl~L~~----~eg~s~~EIA~~lgis~~tVKsrl~RAr~~  174 (197)
T PRK09643        110 -----------PVADRETARVETAIAVQRALMRLPVEQRAALVAVD----MQGYSVADTARMLGVAEGTVKSRCARGRAR  174 (197)
T ss_pred             -----------CCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf             -----------78652031389999999999769998879999999----819999999999893999999999999999


Q ss_pred             HCCHHHHHHHH
Q ss_conf             32967778756
Q gi|254780289|r  667 LKHPSRSKKLR  677 (682)
Q Consensus       667 l~~~~~~~~l~  677 (682)
                      ||.  .-..|+
T Consensus       175 Lr~--~L~~l~  183 (197)
T PRK09643        175 LAE--LLGYLR  183 (197)
T ss_pred             HHH--HHHHHH
T ss_conf             999--999884


No 69 
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=98.79  E-value=2.4e-06  Score=69.08  Aligned_cols=171  Identities=13%  Similarity=0.238  Sum_probs=128.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHH
Q ss_conf             88999999876533211246899987555789998875223567778875443679999887438545731201028989
Q gi|254780289|r  425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV  504 (682)
Q Consensus       425 ~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i  504 (682)
                      .+-.+++.+++.|..   .|-..|++..-..|..+|.++++.--.-.|++||--+-+.+..++|++.+ .+|+   ||-.
T Consensus        48 d~D~eLv~R~~~GD~---~AF~~Ly~ry~~~l~~~a~r~l~d~~dAEDvvQEvFlk~w~~~~~f~~g~-s~f~---tWL~  120 (233)
T PRK12538         48 DEDEELLDRLATDDE---AAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGR-AKFS---TWLY  120 (233)
T ss_pred             CCHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCC-CHHH---HHHH
T ss_conf             978999999996029---99999999999999999999959999999999999999999884477786-7399---9999


Q ss_pred             HHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             99999999722870461420588989999999998776088999789998709998999999986089875536358899
Q gi|254780289|r  505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED  584 (682)
Q Consensus       505 ~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~  584 (682)
                      +-+..+++. .                 .|   +     .|.                         +.+  +. +.+  
T Consensus       121 ~IA~N~~id-~-----------------~R---k-----~r~-------------------------~~~--d~-~~e--  144 (233)
T PRK12538        121 RVVSNRCID-L-----------------RR---K-----PRT-------------------------ENV--DA-VPE--  144 (233)
T ss_pred             HHHHHHHHH-H-----------------HH---H-----HCC-------------------------CCC--CC-CCC--
T ss_conf             999999999-9-----------------97---4-----145-------------------------652--23-444--


Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             86047562389889989999999999999999732998899999998187986746889998996678999999999999
Q gi|254780289|r  585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI  664 (682)
Q Consensus       585 ~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~  664 (682)
                             +.| ..+++...+....+...|..+|..|||+.+.|+.|+|    ...+|.+||+..+|+|---|+..=.+|+
T Consensus       145 -------~~d-~~~~~~~~l~~~e~~~~L~~aL~~Lp~~~R~vl~L~~----~egls~~EIA~~Lgis~~TVKsrL~RAr  212 (233)
T PRK12538        145 -------VAD-GKPDAVSVIERNELSDLLEAAMQRLPEQQRIAVILSY----HENMSNGEIAEVMDTTVAAVESLLKRGR  212 (233)
T ss_pred             -------CCC-CCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             -------456-8988878999999999999999759999999999999----8499999999998929999999999999


Q ss_pred             HHHCCH
Q ss_conf             983296
Q gi|254780289|r  665 RKLKHP  670 (682)
Q Consensus       665 ~~l~~~  670 (682)
                      ++||.-
T Consensus       213 ~~LR~~  218 (233)
T PRK12538        213 QQLRDL  218 (233)
T ss_pred             HHHHHH
T ss_conf             999999


No 70 
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=98.78  E-value=1e-06  Score=71.90  Aligned_cols=168  Identities=17%  Similarity=0.256  Sum_probs=113.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHH
Q ss_conf             99999987653321124689998755578999887522356777887544367999988743854573120102898999
Q gi|254780289|r  427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ  506 (682)
Q Consensus       427 lK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~  506 (682)
                      -.+++.+++.|..   .|-.+++...-..|...|.++++..-.-.|++|+.-+.+.+..++|++...  |   .+|-.+-
T Consensus         6 d~~Li~~~~~GD~---~Af~~L~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~~~~~~~~~~~~~~--~---~~wL~~i   77 (177)
T PRK09638          6 EKELIRRAKKGND---AALTKLLQQHYNFLYGYVLKLTLNPDLAEDLVQETMLKAIENIHQFQGRSK--F---STWLISI   77 (177)
T ss_pred             HHHHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCHH--H---HHHHHHH
T ss_conf             9999999994779---999999999999999999999199999999999999999998877065007--9---9999999


Q ss_pred             HHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             99999972287046142058898999999999877608899978999870999899999998608987553635889986
Q gi|254780289|r  507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS  586 (682)
Q Consensus       507 ~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~  586 (682)
                      +...++ |.                +.+..        |.....+                      ...+.+.      
T Consensus        78 a~n~~~-d~----------------~Rk~~--------r~~~~~~----------------------~~~~~~~------  104 (177)
T PRK09638         78 ASRLYL-DH----------------LRKRK--------REELREE----------------------AATEETL------  104 (177)
T ss_pred             HHHHHH-HH----------------HHHHC--------CCCCCCC----------------------CCCCCCC------
T ss_conf             999999-99----------------99860--------3011000----------------------2333355------


Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             04756238988998999999999999999973299889999999818798674688999899667899999999999998
Q gi|254780289|r  587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK  666 (682)
Q Consensus       587 ~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~  666 (682)
                               .... .+..........+..+|..|||+.+.|+.|||    -..+|..|||+.+|+|-.-|+..=.+|+++
T Consensus       105 ---------~~~~-~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~L~~----~eg~s~~EIA~~l~is~~tVk~~l~rA~~~  170 (177)
T PRK09638        105 ---------RKEK-WETAISGHEWSELLDLLMKLPPELRAPFILKH----YYGYTYEEIAKMLGIPEGTVKSRVHHGLKK  170 (177)
T ss_pred             ---------CCCC-CCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf             ---------6676-11465379999999999759998989999999----919999999999893999999999999999


Q ss_pred             HCC
Q ss_conf             329
Q gi|254780289|r  667 LKH  669 (682)
Q Consensus       667 l~~  669 (682)
                      ||.
T Consensus       171 Lr~  173 (177)
T PRK09638        171 IRK  173 (177)
T ss_pred             HHH
T ss_conf             999


No 71 
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=98.78  E-value=6.2e-07  Score=73.68  Aligned_cols=169  Identities=14%  Similarity=0.244  Sum_probs=115.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CC---CHHHHHHHHHHHHHHHHHHCCCCCCCEEEH
Q ss_conf             26889999998765332112468999875557899988752235-67---778875443679999887438545731201
Q gi|254780289|r  423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR-GL---QFLDLIQEGNIGLMKAAEKFDWCLGYKFST  498 (682)
Q Consensus       423 ~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~-~~---~~~~~~~~~~~~l~~a~~~~~~~~g~~f~t  498 (682)
                      ...++.++++.++.|...   |=.+|++.....|.++|.+++.+ |.   .-.|++|+--+-+.+...+|++.  ..|.|
T Consensus         5 ~~~e~~~Li~~~~~GD~~---Af~~L~~~~~~~l~~~~~~~l~~~~~~~~dAeDlvQevfl~~~~~~~~~~~~--~~f~~   79 (184)
T PRK12512          5 REDEWTDLMRSANAGDAA---AYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAP   79 (184)
T ss_pred             CHHHHHHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCC--CCHHH
T ss_conf             528799999999827899---9999999999999999999988468998899999999999999872314888--85899


Q ss_pred             HHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCC
Q ss_conf             02898999999999722870461420588989999999998776088999789998709998999999986089875536
Q gi|254780289|r  499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET  578 (682)
Q Consensus       499 ya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~  578 (682)
                      |-.--.|..+..++..+                            ++.+.         ++.+.+               
T Consensus        80 WL~~Iarn~~~d~~Rk~----------------------------~~~~~---------~~~~~~---------------  107 (184)
T PRK12512         80 WLFAIARNKLIDALRRR----------------------------GRRVF---------VDIDDF---------------  107 (184)
T ss_pred             HHHHHHHHHHHHHHHHH----------------------------CCCCC---------CCHHHH---------------
T ss_conf             99999999999999974----------------------------37778---------983444---------------


Q ss_pred             CCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             35889986047562389889989999999999999999732998899999998187986746889998996678999999
Q gi|254780289|r  579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ  658 (682)
Q Consensus       579 ~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rq  658 (682)
                                .+.+.+....   +..    ....+..+|..|||+.+.||.|+|    -..+|..||++.+|+|---|+.
T Consensus       108 ----------~~~~~~~~~~---~~~----~~~~l~~~L~~Lp~~~R~vi~L~~----~~g~s~~EIA~~lgis~~tVk~  166 (184)
T PRK12512        108 ----------AETLPSEPAA---ETL----PAGDVGRHLETLPPRQRDVVQSIA----VEGASIKETAAKLSMSEGAVRV  166 (184)
T ss_pred             ----------HHCCCCCCCC---CHH----HHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHH
T ss_conf             ----------2216788876---426----899999999689999999999998----5597999999998919999999


Q ss_pred             HHHHHHHHHCC
Q ss_conf             99999998329
Q gi|254780289|r  659 IEAKAIRKLKH  669 (682)
Q Consensus       659 i~~~a~~~l~~  669 (682)
                      .-.+|+++||.
T Consensus       167 ~l~RA~~~Lr~  177 (184)
T PRK12512        167 ALHRGLAALAA  177 (184)
T ss_pred             HHHHHHHHHHH
T ss_conf             99999999999


No 72 
>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=98.78  E-value=2e-07  Score=77.61  Aligned_cols=182  Identities=26%  Similarity=0.365  Sum_probs=150.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHH
Q ss_conf             99999876533211246899987555789998875223567778875443679999887438545731201028989999
Q gi|254780289|r  428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA  507 (682)
Q Consensus       428 K~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~  507 (682)
                      .+++..++.|..   .|..-+|.-.-.+|-+-|+.|---|-+-.|.+|||.+||.||+.-|...+=..|-.||-..|...
T Consensus         7 ~~~~~~~~~G~~---~a~~~~i~~y~~fv~ak~~~yfl~Gad~edi~qeGmiGlyka~rd~~~~~l~sf~afaelC~trq   83 (198)
T TIGR02859         7 EEIVELAREGDE---KALEYLIEKYKNFVKAKARSYFLVGADKEDIIQEGMIGLYKAIRDYKEDKLSSFKAFAELCVTRQ   83 (198)
T ss_pred             HHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHHEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             899999970118---89999999999998775311013206456566611689999997531567899999999999999


Q ss_pred             HHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCC-CCCC
Q ss_conf             999997228704614205889899999999987760889997899987099989999999860898755363588-9986
Q gi|254780289|r  508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD-EDTS  586 (682)
Q Consensus       508 i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~-~~~~  586 (682)
                      |..+|..-+|--+||..                                               .-|||+.||.+ +.|.
T Consensus        84 iitaiktatrqkhiPln-----------------------------------------------~y~sl~kPiy~~~sdr  116 (198)
T TIGR02859        84 IITAIKTATRQKHIPLN-----------------------------------------------SYVSLNKPIYDEESDR  116 (198)
T ss_pred             HHHHHHHHHHHCCCCCH-----------------------------------------------HHEECCCCCCCCCCHH
T ss_conf             99998876520246520-----------------------------------------------0000256525452014


Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHC-CCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             047562389889989999999999999999732-9988999999981879867468899989966789999999999999
Q gi|254780289|r  587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR  665 (682)
Q Consensus       587 ~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~-l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~  665 (682)
                      +|.|++......+|.+.+....--..+...+.. |+.=|..||....   +|  .++.||+..++-   .+.-|.+ ||.
T Consensus       117 tl~d~~~~~~~~dP~~l~i~~e~~~~~~~~~~~~ls~le~~vl~~yl---~G--~~yqei~~~l~r---~~ksidn-alq  187 (198)
T TIGR02859       117 TLLDVVSEAKVADPEELIISKEEYEKIESKLEELLSDLELKVLVLYL---DG--KSYQEIAEDLNR---HVKSIDN-ALQ  187 (198)
T ss_pred             HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---CC--CHHHHHHHHHHH---HHHHHHH-HHH
T ss_conf             79998854432252777631688999999999999999999999984---57--407889988645---6678999-999


Q ss_pred             HHC
Q ss_conf             832
Q gi|254780289|r  666 KLK  668 (682)
Q Consensus       666 ~l~  668 (682)
                      +.+
T Consensus       188 rvk  190 (198)
T TIGR02859       188 RVK  190 (198)
T ss_pred             HHH
T ss_conf             999


No 73 
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=98.76  E-value=1.7e-06  Score=70.16  Aligned_cols=164  Identities=16%  Similarity=0.136  Sum_probs=115.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEEC
Q ss_conf             24689998755578999887522356777887544367999988743854573120102898999999999722870461
Q gi|254780289|r  442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI  521 (682)
Q Consensus       442 ~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~  521 (682)
                      .+|-.+||..+.+.|..+|.++++.--.-.|++||.-+-..+..++|..   -.++   +|-.+=+...++         
T Consensus        20 ~eaF~~Lv~rh~~~lyr~a~r~~gn~~dAEDlvQEtFlra~r~l~~frg---~~~~---tWL~rIa~N~~~---------   84 (217)
T PRK12533         20 GERFRALVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSCRG---DNAR---PWLLAIVRHTWY---------   84 (217)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCC---CCHH---HHHHHHHHHHHH---------
T ss_conf             9999999999999999999999699999999999999999986776234---4248---999999999999---------


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHH
Q ss_conf             42058898999999999877608899978999870999899999998608987553635889986047562389889989
Q gi|254780289|r  522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL  601 (682)
Q Consensus       522 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~  601 (682)
                              +.+.+..+  ..                               .+.....  .+.+..+.++.  ....+|.
T Consensus        85 --------~~~Rrr~~--~~-------------------------------~~~~~~~--~~~~~~~~~~~--~~~~~pe  119 (217)
T PRK12533         85 --------SEWRRRAN--AH-------------------------------EVAYPDT--LDDADSPDDWQ--PAVEDPL  119 (217)
T ss_pred             --------HHHHHHHC--CC-------------------------------CCCCCCC--CCCCCCCCCCC--CCCCCHH
T ss_conf             --------99997411--23-------------------------------3442111--34432343346--7879999


Q ss_pred             HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             99999999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       602 ~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      ..+........|..+|..|||..+.||.|||    -..+|++||++.+|++---|+.-=.+|-++||.
T Consensus       120 ~~~~~~e~~~~l~~AL~~Lp~~~R~vl~Lr~----~eglS~~EIAeiLgip~gTVKSRL~RAR~~Lr~  183 (217)
T PRK12533        120 ALLLRGEDVRLVNAALAKLPVEYREVLVLRE----LEDMSYREIAAIADVPVGTVMSRLARARRRLAA  183 (217)
T ss_pred             HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             9999889999999999809998868999999----809999999999894999999999999999999


No 74 
>pfam00140 Sigma70_r1_2 Sigma-70 factor, region 1.2.
Probab=98.76  E-value=6.8e-09  Score=89.15  Aligned_cols=35  Identities=51%  Similarity=0.935  Sum_probs=33.1

Q ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             72899999985697688978899999999988999
Q gi|254780289|r  118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM  152 (682)
Q Consensus       118 dDPVRMYLREMG~V~LLTREgEIeIAKRIE~G~~~  152 (682)
                      +|||++||||||++||||+|+||++||+|+.|...
T Consensus         1 ~D~v~~YL~eIg~~pLLt~eEEi~LA~~i~~g~~~   35 (37)
T pfam00140         1 SDSVRLYLREIGRVPLLTAEEEVELARRIEAGDEL   35 (37)
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCHH
T ss_conf             97099999983776789989999999999816373


No 75 
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=98.73  E-value=2.6e-06  Score=68.81  Aligned_cols=84  Identities=17%  Similarity=0.088  Sum_probs=54.6

Q ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHHHHHHHH-HHHHHHHHHHHHC--CHHHHHH-------HHHHHHHHCCCHHHHHHHH
Q ss_conf             7728999999856976889788999999999-8899999998728--2389999-------9999873117103678764
Q gi|254780289|r  117 TDDPVRMYLREMGSIELLSREGEIAIAKRIE-AGRAMMMASLCES--PLTFQAL-------IIWRDELNDGTTLLREIID  186 (682)
Q Consensus       117 tdDPVRMYLREMG~V~LLTREgEIeIAKRIE-~G~~~i~~al~~~--P~ti~~i-------l~~~e~i~~ge~~LrdIID  186 (682)
                      -.|.||+|||+++++||||+|+|+++|+|+- .|......-+..+  ++++...       +.+-|.|++|.+.|-.-|+
T Consensus         4 ~~~~~~~y~~~~~~~plLt~eeE~~L~~~~~~~gD~~Ar~~LI~~NLRLV~~iA~ry~~~g~~l~DLIQeG~iGLi~Ave   83 (289)
T PRK07500          4 DASADRSMIRSAMKAPYLEREEEHALAYRWKDTRDEDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAA   83 (289)
T ss_pred             CCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             53468999999633799999999999999987779999999999858999999987458998978999986999999997


Q ss_pred             HHHCCCCCCCCCCC
Q ss_conf             21013543333333
Q gi|254780289|r  187 LEACIGPESKGGFF  200 (682)
Q Consensus       187 ld~t~~~~~~~~~~  200 (682)
                      .|..-....+++|.
T Consensus        84 kFDp~rG~rFSTYA   97 (289)
T PRK07500         84 RFDPDRDVRFSTYA   97 (289)
T ss_pred             CCCCCCCCCEEEHH
T ss_conf             36988899721101


No 76 
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=98.70  E-value=2e-06  Score=69.77  Aligned_cols=174  Identities=14%  Similarity=0.162  Sum_probs=117.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHH
Q ss_conf             99999876533211246899987555789998875223567778875443679999887438545731201028989999
Q gi|254780289|r  428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA  507 (682)
Q Consensus       428 K~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~  507 (682)
                      ..++++.+.|.   ++|-.+|++..=..|..+|.++.+.--.-.|++|+--+-+.+..++|++.+| +|+||    +-.-
T Consensus        26 ~~Lv~~A~~GD---~~AF~~Ly~~y~~~l~~~~~r~l~d~~~AEDvvQetFlkvw~~~~~~~~~~~-~f~tW----L~~I   97 (206)
T PRK12526         26 QWLILVAISRD---KQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTW----VYTV   97 (206)
T ss_pred             HHHHHHHHHCC---HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCC-HHHHH----HHHH
T ss_conf             99999999658---9999999999999999999999199999999999999999983876586425-29999----9999


Q ss_pred             HHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCE
Q ss_conf             99999722870461420588989999999998776088999789998709998999999986089875536358899860
Q gi|254780289|r  508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH  587 (682)
Q Consensus       508 i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~  587 (682)
                      ......|.                +.+....                                 ...++    ++ +...
T Consensus        98 arN~~~d~----------------lRk~~~~---------------------------------~~~~~----~~-d~~~  123 (206)
T PRK12526         98 MRNAAFDM----------------LRKIKAK---------------------------------KEQNL----GD-DIWP  123 (206)
T ss_pred             HHHHHHHH----------------HHHHHCC---------------------------------CCCCC----CC-HHCH
T ss_conf             99999999----------------9865312---------------------------------22232----10-0000


Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf             47562389889989999999999999999732998899999998187986746889998996678999999999999983
Q gi|254780289|r  588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL  667 (682)
Q Consensus       588 ~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l  667 (682)
                      +.+...+ .. .+.+......+...|..+|..||++.+.|+.|+|    -..+|.+||+..+|+|---|+.-=.+|+.+|
T Consensus       124 ~~~~~~~-~~-~~~~~~~~~~~~~~l~~~l~~LP~~~R~vi~L~~----~egls~~EIA~~l~is~~TVksrl~rAlk~L  197 (206)
T PRK12526        124 IEQALAE-SQ-SESEEFSDHLMDKQILSYIEKLPEAQQTVVKGVY----FQELSQEQLAQQLNVPLGTVKSRLRLALAKL  197 (206)
T ss_pred             HHHCCCC-CC-CCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             4430145-78-8357899899999999999868999888989999----8599999999998939999999999999999


Q ss_pred             CC
Q ss_conf             29
Q gi|254780289|r  668 KH  669 (682)
Q Consensus       668 ~~  669 (682)
                      |-
T Consensus       198 R~  199 (206)
T PRK12526        198 KV  199 (206)
T ss_pred             HH
T ss_conf             99


No 77 
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=98.69  E-value=2.7e-06  Score=68.71  Aligned_cols=170  Identities=16%  Similarity=0.209  Sum_probs=114.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-CCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHH
Q ss_conf             68899999987653321124689998755578999887522356-77788754436799998874385457312010289
Q gi|254780289|r  424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW  502 (682)
Q Consensus       424 i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~-~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~  502 (682)
                      ..+++.++.++..|...   |=.+++...-+.|...+.++.+.. -.-.|++||.-+-+.+...+|++..  .|+|    
T Consensus         2 ~~~l~~Ll~~~~~GD~~---Af~~l~~~y~~~l~~~~~~~l~~~~~~AEDl~Qe~fl~~~~~~~~~~~~~--~~~~----   72 (178)
T PRK12536          2 ESRLKALLLRGLAGDAA---AYRQFLTELARHLRAFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRPDQ--PLTA----   72 (178)
T ss_pred             HHHHHHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCC--CHHH----
T ss_conf             48899999999815699---99999999999999999999099876899999999999999787669999--6899----


Q ss_pred             HHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             89999999997228704614205889899999999987760889997899987099989999999860898755363588
Q gi|254780289|r  503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD  582 (682)
Q Consensus       503 ~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~  582 (682)
                      |+. .|.+..               .++.+.+..        |.+...                           .++.+
T Consensus        73 WL~-~Ia~n~---------------~~d~~R~~~--------r~~~~~---------------------------~~~~~  101 (178)
T PRK12536         73 WVQ-AIARYK---------------LADFLRRRA--------RREALH---------------------------DPLDD  101 (178)
T ss_pred             HHH-HHHHHH---------------HHHHHHHHH--------CCCCCC---------------------------CCCHH
T ss_conf             999-999999---------------999999874--------645445---------------------------75112


Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             99860475623898899899999999999999997329988999999981879867468899989966789999999999
Q gi|254780289|r  583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK  662 (682)
Q Consensus       583 ~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~  662 (682)
                      ..     +....+. ..|      ...+..+..+|..|||+.+.||.|+|    -..+|..||++.+|+|..-|+.-=.+
T Consensus       102 ~~-----~~~~~~~-~~~------~~~~~~l~~~l~~Lp~~~R~~~~l~~----~eg~s~~EIA~~lgis~~tVk~rl~R  165 (178)
T PRK12536        102 EA-----ELFATSD-DEA------AEARRDLGKLLEQLPDRQRLPIVHVK----LEGLSVEETAQLTGLSESAVKVGIHR  165 (178)
T ss_pred             HH-----HCCCCCC-CCH------HHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             32-----0247886-358------99999999999869998999999998----85999999999989299999999999


Q ss_pred             HHHHHCC
Q ss_conf             9998329
Q gi|254780289|r  663 AIRKLKH  669 (682)
Q Consensus       663 a~~~l~~  669 (682)
                      |+++||.
T Consensus       166 a~k~Lr~  172 (178)
T PRK12536        166 GLKALAA  172 (178)
T ss_pred             HHHHHHH
T ss_conf             9999999


No 78 
>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=98.69  E-value=4.6e-07  Score=74.73  Aligned_cols=167  Identities=23%  Similarity=0.355  Sum_probs=120.5

Q ss_pred             HHHHHHH--HHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHH
Q ss_conf             7555789--99887522356777887544367999988743854573120102898999999999722870461420588
Q gi|254780289|r  450 EANLRLV--ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD  527 (682)
Q Consensus       450 ~anlr~v--~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~  527 (682)
                      ..-||++  +-|..++.+| ++-.|++||.   +|.|...|+-=||--=.-++. |-|+=..+.|++.            
T Consensus        17 ~~yLr~La~~~L~~~L~~r-~dpSD~VQe~---~l~A~~~~~~fRG~t~~Ef~~-WLR~IL~~~l~~~------------   79 (190)
T TIGR02984        17 RNYLRLLARVQLDRRLRRR-VDPSDVVQET---LLEAHRDFDQFRGKTEGEFAG-WLRQILANVLADA------------   79 (190)
T ss_pred             HHHHHHHHHHHHHHHHHCC-CCHHHHHHHH---HHHHHHHHHHHCCCCHHHHHH-HHHHHHHHHHHHH------------
T ss_conf             2499999999760884001-5754589999---999998887532898578999-9999999999999------------


Q ss_pred             HHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC--EEEEEECCCCCCCHHHHHH
Q ss_conf             98999999999877608899978999870999899999998608987553635889986--0475623898899899999
Q gi|254780289|r  528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAI  605 (682)
Q Consensus       528 ~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~--~~~~~~~d~~~~~~~~~~~  605 (682)
                              .+.+.+.--|.                       .+.=+||+++-+-.++|  .|.-++.+ +..+|...+.
T Consensus        80 --------~~~h~~~qkRD-----------------------~rrE~~l~~~~~~~~~Ss~~L~~~Laa-~~~sPS~~a~  127 (190)
T TIGR02984        80 --------LRRHLGAQKRD-----------------------IRREQSLDAGAARVDESSVRLEAQLAA-DGPSPSQAAA  127 (190)
T ss_pred             --------HHHHHHHHCCC-----------------------CHHCCCCCCCCCCHHHHHHHHHHHHCC-CCCCCHHHHH
T ss_conf             --------99886642026-----------------------201012012457658879999997518-9998558999


Q ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             9999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       606 ~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      +...-..+..+|+.|||..++||.|||    -+.+++.|||..||.|.-=|+-.-.+||+|||.
T Consensus       128 r~E~~~~L~~AL~~L~e~~REvi~LR~----~EGLS~~EvA~~Md~~~~av~~l~~Ral~~Lr~  187 (190)
T TIGR02984       128 RRESAVRLAQALAKLPEDYREVILLRH----LEGLSFAEVAERMDRSEGAVSMLWVRALARLRQ  187 (190)
T ss_pred             HHHHHHHHHHHHHHCCHHHHHHHHHHH----HHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             977999999999647922589999987----603555899987079758987589999999987


No 79 
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=98.68  E-value=4.7e-06  Score=66.73  Aligned_cols=159  Identities=17%  Similarity=0.155  Sum_probs=114.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEEC
Q ss_conf             24689998755578999887522356777887544367999988743854573120102898999999999722870461
Q gi|254780289|r  442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI  521 (682)
Q Consensus       442 ~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~  521 (682)
                      .+|=.+++..+-..|..+|.++++.--.-.|++|+.-+-+++...+|....  .|.   +|-.+-+...++         
T Consensus        15 e~Af~~L~~~y~~~v~~~~~~~~~d~~~AeD~~Qe~fl~~~~~~~~~~~~~--~~~---~Wl~~ia~N~~~---------   80 (177)
T PRK09415         15 EDLIDEIMNKYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKS--NLK---TWLYRIAINHCK---------   80 (177)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCC--CHH---HHHHHHHHHHHH---------
T ss_conf             999999999999999999999909999999999999999999874558855--499---999999999999---------


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHH
Q ss_conf             42058898999999999877608899978999870999899999998608987553635889986047562389889989
Q gi|254780289|r  522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL  601 (682)
Q Consensus       522 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~  601 (682)
                              +.+.+..+       +...+.+                          .+     .    +.+. ....+|.
T Consensus        81 --------d~~R~~~~-------~~~~~~~--------------------------~~-----~----~~~~-~~~~~~~  109 (177)
T PRK09415         81 --------DYLKSWHN-------KKVIVTE--------------------------DI-----F----TYME-SQKESVE  109 (177)
T ss_pred             --------HHHHHHHC-------CCCCCCH--------------------------HH-----H----HHCC-CCCCCHH
T ss_conf             --------99999871-------3556303--------------------------56-----6----4025-5579989


Q ss_pred             HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             99999999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       602 ~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      +..........+..+|..|||+.+.|+.+||    -...|..|||..+|+|-.-|+..=.+|.++||.
T Consensus       110 ~~~~~~~~~~~l~~~l~~L~~~~r~ii~l~~----~~~~s~~EIA~~l~is~~tV~~rl~Rark~Lr~  173 (177)
T PRK09415        110 EEVIQNAEDERLASAVMSLPIKYREVIYLFY----YEELSIKEIATVTGVNENTIKTRLKKAKELLKK  173 (177)
T ss_pred             HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999769999999999999----809989999998892999999999999999998


No 80 
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=98.67  E-value=3.4e-06  Score=67.90  Aligned_cols=162  Identities=19%  Similarity=0.155  Sum_probs=113.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEEC
Q ss_conf             24689998755578999887522356777887544367999988743854573120102898999999999722870461
Q gi|254780289|r  442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI  521 (682)
Q Consensus       442 ~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~  521 (682)
                      ..|=.+|++..-..|.++|.++++.--.-.|++|+.=+-+.+..++|+...+-+|+|   |..|=+..++|.        
T Consensus         8 ~~afe~Ly~~y~~~ly~~a~~~~~d~~~AEDivQe~Flk~~~~~~~~~~~~~~~~~~---wL~rIa~N~~id--------   76 (185)
T PRK12542          8 YEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKR---YILRVAKNKAID--------   76 (185)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHH---HHHHHHHHHHHH--------
T ss_conf             999999999999999999999949999999999999999999888716655267999---999999999999--------


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHH
Q ss_conf             42058898999999999877608899978999870999899999998608987553635889986047562389889989
Q gi|254780289|r  522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL  601 (682)
Q Consensus       522 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~  601 (682)
                               .+.+..        +.++.                          ++...  .+.      + +....++.
T Consensus        77 ---------~~Rk~k--------~~~~~--------------------------~~~~~--~~~------~-~~~~~~~e  104 (185)
T PRK12542         77 ---------SYRKNK--------RHETF--------------------------LEEYE--RES------I-EAVDENIE  104 (185)
T ss_pred             ---------HHHHHC--------CCCCC--------------------------HHHHH--CCC------C-CCCCCCHH
T ss_conf             ---------999732--------43442--------------------------01321--023------3-56787743


Q ss_pred             HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCH
Q ss_conf             999999999999999732998899999998187986746889998996678999999999999983296
Q gi|254780289|r  602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP  670 (682)
Q Consensus       602 ~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~  670 (682)
                      +..........|..+|..|||+.+.|+.|||    -..+|..||+..+|+|---|+..=.+|+++||.-
T Consensus       105 ~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~----~~gls~~EIA~~L~is~~tVk~rl~RArk~Lr~~  169 (185)
T PRK12542        105 EWEKRKMSEVQIDTLLKELNESNRQVFKYKV----FYNLTYQEISSVMGITEANVRKQFERARKRVQNM  169 (185)
T ss_pred             HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_conf             7999998999999999829998889976799----8399999999998929999999999999999998


No 81 
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=98.66  E-value=2.7e-06  Score=68.70  Aligned_cols=152  Identities=20%  Similarity=0.183  Sum_probs=107.6

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHH
Q ss_conf             99987555789998875223567778875443679999887438545731201028989999999997228704614205
Q gi|254780289|r  446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM  525 (682)
Q Consensus       446 ~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~  525 (682)
                      .++....-..|...|.++++.--.-.|++|+.-+-+.+..+.|+.+   +|.|   |-.+=+...++             
T Consensus         4 E~ly~~y~~~l~~~~~~~~~d~~~AeDl~Qe~flk~~~~~~~~~~~---~~~~---WL~~Ia~n~~~-------------   64 (165)
T PRK09644          4 EEIYKMYINDVYRYLFSLTKSHHLAEDLLQETFYRAYIYLEDYDNQ---KVKP---WLFKVAYHTFI-------------   64 (165)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCC---CHHH---HHHHHHHHHHH-------------
T ss_conf             9999999999999999990999999999999999999988766813---1899---99999999999-------------


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHH
Q ss_conf             88989999999998776088999789998709998999999986089875536358899860475623898899899999
Q gi|254780289|r  526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI  605 (682)
Q Consensus       526 ~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~  605 (682)
                          +.+.+.        .|.+.                         +      +++.       +++....+|.+.+.
T Consensus        65 ----d~~Rk~--------~r~~~-------------------------~------~~~~-------~~~~~~~~~~~~~~   94 (165)
T PRK09644         65 ----DFVRKE--------KKVVF-------------------------V------GTDE-------IETIQAESTEEYAV   94 (165)
T ss_pred             ----HHHHHH--------CCCCC-------------------------C------CHHH-------HCCCCCCCHHHHHH
T ss_conf             ----999974--------47577-------------------------6------5211-------00113588014999


Q ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCH
Q ss_conf             99999999999732998899999998187986746889998996678999999999999983296
Q gi|254780289|r  606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP  670 (682)
Q Consensus       606 ~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~  670 (682)
                      .......+..+|..|||+.+.|+.|||    -...|..|||..+|+|-.-|+..=.+|..+||.-
T Consensus        95 ~~e~~~~l~~~l~~Lp~~~r~v~~L~~----~~~~s~~EIA~~l~is~~tVk~rl~RAr~~Lr~~  155 (165)
T PRK09644         95 AKNSYEKLIQIIHTLPVIEAQAILLCD----VHELTYEEAASVLDLKENTYKSHLFRGRKRLKAL  155 (165)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHH----HHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_conf             899999999998729999999999999----9888999999998939999999999999999999


No 82 
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=98.66  E-value=5.3e-06  Score=66.36  Aligned_cols=164  Identities=18%  Similarity=0.201  Sum_probs=111.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCE
Q ss_conf             21124689998755578999887522356777887544367999988743854573120102898999999999722870
Q gi|254780289|r  439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT  518 (682)
Q Consensus       439 ~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~  518 (682)
                      ...+.+-.+++..+.+.+...+.++++..-.-.||+||..+.++++...|  .-+..|.||.   .+=+...+|      
T Consensus        11 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~--~~~~~~~~wl---~~Ia~n~~i------   79 (182)
T COG1595          11 RGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF--RGRSSFKAWL---YRIARNLAI------   79 (182)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCHHC--CCCCCHHHHH---HHHHHHHHH------
T ss_conf             75178899999999999999999996884309999999999999733311--6788789999---999999999------


Q ss_pred             EECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCC
Q ss_conf             46142058898999999999877608899978999870999899999998608987553635889986047562389889
Q gi|254780289|r  519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV  598 (682)
Q Consensus       519 ~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~  598 (682)
                                 +.+.+..+....                                 ..+..    . .   +...+....
T Consensus        80 -----------D~~R~~~r~~~~---------------------------------~~~~~----~-~---~~~~~~~~~  107 (182)
T COG1595          80 -----------DRLRKRKRRRAR---------------------------------VEEAD----L-L---PEEADPAPD  107 (182)
T ss_pred             -----------HHHHHHHHHCCH---------------------------------HHHCC----C-C---CCCCCCCCH
T ss_conf             -----------999976101320---------------------------------01000----2-4---543456702


Q ss_pred             CHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCH
Q ss_conf             989999999999999999732998899999998187986746889998996678999999999999983296
Q gi|254780289|r  599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP  670 (682)
Q Consensus       599 ~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~  670 (682)
                      .+ +.+........+.++|..|||+++.|+.|+|    -..+|..||++.+|||---|+..-.+|+.+|+..
T Consensus       108 ~~-~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~----~~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~  174 (182)
T COG1595         108 LA-ELLLAEEELERLRRALARLPPRQREAFLLRY----LEGLSYEEIAEILGISVGTVKSRLHRARKKLREQ  174 (182)
T ss_pred             HH-HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_conf             67-8887678999999999839999999999999----8599999999895999999999999999999998


No 83 
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=98.66  E-value=4.5e-06  Score=66.92  Aligned_cols=172  Identities=14%  Similarity=0.177  Sum_probs=106.9

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHH
Q ss_conf             9987555789998875223567-778875443679999887438545731201028989999999997228704614205
Q gi|254780289|r  447 EMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM  525 (682)
Q Consensus       447 ~l~~anlr~v~~~~~~~~~~~~-~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~  525 (682)
                      +|+ .+.+-.+..|.......- .-.|++||.-+-..++.+.|+.  +.+|+||..==.|..+..++...+|..++....
T Consensus        10 ~l~-~~r~~L~~fa~~~L~~~~d~AEDlvQEtflka~~~~~~f~~--~s~f~tWL~~IarN~~id~lR~~~r~~~~~~~~   86 (195)
T PRK12532         10 ELI-ESRKLLLHFARLQLPDHPDLAEDLVQETLLSAYSAGDSFQG--RALVNSWLFAILKNKIIDALRQIGRQRKVFTAL   86 (195)
T ss_pred             HHH-HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf             999-98999999999980898757999999999999986874589--887888999999999999999862766767532


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHH
Q ss_conf             88989999999998776088999789998709998999999986089875536358899860475623898899899999
Q gi|254780289|r  526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI  605 (682)
Q Consensus       526 ~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~  605 (682)
                                             .++.   ++                -+.+..+..++..+  .--...+..+|++.+.
T Consensus        87 -----------------------~~e~---~d----------------~~~~~~~~~~~~~~--~~~~p~~~~~pe~~~~  122 (195)
T PRK12532         87 -----------------------DDEL---LD----------------EAFESHFSQNGHWT--PEGQPQHWNTPEKSLN  122 (195)
T ss_pred             -----------------------CHHH---HH----------------HHHHHHHCCCCCCC--CCCCCCCCCCHHHHHH
T ss_conf             -----------------------0233---32----------------56665420134457--5446555499999999


Q ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             9999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       606 ~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      ...+...+..+|..||++.+.|+.|||    -..++++|||+.+|+|-.-|+..=.+|-.+||.
T Consensus       123 ~~e~~~~l~~~l~~Lp~~~R~vl~L~~----~egls~~EIA~~lgis~~tVks~l~RAR~~Lr~  182 (195)
T PRK12532        123 NNEFQKILQSCLYNLPENTARVFTLKE----ILGFSSDEIQQMCGISTSNYHTIMHRARESLRQ  182 (195)
T ss_pred             HHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             899999999999859999989999999----819999999999895999999999999999999


No 84 
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=98.62  E-value=3.8e-06  Score=67.52  Aligned_cols=165  Identities=18%  Similarity=0.200  Sum_probs=109.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHH
Q ss_conf             99876533211246899987555789998875223567778875443679999887438545731201028989999999
Q gi|254780289|r  431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR  510 (682)
Q Consensus       431 ~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~  510 (682)
                      +++++.|..   .|=.++++..-+.|..++.++++.. .-.|++|+.-+.+.+..++|+..  ..|+|    |+-.-...
T Consensus         2 i~~~~~Gd~---~Af~~ly~~y~~~l~~~~~~~~~~~-~AEDi~Qd~fik~~~~~~~~~~~--~~~~~----wl~~ia~N   71 (175)
T PRK12518          2 IQRCQRGDR---QAFRQLYRRYQQKVRSTLYQLCGRE-LLDDLVQEVFLRVWKGLPKLRNP--AYFST----WLYRITWN   71 (175)
T ss_pred             HHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHCCHH-HHHHHHHHHHHHHHHCCCCCCCC--CHHHH----HHHHHHHH
T ss_conf             898986589---9999999999999999999977998-89999999999998711127982--35999----99999999


Q ss_pred             HHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEE
Q ss_conf             99722870461420588989999999998776088999789998709998999999986089875536358899860475
Q gi|254780289|r  511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD  590 (682)
Q Consensus       511 ~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~  590 (682)
                      ..                ++.+.+..+                                  .+...+.+...+.      
T Consensus        72 ~~----------------~d~~Rk~~r----------------------------------~~~~~~~~~~~~~------   95 (175)
T PRK12518         72 VA----------------TDARRQFAK----------------------------------RPSRIQQDSSLDQ------   95 (175)
T ss_pred             HH----------------HHHHHHHHC----------------------------------CCCCCCCCCCCCC------
T ss_conf             99----------------999999870----------------------------------2432332100024------


Q ss_pred             EECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             6238988998999999999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       591 ~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                        .......|  ..........+..+|..|||+.+.|+.|+|    -...|+.|||+.+|+|-.-|+..=.+|+++||.
T Consensus        96 --~~~~~~~~--~~~~~~~~~~l~~~l~~Lp~~~r~vi~l~~----~~~~s~~EIA~~l~is~~tVk~~l~Ra~k~Lr~  166 (175)
T PRK12518         96 --PSRPSDEP--DLMQLHYQDLVQQGLATLSLEHRAVLVLHD----LEDLPQKEIAEILNIPVGTVKSRLFYARRQLRK  166 (175)
T ss_pred             --CCCCCCCH--HHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             --56788976--999999999999999769999999999999----929999999999895999999999999999999


No 85 
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=98.61  E-value=7.7e-06  Score=65.08  Aligned_cols=176  Identities=14%  Similarity=0.114  Sum_probs=115.1

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHH
Q ss_conf             99875557899988752235677788754436799998874385457312010289899999999972287046142058
Q gi|254780289|r  447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR  526 (682)
Q Consensus       447 ~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~  526 (682)
                      .+|+-.=+-++..|..+.+.--.-.|++||.-+...++.++|+.+..|     -||-.+=+...|+.             
T Consensus        12 ~~~~~~r~~L~r~A~~~l~d~~~AEDlvQEtflka~~~~~~F~g~ss~-----~TWL~~Ia~N~~id-------------   73 (201)
T PRK12545         12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQSAH-----KTWVFGILRNKLID-------------   73 (201)
T ss_pred             HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHH-----HHHHHHHHHHHHHH-------------
T ss_conf             999999999999999990999899999999999999854045875238-----99999999999999-------------


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHH
Q ss_conf             89899999999987760889997899987099989999999860898755363588998604756238988998999999
Q gi|254780289|r  527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ  606 (682)
Q Consensus       527 ~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~  606 (682)
                          .+.+.        .|......+...+              ...-.+|..+..+. +.+.........+.|+..+..
T Consensus        74 ----~lRkr--------~r~~~~~~~d~~~--------------d~e~~~d~~~~~d~-g~w~~~~~p~~~~~Pe~~l~~  126 (201)
T PRK12545         74 ----TLRAR--------RRTINLSALDAEL--------------DGESLLDRELFKDN-GHWAAHAKPRPWPKPETILQQ  126 (201)
T ss_pred             ----HHHHH--------CCCCCCCCCCCCC--------------CCCCCCHHHHHCCC-CCCCCCCCCCCCCCHHHHHHH
T ss_conf             ----99961--------5778855344454--------------63211105540344-543233578889998999999


Q ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHH
Q ss_conf             99999999997329988999999981879867468899989966789999999999999832967
Q gi|254780289|r  607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS  671 (682)
Q Consensus       607 ~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~  671 (682)
                      ..+...+..+|..|||+.+.|+.||+    -...+.+||+..+|+|-.-|+..=.+|-.+||.--
T Consensus       127 ~e~~~~l~~aL~~LP~~~R~v~~Lr~----~egls~~EIA~~L~is~~tVksrL~RAR~~LR~~L  187 (201)
T PRK12545        127 QQFWTLFETCLDHLPEQIGRVFMMRE----FLDFEIDDICTELTLTANHCSVLLYRARTRLRTCL  187 (201)
T ss_pred             HHHHHHHHHHHHHCCHHHHHHHHHHH----HHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999959999988989999----92898999999989699999999999999999999


No 86 
>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=98.61  E-value=3.8e-06  Score=67.48  Aligned_cols=175  Identities=17%  Similarity=0.212  Sum_probs=113.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHH-----HHHHHHHHHHHHHHHCCCCCCCEEEHH
Q ss_conf             889999998765332112468999875557899988752235677788-----754436799998874385457312010
Q gi|254780289|r  425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD-----LIQEGNIGLMKAAEKFDWCLGYKFSTY  499 (682)
Q Consensus       425 ~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~-----~~~~~~~~l~~a~~~~~~~~g~~f~ty  499 (682)
                      .++-+++++++.|..   .|-.+|++..-.-+..+|.+|.+.-..-.|     ++|+.-+-|.+.-+.+++.....|.||
T Consensus         2 ~~~teLi~~~k~GD~---~Af~~L~~~y~~~l~r~a~~~l~~~~~~ed~~~~~lvqe~Flrl~~~~~~~~~~~~~~f~~~   78 (185)
T pfam07638         2 QEVTQLLQQVKDGDA---AATEQLLPLVYDELRRLAGSKLQNERRGHTLQPTALVHEAFVRLVDTEDFPDWSGRGHFFAA   78 (185)
T ss_pred             CHHHHHHHHHHCCCH---HHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHH
T ss_conf             479999999986779---99999999999999999999963532101677899999999999840202367756899999


Q ss_pred             HHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCC
Q ss_conf             28989999999997228704614205889899999999987760889997899987099989999999860898755363
Q gi|254780289|r  500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP  579 (682)
Q Consensus       500 a~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~  579 (682)
                      +.-|+|.-+..+...+.+.-|.                      +   ...                      ..+++  
T Consensus        79 l~~i~~~~~id~~R~~~~~~~~----------------------~---~~~----------------------~~~~~--  109 (185)
T pfam07638        79 AAEAMRRILIDHARRRQRQKRG----------------------G---DVQ----------------------RRELD--  109 (185)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCC----------------------C---CCH----------------------HCCHH--
T ss_conf             9999999999999988866126----------------------6---410----------------------10101--


Q ss_pred             CCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             58899860475623898899899999999999999997329988999999981879867468899989966789999999
Q gi|254780289|r  580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI  659 (682)
Q Consensus       580 ~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi  659 (682)
                        ++        ......++|+....   +.+.+ +.|.+|||+.+.|+.|||    ....|..|||+.+|+|---|+-=
T Consensus       110 --~~--------~~~~~~~~~~~~~~---l~~~~-~~l~~Lpp~~r~v~~L~~----~eglS~~EIAe~Lgis~~TVk~r  171 (185)
T pfam07638       110 --EV--------VDNGDSPNPDLLLD---LDEAL-EQLFSLSPRQARLVELRF----FAGLSNDEIAERLGVSERTVERN  171 (185)
T ss_pred             --HH--------CCCCCCCCHHHHHH---HHHHH-HHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             --10--------01456898788999---99999-998648998888988899----75999999999979699899999


Q ss_pred             HHHHHHHHCC
Q ss_conf             9999998329
Q gi|254780289|r  660 EAKAIRKLKH  669 (682)
Q Consensus       660 ~~~a~~~l~~  669 (682)
                      =.+|..+||.
T Consensus       172 l~~Ar~~Lr~  181 (185)
T pfam07638       172 WALARAWLHR  181 (185)
T ss_pred             HHHHHHHHHH
T ss_conf             9999999998


No 87 
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=98.57  E-value=1.3e-05  Score=63.27  Aligned_cols=171  Identities=15%  Similarity=0.187  Sum_probs=112.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC----CCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEE
Q ss_conf             12688999999876533211246899987555789998875223----56777887544367999988743854573120
Q gi|254780289|r  422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN----RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS  497 (682)
Q Consensus       422 l~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~----~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~  497 (682)
                      .+..+++.++.....|...+-   ..++...-+.+.+++..+..    ..-.-.|++|+.-+-+.+...+|++..  .|+
T Consensus         3 ~~~~~~~~Lv~~~~~GD~~Af---~~L~~r~~~~l~~~~~~~l~r~~~~~~dAeDlvQe~fl~~~~~~~~~~~~~--~~~   77 (184)
T PRK12539          3 SKENELKALMLASLDGDAAAH---RALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLT   77 (184)
T ss_pred             CCHHHHHHHHHHHHCCCHHHH---HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCC--CHH
T ss_conf             977999999999980889999---999999899999999999998439998999999999999998377559998--579


Q ss_pred             HHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCC
Q ss_conf             10289899999999972287046142058898999999999877608899978999870999899999998608987553
Q gi|254780289|r  498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE  577 (682)
Q Consensus       498 tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~  577 (682)
                         +|-.+=+...++                 +.+.+..        +.                        ...+   
T Consensus        78 ---~WL~~Ia~n~~~-----------------d~~R~~~--------~~------------------------~~~~---  102 (184)
T PRK12539         78 ---PWVYAIARYKLI-----------------DHLRRTR--------AS------------------------LADV---  102 (184)
T ss_pred             ---HHHHHHHHHHHH-----------------HHHHHCC--------CC------------------------CCCC---
T ss_conf             ---999999999999-----------------9998514--------55------------------------3448---


Q ss_pred             CCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHH
Q ss_conf             63588998604756238988998999999999999999973299889999999818798674688999899667899999
Q gi|254780289|r  578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR  657 (682)
Q Consensus       578 ~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~r  657 (682)
                       |+.+.+     +.........++       ....+..+|+.|||+.+.|+.|+|    -...|..||+..+|+|-.-|+
T Consensus       103 -~~~~~~-----~~~~~~~~~~~e-------~~~~l~~~l~~Lp~~~r~v~~L~~----~eg~s~~EIA~~lgis~~tVk  165 (184)
T PRK12539        103 -PIDDAD-----ELVAHDDAAAVE-------STLDLGRLLARLPEKMRLAIQAVK----LDGLSVAEAATRSGMSESAVK  165 (184)
T ss_pred             -CCCCCC-----CCCCCCCHHHHH-------HHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHH
T ss_conf             -844344-----456785133188-------999999999849999999999999----949999999999891999999


Q ss_pred             HHHHHHHHHHCC
Q ss_conf             999999998329
Q gi|254780289|r  658 QIEAKAIRKLKH  669 (682)
Q Consensus       658 qi~~~a~~~l~~  669 (682)
                      --=.+|+++||.
T Consensus       166 s~l~Rark~Lr~  177 (184)
T PRK12539        166 VSVHRGLKALAA  177 (184)
T ss_pred             HHHHHHHHHHHH
T ss_conf             999999999999


No 88 
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=98.56  E-value=3.9e-07  Score=75.33  Aligned_cols=93  Identities=17%  Similarity=0.285  Sum_probs=80.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC--HHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHH
Q ss_conf             9999998765332112468999875557899988752235677--78875443679999887438545731201028989
Q gi|254780289|r  427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ--FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV  504 (682)
Q Consensus       427 lK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~--~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i  504 (682)
                      +..++..++.|.   ..|+.++|+.+.+||..++.+++++-+.  -.|+++.|-+|+..|+++||+.+|..|.+||.+-|
T Consensus         5 le~~l~~i~~Gd---~~~re~lI~~y~pfI~k~~s~~~~r~~~~e~DDe~SIgliAfneAI~~y~~~kg~~F~~fA~~vI   81 (237)
T PRK08311          5 IEDILEKIQNGD---EELREELIEEYKPFILKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELVI   81 (237)
T ss_pred             HHHHHHHHHCCC---HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHH
T ss_conf             999999988678---99999999992789999999996777898878299899999999998628335986599999999


Q ss_pred             HHHHHHHHHHCCCEEECC
Q ss_conf             999999997228704614
Q gi|254780289|r  505 KQAITRSIADQSCTIRIP  522 (682)
Q Consensus       505 ~~~i~~~~~~~~~~~r~~  522 (682)
                      +..+.-++..+.+.-..+
T Consensus        82 k~rliDy~Rke~k~~~~~   99 (237)
T PRK08311         82 KRRLIDYIRKEKKHSKVV   99 (237)
T ss_pred             HHHHHHHHHHHCCCCCCC
T ss_conf             999999999740444568


No 89 
>pfam04542 Sigma70_r2 Sigma-70 region 2. Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. 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 though to mediate strand separation, thereby allowing transcription initiation.
Probab=98.54  E-value=2.1e-07  Score=77.40  Aligned_cols=71  Identities=39%  Similarity=0.570  Sum_probs=67.3

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCE
Q ss_conf             98755578999887522356777887544367999988743854573120102898999999999722870
Q gi|254780289|r  448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT  518 (682)
Q Consensus       448 l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~  518 (682)
                      |++.+.++|.++|++|.+.+....|++||+.+++++++++|++.+|.+|+||+.++++..+..++..+.|+
T Consensus         1 L~~~y~~~l~~~~~~~~~~~~~aeDl~Qe~f~~~~~~~~~~~~~~~~~f~~wl~~i~~n~~~d~~Rk~~r~   71 (71)
T pfam04542         1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLLRAVERFDPERGVSFSTWLYTIIRNAIIDALRKQRRT   71 (71)
T ss_pred             CHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             99989999999999883986029999999999999998757961366099899999999999999973999


No 90 
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=98.52  E-value=1.4e-05  Score=62.93  Aligned_cols=157  Identities=18%  Similarity=0.218  Sum_probs=108.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEE
Q ss_conf             12468999875557899988752235677788754436799998874385457312010289899999999972287046
Q gi|254780289|r  441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR  520 (682)
Q Consensus       441 ~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r  520 (682)
                      +.+|=.++...+-+.|...+.++++.--.-.|++|+.-+-+.+.  .|....  .|.   +|-.+-+...++ |.     
T Consensus         1 meeAF~~ly~~y~~~l~~~~~~~~~d~~~AeDl~Qe~flk~~~~--~~~~~~--~~~---~wL~~ia~n~~~-d~-----   67 (166)
T PRK09639          1 MEETFEDLFKQYYQDVVQQIIYIVKDRTQAEDLAQEVFLRLLRS--DWKGIE--NEK---GWLIKSARNVAY-NY-----   67 (166)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHC--CCCCCC--CHH---HHHHHHHHHHHH-HH-----
T ss_conf             98999999999999999999999299999999999999999872--635446--789---999999999999-99-----


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCH
Q ss_conf             14205889899999999987760889997899987099989999999860898755363588998604756238988998
Q gi|254780289|r  521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP  600 (682)
Q Consensus       521 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~  600 (682)
                                 +.+..+...                                 ...+ ...         ........+|
T Consensus        68 -----------~R~~~~~~~---------------------------------~~~~-~~~---------~~~~~~~~~~   93 (166)
T PRK09639         68 -----------FRSEKRHRA---------------------------------RILG-EFQ---------WQEEQIDSSP   93 (166)
T ss_pred             -----------HHHHHHHHH---------------------------------HHCC-CHH---------CCCCCCCCCH
T ss_conf             -----------998840201---------------------------------0000-100---------0134557997


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             999999999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       601 ~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      ++.+........+..+|..|||+.+.|+.+||  . |  +|..||+..+|+|-.-|+..=.+|+++||.
T Consensus        94 e~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~--~-g--~s~~EIA~~l~is~~tVk~~l~RA~~~Lr~  157 (166)
T PRK09639         94 EEIWIRKEEITKVQEVLAKMTERDRTVLLLRF--S-G--YSYKEIAQALGIDESSVGTTLHRAKKKFRK  157 (166)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH--H-C--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             89999899999999998839999999999999--3-8--999999999891999999999999999999


No 91 
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=98.52  E-value=1.3e-05  Score=63.29  Aligned_cols=148  Identities=17%  Similarity=0.201  Sum_probs=109.9

Q ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHH
Q ss_conf             57899988752235677788754436799998874385457312010289899999999972287046142058898999
Q gi|254780289|r  453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV  532 (682)
Q Consensus       453 lr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~  532 (682)
                      =+.|.++|-++++..-.-.|++|+.-+-+.+..++|+. +|  |   .+|-.|=+...|+. .                +
T Consensus         5 ~~~ly~~~~~~~~n~~dAeDi~QevFik~~~~~~~~~~-~~--~---~~WL~~Ia~N~~~d-~----------------~   61 (160)
T PRK09642          5 RHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQF-RG--L---KTWMARIATNHAID-Y----------------K   61 (160)
T ss_pred             HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCC-CC--H---HHHHHHHHHHHHHH-H----------------H
T ss_conf             89999999999099999999999999999984503362-44--9---99999999999999-9----------------9


Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH
Q ss_conf             99999987760889997899987099989999999860898755363588998604756238988998999999999999
Q gi|254780289|r  533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET  612 (682)
Q Consensus       533 ~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~  612 (682)
                      .+..        |.+                        ..+|+.    .+.+    +.+  ....+|++.+........
T Consensus        62 Rk~~--------r~~------------------------~~~~~~----~~~~----~~~--~~~~~~e~~~~~~e~~~~   99 (160)
T PRK09642         62 RKKA--------REN------------------------EELSLC----KETE----ENI--KSSHNIEDLLLTKEQKLL   99 (160)
T ss_pred             HHHH--------CCC------------------------CCCCCC----HHHH----HCC--CCCCCHHHHHHHHHHHHH
T ss_conf             9872--------455------------------------312200----0112----115--677998999998999999


Q ss_pred             HHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       613 ~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      +.++|..|||+.+.|+.|||    -...|+.||+..+|+|-.-|+.-=.+|.++||.
T Consensus       100 l~~~l~~Lp~~~R~v~~L~~----~e~~s~~EIA~~l~is~~tVk~~l~RArk~Lkk  152 (160)
T PRK09642        100 IAQKLRELPENYRDVVLAHY----LEEKSYQEIALQENIEVKTVEMKLYRARKWIKK  152 (160)
T ss_pred             HHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             99999979999999979999----829999999999891999999999999999999


No 92 
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=98.51  E-value=2.7e-05  Score=60.79  Aligned_cols=155  Identities=18%  Similarity=0.168  Sum_probs=108.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEE
Q ss_conf             11246899987555789998875223567778875443679999887438545731201028989999999997228704
Q gi|254780289|r  440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI  519 (682)
Q Consensus       440 e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~  519 (682)
                      .-++|=.+|++.+-..|.+.|-++++.--.-.|++||.-+-+.+..++|+....|+     +|-.+-+  +.        
T Consensus        20 ~~~~AFe~L~~~y~~~ly~~a~~~~~d~~~AeDl~QEtFlk~~~~~~~~~~~~~~~-----tWL~~I~--~~--------   84 (188)
T PRK12517         20 SKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEKAAK-----AWLITIL--RR--------   84 (188)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHH-----HHHHHHH--HH--------
T ss_conf             35999999999999999999999949999999999999999999887647963189-----9999999--99--------


Q ss_pred             ECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCC
Q ss_conf             61420588989999999998776088999789998709998999999986089875536358899860475623898899
Q gi|254780289|r  520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS  599 (682)
Q Consensus       520 r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~  599 (682)
                             ....++.   +.       .+                        ..+.++.           ..+.+.....
T Consensus        85 -------~~~~r~~---r~-------~~------------------------~~~~~~~-----------~~~~~~~~~~  112 (188)
T PRK12517         85 -------ENARRFE---RK-------QF------------------------DLVDIED-----------DSIEDDLSSS  112 (188)
T ss_pred             -------HHHHHHH---HC-------CC------------------------CCCCCCC-----------CCCCCCCCCC
T ss_conf             -------9889998---61-------57------------------------7565220-----------0024666788


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             8999999999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       600 ~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      |++....    ..|..+|..|||+.+.||.|||    -...|..|||..+|+|-.-|+..=.+|..+||.
T Consensus       113 ~e~~~~~----~~l~~~l~~Lp~~~R~vi~L~~----~eg~s~~EIA~~Lgis~~tVksrl~RAr~~Lr~  174 (188)
T PRK12517        113 SEEEMEQ----YWLRRQIAKLDPEYREPLLLQV----IGGFSGEEIAEILDLNKNTVMTRLFRARNQLKE  174 (188)
T ss_pred             CHHHHHH----HHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             1689999----9999999769999999999999----839999999999893999999999999999999


No 93 
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=98.51  E-value=1.9e-05  Score=61.90  Aligned_cols=160  Identities=16%  Similarity=0.140  Sum_probs=101.7

Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHH
Q ss_conf             89998875223567778875443679999887438545731201028989999999997228704614205889899999
Q gi|254780289|r  455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR  534 (682)
Q Consensus       455 ~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~  534 (682)
                      -+...|.++++.--.-.|++||.-+-..+..+.|+...  +|+   ||-.|=+...++.                 .+.+
T Consensus        21 ~L~~fa~~~l~d~~~AEDlvQEtFlka~~~~~~f~~~~--~f~---tWL~~Ia~N~~id-----------------~lRk   78 (191)
T PRK12530         21 QMLKFATLQLKDADLAEDVVQEAFTSALKNIDSFKGQS--ALK---TWIFAILKNKIID-----------------YIRQ   78 (191)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCC--CHH---HHHHHHHHHHHHH-----------------HHHH
T ss_conf             99999999939999999999999999998688637877--299---9999999999999-----------------9998


Q ss_pred             HHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCC--CCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH
Q ss_conf             9999877608899978999870999899999998608987553635--88998604756238988998999999999999
Q gi|254780289|r  535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRET  612 (682)
Q Consensus       535 ~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~--~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~  612 (682)
                              .+|.+...++.                     .-+.|.  .++....-.+..+......|...+....+...
T Consensus        79 --------~~r~~~~~~~~---------------------~~~~~~~~~d~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~  129 (191)
T PRK12530         79 --------RKRFVNESELI---------------------EEESPNSFFDEKGHWKPETYEPSELQDVEQTVYSEEFWLI  129 (191)
T ss_pred             --------HCCCCCCCCCC---------------------CCCCCHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf             --------46667721001---------------------2224100101112234333683021689999999999999


Q ss_pred             HHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       613 ~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      +..+|..|||+.+.|+.|||    -...|.+||++.+|+|-.-|+..=.+|-.+||.
T Consensus       130 l~~~l~~LP~~~R~v~~Lr~----~~~ls~~EIA~~l~is~~tVksrL~RAR~~Lr~  182 (191)
T PRK12530        130 FEICLNKLPAQQARVFMMRE----FLELSSEQICQECHITTSNLHVLLYRARLQLQA  182 (191)
T ss_pred             HHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             99999869999999999999----929999999999896999999999999999999


No 94 
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=98.46  E-value=2.2e-05  Score=61.41  Aligned_cols=156  Identities=13%  Similarity=0.124  Sum_probs=112.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEEC
Q ss_conf             24689998755578999887522356777887544367999988743854573120102898999999999722870461
Q gi|254780289|r  442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI  521 (682)
Q Consensus       442 ~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~  521 (682)
                      .-|=..+.+.+-+.+...+.++++..-.-.|++|+.=+-+.+. +++..-.  .+.+|-.++.|..+..++..+      
T Consensus         9 ~~AFe~Ly~~~~~~l~~~~~~~~~~~~~AeDivQe~Flr~~~~-~~~~~~~--~~~a~L~~iarn~~id~~Rr~------   79 (172)
T PRK09651          9 SLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRN------   79 (172)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHC-CCCCCCC--CHHHHHHHHHHHHHHHHHHHH------
T ss_conf             6699999999999999999999598868999999999999863-8523346--889999999999999999998------


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHH
Q ss_conf             42058898999999999877608899978999870999899999998608987553635889986047562389889989
Q gi|254780289|r  522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL  601 (682)
Q Consensus       522 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~  601 (682)
                                    ....       ...+.+                 ..                    +.+...++|+
T Consensus        80 --------------~~~~-------~~~~~~-----------------~~--------------------~~~~~~~~~e  101 (172)
T PRK09651         80 --------------ALEK-------AYLEML-----------------AL--------------------MPEGGAPSPE  101 (172)
T ss_pred             --------------HHHH-------HHHHHH-----------------HH--------------------CCCCCCCCHH
T ss_conf             --------------8888-------788888-----------------74--------------------7554599988


Q ss_pred             HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf             9999999999999997329988999999981879867468899989966789999999999999832
Q gi|254780289|r  602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK  668 (682)
Q Consensus       602 ~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~  668 (682)
                      ...........+..+|+.|||+.+.|+.|++    -...|..||+..+|+|-.-|+.-=.+||+.++
T Consensus       102 ~~~~~~e~~~~l~~~l~~Lp~~~R~v~~L~~----~egls~~EIA~~lgiS~~tVk~~l~rAlk~c~  164 (172)
T PRK09651        102 ERESQLETLQLLDSMLDGLNGKTREAFLLSQ----LDGLTYSEIAHKLGVSISSVKKYVAKAVEHCL  164 (172)
T ss_pred             HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             9999999999999998709999999999998----83999999999989399999999999999999


No 95 
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=98.46  E-value=1.6e-05  Score=62.57  Aligned_cols=149  Identities=13%  Similarity=0.128  Sum_probs=101.3

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHH
Q ss_conf             99987555789998875223567778875443679999887438545731201028989999999997228704614205
Q gi|254780289|r  446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM  525 (682)
Q Consensus       446 ~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~  525 (682)
                      .++...+-+.|...+.++++..-.-.|++|+.-+-+.+..++|+...  .|.|   |-.+-+...++ |..|        
T Consensus         4 E~Ly~~y~~~l~~~~~~~~~d~~~AEDivQe~flk~~~~~~~~~~~~--~~~~---WL~~IarN~~i-d~~R--------   69 (181)
T PRK09637          4 ESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDGS--SIKS---WLYQIANNTII-DFYR--------   69 (181)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCC--CHHH---HHHHHHHHHHH-HHHH--------
T ss_conf             99999999999999999959999999999999999998522058823--4999---99999999999-9998--------


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHH
Q ss_conf             88989999999998776088999789998709998999999986089875536358899860475623898899899999
Q gi|254780289|r  526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI  605 (682)
Q Consensus       526 ~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~  605 (682)
                              +.        .|....         +                 +.....+               .|.+...
T Consensus        70 --------k~--------~r~~~~---------~-----------------~~~~~~~---------------~~~~~~~   92 (181)
T PRK09637         70 --------KK--------NRSEEL---------P-----------------DDLLFED---------------EEREENA   92 (181)
T ss_pred             --------HH--------CCCCCC---------C-----------------HHHCCCC---------------CCCCHHH
T ss_conf             --------61--------555677---------4-----------------2221467---------------9832249


Q ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             9999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       606 ~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      ...+...+..+|+.|||+.+.|+.|+|    -..+|..||+..+|+|-.-|+.-=.+|..+||.
T Consensus        93 ~~e~~~~l~~~l~~Lp~~~R~v~~L~~----~eg~s~~EIA~~L~is~~tVksrl~RAr~~Lr~  152 (181)
T PRK09637         93 KKELAPCLRPFIDALPEKYAEALRLTE----LEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKE  152 (181)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             999999999999769999989979998----859999999999894999999999999999999


No 96 
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=98.46  E-value=9.9e-06  Score=64.19  Aligned_cols=74  Identities=18%  Similarity=0.287  Sum_probs=67.1

Q ss_pred             ECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             238988998999999999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       592 ~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      ..+....+|.+.+.+......+..+|..||++.+.|+.|||    -...|.+||++.+|+|---|+-.=.+|+++||.
T Consensus        79 ~~~~~~~~p~~~~~~~e~~~~l~~ai~~Lp~~qR~vl~L~~----~egls~~EIA~~l~is~~tVk~~l~RAr~~Lr~  152 (161)
T PRK09047         79 ADDDGAESPEDRLERAQVLQLIEEAIQKLPARQREAFLLRY----WEDMDVAETAAAMGCSEGSVKTHCSRATHTLAK  152 (161)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             56766899999999999999999999819999999989999----987799999999896999999999999999999


No 97 
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=98.44  E-value=2.6e-05  Score=60.87  Aligned_cols=155  Identities=15%  Similarity=0.156  Sum_probs=102.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEEC
Q ss_conf             24689998755578999887522356777887544367999988743854573120102898999999999722870461
Q gi|254780289|r  442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI  521 (682)
Q Consensus       442 ~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~  521 (682)
                      ++|=.+++..+-+.|...+.++++.--.-.|++||.-+-+++..+.|.   |-.|.|   |-.+=+...++ |.      
T Consensus         4 r~afe~ly~~~~~~l~~~~~~~~~d~~~AeDl~QetFlk~~~~~~~~~---~~~~~~---WL~~Ia~N~~~-d~------   70 (161)
T PRK12541          4 KQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYK---GEEIRP---WLFTIAYNAFI-DW------   70 (161)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCC---CCCHHH---HHHHHHHHHHH-HH------
T ss_conf             999999999999999999999939999999999999999998361316---675689---99999999999-99------


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHH
Q ss_conf             42058898999999999877608899978999870999899999998608987553635889986047562389889989
Q gi|254780289|r  522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL  601 (682)
Q Consensus       522 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~  601 (682)
                                +.+..        +.++                         .+++       +..    +  ++.++|+
T Consensus        71 ----------~Rk~~--------~~~~-------------------------~~~~-------~~~----~--~~~~~~~   94 (161)
T PRK12541         71 ----------YRKEK--------KYKT-------------------------TTVE-------EFH----L--PNVPSTE   94 (161)
T ss_pred             ----------HHHHH--------CCCC-------------------------CCHH-------HHC----C--CCCCCCH
T ss_conf             ----------99860--------4465-------------------------5255-------540----4--6899962


Q ss_pred             HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             99999999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       602 ~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      +..........+.++|..|||..+.|+.|||    -..+|..|||+.+|+|-.-|+..=.+|.++||.
T Consensus        95 ~~~~~~~~~~~~~~~l~~Lp~~~R~v~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~RArk~Lr~  158 (161)
T PRK12541         95 HEYFVKHEIASWLDSLSSLPLERRNVLLLRD----YYGFSYKEIAEMTGLSLAKVKIELHRGRKETKS  158 (161)
T ss_pred             HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             7789999999999999819999999999899----749999999999893999999999999999987


No 98 
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=98.44  E-value=2.6e-05  Score=60.92  Aligned_cols=159  Identities=18%  Similarity=0.244  Sum_probs=111.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEEC
Q ss_conf             24689998755578999887522356777887544367999988743854573120102898999999999722870461
Q gi|254780289|r  442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI  521 (682)
Q Consensus       442 ~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~  521 (682)
                      ..|=.++...+=.-+...|.+|++..-.-.|++|+.=+-|...-+.|++..-      -+ |+..-+.....|+      
T Consensus        11 e~al~elf~~~~~~L~~~a~r~~~~~~~AEDivQe~Flkl~~~~~~~~~~~~------~a-wL~~iarN~~id~------   77 (183)
T PRK07037         11 DGALLDVFVDNRSMLVKIARGIVGCASRAEDVVQDAFVKLVEAPNQDAVKQP------VA-YLFQMVRNLAIDH------   77 (183)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCCH------HH-HHHHHHHHHHHHH------
T ss_conf             8999999999999999999999799988999999999999974543441369------99-9999999999999------


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHH
Q ss_conf             42058898999999999877608899978999870999899999998608987553635889986047562389889989
Q gi|254780289|r  522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL  601 (682)
Q Consensus       522 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~  601 (682)
                                +.+....  ..                               .+     +++++.  .+ +.+ ...+|+
T Consensus        78 ----------lRr~~~~--~~-------------------------------~~-----~~~~~~--~~-~~~-~~~~pe  105 (183)
T PRK07037         78 ----------CRRQSLE--NK-------------------------------YH-----GDEDDG--LD-VPS-PEASPE  105 (183)
T ss_pred             ----------HHHHHHH--HH-------------------------------CC-----CCHHHH--CC-CCC-CCCCHH
T ss_conf             ----------9977766--50-------------------------------13-----424442--12-678-899989


Q ss_pred             HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             99999999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       602 ~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      +.+........|..+|..|||+.+.|+.|++    -...|..||++.+|||---|+--=.+|+++||.
T Consensus       106 ~~~~~~e~~~~l~~ai~~LP~~~R~v~~L~~----~eg~s~~EIAe~LgiS~~tVk~~l~rAl~~LR~  169 (183)
T PRK07037        106 AALINRDTLRHVADALDELPARTRAAFEMVR----LRGETLQDIARELNVSQTLVNFMIRDALRHCRK  169 (183)
T ss_pred             HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999819999999989898----739899999999892999999999999999999


No 99 
>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=98.43  E-value=4.5e-07  Score=74.77  Aligned_cols=50  Identities=54%  Similarity=0.882  Sum_probs=46.4

Q ss_pred             HHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       616 ~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      +|+.|||+++.||.|||    ..+.|+.|||+.+|+|..+|+|+..+||.|||.
T Consensus         1 Al~~L~~~~r~ii~l~y----~~~~t~~EIA~~lgis~~~V~~~~~ral~~LR~   50 (50)
T pfam04545         1 ALASLPPREREVLVLRF----GEGLTLEEIGERLGISRERVRQIEKRALRKLRK   50 (50)
T ss_pred             CHHHCCHHHHHHHHHHC----CCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHCC
T ss_conf             97668999999999870----688249999999897999999999999998629


No 100
>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=98.39  E-value=3.2e-06  Score=68.02  Aligned_cols=161  Identities=19%  Similarity=0.318  Sum_probs=131.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHH
Q ss_conf             99999987653321124689998755578999887522356777887544367999988743854573120102898999
Q gi|254780289|r  427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ  506 (682)
Q Consensus       427 lK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~  506 (682)
                      .|..++.|++|...+-   -+||+--===|..++=+-.|....-.|.-||+-|-----+|.||+.|  ||||   |--|=
T Consensus         5 ~Kk~ik~v~~GD~~Af---AdlVdlYKDKiY~l~YRMlGN~HEA~D~AQEAF~RAY~~IDtyd~~~--KFST---WLyRI   76 (187)
T TIGR02948         5 IKKRIKEVKKGDENAF---ADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYVNIDTYDIER--KFST---WLYRI   76 (187)
T ss_pred             HHHHHHHHHHCHHHHH---HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCC--CHHH---HHHHH
T ss_conf             6889999860217888---99999964247777776506743055688888888654114316664--3147---89999


Q ss_pred             HHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             99999972287046142058898999999999877608899978999870999899999998608987553635889986
Q gi|254780289|r  507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS  586 (682)
Q Consensus       507 ~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~  586 (682)
                      |               +.+  +|-++.                                   --+..+.||.||+.-++-
T Consensus        77 A---------------TNl--~IDrlR-----------------------------------KrKPD~yLd~~V~G~dGL  104 (187)
T TIGR02948        77 A---------------TNL--TIDRLR-----------------------------------KRKPDFYLDDEVAGTDGL  104 (187)
T ss_pred             H---------------HHH--HHHHHH-----------------------------------CCCCCCCCCCCCCCCCCC
T ss_conf             9---------------877--886541-----------------------------------348886436755786774


Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCC
Q ss_conf             047562389889989999999999999999732998899999998187986746889998996678
Q gi|254780289|r  587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT  652 (682)
Q Consensus       587 ~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~  652 (682)
                      |+..-++. ....|++.+..-.+++.+.+.+..|||+-|.|+.|.|    =.+.+|.||...+++.
T Consensus       105 T~~sQlaa-~~~~~~d~V~~lE~~~~iQ~~I~~LP~KYR~~ivLKY----~edLSL~EIS~IL~lP  165 (187)
T TIGR02948       105 TMESQLAA-DEASPEDEVVSLELRDTIQEEIEALPEKYRSVIVLKY----MEDLSLKEISEILDLP  165 (187)
T ss_pred             HHHHCCCC-CCCCCHHHHHHHHHHHHHHHHHHHCCHHHCEEHHHHH----HHHHHHHHHHHHHCCC
T ss_conf             00100110-1246214655535678999999743433512224544----4442188899985789


No 101
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=98.37  E-value=0.0001  Score=56.19  Aligned_cols=170  Identities=19%  Similarity=0.136  Sum_probs=109.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHH
Q ss_conf             26889999998765332112468999875557899988752235677788754436799998874385457312010289
Q gi|254780289|r  423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW  502 (682)
Q Consensus       423 ~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~  502 (682)
                      +-..+.+++.+.+.|.+.+   -..+++.+-..|..++.+..|. -.-.|++||--+-+.+...+|....  .|+   ||
T Consensus         9 ~da~~~~Lv~~a~~GD~~A---f~~L~~r~~~~v~r~~~~l~~~-~~AeDl~QEtflk~~~~l~~f~~~~--~f~---tW   79 (195)
T PRK12535          9 NDAHVTELALAAGRGDRAA---LTEFIRATQDDVWRLLAHLGGH-DIADDLTQETYLRVMSALPRFAARS--SAR---TW   79 (195)
T ss_pred             CHHHHHHHHHHHHHCCHHH---HHHHHHHHHHHHHHHHHHHCCH-HHHHHHHHHHHHHHHHHHHHCCCCC--CHH---HH
T ss_conf             8488999999998220999---9999999999999999893799-7799999999999999887707888--799---99


Q ss_pred             HHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             89999999997228704614205889899999999987760889997899987099989999999860898755363588
Q gi|254780289|r  503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD  582 (682)
Q Consensus       503 ~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~  582 (682)
                      -++=+...++ |+.|                +   ...                               .|-....++  
T Consensus        80 L~~Ia~n~~~-d~~R----------------~---~~~-------------------------------~~~~~~~~~--  106 (195)
T PRK12535         80 LLSLARRVWV-DNIR----------------H---DMA-------------------------------RPRKSAVEY--  106 (195)
T ss_pred             HHHHHHHHHH-HHHH----------------H---HHC-------------------------------CCCCCCCCC--
T ss_conf             9999999999-9999----------------8---851-------------------------------666553332--


Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             99860475623898899899999999999999997329988999999981879867468899989966789999999999
Q gi|254780289|r  583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK  662 (682)
Q Consensus       583 ~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~  662 (682)
                       ++...    .|  ...+.....    ...+..+|..|||..+.||.|+|    -..+|.+||+..+|++---|+--=.+
T Consensus       107 -~~~~~----~d--~~~~~~~~~----~~~l~~~l~~Lp~~~R~~l~L~~----~~g~s~~EIA~ilgi~~gTVKsRl~R  171 (195)
T PRK12535        107 -EDTGA----TD--ATNAGIWSE----WIDVRTLIDALPPERREALILTQ----VLGYTYEEAAKIADVRVGTIRSRVAR  171 (195)
T ss_pred             -CCCCC----CC--CCCCHHHHH----HHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             -23566----77--764035777----99999999849998879999999----82998999999989399999999999


Q ss_pred             HHHHHCC
Q ss_conf             9998329
Q gi|254780289|r  663 AIRKLKH  669 (682)
Q Consensus       663 a~~~l~~  669 (682)
                      |..+||-
T Consensus       172 Ar~~Lr~  178 (195)
T PRK12535        172 ARADLVA  178 (195)
T ss_pred             HHHHHHH
T ss_conf             9999999


No 102
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=98.36  E-value=4.8e-05  Score=58.82  Aligned_cols=157  Identities=13%  Similarity=0.148  Sum_probs=103.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEEC
Q ss_conf             24689998755578999887522356777887544367999988743854573120102898999999999722870461
Q gi|254780289|r  442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI  521 (682)
Q Consensus       442 ~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~  521 (682)
                      ..|=..|...+-+.|...+.++++.-..-.|++|+--+-+.+..+.|+. .+-.|.|    |+..-....+.|+      
T Consensus         6 ~~af~~Ly~~~~~~l~~~~~~~~~d~~~AeDivQe~F~k~~~~~~~~~~-~~~~~~~----wL~~Ia~n~~~d~------   74 (171)
T PRK09645          6 AALMRALYDEHAAALWRYALRLTGDRARAEDVVQETLLRAWQHPEVLAD-PTRSARA----WLFTVARNLVIDE------   74 (171)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCC-CCCCHHH----HHHHHHHHHHHHH------
T ss_conf             9999999999999999999999099999999999999999985887066-4141999----9999999999999------


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHH
Q ss_conf             42058898999999999877608899978999870999899999998608987553635889986047562389889989
Q gi|254780289|r  522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL  601 (682)
Q Consensus       522 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~  601 (682)
                                +.+....                                 .....+...          ...+...++..
T Consensus        75 ----------~R~~~~~---------------------------------~~~~~~~~~----------~~~~~~~~~~~  101 (171)
T PRK09645         75 ----------RRSARAR---------------------------------PVEGSPDVL----------GVPEQSTPDEV  101 (171)
T ss_pred             ----------HHHHHCC---------------------------------CCCCCCCHH----------HHCCCCCCCHH
T ss_conf             ----------9987547---------------------------------543444233----------20256883168


Q ss_pred             HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             99999999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       602 ~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      +   .......+..+|..|||+.+.|+.|||    -..+|++|||+.+|+|-.-|+.-=.+|+++||.
T Consensus       102 ~---~~~~~~~l~~ai~~L~~~~r~v~~l~~----~~g~s~~EIA~~l~is~~tVk~~l~ra~~~Lr~  162 (171)
T PRK09645        102 D---AALDRLLIADALAQLSPEHRAVLVRSY----YRGWSTAQIAADLGIPEGTVKSRLHYAVRALRL  162 (171)
T ss_pred             H---HHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             8---999999999999759999887989999----869999999999892999999999999999999


No 103
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=98.34  E-value=5.8e-05  Score=58.12  Aligned_cols=153  Identities=16%  Similarity=0.134  Sum_probs=100.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEEC
Q ss_conf             24689998755578999887522356777887544367999988743854573120102898999999999722870461
Q gi|254780289|r  442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI  521 (682)
Q Consensus       442 ~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~  521 (682)
                      ...++++++ +..-+...|.++++..-.-.|++|+.-+-+.+..++|++..  +|.|   |..+=+...++         
T Consensus         7 ~~~~~~l~e-H~p~L~~fa~r~~~~~~~AEDlvQEtflk~~~~l~~~~~~~--~~~t---WL~~IarN~~~---------   71 (188)
T PRK12546          7 RDPRDELVE-HLPALRAFAISLTRNVAAADDLVQDTVVKAWTNFDKFQEGT--NLRA---WLFTILRNTFY---------   71 (188)
T ss_pred             HHHHHHHHH-HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCC--CHHH---HHHHHHHHHHH---------
T ss_conf             629999999-99999999999919999999999999999999787647653--1388---99999999999---------


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHH
Q ss_conf             42058898999999999877608899978999870999899999998608987553635889986047562389889989
Q gi|254780289|r  522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL  601 (682)
Q Consensus       522 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~  601 (682)
                              +    ..|+    .+|..                          ...+....   +    ....+   +.++
T Consensus        72 --------d----~~Rk----~~r~~--------------------------~~~~~~~~---~----~~~~~---~~~~   99 (188)
T PRK12546         72 --------S----DRRK----HKREV--------------------------EDPEGVHA---A----SLAVK---PAHD   99 (188)
T ss_pred             --------H----HHHH----HCCCC--------------------------CCCCCCCC---C----CCCCC---CCCH
T ss_conf             --------9----9997----44777--------------------------76421112---3----34689---8700


Q ss_pred             HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             99999999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       602 ~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      ...    ....+..+|..|||+.+.||.|+|    -..+|+.||++.+|+|---|+.-=.+|.++||.
T Consensus       100 ~~~----~~~~l~~aL~~LP~~~R~vl~L~~----~egls~~EIAe~Lgis~gTVKsRL~RAR~~Lr~  159 (188)
T PRK12546        100 GRL----AMSDFRAAFAQLPDEQREALILVG----ASGFSYEEAAEMCGVAVGTVKSRANRARARLAE  159 (188)
T ss_pred             HHH----HHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             689----999999999869999988958799----829899999999893999999999999999999


No 104
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=98.32  E-value=0.00011  Score=55.82  Aligned_cols=155  Identities=12%  Similarity=0.091  Sum_probs=103.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEE
Q ss_conf             12468999875557899988752235677788754436799998874385457312010289899999999972287046
Q gi|254780289|r  441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR  520 (682)
Q Consensus       441 ~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r  520 (682)
                      ..++=.+++.+...-+...|.++++..-.-.|++|+.-+-+.+..++|++.  .+|.||.   .+=+...++        
T Consensus         4 ~~~~F~~l~~~~~p~L~~~a~~l~~~~~~AeDlvQe~flk~~~~~~~~~~~--~~~~~Wl---~~IarN~~~--------   70 (164)
T PRK12547          4 TSKNFKQELLAALPSLRAFAVSLSSKHDKADDLVQDTLMKAWAKQDSFQPG--TNLKAWL---FTILRNEFY--------   70 (164)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHH---HHHHHHHHH--------
T ss_conf             799999999998999999999994999999999999999999988876998--8699999---999999999--------


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCH
Q ss_conf             14205889899999999987760889997899987099989999999860898755363588998604756238988998
Q gi|254780289|r  521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP  600 (682)
Q Consensus       521 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~  600 (682)
                               +.+.+        .+|+....+                                  ..   +.++....++
T Consensus        71 ---------d~~Rk--------~~r~~~~~~----------------------------------~~---~~~~~~~~~~   96 (164)
T PRK12547         71 ---------SQMRK--------RGREVQDSD----------------------------------GV---FTARLAVHPA   96 (164)
T ss_pred             ---------HHHHH--------HCCCCCCCC----------------------------------CC---CCCCCCCCCH
T ss_conf             ---------99997--------278776521----------------------------------01---1012568940


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             999999999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       601 ~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      ....  .. ...+..+|..||+..+.|+.|+|    -..+|..||+..+|+|-.-|+.-=.+|..+||.
T Consensus        97 ~~~~--~~-~~~l~~al~~Lp~~~r~v~~L~~----~~g~s~~EIA~~lgis~~tVksrl~rAr~~Lr~  158 (164)
T PRK12547         97 QYGS--LD-LQDFRKALNLLPADQREAIILIG----ASGFSYEEAAEICGCAVGTIKSRVSRARNRLQE  158 (164)
T ss_pred             HHHH--HH-HHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             2436--89-99999999858999999999899----849999999999893999999999999999999


No 105
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=98.27  E-value=0.0001  Score=56.11  Aligned_cols=154  Identities=12%  Similarity=0.156  Sum_probs=101.0

Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHH
Q ss_conf             78999887522356777887544367999988743854573120102898999999999722870461420588989999
Q gi|254780289|r  454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV  533 (682)
Q Consensus       454 r~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~  533 (682)
                      +-+...+.++++.--.-.|++|+.-+-+.+   +++....-.+   -+|..|-+...++. .                +.
T Consensus         6 ~~L~~~~~~~~~~~~~AeDivQd~F~k~~~---~~~~~~~~~~---~a~L~~ia~N~~~d-~----------------~R   62 (159)
T PRK12527          6 RELLRFLSARLGNRQAAEDVAHDAYLRVLE---RSSSAQIEHP---RAFLYRTALNLVVD-R----------------HR   62 (159)
T ss_pred             HHHHHHHHHHHCCHHHHHHHHHHHHHHHHH---HCCCCCCCCH---HHHHHHHHHHHHHH-H----------------HH
T ss_conf             999999999969999999999999999998---6663554569---99999999999999-9----------------99


Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHH
Q ss_conf             99999877608899978999870999899999998608987553635889986047562389889989999999999999
Q gi|254780289|r  534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT  613 (682)
Q Consensus       534 ~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~  613 (682)
                      +..                                 .+...+++.. .+         ......++|++.+........+
T Consensus        63 ~~~---------------------------------~~~~~~~~~~-~~---------~~~~~~~~~~~~~~~~e~~~~l   99 (159)
T PRK12527         63 RHR---------------------------------VRQAEPLEVL-DE---------EERLHSPSPQTRLDLGQRLALL   99 (159)
T ss_pred             HHH---------------------------------HCCCCCHHHH-CC---------CCCCCCCCHHHHHHHHHHHHHH
T ss_conf             987---------------------------------5145530211-10---------1012489869999999999999


Q ss_pred             HHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHCC
Q ss_conf             999732998899999998187986746889998996678999999999999983296777875665179
Q gi|254780289|r  614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG  682 (682)
Q Consensus       614 ~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~~~~~~  682 (682)
                      ..+|+.|||+.+.|+.|+|    -...|..||++.+|+|..-|+.-=.+|+++||.     .|+.|-.|
T Consensus       100 ~~al~~Lp~~~R~v~~L~~----~egls~~EIA~~lgis~~tVk~~l~rA~k~Lr~-----~L~~~e~g  159 (159)
T PRK12527        100 QRALAELPPICRESFLLRK----LEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRV-----RMRQWESG  159 (159)
T ss_pred             HHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH-----HHHHHHCC
T ss_conf             9999869999989998898----739799999999891999999999999999999-----99977673


No 106
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=98.26  E-value=0.00011  Score=55.84  Aligned_cols=171  Identities=18%  Similarity=0.132  Sum_probs=112.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHH
Q ss_conf             12688999999876533211246899987555789998875223567778875443679999887438545731201028
Q gi|254780289|r  422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM  501 (682)
Q Consensus       422 l~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~  501 (682)
                      .+..++-+++.+.+.|..+   |=..|+..+-+-|...+. |.+..-.-.|++||--+-..++..+|+.+.  +|+   |
T Consensus         6 ~dd~~l~aLv~~a~~GD~~---Af~~L~~~~~~~v~r~~~-~l~d~~~AeDl~QEtFlka~~~l~~f~~~s--~f~---t   76 (185)
T PRK09649          6 SDDEAVTALALSAAKGNGR---ALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSARS--SAR---T   76 (185)
T ss_pred             CCHHHHHHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHH-HHCCHHHHHHHHHHHHHHHHHHHHHCCCCC--CHH---H
T ss_conf             4609999999999944799---999999999999999999-938998999999999999999887628876--189---9


Q ss_pred             HHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             98999999999722870461420588989999999998776088999789998709998999999986089875536358
Q gi|254780289|r  502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG  581 (682)
Q Consensus       502 ~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~  581 (682)
                      |-.+=+...++.                 .+.+..        +.|..                         +.    +
T Consensus        77 WL~~IA~N~~~d-----------------~~Rk~~--------~~~~~-------------------------~~----~  102 (185)
T PRK09649         77 WLLAIARHVVAD-----------------HIRHVR--------SRPRT-------------------------TR----G  102 (185)
T ss_pred             HHHHHHHHHHHH-----------------HHHHHH--------CCCCC-------------------------CC----C
T ss_conf             999999999999-----------------999874--------37764-------------------------34----4


Q ss_pred             CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             89986047562389889989999999999999999732998899999998187986746889998996678999999999
Q gi|254780289|r  582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA  661 (682)
Q Consensus       582 ~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~  661 (682)
                      .+.+. +.+  .+......++       ...+..+|..|||..+.||.|||    -..+|++||+..+|++---|+--=.
T Consensus       103 ~~~e~-~~~--~~~~~~~~e~-------~~~l~~al~~Lp~~~R~vl~L~~----~egls~~EIA~~lg~~~gTVKsRl~  168 (185)
T PRK09649        103 ARPEH-LID--GDRHARGFED-------LVEVTTMIADLTTDQREALLLTQ----LLGLSYADAAAVCGCPVGTIRSRVA  168 (185)
T ss_pred             CCHHH-CCC--CCCCCCCHHH-------HHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             57231-158--4311023788-------99999999849999999999899----7299999999998939999999999


Q ss_pred             HHHHHHCC
Q ss_conf             99998329
Q gi|254780289|r  662 KAIRKLKH  669 (682)
Q Consensus       662 ~a~~~l~~  669 (682)
                      +|..+|+-
T Consensus       169 RAR~~L~a  176 (185)
T PRK09649        169 RARDALLA  176 (185)
T ss_pred             HHHHHHHH
T ss_conf             99999997


No 107
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=98.25  E-value=0.00013  Score=55.48  Aligned_cols=155  Identities=14%  Similarity=0.119  Sum_probs=103.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEE
Q ss_conf             12468999875557899988752235677788754436799998874385457312010289899999999972287046
Q gi|254780289|r  441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR  520 (682)
Q Consensus       441 ~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r  520 (682)
                      ...|-.+++.+.+.-+...|.++++.--.-.|++|+.-+-+.+..++|...  -.|.|   |-.+=+..+++        
T Consensus        11 ~~~~F~~l~~~~~p~L~~~a~~l~~~~~dAEDlvQetflk~~~~~~~~~~~--~~~~a---WL~~IarN~~~--------   77 (190)
T PRK12516         11 GTPPFKRELLASLPSLRAFAVSLIGQHDRADDLVQDTIMKAWAKQESFEVG--TNMKA---WLFTILRNEFY--------   77 (190)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHH---HHHHHHHHHHH--------
T ss_conf             872099999998999999999990999999999999999999998635656--77999---99999999999--------


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCH
Q ss_conf             14205889899999999987760889997899987099989999999860898755363588998604756238988998
Q gi|254780289|r  521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP  600 (682)
Q Consensus       521 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~  600 (682)
                               +.+.+.        ++...                          ..+..        +.    +..+..|
T Consensus        78 ---------d~~Rk~--------~r~~~--------------------------~~d~~--------~~----e~~~~~~  102 (190)
T PRK12516         78 ---------TQMRKR--------GREVQ--------------------------DTDGM--------FS----EQLAVHP  102 (190)
T ss_pred             ---------HHHHHC--------CCCCC--------------------------CCCCC--------CC----CCCCCCC
T ss_conf             ---------999961--------68666--------------------------53222--------33----3346895


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             999999999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       601 ~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      ...  .......+..+|..|||+.+.|+.|+|    -..+|.+||+..+|+|---|+.-=.+|.++||.
T Consensus       103 ~~~--~~~~~~~l~~al~~Lp~~~R~vl~L~~----~egls~~EIAe~Lgis~~TVksrl~RAr~~Lr~  165 (190)
T PRK12516        103 SQY--GTLDLQDFRAALDQLPDDQREAIILIG----ASGFAYEEAAEICGCAVGTIKSRVSRARARLQE  165 (190)
T ss_pred             CCC--CHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             420--207799999999819999989999899----829999999999894999999999999999999


No 108
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=98.18  E-value=0.0002  Score=53.93  Aligned_cols=186  Identities=16%  Similarity=0.211  Sum_probs=123.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHH
Q ss_conf             99998765332112468999875557899988752235677788754436799998874385457312010289899999
Q gi|254780289|r  429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI  508 (682)
Q Consensus       429 ~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i  508 (682)
                      ......+.|.   ..|-.++++..-+-+...+.+..+..-+-.|++||.-+-..++.++|+.+.     ...||-.|=+.
T Consensus        11 ~~~a~a~~GD---~~Af~~Lv~~~r~~L~~~cyRmlGs~~dAED~vQEt~lrawr~~~~f~~~~-----~~rtWL~rIat   82 (341)
T PRK08241         11 AGLAAAADGD---RDAFLALAEPHRRELLAHCYRMLGSLHDAEDLVQETLLRAWRSYDRFEGRS-----SLRTWLYRIAT   82 (341)
T ss_pred             HHHHHHHCCC---HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCC-----CCCEEEHHHHH
T ss_conf             9999997479---999999999999999999999809998999999999999985132226556-----64131019899


Q ss_pred             HHHHHHCCCEEECCCHHHHHHHHHH-HHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCE
Q ss_conf             9999722870461420588989999-999998776088999789998709998999999986089875536358899860
Q gi|254780289|r  509 TRSIADQSCTIRIPVHMRDKIHKVV-RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH  587 (682)
Q Consensus       509 ~~~~~~~~~~~r~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~  587 (682)
                      ..|+.                 .+. +..|.....+|......                          ..+.....+..
T Consensus        83 n~cLd-----------------~Lr~r~RR~~~~~l~~~~~~~--------------------------~~~~~~~~~~~  119 (341)
T PRK08241         83 NVCLD-----------------ALEGRARRPLPTGLGPPSADP--------------------------SAALVERPEVP  119 (341)
T ss_pred             HHHHH-----------------HHHHHHCCCCCCCCCCCCCCC--------------------------CCCCCCCCCCC
T ss_conf             99999-----------------998742446744456665665--------------------------44555555666


Q ss_pred             ----EEEEECCCCCCCHHHHHH-HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             ----475623898899899999-999999999997329988999999981879867468899989966789999999999
Q gi|254780289|r  588 ----LGDFIEDKNAVSPLDSAI-QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK  662 (682)
Q Consensus       588 ----~~~~~~d~~~~~~~~~~~-~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~  662 (682)
                          +-|-.-+....+|.+.+. +..++-++..+|..|+|+++.|+.||--+    .++..||+..+|+|-.=|+|.=.+
T Consensus       120 WleP~Pd~~~~~~~~dP~~~~~~rEsv~lA~laaLq~Lpp~QRavlvLRdV~----g~s~~EiAe~Lg~S~aAVks~L~R  195 (341)
T PRK08241        120 WLEPLPDALLDPAAADPAAIVVARESVRLAFVAALQHLPPRQRAVLLLRDVL----GWSAAEVAEALGTSTAAVNSALQR  195 (341)
T ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHEEEEHHHHC----CCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             5466775345667799889988877899999999983999790200129752----998899999978999999999999


Q ss_pred             HHHHHCC
Q ss_conf             9998329
Q gi|254780289|r  663 AIRKLKH  669 (682)
Q Consensus       663 a~~~l~~  669 (682)
                      |=..|+.
T Consensus       196 ARa~L~~  202 (341)
T PRK08241        196 ARATLAE  202 (341)
T ss_pred             HHHHHHH
T ss_conf             9999986


No 109
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=98.18  E-value=0.00017  Score=54.39  Aligned_cols=155  Identities=14%  Similarity=0.134  Sum_probs=104.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCC
Q ss_conf             68999875557899988752235677788754436799998874385457312010289899999999972287046142
Q gi|254780289|r  444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV  523 (682)
Q Consensus       444 AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~  523 (682)
                      +=..+.+-+-..|...+.++.+.--.-.|++|+.-+-|++. ..|...     .+..+|..+-+-..++ |+        
T Consensus        11 ~~~~Ly~~~~~~L~~~~~r~~~~~e~AEDivQd~Flrl~~~-~~~~~~-----~~~~a~Lf~iarNl~~-D~--------   75 (172)
T PRK12523         11 LVGALYRDHRGWLLAWLRRNLACRQRAEDLSQDTFVRLLGR-PELPTP-----REPRAFLAAVAKGLMF-DH--------   75 (172)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHC-CCCCCC-----CCHHHHHHHHHHHHHH-HH--------
T ss_conf             99999999999999999999498868999999999999827-765673-----4599999999999999-99--------


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHH
Q ss_conf             05889899999999987760889997899987099989999999860898755363588998604756238988998999
Q gi|254780289|r  524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS  603 (682)
Q Consensus       524 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~  603 (682)
                              +.+..++..       ..++++                                     .+.+...++|++.
T Consensus        76 --------~Rr~~~~~~-------~~~~~~-------------------------------------~~~~~~~~~~e~~  103 (172)
T PRK12523         76 --------FRRAALEQA-------YLAELA-------------------------------------LVPEAEQPSPEEQ  103 (172)
T ss_pred             --------HHHHHHHHH-------HHHHHH-------------------------------------CCCCCCCCCHHHH
T ss_conf             --------998998850-------088886-------------------------------------2665468997999


Q ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             999999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       604 ~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      .........|..+|+.|||+.+.|+.|++    -..+|..||+..+|+|---|++-=.+||+.++.
T Consensus       104 ~~~~e~~~~l~~al~~Lp~~~R~v~~L~~----~eGls~~EIA~~LgiS~~tVk~~l~rAl~~~~~  165 (172)
T PRK12523        104 HLILEDLKAIDRLLGKLSSKARAAFLYNR----LDGMGHAEIAERLGVSVSRVRQYLAQGLRQCYI  165 (172)
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             99999999999998649999999999999----939999999999893999999999999999999


No 110
>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=98.17  E-value=8.4e-05  Score=56.89  Aligned_cols=131  Identities=18%  Similarity=0.354  Sum_probs=98.4

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHH---HHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             77788754436799998874385457312010289899---999999972287046142058898999999999877608
Q gi|254780289|r  468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK---QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK  544 (682)
Q Consensus       468 ~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~---~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~  544 (682)
                      ..-.||+|+==.-.|+.++.|-+.....|+.   |-.+   .-|.-|+....|                           
T Consensus        36 ~tAEDL~s~vF~~~L~~i~~f~~~~~t~f~~---WLf~iA~N~v~Dyfr~~~r---------------------------   85 (171)
T TIGR02952        36 YTAEDLTSEVFLRVLRKIDSFKEQKNTDFEA---WLFTIARNVVADYFRKSKR---------------------------   85 (171)
T ss_pred             EEHHHHHHHHHHHHHHHHHHHCCCCCCCCHH---HHHHHHHHHHHHHHHCCCC---------------------------
T ss_conf             3114647899999973122101257877224---7899999999988511345---------------------------


Q ss_pred             CCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHH
Q ss_conf             89997899987099989999999860898755363588998604756238988998999999999999999973299889
Q gi|254780289|r  545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE  624 (682)
Q Consensus       545 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re  624 (682)
                                .+.++.+.+..++                           ...++|.+.+....--+.+..++..|+|.+
T Consensus        86 ----------~~~~~~~~~~~l~---------------------------~~e~~P~e~~~~~~~n~~L~~a~~~L~p~q  128 (171)
T TIGR02952        86 ----------RPLLSLDVVKELL---------------------------SAEPSPEEAVLKELANEKLLEAVKKLTPKQ  128 (171)
T ss_pred             ----------CCCCCHHHHHHHH---------------------------HCCCCHHHHHHHHHHHHHHHHHHHHCCHHH
T ss_conf             ----------5210099989887---------------------------348981789998888999999996108323


Q ss_pred             HHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             999999818798674688999899667899999999999998329
Q gi|254780289|r  625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       625 ~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      ++||.|||    +....-.||++.+|.+--=|.+|..+|+++|+.
T Consensus       129 q~viaLrF----~~~L~~~EvA~ilGk~~gavk~Lq~rAv~~L~r  169 (171)
T TIGR02952       129 QEVIALRF----AQNLPIAEVARILGKTEGAVKALQFRAVKKLAR  169 (171)
T ss_pred             HHHHHHHH----CCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHH
T ss_conf             12033321----168838789987268974689999999999873


No 111
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=98.14  E-value=0.00039  Score=51.63  Aligned_cols=155  Identities=14%  Similarity=0.104  Sum_probs=100.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECC
Q ss_conf             46899987555789998875223567778875443679999887438545731201028989999999997228704614
Q gi|254780289|r  443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP  522 (682)
Q Consensus       443 ~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~  522 (682)
                      .|-++.+.+-..=+...|-++++..-.-.||+||.-+-+.+..++|++.  .+|.||   -.+  |.|..+         
T Consensus         5 ~~f~~~~l~~~P~L~~fa~~l~~n~~dAEDlvQEtflk~~~~~~~~~~~--~~~~tW---L~~--IarN~~---------   68 (181)
T PRK12540          5 DSLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPG--SNLPAW---LFT--ILRNLF---------   68 (181)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHH---HHH--HHHHHH---------
T ss_conf             8899999998799999999993999999999999999999849875987--624899---999--999999---------


Q ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHH
Q ss_conf             20588989999999998776088999789998709998999999986089875536358899860475623898899899
Q gi|254780289|r  523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD  602 (682)
Q Consensus       523 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~  602 (682)
                            ++.+.+.        .+.....                                  +..+...+..  .+....
T Consensus        69 ------~~~~Rk~--------~r~~~~~----------------------------------~~~~~~~~~~--~~~~~~   98 (181)
T PRK12540         69 ------RSDYRKR--------RREVEDA----------------------------------DGSYAKTLKS--QPGQNA   98 (181)
T ss_pred             ------HHHHHHH--------CCCCCCC----------------------------------CCCCCCCCCC--CCCHHH
T ss_conf             ------9999983--------5766643----------------------------------2110001468--997356


Q ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHH
Q ss_conf             999999999999997329988999999981879867468899989966789999999999999832967
Q gi|254780289|r  603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS  671 (682)
Q Consensus       603 ~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~  671 (682)
                      ..    ..+.+..+|..||+..+.||.|+|    -..+|.+||++.+|+|---|+--=.+|.+|||---
T Consensus        99 ~~----~~~~l~~al~~Lp~~~R~vl~L~~----~egls~~EIA~iL~is~gTVKsRL~RAr~kLr~~L  159 (181)
T PRK12540         99 HL----EFEEFRAALEKLPQDQREALILVG----ASGFSYEDAAAICGCAVGTIKSRVNRARSKLSALL  159 (181)
T ss_pred             HH----HHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             77----899999999819999989988799----80999999999989499999999999999999998


No 112
>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=98.05  E-value=1.5e-05  Score=62.80  Aligned_cols=55  Identities=31%  Similarity=0.526  Sum_probs=51.2

Q ss_pred             HHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf             99999997329988999999981879867468899989966789999999999999832
Q gi|254780289|r  610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK  668 (682)
Q Consensus       610 ~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~  668 (682)
                      ++.|.++|+.|||+++.|+.|||    -..+|+.|||..+|+|...|++.-.+|+.+||
T Consensus         1 r~~l~~al~~L~~~~r~vl~l~y----~~~~s~~EIa~~lgis~~tVk~~l~rA~~~Lr   55 (55)
T cd06171           1 RERLEEALDKLPEREREVILLRF----GEGLSYEEIAEILGISRSTVRQRLHRALKKLR   55 (55)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
T ss_conf             98999999839999989899999----80999999999989599999999999998758


No 113
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=98.01  E-value=0.00036  Score=51.89  Aligned_cols=150  Identities=12%  Similarity=0.124  Sum_probs=96.8

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHH
Q ss_conf             99987555789998875223567778875443679999887438545731201028989999999997228704614205
Q gi|254780289|r  446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM  525 (682)
Q Consensus       446 ~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~  525 (682)
                      ..++. ++.=+...|.++++.--.-.|++|+.-+-+.+..++|+....     +.+|+.+-+...+|. ..|        
T Consensus         8 ~~~~~-~~P~L~rfa~~l~~d~~dAEDlvQetflk~~~~~~~~~~~~~-----~~~WL~~IarN~~id-~~R--------   72 (182)
T PRK12511          8 FDVID-QLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSGGN-----LRTWLMSILHNAFID-ELR--------   72 (182)
T ss_pred             HHHHH-HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCC-----HHHHHHHHHHHHHHH-HHH--------
T ss_conf             99999-899999999999299999999999999999999886688664-----999999999999999-998--------


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHH
Q ss_conf             88989999999998776088999789998709998999999986089875536358899860475623898899899999
Q gi|254780289|r  526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI  605 (682)
Q Consensus       526 ~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~  605 (682)
                              +..        +.                          +...+. +..         ..+.....+.+...
T Consensus        73 --------r~~--------~~--------------------------~~~~~~-~~~---------~~~~~~~~~~e~~~  100 (182)
T PRK12511         73 --------RRR--------AE--------------------------ARRADE-LVV---------EADASAPAGQEHAV  100 (182)
T ss_pred             --------HCC--------CC--------------------------CCCCCC-CCC---------CCCCCCCCCHHHHH
T ss_conf             --------433--------44--------------------------343331-012---------35556896356899


Q ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             9999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       606 ~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      .   ...+..+|..|||+.+.||.|+|    -..+|..|||+.+|+|---|+.-=.+|..+||.
T Consensus       101 ~---~~~l~~al~~Lp~~~R~vl~L~~----~egls~~EIAe~Lgis~gTVKsrl~RAr~~LR~  157 (182)
T PRK12511        101 R---LAQIRDAFFDLPEEQRAALHLVA----IEGLSYQEAANVLGIPIGTLMSRIGRARAALRA  157 (182)
T ss_pred             H---HHHHHHHHHCCCHHHHHHEEEEE----ECCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             9---99999999869998950112410----079999999999893999999999999999999


No 114
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=97.95  E-value=0.00083  Score=49.04  Aligned_cols=152  Identities=14%  Similarity=0.102  Sum_probs=98.0

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHH
Q ss_conf             99987555789998875223567778875443679999887438545731201028989999999997228704614205
Q gi|254780289|r  446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM  525 (682)
Q Consensus       446 ~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~  525 (682)
                      .+|-..+-+-++.-+.++.+.--.-.|++||--+-+...-+..+.      ..-. .|+.....+...|++|        
T Consensus        12 ~~Lf~~~y~~L~~~~~r~lg~~~~AeDivQe~Flr~~~~~~~~~~------~~~~-a~L~~iArnl~~d~~R--------   76 (168)
T PRK12525         12 GQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI------REPR-ALLTTIARRLMYEGWR--------   76 (168)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCC------CCHH-HHHHHHHHHHHHHHHH--------
T ss_conf             999999999999999999498857999999999999867774554------5889-9999999999999999--------


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHH
Q ss_conf             88989999999998776088999789998709998999999986089875536358899860475623898899899999
Q gi|254780289|r  526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI  605 (682)
Q Consensus       526 ~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~  605 (682)
                              |.....       +..+                        ++    .+         ..+...++|++.+.
T Consensus        77 --------r~~~~~-------~~~~------------------------~~----~~---------~~~~~~~~pe~~~~  104 (168)
T PRK12525         77 --------RQDLER-------AYLQ------------------------SL----AE---------APEAVQPSPEEQWM  104 (168)
T ss_pred             --------HHHHHH-------HHHH------------------------HH----HC---------CCCCCCCCHHHHHH
T ss_conf             --------999999-------8888------------------------88----51---------66656898678999


Q ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf             999999999997329988999999981879867468899989966789999999999999832
Q gi|254780289|r  606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK  668 (682)
Q Consensus       606 ~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~  668 (682)
                      .......+..+|+.|||+.+.|+.|++    -..+|..|||+.+|||.--|..-=.+||+..+
T Consensus       105 ~~e~~~~l~~al~~LP~~~R~vflL~~----~eGlsy~EIAe~LgIS~~tV~~~l~rAl~~c~  163 (168)
T PRK12525        105 VIETLLAIDRLLDGLSGKARAAFLMSQ----LEGLTYVEIGERLGVSLSRIHQYMVEAFKCCY  163 (168)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             999999999998639999999999999----92999999999989799999999999999999


No 115
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=97.94  E-value=0.0011  Score=48.17  Aligned_cols=153  Identities=14%  Similarity=0.190  Sum_probs=99.6

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHH
Q ss_conf             98755578999887522356777887544367999988743854573120102898999999999722870461420588
Q gi|254780289|r  448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD  527 (682)
Q Consensus       448 l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~  527 (682)
                      --++.=+.+.++|.+..+..-.-.|++||.-+-+.++ +++      ..+.-.+|-.|-+...|+.              
T Consensus         5 ~fe~~R~~L~~~AyRmlGs~~DAEDvvQEt~lr~~~~-~~~------~~~~~~aWL~rI~~n~~ld--------------   63 (289)
T PRK09636          5 EFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLRWNNA-DRA------EIRDPRAFLTRVVTRLCLD--------------   63 (289)
T ss_pred             HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCC-CCC------CCCCHHHHHHHHHHHHHHH--------------
T ss_conf             8998799999999998099978999999999998506-842------2347899999999999999--------------


Q ss_pred             HHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHH-HHHHH
Q ss_conf             98999999999877608899978999870999899999998608987553635889986047562389889989-99999
Q gi|254780289|r  528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL-DSAIQ  606 (682)
Q Consensus       528 ~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~-~~~~~  606 (682)
                         .+.+..+....-.|             .                -|..|+-            + ...+|. .....
T Consensus        64 ---~LR~ar~rre~~~g-------------~----------------wlpep~~------------~-~~~~p~~~~~~~   98 (289)
T PRK09636         64 ---RLRSARHRRETYVG-------------P----------------WLPEPVV------------E-DSDDPLEAVVAA   98 (289)
T ss_pred             ---HHHHHHCCCCCCCC-------------C----------------CCCCCCC------------C-CCCCCHHHHHHH
T ss_conf             ---99854016554678-------------7----------------7887667------------8-889935678877


Q ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCH
Q ss_conf             9999999999732998899999998187986746889998996678999999999999983296
Q gi|254780289|r  607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP  670 (682)
Q Consensus       607 ~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~  670 (682)
                      ..+..++..+|..|||+++.|+.||.-.    .++++||+..+|+|-.=|||+-.+|=++|+..
T Consensus        99 e~~~~al~~~L~~L~p~qRav~vLrdv~----g~s~~EIA~iLg~s~~avR~~l~RAR~~l~~~  158 (289)
T PRK09636         99 EDLSLALMLALERLSPLERAAFLLHDVF----GVPFDEIASTLGRSEAACRQLASRARKHVRAA  158 (289)
T ss_pred             HHHHHHHHHHHHHCCHHHHHHHHHHHHH----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_conf             8899999999973999896254049860----99999999998179999999999999987344


No 116
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=97.85  E-value=0.00012  Score=55.66  Aligned_cols=67  Identities=22%  Similarity=0.145  Sum_probs=46.3

Q ss_pred             HHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHC--CHHHHHH-------HHHHHHHHCCCHHHHHHHHH
Q ss_conf             9999998569768897889999999998899999998728--2389999-------99998731171036787642
Q gi|254780289|r  121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES--PLTFQAL-------IIWRDELNDGTTLLREIIDL  187 (682)
Q Consensus       121 VRMYLREMG~V~LLTREgEIeIAKRIE~G~~~i~~al~~~--P~ti~~i-------l~~~e~i~~ge~~LrdIIDl  187 (682)
                      .-.||+++...+|||+|+|+++|.|+.+|.......+..+  .+++...       +.+-|.|++|.+.|-.-|+.
T Consensus        17 l~syl~~i~~~~~Ls~eEE~~La~~~~~GD~~Ar~~LI~~NLRLVvsIAkky~~~g~~l~DLIQEGniGLi~Avek   92 (228)
T PRK05803         17 LVSYVKNNSFPQPLSEEEERKYLELMKQGDEEARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIDS   92 (228)
T ss_pred             HHHHHHCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             9999974788999999999999999984689999999998779999999627799989899999999999999998


No 117
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=97.77  E-value=0.0046  Score=43.16  Aligned_cols=155  Identities=10%  Similarity=0.080  Sum_probs=95.2

Q ss_pred             HHHHHHHHHHHHH-HHHHHHHCCCCC-CHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEEC
Q ss_conf             6899987555789-998875223567-77887544367999988743854573120102898999999999722870461
Q gi|254780289|r  444 AKKEMVEANLRLV-ISVAKKYTNRGL-QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI  521 (682)
Q Consensus       444 AK~~l~~anlr~v-~~~~~~~~~~~~-~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~  521 (682)
                      |=..|...+=.++ -.+.++..+.|- .-.||+|+--+-|.++.+...+.-.-.|   .+|--|-+ .....|+      
T Consensus        14 a~~~Ly~~h~~~L~~~l~~Rl~~~~~~~AeDl~QDvFlrl~~~~~~~~~~~i~~p---~a~L~rIA-~Nl~id~------   83 (178)
T PRK12529         14 KVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQP---RAYLARIA-NCVLVSW------   83 (178)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHH---HHHHHHHH-HHHHHHH------
T ss_conf             9999999999999999999828998354699999999999973444564323348---99999999-9999999------


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHH
Q ss_conf             42058898999999999877608899978999870999899999998608987553635889986047562389889989
Q gi|254780289|r  522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL  601 (682)
Q Consensus       522 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~  601 (682)
                                ..|......       ..+++                 .                   + +.++..++|+
T Consensus        84 ----------~Rr~~~~~~-------~le~~-----------------~-------------------~-~~~~~~pspE  109 (178)
T PRK12529         84 ----------RRRQSLELA-------WLEAL-----------------A-------------------T-LPEPLHPSPE  109 (178)
T ss_pred             ----------HHHHHHHHH-------HHHHH-----------------H-------------------C-CCCCCCCCHH
T ss_conf             ----------998888987-------89988-----------------6-------------------4-7866689989


Q ss_pred             HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             99999999999999973299889999999818798674688999899667899999999999998
Q gi|254780289|r  602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK  666 (682)
Q Consensus       602 ~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~  666 (682)
                      ..+........|..+|+.||||-+.|+.|++    -..+|..||++.+|||.--|.+-=.+||..
T Consensus       110 ~~~~~~e~l~~l~~al~~Lp~r~R~vF~L~r----~eGls~~EIAe~LgiS~~tV~~~l~rAl~~  170 (178)
T PRK12529        110 QQSVILETLHEIDALLDTLRPRVKQAFLMAT----LDGMKQKDIAQALDIALPTVKKYIHQAYVT  170 (178)
T ss_pred             HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf             9999999999999998569978889987998----829999999999895999999999999999


No 118
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=97.66  E-value=0.0049  Score=42.95  Aligned_cols=154  Identities=14%  Similarity=0.133  Sum_probs=98.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCC
Q ss_conf             68999875557899988752235677788754436799998874385457312010289899999999972287046142
Q gi|254780289|r  444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV  523 (682)
Q Consensus       444 AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~  523 (682)
                      |=.++-..+-..+...+.++.+..-.-.|++|+--+-|+..-+..+.      .+-.. |+.+...+.+.|+.|      
T Consensus        11 ~~e~ly~~~~~~L~~~~~r~~g~~~~AEDivQd~Flrl~~~~~~~~~------~~~~a-yL~~iA~n~~id~~R------   77 (167)
T PRK12528         11 TVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQI------IEPRA-FLTTIAKRVLCNHYR------   77 (167)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCC------CCHHH-HHHHHHHHHHHHHHH------
T ss_conf             99999999999999999999398857999999999999965654465------67999-999999999999999------


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHH
Q ss_conf             05889899999999987760889997899987099989999999860898755363588998604756238988998999
Q gi|254780289|r  524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS  603 (682)
Q Consensus       524 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~  603 (682)
                                +......       ..+.+                 ..                    ..+...++|++.
T Consensus        78 ----------~~~~~~~-------~~~~~-----------------~~--------------------~~~~~~~~~e~~  103 (167)
T PRK12528         78 ----------RQDLERA-------YLEAL-----------------AQ--------------------LPERVAPSEEER  103 (167)
T ss_pred             ----------HHHHHHH-------HHHHH-----------------HC--------------------CCCCCCCCHHHH
T ss_conf             ----------9998998-------99887-----------------63--------------------653246985789


Q ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf             99999999999997329988999999981879867468899989966789999999999999832
Q gi|254780289|r  604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK  668 (682)
Q Consensus       604 ~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~  668 (682)
                      +........+..+|+.|||+.+.|+.|+.    -...|..||++.+|+|-.-|+.-=.+|+....
T Consensus       104 ~~~~e~~~~l~~~l~~LP~~~R~vf~L~r----~~gls~~EIA~~LgiS~~tVk~~l~rA~~~c~  164 (167)
T PRK12528        104 AIILETLVELDRLLDGLPPLVKRAFLLAQ----VDGLGYGEIATELGISLATVKRYLNKAAMRCY  164 (167)
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             99999999999998709999999999999----82989999999979799999999999999999


No 119
>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=97.64  E-value=0.0043  Score=43.39  Aligned_cols=164  Identities=13%  Similarity=0.194  Sum_probs=122.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCC
Q ss_conf             68999875557899988752235677788754436799998874385457312010289899999999972287046142
Q gi|254780289|r  444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV  523 (682)
Q Consensus       444 AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~  523 (682)
                      |=+.|....=+-+...|.+|++..-.-.|++|+-=+.|..-=+.++...  .|.+|=.=+||..+..++..+.-      
T Consensus         2 aF~~ly~~Yy~~l~~fA~~yv~~~e~AEdIVqdvF~~lWe~r~~l~~~~--~~~~YL~~~v~N~~ln~Lr~~~~------   73 (167)
T TIGR02985         2 AFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRESLEESE--SIKAYLFTIVKNRCLNYLRHKQV------   73 (167)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCC--CCCHHHHHHHHHHHHHHHHHHHH------
T ss_conf             4889999987999999999836899999999999999973145256213--52179999999989989988999------


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHH
Q ss_conf             05889899999999987760889997899987099989999999860898755363588998604756238988998999
Q gi|254780289|r  524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS  603 (682)
Q Consensus       524 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~  603 (682)
                               ......            ++.+              .  .+..++.-+.             ....+|.+.
T Consensus        74 ---------~~~~~~------------~~~~--------------~--~~~~~~~~~~-------------~l~~~~~~~  103 (167)
T TIGR02985        74 ---------EEKYQE------------ELSE--------------I--EEDEIELRLQ-------------SLEADPEED  103 (167)
T ss_pred             ---------HHHHHH------------HHHH--------------H--HHHHHHHHHH-------------HCCCCCHHH
T ss_conf             ---------999999------------9998--------------6--5567876310-------------036897457


Q ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             999999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       604 ~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      .....|...|..+|+.|||+-|.|+.|-+    -+.+|-.|||..+|||--=|.--=.+||+.||+
T Consensus       104 ~~~~El~~~i~~~~~~LPe~~R~iF~lsr----~eg~s~~EIA~~L~iS~~TVe~hi~~ALk~LR~  165 (167)
T TIGR02985       104 IYSKELEEIIEEAIEKLPEQCREIFILSR----FEGLSNKEIAEELGISVKTVEYHITKALKFLRK  165 (167)
T ss_pred             HHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             87999999999998756898999999988----617986789988489888999999999999987


No 120
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=97.50  E-value=0.014  Score=39.31  Aligned_cols=155  Identities=19%  Similarity=0.247  Sum_probs=100.7

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHH
Q ss_conf             99875557899988752235677788754436799998874385457312010289899999999972287046142058
Q gi|254780289|r  447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR  526 (682)
Q Consensus       447 ~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~  526 (682)
                      +-.+++=+..+++|-+..+..-+-.|++||.-+-+.++-  +..     ...--+|-.|-.-..||.             
T Consensus         9 ~~fe~hR~~L~~~ayRmlGs~~dAED~VQEa~lr~~~~~--~~~-----~~~~~awL~ri~tn~cld-------------   68 (290)
T PRK09635          9 AAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAP--VGD-----IDDERGWLIVVTSRLCLD-------------   68 (290)
T ss_pred             HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCC--CCC-----CCCHHHHHHHHHHHHHHH-------------
T ss_conf             999998999999999980898789999999999997477--312-----357888999999999999-------------


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHH-HH
Q ss_conf             89899999999987760889997899987099989999999860898755363588998604756238988998999-99
Q gi|254780289|r  527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS-AI  605 (682)
Q Consensus       527 ~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~-~~  605 (682)
                          .+.+....      |+                         .|..    +|.....   +  ..+...+|.+. ..
T Consensus        69 ----~LR~~r~r------re-------------------------~~~~----~~~~~~~---~--~~~~~~dp~~~~~~  104 (290)
T PRK09635         69 ----HIKSASTR------RE-------------------------RPQD----IAAWHDG---D--ASVSSVDPADRVTL  104 (290)
T ss_pred             ----HHHHHHHC------CC-------------------------CCCC----CCCCCCC---C--CCCCCCCHHHHHHH
T ss_conf             ----98766522------67-------------------------8766----6777876---7--77888982889887


Q ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             9999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       606 ~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      ...+..++..+|..|+|+|+.|+.||--+|    ++++||+..+|.|-.=+||+=.+|=++|+.
T Consensus       105 ~~~v~~All~~Le~L~P~eRaa~vLrdvfg----~~~~EIA~~Lg~s~~a~Rqll~RAR~~l~~  164 (290)
T PRK09635        105 DDEVRLALLIMLERLGPAERVVFVLHEIFG----LPYQQIATTIGSQASTCRQLAHRARRKINE  164 (290)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHCC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHC
T ss_conf             778999999998629986854552698608----988999999689989999999999998732


No 121
>PRK06930 positive control sigma-like factor; Validated
Probab=97.45  E-value=0.0006  Score=50.11  Aligned_cols=61  Identities=18%  Similarity=0.242  Sum_probs=54.1

Q ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             99999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       605 ~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      ....-+..|.++|+.|+|||++|+.|..    ++..|..|||..+|||+--|.+.=.+|..|++.
T Consensus       100 ~se~d~~~iedALs~Lt~rErevfll~~----~~glsy~EIA~~L~Is~~tV~~~l~RA~~Ki~~  160 (170)
T PRK06930        100 ISEWDKIRIEDALSVLTEREKEVYLMHR----GYGLSYSEIAAYLNIKKSTVQSMIERAEKKIAK  160 (170)
T ss_pred             CCHHHHHHHHHHHHHCCHHHHHHHHHHH----HHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             0389998899999856988889998897----618889999999798899999999999999999


No 122
>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=97.42  E-value=0.0038  Score=43.79  Aligned_cols=143  Identities=20%  Similarity=0.342  Sum_probs=92.8

Q ss_pred             HHHHHHHHHHHHHHHHHCCCE----EECCCHHHHHHHHHHHHHHHHHHH--CCCCCCHHHHHHHCC-------CCHHHHH
Q ss_conf             102898999999999722870----461420588989999999998776--088999789998709-------9989999
Q gi|254780289|r  498 TYAMWWVKQAITRSIADQSCT----IRIPVHMRDKIHKVVRTARRMSNK--IKREPTPEEIAKKLA-------MPVEGVR  564 (682)
Q Consensus       498 tya~~~i~~~i~~~~~~~~~~----~r~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~a~~~~-------~~~~~~~  564 (682)
                      |-+.+|=.++.-|+|-.+...    +|-|.-|++-.-...|      +.  .|+.-+|.-||++.|       +.+-=+|
T Consensus        37 ~~G~p~Al~~lErhvL~k~~~~L~~~r~~~~~vdEV~Q~lR------~rLLl~~~~~ppriaeY~GrGpL~~WvR~~A~R  110 (249)
T TIGR03001        37 AQGEPAALAALERHVLSKVPARLARLRPPEAFVDEVLQRLR------QRLLLPRAEAPPRIAEYSGRGPLLSWVRIVAVR  110 (249)
T ss_pred             HHCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHH------HHCCCCCCCCCHHHHHHCCCCHHHHHHHHHHHH
T ss_conf             61228999999999998735523788998642776579977------642689888621244211652469999999999


Q ss_pred             HHHHHHC---CCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHH----HHHHHHHHHHHHCCCHHHHHHHHHHHCCCCC
Q ss_conf             9998608---98755363588998604756238988998999999----9999999999732998899999998187986
Q gi|254780289|r  565 KVLKITK---EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ----ANLRETTTRVLASLTPREERVLRMRFGIGMN  637 (682)
Q Consensus       565 ~~~~~~~---~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~----~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~  637 (682)
                      -+++..+   .....      +.++.+.++..-....+|+-...+    ..+++++.++|++||+|||..||+.|    =
T Consensus       111 ~A~~L~~~~~~~~~~------e~~~~~~~~~~~~~maDpEl~llr~~~r~~f~~Al~~Al~~L~~rER~LLRLHf----v  180 (249)
T TIGR03001       111 IALELQAQERRHSHL------EEETELAALPAPGSMADPELDLLRERYRQEFRAALREALAALSERERTLLRLHF----V  180 (249)
T ss_pred             HHHHHHHHCCCCCCC------CCCCCHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----H
T ss_conf             999987512444520------023314544068874117899999999999999999987328986876555688----2


Q ss_pred             CCCCHHHHHHHHCCCHHHH
Q ss_conf             7468899989966789999
Q gi|254780289|r  638 TDHTLEEVGKQFCVTRERI  656 (682)
Q Consensus       638 ~~~tl~e~~~~~~~~~er~  656 (682)
                      ...|+++||..|+++|-=|
T Consensus       181 ~~Ls~~r~g~my~~~~STv  199 (249)
T TIGR03001       181 EGLSMDRLGAMYQVHRSTV  199 (249)
T ss_pred             CCCCHHHHHHHHCCCCHHH
T ss_conf             0332999987745775078


No 123
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=97.41  E-value=0.0016  Score=46.85  Aligned_cols=56  Identities=23%  Similarity=0.235  Sum_probs=36.1

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHCC--HHHHHH-------HHHHHHHHCCCHHHHHHHHH
Q ss_conf             688978899999999988999999987282--389999-------99998731171036787642
Q gi|254780289|r  132 ELLSREGEIAIAKRIEAGRAMMMASLCESP--LTFQAL-------IIWRDELNDGTTLLREIIDL  187 (682)
Q Consensus       132 ~LLTREgEIeIAKRIE~G~~~i~~al~~~P--~ti~~i-------l~~~e~i~~ge~~LrdIIDl  187 (682)
                      ||||+|+|+++|+||.+|......-+..+-  +++...       +.+-|.|++|.+.|-.-|+.
T Consensus        37 p~Ls~eeE~~l~~~~~~GD~~Ar~~LI~~NLRLVv~IAkky~~~G~~l~DLIqEGniGLikAvek  101 (239)
T PRK08301         37 PPLSKEEEEVLLNKLPKGDEAVRSILIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNT  101 (239)
T ss_pred             CCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             99899999999999983469999999998789999999757689979899999858999999996


No 124
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=97.27  E-value=0.0031  Score=44.49  Aligned_cols=26  Identities=23%  Similarity=0.296  Sum_probs=22.9

Q ss_pred             CCCCCCHHHHHHHCCCCHHHHHHHHH
Q ss_conf             08899978999870999899999998
Q gi|254780289|r  543 IKREPTPEEIAKKLAMPVEGVRKVLK  568 (682)
Q Consensus       543 ~~~~~~~~~~a~~~~~~~~~~~~~~~  568 (682)
                      .|.+.|.++|++.+|+|.++||.+..
T Consensus       296 ~~~~~TLeevg~~~~vsrERvRQIE~  321 (342)
T COG0568         296 DGEPKTLEELGEEFGISRERVRQIEA  321 (342)
T ss_pred             CCCCCHHHHHHHHHCCCHHHHHHHHH
T ss_conf             99955199999895986999999999


No 125
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=97.10  E-value=0.0011  Score=48.14  Aligned_cols=229  Identities=19%  Similarity=0.234  Sum_probs=94.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHCCCHHHHHHHCCCCCCCHHHHH
Q ss_conf             9999999999998621005778878999999999999999999--------99999712535777763167768989999
Q gi|254780289|r  314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL--------LRLAQSYGIKRDVFLERHQGRELDPHWVS  385 (682)
Q Consensus       314 ~~kl~~eL~e~~~~lkl~~k~iE~L~~~l~~~~k~Ir~~Er~L--------~rl~~k~~i~R~~Fi~~f~gnEt~~~wl~  385 (682)
                      ...++.+|..+-....++...|..++..+..-..+.+..-+++        ..+|++|-----.|+.+.+  |-|.....
T Consensus       344 I~~~q~kL~~ie~~~gl~i~elK~i~r~I~~Ge~~a~~AKkeMiEANLRLVISIAKKYtNRGLqFLDLIQ--EGNiGLMk  421 (620)
T PRK05658        344 IQRLQQELEAIEEETGLTIEELKEINRQISKGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ--EGNIGLMK  421 (620)
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHH--HCCHHHHH
T ss_conf             9999999999999849799999999999999877789999999986189999999983148998789987--44079999


Q ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHH
Q ss_conf             9861355106765543456776532-233332222211268899999987653321124-----------6899987555
Q gi|254780289|r  386 YAKDFPEGEWKNFVACEVDSILKIR-NEIKSISVETGISISEFRHIVSMVRKGECEASI-----------AKKEMVEANL  453 (682)
Q Consensus       386 ~~~~~~~~~~~~~l~~~~~eI~~~q-~kL~~ie~~~gl~i~ElK~i~r~I~~ge~e~~~-----------AK~~l~~anl  453 (682)
                      .+.+.....-..|..-.-..|..+. +.|++=..-+.+|++=+-.|++-++....-.+.           .+-.|-.--.
T Consensus       422 AVdKFeyrrGyKFSTYATWWIRQAITRaIaDqaRTIRiPVHmietinkl~r~~r~l~qe~Grept~eEia~~~~~~~~kv  501 (620)
T PRK05658        422 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERLGMPEDKV  501 (620)
T ss_pred             HHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHH
T ss_conf             99862845597135779999999999999861774015188999999999999999998289999999998949899999


Q ss_pred             HHHHHHHHHHCCC----C----CCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHH
Q ss_conf             7899988752235----6----7778875443679999887438545731201028989999999997228704614205
Q gi|254780289|r  454 RLVISVAKKYTNR----G----LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM  525 (682)
Q Consensus       454 r~v~~~~~~~~~~----~----~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~  525 (682)
                      |=|..|||-=.--    |    -.|.|.|...|.--                     -+-.++...+.++.+        
T Consensus       502 r~vlki~~epiSle~pig~~~ds~lgdfied~~~~~---------------------p~~~~~~~~l~~~~~--------  552 (620)
T PRK05658        502 RKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAEL---------------------PIDAATQESLREQTT--------  552 (620)
T ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---------------------HHHHHHHHHHHHHHH--------
T ss_conf             999986489802438878888764001016899998---------------------799999999999999--------


Q ss_pred             HHHHHHH-HHHHHHHHHH----CCCCCCHHHHHHHCCCCHHHHHHH----HHHHCCCC
Q ss_conf             8898999-9999998776----088999789998709998999999----98608987
Q gi|254780289|r  526 RDKIHKV-VRTARRMSNK----IKREPTPEEIAKKLAMPVEGVRKV----LKITKEPI  574 (682)
Q Consensus       526 ~~~~~~~-~~~~~~~~~~----~~~~~~~~~~a~~~~~~~~~~~~~----~~~~~~~~  574 (682)
                       +.+..+ -|-.+-+...    .|.+.|.||+...++++.++||.+    ++-.++|.
T Consensus       553 -~vl~~Lt~rE~~vl~~RfGi~~~~~~TLeevg~~f~vtRERiRQIEakalrklrhp~  609 (620)
T PRK05658        553 -DVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS  609 (620)
T ss_pred             -HHHHCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCC
T ss_conf             -998479999999999957999999678999998829768989999999999856872


No 126
>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=96.79  E-value=0.0051  Score=42.78  Aligned_cols=53  Identities=23%  Similarity=0.424  Sum_probs=48.0

Q ss_pred             HHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf             999999732998899999998187986746889998996678999999999999983
Q gi|254780289|r  611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL  667 (682)
Q Consensus       611 ~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l  667 (682)
                      +.+.++|+.|||+.+.|+.|+|    -...|..||++.+|+|---|+..=.+|+++|
T Consensus         2 ~~l~~ai~~Lp~~~r~~~~l~~----~~~~s~~eIA~~lg~s~~tVk~~l~RA~~~L   54 (54)
T pfam08281         2 EALLRALEELPPRQREVFLLRY----LEGLSYAEIAELLGISEGTVKSRLSRARKKL   54 (54)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHH----HHCCCHHHHHHHHCCCHHHHHHHHHHHHHCC
T ss_conf             8999999859999998968799----8785999999998949999999999999719


No 127
>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=96.69  E-value=0.0013  Score=47.57  Aligned_cols=190  Identities=11%  Similarity=0.052  Sum_probs=117.2

Q ss_pred             CHHHHHH---HHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCHHHHH
Q ss_conf             2389999---9999873117103678764210135433333334333332110001110001000000001221000011
Q gi|254780289|r  161 PLTFQAL---IIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS  237 (682)
Q Consensus       161 P~ti~~i---l~~~e~i~~ge~~LrdIIDld~t~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~e~~~e~~~~~~  237 (682)
                      +++-+|+   |.+.|.|++|++.|=.-|+.|..-.++.+++++.||-.++.....+++......+++..+.-+.-....-
T Consensus        15 SIAKkY~nRGL~F~DLIQEGn~GL~KAv~KFdy~kGyKFSTYATWWIRQAITRAIADQARtIRiPVHm~ETINk~~~~~R   94 (240)
T TIGR02393        15 SIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIKAER   94 (240)
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             67666304786334367652357898877621357886551157899999999887513720110326678889999989


Q ss_pred             HHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHH
Q ss_conf             11101356666530344310002223345555644421023479876689999999999999875210120007999999
Q gi|254780289|r  238 KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL  317 (682)
Q Consensus       238 ~~~~~~~~~~~~e~e~~~~~~e~e~de~~~sla~~e~eLk~~v~e~l~~i~~~~~kl~k~~~~~~~~~~~~~~~kk~~kl  317 (682)
                      .....-..++..+.-.+..+...+.-.....++..--+|...+-+--+.--..|-+-.        ............-+
T Consensus        95 ~l~Q~~Gr~Pt~EelAe~~g~~~~Kv~~i~~~~~~PiSLe~piG~e~dS~l~DFi~D~--------~~~~P~~~~~~~~l  166 (240)
T TIGR02393        95 KLLQELGREPTDEELAERMGLPVEKVREIKKIAQEPISLETPIGEEEDSSLGDFIEDE--------SIESPEDAAAKELL  166 (240)
T ss_pred             HHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC--------CCCCHHHHHHHHHH
T ss_conf             9998728899877899870899899999998624886566677887777442652574--------44685899999999


Q ss_pred             HHHHHHHHH-HH---------------HH-HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999998-62---------------10-0577887899999999999999999999
Q gi|254780289|r  318 KEKLVKLVG-SL---------------SL-NQSRIDLLVEQLYDISKRIMHNEGELLR  358 (682)
Q Consensus       318 ~~eL~e~~~-~l---------------kl-~~k~iE~L~~~l~~~~k~Ir~~Er~L~r  358 (682)
                      .++|.+.+. .|               .. .++.+|++...+.....+||++|.+.+|
T Consensus       167 ~~~l~~vL~~~L~~rE~~Vl~~RyGL~d~~~~~TLEEVG~~f~VTRERIRQIE~KALR  224 (240)
T TIGR02393       167 REQLEEVLENTLTERERKVLRMRYGLLDGEKPKTLEEVGKEFNVTRERIRQIESKALR  224 (240)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf             9999999860178889999987438998876533788876517871145688899988


No 128
>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=96.57  E-value=0.014  Score=39.33  Aligned_cols=71  Identities=23%  Similarity=0.285  Sum_probs=58.3

Q ss_pred             CCCHHHHHH-HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHH
Q ss_conf             899899999-999999999997329988999999981879867468899989966789999999999999832967
Q gi|254780289|r  597 AVSPLDSAI-QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS  671 (682)
Q Consensus       597 ~~~~~~~~~-~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~  671 (682)
                      ..+|.+.++ ..+|.-+.--+|..|+|-||.|+.||==.+    +.++||+...|.|--=.|||-.+|=+|||.-.
T Consensus        86 ~~dP~e~~E~~eslS~A~L~lLErL~P~ERAVF~LREVF~----y~Y~EIA~~v~kS~ancRQl~~RAr~~lr~~~  157 (287)
T TIGR02957        86 SADPAESVELAESLSMAYLLLLERLSPLERAVFLLREVFD----YDYEEIASIVGKSEANCRQLVSRARRHLRAAR  157 (287)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHC----CCCHHHHHHCCCCHHHHHHHHHHHHHHHHHCC
T ss_conf             5553889988753779999987307978999999998745----88267897606895799999999999997528


No 129
>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=96.51  E-value=0.0015  Score=46.93  Aligned_cols=150  Identities=18%  Similarity=0.253  Sum_probs=101.3

Q ss_pred             HHHHHHHHHHHHHHHHHC-CCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHH
Q ss_conf             998755578999887522-3567778875443679999887438545731201028989999999997228704614205
Q gi|254780289|r  447 EMVEANLRLVISVAKKYT-NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM  525 (682)
Q Consensus       447 ~l~~anlr~v~~~~~~~~-~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~  525 (682)
                      +.+.+.-+=.+-.|.-.+ +--..-.||+|+.=+-+-.+=+++      +=.-=+--|+|+.+.+.-...||-=|+    
T Consensus        10 ~f~~~r~~~L~r~A~lLt~GD~~~AEDLvQ~Al~~~y~rW~Ri------~~~~~~~aYvR~vl~n~~~s~wRrR~~----   79 (165)
T TIGR02983        10 AFVAARYPRLLRTAYLLTAGDPHEAEDLVQEALVRTYVRWDRI------RDADAPDAYVRRVLVNLAISRWRRRRV----   79 (165)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCC------CCCCCCHHHHHHHHHHHHHHHHHHHHH----
T ss_conf             9999999999999999827887569999999999998862215------882540578999999999999998876----


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHH
Q ss_conf             88989999999998776088999789998709998999999986089875536358899860475623898899899999
Q gi|254780289|r  526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI  605 (682)
Q Consensus       526 ~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~  605 (682)
                                ..++                                       |..+         ++|..  +-.+...
T Consensus        80 ----------~~e~---------------------------------------~~~~---------~Pd~~--ga~d~~~   99 (165)
T TIGR02983        80 ----------RLEL---------------------------------------PTEE---------LPDAA--GAPDPAA   99 (165)
T ss_pred             ----------HHHC---------------------------------------CCCC---------CCCCC--CCCCCCC
T ss_conf             ----------4421---------------------------------------4668---------64888--8987531


Q ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCH
Q ss_conf             99999999999732998899999998187986746889998996678999999999999983296
Q gi|254780289|r  606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP  670 (682)
Q Consensus       606 ~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~  670 (682)
                      ...++..|.++|..||+|.+.||.|||    ..+.|=+||+..+|+|-==|+=-=.+||.+||+-
T Consensus       100 ~~~~r~~l~~AL~~LP~rQR~vvVLRY----~eDlSe~~~A~~LG~SvGTVKS~~sRal~~LR~~  160 (165)
T TIGR02983       100 DVALRAALARALRRLPARQRAVVVLRY----YEDLSEAEVAEVLGISVGTVKSRLSRALARLREL  160 (165)
T ss_pred             CHHHHHHHHHHHHHCCHHCCEEEEEEC----CCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
T ss_conf             122699999999735641236723204----5789868999881999322899899999998873


No 130
>TIGR02233 Myxo_sigma_rel Myxococcus probable DNA-binding regulatory protein.
Probab=96.50  E-value=0.0054  Score=42.61  Aligned_cols=59  Identities=20%  Similarity=0.369  Sum_probs=47.2

Q ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHH----HHHHHHHHH
Q ss_conf             999999999999997329988999999981879867468899989966789999----999999999
Q gi|254780289|r  603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI----RQIEAKAIR  665 (682)
Q Consensus       603 ~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~----rqi~~~a~~  665 (682)
                      .-.+..+++++..++++|+|||+.|||+.|    =...||+-||..||+.|-=|    -+....++.
T Consensus         8 ~~~R~~~~~al~~Ala~L~~~eR~lLRLH~----~~gLsldR~~~lY~~hrStvaR~v~~are~Ll~   70 (106)
T TIGR02233         8 EEARQHLSAALSEALAALSERERTLLRLHH----VEGLSLDRLGTLYGVHRSTVARWVAGARELLLE   70 (106)
T ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHH
T ss_conf             999999999999997528963335666776----236558999988478861699999999999999


No 131
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=96.34  E-value=0.0055  Score=42.53  Aligned_cols=62  Identities=18%  Similarity=0.191  Sum_probs=41.0

Q ss_pred             HCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHC--CHHHHHH-------HHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             569768897889999999998899999998728--2389999-------9999873117103678764210
Q gi|254780289|r  128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCES--PLTFQAL-------IIWRDELNDGTTLLREIIDLEA  189 (682)
Q Consensus       128 MG~V~LLTREgEIeIAKRIE~G~~~i~~al~~~--P~ti~~i-------l~~~e~i~~ge~~LrdIIDld~  189 (682)
                      ..+.||||+|+|+++|+|+.+|.......|..+  ++++...       +.+-|.+++|.+.|-.-++.|.
T Consensus        13 ~~k~PlLt~EEe~~L~~~~~~gD~~Ar~~LI~~nLrLV~~iA~ky~~~g~~~~DLiQeG~iGLi~AiekFD   83 (257)
T PRK08215         13 TSKLPVLKNEEMKELFRRMQNGDTSAREKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKAIDNFD   83 (257)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHC
T ss_conf             22489999999999999999388999999999878999999987658998988999987999999999709


No 132
>pfam00196 GerE Bacterial regulatory proteins, luxR family.
Probab=95.94  E-value=0.028  Score=36.96  Aligned_cols=56  Identities=29%  Similarity=0.474  Sum_probs=49.2

Q ss_pred             HHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHH
Q ss_conf             7329988999999981879867468899989966789999999999999832967778756
Q gi|254780289|r  617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR  677 (682)
Q Consensus       617 l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~  677 (682)
                      |++|+|||.+|+++-.     ..+|-.|||..+|||.--|+..-..+++||.-.+|....+
T Consensus         1 l~~LT~RE~~il~~l~-----~G~s~~eIA~~L~is~~TV~~h~~~i~~Kl~v~nr~elv~   56 (58)
T pfam00196         1 LDSLSPREREVLRLLA-----AGKSNKEIADILGISEKTVKVHRSNIMRKLNVHSRVELIR   56 (58)
T ss_pred             CCCCCHHHHHHHHHHH-----HCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHH
T ss_conf             9977999999999998-----0799999999978889999999999999809999999995


No 133
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=95.84  E-value=0.045  Score=35.35  Aligned_cols=60  Identities=20%  Similarity=0.312  Sum_probs=54.1

Q ss_pred             HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHCC
Q ss_conf             32998899999998187986746889998996678999999999999983296777875665179
Q gi|254780289|r  618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG  682 (682)
Q Consensus       618 ~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~~~~~~  682 (682)
                      ..|+|||++||++=     ...+|-.|||..+++|---|+-.-...++||.-.+|....|--.||
T Consensus       136 ~~LT~RE~eVL~li-----a~G~snkeIA~~L~IS~~TVk~h~~~i~~KL~v~~r~el~r~a~~~  195 (196)
T PRK10360        136 DPLTKRERQVAEKL-----AQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVELARRMFDG  195 (196)
T ss_pred             CCCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHCC
T ss_conf             89997999999999-----8799999999996999999999999999981999999999999706


No 134
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=95.84  E-value=0.0099  Score=40.52  Aligned_cols=62  Identities=15%  Similarity=0.081  Sum_probs=40.3

Q ss_pred             HHHHCCCCCCCHHHHHHHHHHHHH-HHHHHHHHHHHC--CHHHHHHHHH-------HHHHHCCCHHHHHHHH
Q ss_conf             998569768897889999999998-899999998728--2389999999-------9873117103678764
Q gi|254780289|r  125 LREMGSIELLSREGEIAIAKRIEA-GRAMMMASLCES--PLTFQALIIW-------RDELNDGTTLLREIID  186 (682)
Q Consensus       125 LREMG~V~LLTREgEIeIAKRIE~-G~~~i~~al~~~--P~ti~~il~~-------~e~i~~ge~~LrdIID  186 (682)
                      |+|++++|+||+|+|.+++++.-. |.......|..+  |+++.....+       -|.+++|.+.|-.-++
T Consensus         1 ~~~~~~~~~Lt~eee~~L~~~~~~~gd~~Ar~~Li~~nlrLV~~iA~~y~~~g~~~~DLiQeG~iGLi~Aie   72 (257)
T PRK08583          1 MKESSQPTKLTKEDVNQWIAEYQENQDEEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIR   72 (257)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             986768999999999999999988199999999999849999999998626898861799999999999987


No 135
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=95.77  E-value=0.029  Score=36.78  Aligned_cols=46  Identities=30%  Similarity=0.423  Sum_probs=42.4

Q ss_pred             CCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             299889999999818798674688999899667899999999999998329
Q gi|254780289|r  619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       619 ~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      -|+.|...||++|     ...+|..||+..+|.||--|--||.+|+.+++.
T Consensus         4 ~Lt~~q~~vL~lR-----~~G~tQ~eIA~~lgTSraNvs~iEk~A~eNIek   49 (139)
T PRK03975          4 FLTERQIEVLRLR-----KRGLTQQEIADILGTSRANISIIEKRARENIEK   49 (139)
T ss_pred             HHHHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             5689999999999-----828979999999773288999999999999999


No 136
>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=95.67  E-value=0.11  Score=32.20  Aligned_cols=68  Identities=21%  Similarity=0.315  Sum_probs=47.9

Q ss_pred             HHHHHHHHCCCCCCCHHHHHHHHHHH------HHHHHHHHHHHHHC-CHHHHHH---HHHHHHHHCCCHHHHHHHHHH
Q ss_conf             99999985697688978899999999------98899999998728-2389999---999987311710367876421
Q gi|254780289|r  121 VRMYLREMGSIELLSREGEIAIAKRI------EAGRAMMMASLCES-PLTFQAL---IIWRDELNDGTTLLREIIDLE  188 (682)
Q Consensus       121 VRMYLREMG~V~LLTREgEIeIAKRI------E~G~~~i~~al~~~-P~ti~~i---l~~~e~i~~ge~~LrdIIDld  188 (682)
                      .--|++.+-..|+||.|+|-.+|+|-      +|+++.|++=|=.. .++..|-   |...|.|++|++.|=--|.-|
T Consensus         3 L~~Yi~~vn~~P~L~~EEE~~LA~r~r~~~Dl~AA~~Lv~SHLRfVv~iArgY~GYGL~~aDLIQEGNIGLMkAVkRF   80 (279)
T TIGR02392         3 LDAYIRAVNRIPMLTAEEEQELAKRLREEGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRF   80 (279)
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHC
T ss_conf             788999997178999889999999865423778999874662478755320367777442443422226655334421


No 137
>PRK00118 putative DNA-binding protein; Validated
Probab=95.58  E-value=0.04  Score=35.72  Aligned_cols=47  Identities=19%  Similarity=0.359  Sum_probs=42.3

Q ss_pred             CCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             299889999999818798674688999899667899999999999998329
Q gi|254780289|r  619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       619 ~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      -|+++.+.++.+.|    ..+.+|.|||..+||||.-|...=.+|...|..
T Consensus        17 LLT~kQ~~~~~lyy----~~DlSl~EIAe~~~iSRQaV~D~ikr~~~~L~~   63 (105)
T PRK00118         17 LLTEKQRNYMELYY----LDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLED   63 (105)
T ss_pred             HCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             75599999999998----854999999899698599999999999999999


No 138
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=95.47  E-value=0.06  Score=34.33  Aligned_cols=52  Identities=13%  Similarity=0.340  Sum_probs=46.9

Q ss_pred             CCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHH
Q ss_conf             299889999999818798674688999899667899999999999998329677787
Q gi|254780289|r  619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK  675 (682)
Q Consensus       619 ~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~  675 (682)
                      .|++||++||++=     ....|-.|||..+|||..-|..-=..|.+||.-++|...
T Consensus       179 ~LT~RE~E~L~W~-----A~GKTs~EIa~IL~ISe~TV~fHl~na~~KL~a~Nr~qA  230 (240)
T PRK10188        179 NFSKREKEILKWT-----AEGKTSAEIAMILSISENTVNFHQKNMQKKFNAPNKTQI  230 (240)
T ss_pred             CCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf             8998999999999-----779999999988399999999999999999589989999


No 139
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=95.45  E-value=0.055  Score=34.66  Aligned_cols=56  Identities=34%  Similarity=0.520  Sum_probs=48.9

Q ss_pred             HHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHH
Q ss_conf             7329988999999981879867468899989966789999999999999832967778756
Q gi|254780289|r  617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR  677 (682)
Q Consensus       617 l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~  677 (682)
                      ++.|+|||.+|+.+-     ...+|-.+|+..+|+|..-|+..-.++++||.-.+|....+
T Consensus         1 l~~LT~rE~~il~~l-----~~G~s~~eIA~~L~is~~TV~~~~~~i~~Kl~v~~r~elv~   56 (58)
T smart00421        1 LASLTPREREVLRLL-----AEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVR   56 (58)
T ss_pred             CCCCCHHHHHHHHHH-----HHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHH
T ss_conf             976189999999999-----81799999998989789899999999999848999999995


No 140
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=95.44  E-value=0.065  Score=34.06  Aligned_cols=56  Identities=16%  Similarity=0.268  Sum_probs=48.9

Q ss_pred             HHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHH
Q ss_conf             7329988999999981879867468899989966789999999999999832967778756
Q gi|254780289|r  617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR  677 (682)
Q Consensus       617 l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~  677 (682)
                      +..|+|||++||++=     ...+|-.|||+.+++|..-|+..-...++||.-.+|.....
T Consensus       141 ~~~Lt~RE~eVL~ll-----~~G~snkeIA~~L~iS~~TV~~h~~~i~~KL~v~~r~el~~  196 (204)
T PRK09958        141 LDSLSKQEISVMRYI-----LDGKDNNDIAEKMFISNKTVSTYKSRLMEKLECKSLMDLYT  196 (204)
T ss_pred             CCCCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHH
T ss_conf             256899999999999-----86999999998978899999999999999848999999999


No 141
>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=95.20  E-value=0.063  Score=34.18  Aligned_cols=47  Identities=19%  Similarity=0.368  Sum_probs=41.7

Q ss_pred             CCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             299889999999818798674688999899667899999999999998329
Q gi|254780289|r  619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       619 ~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      -||++.+.++.+.|    ..+.+|.|||..+||||.-|...=.+|-..|..
T Consensus        17 LLT~KQ~~~~~lyy----~eDlSL~EIAe~~~iSRQaV~D~ikR~~~~L~~   63 (101)
T pfam04297        17 LLTDKQKNYFELYY----LDDLSLSEIAEEFNVSRQAVYDNIKRTEKMLES   63 (101)
T ss_pred             HCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             76599999999998----763989999988198599999999999999999


No 142
>PRK10403 transcriptional regulator NarP; Provisional
Probab=95.14  E-value=0.1  Score=32.54  Aligned_cols=58  Identities=22%  Similarity=0.258  Sum_probs=50.8

Q ss_pred             HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHH
Q ss_conf             329988999999981879867468899989966789999999999999832967778756651
Q gi|254780289|r  618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL  680 (682)
Q Consensus       618 ~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~~~~  680 (682)
                      ..|++||.+||++-     ...+|-.|||..+++|..-|+-.-...++||.-.+|....--|+
T Consensus       152 ~~LT~RE~eVL~ll-----a~G~snkeIA~~L~iS~~TV~~h~~~I~~KLgv~nR~ea~~~~~  209 (215)
T PRK10403        152 SVLTERELDVLHEL-----AQGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVAATILFL  209 (215)
T ss_pred             CCCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf             56899999999999-----86999999999979829999999999999868998999999999


No 143
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=94.98  E-value=0.19  Score=30.47  Aligned_cols=59  Identities=19%  Similarity=0.253  Sum_probs=49.9

Q ss_pred             HHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHH
Q ss_conf             9997329988999999981879867468899989966789999999999999832967778756
Q gi|254780289|r  614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR  677 (682)
Q Consensus       614 ~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~  677 (682)
                      ..-+..|+|||++||++=     ...+|-.|||..+++|.--|.-.-..-++||.-.+|....+
T Consensus       136 ~~~~~~LT~RE~eVL~ll-----~~G~snkeIA~~L~iS~~TV~~h~~~I~~KL~v~~~~elv~  194 (202)
T PRK09390        136 RARIASLSERERQVMDGL-----VAGLSNKVIARDLDISPRTVEVYRANVMTKMQAGSLSELVR  194 (202)
T ss_pred             HHHHCCCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHH
T ss_conf             740066998999999999-----83896899999979878899999999999968898899999


No 144
>PRK09483 response regulator; Provisional
Probab=94.97  E-value=0.11  Score=32.30  Aligned_cols=55  Identities=18%  Similarity=0.299  Sum_probs=48.7

Q ss_pred             HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHH
Q ss_conf             329988999999981879867468899989966789999999999999832967778756
Q gi|254780289|r  618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR  677 (682)
Q Consensus       618 ~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~  677 (682)
                      ..|+|||++|+++-     ...+|-.||+..+++|.--|+-.-...++||.-.+|....+
T Consensus       147 ~~LT~RE~eVl~ll-----~~G~snkeIA~~L~iS~~TV~~h~~~i~~KL~v~~r~el~~  201 (216)
T PRK09483        147 ASLSERELQIMLMI-----TKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDVELTH  201 (216)
T ss_pred             CCCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHH
T ss_conf             56899999999999-----87999999999969899999999999999809999999999


No 145
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=94.93  E-value=0.12  Score=32.05  Aligned_cols=54  Identities=24%  Similarity=0.323  Sum_probs=47.7

Q ss_pred             CCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHH
Q ss_conf             29988999999981879867468899989966789999999999999832967778756
Q gi|254780289|r  619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR  677 (682)
Q Consensus       619 ~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~  677 (682)
                      .|+|||.+||++=     ...+|-.|||..+++|.--|+-.-...++||.-.+|....+
T Consensus       150 ~LT~RE~eVL~ll-----a~G~snkeIA~~L~iS~~TV~~h~~~i~~KLgv~n~~eLv~  203 (216)
T PRK10840        150 RLSPKESEVLRLF-----AEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLN  203 (216)
T ss_pred             CCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHH
T ss_conf             9998999999999-----86999999998969899999999999999829998999999


No 146
>PRK05572 sporulation sigma factor SigF; Validated
Probab=94.89  E-value=0.031  Score=36.61  Aligned_cols=59  Identities=20%  Similarity=0.159  Sum_probs=39.3

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHC--CHHHHHHH-------HHHHHHHCCCHHHHHHHHHH
Q ss_conf             9768897889999999998899999998728--23899999-------99987311710367876421
Q gi|254780289|r  130 SIELLSREGEIAIAKRIEAGRAMMMASLCES--PLTFQALI-------IWRDELNDGTTLLREIIDLE  188 (682)
Q Consensus       130 ~V~LLTREgEIeIAKRIE~G~~~i~~al~~~--P~ti~~il-------~~~e~i~~ge~~LrdIIDld  188 (682)
                      .-|+||+|+|.++|+++.+|.......|..+  ++++...-       .+-|.+++|.+.|-.-++.|
T Consensus         8 ~~~~Ls~eee~~L~~~~~~Gd~~Ar~~Li~~nlrLV~siA~ry~~~g~~~~DLiQeG~iGLi~A~ekF   75 (251)
T PRK05572          8 KKEQLKDEENKELIKKAQDGDKEARDKLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKF   75 (251)
T ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCC
T ss_conf             68999999999999999807999999999985999999998775899998899999999999996225


No 147
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=94.82  E-value=0.11  Score=32.13  Aligned_cols=51  Identities=25%  Similarity=0.449  Sum_probs=41.7

Q ss_pred             HCCCHHHHHHHHHHHCCC---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf             329988999999981879---867468899989966789999999999999832
Q gi|254780289|r  618 ASLTPREERVLRMRFGIG---MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK  668 (682)
Q Consensus       618 ~~l~~re~~v~~~r~g~~---~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~  668 (682)
                      ..|+|||.+||+.=|-.|   ..+..||.++++.||||+-=+-|.=.+|.+||=
T Consensus       154 ~~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl~  207 (215)
T COG3413         154 NDLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLI  207 (215)
T ss_pred             CCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             469999999999999858988876589999999959988899999999999999


No 148
>PRK05949 RNA polymerase sigma factor; Validated
Probab=94.69  E-value=0.41  Score=27.78  Aligned_cols=39  Identities=36%  Similarity=0.525  Sum_probs=35.0

Q ss_pred             CCCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             345777728999999856976889788999999999889
Q gi|254780289|r  112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR  150 (682)
Q Consensus       112 ~e~~rtdDPVRMYLREMG~V~LLTREgEIeIAKRIE~G~  150 (682)
                      .....|.|||++||+|||.+||||+|+||.+|++|..+.
T Consensus        11 ~~~~~~~D~~~~YL~ei~~~pLLt~eeE~~La~~iq~~~   49 (327)
T PRK05949         11 TQPTFTADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMM   49 (327)
T ss_pred             CCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             999899881999999827866889999999999999999


No 149
>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=94.61  E-value=0.15  Score=31.10  Aligned_cols=53  Identities=28%  Similarity=0.433  Sum_probs=47.0

Q ss_pred             CCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHH
Q ss_conf             9988999999981879867468899989966789999999999999832967778756
Q gi|254780289|r  620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR  677 (682)
Q Consensus       620 l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~  677 (682)
                      |+|||.+||.+-     ...+|-.||++.+|+|..-|+-.-..+++||.-.+|.....
T Consensus         1 LT~rE~~il~~~-----~~G~s~~eIA~~L~is~~TV~~~~~~i~~Kl~~~~r~elv~   53 (57)
T cd06170           1 LTPREREVLRLL-----AEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVA   53 (57)
T ss_pred             CCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHH
T ss_conf             988999999999-----80799999999989789999999999999868999999999


No 150
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=94.53  E-value=0.44  Score=27.51  Aligned_cols=38  Identities=37%  Similarity=0.613  Sum_probs=34.5

Q ss_pred             CCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             45777728999999856976889788999999999889
Q gi|254780289|r  113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR  150 (682)
Q Consensus       113 e~~rtdDPVRMYLREMG~V~LLTREgEIeIAKRIE~G~  150 (682)
                      ....|+|||||||||+|+|||||.++||++||+|+.|.
T Consensus        69 ~~~~t~D~vr~YL~eIg~~~LLt~~eEi~La~~i~~~~  106 (385)
T PRK07406         69 KGVYTEDSIRVYLQEIGRIRLLRPDEEIELARKIADLL  106 (385)
T ss_pred             CCCCCCCCHHHHHHHCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             66888884999998627767999999999999999999


No 151
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=94.31  E-value=0.19  Score=30.32  Aligned_cols=52  Identities=21%  Similarity=0.309  Sum_probs=45.2

Q ss_pred             CCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHH
Q ss_conf             299889999999818798674688999899667899999999999998329677787
Q gi|254780289|r  619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK  675 (682)
Q Consensus       619 ~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~  675 (682)
                      .|+|||++||++-     ...+|..||+.++++|-.-|.--...+++||--.+...-
T Consensus       134 ~Lt~rE~eVl~l~-----a~G~s~~eIA~~L~~S~kTv~thr~~~m~KLgv~s~a~L  185 (205)
T PRK11475        134 MLSPTEREILRFM-----SRGYSMPQIAEQLERNIKTIRAHKFNVMSKLGVSSDAGL  185 (205)
T ss_pred             CCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHH
T ss_conf             8985899999999-----769999999999788888999999999998299987999


No 152
>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=94.19  E-value=0.51  Score=27.00  Aligned_cols=85  Identities=16%  Similarity=0.201  Sum_probs=61.3

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHH----HHHHHH-----------------HHHCCCHHHHHHHHHHHCCCCCCCCCHHHH
Q ss_conf             04756238988998999999999----999999-----------------973299889999999818798674688999
Q gi|254780289|r  587 HLGDFIEDKNAVSPLDSAIQANL----RETTTR-----------------VLASLTPREERVLRMRFGIGMNTDHTLEEV  645 (682)
Q Consensus       587 ~~~~~~~d~~~~~~~~~~~~~~~----~~~~~~-----------------~l~~l~~re~~v~~~r~g~~~~~~~tl~e~  645 (682)
                      ++--|..-....+|-....-..|    ..++.+                 .++.|+|||.+||++=     ....|-.||
T Consensus       137 cl~~f~~~~~~~~~~~~~~LelL~P~Lh~AL~rv~~l~~q~~~~~~~~~~~~glLT~RE~EVL~~v-----a~G~sn~eI  211 (247)
T TIGR03020       137 CLYSFSRSSVPLDARHAYFLELLLPYLDSALRRVLFLPNQHRTRPLGERHSAGLITAREAEILAWV-----RDGKTNEEI  211 (247)
T ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHH-----HCCCCHHHH
T ss_conf             599997158899877999999768899999998631643354555556776789998999999999-----879999999


Q ss_pred             HHHHCCCHHHHHHHHHHHHHHHCCHHHHHHH
Q ss_conf             8996678999999999999983296777875
Q gi|254780289|r  646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL  676 (682)
Q Consensus       646 ~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l  676 (682)
                      |..++||..-|+.--..+++||.-.+|....
T Consensus       212 A~~L~iS~~TVk~H~~~i~~KL~v~nR~qAV  242 (247)
T TIGR03020       212 AAILGISSLTVKNHLQHIFKKLDVRNRAQAV  242 (247)
T ss_pred             HHHHCCCHHHHHHHHHHHHHHCCCCCHHHHH
T ss_conf             9994979999999999999980999899999


No 153
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=94.19  E-value=0.25  Score=29.49  Aligned_cols=58  Identities=26%  Similarity=0.373  Sum_probs=49.8

Q ss_pred             HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHH
Q ss_conf             329988999999981879867468899989966789999999999999832967778756651
Q gi|254780289|r  618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL  680 (682)
Q Consensus       618 ~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~~~~  680 (682)
                      ..|++||..|+++--   .|  +|..||+..+++|..-|+..-..+.+||...+|...+.-+.
T Consensus         3 ~~Lt~rE~~~~~l~~---~G--~s~~eia~~l~is~~tV~~h~~~i~~Kl~~~~r~~~~~~~~   60 (65)
T COG2771           3 ADLTPREREILRLVA---QG--KSNKEIARILGISEETVKTHLRNIYRKLGVKNRVELVALAL   60 (65)
T ss_pred             CCCCHHHHHHHHHHH---CC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf             113888999999998---69--98999999987799999999999999977586999999999


No 154
>PRK10651 transcriptional regulator NarL; Provisional
Probab=94.18  E-value=0.2  Score=30.29  Aligned_cols=54  Identities=20%  Similarity=0.361  Sum_probs=47.7

Q ss_pred             HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHH
Q ss_conf             32998899999998187986746889998996678999999999999983296777875
Q gi|254780289|r  618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL  676 (682)
Q Consensus       618 ~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l  676 (682)
                      ..|+|||.+||++-     ...+|-.|||..+++|-.-|+-.-...++||.-.+|....
T Consensus       154 ~~LT~RE~eVL~ll-----~~G~snkeIA~~L~iS~~TV~~h~~~i~~KLgv~nr~ea~  207 (216)
T PRK10651        154 NQLTPRERDILKLI-----AQGLSNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAA  207 (216)
T ss_pred             CCCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHH
T ss_conf             34898999999999-----8599999999996978999999999999984899999999


No 155
>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=94.17  E-value=0.52  Score=26.96  Aligned_cols=159  Identities=19%  Similarity=0.276  Sum_probs=120.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHH
Q ss_conf             99999876533211246899987555789998875223567778875443679999887438545731201028989999
Q gi|254780289|r  428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA  507 (682)
Q Consensus       428 K~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~  507 (682)
                      ..+++++++|+.   +|-+=||.=-=+=|+++.-+|....-...|.-||.=|-=-+|+..|=-.     |.|=||--|=|
T Consensus         9 ~~Lv~RVQrG~k---~AF~lLV~KYQ~kv~~Lv~Ryv~~~~e~~DVAQe~FvkAYRAl~~FRGd-----saFYTWLyRIa   80 (192)
T TIGR02939         9 LELVERVQRGEK---QAFDLLVRKYQHKVVSLVGRYVRDSEEVEDVAQEAFVKAYRALASFRGD-----SAFYTWLYRIA   80 (192)
T ss_pred             HHHHHHHHCCCH---HHHHHHHHHHHHHHHHHHHHHHCCHHCCCCHHHHHHHHHHHHHCCCCCC-----HHHHHHHHHHH
T ss_conf             899888733223---5677788999999999998761481003401477899999751235551-----36789999999


Q ss_pred             HHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHH-HHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             99999722870461420588989999999998776088999789-99870999899999998608987553635889986
Q gi|254780289|r  508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE-IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS  586 (682)
Q Consensus       508 i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~  586 (682)
                      |.                         +++.++-..||.|.... +                        |  ..+-+..
T Consensus        81 vN-------------------------TAKNyLVaq~Rr~p~~dg~------------------------~--~edAE~F  109 (192)
T TIGR02939        81 VN-------------------------TAKNYLVAQGRRPPTSDGV------------------------E--AEDAEQF  109 (192)
T ss_pred             HH-------------------------HHHHHHHHCCCCCCCCCCC------------------------C--CHHHHCC
T ss_conf             98-------------------------8777664247988744567------------------------6--0433120


Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCC
Q ss_conf             04756238988998999999999999999973299889999999818798674688999899667
Q gi|254780289|r  587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV  651 (682)
Q Consensus       587 ~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~  651 (682)
                      .-+|-+-  +..+|+..++...|...+..+|..||+-=+.=|.||=    -...++|||++.|+-
T Consensus       110 ~~a~~Lr--~~~tPE~~ll~~el~~~v~~a~~aLPE~Lr~Ai~LRE----leGLSYe~IA~~MdC  168 (192)
T TIGR02939       110 EEADALR--DIDTPERLLLSRELEQTVNKALEALPEDLRTAITLRE----LEGLSYEDIAEIMDC  168 (192)
T ss_pred             CCCCCCC--CCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----CCCCCHHHHHHHCCC
T ss_conf             0267665--5666167999999999999998617267874544651----268787888733069


No 156
>PRK13870 transcriptional regulator TraR; Provisional
Probab=94.10  E-value=0.53  Score=26.86  Aligned_cols=51  Identities=24%  Similarity=0.318  Sum_probs=45.7

Q ss_pred             CCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHH
Q ss_conf             99889999999818798674688999899667899999999999998329677787
Q gi|254780289|r  620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK  675 (682)
Q Consensus       620 l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~  675 (682)
                      |+|||+++|+.=     ....|-.|||..+|||..-|+-.=..|.+||.-.+|...
T Consensus       174 LT~RE~E~L~W~-----A~GKT~~EIA~ILgISe~TV~fHl~na~~KL~a~nr~qA  224 (234)
T PRK13870        174 LDPKEATYLRWI-----AVGMTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHL  224 (234)
T ss_pred             CCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf             997999999999-----789989999999798899999999999999589989999


No 157
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=94.03  E-value=0.24  Score=29.53  Aligned_cols=54  Identities=22%  Similarity=0.253  Sum_probs=47.6

Q ss_pred             CCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHH
Q ss_conf             29988999999981879867468899989966789999999999999832967778756
Q gi|254780289|r  619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR  677 (682)
Q Consensus       619 ~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~  677 (682)
                      .|+|||.+|+++-     ...+|-.|||..+++|.--|+-.-...++||.-.+|....+
T Consensus       149 ~Lt~RE~eVL~ll-----~~G~snkeIA~~L~iS~~TV~~h~~~I~~KL~v~nr~elv~  202 (210)
T PRK09935        149 PLSNREVTVLRYL-----ANGLSNKEIAEQLLLSNKTISAHKSNIYGKLGLHSIVELID  202 (210)
T ss_pred             CCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHH
T ss_conf             9998999999999-----86999999998949889999999999999819999999999


No 158
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=93.96  E-value=0.47  Score=27.29  Aligned_cols=37  Identities=41%  Similarity=0.636  Sum_probs=33.6

Q ss_pred             CCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             7777289999998569768897889999999998899
Q gi|254780289|r  115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA  151 (682)
Q Consensus       115 ~rtdDPVRMYLREMG~V~LLTREgEIeIAKRIE~G~~  151 (682)
                      ..++|||++||+|+|.+||||+|+|+.+|++|+.|..
T Consensus         5 ~~~~d~~~~Yl~ei~~~~LLt~eeE~~la~~i~~~~~   41 (318)
T PRK07405          5 KTATDLVRTYLREIGRVPLLTHEEEILYGKQVQRLMA   41 (318)
T ss_pred             CCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             7898759999998177679999999999999999988


No 159
>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=93.90  E-value=0.58  Score=26.59  Aligned_cols=53  Identities=17%  Similarity=0.235  Sum_probs=46.7

Q ss_pred             HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHH
Q ss_conf             3299889999999818798674688999899667899999999999998329677787
Q gi|254780289|r  618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK  675 (682)
Q Consensus       618 ~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~  675 (682)
                      ..|+|||++||++=     ...+|--|||..+|||..-|+..=..|.+||.-.+|...
T Consensus       170 ~~LT~RE~E~L~w~-----A~Gkt~~eIa~iL~iSe~TV~~hl~~a~~KLga~nr~qA  222 (232)
T TIGR03541       170 GVLSEREREVLAWT-----ALGRRQADIAAILGISERTVENHLRSARRKLGVATTAQA  222 (232)
T ss_pred             CCCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf             99898999999999-----879999999999698999999999999998489999999


No 160
>pfam04967 HTH_10 HTH DNA binding domain.
Probab=93.67  E-value=0.28  Score=29.05  Aligned_cols=48  Identities=25%  Similarity=0.484  Sum_probs=37.0

Q ss_pred             CCHHHHHHHHHHHCCC---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf             9988999999981879---86746889998996678999999999999983
Q gi|254780289|r  620 LTPREERVLRMRFGIG---MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL  667 (682)
Q Consensus       620 l~~re~~v~~~r~g~~---~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l  667 (682)
                      |++|+++||..=|-.|   ..+..|+.||+..||||+--+-..=.+|.+|+
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 161
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=93.04  E-value=0.46  Score=27.34  Aligned_cols=56  Identities=23%  Similarity=0.363  Sum_probs=48.8

Q ss_pred             HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHHH
Q ss_conf             3299889999999818798674688999899667899999999999998329677787566
Q gi|254780289|r  618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS  678 (682)
Q Consensus       618 ~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~~  678 (682)
                      ..|+|||..|+++-     ...+|-.|||.++++|---|+-.-...++||.-.+|.....-
T Consensus       147 ~~LT~RE~eVl~ll-----a~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~v~~Rtea~~~  202 (211)
T COG2197         147 ELLTPRELEVLRLL-----AEGLSNKEIAEELNLSEKTVKTHVSNILRKLGVRNRTEAAIR  202 (211)
T ss_pred             CCCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHH
T ss_conf             78998999999999-----879988999999787898999999999998399989999999


No 162
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=92.92  E-value=0.8  Score=25.46  Aligned_cols=68  Identities=21%  Similarity=0.304  Sum_probs=54.0

Q ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHH
Q ss_conf             9999999997329988999999981879867468899989966789999999999999832967778756651
Q gi|254780289|r  608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL  680 (682)
Q Consensus       608 ~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~~~~  680 (682)
                      .....+...|++|+|||++|+..=-     ..++=-+|+..+|+|---|--..+..++|++.-+-+..++-++
T Consensus       131 ~~~~~~~~~l~tLT~RERqVl~~vV-----~G~~NKqIA~dLgiS~rTVe~HRanvM~Km~a~SlaeLvr~a~  198 (202)
T COG4566         131 DRQAAIRARLATLTPRERQVLDLVV-----RGLMNKQIAFDLGISERTVELHRANVMEKMQARSLAELVRMAL  198 (202)
T ss_pred             HHHHHHHHHHHHCCHHHHHHHHHHH-----CCCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHH
T ss_conf             7899999999866988999999998-----3763089999839866459999999999973331999999998


No 163
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family.
Probab=92.81  E-value=0.6  Score=26.42  Aligned_cols=29  Identities=45%  Similarity=0.861  Sum_probs=28.5

Q ss_pred             CHHHHHHHHHCCCCCCCHHHHHHHHHHHH
Q ss_conf             28999999856976889788999999999
Q gi|254780289|r  119 DPVRMYLREMGSIELLSREGEIAIAKRIE  147 (682)
Q Consensus       119 DPVRMYLREMG~V~LLTREgEIeIAKRIE  147 (682)
                      |+||.||+|||.|||||.|+||++|++|-
T Consensus         1 D~Vr~YL~eIGRvPLLt~eEEI~LArqVQ   29 (336)
T TIGR02997         1 DLVRLYLQEIGRVPLLTPEEEIELARQVQ   29 (336)
T ss_pred             CCCHHHHHHCCCCCCCCHHHHHHHHHHHH
T ss_conf             92004445056678987688999989999


No 164
>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=92.74  E-value=0.2  Score=30.24  Aligned_cols=45  Identities=29%  Similarity=0.473  Sum_probs=41.7

Q ss_pred             CCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             99889999999818798674688999899667899999999999998329
Q gi|254780289|r  620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       620 l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      |+++...||.||     ....+=+|||+.++-||.=|--||.+|+.+..-
T Consensus         7 LTe~Q~kVL~lR-----~kGl~Q~eIAk~LkTtRaNvS~iEkrA~EnIeK   51 (142)
T TIGR00721         7 LTERQIKVLELR-----EKGLKQKEIAKILKTTRANVSIIEKRALENIEK   51 (142)
T ss_pred             CHHHHHHHHHHH-----HCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHH
T ss_conf             406568999986-----338887889877267201378988874432377


No 165
>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=92.42  E-value=0.92  Score=24.98  Aligned_cols=135  Identities=19%  Similarity=0.252  Sum_probs=77.1

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             67778875443679999887438545731201028989999999997228704614205889899999999987760889
Q gi|254780289|r  467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE  546 (682)
Q Consensus       467 ~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~  546 (682)
                      --+-.|++||.++-++.-.+.|++..+|      ..|.++     ||               .|++..    .....||.
T Consensus        25 ~~dadDv~QEt~v~~~~k~~~f~~~~~F------~aWa~~-----iA---------------rn~vl~----~~r~~~R~   74 (163)
T TIGR02989        25 RDDADDVLQETFVTAWRKFDEFDPGTDF------GAWARG-----IA---------------RNKVLN----HRRKLGRD   74 (163)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHCCCCCC------HHHHHH-----HH---------------HHHHHH----HHHHCCCC
T ss_conf             5658889999999998607751789897------678999-----99---------------999999----98730244


Q ss_pred             CCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHH
Q ss_conf             99789998709998999999986089875536358899860475623898899899999999999999997329988999
Q gi|254780289|r  547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER  626 (682)
Q Consensus       547 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~  626 (682)
                      +..      +..--+++-..|..     .++.+.-.+.                     .+.-..+|..=|..||++.+.
T Consensus        75 ~~~------l~~f~D~l~e~lA~-----~~~~~~~~~~---------------------~~~~~~AL~~C~~~L~~~~R~  122 (163)
T TIGR02989        75 RER------LVVFDDELLEALAA-----ELEEAEEADR---------------------SEDELQALEGCLEKLPERQRE  122 (163)
T ss_pred             CHH------HHHHHHHHHHHHHH-----HHHHHHCCCC---------------------CHHHHHHHHHHHHHCCHHHHH
T ss_conf             127------77625999999999-----8755522788---------------------178999999878635978899


Q ss_pred             HHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf             99998187986746889998996678999999999999983
Q gi|254780289|r  627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL  667 (682)
Q Consensus       627 v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l  667 (682)
                      +|.+||+=    ..+++.|+.+.|.|-..|+|-=.+.-..|
T Consensus       123 Ll~~rY~~----G~~~~~~A~~~g~~~~A~~~~L~R~R~~L  159 (163)
T TIGR02989       123 LLQLRYQR----GVSLEALAEQLGRTVNAVYKALSRLRVRL  159 (163)
T ss_pred             HHHHHHCC----CCCHHHHHHHHCCHHHHHHHHHHHHHHHH
T ss_conf             99998227----97878999884713899999999999997


No 166
>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=91.97  E-value=0.62  Score=26.32  Aligned_cols=77  Identities=18%  Similarity=0.210  Sum_probs=59.6

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             04756238988998999999999999999973299889999999818798674688999899667899999999999998
Q gi|254780289|r  587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK  666 (682)
Q Consensus       587 ~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~  666 (682)
                      .+|++--=++...|+.........+.+...|+.||+--|.||.||.    -.+.+..||+..+|+|--.|--.==+|=+.
T Consensus        81 ~~~~~~~l~~~~~pE~~~~~K~~~e~~~~~l~~Lpe~yr~vl~Lr~----~~efSYkEia~~~n~sl~~vK~~LfRaR~e  156 (162)
T TIGR02950        81 LIGELELLDPVESPEHELLIKEELEELTKHLSSLPENYRTVLLLRE----FKEFSYKEIAELLNLSLAKVKSELFRARKE  156 (162)
T ss_pred             HHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf             2000131276441089999999999999998527087656567543----126688899998456022100444487799


Q ss_pred             H
Q ss_conf             3
Q gi|254780289|r  667 L  667 (682)
Q Consensus       667 l  667 (682)
                      |
T Consensus       157 L  157 (162)
T TIGR02950       157 L  157 (162)
T ss_pred             H
T ss_conf             9


No 167
>TIGR02895 spore_sigI RNA polymerase sigma-I factor; InterPro: IPR014244   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 transcription factor Sigma-I. This protein is found in endospore-forming species in the Firmicutes lineage of bacteria, such as Bacillus subtilis, but is not universally present among such species. Sigma-I was shown to be induced by heat shock  in B. subtilis and is suggested by its phylogenetic profile to be connected to the program of sporulation .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=91.22  E-value=0.69  Score=25.99  Aligned_cols=77  Identities=17%  Similarity=0.236  Sum_probs=66.6

Q ss_pred             HHH-HHHHHHHHHHHHHHHHHHHCCCCC--CHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCE
Q ss_conf             246-899987555789998875223567--77887544367999988743854573120102898999999999722870
Q gi|254780289|r  442 SIA-KKEMVEANLRLVISVAKKYTNRGL--QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT  518 (682)
Q Consensus       442 ~~A-K~~l~~anlr~v~~~~~~~~~~~~--~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~  518 (682)
                      ..+ +.+||+-.=.|.++++-+.|+|=+  .-.|=.+-|-+.+=-||++|++.+|-.|-.+|.--|+--+--++..+.++
T Consensus         8 ~~~l~e~LI~~Y~PFI~k~vs~~~~ryId~~~DDE~SIGL~AFnEAI~sY~~~KG~sFL~FA~l~IkRr~IDy~R~n~k~   87 (225)
T TIGR02895         8 NEELREELIRQYKPFIAKLVSSVCKRYIDTKEDDELSIGLIAFNEAIESYDLNKGKSFLSFAKLIIKRRVIDYIRKNQKY   87 (225)
T ss_pred             CHHHHHHHHHHHCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             06899999885146899999998633068888832558899999899873143562169999998899988888741112


No 168
>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=90.64  E-value=1.4  Score=23.64  Aligned_cols=155  Identities=23%  Similarity=0.287  Sum_probs=92.7

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHH-HHHHHHHHHC
Q ss_conf             356777887544367999988743854573120102898999999999722870461420588989999-9999987760
Q gi|254780289|r  465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV-RTARRMSNKI  543 (682)
Q Consensus       465 ~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~-~~~~~~~~~~  543 (682)
                      |.-.+-.|||||--+===++-++||-+-|+|     +|--|=|-.-|+                 +-+. |..+...-+.
T Consensus        27 GS~~eAeDlVQeTllrAW~~~~~FeGrSS~R-----~WLYrIATN~CL-----------------~~L~~R~~r~~~~~~   84 (329)
T TIGR02960        27 GSLHEAEDLVQETLLRAWRAREKFEGRSSLR-----AWLYRIATNACL-----------------DALKARRRRARPLEL   84 (329)
T ss_pred             CCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC-----HHHHHHHHHHHH-----------------HHHHCCCCCCCCCCC
T ss_conf             6521144678999999731003315776630-----678898999999-----------------987423224653347


Q ss_pred             CCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHH-HHHHHHHHHHHHHCCCH
Q ss_conf             88999789998709998999999986089875536358899860475623898899899999-99999999999732998
Q gi|254780289|r  544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI-QANLRETTTRVLASLTP  622 (682)
Q Consensus       544 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~-~~~~~~~~~~~l~~l~~  622 (682)
                      +-.|+++--|+            +....+.-=|+ |.   -|..|-+  .++.+..|+..+. +++.+-+-.-+|.-|||
T Consensus        85 ~~rp~~~~~Aa------------~~~~~e~~WLe-P~---Pd~~L~~--~~p~aa~P~~~~~~~EsvrLAF~AAlQ~LpP  146 (329)
T TIGR02960        85 SARPSAEGRAA------------LSLAAEVTWLE-PL---PDVELDL--VLPAAADPEAAAVARESVRLAFVAALQLLPP  146 (329)
T ss_pred             CCCCCCCCCCC------------CCCCCCCCCCC-CC---CCCCCCC--CCCCCCCHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             78747887744------------20367887667-88---6021752--3688887112332114689999999874881


Q ss_pred             HHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             89999999818798674688999899667899999999999
Q gi|254780289|r  623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA  663 (682)
Q Consensus       623 re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a  663 (682)
                      |.|.||.||=-+|    ..=.||++-+|-|--=|.=.=.+|
T Consensus       147 rQRAvL~LRdvlG----w~A~E~A~~L~~s~ASVnSaLQRA  183 (329)
T TIGR02960       147 RQRAVLLLRDVLG----WKAAEVAELLGTSVASVNSALQRA  183 (329)
T ss_pred             HHHHHHHHHHHHC----CCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             4578999898835----555689987438326786588887


No 169
>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=90.40  E-value=1.4  Score=23.49  Aligned_cols=162  Identities=19%  Similarity=0.259  Sum_probs=110.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHH
Q ss_conf             99876533211246899987555789998875223567778875443679999887438545731201028989999999
Q gi|254780289|r  431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR  510 (682)
Q Consensus       431 ~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~  510 (682)
                      +++--+|.   ..|=..||+.|==-...+|=.|++.--+-+|.|||...==-.+++|-   +.-+|  +-||-+|==|..
T Consensus         7 v~~a~~Gn---~~aF~~Li~~~ke~LYk~Af~Yvkne~DALd~i~EtvyKAY~sI~kL---k~~~Y--F~TW~trILIn~   78 (173)
T TIGR02954         7 VKKAIRGN---KEAFESLIKKNKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIEKL---KHPEY--FNTWLTRILINE   78 (173)
T ss_pred             HHHHHHCC---HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHH---CCCCC--CHHHHHHHHHHH
T ss_conf             99987249---34789999984366857665440673405899999999999989983---36100--025678999999


Q ss_pred             HHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEE
Q ss_conf             99722870461420588989999999998776088999789998709998999999986089875536358899860475
Q gi|254780289|r  511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD  590 (682)
Q Consensus       511 ~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~  590 (682)
                      ||.              .++|                                      -+.-|-++.+....+.     
T Consensus        79 ci~--------------lL~K--------------------------------------~kk~i~~~~~~~~~~~-----  101 (173)
T TIGR02954        79 CID--------------LLKK--------------------------------------KKKVILFDKNTKIEKK-----  101 (173)
T ss_pred             HHH--------------HHHC--------------------------------------CCCEEECCCCCCHHHH-----
T ss_conf             999--------------9843--------------------------------------8975306887101223-----


Q ss_pred             EECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             6238988998999999999999999973299889999999818798674688999899667899999999999998329
Q gi|254780289|r  591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       591 ~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                          ....+-.+.++.    ..|-.||.+|.+.++.+|.|||    -.+.|-.||++.|+.+--=|---=.||+.+||.
T Consensus       102 ----~~~~~~~~~lef----~dLy~Ai~~L~~~~~t~IIL~Y----y~DL~I~eIa~vM~~P~gTvKtyl~Ra~~~lk~  168 (173)
T TIGR02954       102 ----ECEVDADERLEF----EDLYKAIDTLNDKYKTAIILRY----YHDLKIKEIAEVMNKPEGTVKTYLRRAKKKLKK  168 (173)
T ss_pred             ----HCCCCHHHHHCH----HHHHHHHHHHHHHHHHHHHHHH----CCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHH
T ss_conf             ----216686886258----6899999731145440264332----179984259985168985178999999999888


No 170
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=90.10  E-value=1.5  Score=23.43  Aligned_cols=54  Identities=15%  Similarity=0.292  Sum_probs=46.9

Q ss_pred             CCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHH
Q ss_conf             29988999999981879867468899989966789999999999999832967778756
Q gi|254780289|r  619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR  677 (682)
Q Consensus       619 ~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~  677 (682)
                      .|++||++||++=     ....|=.||++.+.||---|+-.-..-++||.--+|.....
T Consensus       155 ~LT~RE~eIL~ll-----a~G~sNkEIA~~L~iSe~TVk~H~~~I~~KL~v~~R~qav~  208 (216)
T PRK10100        155 LLTHREKEILNKL-----RIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAVS  208 (216)
T ss_pred             CCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHH
T ss_conf             9998999999999-----87999999998949889899999999999809999999999


No 171
>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=88.68  E-value=1.9  Score=22.56  Aligned_cols=161  Identities=20%  Similarity=0.298  Sum_probs=88.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HCCCCCC----------HHHHHHHHHHHHHHHHHHCCC
Q ss_conf             8999999876533211246899987555789998875-----2235677----------788754436799998874385
Q gi|254780289|r  426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK-----YTNRGLQ----------FLDLIQEGNIGLMKAAEKFDW  490 (682)
Q Consensus       426 ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~-----~~~~~~~----------~~~~~~~~~~~l~~a~~~~~~  490 (682)
                      .+.+|....+.|...+.   ++|...----.-.||.+     -.|.+|+          --+||.|.-+=|+...+.=.+
T Consensus         3 ~vt~ll~~~~~Gd~~A~---~~L~~~~Y~~LR~~A~~~~~~~~~~~~Lq~~~~~~ci~stT~LV~EAylrL~~t~~~~~~   79 (194)
T TIGR02999         3 PVTELLQQWQNGDQAAR---DQLFPALYQELRRIARRELRRERSGQTLQVEVLAVCIDSTTALVHEAYLRLVDTQDEQEW   79 (194)
T ss_pred             HHHHHHHHHHCCCHHHH---HHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCHHHHHHHHHHHHHCCCCHHHH
T ss_conf             59999998836458899---999999999999999999985103665204467751046678899876642123202322


Q ss_pred             C-CCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             4-573120102898999999999722870461420588989999999998776088999789998709998999999986
Q gi|254780289|r  491 C-LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI  569 (682)
Q Consensus       491 ~-~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  569 (682)
                      . |++=|+.=|     +++.|=+-||+|                   ++..++-|                        -
T Consensus        80 ~~r~HF~~~AA-----~aMRrIL~D~AR-------------------~~~~~KRG------------------------g  111 (194)
T TIGR02999        80 SDRRHFFAAAA-----KAMRRILVDHAR-------------------RRRAQKRG------------------------G  111 (194)
T ss_pred             CCHHHHHHHHH-----HHHHHHHHHHHH-------------------HHHHHCCC------------------------C
T ss_conf             25088999999-----999999999999-------------------99874136------------------------7


Q ss_pred             HCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHH
Q ss_conf             08987553635889986047562389889989999999999999999732998899999998187986746889998996
Q gi|254780289|r  570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF  649 (682)
Q Consensus       570 ~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~  649 (682)
                      ...-++|    ++..        +   ...|+....-..| +..-.-|+...||-.+|+.|||  -+|  +|.+|||..+
T Consensus       112 ~~~~~~l----~~~~--------~---~~~~~~~~~L~~L-d~aL~~L~~~~Pr~a~~veLr~--F~G--l~~~E~A~~L  171 (194)
T TIGR02999       112 GAVRVSL----DEVL--------P---DAEADADEELLDL-DDALDKLAQVDPRQAEVVELRF--FAG--LTVEEIAELL  171 (194)
T ss_pred             CCCCCCC----CCCC--------C---CCCCCCHHHHHHH-HHHHHHHHHCCHHHHHHHHHHH--HCC--CCHHHHHHHH
T ss_conf             7633552----0000--------1---3577740359999-9999877400678899885311--048--8989999986


Q ss_pred             CCCHHHHH
Q ss_conf             67899999
Q gi|254780289|r  650 CVTRERIR  657 (682)
Q Consensus       650 ~~~~er~r  657 (682)
                      +||.-=|.
T Consensus       172 ~~S~~Tv~  179 (194)
T TIGR02999       172 GVSVRTVE  179 (194)
T ss_pred             CCCHHHHH
T ss_conf             88887899


No 172
>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=87.98  E-value=1.7  Score=22.80  Aligned_cols=37  Identities=19%  Similarity=0.279  Sum_probs=18.4

Q ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHCCC-CHHHHHHHH
Q ss_conf             9999999987760889997899987099-989999999
Q gi|254780289|r  531 KVVRTARRMSNKIKREPTPEEIAKKLAM-PVEGVRKVL  567 (682)
Q Consensus       531 ~~~~~~~~~~~~~~~~~~~~~~a~~~~~-~~~~~~~~~  567 (682)
                      ++...-+.+..++|..||..||++.+|+ |..-|...+
T Consensus        10 ~il~~I~~~~~~~G~~Pt~rEI~~~~g~~S~s~v~~~l   47 (65)
T pfam01726        10 EVLDFIKASIEETGYPPSRREIAQALGLRSPNAAEEHL   47 (65)
T ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHHCCCCHHHHHHHH
T ss_conf             99999999999828898799999993899809999999


No 173
>PRK12423 LexA repressor; Provisional
Probab=87.57  E-value=1  Score=24.66  Aligned_cols=41  Identities=20%  Similarity=0.223  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCC-CHHHHHHHH
Q ss_conf             89899999999987760889997899987099-989999999
Q gi|254780289|r  527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAM-PVEGVRKVL  567 (682)
Q Consensus       527 ~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~-~~~~~~~~~  567 (682)
                      ..-.++...-+++..++|..||..|||+.+|+ |..-|..-+
T Consensus         6 ~kQ~~iL~fI~~~~~~~G~~Pt~rEI~~~~g~~S~~~v~~hl   47 (202)
T PRK12423          6 PKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHV   47 (202)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCHHHHHHH
T ss_conf             999999999999999629898899999982999867899999


No 174
>PRK04841 transcriptional regulator MalT; Provisional
Probab=87.53  E-value=2.2  Score=22.05  Aligned_cols=54  Identities=22%  Similarity=0.258  Sum_probs=47.1

Q ss_pred             CCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHH
Q ss_conf             29988999999981879867468899989966789999999999999832967778756
Q gi|254780289|r  619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR  677 (682)
Q Consensus       619 ~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~  677 (682)
                      .|++||.+||++=     ....|=.||+..++||-.-|.-.=..-.+||.-.+|...+.
T Consensus       838 ~LT~RE~eVL~lL-----a~GlSNkeIA~~L~IS~~TVK~HlrnIy~KLgV~sR~~AV~  891 (903)
T PRK04841        838 PLTQREWQVLGLI-----YSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEAVQ  891 (903)
T ss_pred             CCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHH
T ss_conf             9799999999999-----76899999998819987699999999985659998999999


No 175
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=86.54  E-value=0.49  Score=27.14  Aligned_cols=12  Identities=25%  Similarity=0.733  Sum_probs=5.1

Q ss_pred             CCCCCCCCCCCC
Q ss_conf             987553635889
Q gi|254780289|r  572 EPISLETPIGDE  583 (682)
Q Consensus       572 ~~~sl~~~~~~~  583 (682)
                      .|||...|-|++
T Consensus        66 spv~i~v~aGe~   77 (143)
T COG1356          66 SPVSITVKAGED   77 (143)
T ss_pred             CCEEEEECCCCC
T ss_conf             975898558884


No 176
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=86.27  E-value=0.33  Score=28.49  Aligned_cols=41  Identities=15%  Similarity=0.422  Sum_probs=34.3

Q ss_pred             HHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHH
Q ss_conf             999997329988999999981879867468899989966789999
Q gi|254780289|r  612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI  656 (682)
Q Consensus       612 ~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~  656 (682)
                      ...++++.|||++++|+-|+|    -....--|||+.+.+||.-|
T Consensus       100 eF~DLISiL~~~QKkIIYmKF----f~~~kdieIak~L~ISRQsV  140 (142)
T TIGR03209       100 EFNDLISILPNKQKKIIYMKF----FEDMKEIDIAKKLHISRQSV  140 (142)
T ss_pred             HHHHHHHHCCCCHHEEEHHHH----HHHHHHHHHHHHHCCHHHHH
T ss_conf             298899857940010115899----87777857999953028751


No 177
>PRK00215 LexA repressor; Validated
Probab=85.71  E-value=2.4  Score=21.76  Aligned_cols=41  Identities=20%  Similarity=0.306  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCHHHHHHHCCC-CHHHHHHHHH
Q ss_conf             9899999999987760889997899987099-9899999998
Q gi|254780289|r  528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAM-PVEGVRKVLK  568 (682)
Q Consensus       528 ~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~-~~~~~~~~~~  568 (682)
                      ...++..--+++..++|+.||..|||+.+|+ |..-|...++
T Consensus         5 kQ~~il~fI~~~~~~~g~~Ps~rEI~~~~g~~S~~tV~~~l~   46 (204)
T PRK00215          5 RQQEILDFIKDRIEETGYPPSRREIADALGLRSPSAVHEHLK   46 (204)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHH
T ss_conf             999999999999997488998999999809998189999999


No 178
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=84.17  E-value=2.6  Score=21.42  Aligned_cols=36  Identities=28%  Similarity=0.492  Sum_probs=21.6

Q ss_pred             CCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             9988999999981879867468899989966789999999
Q gi|254780289|r  620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI  659 (682)
Q Consensus       620 l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi  659 (682)
                      |+.+....+.+.|    .-+.+|.||+..|+|||.-|-+-
T Consensus        18 LT~KQ~~Y~~lyy----~dDlSl~EIAee~~VSRqAIyDn   53 (105)
T COG2739          18 LTKKQKNYLELYY----LDDLSLSEIAEEFNVSRQAIYDN   53 (105)
T ss_pred             HHHHHHHHHHHHH----HHHCCHHHHHHHHCCCHHHHHHH
T ss_conf             8688999999999----81166999999957509999999


No 179
>PRK10869 recombination and repair protein; Provisional
Probab=84.01  E-value=3.1  Score=20.80  Aligned_cols=109  Identities=10%  Similarity=0.181  Sum_probs=52.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCCCCCCHHHHHHHHHCCC
Q ss_conf             99999999999998621005778878999999999999999999999997125357777631677689899999861355
Q gi|254780289|r  313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPE  392 (682)
Q Consensus       313 k~~kl~~eL~e~~~~lkl~~k~iE~L~~~l~~~~k~Ir~~Er~L~rl~~k~~i~R~~Fi~~f~gnEt~~~wl~~~~~~~~  392 (682)
                      ...++...|......+.+.|.+++.+-+.+.           .|.++++|++++-++.+..+..                
T Consensus       276 ~l~e~~~~L~~~~~~le~Dp~~Le~ie~RL~-----------~i~~L~RKyg~~~eeLl~~~~~----------------  328 (553)
T PRK10869        276 QIQEASDELRHYLDRLDLDPNRLFELEQRLS-----------KQISLARKHHVSPEELPQHHQS----------------  328 (553)
T ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHH-----------HHHHHHHHHCCCHHHHHHHHHH----------------
T ss_conf             9999999999998735688476899999999-----------9999998839999999999999----------------


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             10676554345677653223333222221126889999998765332112468999875557
Q gi|254780289|r  393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR  454 (682)
Q Consensus       393 ~~~~~~l~~~~~eI~~~q~kL~~ie~~~gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr  454 (682)
                            +......+......+..++.+......++......++..++++-..=.+-|...|.
T Consensus       329 ------l~~eL~~l~~~~~~l~~L~~~~~~~~~~~~~~A~~Ls~~R~~aA~~L~~~I~~~L~  384 (553)
T PRK10869        329 ------LLEEQQQLDDQEDKLETLALAVEKHHQQALETARKLHQSRQRYAKELAKLITQSMH  384 (553)
T ss_pred             ------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             ------99999863087999999999999999999999999999999999999999999986


No 180
>pfam02650 HTH_WhiA Sporulation Regulator WhiA C terminal domain. This domain is found at the C terminal of the sporulation regulator WhiA. It is predicted to form a DNA binding helix-turn-helix structure. WhiA is a distant homologue of LAGLIDADG homing endonucleases.
Probab=82.23  E-value=3.1  Score=20.81  Aligned_cols=42  Identities=29%  Similarity=0.579  Sum_probs=33.3

Q ss_pred             HHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHC--CCHH----HHHHHHH
Q ss_conf             7329988999999981879867468899989966--7899----9999999
Q gi|254780289|r  617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC--VTRE----RIRQIEA  661 (682)
Q Consensus       617 l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~--~~~e----r~rqi~~  661 (682)
                      +..||+..+.+..+|.   ...+.||.|+|+.+.  ||+-    |.|.|+.
T Consensus       141 l~~Lp~~l~~~a~lRl---~~Pd~SL~ELgell~p~isKSgvnhRlrKi~~  188 (191)
T pfam02650       141 LDNLPEKLREIAQLRL---ENPDASLKELGELLDPPITKSGVNHRLRKLEK  188 (191)
T ss_pred             CCCCCHHHHHHHHHHH---HCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHH
T ss_conf             1219999999999999---69656799999883799788999899999998


No 181
>COG1809 (2R)-phospho-3-sulfolactate synthase (PSL synthase, CoM    biosynthesis) [Coenzyme transport and metabolism]
Probab=82.06  E-value=3.1  Score=20.81  Aligned_cols=24  Identities=17%  Similarity=0.332  Sum_probs=18.6

Q ss_pred             CCCCHHHHHHHHHHHHHCCCEEEC
Q ss_conf             359988899999999847977832
Q gi|254780289|r   56 DEVSSEQMEDTVAMLSNMGINVVD   79 (682)
Q Consensus        56 d~~~~e~ie~i~~~L~~~GI~Vve   79 (682)
                      ...+.|++..-+++..+.||.|+-
T Consensus        55 ~Li~kd~V~ekid~y~e~~i~v~p   78 (258)
T COG1809          55 SLIDKDQVKEKIDMYKENDIYVFP   78 (258)
T ss_pred             CCCCHHHHHHHHHHHHHCCCEECC
T ss_conf             466289999999999975935657


No 182
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=81.76  E-value=3.7  Score=20.18  Aligned_cols=13  Identities=23%  Similarity=0.401  Sum_probs=6.1

Q ss_pred             HHHHHHHHHHHHC
Q ss_conf             8899999999847
Q gi|254780289|r   61 EQMEDTVAMLSNM   73 (682)
Q Consensus        61 e~ie~i~~~L~~~   73 (682)
                      .-+.||+..+...
T Consensus       147 Aa~~Di~~~~~~R  159 (443)
T PRK00286        147 AAIRDILTVLSRR  159 (443)
T ss_pred             HHHHHHHHHHHCC
T ss_conf             8999999998504


No 183
>PRK09954 hypothetical protein; Provisional
Probab=80.39  E-value=4.1  Score=19.84  Aligned_cols=43  Identities=16%  Similarity=0.288  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHHCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHCCC
Q ss_conf             9999999787848867899975268435998889999999984797
Q gi|254780289|r   30 SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGI   75 (682)
Q Consensus        30 ~ik~LI~~gke~GylTydeIn~~LP~d~~~~e~ie~i~~~L~~~GI   75 (682)
                      .=|+++++=|+..|++..||-+.|.   .+-.-+=.-++-|..-|+
T Consensus         4 re~~il~~i~~~p~i~q~ela~~lg---isrs~va~hi~~l~~kg~   46 (362)
T PRK09954          4 REKEILAILRRNPLIQQNEIADILQ---ISRSRVAAHIMDLMRKGR   46 (362)
T ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHC---CCHHHHHHHHHHHHHCCE
T ss_conf             8999999998789958999999979---879999999998875476


No 184
>PRK13239 alkylmercury lyase; Provisional
Probab=79.79  E-value=4.1  Score=19.83  Aligned_cols=28  Identities=36%  Similarity=0.406  Sum_probs=25.9

Q ss_pred             CCCCCCHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf             0889997899987099989999999860
Q gi|254780289|r  543 IKREPTPEEIAKKLAMPVEGVRKVLKIT  570 (682)
Q Consensus       543 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~  570 (682)
                      .|++.|++.||+.+|+|+++|+.+|...
T Consensus        33 ~G~PVs~~~LA~~~g~~~e~v~~~L~~~   60 (206)
T PRK13239         33 KGRPVSRETLAGALGWPVEEVAAVLEQA   60 (206)
T ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHHHC
T ss_conf             6999999999988699999999999857


No 185
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=79.62  E-value=4.3  Score=19.66  Aligned_cols=46  Identities=26%  Similarity=0.415  Sum_probs=26.1

Q ss_pred             CCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHH
Q ss_conf             998999999986089875536358899860475623898899899999
Q gi|254780289|r  558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI  605 (682)
Q Consensus       558 ~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~  605 (682)
                      ...+.|..+.-.++-||  =.-||-+-|.++.||++|--+++|..+++
T Consensus       212 FNdE~vaRAi~~s~iPv--ISAVGHEtD~tL~DfVAD~RApTPTaAAE  257 (440)
T COG1570         212 FNDEIVARAIAASRIPV--ISAVGHETDFTLADFVADLRAPTPTAAAE  257 (440)
T ss_pred             CCHHHHHHHHHHCCCCE--EEECCCCCCCCHHHHHHHCCCCCCHHHHH
T ss_conf             58099999998079985--84066677752877643134799668788


No 186
>PRK09191 two-component response regulator; Provisional
Probab=79.50  E-value=4.4  Score=19.63  Aligned_cols=124  Identities=14%  Similarity=0.103  Sum_probs=62.7

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCC--HH
Q ss_conf             9875557899988752235677788754436799998874385457312010289899999999972287046142--05
Q gi|254780289|r  448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HM  525 (682)
Q Consensus       448 l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~--~~  525 (682)
                      -|-.||.++---|+--+|.--.=..+++.---.|+-.-+.|+...+-|..-|..+   +.|-....-+.....-|.  ..
T Consensus         6 ~ia~~LPyLRRYARALTGsQ~~GD~yV~a~LEallad~~~~~~~~~~Rv~Ly~~f---~~iw~s~~~~~~~~~~~~~~~~   82 (261)
T PRK09191          6 RIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEASSPRVGLYRLF---HRIWSSAGANDPEPESPFEARA   82 (261)
T ss_pred             HHHHHCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCHHCCCCCCHHHHHHHHH---HHHHHHCCCCCCCCCCCCHHHH
T ss_conf             8887583999999986178201899999999999809220267775589999999---9999725999888876300689


Q ss_pred             HHHHHHHHHHHHHHHH-HCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCC
Q ss_conf             8898999999999877-608899978999870999899999998608987
Q gi|254780289|r  526 RDKIHKVVRTARRMSN-KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI  574 (682)
Q Consensus       526 ~~~~~~~~~~~~~~~~-~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  574 (682)
                      ...+.++....|+.+- -.=-.=+.+|+|+.||++.+++...+..++.-+
T Consensus        83 ~~~L~~ltp~~RqAlLL~alEgFs~~eaA~Il~v~~~e~~~l~~~A~~ei  132 (261)
T PRK09191         83 ERRLSAITPLPRQAFLLTALEGFSEEEAAEILGVDPAEVAALLDDASREI  132 (261)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             99987489303499998988289889999997899999999999999999


No 187
>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=77.68  E-value=4.9  Score=19.24  Aligned_cols=55  Identities=22%  Similarity=0.301  Sum_probs=45.3

Q ss_pred             HHHHHHHHHHCC-CHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf             999999997329-98899999998187986746889998996678999999999999983
Q gi|254780289|r  609 LRETTTRVLASL-TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL  667 (682)
Q Consensus       609 ~~~~~~~~l~~l-~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l  667 (682)
                      -+..+.++++.| +|-++.||+|.|    -...+.-+|+..++.||.-+--+-.+|++-|
T Consensus        44 ~r~El~rlI~~l~np~~RtvL~m~Y----id~~~~~~v~e~l~~Sr~Tyyr~~r~Ai~~L   99 (100)
T pfam07374        44 RKLELGRLIDKLENPDSRTILRMVY----IDKMTVWQVCDKLNCSRTTYYRKLRVAIKEL   99 (100)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHEEEE----ECCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
T ss_conf             9999999998457802213111434----4347499999997666678999999999852


No 188
>pfam04963 Sigma54_CBD Sigma-54 factor, core binding domain. This domain makes a direct interaction with the core RNA polymerase, to form an enhancer dependent holoenzyme. The centre of this domain contains a very weak similarity to a helix-turn-helix motif which may represent the other DNA binding domain.
Probab=76.78  E-value=5.2  Score=19.06  Aligned_cols=129  Identities=16%  Similarity=0.194  Sum_probs=59.9

Q ss_pred             HHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHH---HCCC-CCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             99999972287046142058898999999999877---6088-9997899987099989999999860898755363588
Q gi|254780289|r  507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN---KIKR-EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD  582 (682)
Q Consensus       507 ~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~---~~~~-~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~  582 (682)
                      +...++..|-+...++-..       ..++..+..   +.|. .-+.++||..++++.++|..+++..+   +|| |.|=
T Consensus        16 sL~e~L~~Ql~~~~l~~~e-------~~ia~~iI~~LD~~GyL~~~~~eia~~~~~~~~~ie~~l~~iQ---~le-P~GI   84 (195)
T pfam04963        16 SLRDHLLEQLELAPFSDAD-------RLIALALIDALDDTGYLQASLEEIAESLGVELDEVEAVLAVLQ---QFD-PAGV   84 (195)
T ss_pred             CHHHHHHHHHCCCCCCHHH-------HHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH---CCC-CCCC
T ss_conf             9999999998146999999-------9999999962697776387999999880878999999999997---489-9823


Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             99860475623898899899999999999999997329988999999981879867468899989966789999999999
Q gi|254780289|r  583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK  662 (682)
Q Consensus       583 ~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~  662 (682)
                      .             +.+     ...+|.-++... ..-.+--..|+.-.|..-  ..+.+..|.+.+|+|.+.|+..-..
T Consensus        85 g-------------Arn-----L~EcL~lQL~~~-~~~~~~a~~ii~~~le~l--~~~~~~~i~k~l~~s~~~i~~a~~~  143 (195)
T pfam04963        85 G-------------ARD-----LSECLLLQLRQL-DRWLDPAMEALVDHLELL--ARRDFATLKRICGVDEEDLREMIEE  143 (195)
T ss_pred             C-------------CCC-----HHHHHHHHHHHC-CCCHHHHHHHHHHHHHHH--HCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             5-------------088-----999999998652-865689999999889998--5268999999969199999999999


Q ss_pred             HHHHHC
Q ss_conf             999832
Q gi|254780289|r  663 AIRKLK  668 (682)
Q Consensus       663 a~~~l~  668 (682)
                       +++|.
T Consensus       144 -I~~Ln  148 (195)
T pfam04963       144 -IRSLN  148 (195)
T ss_pred             -HHHCC
T ss_conf             -99679


No 189
>PRK13558 bacterio-opsin activator; Provisional
Probab=76.28  E-value=5.3  Score=18.97  Aligned_cols=55  Identities=15%  Similarity=0.108  Sum_probs=44.9

Q ss_pred             HHHHHHCCCHHHHHHHHHHHCC---CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf             9999732998899999998187---986746889998996678999999999999983
Q gi|254780289|r  613 TTRVLASLTPREERVLRMRFGI---GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL  667 (682)
Q Consensus       613 ~~~~l~~l~~re~~v~~~r~g~---~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l  667 (682)
                      ...+...|++|.+.+|+.=|==   .-.++.|=+||+..+|||+--.-|.=.+|-+||
T Consensus       610 ~~aL~e~LTDRQ~eaLqtAY~sGyFEwPR~sTGeElAesLgIS~pTfhqHLRaaerKL  667 (674)
T PRK13558        610 REELRNDLTDRQLTALQKAYVSGYFEWPRRAEGKQLAESMDIVPSTYHQHLQAAKQKL  667 (674)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHH
T ss_conf             9999876049899999999864757788778789999870988388999999999999


No 190
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=74.42  E-value=5.9  Score=18.62  Aligned_cols=39  Identities=23%  Similarity=0.307  Sum_probs=29.7

Q ss_pred             HHHHHHHH-C-CCCCCHHHHHHHCCCCHHHHHHHHHHHCCC
Q ss_conf             99998776-0-889997899987099989999999860898
Q gi|254780289|r  535 TARRMSNK-I-KREPTPEEIAKKLAMPVEGVRKVLKITKEP  573 (682)
Q Consensus       535 ~~~~~~~~-~-~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  573 (682)
                      .+++-+|+ + --.-|.++||+.|+++..++.+++.+.++|
T Consensus        10 ~Tk~elqan~el~~LS~~~iA~~Ln~t~~~lekil~~tqr~   50 (97)
T COG4367          10 RTKQELQANFELCPLSDEEIATALNWTEVKLEKILQVTQRP   50 (97)
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHCC
T ss_conf             88999997544064529999999588799999999885064


No 191
>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=73.17  E-value=2.7  Score=21.26  Aligned_cols=41  Identities=29%  Similarity=0.430  Sum_probs=21.6

Q ss_pred             HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             329988999999981879867468899989966789999999999
Q gi|254780289|r  618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK  662 (682)
Q Consensus       618 ~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~  662 (682)
                      ...+|..-.|=.+|--||.    |...+|.++||++.||-+||.-
T Consensus        21 ~~~~P~~GWvR~~R~ALGm----s~~QLA~RlGV~p~Rv~~~E~~   61 (150)
T TIGR02612        21 ALKTPKKGWVRAIRKALGM----SGAQLAARLGVTPQRVEAIEKS   61 (150)
T ss_pred             CCCCCCCCCHHHHHHHHCC----CHHHHHHHCCCCHHHHHHHHHH
T ss_conf             5387688616889877251----5788766528973779998888


No 192
>PRK09247 ATP-dependent DNA ligase; Validated
Probab=73.15  E-value=3.8  Score=20.12  Aligned_cols=27  Identities=26%  Similarity=0.342  Sum_probs=13.1

Q ss_pred             HHHHHHHHHHCCCCCCCCCHHHHHHHH
Q ss_conf             899999998187986746889998996
Q gi|254780289|r  623 REERVLRMRFGIGMNTDHTLEEVGKQF  649 (682)
Q Consensus       623 re~~v~~~r~g~~~~~~~tl~e~~~~~  649 (682)
                      |=-+|+|.|.--.-..--|+++|-+.|
T Consensus       507 RFPR~~r~R~DK~~~ea~t~~~~~~l~  533 (537)
T PRK09247        507 RFPRILRWRWDKPAAEADRLETLQALL  533 (537)
T ss_pred             ECCCEEEECCCCCHHHCCCHHHHHHHH
T ss_conf             747210452999936683999999999


No 193
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=72.26  E-value=5.2  Score=19.06  Aligned_cols=38  Identities=26%  Similarity=0.288  Sum_probs=17.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             68899999987653321124689998755578999887522
Q gi|254780289|r  424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT  464 (682)
Q Consensus       424 i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~  464 (682)
                      +.+-..|...|..+..+.-   .+++..+++.+.+...++.
T Consensus       185 ~~eH~~il~ai~~~d~~~A---~~~m~~Hl~~~~~~~~~~~  222 (230)
T COG1802         185 IDEHRAILEALEARDAEAA---AEAMRQHLRRARSRLLEAL  222 (230)
T ss_pred             HHHHHHHHHHHHCCCHHHH---HHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999993999999---9999999999999999985


No 194
>pfam05263 DUF722 Protein of unknown function (DUF722). This family contains several bacteriophage proteins of unknown function.
Probab=71.50  E-value=6.8  Score=18.13  Aligned_cols=51  Identities=18%  Similarity=0.343  Sum_probs=40.2

Q ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             99999999973299889999999818798674688999899667899999999
Q gi|254780289|r  608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE  660 (682)
Q Consensus       608 ~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~  660 (682)
                      ..++.+.....+|.+-+++||.+|||  .....|--.|+..++|+--.++-+.
T Consensus        70 ~qk~~id~~~~~~~~~~k~ii~lrY~--~r~~~sW~~Va~~l~i~er~~~~~~  120 (130)
T pfam05263        70 RQKEILDNFYKVLTEEEKRIIELRYK--GRNGMTWYQVAQELDISEKKAKRIY  120 (130)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHC--CCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             99999999999851899999999867--6467549999999651199999999


No 195
>KOG0996 consensus
Probab=71.09  E-value=6.9  Score=18.06  Aligned_cols=54  Identities=13%  Similarity=0.314  Sum_probs=33.6

Q ss_pred             CCHHHHHHHHHHHHHCCCC-------CHHHHH-------HHCCCCCCC------------------HHHHHHHHHHHHHC
Q ss_conf             0289999999978784886-------789997-------526843599------------------88899999999847
Q gi|254780289|r   26 FSDDSWKKMIKLARQRGYV-------TIEELN-------AFLPPDEVS------------------SEQMEDTVAMLSNM   73 (682)
Q Consensus        26 ~~~~~ik~LI~~gke~Gyl-------TydeIn-------~~LP~d~~~------------------~e~ie~i~~~L~~~   73 (682)
                      ++..++-.||..+-..+-+       +|..|.       +.+|+..|.                  +...-+|...|...
T Consensus       139 iR~~klS~LIh~S~~~~~l~SCsV~vhFq~iiD~~~~~~E~vp~s~~~ItRtA~~~NsSkY~Ingk~as~~~V~~lLk~~  218 (1293)
T KOG0996         139 IRSKKLSALIHKSDGHPNLQSCSVEVHFQKIIDKPGGTYEVVPDSEFTITRTAFRDNSSKYYINGKEASFKDVTKLLKSH  218 (1293)
T ss_pred             HHHHHHHHHHHCCCCCCCCCCEEEEEEEEEEECCCCCCEEECCCCEEEEEEHHHHCCCCEEEECCCCCCHHHHHHHHHHC
T ss_conf             76778999883447899876304887643323168986221379705897435407873276778504299999999866


Q ss_pred             CCEEEC
Q ss_conf             977832
Q gi|254780289|r   74 GINVVD   79 (682)
Q Consensus        74 GI~Vve   79 (682)
                      ||++-.
T Consensus       219 gIDleH  224 (1293)
T KOG0996         219 GIDLEH  224 (1293)
T ss_pred             CCCCCC
T ss_conf             978766


No 196
>PRK13869 plasmid-partitioning protein RepA; Provisional
Probab=71.02  E-value=7  Score=18.05  Aligned_cols=13  Identities=15%  Similarity=0.312  Sum_probs=5.9

Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             7887544367999
Q gi|254780289|r  470 FLDLIQEGNIGLM  482 (682)
Q Consensus       470 ~~~~~~~~~~~l~  482 (682)
                      +.||=..||+..+
T Consensus       155 lIDLDPQgnlS~~  167 (405)
T PRK13869        155 AVDLDPQASLSAL  167 (405)
T ss_pred             EEECCHHHHHHHH
T ss_conf             9964561788898


No 197
>COG1481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=70.77  E-value=7  Score=18.01  Aligned_cols=45  Identities=24%  Similarity=0.409  Sum_probs=34.7

Q ss_pred             HHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCC--CHH----HHHHHHHHHH
Q ss_conf             73299889999999818798674688999899667--899----9999999999
Q gi|254780289|r  617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV--TRE----RIRQIEAKAI  664 (682)
Q Consensus       617 l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~--~~e----r~rqi~~~a~  664 (682)
                      |..||++.+++..+|-   ..++.||+|+|+.+..  |+-    |.|.|..-|-
T Consensus       251 l~~lpe~l~e~a~LRl---~hpd~SLeeLg~~l~~~iSKSGvnHrlrkl~kia~  301 (308)
T COG1481         251 LEKLPEKLREAALLRL---EHPDASLEELGELLEPPISKSGVNHRLRKLKKIAE  301 (308)
T ss_pred             HHHCCHHHHHHHHHHH---CCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHH
T ss_conf             3117988999999973---38051099999985584368888889999999999


No 198
>pfam02601 Exonuc_VII_L Exonuclease VII, large subunit. This family consist of exonuclease VII, large subunit EC:3.1.11.6 This enzyme catalyses exonucleolytic cleavage in either 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. This exonuclease VII enzyme is composed of one large subunit and 4 small ones.
Probab=70.09  E-value=7.3  Score=17.91  Aligned_cols=45  Identities=16%  Similarity=0.277  Sum_probs=18.4

Q ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHC
Q ss_conf             999999997878488678999752684359988899999999847
Q gi|254780289|r   29 DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNM   73 (682)
Q Consensus        29 ~~ik~LI~~gke~GylTydeIn~~LP~d~~~~e~ie~i~~~L~~~   73 (682)
                      ..++..+..-+++++...=.|.-+.-++.-.+..|=..+..++.+
T Consensus        26 Aa~~Di~~~~~~r~p~~~i~l~p~~VQG~~a~~~I~~ai~~~~~~   70 (295)
T pfam02601        26 AAYQDFLRTARRRGPLVEIEIYPTLVQGDGAAESIVSALERANER   70 (295)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHC
T ss_conf             899999999998199967999473576504899999999999846


No 199
>cd04981 IgV_H Immunoglobulin (Ig) heavy chain (H), variable (V) domain. IgV_H: Immunoglobulin (Ig) heavy chain (H), variable (V) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determine the type of immunoglobulin: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which can associate with any of the heavy chains. This family includes alpha, gamma, delta, epsilon, and mu heavy chains.
Probab=68.95  E-value=0.31  Score=28.70  Aligned_cols=21  Identities=33%  Similarity=0.851  Sum_probs=17.6

Q ss_pred             CCCEEEHHHHHHHHHHHHHHH
Q ss_conf             573120102898999999999
Q gi|254780289|r  492 LGYKFSTYAMWWVKQAITRSI  512 (682)
Q Consensus       492 ~g~~f~tya~~~i~~~i~~~~  512 (682)
                      .||-|++|+..||||+=-+.+
T Consensus        22 SGftf~~y~m~WVRQaPGkgL   42 (117)
T cd04981          22 SGFTFTSYGVNWVRQAPGKGL   42 (117)
T ss_pred             CCCCHHHCEEEEEEECCCCCE
T ss_conf             066966691689985899982


No 200
>TIGR02168 SMC_prok_B chromosome segregation protein SMC; InterPro: IPR011890   The SMC (structural maintenance of chromosomes) family of proteins, exist in virtually all organisms including both bacteria and archaea. The SMC proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms and form three types of heterodimer (SMC1SMC3, SMC2SMC4, SMC5SMC6), which are core components of large multiprotein complexes. The best known complexes are cohesin, which is responsible for sister-chromatid cohesion, and condensin, which is required for full chromosome condensation in mitosis.     SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and share a five-domain structure, with globular N- and C-terminal (IPR003395 from INTERPRO) domains separated by a long (circa 100 nm or 900 residues) coiled coil segment in the centre of which is a globular ''hinge'' domain, characterised by a set of four highly conserved glycine residues that are typical of flexible regions in a protein. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif (XXXXD, where X is any hydrophobic residue), and a LSGG motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases .    All SMC proteins appear to form dimers, either forming homodimers with themselves, as in the case of prokaryotic SMC proteins, or heterodimers between different but related SMC proteins. The dimers are arranged in an antiparallel alignment. This orientation brings the N- and C-terminal globular domains (from either different or identical protamers) together, which unites an ATP binding site (Walker A motif) within the N-terminal domain with a Walker B motif (DA box) within the C-terminal domain, to form a potentially functional ATPase. Protein interaction and microscopy data suggest that SMC dimers form a ring-like structure which might embrace DNA molecules. Non-SMC subunits associate with the SMC amino- and carboxy-terminal domains. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences.   SMCs share not only sequence similarity but also structural similarity with ABC proteins. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression . The smc gene is often associated with scpB (IPR005234 from INTERPRO) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle , , .; GO: 0005515 protein binding, 0005524 ATP binding, 0005694 chromosome.
Probab=68.56  E-value=7.8  Score=17.68  Aligned_cols=28  Identities=18%  Similarity=0.298  Sum_probs=9.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999998765332112468999875557
Q gi|254780289|r  427 FRHIVSMVRKGECEASIAKKEMVEANLR  454 (682)
Q Consensus       427 lK~i~r~I~~ge~e~~~AK~~l~~anlr  454 (682)
                      +..+-.++...+.....|+.++-+++=|
T Consensus       468 l~~~~~~~~~~~~~~~~~~~~l~~~~~r  495 (1191)
T TIGR02168       468 LEELREELEEAEQALDAAKRELAQLQAR  495 (1191)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999999999999999


No 201
>cd00228 eu-GS Eukaryotic Glutathione Synthetase (eu-GS); catalyses the production of glutathione from gamma-glutamylcysteine and glycine in an ATP-dependent manner. Belongs to the ATP-grasp superfamily.
Probab=67.05  E-value=5.4  Score=18.94  Aligned_cols=128  Identities=16%  Similarity=0.235  Sum_probs=70.1

Q ss_pred             HHHHCCCCCCCEEEHH---HHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCH
Q ss_conf             8874385457312010---2898999999999722870461420588989999999998776088999789998709998
Q gi|254780289|r  484 AAEKFDWCLGYKFSTY---AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV  560 (682)
Q Consensus       484 a~~~~~~~~g~~f~ty---a~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~  560 (682)
                      .|.-.=+|-||-.+-|   +.|=.|-     .-.+++.|+||.-..+     .-.+++..|.+-.   |.-|...+ -..
T Consensus       257 eVavVYfRaGY~P~dY~se~~W~aRl-----~lE~S~AIKcPsi~~q-----LaGtKKVQQ~La~---p~vLerFl-~~~  322 (471)
T cd00228         257 EVAVVYFRAGYTPDDYPSESEWEARL-----LMERSSAIKCPSISTQ-----LAGTKKIQQELAE---PGVLERFL-PNP  322 (471)
T ss_pred             EEEEEEECCCCCCCCCCCHHHHHHHH-----HHHHCCCCCCCCHHHH-----HHCCHHHHHHHCC---HHHHHHHC-CCH
T ss_conf             99999973777802389878889999-----9986377148899998-----6242999998668---30998870-899


Q ss_pred             HHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHH--------HHHHHHHHHHHHHCCCH---HHHHHHH
Q ss_conf             999999986089875536358899860475623898899899999--------99999999999732998---8999999
Q gi|254780289|r  561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI--------QANLRETTTRVLASLTP---REERVLR  629 (682)
Q Consensus       561 ~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~--------~~~~~~~~~~~l~~l~~---re~~v~~  629 (682)
                      +++..+.+....-.|||..  +.++.....-     ..+|+..+.        ...-.+.|...|..|++   |.+-||.
T Consensus       323 ~~~~~lr~tFa~ly~Ld~~--~~g~~~~~~A-----~~~P~~yVLKPQREGGGNNiyg~dI~~~L~~l~~~ee~~ayILM  395 (471)
T cd00228         323 EEVAKLRATFAGLYSLDDT--EEGDEIVRKA-----LEKPELFVLKPQREGGGNNIYGEEMREALLKLQGSEERAAYILM  395 (471)
T ss_pred             HHHHHHHHHHHCCCCCCCC--CCHHHHHHHH-----HHCHHHEEECCCCCCCCCCHHHHHHHHHHHHCCCHHHHCCEEEE
T ss_conf             9999999973114047874--0128999998-----83913125647465760001108999999856982441530165


Q ss_pred             HHH
Q ss_conf             981
Q gi|254780289|r  630 MRF  632 (682)
Q Consensus       630 ~r~  632 (682)
                      -|.
T Consensus       396 erI  398 (471)
T cd00228         396 EKI  398 (471)
T ss_pred             ECC
T ss_conf             145


No 202
>PRK11414 putative DNA-binding transcriptional regulator; Provisional
Probab=66.64  E-value=7.9  Score=17.63  Aligned_cols=16  Identities=13%  Similarity=0.347  Sum_probs=7.5

Q ss_pred             HHHHHHHHHHHHHHHH
Q ss_conf             9998755578999887
Q gi|254780289|r  446 KEMVEANLRLVISVAK  461 (682)
Q Consensus       446 ~~l~~anlr~v~~~~~  461 (682)
                      ..++++|..+=..|+.
T Consensus       129 ~~~~~~d~~FH~~i~~  144 (221)
T PRK11414        129 EQIINANRLFRLAIYH  144 (221)
T ss_pred             HHHHHHHHHHHHHHHH
T ss_conf             9999999999999998


No 203
>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=65.23  E-value=8.9  Score=17.20  Aligned_cols=35  Identities=20%  Similarity=0.378  Sum_probs=23.5

Q ss_pred             CCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHH
Q ss_conf             299889999999818798674688999899667899999
Q gi|254780289|r  619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR  657 (682)
Q Consensus       619 ~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~r  657 (682)
                      .|++-...-++-++  ..|  .|..+|+..|||||.-|-
T Consensus         5 ~lt~~q~~~ar~l~--~~G--~~~~~iA~~~GVsr~Tiy   39 (42)
T cd00569           5 KLTPEQIEEARRLL--AAG--ESVAEIARRLGVSRSTLY   39 (42)
T ss_pred             CCCHHHHHHHHHHH--HCC--CCHHHHHHHHCCCHHHHH
T ss_conf             69999999999999--978--989999999797999998


No 204
>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=64.41  E-value=9.2  Score=17.09  Aligned_cols=47  Identities=13%  Similarity=0.221  Sum_probs=34.0

Q ss_pred             ECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHH
Q ss_conf             61420588989999999998776088999789998709998999999
Q gi|254780289|r  520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV  566 (682)
Q Consensus       520 r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~  566 (682)
                      +||-..+..+-...|.-.++...--.--+-+|||+.+|++...||+=
T Consensus         1 kIP~ati~RLp~Y~R~L~~L~~~g~~~vSS~eLa~~~gv~~aqiRKD   47 (49)
T pfam06971         1 KIPEATIKRLPLYYRYLEELLEEGVERVSSKELSEAIGIDAAQIRKD   47 (49)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHCCCCEECHHHHHHHHCCCHHHHHCC
T ss_conf             98889999999999999999985990497999999979399996142


No 205
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=63.62  E-value=7.7  Score=17.69  Aligned_cols=24  Identities=42%  Similarity=0.527  Sum_probs=19.4

Q ss_pred             CCCCHHHHHHHCCCCHHHHHHHHH
Q ss_conf             899978999870999899999998
Q gi|254780289|r  545 REPTPEEIAKKLAMPVEGVRKVLK  568 (682)
Q Consensus       545 ~~~~~~~~a~~~~~~~~~~~~~~~  568 (682)
                      -+.|.++||+.+|+.+..||++|-
T Consensus        35 ~evTDEeiAe~~gi~lN~VRk~LY   58 (178)
T PRK06266         35 GEVTDEEIAEQTGIKLNTVRKILY   58 (178)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             657899999996997899999999


No 206
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=63.56  E-value=9.5  Score=16.98  Aligned_cols=68  Identities=18%  Similarity=0.217  Sum_probs=42.6

Q ss_pred             CCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf             899978999870999899999998608987553635889986047562389889989999999999999999732
Q gi|254780289|r  545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS  619 (682)
Q Consensus       545 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~  619 (682)
                      ++-|..+||+.+|+.+..|..+.+-    -.+.||.|-   ..|-.|....-.......++....+..|.++++.
T Consensus       348 kPL~lkdiA~~lglheSTVSRav~~----Kyi~tp~G~---~~lk~fFs~~~~~~~g~~~S~~~ik~~i~~lI~~  415 (461)
T PRK05932        348 KPLVLKDIAEALGMHESTISRATTN----KYMATPRGI---FELKYFFSSAVSTDSGGEASSTAIRALIKKLIAA  415 (461)
T ss_pred             CCCCHHHHHHHCCCCHHHHHHHHHC----CEECCCCCE---EEHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             6763999998739981258898716----611489744---6699974230578886201399999999999984


No 207
>TIGR01637 phage_arpU phage transcriptional regulator, ArpU family; InterPro: IPR006524   These sequences represent a family of phage proteins, including ArpU, called a putative autolysin regulatory protein. ArpU was described as a regulator of cellular muramidase-2 of Enterococcus hirae but appears to have been cloned from a prophage. This family appears related to the RinA family of bacteriophage transcriptional activators and to some sporulation-specific sigma factors. This group of sequences could be a phage transcriptional activator family..
Probab=63.54  E-value=9.5  Score=16.98  Aligned_cols=56  Identities=9%  Similarity=0.207  Sum_probs=43.9

Q ss_pred             HHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf             9999997329988999999981879867468899989966789999999999999832
Q gi|254780289|r  611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK  668 (682)
Q Consensus       611 ~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~  668 (682)
                      ..+..++..|++++|.||...|  -......=-.|-..+|+|.-..-.+-.+|+-+|-
T Consensus        75 ~~v~~~~~~L~~~~R~Il~~~Y--~~~~~~~D~~i~~el~~s~~~Yy~~K~rA~l~lA  130 (139)
T TIGR01637        75 NAVSKAINQLDEISRQILYDKY--LEEDKKSDYQIMNELGYSHSQYYRIKKRALLRLA  130 (139)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHH--HCHHHHCCHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             9999998408888999999971--0455303788888743777899999999999999


No 208
>pfam02001 DUF134 Protein of unknown function DUF134. This family of archaeal proteins has no known function.
Probab=61.73  E-value=10  Score=16.74  Aligned_cols=46  Identities=24%  Similarity=0.272  Sum_probs=38.9

Q ss_pred             CCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf             29988999999981879867468899989966789999999999999832
Q gi|254780289|r  619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK  668 (682)
Q Consensus       619 ~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~  668 (682)
                      .|++-|-+.|||-.    ...+|-+|-+..+||||--+--|-..|-+|+-
T Consensus        36 ~L~~dE~EAiRL~D----~egl~QeeaA~~MgVSR~Tf~ril~~ARkKvA   81 (100)
T pfam02001        36 IITLDEFEAIRLVD----YEDYTQEEAAKLMGISRRTVWRLLTSARKKIA   81 (100)
T ss_pred             EECHHHHHHHHHHH----HCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHH
T ss_conf             73499999999873----60798999998849769999999999999999


No 209
>pfam04748 Polysacc_deac_2 Divergent polysaccharide deacetylase. This family is divergently related to pfam01522 (personal obs:Yeats C).
Probab=61.54  E-value=10  Score=16.72  Aligned_cols=141  Identities=21%  Similarity=0.237  Sum_probs=76.0

Q ss_pred             CCCCCCCHHCCHHHHHHHHHHHHHC-CCCCHHHHHHHCCCCCCCHHH-HHHHHHHHHHCCCEEECCCCCCCCCCCCCCCC
Q ss_conf             6555443020289999999978784-886789997526843599888-99999999847977832784100001236432
Q gi|254780289|r   17 DSDDSLVFDFSDDSWKKMIKLARQR-GYVTIEELNAFLPPDEVSSEQ-MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLD   94 (682)
Q Consensus        17 ~~~~~~~~d~~~~~ik~LI~~gke~-GylTydeIn~~LP~d~~~~e~-ie~i~~~L~~~GI~Vve~~~~~~~~~~~~~~~   94 (682)
                      .+......++..+.++..+.....+ .+...  +|+|..+.....++ |..++..|.+.|.-.+|+..........-...
T Consensus        62 ~gp~~L~~~~~~~~i~~~l~~~l~~~p~avG--vnNhmGS~~t~~~~~m~~vl~~l~~~gl~fvDS~Tt~~S~a~~~A~~  139 (213)
T pfam04748        62 PGPGTLTVGMSAEEIEKRLEAALSRVPYAVG--VNNHMGSRFTADRAAMRWVMEELKKRGLFFVDSRTSGRSVAPKLAKE  139 (213)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHCCCCEE--EECCCCCCCCCCHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHH
T ss_conf             9977588899999999999999987888489--95466755416999999999999877988991477766589999998


Q ss_pred             CCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH
Q ss_conf             11011122334444200345777728999999856976889788999999999889999999872823899999999873
Q gi|254780289|r   95 LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL  174 (682)
Q Consensus        95 ~~~~~~~e~~~~~~~~~~e~~rtdDPVRMYLREMG~V~LLTREgEIeIAKRIE~G~~~i~~al~~~P~ti~~il~~~e~i  174 (682)
                      ..-....-    ....|  ...+.+.|+-+|++.           +.+||+  .|.  ++..-.-+|.|+..+..|...+
T Consensus       140 ~gvp~~~r----dvfLD--~~~~~~~I~~ql~~~-----------~~~A~~--~G~--aI~Igh~~p~Tl~~L~~~~~~l  198 (213)
T pfam04748       140 LGVPAAKR----DVFLD--NEQTEAAIRRQLDQA-----------AALARK--EGS--AIAIGHPHPETIAALKEWLPEL  198 (213)
T ss_pred             CCCCEEEE----EEECC--CCCCHHHHHHHHHHH-----------HHHHHH--CCC--EEEEECCCHHHHHHHHHHHHHH
T ss_conf             39986761----03147--999999999999999-----------999986--395--7999779989999999986577


Q ss_pred             HCCCHH
Q ss_conf             117103
Q gi|254780289|r  175 NDGTTL  180 (682)
Q Consensus       175 ~~ge~~  180 (682)
                      ....+.
T Consensus       199 ~~~gi~  204 (213)
T pfam04748       199 RARGIE  204 (213)
T ss_pred             HHCCEE
T ss_conf             658879


No 210
>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=60.98  E-value=10  Score=16.65  Aligned_cols=267  Identities=16%  Similarity=0.187  Sum_probs=130.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHCCCHHHHHHH-----CC-CCCCCHHHHHH
Q ss_conf             99999999999862100577887899999--999999999999999999712535777763-----16-77689899999
Q gi|254780289|r  315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLY--DISKRIMHNEGELLRLAQSYGIKRDVFLER-----HQ-GRELDPHWVSY  386 (682)
Q Consensus       315 ~kl~~eL~e~~~~lkl~~k~iE~L~~~l~--~~~k~Ir~~Er~L~rl~~k~~i~R~~Fi~~-----f~-gnEt~~~wl~~  386 (682)
                      +.+-..|.+.+..=.+-..-++.+.+.+.  .-...+...-..|.++ +=.||--.++.+-     -. -...++.|...
T Consensus       134 ~~ia~~iI~~Ld~~GYL~~~~e~~~~~~~~~~~~~~v~~vl~~~Q~L-dP~GvgAr~L~EcL~LQl~~~~~~~~~~~~~~  212 (477)
T TIGR02395       134 RKIALYIIDALDEDGYLEEDLEEIADELEIEVSEEEVEKVLELIQRL-DPAGVGARDLQECLLLQLERRLDEDDTPLREL  212 (477)
T ss_pred             HHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHCC-CCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHH
T ss_conf             99999998501788852578899999728898888999999998423-88850117889999999865338998789999


Q ss_pred             HHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHH-----HHHHHHHHHHHHHH--H-------
Q ss_conf             8613551067655434567765322333322222112-6889999998765-----33211246899987--5-------
Q gi|254780289|r  387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS-ISEFRHIVSMVRK-----GECEASIAKKEMVE--A-------  451 (682)
Q Consensus       387 ~~~~~~~~~~~~l~~~~~eI~~~q~kL~~ie~~~gl~-i~ElK~i~r~I~~-----ge~e~~~AK~~l~~--a-------  451 (682)
                      ....-......        +  +.+++..+...++++ ..+++....-|+.     |..=........|-  .       
T Consensus       213 a~~i~~~~~~~--------L--~~~~~~~l~~~~~~~~~~~~~~a~~~i~~L~P~Pg~~f~~~~~~~y~~~~PD~~v~~~  282 (477)
T TIGR02395       213 ALNILLEHLEL--------L--AEKDFKRLAKKLGLSSEEELKEALDLIKSLSPKPGKEFADPEEEEYVIVKPDVIVTKK  282 (477)
T ss_pred             HHHHHHHHHHH--------H--HHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCHHHHCCCCCCEEEEECCEEEEEEE
T ss_conf             99998755679--------9--9853555798707998899999999997079986032236777603787364899883


Q ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHH
Q ss_conf             55789998875223567778875443679999887438545731201028989999999997228704614205889899
Q gi|254780289|r  452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK  531 (682)
Q Consensus       452 nlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~  531 (682)
                      |=.|+|    ...++++|-..+-+.+.-.+-+ .++=+          +.-|+++...+|=    |.|+.=--=.+|+.|
T Consensus       283 ~~~~~~----~l~~~~~P~~~~~~~y~~~~~~-~~~~~----------~~~yl~~k~~eA~----wL~~~l~~R~~TL~~  343 (477)
T TIGR02395       283 NGEWVV----ELNKRSLPELRINEEYFKLLKK-AEKEA----------AQQYLKEKLQEAR----WLIKALEQREETLLR  343 (477)
T ss_pred             CCEEEE----EECCCCCCEEEECHHHHHHHHH-HHHHH----------HHHHHHHHHHHHH----HHHHHHHHHHHHHHH
T ss_conf             878899----8737777614431868899874-22357----------8899999999999----999999998999999


Q ss_pred             HH----HHHHHHHH---HCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCC-CCCHHHH
Q ss_conf             99----99999877---6088999789998709998999999986089875536358899860475623898-8998999
Q gi|254780289|r  532 VV----RTARRMSN---KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN-AVSPLDS  603 (682)
Q Consensus       532 ~~----~~~~~~~~---~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~-~~~~~~~  603 (682)
                      +.    ...+.++.   ..=|+-|..+||+.+|+.+..|..+-+    -=+|.||.|=   ..|-.|....- ...+...
T Consensus       344 v~~~Iv~~Q~~FF~~g~~~LkPL~L~~vA~el~~heSTiSRai~----~KYl~T~~G~---f~Lk~FFS~~v~~~~~~~~  416 (477)
T TIGR02395       344 VAEAIVERQKDFFEGGPAALKPLTLREVAEELGLHESTISRAIN----NKYLQTPRGV---FELKYFFSSGVSTESAEGE  416 (477)
T ss_pred             HHHHHHHHHHHHHHCCHHCCCCCCHHHHHHHHCCCCCCEEEEEC----CCEEECCCCC---HHHHHHCCHHHCCCCCCHH
T ss_conf             99999999999841452006886389999885889872463317----7357607640---3365431201203456503


Q ss_pred             HHHHHHHHHHHHHHH
Q ss_conf             999999999999973
Q gi|254780289|r  604 AIQANLRETTTRVLA  618 (682)
Q Consensus       604 ~~~~~~~~~~~~~l~  618 (682)
                      ++....|..|.++++
T Consensus       417 ~S~~~ik~~~~~lI~  431 (477)
T TIGR02395       417 ASSTAIKALIKELIA  431 (477)
T ss_pred             HHHHHHHHHHHHHHH
T ss_conf             469999999999997


No 211
>COG2856 Predicted Zn peptidase [Amino acid transport and metabolism]
Probab=59.49  E-value=10  Score=16.73  Aligned_cols=16  Identities=25%  Similarity=0.306  Sum_probs=5.6

Q ss_pred             HHHHHCCCHHHHHHHC
Q ss_conf             9997125357777631
Q gi|254780289|r  359 LAQSYGIKRDVFLERH  374 (682)
Q Consensus       359 l~~k~~i~R~~Fi~~f  374 (682)
                      .+...-||...|.+.|
T Consensus       112 FAa~lLmP~~~l~~~~  127 (213)
T COG2856         112 FAAELLMPEEVLRERL  127 (213)
T ss_pred             HHHHHHCCHHHHHHHH
T ss_conf             9999837849998632


No 212
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147; InterPro: IPR011873    This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterised..
Probab=57.50  E-value=12  Score=16.22  Aligned_cols=118  Identities=24%  Similarity=0.366  Sum_probs=76.2

Q ss_pred             HHHHHHHCCCCC-CHHHHHHHCC--CCHHHHHHHHHHHCCCCCCCCCCCCCC-CCEEEEEECCCCCC-CHHHHH------
Q ss_conf             999877608899-9789998709--998999999986089875536358899-86047562389889-989999------
Q gi|254780289|r  536 ARRMSNKIKREP-TPEEIAKKLA--MPVEGVRKVLKITKEPISLETPIGDED-TSHLGDFIEDKNAV-SPLDSA------  604 (682)
Q Consensus       536 ~~~~~~~~~~~~-~~~~~a~~~~--~~~~~~~~~~~~~~~~~sl~~~~~~~~-~~~~~~~~~d~~~~-~~~~~~------  604 (682)
                      .|.+..-.+-.| .+++||..+.  +|+..|+..+...-+ ++|   |-.++ +....  ..|+.+. ++.+..      
T Consensus       132 iRe~~~~~~~~~~~~~~la~~~~P~IS~~qvk~sl~LL~~-l~l---i~K~~q~G~y~--~~~~~vs~~g~e~~~~av~~  205 (281)
T TIGR02147       132 IRELVAVMPFADDDPEELAKRLKPKISAEQVKESLDLLER-LGL---IKKNEQDGFYK--QTDKAVSMTGSEVIPLAVRQ  205 (281)
T ss_pred             HHHHHHHCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHH-CCC---CEEECCCCCEE--EECCCEEECCHHHHHHHHHH
T ss_conf             9999875489999868999870798578999999999862-332---01103058767--60760660746568999999


Q ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             9999999999997329988999999981879867468899989966789999999999
Q gi|254780289|r  605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK  662 (682)
Q Consensus       605 ~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~  662 (682)
                      -...+-+.=.++|..+|+-+|.|=-+=||+...   |+.+|-+....=|-.|..|=++
T Consensus       206 y~~Q~~~La~~al~~~~~~~R~~S~~T~g~~~~---~y~~i~~~i~~fR~~~~~~~~~  260 (281)
T TIGR02147       206 YQKQMIDLAKEALDALPPEERDVSTVTLGISEE---AYKEIVKKIQEFRKEVLAIAAK  260 (281)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCEEEEEECCCHH---HHHHHHHHHHHHHHHHHHHHHC
T ss_conf             879999999999971789876313003233599---9999999999999999999841


No 213
>COG3824 Predicted Zn-dependent protease [General function prediction only]
Probab=57.33  E-value=4.6  Score=19.48  Aligned_cols=27  Identities=26%  Similarity=0.570  Sum_probs=22.1

Q ss_pred             CCCCC-HHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             67468-8999899667899999999999
Q gi|254780289|r  637 NTDHT-LEEVGKQFCVTRERIRQIEAKA  663 (682)
Q Consensus       637 ~~~~t-l~e~~~~~~~~~er~rqi~~~a  663 (682)
                      .-.|| ++|||-.||+|-+++-|||..|
T Consensus       108 ~vthvliHEIgHhFGLsDdd~~rie~~a  135 (136)
T COG3824         108 QVTHVLIHEIGHHFGLSDDDLERIEWAA  135 (136)
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHHCC
T ss_conf             7443023532212387776898754303


No 214
>KOG2727 consensus
Probab=57.03  E-value=12  Score=16.17  Aligned_cols=54  Identities=22%  Similarity=0.324  Sum_probs=40.0

Q ss_pred             HHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHH
Q ss_conf             989999999997228704614205889899999999987760889997899987099989999999
Q gi|254780289|r  502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL  567 (682)
Q Consensus       502 ~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~  567 (682)
                      |-+|+.|.|-|-+            .++-+...++-.+.+..||-|-..+--+.+||+..++...+
T Consensus       922 ~~l~hGIa~miWn------------~fl~~~fqaa~~lv~KvGr~PkDk~crkdigms~~k~~eFL  975 (1244)
T KOG2727         922 PRLRHGIARMIWN------------KFLFMVFQAAVNLVEKVGRRPKDKECRKDIGMSEVKLEEFL  975 (1244)
T ss_pred             HHHHCCHHHHHHH------------HHHHHHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCHHHHHH
T ss_conf             6886214999998------------89999999999999984789732677874175400079999


No 215
>pfam10078 DUF2316 Uncharacterized protein conserved in bacteria (DUF2316). Members of this family of hypothetical bacterial proteins have no known function.
Probab=57.03  E-value=12  Score=16.17  Aligned_cols=37  Identities=24%  Similarity=0.306  Sum_probs=27.1

Q ss_pred             HHHHHHHH-C-CCCCCHHHHHHHCCCCHHHHHHHHHHHC
Q ss_conf             99998776-0-8899978999870999899999998608
Q gi|254780289|r  535 TARRMSNK-I-KREPTPEEIAKKLAMPVEGVRKVLKITK  571 (682)
Q Consensus       535 ~~~~~~~~-~-~~~~~~~~~a~~~~~~~~~~~~~~~~~~  571 (682)
                      ++++-+|+ + --.-|.+++|..|++|+++|..+|.+.+
T Consensus        10 ~T~~ELqeNf~~~~ls~~~iA~dL~~s~~~ve~vL~m~~   48 (89)
T pfam10078        10 ATRKELQANFELSGLTIEQVAKDLNTTPEKVEALLQLKQ   48 (89)
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCC
T ss_conf             999999999988389899999894999999999997346


No 216
>pfam12324 HTH_15 Helix-turn-helix domain of alkylmercury lyase. Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This is the N terminal helix-turn-helix domain associated with pfam03243.
Probab=56.81  E-value=12  Score=16.14  Aligned_cols=36  Identities=33%  Similarity=0.304  Sum_probs=28.8

Q ss_pred             HHHHHHH--CCCCCCHHHHHHHCCCCHHHHHHHHHHHC
Q ss_conf             9998776--08899978999870999899999998608
Q gi|254780289|r  536 ARRMSNK--IKREPTPEEIAKKLAMPVEGVRKVLKITK  571 (682)
Q Consensus       536 ~~~~~~~--~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  571 (682)
                      .+-+++.  .|++-|++.||..+|.|+++|+.+|....
T Consensus        26 ~~~LLr~La~G~PVt~~~LA~a~g~~~e~V~~~L~~~p   63 (77)
T pfam12324        26 FRPLLRMLADGRPVTREDLAGATGKPVERVAKVLAQAP   63 (77)
T ss_pred             HHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHCC
T ss_conf             99999999479986899999896989999999998588


No 217
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=56.67  E-value=12  Score=16.13  Aligned_cols=22  Identities=18%  Similarity=0.422  Sum_probs=9.2

Q ss_pred             HHHHHHHHHHHHHCCCCCCHHHHHH
Q ss_conf             5557899988752235677788754
Q gi|254780289|r  451 ANLRLVISVAKKYTNRGLQFLDLIQ  475 (682)
Q Consensus       451 anlr~v~~~~~~~~~~~~~~~~~~~  475 (682)
                      +.|..+..||+-+   |+++.+|+.
T Consensus        47 PSl~tL~kIa~aL---~v~l~~lf~   68 (185)
T PRK09943         47 PAISTLQKLLKVY---GLSLSEFFS   68 (185)
T ss_pred             CCHHHHHHHHHHH---CCCHHHHHC
T ss_conf             9999999999984---999999827


No 218
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=55.86  E-value=11  Score=16.34  Aligned_cols=19  Identities=21%  Similarity=0.382  Sum_probs=8.0

Q ss_pred             HHHHHHHHHHHHHHHHHHC
Q ss_conf             9998755578999887522
Q gi|254780289|r  446 KEMVEANLRLVISVAKKYT  464 (682)
Q Consensus       446 ~~l~~anlr~v~~~~~~~~  464 (682)
                      ....++.+.|-..||.--.
T Consensus       145 ~~~~~aD~~FH~aIa~as~  163 (241)
T COG2186         145 EAFAEADLAFHLAIAEASG  163 (241)
T ss_pred             HHHHHHHHHHHHHHHHHCC
T ss_conf             1207889999999999839


No 219
>pfam01698 FLO_LFY Floricaula / Leafy protein. This family consists of various plant development proteins which are homologues of floricaula (FLO) and Leafy (LFY) proteins which are floral meristem identity proteins. Mutations in the sequences of these proteins affect flower and leaf development.
Probab=55.78  E-value=12  Score=16.12  Aligned_cols=43  Identities=21%  Similarity=0.410  Sum_probs=22.7

Q ss_pred             HHHHHHHHHHHHCC--CCCHHHHHHH------CCCCCCCHHHHHHHHHHHHHC
Q ss_conf             99999999787848--8678999752------684359988899999999847
Q gi|254780289|r   29 DSWKKMIKLARQRG--YVTIEELNAF------LPPDEVSSEQMEDTVAMLSNM   73 (682)
Q Consensus        29 ~~ik~LI~~gke~G--ylTydeIn~~------LP~d~~~~e~ie~i~~~L~~~   73 (682)
                      -.++.|=.+-+.=|  |.|-+-|.+.      |  -.+.-+.+|+.|..|.+.
T Consensus        44 ~~l~gLEdLF~~YGVRy~TaAKIaELGFTasTL--v~MkdeELDdMM~sLs~i   94 (382)
T pfam01698        44 RKLRGLEELFQAYGVRYYTAAKIAELGFTVSTL--VNMKDEELDDMMNSLSHI   94 (382)
T ss_pred             CCCCCHHHHHHHCCCHHHHHHHHHHHCCHHHHH--HCCCHHHHHHHHHHHHHH
T ss_conf             553449999884285199999999715449876--467688999999999976


No 220
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=55.37  E-value=13  Score=15.97  Aligned_cols=21  Identities=43%  Similarity=0.474  Sum_probs=10.8

Q ss_pred             CHHHHHHHHCCCHHHHHHHHH
Q ss_conf             889998996678999999999
Q gi|254780289|r  641 TLEEVGKQFCVTRERIRQIEA  661 (682)
Q Consensus       641 tl~e~~~~~~~~~er~rqi~~  661 (682)
                      |=++.|+..||||.-|-.||.
T Consensus        16 tQ~elA~~vgVsRQTi~~iEk   36 (68)
T COG1476          16 TQEELAKLVGVSRQTIIAIEK   36 (68)
T ss_pred             CHHHHHHHCCCCHHHHHHHHC
T ss_conf             899999991957999999991


No 221
>KOG2773 consensus
Probab=55.19  E-value=13  Score=15.95  Aligned_cols=171  Identities=15%  Similarity=0.138  Sum_probs=82.5

Q ss_pred             HHHHHHHHHHHHHHHHH-HHCCCHHHHHHHCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999-71253577776316776898999998613551067655434567765322333322222112
Q gi|254780289|r  345 ISKRIMHNEGELLRLAQ-SYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS  423 (682)
Q Consensus       345 ~~k~Ir~~Er~L~rl~~-k~~i~R~~Fi~~f~gnEt~~~wl~~~~~~~~~~~~~~l~~~~~eI~~~q~kL~~ie~~~gl~  423 (682)
                      +-..|......+.+-|. -..+|..+.+..|..-..             ...+..+.........+.+.|..+...+-..
T Consensus       193 lwD~ile~Ri~lQKa~~~anqLP~~ev~~lf~sd~~-------------ee~st~lke~~k~l~kll~~ll~lr~~ll~~  259 (483)
T KOG2773         193 LWDNILELRIKLQKADDDANQLPQPEVLSLFKSDDE-------------EELSTALKELAKNLKKLLQSLLKLREALLTK  259 (483)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCC-------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             999899888888875555530787066787631663-------------6677899999999999999999999998623


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHCCCCC-CHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHH
Q ss_conf             6889999998765332112468999875557899--98875223567-77887544367999988743854573120102
Q gi|254780289|r  424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI--SVAKKYTNRGL-QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA  500 (682)
Q Consensus       424 i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~--~~~~~~~~~~~-~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya  500 (682)
                      ...-..++..=+.-+..  .-+..|-+--++.+-  +--..|+|..| .|.|.+|-.+-|...--.+|-.-         
T Consensus       260 ~~~~~~~v~~k~~~E~~--~~~~~l~~~~~~i~sl~~~~~~yrN~~L~KW~dkt~~~sg~a~~~~~kf~~~---------  328 (483)
T KOG2773         260 YPNTTKIVNAKKSFESG--KFKRSLKEFSLEINSLDFFLLEYRNKVLRKWHDKTQLASGGAAPKCKKFLIP---------  328 (483)
T ss_pred             CCHHHHHHHCCCCCCCC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHCC---------
T ss_conf             73045564057742245--3016688999999888999999989999987412453166322110234054---------


Q ss_pred             HHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHH
Q ss_conf             898999999999722870461420588989999999998776088999789
Q gi|254780289|r  501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE  551 (682)
Q Consensus       501 ~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  551 (682)
                       +-|-+.|..+..+..|.++           -+++.|..+.-+++-|-+..
T Consensus       329 -~~i~~Qi~~~l~d~erl~~-----------rtq~~r~~~~v~~~~pe~a~  367 (483)
T KOG2773         329 -FSINFQIEHFLDDPERLVK-----------RTQTMRRKFSVLARFPENAQ  367 (483)
T ss_pred             -CHHHHHHHHHHHCHHHHHH-----------HHHHCCCCCCCCCCCCCHHC
T ss_conf             -3178999998618999998-----------75321331232345760210


No 222
>pfam08279 HTH_11 HTH domain. This family includes helix-turn-helix domains in a wide variety of proteins.
Probab=53.92  E-value=13  Score=15.80  Aligned_cols=22  Identities=27%  Similarity=0.450  Sum_probs=12.5

Q ss_pred             CCHHHHHHHCCCCHHHHHHHHH
Q ss_conf             9978999870999899999998
Q gi|254780289|r  547 PTPEEIAKKLAMPVEGVRKVLK  568 (682)
Q Consensus       547 ~~~~~~a~~~~~~~~~~~~~~~  568 (682)
                      -|..+||+.|++|..-|..-++
T Consensus        16 vt~~~La~~l~VSr~TV~rdi~   37 (55)
T pfam08279        16 ISGQELAEKLGVSRRTIRRDIK   37 (55)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHH
T ss_conf             1899999996988999999999


No 223
>PRK11564 stationary phase inducible protein CsiE; Provisional
Probab=53.61  E-value=14  Score=15.77  Aligned_cols=48  Identities=13%  Similarity=0.263  Sum_probs=24.5

Q ss_pred             HHHHHHHHHCCCCCHHHHHHHCC-CCCCCHHHHHHHHHHHHHC-CCEEEC
Q ss_conf             99999787848867899975268-4359988899999999847-977832
Q gi|254780289|r   32 KKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNM-GINVVD   79 (682)
Q Consensus        32 k~LI~~gke~GylTydeIn~~LP-~d~~~~e~ie~i~~~L~~~-GI~Vve   79 (682)
                      -=|+.+--....||-+.+.+.|- +...-..++.++-.-|..- ++.+.-
T Consensus        19 ~ill~Ll~~~e~vtl~~L~~~l~VSr~Ti~~DLk~l~~~L~~y~~L~L~~   68 (426)
T PRK11564         19 QILLMLFQPGLTVTLETISQLNGVDDDIARQDIAETAREIQRYHHLTLTT   68 (426)
T ss_pred             HHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCEEEEE
T ss_conf             99999977999734999999969988899999999999983008869998


No 224
>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=53.28  E-value=14  Score=15.73  Aligned_cols=25  Identities=24%  Similarity=0.238  Sum_probs=20.3

Q ss_pred             CCHHHHHHHCCCCHHHHHHHHHHHC
Q ss_conf             9978999870999899999998608
Q gi|254780289|r  547 PTPEEIAKKLAMPVEGVRKVLKITK  571 (682)
Q Consensus       547 ~~~~~~a~~~~~~~~~~~~~~~~~~  571 (682)
                      -|++|.|+.||+|...|.++.+-..
T Consensus         2 lTv~EaA~yLgv~~~t~~~l~~~g~   26 (49)
T TIGR01764         2 LTVEEAAEYLGVSKSTVYRLIEEGE   26 (49)
T ss_pred             CCHHHHHHHCCCCHHHHHHHHHCCC
T ss_conf             8778899771999057899997189


No 225
>PRK07023 short chain dehydrogenase; Provisional
Probab=53.27  E-value=14  Score=15.73  Aligned_cols=89  Identities=16%  Similarity=0.034  Sum_probs=56.1

Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHH
Q ss_conf             78999887522356777887544367999988743854573120102898999999999722870461420588989999
Q gi|254780289|r  454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV  533 (682)
Q Consensus       454 r~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~  533 (682)
                      -.+.|++-.....|...-----.|-.|++++.-.- ..+|.|..+.+--||.-.+++.+......   +..+.       
T Consensus       133 InisS~a~~~~~~~~~~Y~aSKaal~~~t~sla~E-~~~~IrVn~V~PG~v~T~m~~~~~~~~~~---~~~~~-------  201 (243)
T PRK07023        133 LHISSGAARNAYAGWSVYCATKAALDHHARAVALE-ANRALRIVSLAPGVVDTGMQATIRATDEE---RFPMR-------  201 (243)
T ss_pred             EEEECHHHCCCCCCCHHHHHHHHHHHHHHHHHHHH-CCCCCEEEEEECCCCCCHHHHHHHHCCCC---CHHHH-------
T ss_conf             57833111678999668999999999999999986-79998899996377977466787545830---07999-------


Q ss_pred             HHHHHHHHHCCCCCCHHHHHH
Q ss_conf             999998776088999789998
Q gi|254780289|r  534 RTARRMSNKIKREPTPEEIAK  554 (682)
Q Consensus       534 ~~~~~~~~~~~~~~~~~~~a~  554 (682)
                       ..-.-.+.+||-.||+|+|.
T Consensus       202 -~~~~~~~p~GR~g~PedVA~  221 (243)
T PRK07023        202 -ERFRQLKASGALSTPEDAAR  221 (243)
T ss_pred             -HHHHHCCCCCCCCCHHHHHH
T ss_conf             -99870688899768999999


No 226
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=52.94  E-value=14  Score=15.69  Aligned_cols=19  Identities=26%  Similarity=0.356  Sum_probs=13.7

Q ss_pred             CCCCCHHHHHHHCCCCHHH
Q ss_conf             8899978999870999899
Q gi|254780289|r  544 KREPTPEEIAKKLAMPVEG  562 (682)
Q Consensus       544 ~~~~~~~~~a~~~~~~~~~  562 (682)
                      ..--|.||||+.+|+|+..
T Consensus        19 nPF~TDeeLa~~f~VSiqT   37 (185)
T PRK04424         19 NPFITDEELAEKFGVSIQT   37 (185)
T ss_pred             CCCCCHHHHHHHCCCEEEE
T ss_conf             8998779999860957778


No 227
>pfam02885 Glycos_trans_3N Glycosyl transferase family, helical bundle domain. This family includes anthranilate phosphoribosyltransferase (TrpD), thymidine phosphorylase. All these proteins can transfer a phosphorylated ribose substrate.
Probab=52.56  E-value=14  Score=15.65  Aligned_cols=47  Identities=23%  Similarity=0.218  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHCCCCCHHHHHHHCC---CCCCCHHHHHHHHHHHHHCCCEE
Q ss_conf             999999787848867899975268---43599888999999998479778
Q gi|254780289|r   31 WKKMIKLARQRGYVTIEELNAFLP---PDEVSSEQMEDTVAMLSNMGINV   77 (682)
Q Consensus        31 ik~LI~~gke~GylTydeIn~~LP---~d~~~~e~ie~i~~~L~~~GI~V   77 (682)
                      ++.+|++=...+-||++|+..++-   ++.+++.|+-.+...|...|...
T Consensus         2 ~~~~l~kl~~g~~Ls~~e~~~~~~~i~~g~~s~~qi~afL~al~~kget~   51 (66)
T pfam02885         2 IKELIKKLLRGEDLSREEAEALMDAIMSGEASDAQIAAFLMALRIKGETP   51 (66)
T ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCH
T ss_conf             89999999859997999999999999869999999999999999839999


No 228
>pfam06239 ECSIT Evolutionarily conserved signalling intermediate in Toll pathway. Activation of NF-kappaB as a consequence of signaling through the Toll and IL-1 receptors is a major element of innate immune responses. ECSIT plays an important role in signalling to NF-kappaB, functioning as the intermediate in the signaling pathways between TRAF-6 and MEKK-1.
Probab=52.02  E-value=14  Score=15.59  Aligned_cols=27  Identities=4%  Similarity=0.007  Sum_probs=14.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             532233332222211268899999987
Q gi|254780289|r  408 KIRNEIKSISVETGISISEFRHIVSMV  434 (682)
Q Consensus       408 ~~q~kL~~ie~~~gl~i~ElK~i~r~I  434 (682)
                      -+..-|..+|.+--+|-.|...+.-.|
T Consensus       122 cai~vLeqME~~gV~Pd~E~~~ll~~i  148 (229)
T pfam06239       122 CAIDVLEQMENHGVMPDKETEFLLVNI  148 (229)
T ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHH
T ss_conf             999999999983888958999999999


No 229
>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=51.96  E-value=13  Score=15.90  Aligned_cols=40  Identities=10%  Similarity=0.244  Sum_probs=26.4

Q ss_pred             HHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCC
Q ss_conf             9987760889997899987099989999999860898755363
Q gi|254780289|r  537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP  579 (682)
Q Consensus       537 ~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~  579 (682)
                      .+++..+  .-|..++|+.||+|...+..+.. .+.+||-|+-
T Consensus        13 eEfL~PL--g~s~~~LA~~LgVsr~~~sriv~-~~~~iT~dmA   52 (81)
T TIGR02607        13 EEFLEPL--GLSVRALAKALGVSRSTLSRIVN-GRRGITADMA   52 (81)
T ss_pred             HHHHHCC--CHHHHHHHHHCCCCHHHHHHHHH-CCCCCCHHHH
T ss_conf             7752104--70689999870999788888874-4899888899


No 230
>PRK02842 light-independent protochlorophyllide reductase subunit N; Provisional
Probab=51.71  E-value=11  Score=16.41  Aligned_cols=45  Identities=27%  Similarity=0.378  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHHCCC-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             88999999981879-8674688999899667899999999999998
Q gi|254780289|r  622 PREERVLRMRFGIG-MNTDHTLEEVGKQFCVTRERIRQIEAKAIRK  666 (682)
Q Consensus       622 ~re~~v~~~r~g~~-~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~  666 (682)
                      .|-.++|..-|-+| +|+..-++.++..|||+.++++..++.+..+
T Consensus       232 ~RGa~~i~ApFP~G~eGT~~Wl~aiA~~fgv~~~~~~~~~~~~~aR  277 (425)
T PRK02842        232 ERGAKVLTAPFPLGPEGTRAWLEAAAAAFGIDPDGLEEREAPAWER  277 (425)
T ss_pred             HCCCCEECCCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf             5298310578987840169999999998499888899888878888


No 231
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=51.57  E-value=12  Score=16.22  Aligned_cols=26  Identities=35%  Similarity=0.360  Sum_probs=14.7

Q ss_pred             CCCCCHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             88999789998709998999999986
Q gi|254780289|r  544 KREPTPEEIAKKLAMPVEGVRKVLKI  569 (682)
Q Consensus       544 ~~~~~~~~~a~~~~~~~~~~~~~~~~  569 (682)
                      ..+-|..||++.+|||...|..+++-
T Consensus        39 ~~Pmtl~Ei~E~lg~Sks~vS~~lkk   64 (177)
T COG1510          39 RKPLTLDEIAEALGMSKSNVSMGLKK   64 (177)
T ss_pred             CCCCCHHHHHHHHCCCCCHHHHHHHH
T ss_conf             99966999999977780128899999


No 232
>PRK01381 Trp operon repressor; Provisional
Probab=50.53  E-value=15  Score=15.42  Aligned_cols=42  Identities=24%  Similarity=0.261  Sum_probs=24.2

Q ss_pred             HHHHHHHC-CCHHHHHHHHHHHCCCC---CCCCCHHHHHHHHCCCH
Q ss_conf             99999732-99889999999818798---67468899989966789
Q gi|254780289|r  612 TTTRVLAS-LTPREERVLRMRFGIGM---NTDHTLEEVGKQFCVTR  653 (682)
Q Consensus       612 ~~~~~l~~-l~~re~~v~~~r~g~~~---~~~~tl~e~~~~~~~~~  653 (682)
                      ....+|.. |+|.|+.-|..|+-|-.   ...++-.||++.+||+=
T Consensus        24 ~~~~ll~~lLTp~Er~al~~R~~I~~~Ll~ge~sQReIa~~lgvsi   69 (99)
T PRK01381         24 LHLPLLTLLLTPDEREALGTRVRIVEELLRGELSQREIKQELGVGI   69 (99)
T ss_pred             HHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCC
T ss_conf             6999999978999999999999999999948764999999849740


No 233
>PRK01388 arginine deiminase; Provisional
Probab=50.34  E-value=12  Score=16.27  Aligned_cols=42  Identities=17%  Similarity=0.135  Sum_probs=35.5

Q ss_pred             HHHCCCCCHHHHHHHCCCCCCCHHHH----HHHHHHHHHCCCEEEC
Q ss_conf             87848867899975268435998889----9999999847977832
Q gi|254780289|r   38 ARQRGYVTIEELNAFLPPDEVSSEQM----EDTVAMLSNMGINVVD   79 (682)
Q Consensus        38 gke~GylTydeIn~~LP~d~~~~e~i----e~i~~~L~~~GI~Vve   79 (682)
                      |.|-.+||-+-+.+.|=+|++..+..    +.....|.+.||+|+.
T Consensus        24 G~El~~ltP~~~~~lLFddi~~l~~A~~EHd~f~~~Lr~~GveV~~   69 (410)
T PRK01388         24 GLELERLTPSNCDELLFDDVPWVERAQKEHDAFAQTLRERGVEVLY   69 (410)
T ss_pred             CHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCEEEE
T ss_conf             5898855911146651055658999999999999999868988998


No 234
>TIGR02865 spore_II_E stage II sporulation protein E; InterPro: IPR014221   This entry contains the stage II sporulation protein E (SpoIIE), which is a multiple membrane spanning protein with two separable functions. It plays a role in the switch to polar cell division during sporulation and it has phosphatase activity, located in the C-terminal region, which is required to activate sigma-F. All members of this entry are found in endospore-forming Gram-positive bacteria. A homologous protein, not a member of this entry, is found in the Cyanobacterium-like (and presumably non-spore-forming) photosynthesizer Heliobacillus mobilis..
Probab=50.05  E-value=15  Score=15.37  Aligned_cols=64  Identities=17%  Similarity=0.213  Sum_probs=31.8

Q ss_pred             CCCCCCC-CCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHC-CCHHHH-----HHHHHHHCCC
Q ss_conf             9875536-35889986047562389889989999999999999999732-998899-----9999981879
Q gi|254780289|r  572 EPISLET-PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREE-----RVLRMRFGIG  635 (682)
Q Consensus       572 ~~~sl~~-~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~-l~~re~-----~v~~~r~g~~  635 (682)
                      +.||=|. ..|+=.+..+.-.|.|-=..-|.-..+....=..|.+.+.. +++.=+     -||.+||+=+
T Consensus       590 e~vSGDSY~~~~L~~Gky~~~iSDGMG~G~~A~~ES~a~~~LlEk~l~~Gf~~~~AI~tvNSil~LrF~~~  660 (794)
T TIGR02865       590 ELVSGDSYSFGKLSAGKYAVAISDGMGSGPEAAQESSACVRLLEKFLESGFDREVAIKTVNSILSLRFSED  660 (794)
T ss_pred             CCCCCCEEEEEECCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCC
T ss_conf             94016556776317970799985479981889999999999999999707887689999889973148998


No 235
>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=50.04  E-value=15  Score=15.36  Aligned_cols=32  Identities=25%  Similarity=0.269  Sum_probs=22.1

Q ss_pred             HHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHH
Q ss_conf             99998776088999789998709998999999
Q gi|254780289|r  535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKV  566 (682)
Q Consensus       535 ~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~  566 (682)
                      .+.++..+.|-.-+.-+||+.|++|...|+.=
T Consensus        11 kA~eiy~~s~G~~~l~~IA~~L~vs~~~IrkW   42 (60)
T pfam10668        11 KAKEMWKESGGTMKLKDIANKLNVSESQIRKW   42 (60)
T ss_pred             HHHHHHHHCCCCEEHHHHHHHHCCCHHHHHHC
T ss_conf             99999998289644999999968798887603


No 236
>pfam11913 DUF3431 Protein of unknown function (DUF3431). This family of proteins are functionally uncharacterized. This protein is found in eukaryotes. Proteins in this family are typically between 291 to 390 amino acids in length. This protein has a conserved NLRC sequence motif.
Probab=49.36  E-value=2.8  Score=21.22  Aligned_cols=24  Identities=33%  Similarity=0.517  Sum_probs=18.5

Q ss_pred             HHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             899667899999999999998329
Q gi|254780289|r  646 GKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       646 ~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      +.+|.||||||||.-..-..++|.
T Consensus       158 CaQFaVsre~Ir~rP~~~Y~~~r~  181 (222)
T pfam11913       158 CAQFAVSRERIRKRPREDYVRYRQ  181 (222)
T ss_pred             EEEEEEEHHHHHHCCHHHHHHHHH
T ss_conf             342326399998689999999999


No 237
>KOG3099 consensus
Probab=49.30  E-value=16  Score=15.28  Aligned_cols=11  Identities=18%  Similarity=0.425  Sum_probs=4.0

Q ss_pred             CCCCCCHHHHH
Q ss_conf             67768989999
Q gi|254780289|r  375 QGRELDPHWVS  385 (682)
Q Consensus       375 ~gnEt~~~wl~  385 (682)
                      .+|+....|+.
T Consensus       109 ~~~~va~e~la  119 (340)
T KOG3099         109 SGNEVAAEILA  119 (340)
T ss_pred             CCCCHHHHHHH
T ss_conf             77621499987


No 238
>pfam12128 DUF3584 Protein of unknown function (DUF3584). This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 943 to 1234 amino acids in length. There are two conserved sequence motifs: GKT and YLP.
Probab=48.51  E-value=16  Score=15.19  Aligned_cols=16  Identities=31%  Similarity=0.364  Sum_probs=10.3

Q ss_pred             HHHHHHHHHHCCCCCC
Q ss_conf             6799998874385457
Q gi|254780289|r  478 NIGLMKAAEKFDWCLG  493 (682)
Q Consensus       478 ~~~l~~a~~~~~~~~g  493 (682)
                      --.+.+++++|+.--.
T Consensus       907 ~~~~~~~~~~f~~~~~  922 (1192)
T pfam12128       907 SGDLKKFVERFDGVIA  922 (1192)
T ss_pred             HHHHHHHHHHHHHHHH
T ss_conf             9999999999899998


No 239
>pfam02682 AHS1 Allophanate hydrolase subunit 1. This family is the first subunit of allophanate hydrolase.
Probab=48.27  E-value=16  Score=15.17  Aligned_cols=47  Identities=28%  Similarity=0.317  Sum_probs=33.7

Q ss_pred             HHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCC
Q ss_conf             722870461420588989999999998776088999789998709998999999986089875
Q gi|254780289|r  513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS  575 (682)
Q Consensus       513 ~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~s  575 (682)
                      ...+++++|||.--..                --|..+++|+..|++.++|-++.....-.|.
T Consensus        82 ~~~~~~~~IPV~Yd~~----------------~gpDL~~va~~~gLs~~evI~~Hs~~~y~V~  128 (202)
T pfam02682        82 AAPSRIIEIPVCYGGE----------------FGPDLEEVAEHNGLSVEEVIRLHSAAEYRVY  128 (202)
T ss_pred             CCCCCEEEEEEEECCC----------------CCCCHHHHHHHHCCCHHHHHHHHHCCCEEEE
T ss_conf             6898489997688996----------------6879999999839499999999856787999


No 240
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=47.98  E-value=16  Score=15.13  Aligned_cols=46  Identities=20%  Similarity=0.267  Sum_probs=18.9

Q ss_pred             HHHHHHHHHHHHHC-C-CCCHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCE
Q ss_conf             89999999978784-8-8678999752684359988899999999847977
Q gi|254780289|r   28 DDSWKKMIKLARQR-G-YVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN   76 (682)
Q Consensus        28 ~~~ik~LI~~gke~-G-ylTydeIn~~LP~d~~~~e~ie~i~~~L~~~GI~   76 (682)
                      -+.|+..|--|.=. | .|+-.+|.+-|.   ++---+=+.+..|...|+-
T Consensus        17 ~~~lr~~I~~g~l~pG~~L~E~~La~~~g---VSRtpvREAL~~L~~eGlv   64 (212)
T TIGR03338        17 QDEIERAILSGELPPGAKLNESDIAARLG---VSRGPVREAFRALEEAGLV   64 (212)
T ss_pred             HHHHHHHHHCCCCCCCCCCCHHHHHHHHC---CCHHHHHHHHHHHHHCCCH
T ss_conf             99999999839999909818999999889---6949999999999986963


No 241
>TIGR01026 fliI_yscN ATPase FliI/YscN family; InterPro: IPR005714    Proteins in this entry show extensive homology to the ATP synthase F1 beta subunit, and are involved in type III protein secretion. They fall into the two separate functional groups outlined below.   The first group, exemplified by the Salmonella typhimurium FliI protein (P26465 from SWISSPROT), is needed for flagellar assembly. Most structural components of the bacterial flagellum are translocated through the central channel of the growing flagellar structure by the type III flagellar protein-export apparatus in an ATPase-driven manner, to be assembled at the growing end. FliI is the ATPase that couples ATP hydrolysis to the translocation reaction , .   The second group couples ATP hydrolysis to protein translocation in non-flagellar type III secretion systems. Often these systems are involved in virulence and pathogenicity. YscN (P40290 from SWISSPROT) from pathogenic Yersinia species, for example, energises the injection of antihost factors directly into eukaryotic cells, thus overcoming host defences .; GO: 0016887 ATPase activity, 0009058 biosynthetic process, 0015031 protein transport, 0005737 cytoplasm.
Probab=47.46  E-value=17  Score=15.08  Aligned_cols=41  Identities=17%  Similarity=0.293  Sum_probs=33.8

Q ss_pred             HHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCH
Q ss_conf             99999997228704614205889899999999987760889997
Q gi|254780289|r  506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP  549 (682)
Q Consensus       506 ~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  549 (682)
                      -+|-.|++||...|=+   |.+.+.++-++.|++--..|-+||.
T Consensus       253 t~iAEYFrdqGk~VlL---lmDSvTRfA~AqREiGLA~GEPP~~  293 (455)
T TIGR01026       253 TAIAEYFRDQGKDVLL---LMDSVTRFAMAQREIGLAAGEPPAT  293 (455)
T ss_pred             HHHHHHHHHCCCEEEE---EHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             2543546521870562---0202789988988998743777777


No 242
>TIGR02546 III_secr_ATP type III secretion apparatus H+-transporting two-sector ATPase; InterPro: IPR013380    Proteins in this entry are found in a variety of bacteria, and are predicted to be ATPases involved in type III secretion systems. One example is YscN (P40290 from SWISSPROT) from Yersinia enterocolitica, which is thought to energise the YOP (Yersinia outer protein) secretion system .; GO: 0046961 hydrogen ion transporting ATPase activity rotational mechanism, 0030254 protein secretion by the type III secretion system.
Probab=47.46  E-value=17  Score=15.08  Aligned_cols=43  Identities=21%  Similarity=0.318  Sum_probs=35.6

Q ss_pred             HHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHH
Q ss_conf             9999999722870461420588989999999998776088999789
Q gi|254780289|r  506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE  551 (682)
Q Consensus       506 ~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  551 (682)
                      -+|-.|+.||.+.|=+   |.+++.++-|+.|+.--..|-+|+-..
T Consensus       232 TaIAEYFRDQGk~VlL---mmDSlTRfARA~REiGLAaGEP~aR~G  274 (430)
T TIGR02546       232 TAIAEYFRDQGKRVLL---MMDSLTRFARALREIGLAAGEPPARRG  274 (430)
T ss_pred             HHHHHHHHHCCCEEEE---EEECHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             7999999973990798---840277999998778875378400257


No 243
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=47.04  E-value=17  Score=15.03  Aligned_cols=24  Identities=25%  Similarity=0.213  Sum_probs=13.0

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCEE
Q ss_conf             754436799998874385457312
Q gi|254780289|r  473 LIQEGNIGLMKAAEKFDWCLGYKF  496 (682)
Q Consensus       473 ~~~~~~~~l~~a~~~~~~~~g~~f  496 (682)
                      ||-.||+|-.=+--.+=.++||+.
T Consensus        89 lvGaGnLG~AL~~y~gf~~~gf~I  112 (211)
T PRK05472         89 LVGAGNLGRALLNYNGFKKRGFKI  112 (211)
T ss_pred             EECCCHHHHHHHHCCCHHHCCCEE
T ss_conf             988877999998487623189789


No 244
>pfam04760 IF2_N Translation initiation factor IF-2, N-terminal region. This conserved feature at the N-terminus of bacterial translation initiation factor IF2 has recently had its structure solved. It shows structural similarity to the tRNA anticodon Stem Contact Fold domains of the methionyl-tRNA and glutaminyl-tRNA synthetases, and a similar fold is also found in the B5 domain of the phenylalanine-tRNA synthetase.
Probab=46.22  E-value=17  Score=14.94  Aligned_cols=34  Identities=18%  Similarity=0.067  Sum_probs=23.3

Q ss_pred             CCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             9978999870999899999998608987553635
Q gi|254780289|r  547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI  580 (682)
Q Consensus       547 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~  580 (682)
                      -|+.|+|+.||++..+|-+.+-...-.+|.+..+
T Consensus         4 itV~elA~~l~~~~~~vi~~L~~~Gi~~~~n~~l   37 (52)
T pfam04760         4 IRVYELAKELGVSSKELIKKLFKLGIMKTHNSTL   37 (52)
T ss_pred             EEHHHHHHHHCCCHHHHHHHHHHCCCEECCCCCC
T ss_conf             7399999998888999999999879855677745


No 245
>COG2316 Predicted hydrolase (HD superfamily) [General function prediction only]
Probab=45.02  E-value=14  Score=15.75  Aligned_cols=19  Identities=32%  Similarity=0.361  Sum_probs=11.0

Q ss_pred             HHHHHCCCHHHHHHHHHHH
Q ss_conf             9899667899999999999
Q gi|254780289|r  645 VGKQFCVTRERIRQIEAKA  663 (682)
Q Consensus       645 ~~~~~~~~~er~rqi~~~a  663 (682)
                      -|=--|++|++|||+|.-.
T Consensus       171 K~FAaG~~Rd~vR~~E~lG  189 (212)
T COG2316         171 KGFAAGVNRDEVRQAEELG  189 (212)
T ss_pred             HHHHCCCCHHHHHHHHHHC
T ss_conf             5554158899999999919


No 246
>PRK04217 hypothetical protein; Provisional
Probab=44.60  E-value=18  Score=14.76  Aligned_cols=45  Identities=29%  Similarity=0.295  Sum_probs=36.9

Q ss_pred             CCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf             9988999999981879867468899989966789999999999999832
Q gi|254780289|r  620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK  668 (682)
Q Consensus       620 l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~  668 (682)
                      |+.-|-+.|||-.    ...+|-+|-+..+||||--+--|-..|-+|+-
T Consensus        43 LtvdE~EaiRL~D----~egl~qeeaA~~M~VSR~Tf~ril~~AR~KvA   87 (110)
T PRK04217         43 MTYEEFEALRLVD----YEGLTQEEAGKRMGVSRGTVWRALTSARKKVA   87 (110)
T ss_pred             ECHHHHHHHHHHH----HCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHH
T ss_conf             1199999999873----60798999998849769999999999999999


No 247
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=44.32  E-value=18  Score=14.73  Aligned_cols=45  Identities=24%  Similarity=0.248  Sum_probs=35.1

Q ss_pred             CCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf             2998899999998187986746889998996678999999999999983
Q gi|254780289|r  619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL  667 (682)
Q Consensus       619 ~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l  667 (682)
                      .|+.-|-+.|||.+    ....|-+|-|.++||||--+--+=..|..|.
T Consensus        33 ~lt~eElEAlRLvD----~~~l~QeeAA~rMgISr~Tfwr~l~sAR~Kv   77 (99)
T COG1342          33 ILTIEELEALRLVD----YEGLTQEEAALRMGISRQTFWRLLTSARKKV   77 (99)
T ss_pred             EECHHHHHHHHHHH----HHHCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             52299988999886----8610578999984642999999999999999


No 248
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=44.25  E-value=18  Score=14.72  Aligned_cols=40  Identities=20%  Similarity=0.276  Sum_probs=20.3

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHH
Q ss_conf             7778875443679999887438545731201028989999
Q gi|254780289|r  468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA  507 (682)
Q Consensus       468 ~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~  507 (682)
                      -+-.||.||...-+|.++.+=|..--|-|----.-||-|.
T Consensus        42 WDaEDLaQet~~Kviq~~~~k~~~~a~l~kIArNqW~Dql   81 (228)
T PRK06704         42 WDGEDLAQETVCKVLQKYSNKDICMTLVYKIARNRWLDQI   81 (228)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             6578899999999999987622179999999998999998


No 249
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=44.17  E-value=18  Score=14.71  Aligned_cols=49  Identities=16%  Similarity=0.093  Sum_probs=32.6

Q ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCC---HHHHHHHHHHHHHCCCEEEC
Q ss_conf             89999999978784886789997526843599---88899999999847977832
Q gi|254780289|r   28 DDSWKKMIKLARQRGYVTIEELNAFLPPDEVS---SEQMEDTVAMLSNMGINVVD   79 (682)
Q Consensus        28 ~~~ik~LI~~gke~GylTydeIn~~LP~d~~~---~e~ie~i~~~L~~~GI~Vve   79 (682)
                      |+...+|+.+=.+ ..+|-+||...|.  +.+   -..|..|=..|.+.+|-.+.
T Consensus         3 n~Rq~~il~lL~~-~~lt~~eLA~~L~--VS~RTIR~DI~~iN~~L~~~~i~~~~   54 (585)
T PRK09863          3 NERELKIVDLLEQ-QDRSGGELAQQLG--VSRRTIVRDIAYINFTLNGKAIGSIS   54 (585)
T ss_pred             CHHHHHHHHHHHC-CCCCHHHHHHHCC--CCCHHHHHHHHHHHHHHHHCCEEEEE
T ss_conf             6799999999975-9999899998749--97117899999999998418518984


No 250
>TIGR01632 L11_bact ribosomal protein L11; InterPro: IPR006519   Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , .   Ribosomal protein L11 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L11 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities , groups bacterial, chloroplast, cyanelle, and most mitochondrial forms of ribosomal protein L11. L11 is a protein of 140 to 165 amino-acid residues. In E. coli, the C-terminal half of L11 has been shown  to be in an extended and loosely folded conformation and is likely to be buried within the ribosomal structure. This entry represents the bacterial, chloroplast and mitochondrial forms. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome.
Probab=44.07  E-value=18  Score=14.70  Aligned_cols=38  Identities=21%  Similarity=0.549  Sum_probs=20.5

Q ss_pred             CCCCHHHHHHH----CCCCCCCHHHHHHHHHHH----HHCCCEEEC
Q ss_conf             88678999752----684359988899999999----847977832
Q gi|254780289|r   42 GYVTIEELNAF----LPPDEVSSEQMEDTVAML----SNMGINVVD   79 (682)
Q Consensus        42 GylTydeIn~~----LP~d~~~~e~ie~i~~~L----~~~GI~Vve   79 (682)
                      |-||..+|.+.    ++|+.++.-.||.++-++    -.|||+|++
T Consensus        99 G~it~~q~~eIA~~K~~D~~ln~~~~EaA~k~I~GtAkSMGi~v~~  144 (144)
T TIGR01632        99 GKITRKQVREIAEIKMSDERLNTKDLEAAMKIIAGTAKSMGIEVVG  144 (144)
T ss_pred             EEECHHHHHHHHHHHCCCCCCCHHCHHHHHHHHCCCCCCCCEEECC
T ss_conf             2012788899998616898888102553154300000218615259


No 251
>pfam02638 DUF187 Uncharacterized BCR, COG1649.
Probab=43.99  E-value=13  Score=15.87  Aligned_cols=20  Identities=20%  Similarity=0.513  Sum_probs=12.4

Q ss_pred             CCHHHHHHHHHHHHHCCCEE
Q ss_conf             99888999999998479778
Q gi|254780289|r   58 VSSEQMEDTVAMLSNMGINV   77 (682)
Q Consensus        58 ~~~e~ie~i~~~L~~~GI~V   77 (682)
                      .++.++.+.+..|.++|++-
T Consensus        56 ~~~~q~~e~i~~L~~lnfNt   75 (394)
T pfam02638        56 PDPVQLQEAIALLDDLNFNT   75 (394)
T ss_pred             CCHHHHHHHHHHHHHCCCCE
T ss_conf             89899999999999869987


No 252
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=43.97  E-value=19  Score=14.69  Aligned_cols=33  Identities=15%  Similarity=0.138  Sum_probs=21.8

Q ss_pred             HHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHC
Q ss_conf             877608899978999870999899999998608
Q gi|254780289|r  539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK  571 (682)
Q Consensus       539 ~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  571 (682)
                      +....++.-+-++||+.||+|..-|-+..+..+
T Consensus        12 l~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr   44 (79)
T COG1654          12 LLLLTGNFVSGEKLAEELGISRTAVWKHIQQLR   44 (79)
T ss_pred             HHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             997379966689999997865999999999999


No 253
>pfam01371 Trp_repressor Trp repressor protein. This protein binds to tryptophan and represses transcription of the Trp operon.
Probab=43.86  E-value=19  Score=14.68  Aligned_cols=44  Identities=23%  Similarity=0.345  Sum_probs=22.9

Q ss_pred             HHHHHHC-CCHHHHHHHHHHHCCCC---CCCCCHHHHHHHHCCCHHHH
Q ss_conf             9999732-99889999999818798---67468899989966789999
Q gi|254780289|r  613 TTRVLAS-LTPREERVLRMRFGIGM---NTDHTLEEVGKQFCVTRERI  656 (682)
Q Consensus       613 ~~~~l~~-l~~re~~v~~~r~g~~~---~~~~tl~e~~~~~~~~~er~  656 (682)
                      +...+.. ++|.|..-+..||-+-.   ...+|..+|.+..|+|---|
T Consensus        19 ~~~f~~dl~T~~E~~ala~R~~va~~LL~~~~syreI~~~~g~S~aTI   66 (88)
T pfam01371        19 CYAFLTDLLTPDEREALAQRLRIAKELLRGELSQREIAQELGASIATI   66 (88)
T ss_pred             HHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHH
T ss_conf             999999839999999999999999999978998999999859852314


No 254
>pfam04931 DNA_pol_phi DNA polymerase phi. This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.
Probab=43.77  E-value=19  Score=14.67  Aligned_cols=16  Identities=25%  Similarity=0.387  Sum_probs=7.9

Q ss_pred             HHHHHHHHHHHHHHHC
Q ss_conf             9999999999999732
Q gi|254780289|r  604 AIQANLRETTTRVLAS  619 (682)
Q Consensus       604 ~~~~~~~~~~~~~l~~  619 (682)
                      ......+.++..+|..
T Consensus       699 ~~d~~~~~aL~~al~~  714 (784)
T pfam04931       699 PIDKAVRRALPKVLNL  714 (784)
T ss_pred             HHHHHHHHHHHHHCCC
T ss_conf             6679999999984068


No 255
>TIGR00169 leuB 3-isopropylmalate dehydrogenase; InterPro: IPR004429   Several NAD- or NADP-dependent dehydrogenases, including 3-isopropylmalate dehydrogenase, tartrate dehydrogenase, and the dimeric forms of isocitrate dehydrogenase, share a nucleotide binding domain unrelated to that of lactate dehydrogenase and its homologs. These enzymes dehydrogenate their substates at a H-C-OH site adjacent to a H-C-COOH site; the latter carbon, now adjacent to a carbonyl group, readily decarboxylates. Among these decarboxylating dehydrogenases of hydroxyacids, overall sequence homology indicates evolutionary history rather than actual substrate or cofactor specifity, which may be toggled experimentally by replacement of just a few amino acids. 3-isopropylmalate dehydrogenase is an NAD-dependent enzyme and should have a sequence resembling HGSAPDI around residue 340. The subtrate binding loop should include a sequence resembling E[KQR]X(0,1)LLXXR around residue 115.; GO: 0003862 3-isopropylmalate dehydrogenase activity, 0009098 leucine biosynthetic process, 0005737 cytoplasm.
Probab=43.71  E-value=8.2  Score=17.50  Aligned_cols=82  Identities=23%  Similarity=0.337  Sum_probs=52.5

Q ss_pred             HHHHHHHHHCCCEEEC--CCHHHHHHHHHH--HHHHHHHHHCCCCCCHHHHHH-HC-CCCHHHH---HHHHHHHCCCCCC
Q ss_conf             9999999722870461--420588989999--999998776088999789998-70-9998999---9999860898755
Q gi|254780289|r  506 QAITRSIADQSCTIRI--PVHMRDKIHKVV--RTARRMSNKIKREPTPEEIAK-KL-AMPVEGV---RKVLKITKEPISL  576 (682)
Q Consensus       506 ~~i~~~~~~~~~~~r~--~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~a~-~~-~~~~~~~---~~~~~~~~~~~sl  576 (682)
                      +-|.|.=+.-|+.-|-  ||.-+++.|-+.  +.+|+...         |+++ .. ++.+++.   -.+|...+.|-++
T Consensus       171 ~RIaR~AFe~A~kr~~P~~vTSvDKANVL~sS~LWR~~V~---------e~~~~eYPdv~L~H~yiDnAAM~Lvk~P~~f  241 (370)
T TIGR00169       171 ERIARVAFEMARKRRKPLKVTSVDKANVLESSRLWRKTVE---------EIAKEEYPDVELEHQYIDNAAMQLVKSPRQF  241 (370)
T ss_pred             HHHHHHHHHHHHHCCCCCCEEEECHHHHHHHHHHHHHHHH---------HHHHCCCCCEEECCCHHHHHHHHHHCCCCCC
T ss_conf             7899999999985488985321001204554378999999---------9984688805730215878876753286504


Q ss_pred             C-CCCCCCCCCEEEEEECCCCCCC
Q ss_conf             3-6358899860475623898899
Q gi|254780289|r  577 E-TPIGDEDTSHLGDFIEDKNAVS  599 (682)
Q Consensus       577 ~-~~~~~~~~~~~~~~~~d~~~~~  599 (682)
                      | .-|-+   --|||+|.|..+.-
T Consensus       242 DGV~vT~---N~FGDIlSDeAsvi  262 (370)
T TIGR00169       242 DGVVVTG---NLFGDILSDEASVI  262 (370)
T ss_pred             CCEEEEC---CCCCHHHHHHHHHH
T ss_conf             8667726---53300688888763


No 256
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=43.39  E-value=19  Score=14.63  Aligned_cols=26  Identities=27%  Similarity=0.431  Sum_probs=15.4

Q ss_pred             CCCCCHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             88999789998709998999999986
Q gi|254780289|r  544 KREPTPEEIAKKLAMPVEGVRKVLKI  569 (682)
Q Consensus       544 ~~~~~~~~~a~~~~~~~~~~~~~~~~  569 (682)
                      .+-|+-.|||+.+|+|.-.|++++..
T Consensus        29 ~~LPsE~eLa~~f~VSR~TvRkAL~~   54 (236)
T COG2188          29 DKLPSERELAEQFGVSRMTVRKALDE   54 (236)
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             95959899999979889999999999


No 257
>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=42.86  E-value=19  Score=14.57  Aligned_cols=67  Identities=18%  Similarity=0.288  Sum_probs=38.3

Q ss_pred             CCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHH
Q ss_conf             573120102898999999999722870461420588989999999998776088999789998709998999999
Q gi|254780289|r  492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV  566 (682)
Q Consensus       492 ~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~  566 (682)
                      -|-+|.--..=-.|.++.+.....   -.++.-+..++     .-+++....---.|++++|+..|+|+++|+..
T Consensus        22 ~G~~f~l~idd~LRaAvr~~~~~~---~~~~~e~~~~l-----spreIQarIRaGas~eevA~~~g~~~~rVerf   88 (169)
T pfam11268        22 DGERFRLPVDDRLRAALRGDRARL---GQVEIEVDPTL-----SPREIQARIRAGASAEEVAEAAGVPEERVERF   88 (169)
T ss_pred             CCCEEEEECCHHHHHHHCCCCCCC---CCCCCCCCCCC-----CHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHC
T ss_conf             999898874879999873566666---76643447888-----98999999887999999999959999998742


No 258
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=42.72  E-value=19  Score=14.55  Aligned_cols=25  Identities=12%  Similarity=0.085  Sum_probs=14.8

Q ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             8674688999899667899999999
Q gi|254780289|r  636 MNTDHTLEEVGKQFCVTRERIRQIE  660 (682)
Q Consensus       636 ~~~~~tl~e~~~~~~~~~er~rqi~  660 (682)
                      .|.+....-=.+.+|++-+..|||.
T Consensus       255 ~G~~~~~~ln~r~igl~L~~l~~ip  279 (321)
T COG2390         255 NGQPVDTPLNDRVIGLSLDDLRQIP  279 (321)
T ss_pred             CCCCCCCCCCCCEECCCHHHHHCCC
T ss_conf             9988555565716437788973278


No 259
>pfam09339 HTH_IclR IclR helix-turn-helix domain.
Probab=42.64  E-value=19  Score=14.54  Aligned_cols=30  Identities=17%  Similarity=0.278  Sum_probs=23.2

Q ss_pred             HHHCCCCCCHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             776088999789998709998999999986
Q gi|254780289|r  540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKI  569 (682)
Q Consensus       540 ~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  569 (682)
                      ....+++.+..|||..+|+|...|..++..
T Consensus        12 ~~~~~~~~~l~eia~~~gl~kstv~RlL~t   41 (52)
T pfam09339        12 LAEAPGGLSLTEIARRTGLPKSTAHRLLQT   41 (52)
T ss_pred             HHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             862899989999999989199999999999


No 260
>PRK04483 threonyl-tRNA synthetase; Validated
Probab=42.28  E-value=11  Score=16.61  Aligned_cols=36  Identities=14%  Similarity=0.158  Sum_probs=18.2

Q ss_pred             HHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH
Q ss_conf             8569768897889999999998899999998728238999999998
Q gi|254780289|r  127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRD  172 (682)
Q Consensus       127 EMG~V~LLTREgEIeIAKRIE~G~~~i~~al~~~P~ti~~il~~~e  172 (682)
                      +=|+|++||.+.+        +|...+.+..+.  +....+..+|-
T Consensus        53 ~D~~leiiT~~d~--------egl~v~rHS~AH--vla~Av~~l~p   88 (634)
T PRK04483         53 HDASLRIITAKDA--------EGVEIIRHSCAH--LVGHAVKQLYP   88 (634)
T ss_pred             CCCEEEEECCCCH--------HHHHHHHHHHHH--HHHHHHHHHCC
T ss_conf             9978999569997--------899999999999--99999999779


No 261
>TIGR00373 TIGR00373 conserved hypothetical protein TIGR00373; InterPro: IPR005241    This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain. .
Probab=42.01  E-value=20  Score=14.47  Aligned_cols=46  Identities=26%  Similarity=0.300  Sum_probs=27.2

Q ss_pred             CCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEE
Q ss_conf             9997899987099989999999860898755363588998604756
Q gi|254780289|r  546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF  591 (682)
Q Consensus       546 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~  591 (682)
                      +-|.++||..||+.+.-||++|=..=+.--.|=--.-|+++.+...
T Consensus        30 e~Tdeeis~elg~klN~vRk~Ly~LYdagladYkR~kD~eT~Wy~Y   75 (168)
T TIGR00373        30 EVTDEEISKELGIKLNVVRKLLYKLYDAGLADYKRRKDDETNWYEY   75 (168)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHCCEEEEEEECCCCCCCCEEE
T ss_conf             7477888888384055788999987303010002136898885236


No 262
>TIGR02169 SMC_prok_A chromosome segregation protein SMC; InterPro: IPR011891   The SMC (structural maintenance of chromosomes) family of proteins, exist in virtually all organisms including both bacteria and archaea. The SMC proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms and form three types of heterodimer (SMC1SMC3, SMC2SMC4, SMC5SMC6), which are core components of large multiprotein complexes. The best known complexes are cohesin, which is responsible for sister-chromatid cohesion, and condensin, which is required for full chromosome condensation in mitosis.     SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and share a five-domain structure, with globular N- and C-terminal (IPR003395 from INTERPRO) domains separated by a long (circa 100 nm or 900 residues) coiled coil segment in the centre of which is a globular ''hinge'' domain, characterised by a set of four highly conserved glycine residues that are typical of flexible regions in a protein. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif (XXXXD, where X is any hydrophobic residue), and a LSGG motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases .    All SMC proteins appear to form dimers, either forming homodimers with themselves, as in the case of prokaryotic SMC proteins, or heterodimers between different but related SMC proteins. The dimers are arranged in an antiparallel alignment. This orientation brings the N- and C-terminal globular domains (from either different or identical protamers) together, which unites an ATP binding site (Walker A motif) within the N-terminal domain with a Walker B motif (DA box) within the C-terminal domain, to form a potentially functional ATPase. Protein interaction and microscopy data suggest that SMC dimers form a ring-like structure which might embrace DNA molecules. Non-SMC subunits associate with the SMC amino- and carboxy-terminal domains. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences.   SMCs share not only sequence similarity but also structural similarity with ABC proteins. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression .    This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by IPR011890 from INTERPRO. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent ..
Probab=41.71  E-value=20  Score=14.44  Aligned_cols=51  Identities=20%  Similarity=0.039  Sum_probs=22.0

Q ss_pred             CCCHHHHH---HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCHHHHH
Q ss_conf             88978899---9999999889999999872823899999999873117103678
Q gi|254780289|r  133 LLSREGEI---AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE  183 (682)
Q Consensus       133 LLTREgEI---eIAKRIE~G~~~i~~al~~~P~ti~~il~~~e~i~~ge~~Lrd  183 (682)
                      |+++-+|+   .+++.+++-..+....-.+-...=..+-.+-.++..-..++..
T Consensus       239 L~~~k~e~e~~~ll~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~  292 (1202)
T TIGR02169       239 LKKEKREYEGYLLLKEKEALEKQKEAIEKQLAELEEELEKLTEEIEELEKRLEE  292 (1202)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999988899999999999999999999999999999999999999999999999


No 263
>PRK12444 threonyl-tRNA synthetase; Reviewed
Probab=41.67  E-value=12  Score=16.30  Aligned_cols=22  Identities=9%  Similarity=0.135  Sum_probs=9.5

Q ss_pred             CCEEEHHHHHHHHHHHHHHHHH
Q ss_conf             7312010289899999999972
Q gi|254780289|r  493 GYKFSTYAMWWVKQAITRSIAD  514 (682)
Q Consensus       493 g~~f~tya~~~i~~~i~~~~~~  514 (682)
                      |.-|=.---|.|++.+..++.+
T Consensus       265 G~~fwlP~G~~i~~~le~~~r~  286 (639)
T PRK12444        265 GMPFYLPKGQIIRNELEAFLRE  286 (639)
T ss_pred             CCEEEECCHHHHHHHHHHHHHH
T ss_conf             7447846786999999999999


No 264
>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=41.15  E-value=20  Score=14.38  Aligned_cols=23  Identities=26%  Similarity=0.170  Sum_probs=14.7

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             68899989966789999999999
Q gi|254780289|r  640 HTLEEVGKQFCVTRERIRQIEAK  662 (682)
Q Consensus       640 ~tl~e~~~~~~~~~er~rqi~~~  662 (682)
                      .|.++++..-|||+-.|.+||.-
T Consensus        16 lTQ~~LA~~aGvs~~~Is~iE~G   38 (58)
T TIGR03070        16 LTQADLADLAGVGLRFIRDIEKG   38 (58)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHCC
T ss_conf             98999998819989999999789


No 265
>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=41.03  E-value=20  Score=14.37  Aligned_cols=43  Identities=9%  Similarity=0.198  Sum_probs=23.8

Q ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCC
Q ss_conf             99999999999732998899999998187986746889998996678
Q gi|254780289|r  606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT  652 (682)
Q Consensus       606 ~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~  652 (682)
                      ...+...|..+|..||...++-|++-    +-+..|=-||++.+|||
T Consensus        87 ~~e~~~Cl~~~i~~LP~~~r~a~~L~----el~G~sQ~e~A~kLGlS  129 (170)
T TIGR02959        87 VKELSQCLRPMIKELPDEYREAIRLT----ELEGLSQKEIAEKLGLS  129 (170)
T ss_pred             HHHHHHHHHHHHHHCCHHHHHHHHHH----HCCCCCHHHHHHHCCCC
T ss_conf             45688888998875698678898887----50799827998761753


No 266
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=40.55  E-value=21  Score=14.31  Aligned_cols=18  Identities=22%  Similarity=0.375  Sum_probs=8.0

Q ss_pred             HHHHHCCCCHHHHHHHHH
Q ss_conf             999870999899999998
Q gi|254780289|r  551 EIAKKLAMPVEGVRKVLK  568 (682)
Q Consensus       551 ~~a~~~~~~~~~~~~~~~  568 (682)
                      +||..+|++.+.|..+++
T Consensus       178 ~lA~~lG~tretvsR~L~  195 (236)
T PRK09392        178 TLASYLGMTPENLSRAFA  195 (236)
T ss_pred             HHHHHHCCCHHHHHHHHH
T ss_conf             999987898999999999


No 267
>cd02758 MopB_Tetrathionate-Ra The MopB_Tetrathionate-Ra CD contains tetrathionate reductase, subunit A, (TtrA) and other related proteins. The Salmonella enterica tetrathionate reductase catalyses the reduction of trithionate but not sulfur or thiosulfate. Members of this CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=40.22  E-value=21  Score=14.28  Aligned_cols=22  Identities=5%  Similarity=0.098  Sum_probs=10.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             3322222112688999999876
Q gi|254780289|r  414 KSISVETGISISEFRHIVSMVR  435 (682)
Q Consensus       414 ~~ie~~~gl~i~ElK~i~r~I~  435 (682)
                      ....+.+|++...+.++.+++.
T Consensus       342 e~~AeitGVpa~~I~~lArEfa  363 (735)
T cd02758         342 EEYAEICGVPEAKIIELAKEFT  363 (735)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHH
T ss_conf             9999886989999999999998


No 268
>pfam11633 Nsp3 Replicase polyprotein 1ab. This family of proteins represents Nsp3, the product of ORF1a in group 2 coronavirus.This is the largest replicase subunit.
Probab=40.08  E-value=17  Score=14.89  Aligned_cols=39  Identities=13%  Similarity=0.311  Sum_probs=26.2

Q ss_pred             CCCCCCCCHHCCHHHHHHHHHHHHHCCCCC-----HHHHHHHCC
Q ss_conf             465554430202899999999787848867-----899975268
Q gi|254780289|r   16 EDSDDSLVFDFSDDSWKKMIKLARQRGYVT-----IEELNAFLP   54 (682)
Q Consensus        16 ~~~~~~~~~d~~~~~ik~LI~~gke~GylT-----ydeIn~~LP   54 (682)
                      .+.....+++..-..++.++.-||++|+++     |.-+++.|-
T Consensus        10 a~~~~~~~l~~v~~~~r~mv~hake~g~l~pIc~Dy~A~~k~Lk   53 (142)
T pfam11633        10 APPAKPELLGVVSESFRAMVRHAKETGLLCPICIDYPAFMKVLK   53 (142)
T ss_pred             CCCCCCCEEEEEEHHHHHHHHHHHHCCCEEEEEECCHHHHHHHH
T ss_conf             89999776777633189999866632835579965288999998


No 269
>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]
Probab=39.99  E-value=21  Score=14.25  Aligned_cols=30  Identities=20%  Similarity=0.531  Sum_probs=18.8

Q ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHH
Q ss_conf             578999887522356777887544367999988743854573120102
Q gi|254780289|r  453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA  500 (682)
Q Consensus       453 lr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya  500 (682)
                      .-.||-||    ..|.|+.-|+.              |..|.-|.+|-
T Consensus        87 vDvVvGIa----~sGvPlAt~vA--------------~elg~elaiY~  116 (203)
T COG0856          87 VDVVVGIA----ISGVPLATMVA--------------YELGKELAIYH  116 (203)
T ss_pred             EEEEEEEE----ECCCCHHHHHH--------------HHHCCCEEEEE
T ss_conf             46899885----06862899999--------------97378469981


No 270
>PRK04140 hypothetical protein; Provisional
Probab=39.98  E-value=21  Score=14.25  Aligned_cols=15  Identities=20%  Similarity=0.605  Sum_probs=5.7

Q ss_pred             HHHHHHHHHHCCCEE
Q ss_conf             999999998479778
Q gi|254780289|r   63 MEDTVAMLSNMGINV   77 (682)
Q Consensus        63 ie~i~~~L~~~GI~V   77 (682)
                      |++++.+|...|..|
T Consensus         6 i~~v~~~L~~~gf~v   20 (319)
T PRK04140          6 ISEVIDLLESAGFKV   20 (319)
T ss_pred             HHHHHHHHHHCCCEE
T ss_conf             999999999879579


No 271
>pfam09286 Pro-kuma_activ Pro-kumamolisin, activation domain. Members of this family are found in various subtilase propeptides, and adopt a ferredoxin-like fold, with an alpha+beta sandwich. Cleavage of the domain results in activation of the peptide.
Probab=39.94  E-value=21  Score=14.24  Aligned_cols=37  Identities=30%  Similarity=0.417  Sum_probs=29.8

Q ss_pred             CCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEEECC
Q ss_conf             4886789997526843599888999999998479778327
Q gi|254780289|r   41 RGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG   80 (682)
Q Consensus        41 ~GylTydeIn~~LP~d~~~~e~ie~i~~~L~~~GI~Vve~   80 (682)
                      ..|||.+|+.+.+.+   +.+.++.|...|...||.+...
T Consensus        45 g~~Lt~~e~~~~~~p---s~~~~~~V~~wL~~~g~~~~~~   81 (141)
T pfam09286        45 GKHLSREEVAALFAP---SQETVDAVRAWLESAGITVERA   81 (141)
T ss_pred             CCCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCCEEEE
T ss_conf             666899999988789---9999999999999869954885


No 272
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=39.59  E-value=21  Score=14.21  Aligned_cols=100  Identities=12%  Similarity=0.133  Sum_probs=51.7

Q ss_pred             CCCHHHHHHHCCCCHHHHHHHHHHHCC--CCCCCCCCCCCCCC--EEE-EEECCCCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             999789998709998999999986089--87553635889986--047-5623898899899999999999999997329
Q gi|254780289|r  546 EPTPEEIAKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTS--HLG-DFIEDKNAVSPLDSAIQANLRETTTRVLASL  620 (682)
Q Consensus       546 ~~~~~~~a~~~~~~~~~~~~~~~~~~~--~~sl~~~~~~~~~~--~~~-~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l  620 (682)
                      .-|.++||+.||++...||+++....+  -++-..--..++++  ..- -+--     +  .......++..+..++..|
T Consensus        15 ~v~dedLa~~l~~~~n~vRkiL~~L~e~~lv~~~~~rek~~~~~~~~~yyw~i-----~--y~~~~~~vk~k~~~~~~~L   87 (147)
T smart00531       15 CVTEEDLAELLGIKQKQLRKILYLLYDEKLIKIDYKREKDPETKTWYRYYWYI-----N--YDTLLDVVKYKLDKMRKRL   87 (147)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEEEEECCCCCEEEEEEEEE-----C--HHHHHHHHHHHHHHHHHHH
T ss_conf             70799999997999999999999999779646899987758886599999997-----7--9999999999999999999


Q ss_pred             CHHHHHHH-HHHHC-CCCCCCCCHHHHHHHHCCC
Q ss_conf             98899999-99818-7986746889998996678
Q gi|254780289|r  621 TPREERVL-RMRFG-IGMNTDHTLEEVGKQFCVT  652 (682)
Q Consensus       621 ~~re~~v~-~~r~g-~~~~~~~tl~e~~~~~~~~  652 (682)
                      ..|.+.=. ...|- -.++..+|..|+.+.++.+
T Consensus        88 ~~~l~~e~~~~~Y~C~~C~~ryt~~eA~~l~~~~  121 (147)
T smart00531       88 EDKLEDETNNAYYKCPNCQSKYTFLEANQLLDMD  121 (147)
T ss_pred             HHHHHHCCCCCEEECCCCCCEECHHHHHHHCCCC
T ss_conf             9998627489878899999786299998841899


No 273
>COG2049 DUR1 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]
Probab=39.58  E-value=21  Score=14.21  Aligned_cols=42  Identities=26%  Similarity=0.316  Sum_probs=31.5

Q ss_pred             CEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCC
Q ss_conf             7046142058898999999999877608899978999870999899999998608987
Q gi|254780289|r  517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI  574 (682)
Q Consensus       517 ~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  574 (682)
                      |+|.|||+--.                ..-|..+++|+.-|+++++|-.+.....--|
T Consensus        84 ~~IeIPV~Y~~----------------~~GpDL~~va~~~gls~~evI~~Hs~~~Y~V  125 (223)
T COG2049          84 RLIEIPVVYGG----------------EYGPDLAEVARHNGLSVEEVIELHSSTEYRV  125 (223)
T ss_pred             CEEEEEEEECC----------------CCCCCHHHHHHHCCCCHHHHHHHHCCCCEEE
T ss_conf             76997007689----------------8898899999881999999999725785599


No 274
>TIGR01279 DPOR_bchN light-independent protochlorophyllide reductase, N subunit; InterPro: IPR005970    Synonym: dark protochlorophyllide reductase    Protochlorophyllide reductase catalyzes the reductive formation of chlorophyllide from protochlorophyllide during biosynthesis of chlorophylls and bacteriochlorophylls. The light-independent (dark) form of protochlorophyllide reductase plays a key role in the ability of gymnosperms, algae, and photosynthetic bacteria to form chlorophyll in the dark. Genetic and sequence analyses have indicated that dark protochlorophyllide reductase consists of three protein subunits that exhibit significant sequence similarity to the three subunits of nitrogenase, which catalyzes the reductive formation of ammonia from dinitrogen. Dark protochlorophyllide reductase activity was shown to be dependent on the presence of all three subunits, ATP, and the reductant dithionite.    This enzyme describes the N subunit of the dark form protochlorophyllide reductase, a nitrogenase-like enzyme . ; GO: 0016730 oxidoreductase activity acting on iron-sulfur proteins as donors, 0015995 chlorophyll biosynthetic process, 0019685 photosynthesis dark reaction.
Probab=39.43  E-value=6  Score=18.57  Aligned_cols=58  Identities=26%  Similarity=0.381  Sum_probs=32.4

Q ss_pred             HHHHHHHCCCH-HHHHHHHHHHCCC-CCCCCCHHHHHHHHCCCHHHHHHHHH----HHHHHHCC
Q ss_conf             99999732998-8999999981879-86746889998996678999999999----99998329
Q gi|254780289|r  612 TTTRVLASLTP-REERVLRMRFGIG-MNTDHTLEEVGKQFCVTRERIRQIEA----KAIRKLKH  669 (682)
Q Consensus       612 ~~~~~l~~l~~-re~~v~~~r~g~~-~~~~~tl~e~~~~~~~~~er~rqi~~----~a~~~l~~  669 (682)
                      .|.+...+|.- |-.+||--=|=+| +|+..=||.|+..|||.-.|+..=++    +|-++|+|
T Consensus       242 yL~~ta~~L~~eR~~~~L~~~FPfGPDGT~~f~e~ia~~fG~~~~~l~er~aPrre~aW~~l~~  305 (458)
T TIGR01279       242 YLSDTATTLRRERGAKVLSALFPFGPDGTRRFLEAIAAEFGIEVDKLSEREAPRREQAWRALEP  305 (458)
T ss_pred             HHHHHHHHHHHHCCCEEECCCCCCCCCHHHHHHHHHHHHHCCCCCCCCHHHCHHHHHHHHHHHH
T ss_conf             1889999998502665611578988516899999999985982122001101028999999888


No 275
>TIGR00223 panD aspartate 1-decarboxylase; InterPro: IPR003190 Decarboxylation of aspartate is the major route of alanine production in bacteria, and is catalysed by the enzyme aspartate decarboxylase. The enzyme is translated as an inactive proenzyme of two chains, A and B. This family contains both chains of aspartate decarboxylase.; GO: 0004068 aspartate 1-decarboxylase activity, 0006523 alanine biosynthetic process.
Probab=39.11  E-value=5.8  Score=18.70  Aligned_cols=53  Identities=25%  Similarity=0.235  Sum_probs=33.8

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHH-HHH
Q ss_conf             9987555789998875223567778875443679999887438545731201028989-999
Q gi|254780289|r  447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV-KQA  507 (682)
Q Consensus       447 ~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i-~~~  507 (682)
                      ...+|||-+|=||+        ==.||+...-+===.+|+=.+..=|-|||||+..-= |++
T Consensus        14 ~vT~AnLnY~GSit--------IDeDl~daag~lenekv~IvnvnNG~RfsTY~I~gkkRGs   67 (127)
T TIGR00223        14 TVTEANLNYVGSIT--------IDEDLLDAAGLLENEKVDIVNVNNGKRFSTYVIAGKKRGS   67 (127)
T ss_pred             EEEECCCCEEEEEE--------HHHHHHHHHHCCCCCEEEEEECCCCCCEEEEEECCCCCCC
T ss_conf             76323674365332--------5467999851289984899866899712346651423587


No 276
>PRK10286 O-6-alkylguanine-DNA:cysteine-protein methyltransferase; Provisional
Probab=38.64  E-value=22  Score=14.10  Aligned_cols=78  Identities=15%  Similarity=0.111  Sum_probs=56.6

Q ss_pred             HHHHHHHHHHHHHCCCEE-ECCCHHHHHHHHHHHHHHHHHHH-CCCCCCHHHHHHHCCCCHHHHHHHH-HHHCCCCCCCC
Q ss_conf             989999999997228704-61420588989999999998776-0889997899987099989999999-86089875536
Q gi|254780289|r  502 WWVKQAITRSIADQSCTI-RIPVHMRDKIHKVVRTARRMSNK-IKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLET  578 (682)
Q Consensus       502 ~~i~~~i~~~~~~~~~~~-r~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~sl~~  578 (682)
                      -+|.+.+..+++-.-... -+|+++..+- +-.++...+.+- .|.--|-.+||+.+|.|.. +|.+- .+.+.|+++-.
T Consensus        60 ~~i~~~l~~YF~G~~~~f~~~pl~~~gt~-Fq~~Vw~~l~~Ip~G~t~sY~~lA~~~g~p~a-~RAVg~A~~~Np~~i~i  137 (171)
T PRK10286         60 GGLSDKLRDYFAGNLSIIDTLPTATGGTP-FQREVWQTLRTIPCGQVMHYGQLAEQLGRPGA-ARAVGAANGSNPISIVV  137 (171)
T ss_pred             HHHHHHHHHHHCCCCCCCCCCCCCCCCCH-HHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCH-HHHHHHHHHCCCCCCCC
T ss_conf             78999999998789776785675789999-99999999955899886729999999679854-89999998429988736


Q ss_pred             CCC
Q ss_conf             358
Q gi|254780289|r  579 PIG  581 (682)
Q Consensus       579 ~~~  581 (682)
                      |-+
T Consensus       138 PCH  140 (171)
T PRK10286        138 PCH  140 (171)
T ss_pred             CCC
T ss_conf             884


No 277
>cd06569 GH20_Sm-chitobiase-like The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i) a chitinase hydrolyzes the chitin to oligosaccharides and disaccharides such as di-N-acetyl-D-glucosamine and chitobiose, ii) chitobiase then further degrades these oligomers into monomers. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself.
Probab=38.62  E-value=22  Score=14.10  Aligned_cols=50  Identities=14%  Similarity=0.192  Sum_probs=36.7

Q ss_pred             HHHHHHHHHHCCCCCHHHHHHHCC------------CCCCCHHHHHHHHHHHHHCCCEEECCC
Q ss_conf             999999787848867899975268------------435998889999999984797783278
Q gi|254780289|r   31 WKKMIKLARQRGYVTIEELNAFLP------------PDEVSSEQMEDTVAMLSNMGINVVDGD   81 (682)
Q Consensus        31 ik~LI~~gke~GylTydeIn~~LP------------~d~~~~e~ie~i~~~L~~~GI~Vve~~   81 (682)
                      .=+|-+.|-.+|| +..|....+|            .+.++.++|-+|+.+=...||.|+-+.
T Consensus        56 yP~Lt~~Ga~r~~-~~~e~~~~~p~~~~~~~~~~~~~g~YT~~di~eiV~YA~~RgI~VIPEI  117 (445)
T cd06569          56 LPELTEVGAKRCH-DLSETTCLLPQLGSGPDTNNSGSGYYSRADYIEILKYAKARHIEVIPEI  117 (445)
T ss_pred             CCHHHHHHCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCEEEECC
T ss_conf             8526565120566-6433334464336787777776884689999999999997599886506


No 278
>pfam01381 HTH_3 Helix-turn-helix. This large family of DNA binding helix-turn helix proteins includes Cro and CI.
Probab=38.60  E-value=22  Score=14.09  Aligned_cols=23  Identities=30%  Similarity=0.455  Sum_probs=17.2

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             68899989966789999999999
Q gi|254780289|r  640 HTLEEVGKQFCVTRERIRQIEAK  662 (682)
Q Consensus       640 ~tl~e~~~~~~~~~er~rqi~~~  662 (682)
                      .|..++|+..|||+..|.++|..
T Consensus        10 ~tq~~lA~~~gis~~~is~~E~g   32 (55)
T pfam01381        10 LSQEELAEKLGVSRSTISKIENG   32 (55)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHCC
T ss_conf             98999999989699999999879


No 279
>pfam05049 IIGP Interferon-inducible GTPase (IIGP). Interferon-inducible GTPase (IIGP) is thought to play a role in in intracellular defence. IIGP is predominantly associated with the Golgi apparatus and also localizes to the endoplasmic reticulum and exerts a distinct role in IFN-induced intracellular membrane trafficking or processing.
Probab=38.55  E-value=22  Score=14.09  Aligned_cols=36  Identities=28%  Similarity=0.314  Sum_probs=23.1

Q ss_pred             CCCCCCCHHHHHHHHHCCCCC-----C----CHHHHHHHHHHHHH
Q ss_conf             457777289999998569768-----8----97889999999998
Q gi|254780289|r  113 ADRSTDDPVRMYLREMGSIEL-----L----SREGEIAIAKRIEA  148 (682)
Q Consensus       113 e~~rtdDPVRMYLREMG~V~L-----L----TREgEIeIAKRIE~  148 (682)
                      ..|.++=|..-||.+|+=-.-     .    =++-.|.+||.|..
T Consensus        95 G~gt~~f~~~~Yl~~~~f~~yDfFiiiss~rf~~n~v~LAk~i~~  139 (375)
T pfam05049        95 GLGATNFTVETYLEEMKFSEYDFFIIISSERFSLNDVKLAKAIQR  139 (375)
T ss_pred             CCCCCCCCHHHHHHHCCCCCCCEEEEEECCCCCHHHHHHHHHHHH
T ss_conf             999899898999987485647789999677543201899999998


No 280
>CHL00059 atpA ATP synthase CF1 alpha subunit
Probab=38.14  E-value=22  Score=14.04  Aligned_cols=49  Identities=22%  Similarity=0.291  Sum_probs=31.4

Q ss_pred             HHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHH
Q ss_conf             0289899999999972287046142058898999999999877608899978
Q gi|254780289|r  499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE  550 (682)
Q Consensus       499 ya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  550 (682)
                      |.++|.-.+|-.++.||.+-+=+   +.+.+.|+-.+.|++.--+||+|+-+
T Consensus       237 ~~Apyaa~aIAEyFrdqGkdVLl---v~DdLTr~A~A~REisLllgrPPgre  285 (501)
T CHL00059        237 YLAPYTGAALAEYFMYRERHTLI---IYDDLSKQAQAYRQMSLLLRRPPGRE  285 (501)
T ss_pred             HHHHHHHHHHHHHHHHCCCEEEE---EEECCHHHHHHHHHHHHHCCCCCCCC
T ss_conf             99999999999999977982899---98682698899999898648999766


No 281
>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=37.84  E-value=23  Score=14.01  Aligned_cols=22  Identities=41%  Similarity=0.462  Sum_probs=10.9

Q ss_pred             CCHHHHHHHCCCCHHHHHHHHH
Q ss_conf             9978999870999899999998
Q gi|254780289|r  547 PTPEEIAKKLAMPVEGVRKVLK  568 (682)
Q Consensus       547 ~~~~~~a~~~~~~~~~~~~~~~  568 (682)
                      .|-++||+.+|++.+.|..+++
T Consensus        26 ltr~eiA~~lG~t~eTVsR~l~   47 (67)
T cd00092          26 LTRQEIADYLGLTRETVSRTLK   47 (67)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHH
T ss_conf             7999999997890999999999


No 282
>smart00787 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association.
Probab=37.75  E-value=23  Score=14.00  Aligned_cols=36  Identities=19%  Similarity=0.219  Sum_probs=24.2

Q ss_pred             HHHHHHHH-CCCCCCCHHHHH--HHHHHHHHHHHHHHHH
Q ss_conf             99999985-697688978899--9999999889999999
Q gi|254780289|r  121 VRMYLREM-GSIELLSREGEI--AIAKRIEAGRAMMMAS  156 (682)
Q Consensus       121 VRMYLREM-G~V~LLTREgEI--eIAKRIE~G~~~i~~a  156 (682)
                      .-=|..-+ .+||+|.=-.-.  ++-|+|+.|+..+...
T Consensus        51 l~d~v~A~~~~iP~LELY~~sC~EL~~~I~egr~~~~~~   89 (312)
T smart00787       51 LDQYVVAGYCTVPLLELYQFSCKELKKYISEGRDLFKEI   89 (312)
T ss_pred             HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999715886099999999999999999889999999


No 283
>PRK11637 hypothetical protein; Provisional
Probab=37.67  E-value=23  Score=13.99  Aligned_cols=26  Identities=15%  Similarity=0.220  Sum_probs=8.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             05778878999999999999999999
Q gi|254780289|r  331 NQSRIDLLVEQLYDISKRIMHNEGEL  356 (682)
Q Consensus       331 ~~k~iE~L~~~l~~~~k~Ir~~Er~L  356 (682)
                      ....|+.+...+.....++......+
T Consensus        77 ~~~eI~~l~~~i~~l~~~~~~~~~~l  102 (404)
T PRK11637         77 LNKQIDEMNASIAKLEQQKAAQERSL  102 (404)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999999


No 284
>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=37.65  E-value=23  Score=13.99  Aligned_cols=27  Identities=22%  Similarity=0.405  Sum_probs=19.5

Q ss_pred             CCCCCHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf             889997899987099989999999860
Q gi|254780289|r  544 KREPTPEEIAKKLAMPVEGVRKVLKIT  570 (682)
Q Consensus       544 ~~~~~~~~~a~~~~~~~~~~~~~~~~~  570 (682)
                      .+-|+..+||+.++++..-|+++++..
T Consensus        22 ~~LPs~~~La~~~~vSr~tvr~Al~~L   48 (64)
T pfam00392        22 DKLPSERELAAEFGVSRTTVREALRRL   48 (64)
T ss_pred             CCCHHHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             998479999999796999999999999


No 285
>KOG0976 consensus
Probab=37.45  E-value=23  Score=13.97  Aligned_cols=55  Identities=18%  Similarity=0.255  Sum_probs=36.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5677653223333222221126889999998765332112468999875557899
Q gi|254780289|r  403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI  457 (682)
Q Consensus       403 ~~eI~~~q~kL~~ie~~~gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~  457 (682)
                      ++.+....+.|..+..+..--+.++|.-+-++..|.+.-..||++|-+|-=||-.
T Consensus       374 k~nve~elqsL~~l~aerqeQidelKn~if~~e~~~~dhe~~kneL~~a~ekld~  428 (1265)
T KOG0976         374 KENVEEELQSLLELQAERQEQIDELKNHIFRLEQGKKDHEAAKNELQEALEKLDL  428 (1265)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_conf             9879999999999999999999999875554664110267788899999999988


No 286
>COG5174 TFA2 Transcription initiation factor IIE, beta subunit [Transcription]
Probab=37.44  E-value=23  Score=13.97  Aligned_cols=41  Identities=20%  Similarity=0.183  Sum_probs=26.8

Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHCCCCHH-HHHHHHHHHCCC
Q ss_conf             99999987760889997899987099989-999999860898
Q gi|254780289|r  533 VRTARRMSNKIKREPTPEEIAKKLAMPVE-GVRKVLKITKEP  573 (682)
Q Consensus       533 ~~~~~~~~~~~~~~~~~~~~a~~~~~~~~-~~~~~~~~~~~~  573 (682)
                      ...+-++++++||+-+.+||+..|.|+.. .+..+++..+++
T Consensus        85 lh~aieylk~~~~P~~~eEi~dyls~~l~~~~v~Llkk~~ri  126 (285)
T COG5174          85 LHAAIEYLKQHDRPLSFEEIKDYLSIDLHNNYVLLLKKKRRI  126 (285)
T ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHCCCCCHHHHHHHHHCCCC
T ss_conf             999999999718965599998886476654699998650472


No 287
>smart00796 AHS1 Allophanate hydrolase subunit 1. This domain represents subunit 1 of allophanate hydrolase (AHS1).
Probab=37.07  E-value=13  Score=15.86  Aligned_cols=48  Identities=19%  Similarity=0.256  Sum_probs=34.2

Q ss_pred             HHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCC
Q ss_conf             9972287046142058898999999999877608899978999870999899999998608987
Q gi|254780289|r  511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI  574 (682)
Q Consensus       511 ~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  574 (682)
                      .....+++++|||.--..                --|..+.+|+..|+++++|.+......--|
T Consensus        81 ~~~~~~r~~~IPV~Yd~~----------------~gpDL~~va~~~gls~~evI~~H~~~~y~V  128 (201)
T smart00796       81 ALEVPGRIIEIPVCYGGE----------------FGPDLEFVARHNGLSVDEVIRLHSAAEYRV  128 (201)
T ss_pred             CCCCCCCEEEEEEEECCC----------------CCCCHHHHHHHHCCCHHHHHHHHHCCCEEE
T ss_conf             357898389998587998----------------777999999884959999999973689899


No 288
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=37.01  E-value=23  Score=13.92  Aligned_cols=29  Identities=17%  Similarity=0.052  Sum_probs=21.8

Q ss_pred             HCCCCCCHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf             60889997899987099989999999860
Q gi|254780289|r  542 KIKREPTPEEIAKKLAMPVEGVRKVLKIT  570 (682)
Q Consensus       542 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  570 (682)
                      .-|+..+..+||+..++|..-+.++++..
T Consensus        20 ~~~~~~~~~~Ia~~~~is~~~l~kIl~~L   48 (153)
T PRK11920         20 NDGKLSRIPEIARAYGVSELFLFKILQPL   48 (153)
T ss_pred             CCCCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             89997679999988891999999999999


No 289
>pfam06953 ArsD Arsenical resistance operon trans-acting repressor ArsD. This family consists of several bacterial arsenical resistance operon trans-acting repressor ArsD proteins. ArsD is a trans-acting repressor of the arsRDABC operon that confers resistance to arsenicals and antimonials in Escherichia coli. It possesses two-pairs of vicinal cysteine residues, Cys(12)-Cys(13) and Cys(112)-Cys(113), that potentially form separate binding sites for the metalloids that trigger dissociation of ArsD from the operon. However, as a homodimer it has four vicinal cysteine pairs.
Probab=36.75  E-value=19  Score=14.56  Aligned_cols=21  Identities=33%  Similarity=0.423  Sum_probs=17.7

Q ss_pred             HCCCCCCHHHHHHHCCCCHHH
Q ss_conf             608899978999870999899
Q gi|254780289|r  542 KIKREPTPEEIAKKLAMPVEG  562 (682)
Q Consensus       542 ~~~~~~~~~~~a~~~~~~~~~  562 (682)
                      ..||.||-+|+|+.+|++...
T Consensus        84 ~~G~YPt~eEla~w~gi~~~~  104 (119)
T pfam06953        84 KTGRYPTREELARWAGITLSP  104 (119)
T ss_pred             EECCCCCHHHHHHHHCCCCCC
T ss_conf             815699999999996998776


No 290
>TIGR02237 recomb_radB DNA repair and recombination protein RadB; InterPro: IPR011939    This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA, eukaryotic RAD51 (IPR011941 from INTERPRO) and DMC1 (IPR011940 from INTERPRO), and archaeal RadA (IPR011938 from INTERPRO) ,, .; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0008094 DNA-dependent ATPase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=36.64  E-value=17  Score=14.90  Aligned_cols=22  Identities=27%  Similarity=0.409  Sum_probs=12.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             2468999875557899988752
Q gi|254780289|r  442 SIAKKEMVEANLRLVISVAKKY  463 (682)
Q Consensus       442 ~~AK~~l~~anlr~v~~~~~~~  463 (682)
                      ......++..=|.+..++|+|+
T Consensus       127 ~~~~~~~l~~Ql~~Ll~lArk~  148 (223)
T TIGR02237       127 QISLNRELARQLTLLLSLARKK  148 (223)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHC
T ss_conf             6799999999999999998764


No 291
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=36.28  E-value=24  Score=13.83  Aligned_cols=56  Identities=18%  Similarity=0.227  Sum_probs=40.7

Q ss_pred             CCCHHCCHHHHHHHHHHHHHC-C-CC-CHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEEEC
Q ss_conf             443020289999999978784-8-86-78999752684359988899999999847977832
Q gi|254780289|r   21 SLVFDFSDDSWKKMIKLARQR-G-YV-TIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD   79 (682)
Q Consensus        21 ~~~~d~~~~~ik~LI~~gke~-G-yl-TydeIn~~LP~d~~~~e~ie~i~~~L~~~GI~Vve   79 (682)
                      .++-|..-+.|+..|--|.=+ | -| |-.+|.+.|.   +|---+=..+..|...|+-.+.
T Consensus         6 ~~l~e~V~~~ir~~I~~g~l~pG~~LP~E~eLae~~g---VSR~~VREAL~~L~~~GlV~~~   64 (251)
T PRK09990          6 RPIADVVAERIERLIVDGVLKVGQALPSERRLTEKLG---VSRSALREGLKVLRGRGIIETA   64 (251)
T ss_pred             CCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHC---CCHHHHHHHHHHHHHCCCEEEE
T ss_conf             7399999999999998099999297923999999989---7959999999999988997985


No 292
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=36.16  E-value=24  Score=13.82  Aligned_cols=48  Identities=19%  Similarity=0.315  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHHHHHHCCCCC-CCEEEHH-------------------------HHHHHHHHHHHHHHHCCCEEE
Q ss_conf             75443679999887438545-7312010-------------------------289899999999972287046
Q gi|254780289|r  473 LIQEGNIGLMKAAEKFDWCL-GYKFSTY-------------------------AMWWVKQAITRSIADQSCTIR  520 (682)
Q Consensus       473 ~~~~~~~~l~~a~~~~~~~~-g~~f~ty-------------------------a~~~i~~~i~~~~~~~~~~~r  520 (682)
                      |.|+|.-.+-+||...+|++ |.+++.-                         ...=|..+|..|+.+-+|-++
T Consensus       381 ly~~g~caitkav~~inWr~Ygl~q~p~gP~~v~VhvaSt~VPftsesKEaIAd~pEI~~EIrlAl~e~~R~L~  454 (533)
T PRK04184        381 LYDEGACVITKAVESINWKRYGLSQPPDAPLVVLVHVASTKVPYTSEGKEAIADVPEIEKEIRLALMEAARKLK  454 (533)
T ss_pred             EECCCCCHHHHHHHHCCHHHCCCCCCCCCCEEEEEEEEECCCCCCCCCHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             21266417888877478565187899998789999962068896774355433778999999999999999999


No 293
>TIGR01436 glu_cys_lig_pln glutamate--cysteine ligase; InterPro: IPR011556   These sequences represent one of two highly dissimilar forms of glutamate--cysteine ligase (gamma-glutamylcysteine synthetase), an enzyme of glutathione biosynthesis. The other group is represented by IPR006335 from INTERPRO. This form is found in plants (with a probable transit peptide), root nodule and other bacteria, but not Escherichia coli and closely related species. ; GO: 0004357 glutamate-cysteine ligase activity, 0006750 glutathione biosynthetic process, 0009507 chloroplast.
Probab=35.62  E-value=24  Score=13.76  Aligned_cols=87  Identities=15%  Similarity=0.266  Sum_probs=44.2

Q ss_pred             CCCCCHHHHHHHCCC--CHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHH-----HHHHHHHHHH
Q ss_conf             889997899987099--989999999860898755363588998604756238988998999999-----9999999999
Q gi|254780289|r  544 KREPTPEEIAKKLAM--PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-----ANLRETTTRV  616 (682)
Q Consensus       544 ~~~~~~~~~a~~~~~--~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~-----~~~~~~~~~~  616 (682)
                      |-.|+...=..+|..  |.-+.+.-|.+-          |-|+.+.        ...+..-+...     ..+-.++.++
T Consensus       284 ge~P~l~DW~~HLsT~FPeVRLK~YLEmR----------GADgg~~--------~~lcAlpAfW~glLyD~~~L~aa~D~  345 (446)
T TIGR01436       284 GELPILSDWEDHLSTLFPEVRLKRYLEMR----------GADGGSA--------RRLCALPAFWVGLLYDEEALDAALDL  345 (446)
T ss_pred             CCCCCCCCHHHHHHCCCCCHHHHHHHHCC----------CCCCCCC--------CCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             88876544143540247511211122112----------6675443--------21311367777786336789999988


Q ss_pred             HHCCCHHHHHHHHH---HHCCCCC--CCCCHHHHHHH
Q ss_conf             73299889999999---8187986--74688999899
Q gi|254780289|r  617 LASLTPREERVLRM---RFGIGMN--TDHTLEEVGKQ  648 (682)
Q Consensus       617 l~~l~~re~~v~~~---r~g~~~~--~~~tl~e~~~~  648 (682)
                      ++.=++-|++-||.   |-||-+-  ...+|..||.+
T Consensus       346 ~k~Ws~~er~~lrnevP~~gLkTl~~~g~sl~~lg~~  382 (446)
T TIGR01436       346 VKDWSMEERERLRNEVPKKGLKTLIRDGISLKDLGRD  382 (446)
T ss_pred             HHCCCHHHHHHHHHHCCHHHHCCCCCCCHHHHHHHHH
T ss_conf             6238988998776521421311668762679999999


No 294
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=35.43  E-value=24  Score=13.74  Aligned_cols=19  Identities=11%  Similarity=0.281  Sum_probs=10.2

Q ss_pred             HHHHHHHHHHHHHHHHHCC
Q ss_conf             9987555789998875223
Q gi|254780289|r  447 EMVEANLRLVISVAKKYTN  465 (682)
Q Consensus       447 ~l~~anlr~v~~~~~~~~~  465 (682)
                      ....++..|-..||.--.|
T Consensus       143 ~~~~~D~~FH~~Ia~AsgN  161 (257)
T PRK10225        143 SSESGDMQFHLAIAEATHN  161 (257)
T ss_pred             HHHHHHHHHHHHHHHHCCC
T ss_conf             6999999999999998599


No 295
>COG0853 PanD Aspartate 1-decarboxylase [Coenzyme metabolism]
Probab=35.25  E-value=4.9  Score=19.26  Aligned_cols=50  Identities=26%  Similarity=0.244  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHH
Q ss_conf             9875557899988752235677788754436799998874385457312010289899
Q gi|254780289|r  448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK  505 (682)
Q Consensus       448 l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~  505 (682)
                      ..+|||-+|=||+        ==.||.....|==...|+=++..-|-|||||+..-=|
T Consensus        14 VT~A~L~Y~GSit--------ID~dlldaagile~EkV~I~N~nNGaRf~TYvI~g~r   63 (126)
T COG0853          14 VTEADLNYVGSIT--------IDEDLLDAAGILENEKVDIVNVNNGARFSTYVIAGER   63 (126)
T ss_pred             EEECCCCEEEEEE--------ECHHHHHHCCCCCCCEEEEEECCCCCEEEEEEEECCC
T ss_conf             8502330477688--------8999996538987766899988888378999987268


No 296
>PRK09526 lacI lac repressor; Reviewed
Probab=35.14  E-value=25  Score=13.70  Aligned_cols=29  Identities=17%  Similarity=0.295  Sum_probs=16.2

Q ss_pred             HHHHHHCC-CCCCCHHHHHHHHHHHHHCCC
Q ss_conf             99975268-435998889999999984797
Q gi|254780289|r   47 EELNAFLP-PDEVSSEQMEDTVAMLSNMGI   75 (682)
Q Consensus        47 deIn~~LP-~d~~~~e~ie~i~~~L~~~GI   75 (682)
                      .-++.+|- ...++++--+.|.....++|.
T Consensus        20 sTVSrvLn~~~~vs~~tr~rV~~~a~elgY   49 (342)
T PRK09526         20 QTVSRVLNQASHVSAKTREKVEAAMAELNY   49 (342)
T ss_pred             HHHHHHHCCCCCCCHHHHHHHHHHHHHHCC
T ss_conf             999999789799999999999999998399


No 297
>PRK11886 biotin--protein ligase; Provisional
Probab=35.05  E-value=25  Score=13.69  Aligned_cols=49  Identities=14%  Similarity=0.266  Sum_probs=39.3

Q ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEEEC
Q ss_conf             8999999997878488678999752684359988899999999847977832
Q gi|254780289|r   28 DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD   79 (682)
Q Consensus        28 ~~~ik~LI~~gke~GylTydeIn~~LP~d~~~~e~ie~i~~~L~~~GI~Vve   79 (682)
                      .+++-+|+++=+...|++=++|.+.|.   ++-..+=+-+..|.++|+.|.-
T Consensus         3 ~~~~~~lL~~L~~g~~~SGe~la~~Lg---vSR~aVwK~i~~L~~~G~~I~s   51 (319)
T PRK11886          3 YEKMLQLLSLLADGDFHSGEQLAEELG---ISRAAIWKHIQTLEEWGLDIFS   51 (319)
T ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHC---CCHHHHHHHHHHHHHCCCEEEE
T ss_conf             789999999973799296999999879---8899999999999977973999


No 298
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=34.86  E-value=25  Score=13.67  Aligned_cols=79  Identities=15%  Similarity=0.167  Sum_probs=38.8

Q ss_pred             HHHHHHHHHHHHHHCCCEEECCCHHH-HHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHH--HHCCCCCCC
Q ss_conf             89899999999972287046142058-898999999999877608899978999870999899999998--608987553
Q gi|254780289|r  501 MWWVKQAITRSIADQSCTIRIPVHMR-DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLE  577 (682)
Q Consensus       501 ~~~i~~~i~~~~~~~~~~~r~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~sl~  577 (682)
                      --+|-+.+.+........-++|-.+. .|+.   ++...+....|.+-|.+|+|+.+|+|.-.+++-|.  ....-+..+
T Consensus       135 Q~~iD~l~~~~~~~~~~~~~lPKGl~~~TL~---~i~~~l~~~~~~~~sa~eva~~~giSRvTaRRYLe~L~~~g~~~~~  211 (239)
T PRK10430        135 QAELDQLIHGSSSNEQDPRRLPKGLTPQTLR---TLCQWIDAHQDYEFSTDELANEVNISRVSCRKYLIWLVNCHILFTS  211 (239)
T ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCCCHHHHH---HHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEEE
T ss_conf             9999999850578888766699999999999---9999998279998469999988585298899999999868958998


Q ss_pred             CCCCC
Q ss_conf             63588
Q gi|254780289|r  578 TPIGD  582 (682)
Q Consensus       578 ~~~~~  582 (682)
                      .-.|.
T Consensus       212 ~~YG~  216 (239)
T PRK10430        212 IHYGV  216 (239)
T ss_pred             ECCCC
T ss_conf             35789


No 299
>PRK11753 cAMP-regulatory protein; Provisional
Probab=34.72  E-value=25  Score=13.65  Aligned_cols=26  Identities=23%  Similarity=0.447  Sum_probs=15.3

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf             468899989966789999999999999832
Q gi|254780289|r  639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK  668 (682)
Q Consensus       639 ~~tl~e~~~~~~~~~er~rqi~~~a~~~l~  668 (682)
                      +.|-+|+|..+|+|||.|-    ++|++|+
T Consensus       168 ~lt~~eLA~~lG~sretvs----R~L~~L~  193 (211)
T PRK11753        168 KITRQEIGRIVGCSREMVG----RVLKMLE  193 (211)
T ss_pred             CCCHHHHHHHHCCCHHHHH----HHHHHHH
T ss_conf             4699999988699899999----9999999


No 300
>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=34.36  E-value=25  Score=13.61  Aligned_cols=29  Identities=21%  Similarity=0.266  Sum_probs=22.6

Q ss_pred             HCCCCCCHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf             60889997899987099989999999860
Q gi|254780289|r  542 KIKREPTPEEIAKKLAMPVEGVRKVLKIT  570 (682)
Q Consensus       542 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  570 (682)
                      +.+..++..+||+.||++..-|..+++-.
T Consensus        16 ~~~~~v~~~~iA~~L~Vs~~SVt~mlkkL   44 (58)
T pfam01325        16 EEKGVVKTKDLAERLNVSPSTVSEMLKKL   44 (58)
T ss_pred             CCCCCEEHHHHHHHHCCCCHHHHHHHHHH
T ss_conf             26996129999999599925299999999


No 301
>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=33.87  E-value=26  Score=13.56  Aligned_cols=26  Identities=31%  Similarity=0.482  Sum_probs=17.9

Q ss_pred             CCCCHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf             89997899987099989999999860
Q gi|254780289|r  545 REPTPEEIAKKLAMPVEGVRKVLKIT  570 (682)
Q Consensus       545 ~~~~~~~~a~~~~~~~~~~~~~~~~~  570 (682)
                      +-|+..+||+.+|+|..-|+.++...
T Consensus        24 ~LPs~~~La~~~~vSr~tvr~Al~~L   49 (66)
T cd07377          24 RLPSERELAEELGVSRTTVREALREL   49 (66)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             99279999999798889999999999


No 302
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=33.75  E-value=22  Score=14.11  Aligned_cols=25  Identities=24%  Similarity=0.125  Sum_probs=14.4

Q ss_pred             CCCHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf             9997899987099989999999860
Q gi|254780289|r  546 EPTPEEIAKKLAMPVEGVRKVLKIT  570 (682)
Q Consensus       546 ~~~~~~~a~~~~~~~~~~~~~~~~~  570 (682)
                      .-++-|+|+..|++++.||..-++.
T Consensus         7 ~m~IgelAk~~gvs~~tIRyYE~~G   31 (144)
T PRK13752          7 NLTIGVFAKAAGVNVETIRFYQRKG   31 (144)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHCC
T ss_conf             3829999999789845667987259


No 303
>PRK13394 3-hydroxybutyrate dehydrogenase; Provisional
Probab=33.25  E-value=26  Score=13.48  Aligned_cols=110  Identities=15%  Similarity=0.061  Sum_probs=61.5

Q ss_pred             HHHHHHHHHHHHHH----HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHH-H
Q ss_conf             21124689998755----578999887522356777887544367999988743854573120102898999999999-7
Q gi|254780289|r  439 CEASIAKKEMVEAN----LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI-A  513 (682)
Q Consensus       439 ~e~~~AK~~l~~an----lr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~-~  513 (682)
                      .-++.+-..|++.+    .-.+.|++-.....+...------|.+||.|++-+-=-..|.+.-+.+--||+-.+.... .
T Consensus       121 ~~~~~~~p~M~k~~~~G~IVnisS~~~~~~~~~~~~Y~asKaal~~ltk~lA~E~a~~gIrVN~V~PG~i~T~~~~~~~~  200 (262)
T PRK13394        121 LTTKAALKHMYKDDRGGVVIYMGSVHSHEASPLKSAYVTAKHGLLGLARVLAKEGAKHNVRSHVVCPGFVRTPLVDKQIP  200 (262)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEECCHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEEECCCCCCHHHHHCH
T ss_conf             99999999999837996899974577676799976899999999999999999852319699999758788702331365


Q ss_pred             HCCCEEECCCHHHHHHHHHHHHHHHHH--HHCCCCCCHHHHHHHC
Q ss_conf             228704614205889899999999987--7608899978999870
Q gi|254780289|r  514 DQSCTIRIPVHMRDKIHKVVRTARRMS--NKIKREPTPEEIAKKL  556 (682)
Q Consensus       514 ~~~~~~r~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~a~~~  556 (682)
                      +.+.-..+.  .-      ....+.+.  .-.||-.+|+|+|...
T Consensus       201 ~~~~~~~~~--~~------~~~~~~~~~~~p~~r~g~p~dvA~~v  237 (262)
T PRK13394        201 EQAKELGIS--EE------EVVKKVMLGKTVDGVFTTVEDVAQTV  237 (262)
T ss_pred             HHHHHCCCC--HH------HHHHHHHHCCCCCCCCCCHHHHHHHH
T ss_conf             578763788--58------99999986179988972999999999


No 304
>TIGR02018 his_ut_repres histidine utilization repressor; InterPro: IPR010248   This entry represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.; GO: 0003677 DNA binding, 0016564 transcription repressor activity, 0006547 histidine metabolic process, 0045892 negative regulation of transcription DNA-dependent.
Probab=33.08  E-value=26  Score=13.46  Aligned_cols=68  Identities=25%  Similarity=0.354  Sum_probs=47.3

Q ss_pred             HHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHH-HHCCCCCCCCCCC
Q ss_conf             899999999972287046142058898999999999877608899978999870999899999998-6089875536358
Q gi|254780289|r  503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK-ITKEPISLETPIG  581 (682)
Q Consensus       503 ~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~sl~~~~~  581 (682)
                      =|||.|.+.|.-..|   -|                    .-|-|+-.||++.+|+|.=.|.++|+ .+..- -|.--= 
T Consensus         5 rik~~I~~~I~SG~W---~~--------------------g~R~PsE~EL~~~~G~SRMTvnrALreLt~~G-~l~R~q-   59 (234)
T TIGR02018         5 RIKQDILERIRSGEW---PP--------------------GHRIPSENELVAQFGVSRMTVNRALRELTDAG-LLERRQ-   59 (234)
T ss_pred             HHHHHHHHCCCCCCC---CC--------------------CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC-CEEEEC-
T ss_conf             899999962578888---87--------------------67568779999774872335789999887568-188127-


Q ss_pred             CCCCCEEEEEECC--CCCCCH
Q ss_conf             8998604756238--988998
Q gi|254780289|r  582 DEDTSHLGDFIED--KNAVSP  600 (682)
Q Consensus       582 ~~~~~~~~~~~~d--~~~~~~  600 (682)
                           -+|.||.-  +...++
T Consensus        60 -----g~GTFVA~ae~k~~s~   75 (234)
T TIGR02018        60 -----GVGTFVARAEPKAQSA   75 (234)
T ss_pred             -----CCEEEECCCCCCCCCH
T ss_conf             -----8500441777653101


No 305
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=32.69  E-value=27  Score=13.42  Aligned_cols=36  Identities=19%  Similarity=0.288  Sum_probs=24.2

Q ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHH
Q ss_conf             9999999877608899978999870999899999998
Q gi|254780289|r  532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK  568 (682)
Q Consensus       532 ~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~  568 (682)
                      +.+..-..+|..+| -+..+||+.+|+|...|..-.+
T Consensus         9 ~D~~IL~~L~~d~r-~~~~eia~~lglS~~~v~~Ri~   44 (154)
T COG1522           9 IDRRILRLLQEDAR-ISNAELAERVGLSPSTVLRRIK   44 (154)
T ss_pred             HHHHHHHHHHHCCC-CCHHHHHHHHCCCHHHHHHHHH
T ss_conf             99999999997276-5799999997979899999999


No 306
>cd06919 Asp_decarbox Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent  decarboxylase in beta-alanine production. Decarboxylation of aspartate is  the major route of beta-alanine production in bacteria, and is catalyzed  by the enzyme L-aspartate decarboxylase (ADC), EC:4.1.1.11 which  requires a pyruvoyl group for its activity. The pyruvoyl cofactor is  covalently bound to the enzyme. The protein is synthesized as a  proenzyme and cleaved via self-processing at Gly23-Ser24 to yield an  alpha chain (C-terminal fragment) and beta chain (N-terminal fragment),  and the pyruvoyl group. Beta-alanine is required for the biosynthesis of  pantothenate, in which the enzyme plays a critical regulatory role. The  active site of the tetrameric enzyme is located at the interface of two  subunits, with a Lysine and a Histidine from the beta chain of one  subunit forming the active site with residues from the alpha chain of  the adjacent subunit. This alignment 
Probab=32.59  E-value=4.7  Score=19.38  Aligned_cols=35  Identities=20%  Similarity=0.180  Sum_probs=23.0

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHH
Q ss_conf             88754436799998874385457312010289899
Q gi|254780289|r  471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK  505 (682)
Q Consensus       471 ~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~  505 (682)
                      .||+...+|---.-|+=++..-|-||+|||.+--|
T Consensus        29 ~~Lm~aa~i~~~E~V~V~N~~NG~Rf~TYvI~g~~   63 (111)
T cd06919          29 EDLLEAAGILPYEKVLVVNVNNGARFETYVIPGER   63 (111)
T ss_pred             HHHHHHCCCCCCCEEEEEECCCCCEEEEEEEECCC
T ss_conf             99998759998988999989899478999986468


No 307
>TIGR02513 type_III_yscB type III secretion system chaperone, YscB family; InterPro: IPR013353    Members of this family include YscB of Yersinia and functionally equivalent (but differently named) proteins from type III secretion systems of other pathogens that affect animal cells. YscB acts, along with SycN (IPR012673 from INTERPRO), as a chaperone for YopN, a key part of a complex that regulates type III secretion so that it responds to contact with the eukaryotic target cell..
Probab=32.30  E-value=10  Score=16.78  Aligned_cols=103  Identities=18%  Similarity=0.301  Sum_probs=68.9

Q ss_pred             HHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             99877608899978999870999899999998608987553635889986047562389889989999999999999999
Q gi|254780289|r  537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV  616 (682)
Q Consensus       537 ~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~  616 (682)
                      +.+...+|+.|-+..=--...+.+++..-+++--..-+-|++|+.             .....|-+......||..+..+
T Consensus         5 ~~LA~~LG~gPFvAd~~G~Y~l~iD~~~l~l~~~g~~lll~tpL~-------------~~~~~~~~~~~~~lLk~llq~~   71 (140)
T TIGR02513         5 KSLAERLGQGPFVADRQGAYHLEIDKLTLLLKQHGSELLLETPLE-------------LRFLEPKDDQQVELLKRLLQQV   71 (140)
T ss_pred             HHHHHHCCCCCCEECCCCCEEEEECCEEEEEECCCCHHHHHCCCC-------------CCCCCCCCHHHHHHHHHHHHHH
T ss_conf             899987289983107986157878363566201363442405456-------------3214757704789999999999


Q ss_pred             HH---------CCCHHHHHHHHHHHCCCCCCCCCHHHH-HHHHCCC
Q ss_conf             73---------299889999999818798674688999-8996678
Q gi|254780289|r  617 LA---------SLTPREERVLRMRFGIGMNTDHTLEEV-GKQFCVT  652 (682)
Q Consensus       617 l~---------~l~~re~~v~~~r~g~~~~~~~tl~e~-~~~~~~~  652 (682)
                      ++         +|+.-++-||..|.+|..-.++.|+++ +++.+|-
T Consensus        72 ~~w~r~~P~~L~ld~~~~LiL~arl~l~~ld~~~L~~~L~~~~~ll  117 (140)
T TIGR02513        72 LKWLRRYPQALVLDADGQLILEARLRLDELDNDQLEELLAKHVNLL  117 (140)
T ss_pred             HHHHHCCCCEEEECCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHH
T ss_conf             9875138836866553111888655211589889999999999999


No 308
>TIGR02267 TIGR02267 Myxococcus xanthus paralogous family TIGR02267; InterPro: IPR011753   This family consists of at least 7 paralogs in Myxococcus xanthus, a member of the Deltaproteobacteria. The function is unknown..
Probab=32.20  E-value=27  Score=13.36  Aligned_cols=24  Identities=29%  Similarity=0.361  Sum_probs=13.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999876533211246899987
Q gi|254780289|r  427 FRHIVSMVRKGECEASIAKKEMVE  450 (682)
Q Consensus       427 lK~i~r~I~~ge~e~~~AK~~l~~  450 (682)
                      |+++.++|+.|=.+.-+|=.+|++
T Consensus        62 L~e~~~RIr~GS~RL~rAL~~a~~   85 (123)
T TIGR02267        62 LKEISRRIREGSRRLSRALTEAVR   85 (123)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999988865644899999999986


No 309
>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=32.08  E-value=27  Score=13.35  Aligned_cols=23  Identities=30%  Similarity=0.265  Sum_probs=17.0

Q ss_pred             CHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf             97899987099989999999860
Q gi|254780289|r  548 TPEEIAKKLAMPVEGVRKVLKIT  570 (682)
Q Consensus       548 ~~~~~a~~~~~~~~~~~~~~~~~  570 (682)
                      |+.|+|+.+|+|+..++---+..
T Consensus         2 tIgevAk~~gvs~~TlRyYE~~G   24 (108)
T cd01107           2 TIGEFAKLSNLSIKALRYYDKIG   24 (108)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHCC
T ss_conf             78999999895999999999859


No 310
>pfam12129 Phtf-FEM1B_bdg Male germ-cell putative homeodomain transcription factor. This domain is found in bacteria and eukaryotes, and is typically between 101 and 140 amino acids in length. Phtf proteins do not display any sequence similarity to known or predicted proteins, but their conservation among species suggests an essential function. The 84 kDa Phtf1 protein is an integral membrane protein, anchored to a cell membrane by six to eight trans-membrane domains, that is associated with a domain of the endoplasmic reticulum (ER) juxtaposed to the Golgi apparatus. It is present during meiosis and spermiogenesis, and, by the end of spermiogenesis, is released from the mature spermatozoon within the residual bodies. Phtf1 enhances the binding of FEM1B -feminisation homologue 1B - to cell membranes. Fem-1 was initially identified in the signaling pathway for sex determination, as well as being implicated in apoptosis, but its biochemical role is still unclear, and neither FEM1B nor PHT
Probab=31.91  E-value=20  Score=14.51  Aligned_cols=57  Identities=21%  Similarity=0.347  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHH
Q ss_conf             24689998755578999887522356777887544367999988743854573120102898999999999
Q gi|254780289|r  442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI  512 (682)
Q Consensus       442 ~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~  512 (682)
                      ..-|.++|--.|--=.+-+|-     -|..-+..-...|+++.+         =|.-|+-|||.|--.+.+
T Consensus        42 ~~lK~dLIDVDLVRGStF~KA-----KP~~~w~svtr~gi~Rvl---------f~P~y~~WWiQqTS~~iF   98 (159)
T pfam12129        42 GHLKPDLIDVDLVRGSTFAKA-----KPELPWTSLTRKGAVRVV---------FFPIFAKWWVQVTSPRIF   98 (159)
T ss_pred             CCCCCCCEEEEEECCCCCCCC-----CCCCCHHHHHHHHHHHHH---------HHHHHHHHHHHHCCHHHH
T ss_conf             788800133320126665666-----887749999999999999---------999999999985227899


No 311
>pfam00325 Crp Bacterial regulatory proteins, crp family.
Probab=31.75  E-value=28  Score=13.31  Aligned_cols=21  Identities=38%  Similarity=0.532  Sum_probs=11.8

Q ss_pred             CHHHHHHHCCCCHHHHHHHHH
Q ss_conf             978999870999899999998
Q gi|254780289|r  548 TPEEIAKKLAMPVEGVRKVLK  568 (682)
Q Consensus       548 ~~~~~a~~~~~~~~~~~~~~~  568 (682)
                      +-.+||..+|++.+.|..++.
T Consensus         4 srqdIadylGlt~ETVsR~l~   24 (32)
T pfam00325         4 SRQEIADYLGLTRETVSRLLK   24 (32)
T ss_pred             CHHHHHHHHCCHHHHHHHHHH
T ss_conf             588999984725999999999


No 312
>PRK00876 nadE NAD synthetase; Reviewed
Probab=31.67  E-value=28  Score=13.30  Aligned_cols=35  Identities=17%  Similarity=0.226  Sum_probs=24.9

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHH
Q ss_conf             746889998996678999999999999983296777
Q gi|254780289|r  638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS  673 (682)
Q Consensus       638 ~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~  673 (682)
                      ...+.+++++.+|+|.|.|..+-.. +..-||.+|-
T Consensus       277 ~~~~~~~~~~~~g~~~e~v~~v~~~-i~~kr~~t~~  311 (325)
T PRK00876        277 HGVPAEVVAAALGLTPEQVERVWRD-IEAKRRTTRY  311 (325)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHH-HHHHHHHCCC
T ss_conf             4999999998839899999999999-9987530210


No 313
>PRK03837 transcriptional regulator NanR; Provisional
Probab=31.65  E-value=28  Score=13.29  Aligned_cols=51  Identities=20%  Similarity=0.335  Sum_probs=25.6

Q ss_pred             CHHCCHHHHHHHHHHHHHC-C-CC-CHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCE
Q ss_conf             3020289999999978784-8-86-78999752684359988899999999847977
Q gi|254780289|r   23 VFDFSDDSWKKMIKLARQR-G-YV-TIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN   76 (682)
Q Consensus        23 ~~d~~~~~ik~LI~~gke~-G-yl-TydeIn~~LP~d~~~~e~ie~i~~~L~~~GI~   76 (682)
                      +-|.--+.|+..|--|.=+ | -| |-.+|.+-|.   ++---+=+.+..|...|+-
T Consensus        15 l~e~V~~~lr~~I~~g~l~pG~rLp~E~eLae~lg---VSRtpVREAL~~L~~~GlV   68 (243)
T PRK03837         15 LSEEVEERLEQMIRSGEFGPGEQLPSERELMAFFG---VGRPSVREALQALKRKGLV   68 (243)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHC---CCHHHHHHHHHHHHHCCCE
T ss_conf             99999999999998399999497935999999979---6978999999999988998


No 314
>COG1649 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.50  E-value=27  Score=13.39  Aligned_cols=23  Identities=13%  Similarity=0.241  Sum_probs=15.2

Q ss_pred             CCCCCHHHHHHHHHHHHHCCCEE
Q ss_conf             43599888999999998479778
Q gi|254780289|r   55 PDEVSSEQMEDTVAMLSNMGINV   77 (682)
Q Consensus        55 ~d~~~~e~ie~i~~~L~~~GI~V   77 (682)
                      ...++..++-+++..|..||++=
T Consensus        58 ~v~~~~~el~~~ld~l~~ln~NT   80 (418)
T COG1649          58 RVLFQRQELKDILDDLQKLNFNT   80 (418)
T ss_pred             CCCCCHHHHHHHHHHHHHCCCCE
T ss_conf             41036999999999999709852


No 315
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=31.43  E-value=28  Score=13.27  Aligned_cols=22  Identities=41%  Similarity=0.392  Sum_probs=13.0

Q ss_pred             CCHHHHHHHCCCCHHHHHHHHH
Q ss_conf             9978999870999899999998
Q gi|254780289|r  547 PTPEEIAKKLAMPVEGVRKVLK  568 (682)
Q Consensus       547 ~~~~~~a~~~~~~~~~~~~~~~  568 (682)
                      -|..|||+.+|.+...|++.++
T Consensus        62 ~Ti~EIAeelG~TeqTir~hlk   83 (182)
T COG1318          62 MTISEIAEELGRTEQTVRNHLK   83 (182)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHH
T ss_conf             7499999996877999999975


No 316
>pfam00382 TFIIB Transcription factor TFIIB repeat.
Probab=31.24  E-value=28  Score=13.25  Aligned_cols=67  Identities=18%  Similarity=0.169  Sum_probs=35.7

Q ss_pred             HHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH
Q ss_conf             89998709998999999986089875536358899860475623898899899999999999999997329988999999
Q gi|254780289|r  550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR  629 (682)
Q Consensus       550 ~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~  629 (682)
                      ..++..||+|..-...+..+.+.......-                ..-+|.-.+.-...                  +.
T Consensus         2 ~r~~~~L~L~~~i~~~A~~i~~~~~~~~~~----------------~Grs~~~iaaA~iY------------------~A   47 (71)
T pfam00382         2 KRFADALELPKKVADAANELAKLALDDNLL----------------KGRSPESIAAACLY------------------IA   47 (71)
T ss_pred             HHHHHHCCCCHHHHHHHHHHHHHHHHCCCC----------------CCCCHHHHHHHHHH------------------HH
T ss_conf             688977799889999999999999885874----------------69989999999999------------------99


Q ss_pred             HHHCCCCCCCCCHHHHHHHHCCCH
Q ss_conf             981879867468899989966789
Q gi|254780289|r  630 MRFGIGMNTDHTLEEVGKQFCVTR  653 (682)
Q Consensus       630 ~r~g~~~~~~~tl~e~~~~~~~~~  653 (682)
                      -|   ..+.|+|+.||+..+|||.
T Consensus        48 cr---~~~~~rt~~eia~v~~vs~   68 (71)
T pfam00382        48 CR---LEEVKRTLKEISSVAQVSE   68 (71)
T ss_pred             HH---HCCCCCCHHHHHHHHCCCC
T ss_conf             99---8089989999999968987


No 317
>PRK00413 thrS threonyl-tRNA synthetase; Reviewed
Probab=31.10  E-value=19  Score=14.52  Aligned_cols=10  Identities=10%  Similarity=0.567  Sum_probs=3.9

Q ss_pred             CCCCCCCHHH
Q ss_conf             6976889788
Q gi|254780289|r  129 GSIELLSREG  138 (682)
Q Consensus       129 G~V~LLTREg  138 (682)
                      |+++++|-+.
T Consensus        53 ~~leiit~~d   62 (639)
T PRK00413         53 ATVEIVTADD   62 (639)
T ss_pred             CEEEEECCCC
T ss_conf             7899946999


No 318
>KOG1495 consensus
Probab=30.83  E-value=14  Score=15.61  Aligned_cols=62  Identities=31%  Similarity=0.397  Sum_probs=41.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHH--HCCCCCCCEE---------EHHHHHHHH
Q ss_conf             46899987555789998875223567778875443679999887--4385457312---------010289899
Q gi|254780289|r  443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE--KFDWCLGYKF---------STYAMWWVK  505 (682)
Q Consensus       443 ~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~--~~~~~~g~~f---------~tya~~~i~  505 (682)
                      ..|+=-+.||-++|+--|-.-..-|-..+||+|- |+-++|++=  --.|+..+.|         -||+||-+-
T Consensus        79 ~~~Dy~~sa~S~lvIiTAGarq~~gesRL~lvQr-NV~ifK~iip~lv~ySpd~~llvvSNPVDilTYv~wKLS  151 (332)
T KOG1495          79 ASKDYSVSANSKLVIITAGARQSEGESRLDLVQR-NVDIFKAIIPALVKYSPDCILLVVSNPVDILTYVTWKLS  151 (332)
T ss_pred             ECCCCCCCCCCCEEEEECCCCCCCCCHHHHHHHH-HHHHHHHHHHHHHHCCCCEEEEEECCCHHHHHHHHHHHC
T ss_conf             6676323479868999567778987178999998-899999987888504887089996580378888889871


No 319
>COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]
Probab=30.82  E-value=29  Score=13.19  Aligned_cols=40  Identities=13%  Similarity=0.333  Sum_probs=32.6

Q ss_pred             HHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             9999999998776088999789998709998999999986
Q gi|254780289|r  530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI  569 (682)
Q Consensus       530 ~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  569 (682)
                      -++.++...+.+.++++-+.++||..+|||...+....+.
T Consensus       220 ~~l~~~i~~me~nle~plsl~~LA~~~~~S~R~leRlF~~  259 (328)
T COG4977         220 PRLLRAIELMEANLEEPLSLEELADRAGLSRRQLERLFRA  259 (328)
T ss_pred             HHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             7899999999986538868999999968788789999999


No 320
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=30.65  E-value=29  Score=13.17  Aligned_cols=27  Identities=26%  Similarity=0.401  Sum_probs=20.3

Q ss_pred             CCCCCHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf             889997899987099989999999860
Q gi|254780289|r  544 KREPTPEEIAKKLAMPVEGVRKVLKIT  570 (682)
Q Consensus       544 ~~~~~~~~~a~~~~~~~~~~~~~~~~~  570 (682)
                      .+-|+..+||+.+++|..-|+++++..
T Consensus        18 ~~LPs~~~la~~~~vSr~tvr~A~~~L   44 (60)
T smart00345       18 DKLPSERELAAQLGVSRTTVREALSRL   44 (60)
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             988109999999894999999999999


No 321
>KOG4021 consensus
Probab=30.61  E-value=24  Score=13.78  Aligned_cols=13  Identities=15%  Similarity=0.524  Sum_probs=7.3

Q ss_pred             CCCEEEHHHHHHH
Q ss_conf             5731201028989
Q gi|254780289|r  492 LGYKFSTYAMWWV  504 (682)
Q Consensus       492 ~g~~f~tya~~~i  504 (682)
                      |.|-||+|---|-
T Consensus       176 R~~Dys~~yg~~t  188 (239)
T KOG4021         176 RNFDYSQWYGSWT  188 (239)
T ss_pred             CCCCHHHHCCCCC
T ss_conf             4475677515122


No 322
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=30.35  E-value=29  Score=13.14  Aligned_cols=23  Identities=30%  Similarity=0.452  Sum_probs=12.7

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             68899989966789999999999
Q gi|254780289|r  640 HTLEEVGKQFCVTRERIRQIEAK  662 (682)
Q Consensus       640 ~tl~e~~~~~~~~~er~rqi~~~  662 (682)
                      .|..++|+..|+|.-.|.++|.-
T Consensus        11 lsq~~lA~~~gis~~~is~~E~g   33 (56)
T smart00530       11 LTQEELAEKLGVSRSTLSRIENG   33 (56)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHCC
T ss_conf             99999999989599999999979


No 323
>TIGR03337 phnR transcriptional regulator protein. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.
Probab=30.29  E-value=29  Score=13.13  Aligned_cols=45  Identities=13%  Similarity=0.135  Sum_probs=25.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             222112688999999876533211246899987555789998875223567
Q gi|254780289|r  418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL  468 (682)
Q Consensus       418 ~~~gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~  468 (682)
                      -..|-.+.--.++.++..-...-+++|=+.|+...|--      +..++|.
T Consensus        19 ~~~G~~LPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~------r~~G~GT   63 (231)
T TIGR03337        19 LLPGDKLPSERDLGERFNTTRVTIREALQQLEAEGLIY------REDRRGW   63 (231)
T ss_pred             CCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE------EECCCEE
T ss_conf             99959785899999997979999999999999879969------9668667


No 324
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=30.23  E-value=29  Score=13.12  Aligned_cols=29  Identities=14%  Similarity=0.248  Sum_probs=17.7

Q ss_pred             CCCCHHHHHHHCCCCHHHHHHHHHHHCCC
Q ss_conf             89997899987099989999999860898
Q gi|254780289|r  545 REPTPEEIAKKLAMPVEGVRKVLKITKEP  573 (682)
Q Consensus       545 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  573 (682)
                      |.-|..|+|+..|+|+.-+..+-+-...|
T Consensus        17 rGmT~~eLAe~AGIS~s~LSqIE~Gk~NP   45 (119)
T PRK13890         17 RHMTKKELSDRSGVSISFLSDLTTGKANP   45 (119)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHCCCCCC
T ss_conf             59979999988298899999997799898


No 325
>cd02986 DLP Dim1 family, Dim1-like protein (DLP) subfamily; DLP is a novel protein which shares 38% sequence identity to Dim1. Like Dim1, it is also implicated in pre-mRNA splicing and cell cycle progression. DLP is located in the nucleus and has been shown to interact with the U5 small nuclear ribonucleoprotein particle (snRNP)-specific 102kD protein (or Prp6). Dim1 protein, also known as U5 snRNP-specific 15kD protein is a component of U5 snRNP, which pre-assembles with U4/U6 snRNPs to form a [U4/U6:U5] tri-snRNP complex required for pre-mRNA splicing. Dim1 adopts a thioredoxin fold but does not contain the redox active CXXC motif.
Probab=30.01  E-value=28  Score=13.23  Aligned_cols=18  Identities=17%  Similarity=0.143  Sum_probs=15.5

Q ss_pred             CCCCCCCCCHHHHHHHHH
Q ss_conf             034577772899999985
Q gi|254780289|r  111 DSADRSTDDPVRMYLREM  128 (682)
Q Consensus       111 ~~e~~rtdDPVRMYLREM  128 (682)
                      -.-+||..||+.|.|-|+
T Consensus        18 ViRFGr~~d~~Cm~mDei   35 (114)
T cd02986          18 VLRFGRDEDAVCLQLDDI   35 (114)
T ss_pred             EEEECCCCCCHHHHHHHH
T ss_conf             998469999349889899


No 326
>TIGR02404 trehalos_R_Bsub trehalose operon repressor; InterPro: IPR012770    This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from Escherichia coli..
Probab=29.96  E-value=30  Score=13.09  Aligned_cols=33  Identities=24%  Similarity=0.333  Sum_probs=25.1

Q ss_pred             HHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCC
Q ss_conf             760889997899987099989999999860898
Q gi|254780289|r  541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP  573 (682)
Q Consensus       541 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  573 (682)
                      +.--.=||-.+|++..+.|.+.||+|+....+.
T Consensus        19 k~G~~LPSE~~L~~~Y~~SReTvRKAL~~L~~~   51 (236)
T TIGR02404        19 KEGDLLPSEHELMEQYGASRETVRKALNLLTEA   51 (236)
T ss_pred             CCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf             887738887899986068745889999999857


No 327
>PRK09973 putative outer membrane lipoprotein; Provisional
Probab=29.72  E-value=30  Score=13.06  Aligned_cols=28  Identities=14%  Similarity=0.381  Sum_probs=15.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             0057788789999999999999999999
Q gi|254780289|r  330 LNQSRIDLLVEQLYDISKRIMHNEGELL  357 (682)
Q Consensus       330 l~~k~iE~L~~~l~~~~k~Ir~~Er~L~  357 (682)
                      -++.++++|...+..+|.+|.+++..+.
T Consensus        21 sn~~kv~qLsSdVqtLN~KVdqLs~Dv~   48 (85)
T PRK09973         21 VNEQKVNQLASNVQTLNAKIARLEQDMK   48 (85)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             5558899998889999999999998899


No 328
>PRK12824 acetoacetyl-CoA reductase; Provisional
Probab=29.61  E-value=30  Score=13.05  Aligned_cols=99  Identities=20%  Similarity=0.153  Sum_probs=61.1

Q ss_pred             HHHHHHHHHHHH---HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCC
Q ss_conf             124689998755---57899988752235677788754436799998874385457312010289899999999972287
Q gi|254780289|r  441 ASIAKKEMVEAN---LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC  517 (682)
Q Consensus       441 ~~~AK~~l~~an---lr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~  517 (682)
                      ++.+-..|.+.+   .-.+.|++-.....|..------.|-+||.|..-+-=..+|.+.-+.+--||.-.+....     
T Consensus       119 ~~~~~~~m~~~~~G~IVnisS~~~~~~~~~~~~Y~asKaal~~ltk~lA~E~a~~gIrvN~I~PG~i~T~~~~~~-----  193 (245)
T PRK12824        119 TQPLFPAMCEQGYGRIINISSVNGLKGQFGQTNYSAAKAGMIGFTKALASEGARYGITVNCIAPGYIATPMVEQA-----  193 (245)
T ss_pred             HHHHHHHHHHCCCCEEEEECCHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCEEEEEEEECCCCCCCCHHC-----
T ss_conf             999999999839955999746775778899689999999999999999999725491999997446878210005-----


Q ss_pred             EEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHC
Q ss_conf             046142058898999999999877608899978999870
Q gi|254780289|r  518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL  556 (682)
Q Consensus       518 ~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~  556 (682)
                          +-...+.      ...  ..-+||-.+|+|+|...
T Consensus       194 ----~~e~~~~------~~~--~~Pl~R~g~peevA~~v  220 (245)
T PRK12824        194 ----GPEVLQS------IKN--QIPMKRLGTPEEIAAAV  220 (245)
T ss_pred             ----CHHHHHH------HHH--CCCCCCCCCHHHHHHHH
T ss_conf             ----9999999------985--69988987899999999


No 329
>pfam02969 TAF TATA box binding protein associated factor (TAF). TAF proteins adopt a histone-like fold.
Probab=29.57  E-value=30  Score=13.04  Aligned_cols=46  Identities=22%  Similarity=0.386  Sum_probs=22.9

Q ss_pred             HHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHH
Q ss_conf             9999981879867468899989966789999999999999832967778
Q gi|254780289|r  626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK  674 (682)
Q Consensus       626 ~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~  674 (682)
                      +++.--.||+.-.+-....++..   ..-|||||=..|++=+||..|.+
T Consensus        10 k~iAeS~Gi~~l~de~a~~La~d---veyRl~eiiqeA~KFMrhskR~~   55 (66)
T pfam02969        10 KVIAESLGITNLSDEAAALLAED---VEYRLKEIVQDAAKFMRHSKRQK   55 (66)
T ss_pred             HHHHHHCCCCCCCHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             99999949888999999998999---99999999999999999867577


No 330
>KOG0697 consensus
Probab=29.57  E-value=30  Score=13.04  Aligned_cols=35  Identities=17%  Similarity=0.354  Sum_probs=27.5

Q ss_pred             CHHHHHH--------HHHHHHHCCCCCHHHHHHHCCCCCCCHH
Q ss_conf             2899999--------9997878488678999752684359988
Q gi|254780289|r   27 SDDSWKK--------MIKLARQRGYVTIEELNAFLPPDEVSSE   61 (682)
Q Consensus        27 ~~~~ik~--------LI~~gke~GylTydeIn~~LP~d~~~~e   61 (682)
                      +++.++.        .++.|-..|||.+||+-..|++..-.+|
T Consensus        81 sse~F~~~~k~gsv~~~~~GIrtGFL~iDE~mr~~~~~~~~~d  123 (379)
T KOG0697          81 SSEEFRGMTKNGSVENVEKGIRTGFLSIDEIMRTLSDISKGSD  123 (379)
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHCCEEHHHHHHHHHHHHCCCC
T ss_conf             3587763124785889986676340018888765155421344


No 331
>pfam05635 Ribosomal_S23p S23 ribosomal protein. This family consists of bacterial 23S rRNA proteins.
Probab=29.56  E-value=30  Score=13.04  Aligned_cols=13  Identities=23%  Similarity=0.457  Sum_probs=4.6

Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             1268899999987
Q gi|254780289|r  422 ISISEFRHIVSMV  434 (682)
Q Consensus       422 l~i~ElK~i~r~I  434 (682)
                      ++..++..+...+
T Consensus        88 i~~~~~~~l~~~~  100 (110)
T pfam05635        88 ISEEEYEELLEEL  100 (110)
T ss_pred             CCHHHHHHHHHHH
T ss_conf             9999999999999


No 332
>TIGR01942 pcnB poly(A) polymerase; InterPro: IPR010206   This entry describes the pcnB family of poly(A) polymerases (also known as plasmid copy number protein). These enzymes sequentially add adenosine nucleotides to the 3' end of RNAs, targeting them for degradation by the cell , . This was originally described for anti-sense RNAs, but was later demonstrated for mRNAs as well . Members of this family are as yet limited to the gamma- and beta-proteobacteria, with putative members in the Chlamydiacae and spirochetes. This family has homology to tRNA nucleotidyltransferase.; GO: 0003723 RNA binding, 0004652 polynucleotide adenylyltransferase activity, 0006378 mRNA polyadenylation.
Probab=29.53  E-value=18  Score=14.70  Aligned_cols=12  Identities=33%  Similarity=0.883  Sum_probs=7.2

Q ss_pred             CCEEEHHHHHHH
Q ss_conf             731201028989
Q gi|254780289|r  493 GYKFSTYAMWWV  504 (682)
Q Consensus       493 g~~f~tya~~~i  504 (682)
                      |-.-.+||.||-
T Consensus       392 g~~~~~~~~W~~  403 (448)
T TIGR01942       392 GKEEAKLAEWWT  403 (448)
T ss_pred             CCCCHHHHHHHH
T ss_conf             430012544456


No 333
>PRK04406 hypothetical protein; Provisional
Probab=29.44  E-value=30  Score=13.03  Aligned_cols=52  Identities=15%  Similarity=0.190  Sum_probs=42.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             9999999999999862100577887899999999999999999999999712
Q gi|254780289|r  313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG  364 (682)
Q Consensus       313 k~~kl~~eL~e~~~~lkl~~k~iE~L~~~l~~~~k~Ir~~Er~L~rl~~k~~  364 (682)
                      ....+...|.++-+.+-|--..|+.|.+.+......|..+...+.-++.+.+
T Consensus         5 ~~~~Le~Ri~eLE~rlAFQE~tIeeLN~~v~~qq~~i~~lq~qlr~L~~klk   56 (75)
T PRK04406          5 TIEQLEERINDLECQLAFQEQTIEELNDALSQQQLLITKMQDQMKYVVGKVK   56 (75)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             8999999999999999978999999999999999999999999999999998


No 334
>PRK13209 L-xylulose 5-phosphate 3-epimerase; Reviewed
Probab=29.07  E-value=31  Score=12.98  Aligned_cols=48  Identities=25%  Similarity=0.455  Sum_probs=20.6

Q ss_pred             HHHHHHHHHHHCCC----CCHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEE
Q ss_conf             99999997878488----6789997526843599888999999998479778
Q gi|254780289|r   30 SWKKMIKLARQRGY----VTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV   77 (682)
Q Consensus        30 ~ik~LI~~gke~Gy----lTydeIn~~LP~d~~~~e~ie~i~~~L~~~GI~V   77 (682)
                      .+++-+.++|+=||    ++.||=.+.++.=..+.+++..|...+.+.||.|
T Consensus        22 sw~e~~~~ak~~Gfd~iElsiDe~d~~~~rL~w~~~~~~~ir~~~~~~gi~i   73 (283)
T PRK13209         22 CWLEKLRIAKTAGFDFVEMSVDETDERLARLDWSREQRLALVNALVETGFRV   73 (283)
T ss_pred             CHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCC
T ss_conf             9999999999859987998426853100358999999999999999819986


No 335
>PRK05557 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Validated
Probab=28.81  E-value=31  Score=12.95  Aligned_cols=97  Identities=20%  Similarity=0.237  Sum_probs=58.7

Q ss_pred             HHHHHHHHHHHH---HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCC
Q ss_conf             124689998755---57899988752235677788754436799998874385457312010289899999999972287
Q gi|254780289|r  441 ASIAKKEMVEAN---LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC  517 (682)
Q Consensus       441 ~~~AK~~l~~an---lr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~  517 (682)
                      ++.+-..|.+.+   .-.+-|++-.+...+...-----.|-.||+|+.-+.=-.+|.|..+-+-=||.-.+++.+     
T Consensus       122 ~~~~~p~m~~~~~G~IVnisS~~~~~~~~~~~~Y~asKaal~~lt~~lA~e~~~~gIrvN~V~PG~i~T~~~~~~-----  196 (248)
T PRK05557        122 TKAVARPMMKQRSGRIINISSVVGLMGNPGQANYAASKAGVIGFTKSLARELASRGITVNAVAPGFIETDMTDAL-----  196 (248)
T ss_pred             HHHHHHHHHHCCCCEEEEECCHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCEEEEEEEECCCCCCCCCCC-----
T ss_conf             999999999706971899804665678999555699999999999999998533194999997488877542117-----


Q ss_pred             EEECCCHHHHHHHHHHHHHHHH--HHHCCCCCCHHHHHHHC
Q ss_conf             0461420588989999999998--77608899978999870
Q gi|254780289|r  518 TIRIPVHMRDKIHKVVRTARRM--SNKIKREPTPEEIAKKL  556 (682)
Q Consensus       518 ~~r~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~a~~~  556 (682)
                          +-.          ....+  ..-++|-.+|+|+|...
T Consensus       197 ----~~~----------~~~~~~~~~pl~R~~~p~dva~~v  223 (248)
T PRK05557        197 ----PED----------VKEAILAQIPLGRLGQPEEIASAV  223 (248)
T ss_pred             ----CHH----------HHHHHHHCCCCCCCCCHHHHHHHH
T ss_conf             ----999----------999998579999980999999999


No 336
>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=28.73  E-value=31  Score=12.94  Aligned_cols=23  Identities=17%  Similarity=0.147  Sum_probs=16.6

Q ss_pred             CCCHHHHHHHCCCCHHHHHHHHH
Q ss_conf             99978999870999899999998
Q gi|254780289|r  546 EPTPEEIAKKLAMPVEGVRKVLK  568 (682)
Q Consensus       546 ~~~~~~~a~~~~~~~~~~~~~~~  568 (682)
                      ..+..+.|..++++..-|..-++
T Consensus        18 G~S~~eaA~~F~Is~~Tv~rWlk   40 (120)
T pfam01710        18 GGSITEASKVFQIGRATIYRWLK   40 (120)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             99999999993702999999985


No 337
>pfam04100 Vps53_N Vps53-like, N-terminal. Vps53 complexes with Vps52 and Vps54 to form a multi- subunit complex involved in regulating membrane trafficking events.
Probab=28.30  E-value=31  Score=12.88  Aligned_cols=28  Identities=14%  Similarity=0.421  Sum_probs=17.4

Q ss_pred             CHHHHHHHCCCCCCCHHHHHHHHHHHHHC
Q ss_conf             78999752684359988899999999847
Q gi|254780289|r   45 TIEELNAFLPPDEVSSEQMEDTVAMLSNM   73 (682)
Q Consensus        45 TydeIn~~LP~d~~~~e~ie~i~~~L~~~   73 (682)
                      .-+-||..||++. +...|++++..++.-
T Consensus         6 pv~~iN~lFp~e~-SL~~id~~i~~l~~~   33 (375)
T pfam04100         6 ALEYINQLFPTEQ-SLTNIDSLIQKIQEE   33 (375)
T ss_pred             HHHHHHHHCCCHH-HHHHHHHHHHHHHHH
T ss_conf             8999988599968-886179999999999


No 338
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=28.26  E-value=31  Score=12.88  Aligned_cols=31  Identities=16%  Similarity=0.190  Sum_probs=25.5

Q ss_pred             HHHCCCCCCHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf             7760889997899987099989999999860
Q gi|254780289|r  540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKIT  570 (682)
Q Consensus       540 ~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  570 (682)
                      ....+++.+..|||+.+|+|...+..++...
T Consensus        14 l~~~~~~~sl~eia~~~~l~ksT~~RlL~tL   44 (91)
T smart00346       14 LAEEPGGLTLAELAERLGLSKSTAHRLLNTL   44 (91)
T ss_pred             HHHCCCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             9728999899999999890999999999999


No 339
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=28.18  E-value=32  Score=12.87  Aligned_cols=18  Identities=11%  Similarity=0.209  Sum_probs=9.6

Q ss_pred             CCCHHHHHHHHCCCHHHH
Q ss_conf             468899989966789999
Q gi|254780289|r  639 DHTLEEVGKQFCVTRERI  656 (682)
Q Consensus       639 ~~tl~e~~~~~~~~~er~  656 (682)
                      |.|=+++|...|+|||.|
T Consensus       173 ~lT~~dLA~~lG~trETV  190 (224)
T PRK09391        173 PMSRRDIADYLGLTIETV  190 (224)
T ss_pred             CCCHHHHHHHHCCCHHHH
T ss_conf             579999998879979999


No 340
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=28.10  E-value=32  Score=12.86  Aligned_cols=37  Identities=11%  Similarity=0.116  Sum_probs=27.9

Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             9999998776088999789998709998999999986
Q gi|254780289|r  533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI  569 (682)
Q Consensus       533 ~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  569 (682)
                      .++...+.+.+..+.|.++||+.+|+|......+.+.
T Consensus         8 ~~~~~yI~~h~~~~i~l~~lA~~~~~S~~~l~r~Fk~   44 (107)
T PRK10219          8 QTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRT   44 (107)
T ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             9999999986699999999998989399999999999


No 341
>pfam02261 Asp_decarbox Aspartate decarboxylase. Decarboxylation of aspartate is the major route of beta-alanine production in bacteria, and is catalysed by the enzyme aspartate decarboxylase EC:4.1.1.11 which requires a pyruvoyl group for its activity. It is synthesized initially as a proenzyme which is then proteolytically cleaved to an alpha (C-terminal) and beta (N-terminal) subunit and a pyruvoyl group. This family contains both chains of aspartate decarboxylase.
Probab=28.07  E-value=6.4  Score=18.36  Aligned_cols=35  Identities=20%  Similarity=0.219  Sum_probs=21.6

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHH
Q ss_conf             87544367999988743854573120102898999
Q gi|254780289|r  472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ  506 (682)
Q Consensus       472 ~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~  506 (682)
                      ||+...+|---.-|+=++..-|-||+|||.+--+.
T Consensus        31 ~Lm~aagi~~~E~V~V~Nv~NG~R~~TYvI~g~~g   65 (116)
T pfam02261        31 DLLDAAGILEYEKVQIVNVNNGERFETYVIPGERG   65 (116)
T ss_pred             HHHHHCCCCCCCEEEEEECCCCCEEEEEEEECCCC
T ss_conf             99987599989889999898996899998864799


No 342
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=28.00  E-value=32  Score=12.85  Aligned_cols=37  Identities=19%  Similarity=0.261  Sum_probs=22.7

Q ss_pred             HHHHCCCCC------CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             998187986------74688999899667899999999999998329
Q gi|254780289|r  629 RMRFGIGMN------TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       629 ~~r~g~~~~------~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
                      .-+||-.+.      -|.|-+++|...|+|||.|-    +.|++|+.
T Consensus       168 ~~~~g~~~~~~~~i~l~lt~~dLA~~lG~trEtVs----R~L~~L~~  210 (235)
T PRK11161        168 SRRFAQRGFSPREFRLTMTRGDIGNYLGLTVETIS----RLLGRFQK  210 (235)
T ss_pred             HHHHCCCCCCCCEEEECCCHHHHHHHHCCCHHHHH----HHHHHHHH
T ss_conf             99838778888779823789999988789899999----99999997


No 343
>cd01667 TGS_ThrRS_N TGS _ThrRS_N:  ThrRS (threonyl-tRNA Synthetase)  is a class II tRNA synthetase that couples threonine to its cognate tRNA.  In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase, and SpoT proteins where it occurs. The TGS domain is thought to interact with the tRNA acceptor arm along with an adjacent N-terminal domain. The specific function of TGS is not well understood.
Probab=27.90  E-value=9.3  Score=17.06  Aligned_cols=47  Identities=19%  Similarity=0.289  Sum_probs=36.5

Q ss_pred             CCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEE
Q ss_conf             08899978999870999899999998608987553635889986047
Q gi|254780289|r  543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG  589 (682)
Q Consensus       543 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~  589 (682)
                      +....|+.++|+.++-+..+-.-+.+++.+.+-|..|+.+|..-.+.
T Consensus        13 ~~~~~T~~eiA~~i~~~l~k~~vaa~vng~l~DL~~~i~~d~~v~~i   59 (61)
T cd01667          13 FPKGTTPLDIAKSISPGLAKKAVAAKVNGELVDLSRPLEEDCELEII   59 (61)
T ss_pred             CCCCCCHHHHHHHHCHHHHCCEEEEEECCEEECCCCCCCCCCEEEEE
T ss_conf             78998999999985966341379999999998357412699999998


No 344
>pfam09413 DUF2007 Protein of unknown function (DUF2007). This is a family of proteins with unknown function.
Probab=27.90  E-value=25  Score=13.64  Aligned_cols=11  Identities=36%  Similarity=0.579  Sum_probs=4.0

Q ss_pred             HHHHHHCCCEE
Q ss_conf             99998479778
Q gi|254780289|r   67 VAMLSNMGINV   77 (682)
Q Consensus        67 ~~~L~~~GI~V   77 (682)
                      -+.|.+.||..
T Consensus        16 ~aLL~~agI~~   26 (68)
T pfam09413        16 QALLKGAGIEA   26 (68)
T ss_pred             HHHHHHCCCCE
T ss_conf             99971279977


No 345
>COG3711 BglG Transcriptional antiterminator [Transcription]
Probab=27.77  E-value=32  Score=12.82  Aligned_cols=54  Identities=17%  Similarity=0.175  Sum_probs=40.2

Q ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCH-HHHHHHHHHHHHCCCEEECCCC
Q ss_conf             99999999787848867899975268435998-8899999999847977832784
Q gi|254780289|r   29 DSWKKMIKLARQRGYVTIEELNAFLPPDEVSS-EQMEDTVAMLSNMGINVVDGDD   82 (682)
Q Consensus        29 ~~ik~LI~~gke~GylTydeIn~~LP~d~~~~-e~ie~i~~~L~~~GI~Vve~~~   82 (682)
                      ..-.-|..+--+++++|-.++.+.|.=.--+. -.|..|-..|.+-|+.++....
T Consensus         5 ~~~~~l~~l~~~~~~~~~~~la~~l~vS~Rti~~~i~~In~~l~~~~~~~~~~~~   59 (491)
T COG3711           5 RREQLLLLLLLKNPLLTIKELAEQLGVSRRTIRYDIKKINESLEEGGIPIIKRKG   59 (491)
T ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCEEEECCC
T ss_conf             7899999987346886999999996976744988899999888618850244378


No 346
>PRK05629 hypothetical protein; Validated
Probab=27.62  E-value=32  Score=12.80  Aligned_cols=43  Identities=28%  Similarity=0.283  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHC
Q ss_conf             98999999999877608899978999870999899999998608
Q gi|254780289|r  528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK  571 (682)
Q Consensus       528 ~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  571 (682)
                      .+....|.-.++.+..|+ .+..+||..||+++=.|+.++.-++
T Consensus       244 ~L~~~~r~l~~~~~~~~~-~~~~~iA~~Lgv~P~~vkk~~~qar  286 (331)
T PRK05629        244 ALSMKVGQIARLYSTRGR-INGFELAKELGMPPFVVEKTAKVAR  286 (331)
T ss_pred             HHHHHHHHHHHHHHHHCC-CCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             999999999999975169-9989999883999899999999982


No 347
>KOG2822 consensus
Probab=27.52  E-value=12  Score=16.16  Aligned_cols=28  Identities=18%  Similarity=0.323  Sum_probs=19.4

Q ss_pred             HHHHHHHCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             99887522356777887544367999988
Q gi|254780289|r  457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAA  485 (682)
Q Consensus       457 ~~~~~~~~~~~~~~~~~~~~~~~~l~~a~  485 (682)
                      +..-+=|++. ..++|++.-+-+|.+-++
T Consensus       203 v~lgRiY~GM-HgvlDi~sG~ligvl~~~  230 (407)
T KOG2822         203 VCLGRIYCGM-HGVLDIVSGLLIGVLILI  230 (407)
T ss_pred             HHHHHHHHCC-HHHHHHHHHHHHHHHHHH
T ss_conf             9987787041-488898740698887855


No 348
>pfam02082 Rrf2 Transcriptional regulator. This family is related to pfam001022 and other transcription regulation families (personal obs: Yeats C).
Probab=27.49  E-value=32  Score=12.78  Aligned_cols=46  Identities=22%  Similarity=0.218  Sum_probs=32.6

Q ss_pred             CCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEE
Q ss_conf             8899978999870999899999998608987553635889986047
Q gi|254780289|r  544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG  589 (682)
Q Consensus       544 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~  589 (682)
                      +..-+..+||+.+++|..-++++++..+..--+.+--|-.|+..|.
T Consensus        22 ~~~~s~~~iA~~~~i~~~~l~kil~~L~~~gli~s~rG~~GGy~L~   67 (82)
T pfam02082        22 EGPVTSEEIAERQNISPVYLRKILAKLRKAGLVKSVRGPGGGYRLA   67 (82)
T ss_pred             CCEECHHHHHHHHCCCHHHHHHHHHHHHCCCCEEECCCCCCCCCCC
T ss_conf             9849599999878909999999999810279825658999881134


No 349
>TIGR03324 alt_F1F0_F1_al alternate F1F0 ATPase, F1 subunit alpha. A small number of taxonomically diverse prokaryotic species, including Methanosarcina barkeri, have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 alpha subunit of this apparent second ATP synthase.
Probab=27.25  E-value=33  Score=12.75  Aligned_cols=50  Identities=22%  Similarity=0.349  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHH
Q ss_conf             02898999999999722870461420588989999999998776088999789
Q gi|254780289|r  499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE  551 (682)
Q Consensus       499 ya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  551 (682)
                      |-++|.-.+|-.++.||.+-+=+   +.+.+.|+-.+.|++.-.+||+|+-+-
T Consensus       236 ~~Apyaa~aiAEyFrd~G~dVLl---v~DdLTr~A~A~REisLll~rpPgrea  285 (497)
T TIGR03324       236 YIAPYAATSIGEHFMEQGRDVLI---VYDDLTQHARAYRELSLLLRRPPGREA  285 (497)
T ss_pred             HHHHHHHHHHHHHHHHCCCEEEE---EEECHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             88789999999999968974899---997806999999999986489998778


No 350
>cd00907 Bacterioferritin Bacterioferritin, ferritin-like diiron-binding domain. Bacterioferritins, also known as cytochrome b1, are members of a broad superfamily of ferritin-like diiron-carboxylate proteins. Similar to ferritin in architecture, Bfr forms an oligomer of 24 subunits that assembles to form a hollow sphere with 432 symmetry. Up to 12 heme cofactor groups (iron protoporphyrin IX or coproporphyrin III) are bound between dimer pairs. The role of the heme is unknown, although it may be involved in mediating iron-core reduction and iron release. Each subunit is composed of a four-helix bundle which carries a diiron ferroxidase center; it is here that initial oxidation of ferrous iron by molecular oxygen occurs, facilitating the detoxification of iron, protection against dioxygen and radical products, and storage of ferric-hydroxyphosphate at the core. Some bacterioferritins are composed of two subunit types, one conferring heme-binding ability (alpha) and the other (beta) best
Probab=27.23  E-value=33  Score=12.75  Aligned_cols=14  Identities=14%  Similarity=0.157  Sum_probs=5.1

Q ss_pred             HHHHHHHHHHHCCC
Q ss_conf             99999999971253
Q gi|254780289|r  353 EGELLRLAQSYGIK  366 (682)
Q Consensus       353 Er~L~rl~~k~~i~  366 (682)
                      +.-+.|+..-.|.|
T Consensus        55 ~~l~~rIl~LgG~P   68 (153)
T cd00907          55 DKLIERILFLEGLP   68 (153)
T ss_pred             HHHHHHHHHCCCCC
T ss_conf             99999999839998


No 351
>pfam02271 UCR_14kD Ubiquinol-cytochrome C reductase complex 14kD subunit. The ubiquinol-cytochrome C reductase complex (cytochrome bc1 complex) is a respiratory multienzyme complex. This Pfam family represents the 14kD (or VI) subunit of the complex which is not directly involved in electron transfer, but has a role in assembly of the complex.
Probab=27.08  E-value=33  Score=12.73  Aligned_cols=45  Identities=20%  Similarity=0.330  Sum_probs=31.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             8999875557899988752235677788754436799998874385
Q gi|254780289|r  445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW  490 (682)
Q Consensus       445 K~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~  490 (682)
                      ...++..-=+|-++. -.|...||-+.||+-|-|--.-+|+.|--.
T Consensus         7 l~~~~~p~a~w~~na-sgyrk~GL~~DDll~ee~~~v~eAL~RLP~   51 (105)
T pfam02271         7 LSKLLKPLAKWYFNA-AGYRQLGLRYDDLIPEENPDVQEALRRLPR   51 (105)
T ss_pred             HHHHHHHHHHHHHHH-HCHHHCCCCHHHCCCCCCHHHHHHHHHCCH
T ss_conf             999999999999998-452221663864568799899999986899


No 352
>pfam03917 GSH_synth_ATP Eukaryotic glutathione synthase, ATP binding domain.
Probab=26.94  E-value=33  Score=12.71  Aligned_cols=128  Identities=17%  Similarity=0.255  Sum_probs=72.4

Q ss_pred             HHHHCCCCCCCEEEHH---HHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCH
Q ss_conf             8874385457312010---2898999999999722870461420588989999999998776088999789998709998
Q gi|254780289|r  484 AAEKFDWCLGYKFSTY---AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV  560 (682)
Q Consensus       484 a~~~~~~~~g~~f~ty---a~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~  560 (682)
                      .|.-.=+|-||-.+-|   +.|=.     |-.-.+++.|++|.-     .--.-.+++..|.+-.   |.-|. ++.-..
T Consensus       256 eVavVYfRaGY~P~dY~se~~W~a-----Rl~lE~S~AIKcPsi-----~~qLaGtKKVQQ~La~---p~vLe-rFl~~~  321 (469)
T pfam03917       256 EVAVVYFRAGYTPDDYPSESEWEA-----RLLMEQSSAIKCPSI-----STQLAGTKKIQQELAK---PGVLE-RFLENK  321 (469)
T ss_pred             EEEEEEEECCCCCCCCCCHHHHHH-----HHHHHHCCCCCCCCH-----HHHHHCCHHHHHHHCC---HHHHH-HHCCCH
T ss_conf             899999707768133798788999-----999986377148899-----9986242999998668---54998-872999


Q ss_pred             HHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHH--------HHHHHHHHHHHHHCCCH---HHHHHHH
Q ss_conf             999999986089875536358899860475623898899899999--------99999999999732998---8999999
Q gi|254780289|r  561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI--------QANLRETTTRVLASLTP---REERVLR  629 (682)
Q Consensus       561 ~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~--------~~~~~~~~~~~l~~l~~---re~~v~~  629 (682)
                      +++..+.+....-.|||..  +.++.....     ....|+..+.        ...-.+.|...|..|++   |.+-||.
T Consensus       322 ~~~~~lr~tFa~ly~Ld~~--~~g~~~v~~-----A~~~P~~yVLKPQREGGGNNiyg~dI~~~L~~l~~~ee~~ayILM  394 (469)
T pfam03917       322 EDIAKLRKTFAGLWSLDDT--EEGDEIVKL-----AIEKPELFVLKPQREGGGNNIYGDDMREALLKLQKSEERAAYILM  394 (469)
T ss_pred             HHHHHHHHHHCCCCCCCCC--CCCHHHHHH-----HHHCHHHEEECCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHEEE
T ss_conf             9999999972346306875--121999999-----874945246647676760001107999999856881231101043


Q ss_pred             HHH
Q ss_conf             981
Q gi|254780289|r  630 MRF  632 (682)
Q Consensus       630 ~r~  632 (682)
                      -|.
T Consensus       395 erI  397 (469)
T pfam03917       395 ERI  397 (469)
T ss_pred             ECC
T ss_conf             035


No 353
>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=26.92  E-value=33  Score=12.71  Aligned_cols=43  Identities=21%  Similarity=0.211  Sum_probs=34.8

Q ss_pred             HHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHC
Q ss_conf             8999999999877608899978999870999899999998608
Q gi|254780289|r  529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK  571 (682)
Q Consensus       529 ~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  571 (682)
                      -..+.++--.++.+.|++-.-++||+.++.+...||+.|...+
T Consensus         6 Qr~IL~aLI~lY~~~~~pVks~~IAe~l~~spgTIRN~M~~L~   48 (79)
T pfam03444         6 QKEILQALINLYRKKGRAVKGEEIADIIGRNPGTVRNQMQSLK   48 (79)
T ss_pred             HHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             9999999999999729986679999998789088999999999


No 354
>PRK06200 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase; Provisional
Probab=26.81  E-value=33  Score=12.69  Aligned_cols=94  Identities=13%  Similarity=0.173  Sum_probs=48.6

Q ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHH-HH
Q ss_conf             55789998875223567778875443679999887438545731201028989999999997228704614205889-89
Q gi|254780289|r  452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK-IH  530 (682)
Q Consensus       452 nlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~-~~  530 (682)
                      ..-++.|++-.+...|.+.------|-.||.|+.-. ++..+.|.-+-+-.||.-.+.....       .  .+.+. ..
T Consensus       137 ~iI~~~S~~~~~~~~~~~~Y~asKaal~~ltr~lA~-ela~~IrVN~I~PG~i~T~~~~~~~-------~--~~~~~~~~  206 (263)
T PRK06200        137 SIIFTLSNSSFYPGGGGPLYTASKHAVVGLVRQLAY-ELAPKIRVNGVAPGGTVTDLRGPAS-------L--GQGETSIS  206 (263)
T ss_pred             EEEEECCHHHCCCCCCCHHHHHHHHHHHHHHHHHHH-HHCCCCEEEEEECCCCCCCCCCCCC-------C--CHHHHHHC
T ss_conf             799982202125889856789999999999999999-9779988999962889888644211-------2--14665420


Q ss_pred             HHHHHHHHHH--HHCCCCCCHHHHHHH
Q ss_conf             9999999987--760889997899987
Q gi|254780289|r  531 KVVRTARRMS--NKIKREPTPEEIAKK  555 (682)
Q Consensus       531 ~~~~~~~~~~--~~~~~~~~~~~~a~~  555 (682)
                      ........+.  .-+||-++|+|+|..
T Consensus       207 ~~~~~~~~~~~~~Pl~R~g~p~dia~~  233 (263)
T PRK06200        207 DVPGLADMIAAITPLQFAPQPEDHTGP  233 (263)
T ss_pred             CCHHHHHHHHHCCCCCCCCCHHHHHHH
T ss_conf             468899999717998998399999999


No 355
>PRK02119 hypothetical protein; Provisional
Probab=26.74  E-value=33  Score=12.69  Aligned_cols=50  Identities=14%  Similarity=0.213  Sum_probs=40.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             99999999999862100577887899999999999999999999999712
Q gi|254780289|r  315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG  364 (682)
Q Consensus       315 ~kl~~eL~e~~~~lkl~~k~iE~L~~~l~~~~k~Ir~~Er~L~rl~~k~~  364 (682)
                      ..+...|.++-.++-|--..|+.|-+.+......|..+...+.-++.+.+
T Consensus         5 ~~Le~Ri~~LE~rlAFQe~tIe~LNq~v~~Qq~~i~~l~~ql~~L~~rlk   54 (73)
T PRK02119          5 QMLENRIAELEMKIAFQENLLEELNQALIQQQFVIDKMQVQLRHMANKLK   54 (73)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999978989999999999999999999999999999998


No 356
>smart00491 HELICc2 helicase superfamily c-terminal domain.
Probab=26.59  E-value=33  Score=12.67  Aligned_cols=48  Identities=19%  Similarity=0.049  Sum_probs=23.6

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHCCCCCCCEEE--HHHHHHHHHHHHHHHHH
Q ss_conf             6777887544367999988743854573120--10289899999999972
Q gi|254780289|r  467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS--TYAMWWVKQAITRSIAD  514 (682)
Q Consensus       467 ~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~--tya~~~i~~~i~~~~~~  514 (682)
                      |+||.-.-..=..--+.-.++.-...|+++.  .=|...++|+|-|.|..
T Consensus        77 glP~p~~~d~~~~~r~~y~~~~~~~~~~~~~y~~~a~~~v~QaiGR~IR~  126 (142)
T smart00491       77 GIPFPNPDSPILRARLEYLDEKGGIRPFDEVYLFDAMRALAQAIGRAIRH  126 (142)
T ss_pred             ECCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHCCCCCC
T ss_conf             08999999999999999999864899833112589999999982967546


No 357
>TIGR02470 sucr_synth sucrose synthase; InterPro: IPR012820    This entry represents sucrose synthase an enzyme that despite its name, generally uses rather produces sucrose. Sucrose plus UDP (or ADP) becomes D-fructose plus UDP-glucose (or ADP-glucose), which is then available for cell wall (or starch) biosynthesis. The enzyme is homologous to sucrose phosphate synthase, which catalyses the penultimate step in sucrose synthesis. Sucrose synthase is found, so far, exclusively in plants and cyanobacteria.; GO: 0016157 sucrose synthase activity.
Probab=26.28  E-value=29  Score=13.17  Aligned_cols=62  Identities=19%  Similarity=0.345  Sum_probs=44.9

Q ss_pred             HCCCEEECCCHHHHH------HH---------HH-HHHHHHHHHHCCCCCCH------------HHHHHHCCCCHHHHHH
Q ss_conf             228704614205889------89---------99-99999987760889997------------8999870999899999
Q gi|254780289|r  514 DQSCTIRIPVHMRDK------IH---------KV-VRTARRMSNKIKREPTP------------EEIAKKLAMPVEGVRK  565 (682)
Q Consensus       514 ~~~~~~r~~~~~~~~------~~---------~~-~~~~~~~~~~~~~~~~~------------~~~a~~~~~~~~~~~~  565 (682)
                      +++++.|||...-.-      |+         .+ .-+.+++..+++-.|..            -=||.+||++--.|..
T Consensus       343 ~~~~ILRVPFr~~nG~~~~~WISRFeiWPYLE~FA~D~~~e~~~el~g~PDLIIGNYSDGNLVA~LLA~kLgVTQC~IAH  422 (790)
T TIGR02470       343 EHAHILRVPFRTENGIILRKWISRFEIWPYLETFAEDAEKEILAELQGKPDLIIGNYSDGNLVASLLARKLGVTQCTIAH  422 (790)
T ss_pred             CCCEEEECCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEECCCCHHHHHHHHHHHCCCCCCCHHH
T ss_conf             85316421664347730036633012472045668999999999846899706732563589999998533622220333


Q ss_pred             HHHHHCCCCC
Q ss_conf             9986089875
Q gi|254780289|r  566 VLKITKEPIS  575 (682)
Q Consensus       566 ~~~~~~~~~s  575 (682)
                      +|.-++.|-|
T Consensus       423 ALEKtKY~~S  432 (790)
T TIGR02470       423 ALEKTKYPDS  432 (790)
T ss_pred             HCCCCCCCCC
T ss_conf             1334367664


No 358
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=26.19  E-value=34  Score=12.61  Aligned_cols=26  Identities=23%  Similarity=0.180  Sum_probs=21.8

Q ss_pred             CCCCCCHHHHHHHCCCCHHHHHHHHH
Q ss_conf             08899978999870999899999998
Q gi|254780289|r  543 IKREPTPEEIAKKLAMPVEGVRKVLK  568 (682)
Q Consensus       543 ~~~~~~~~~~a~~~~~~~~~~~~~~~  568 (682)
                      ...+-|.++||+.|+.+...|.++++
T Consensus        39 ~~~~~tvdelae~lnr~rStv~rsl~   64 (126)
T COG3355          39 ENGPLTVDELAEILNRSRSTVYRSLQ   64 (126)
T ss_pred             HCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             46995799999997831999999999


No 359
>TIGR01572 A_thl_para_3677 Arabidopsis paralogous family TIGR01572; InterPro: IPR006462   These sequences comprise a paralogous family of hypothetical proteins in Arabidopsis thaliana. No homologs are detected from other species. Length heterogeneity within the family is attributable partly to a 21-residue repeat present in from zero to three tandem copies. The proteins have no known function..
Probab=26.17  E-value=8.5  Score=17.35  Aligned_cols=42  Identities=29%  Similarity=0.415  Sum_probs=35.7

Q ss_pred             HHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHH
Q ss_conf             9887522356777887544367999988743854573120102
Q gi|254780289|r  458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA  500 (682)
Q Consensus       458 ~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya  500 (682)
                      ++.|-|..-||..--..+--|+-|| +|+||+.++-+-.|||=
T Consensus        46 ~lVk~yA~~GLHrYN~l~G~nl~L~-~v~kFNm~~~~~~s~Yy   87 (290)
T TIGR01572        46 DLVKLYALVGLHRYNVLEGTNLELD-AVKKFNMKLMCALSSYY   87 (290)
T ss_pred             CEEEEEEECCCHHHHHCCCCCCCCC-CHHHHHHHHHHHCCCCE
T ss_conf             2153320002200000268752000-02245578764027421


No 360
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator; InterPro: IPR014290   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 proteins belonging to the Rtf2 family of transcriptional regulators and are found, typically, as the first gene of the SUF operon. They are found only in a subset of the genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role..
Probab=26.14  E-value=34  Score=12.61  Aligned_cols=52  Identities=19%  Similarity=0.207  Sum_probs=31.5

Q ss_pred             HHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEE
Q ss_conf             9877608899978999870999899999998608987553635889986047
Q gi|254780289|r  538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG  589 (682)
Q Consensus       538 ~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~  589 (682)
                      .+.+.-...=++.+||+..|+....|+++|+...+.-=.+-.=|=.|+..|.
T Consensus        17 ~lA~~~~~~ySAA~lA~~tgL~~pTvsK~Lk~L~~A~lV~S~RGv~GGY~La   68 (130)
T TIGR02944        17 VLAQADEQTYSAAELAEQTGLEAPTVSKILKALSEAGLVTSKRGVEGGYTLA   68 (130)
T ss_pred             HHHCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCCCCCCCCHHHHHH
T ss_conf             9852899700688878645988604789988764287532434643004620


No 361
>PRK00901 methylated-DNA--protein-cysteine methyltransferase; Provisional
Probab=25.88  E-value=34  Score=12.57  Aligned_cols=75  Identities=16%  Similarity=0.213  Sum_probs=54.8

Q ss_pred             HHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHH-CCCCCCHHHHHHHCCCCHHHHHHHH-HHHCCCCCCCCCCC
Q ss_conf             99999999722870461420588989999999998776-0889997899987099989999999-86089875536358
Q gi|254780289|r  505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK-IKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIG  581 (682)
Q Consensus       505 ~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~sl~~~~~  581 (682)
                      .+.+..+++......-+|.++..| .+-.++.+.+.+- .|.--|-.+||+.+|-|. -+|.+- .+.+.|+++=-|-+
T Consensus        48 ~~qL~~YF~g~~~~f~lpl~~~GT-~FQ~~VW~~L~~IP~G~t~sY~~lA~~ig~p~-a~RAVG~A~g~Npi~iiIPCH  124 (155)
T PRK00901         48 NKQLEEYFRGKRKKFDLPLAPQGT-EFQKKVWKALQEIPYGETRSYGEIAKNIGNPK-ACRAVGLANNKNPIPIFIPCH  124 (155)
T ss_pred             HHHHHHHHCCCCCCCCCCCCCCCC-HHHHHHHHHHCCCCCCCCEEHHHHHHHHCCCC-CCHHHHHHHHCCCCCCCCCCC
T ss_conf             999999985998655521268999-99999999748479976300999999938996-217999998309977536897


No 362
>TIGR01097 3A0109s02M phosphonate ABC transporter, permease protein; InterPro: IPR005769    Bacterial binding protein-dependent transport systems ,  are multicomponent systems typically composed of a periplasmic substrate-binding protein, one or two reciprocally homologous integral inner-membrane proteins and one or two peripheral membrane ATP-binding proteins that couple energy to the active transport system. The integral inner-membrane proteins translocate the substrate across the membrane. It has been shown ,  that most of these proteins contain a conserved region located about 80 to 100 residues from their C-terminal extremity. This region seems  to be located in a cytoplasmic loop between two transmembrane domains. Apart from the conserved region, the sequence of these proteins is quite divergent, and they have a variable number of transmembrane helices.    These proteins represent a family of phosphonate uptake transporters., probably responsible for the transport of phosphonate across the inner membrane. ; GO: 0015604 phosphonate transmembrane transporter activity, 0015716 phosphonate transport, 0005887 integral to plasma membrane.
Probab=25.60  E-value=22  Score=14.10  Aligned_cols=12  Identities=33%  Similarity=0.639  Sum_probs=8.8

Q ss_pred             HHHHHHHHHHHH
Q ss_conf             898999999999
Q gi|254780289|r  501 MWWVKQAITRSI  512 (682)
Q Consensus       501 ~~~i~~~i~~~~  512 (682)
                      .|||||-++|-.
T Consensus        37 n~W~~~~VRRLM   48 (192)
T TIGR01097        37 NPWVRQIVRRLM   48 (192)
T ss_pred             CCCCCHHHHHHH
T ss_conf             842104789999


No 363
>PTZ00183 centrin; Provisional
Probab=25.60  E-value=35  Score=12.54  Aligned_cols=54  Identities=15%  Similarity=0.270  Sum_probs=30.2

Q ss_pred             CCCHHCCHHHHHHHHHHHH-----HCCCCCHHHHHHHCCCCC--CCHHHHHHHHHHHHHCC
Q ss_conf             4430202899999999787-----848867899975268435--99888999999998479
Q gi|254780289|r   21 SLVFDFSDDSWKKMIKLAR-----QRGYVTIEELNAFLPPDE--VSSEQMEDTVAMLSNMG   74 (682)
Q Consensus        21 ~~~~d~~~~~ik~LI~~gk-----e~GylTydeIn~~LP~d~--~~~e~ie~i~~~L~~~G   74 (682)
                      ...-+.+.+.+++|-+.-+     ..|+|+..|+-.+|..-.  .+.+.+..++..+...|
T Consensus        16 ~~~~~ls~eq~~elke~F~~~D~d~dG~Is~~El~~~L~~lG~~~t~~el~~i~~~~D~d~   76 (168)
T PTZ00183         16 SIRPELNEEQKLEIREAFDLFDTDGTGYIDVKELKVAMRALGFEPKKEEIKRMIADVDKDG   76 (168)
T ss_pred             HHCCCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCC
T ss_conf             2002699999999999999986998696979999999999089999999999998628789


No 364
>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=25.50  E-value=33  Score=12.66  Aligned_cols=23  Identities=17%  Similarity=0.251  Sum_probs=14.6

Q ss_pred             CHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf             97899987099989999999860
Q gi|254780289|r  548 TPEEIAKKLAMPVEGVRKVLKIT  570 (682)
Q Consensus       548 ~~~~~a~~~~~~~~~~~~~~~~~  570 (682)
                      |+.|+|+.+|+|+..++.--++.
T Consensus         2 tIgelA~~~gvs~~TiRyYE~~G   24 (120)
T cd04781           2 DIAEVARQSGLPASTLRYYEEKG   24 (120)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHCC
T ss_conf             68999999886889898999649


No 365
>pfam08726 efhand_Ca_insen Ca2+ insensitive EF hand. EF hands are helix-loop-helix binding motifs involved in the regulation of many cellular processes. EF hands usually bind to Ca2+ ions which causes a major conformational change that allows the protein to interact with its designated targets. This domain corresponds to an EF hand which has partially or entirely lost its calcium-binding properties. The calcium insensitive EF hand is still able to mediate protein-protein recognition.
Probab=25.47  E-value=35  Score=12.52  Aligned_cols=27  Identities=33%  Similarity=0.645  Sum_probs=21.0

Q ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHCCCCC
Q ss_conf             899999999787848867899975268435
Q gi|254780289|r   28 DDSWKKMIKLARQRGYVTIEELNAFLPPDE   57 (682)
Q Consensus        28 ~~~ik~LI~~gke~GylTydeIn~~LP~d~   57 (682)
                      .+.+|.|   +..+.|||-.||..+||++.
T Consensus         9 ~~sFr~l---A~~KpYVT~~dLr~~L~pdq   35 (69)
T pfam08726         9 EQSFRAL---AEGKPYVTEEDLRRALTPEQ   35 (69)
T ss_pred             HHHHHHH---HCCCCCCCHHHHHHHCCHHH
T ss_conf             9999998---48998107999997689999


No 366
>pfam09184 PPP4R2 PPP4R2. PPP4R2 (protein phosphatase 4 core regulatory subunit R2) is the regulatory subunit of the histone H2A phosphatase complex. It has been shown to confer resistance to the anticancer drug cisplatin in yeast, and may confer resistance in higher eukaryotes.
Probab=25.17  E-value=35  Score=12.48  Aligned_cols=11  Identities=9%  Similarity=0.301  Sum_probs=3.6

Q ss_pred             HHHHHHHHHHH
Q ss_conf             99999862100
Q gi|254780289|r  321 LVKLVGSLSLN  331 (682)
Q Consensus       321 L~e~~~~lkl~  331 (682)
                      +.+.|..+-|+
T Consensus        89 ~~~~F~~~PFT   99 (285)
T pfam09184        89 IVTNFNGIPFT   99 (285)
T ss_pred             HHHHCCCCCHH
T ss_conf             99743688718


No 367
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=25.05  E-value=35  Score=12.46  Aligned_cols=35  Identities=11%  Similarity=0.174  Sum_probs=19.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             22112688999999876533211246899987555
Q gi|254780289|r  419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANL  453 (682)
Q Consensus       419 ~~gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anl  453 (682)
                      ..|-.+.--.++.++......-+++|=+.|+...|
T Consensus        24 ~~G~~LPsE~eLa~~~~VSR~TvR~Al~~L~~eGl   58 (239)
T PRK09764         24 KPGDALPTESALQTEFGVSRVTVRQALRQLVEQQI   58 (239)
T ss_pred             CCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCC
T ss_conf             99599929999999979799999999999997899


No 368
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=25.00  E-value=36  Score=12.46  Aligned_cols=110  Identities=17%  Similarity=0.182  Sum_probs=55.5

Q ss_pred             HHHHHHHHHH---CCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHH
Q ss_conf             9999998776---0889997899987099989999999860898755363588998604756238988998999999999
Q gi|254780289|r  533 VRTARRMSNK---IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL  609 (682)
Q Consensus       533 ~~~~~~~~~~---~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~  609 (682)
                      .+....++..   .-++-|..+||+.+|+.+..|..+.+-    -.+.+|.|=   ..|-.|....-........+....
T Consensus       347 v~~Q~~Ff~~G~~~lkPL~lkdiA~~lglheSTVSRav~~----Kyi~tp~Gi---~~lk~FFs~~~~~~~g~~~S~~~i  419 (475)
T PRK12469        347 VARQRDFFRYGEIALKPLVLRDVAEELGLHESTVSRATGN----KYMATPRGT---FEFKHFFPRKLEAAGGGECSAAAV  419 (475)
T ss_pred             HHHHHHHHHCCCCCCCCCCHHHHHHHHCCCCCHHHHHHCC----CEECCCCCE---EEHHHHHHHCCCCCCCCCCCHHHH
T ss_conf             9999999847850036734999999819982037688627----502379854---669986232056899741149999


Q ss_pred             HHHHHHHHH------CCCHHHH-HHHHHHHCCCCCCCCCHHHHHHHHCC
Q ss_conf             999999973------2998899-99999818798674688999899667
Q gi|254780289|r  610 RETTTRVLA------SLTPREE-RVLRMRFGIGMNTDHTLEEVGKQFCV  651 (682)
Q Consensus       610 ~~~~~~~l~------~l~~re~-~v~~~r~g~~~~~~~tl~e~~~~~~~  651 (682)
                      +..|.+++.      .|+...= .+|.-+ ||..-+ +|-.--=..+|+
T Consensus       420 k~~I~~lI~~Ed~~kPlSD~~I~~~L~~~-Gi~IaR-RTVAKYRe~L~I  466 (475)
T PRK12469        420 RALIKDMIAAEQATDPLSDVALAERLAGR-GILLAR-RTVAKYRQAMKI  466 (475)
T ss_pred             HHHHHHHHHHCCCCCCCCHHHHHHHHHHC-CCCEEE-CCHHHHHHHCCC
T ss_conf             99999999844899998999999999977-998763-257999987399


No 369
>TIGR01736 FGAM_synth_II phosphoribosylformylglycinamidine synthase II; InterPro: IPR010074   Phosphoribosylformylglycinamidine synthase is a single, long polypeptide in most bacteria. Three proteins are required in Bacillus subtilis and many other species. This is the longest of the three and is designated PurL, phosphoribosylformylglycinamidine synthase II, or FGAM synthase II.; GO: 0004642 phosphoribosylformylglycinamidine synthase activity, 0006189 'de novo' IMP biosynthetic process, 0005737 cytoplasm.
Probab=24.99  E-value=36  Score=12.46  Aligned_cols=18  Identities=33%  Similarity=0.375  Sum_probs=11.4

Q ss_pred             HHHCCCCCCHHHHHHHCC
Q ss_conf             776088999789998709
Q gi|254780289|r  540 SNKIKREPTPEEIAKKLA  557 (682)
Q Consensus       540 ~~~~~~~~~~~~~a~~~~  557 (682)
                      +..+||+|+.-|+|-.-.
T Consensus        13 F~~LGRePn~~E~~~f~~   30 (763)
T TIGR01736        13 FKELGREPNDTELAMFEA   30 (763)
T ss_pred             HHHHCCCHHHHHHHHHHH
T ss_conf             997388834899999985


No 370
>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=24.87  E-value=36  Score=12.44  Aligned_cols=23  Identities=26%  Similarity=0.160  Sum_probs=17.0

Q ss_pred             CHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf             97899987099989999999860
Q gi|254780289|r  548 TPEEIAKKLAMPVEGVRKVLKIT  570 (682)
Q Consensus       548 ~~~~~a~~~~~~~~~~~~~~~~~  570 (682)
                      |+-|+|+.+|+|+..++---++.
T Consensus         2 ~Ige~Ak~~gvs~~TLRyYe~~G   24 (97)
T cd04782           2 TTGEFAKLCGISKQTLFHYDKIG   24 (97)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHCC
T ss_conf             78999999896999999999669


No 371
>TIGR00270 TIGR00270 conserved hypothetical protein TIGR00270; InterPro: IPR004451 This family of conserved hypothetical proteins includes proteins of unknown function from archaebacteria..
Probab=24.81  E-value=36  Score=12.43  Aligned_cols=63  Identities=30%  Similarity=0.478  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCC-------------CCCCCCCC----------
Q ss_conf             5889899999999987760889997899987099989999999860898-------------75536358----------
Q gi|254780289|r  525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP-------------ISLETPIG----------  581 (682)
Q Consensus       525 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~-------------~sl~~~~~----------  581 (682)
                      ++|-...+.|..|+     =|.-+.|+||+.+.+-+.-+.++-+.--+|             ++|--.|+          
T Consensus        80 lvEdyg~iIR~eRE-----KRgwS~E~LAkki~eK~S~i~kiE~~e~eP~~k~~~kLEkllkIkL~E~~~e~~~ekseG~  154 (169)
T TIGR00270        80 LVEDYGRIIREERE-----KRGWSREELAKKIKEKASVIKKIEREELEPEEKVVKKLEKLLKIKLLEKVEEEKLEKSEGR  154 (169)
T ss_pred             HHHHHHHHHHHHCC-----CCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCCCCEECCCCC
T ss_conf             66432254220001-----4687878999987410678888754037988899999888835010023571000015788


Q ss_pred             CCCCCEEEEEE
Q ss_conf             89986047562
Q gi|254780289|r  582 DEDTSHLGDFI  592 (682)
Q Consensus       582 ~~~~~~~~~~~  592 (682)
                      +....|||||+
T Consensus       155 ~~~g~TlGD~~  165 (169)
T TIGR00270       155 DERGATLGDVV  165 (169)
T ss_pred             CCCCCCCCCEE
T ss_conf             76787423466


No 372
>COG3904 Predicted periplasmic protein [Function unknown]
Probab=24.75  E-value=25  Score=13.64  Aligned_cols=29  Identities=21%  Similarity=0.126  Sum_probs=13.6

Q ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             8674688999899667899999999999998
Q gi|254780289|r  636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRK  666 (682)
Q Consensus       636 ~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~  666 (682)
                      +|-+.+|-+..+...-  -|||||-.|-+--
T Consensus       202 MgigpgLlq~ml~tpp--~dir~l~~kem~~  230 (245)
T COG3904         202 MGIGPGLLQMMLATPP--SDIRQLGLKEMTA  230 (245)
T ss_pred             CCCCHHHHHHHHCCCH--HHHHHHHHHHHHH
T ss_conf             0898799999860894--7655513778765


No 373
>pfam10500 SR-25 Nuclear RNA-splicing-associated protein. SR-25, otherwise known as ADP-ribosylation factor-like factor 6-interacting protein 4, is expressed in virtually all tissues. At the N-terminus there is a repeat of serine-arginine (SR repeat), and towards the middle of the protein there are clusters of both serines and of basic amino acids. The presence of many nuclear localisation signals strongly implies that this is a nuclear protein that may contribute to RNA splicing. SR-25 is also implicated, along with heat-shock-protein-27, as a mediator in the Rac1 (GTPase ras-related C3 botulinum toxin substrate 1) signalling pathway.
Probab=24.71  E-value=36  Score=12.42  Aligned_cols=47  Identities=28%  Similarity=0.390  Sum_probs=24.7

Q ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             999999999997329988999999981879867468899989966789999999999999
Q gi|254780289|r  606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR  665 (682)
Q Consensus       606 ~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~  665 (682)
                      ...-...+..+.+.-+-|-+-|-      |+|+  -||||     |||||-.+|-.+|-+
T Consensus        14 ~e~rQsviRrv~DpeTGR~RLIk------GdgE--ilEEi-----VsrerHk~INkqaT~   60 (74)
T pfam10500        14 YEARQSVIRKVVDPETGRTRLIK------GDGE--ILEEI-----VSKERHKEINKQATR   60 (74)
T ss_pred             HHHHHHHHHHHCCCCCCCEEEEC------CCHH--HHHHH-----HHHHHHHHHHHHHHC
T ss_conf             99999889885076657542441------7628--99999-----828889999887421


No 374
>KOG4697 consensus
Probab=24.64  E-value=36  Score=12.41  Aligned_cols=26  Identities=27%  Similarity=0.507  Sum_probs=20.4

Q ss_pred             CCCCCCEEEHHHHHHHHHHHHHHHHH
Q ss_conf             85457312010289899999999972
Q gi|254780289|r  489 DWCLGYKFSTYAMWWVKQAITRSIAD  514 (682)
Q Consensus       489 ~~~~g~~f~tya~~~i~~~i~~~~~~  514 (682)
                      -+-.+-+|.|-++||+-|-|+--|.-
T Consensus       107 ~~~Ynr~fPsqfsWw~LqVis~tI~~  132 (160)
T KOG4697         107 VFLYNRKFPSQFSWWFLQVISSTILI  132 (160)
T ss_pred             HHHCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             01123568750179999999887998


No 375
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=24.57  E-value=36  Score=12.40  Aligned_cols=22  Identities=5%  Similarity=0.231  Sum_probs=11.6

Q ss_pred             CCHHHHHHHCCCCHHHHHHHHH
Q ss_conf             9978999870999899999998
Q gi|254780289|r  547 PTPEEIAKKLAMPVEGVRKVLK  568 (682)
Q Consensus       547 ~~~~~~a~~~~~~~~~~~~~~~  568 (682)
                      -+..+||+..++|..-+.+++.
T Consensus        26 vsi~eIAe~~~Is~~~LekIl~   47 (164)
T PRK10857         26 VPLADISERQGISLSYLEQLFS   47 (164)
T ss_pred             ECHHHHHHHHCCCHHHHHHHHH
T ss_conf             9499999887919999999999


No 376
>PRK05449 aspartate alpha-decarboxylase; Provisional
Probab=24.45  E-value=8.1  Score=17.54  Aligned_cols=35  Identities=20%  Similarity=0.229  Sum_probs=19.2

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHH
Q ss_conf             87544367999988743854573120102898999
Q gi|254780289|r  472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ  506 (682)
Q Consensus       472 ~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~  506 (682)
                      ||....+|---..|+=++..-|-||+|||.+--+.
T Consensus        31 ~Lm~aagi~~~E~V~V~Nv~NG~Rf~TYvI~g~~G   65 (126)
T PRK05449         31 DLLDAAGILENEKVDIVNVNNGARFETYVIKGERG   65 (126)
T ss_pred             HHHHHCCCCCCCEEEEEECCCCCEEEEEEEECCCC
T ss_conf             99987599989889999898995899999864798


No 377
>KOG3361 consensus
Probab=24.35  E-value=36  Score=12.37  Aligned_cols=80  Identities=34%  Similarity=0.344  Sum_probs=39.8

Q ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCC---CCCEE-----------EHHHHHHHHHHHHHHHHHCCC
Q ss_conf             5578999887522356777887544367999988743854---57312-----------010289899999999972287
Q gi|254780289|r  452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC---LGYKF-----------STYAMWWVKQAITRSIADQSC  517 (682)
Q Consensus       452 nlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~---~g~~f-----------~tya~~~i~~~i~~~~~~~~~  517 (682)
                      |-|-|-|.-|+-+|-|.-+----+-|  -+||--=|+|-.   -..||           |.|||-||+.--.        
T Consensus        39 nPRNVGSldK~dpnVGtGlVGAPACG--DVMkLqIkvd~~g~I~dakFKTFGCGSAIASSS~aTewvkgkt~--------  108 (157)
T KOG3361          39 NPRNVGSLDKNDPNVGTGLVGAPACG--DVMKLQIKVDDSGVIEDAKFKTFGCGSAIASSSLATEWVKGKTL--------  108 (157)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCC--CEEEEEEEECCCCCEEEEEEEECCCCHHHHHHHHHHHHHCCCCH--------
T ss_conf             86555766789997655553576522--00048889779982887665211563476666889999835628--------


Q ss_pred             EEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHH
Q ss_conf             046142058898999999999877608899978999870999899999
Q gi|254780289|r  518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK  565 (682)
Q Consensus       518 ~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~  565 (682)
                               +...++               ...|||++|.+|.-|..-
T Consensus       109 ---------dea~kI---------------kNteIAKeL~LPPVKLHC  132 (157)
T KOG3361         109 ---------DEALKI---------------KNTEIAKELSLPPVKLHC  132 (157)
T ss_pred             ---------HHHHHC---------------CCHHHHHHCCCCCHHHHH
T ss_conf             ---------897711---------------318889761699601346


No 378
>PRK08643 acetoin reductase; Validated
Probab=24.32  E-value=37  Score=12.36  Aligned_cols=107  Identities=21%  Similarity=0.200  Sum_probs=59.4

Q ss_pred             HHHHHHHHHHHH--HHHH--HHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCC
Q ss_conf             124689998755--5789--998875223567778875443679999887438545731201028989999999997228
Q gi|254780289|r  441 ASIAKKEMVEAN--LRLV--ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS  516 (682)
Q Consensus       441 ~~~AK~~l~~an--lr~v--~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~  516 (682)
                      ++.+-+.|.+.+  -+.|  .|++-.....+...------|-+||.|+.-+-=-.+|.|.-.-+-.||+-.+...+.++.
T Consensus       118 ~~~~~~~m~~~~~~G~IVnisS~~~~~~~~~~~~Y~asKaav~~ltkslA~ela~~gIrVN~V~PG~i~T~~~~~~~~~~  197 (256)
T PRK08643        118 IQAAQEQFKKLGHGGKIINATSQAGVEGNPGLSVYGSTKFAVRGLTQTAARDLASEGITVNAYAPGIVKTPMMFDIAHEV  197 (256)
T ss_pred             HHHHHHHHHHHCCCCEEEEEECCHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEECCCCCCHHHHHHHHH
T ss_conf             99999999982899279998321013589984899999999999999999998775918999960668870456677887


Q ss_pred             CE-EECCCHHHHHHHHHHHHHHHHHH--HCCCCCCHHHHHHHC
Q ss_conf             70-46142058898999999999877--608899978999870
Q gi|254780289|r  517 CT-IRIPVHMRDKIHKVVRTARRMSN--KIKREPTPEEIAKKL  556 (682)
Q Consensus       517 ~~-~r~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~a~~~  556 (682)
                      .. ...|.         .....++..  -+||..+|+|+|...
T Consensus       198 ~~~~~~~~---------~~~~~~~~~~ipl~R~g~pedia~~v  231 (256)
T PRK08643        198 GENAGKPD---------EWGMEQFAKDITLKRLSEPEDVANVV  231 (256)
T ss_pred             HHHCCCCH---------HHHHHHHHHCCCCCCCCCHHHHHHHH
T ss_conf             87628975---------89999998359999986899999999


No 379
>smart00492 HELICc3 helicase superfamily c-terminal domain.
Probab=24.18  E-value=35  Score=12.46  Aligned_cols=30  Identities=20%  Similarity=0.149  Sum_probs=14.6

Q ss_pred             HHHCCCCCCCEEEH-H-HHHHHHHHHHHHHHH
Q ss_conf             87438545731201-0-289899999999972
Q gi|254780289|r  485 AEKFDWCLGYKFST-Y-AMWWVKQAITRSIAD  514 (682)
Q Consensus       485 ~~~~~~~~g~~f~t-y-a~~~i~~~i~~~~~~  514 (682)
                      .+++....+|.+.. + |.-.++|++-|+|..
T Consensus        94 ~~~~~~~~~~~~~~~~~A~r~v~Qa~GR~IR~  125 (141)
T smart00492       94 LRDKGQIRPFDFVSLPDAMRTLAQCVGRLIRG  125 (141)
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             99856998424665899999999986875457


No 380
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=24.08  E-value=37  Score=12.33  Aligned_cols=23  Identities=26%  Similarity=0.423  Sum_probs=13.8

Q ss_pred             CCCHHHHHHHCCCCHHHHHHHHH
Q ss_conf             99978999870999899999998
Q gi|254780289|r  546 EPTPEEIAKKLAMPVEGVRKVLK  568 (682)
Q Consensus       546 ~~~~~~~a~~~~~~~~~~~~~~~  568 (682)
                      +.|.++||+.+++|...+....+
T Consensus         1 plsl~~lA~~~~~S~~~l~~~f~   23 (84)
T smart00342        1 PLTLEDLAEALGMSPRHLQRLFK   23 (84)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             98999999988909999999999


No 381
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=24.03  E-value=37  Score=12.33  Aligned_cols=47  Identities=17%  Similarity=0.126  Sum_probs=20.9

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCC--CCCEEEHHHHHHHHHHHHHHHHHCCCEEECCC
Q ss_conf             7887544367999988743854--57312010289899999999972287046142
Q gi|254780289|r  470 FLDLIQEGNIGLMKAAEKFDWC--LGYKFSTYAMWWVKQAITRSIADQSCTIRIPV  523 (682)
Q Consensus       470 ~~~~~~~~~~~l~~a~~~~~~~--~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~  523 (682)
                      .-|.+.   +|+|+|.....++  .-+....|--+++-+-    +.-.--||+.|.
T Consensus       246 ~nD~~A---~g~~~~l~~~g~~VP~DisvigfDd~~~~~~----~~P~LTtv~~~~  294 (335)
T PRK10703        246 GGDIMA---MGAICAADEMGLRVPQDISVIGYDNVRNARY----FTPALTTIHQPK  294 (335)
T ss_pred             CCHHHH---HHHHHHHHHCCCCCCCCEEEEEECCCHHHHH----CCCCCEEEECCH
T ss_conf             875999---9999999971999999749999888289982----589827998299


No 382
>COG2344 AT-rich DNA-binding protein [General function prediction only]
Probab=23.87  E-value=37  Score=12.30  Aligned_cols=29  Identities=17%  Similarity=0.347  Sum_probs=13.6

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCEEEHHHHHH
Q ss_conf             7544367999988743854573120102898
Q gi|254780289|r  473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW  503 (682)
Q Consensus       473 ~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~  503 (682)
                      +|-.||+|  +|+=-|......+|---+.+=
T Consensus        89 iVG~GnlG--~All~Y~f~~~~~~~iv~~FD  117 (211)
T COG2344          89 IVGVGNLG--RALLNYNFSKKNGMKIVAAFD  117 (211)
T ss_pred             EECCCHHH--HHHHCCCCHHHCCCEEEEEEC
T ss_conf             99057088--898607423326935999961


No 383
>PRK09281 F0F1 ATP synthase subunit alpha; Validated
Probab=23.78  E-value=37  Score=12.29  Aligned_cols=45  Identities=20%  Similarity=0.222  Sum_probs=18.0

Q ss_pred             HHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             898999999999722870461420588989999999998776088999
Q gi|254780289|r  501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT  548 (682)
Q Consensus       501 ~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~  548 (682)
                      ++|.--+|-.++.||.+-+=+   +.+.+.|+-.+.|++.--+||+|+
T Consensus       238 Apyaa~aIAEyFrd~G~dVLl---v~DdLtr~A~A~REisLll~rPPg  282 (502)
T PRK09281        238 APYAGCAMGEYFMDNGKDALI---VYDDLSKQAVAYRQLSLLLRRPPG  282 (502)
T ss_pred             HHHHHHHHHHHHHHCCCCEEE---EEECHHHHHHHHHHHHHHCCCCCC
T ss_conf             999999999999967994899---985568999999888986279987


No 384
>PRK13805 bifunctional acetaldehyde-CoA/alcohol dehydrogenase; Provisional
Probab=23.62  E-value=38  Score=12.27  Aligned_cols=137  Identities=12%  Similarity=0.164  Sum_probs=82.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHH---HHHHHHHH-----------HHHHHHHHHHHHHHCCC-CCCHHHHHHHHHHHHHHHHH
Q ss_conf             12688999999876533211---24689998-----------75557899988752235-67778875443679999887
Q gi|254780289|r  422 ISISEFRHIVSMVRKGECEA---SIAKKEMV-----------EANLRLVISVAKKYTNR-GLQFLDLIQEGNIGLMKAAE  486 (682)
Q Consensus       422 l~i~ElK~i~r~I~~ge~e~---~~AK~~l~-----------~anlr~v~~~~~~~~~~-~~~~~~~~~~~~~~l~~a~~  486 (682)
                      +...-++-+.+.+.+.....   ..|+..|.           .|.|-+|.++|....+. +++    .-.+|--|+-.|=
T Consensus       677 ~Al~Ai~li~~~L~~a~~~g~~d~eARe~M~~As~~AG~AF~na~lG~~HamaH~lG~~~~ip----HG~aNAilLP~Vi  752 (862)
T PRK13805        677 LALQAIKLVFEYLPRSYKNGAKDPEAREKMHNAATIAGMAFANAFLGICHSMAHKLGAEFHIP----HGRANAILIPHVI  752 (862)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCC----HHHHHHHHHHHHH
T ss_conf             999999999999999996899889999999999999999996851788788624751486865----5889999989999


Q ss_pred             HCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCH-HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHH
Q ss_conf             43854573120102898999999999722870461420-58898999999999877608899978999870999899999
Q gi|254780289|r  487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK  565 (682)
Q Consensus       487 ~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~  565 (682)
                      +|....-.||.++..|-.-.+..|+ ++-++.+-++.+ ..+...++...-++|...+|=+.+..+    +|++.++...
T Consensus       753 ~fNa~~p~k~~~~p~y~~~~a~ery-a~iA~~lGl~~~s~~e~~~~li~ai~~L~~~lgiP~~L~e----~GV~e~df~~  827 (862)
T PRK13805        753 RYNATDPTKQAAFPQYEYPRADERY-AEIARHLGLPGDTTEEKVESLIKAIEELKAELGIPMSIKE----AGVDEADFLA  827 (862)
T ss_pred             HHHCCCCCCCCCCCCCCCCCHHHHH-HHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHH----CCCCHHHHHH
T ss_conf             9745575322333212333168999-9999983999999899999999999999997699998898----2989899886


Q ss_pred             HH
Q ss_conf             99
Q gi|254780289|r  566 VL  567 (682)
Q Consensus       566 ~~  567 (682)
                      .+
T Consensus       828 ~l  829 (862)
T PRK13805        828 KV  829 (862)
T ss_pred             HH
T ss_conf             69


No 385
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=23.58  E-value=38  Score=12.26  Aligned_cols=21  Identities=43%  Similarity=0.531  Sum_probs=11.6

Q ss_pred             CHHHHHHHCCCCHHHHHHHHH
Q ss_conf             978999870999899999998
Q gi|254780289|r  548 TPEEIAKKLAMPVEGVRKVLK  568 (682)
Q Consensus       548 ~~~~~a~~~~~~~~~~~~~~~  568 (682)
                      |-++||+.+|++.+-|..+++
T Consensus        10 t~~~iA~~lG~tretvsR~l~   30 (48)
T smart00419       10 TRQEIAELLGLTRETVSRTLK   30 (48)
T ss_pred             CHHHHHHHHCCCHHHHHHHHH
T ss_conf             999999997997999999999


No 386
>COG4477 EzrA Negative regulator of septation ring formation [Cell division and chromosome partitioning]
Probab=23.20  E-value=38  Score=12.21  Aligned_cols=22  Identities=23%  Similarity=0.409  Sum_probs=9.5

Q ss_pred             CCC--HHHHHHHHHHHHHHHHHHC
Q ss_conf             677--7887544367999988743
Q gi|254780289|r  467 GLQ--FLDLIQEGNIGLMKAAEKF  488 (682)
Q Consensus       467 ~~~--~~~~~~~~~~~l~~a~~~~  488 (682)
                      |+|  |++|.-.+---+--.+.+|
T Consensus       440 GlPe~~l~l~~~~~~~i~~l~~eL  463 (570)
T COG4477         440 GLPETFLSLFFTAGHEIQDLMKEL  463 (570)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             995999999971006899999998


No 387
>PRK08219 short chain dehydrogenase; Provisional
Probab=23.13  E-value=38  Score=12.20  Aligned_cols=81  Identities=14%  Similarity=0.033  Sum_probs=42.2

Q ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHH
Q ss_conf             57899988752235677788754436799998874385457312010289899999999972287046142058898999
Q gi|254780289|r  453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV  532 (682)
Q Consensus       453 lr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~  532 (682)
                      .-.|.|++-....-|...------|-.||+++.-. ++..|.|..+-+--||+-.+++.+.++..               
T Consensus       123 IV~isS~~g~~~~~~~~~Y~aSKaAl~~l~~~L~~-e~~~~IrVn~I~PG~v~T~m~~~~~~~~~---------------  186 (226)
T PRK08219        123 VVFINSGAGLNASPGWASYAASKFALRALADALRE-EEAGNVRVTSVHPGRTATDMQRELVAQEG---------------  186 (226)
T ss_pred             EEEEECHHHCCCCCCCHHHHHHHHHHHHHHHHHHH-HCCCCEEEEEEEECCCCCCCCHHHHHHHH---------------
T ss_conf             99994767648899974799999999999999998-66998499999708997865355676543---------------


Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHH
Q ss_conf             99999987760889997899987
Q gi|254780289|r  533 VRTARRMSNKIKREPTPEEIAKK  555 (682)
Q Consensus       533 ~~~~~~~~~~~~~~~~~~~~a~~  555 (682)
                            .....||-.+|+|+|+.
T Consensus       187 ------~~~~~~r~~~PedVA~~  203 (226)
T PRK08219        187 ------REYDPARFLRPETVAAA  203 (226)
T ss_pred             ------CCCCCCCCCCHHHHHHH
T ss_conf             ------03787679699999999


No 388
>TIGR01004 PulS_OutS lipoprotein, PulS/OutS family; InterPro: IPR005699    This family comprises lipoproteins from four gamma proteobacterial species: PulS protein of Klebsiella pneumoniae (P20440 from SWISSPROT), the OutS protein of Erwinia chrysanthemi (Q01567 from SWISSPROT) and Pectobacterium chrysanthemi, and the functionally uncharacterised E. coli protein EtpO. PulS and OutS have been shown to interact with and facilitate insertion of secretins into the outer membrane, suggesting a chaperone-like, or piloting function for members of this family.; GO: 0008565 protein transporter activity, 0006886 intracellular protein transport.
Probab=23.01  E-value=39  Score=12.18  Aligned_cols=61  Identities=16%  Similarity=0.286  Sum_probs=42.8

Q ss_pred             HHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHH
Q ss_conf             87522356777887544367999988743854573120102898999999999722870461420588989999999998
Q gi|254780289|r  460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM  539 (682)
Q Consensus       460 ~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~  539 (682)
                      |-||...-|.-.||=.+|.|  .                      +.||.=++...|-+++        .+.+.+.+.++
T Consensus        56 a~rYLk~~CnRSDLPdd~~I--l----------------------~~A~nva~~kGW~~~~--------~~~l~q~S~~l  103 (136)
T TIGR01004        56 AARYLKVKCNRSDLPDDEAI--L----------------------KVAVNVAVKKGWDSLD--------AEDLSQRSEDL  103 (136)
T ss_pred             HHHHHHHCCCCCCCCCHHHH--H----------------------HHHHHHHHHHCCCCCC--------HHHHHHHHHHH
T ss_conf             98886420677899700579--9----------------------9999987563124500--------56688878999


Q ss_pred             HHHCCCCCCHHHH
Q ss_conf             7760889997899
Q gi|254780289|r  540 SNKIKREPTPEEI  552 (682)
Q Consensus       540 ~~~~~~~~~~~~~  552 (682)
                      ++.+-++-||+.+
T Consensus       104 Y~~L~~DsTPea~  116 (136)
T TIGR01004       104 YQRLLKDSTPEAT  116 (136)
T ss_pred             HHHHHCCCCCCCC
T ss_conf             9886148886630


No 389
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=23.00  E-value=39  Score=12.18  Aligned_cols=51  Identities=20%  Similarity=0.261  Sum_probs=30.1

Q ss_pred             HHCCHHHHHHHHHHHHHC-C-CC-CHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEE
Q ss_conf             020289999999978784-8-86-789997526843599888999999998479778
Q gi|254780289|r   24 FDFSDDSWKKMIKLARQR-G-YV-TIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV   77 (682)
Q Consensus        24 ~d~~~~~ik~LI~~gke~-G-yl-TydeIn~~LP~d~~~~e~ie~i~~~L~~~GI~V   77 (682)
                      .|..-+.|++.|--|.=+ | .| +-.+|.+.|.   ++---+=+.+..|..+|+-.
T Consensus        12 ~e~V~~~L~~~I~~G~l~pGd~LPsE~eLA~~lg---VSR~~VREAL~~L~~~GlV~   65 (254)
T PRK09464         12 SDVIEQQLEFLILEGTLRPGEKLPPERELAKQFD---VSRPSLREAIQRLEAKGLLL   65 (254)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHC---CCCHHHHHHHHHHHHCCCEE
T ss_conf             9999999999998499999396936999999868---99559999999999889989


No 390
>PRK12274 serine/threonine protein kinase; Provisional
Probab=22.95  E-value=39  Score=12.17  Aligned_cols=52  Identities=27%  Similarity=0.326  Sum_probs=36.3

Q ss_pred             CCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHH--------HCCCHHHHHHHHHH
Q ss_conf             358899860475623898899899999999999999997--------32998899999998
Q gi|254780289|r  579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL--------ASLTPREERVLRMR  631 (682)
Q Consensus       579 ~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l--------~~l~~re~~v~~~r  631 (682)
                      .+|+|+...+.||-- .....|--...+..-++.+..+|        +.|+|+|+.+|.-.
T Consensus       104 L~~~dg~p~liDFQl-A~~~~rr~~~~Rila~eDlrhllK~kr~y~~e~Ltp~e~~~L~r~  163 (198)
T PRK12274        104 LVQEDGSPAVIDFQL-AVRGNPRARWMRLLAREDLRHLLKHKRMYCPAALTPVERRVLKRT  163 (198)
T ss_pred             EECCCCCEEEEEEEE-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHH
T ss_conf             887999978897441-002363038999999998999999888638988998999999840


No 391
>pfam10498 IFT57 Intra-flagellar transport protein 57. Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.
Probab=22.90  E-value=39  Score=12.17  Aligned_cols=28  Identities=18%  Similarity=0.213  Sum_probs=16.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             0577887899999999999999999999
Q gi|254780289|r  331 NQSRIDLLVEQLYDISKRIMHNEGELLR  358 (682)
Q Consensus       331 ~~k~iE~L~~~l~~~~k~Ir~~Er~L~r  358 (682)
                      ....++.|...+-....+|.+.|+.|..
T Consensus       235 ~~~~L~kl~~d~~~~LekI~sREk~lN~  262 (355)
T pfam10498       235 TKQYLKKLSQDLSKALEKISSREKHLNN  262 (355)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             8999999999999999999889999987


No 392
>TIGR03103 trio_acet_GNAT GNAT-family acetyltransferase TIGR03103. Members of this protein family belong to the GNAT family of acetyltransferases. Each is part of a conserved three-gene cassette sparsely distributed across at least twenty different species known so far, including alpha, beta, and gamma Proteobacteria, Mycobacterium, and Prosthecochloris, which is a member of the Chlorobi. The other two members of the cassette are a probable protease and an asparagine synthetase family protein.
Probab=22.85  E-value=31  Score=12.95  Aligned_cols=62  Identities=8%  Similarity=0.234  Sum_probs=36.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCH
Q ss_conf             5322333322222112688999999876533----------21124689998755578999887522356777
Q gi|254780289|r  408 KIRNEIKSISVETGISISEFRHIVSMVRKGE----------CEASIAKKEMVEANLRLVISVAKKYTNRGLQF  470 (682)
Q Consensus       408 ~~q~kL~~ie~~~gl~i~ElK~i~r~I~~ge----------~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~  470 (682)
                      .++..|.++...+.|++-.=|.+.+++-..-          .....|-.=+-+.. ++||.=+..-.++|...
T Consensus       278 ~creslSelTSAvAms~c~DK~lT~rll~~AG~~VP~~~~~~~~~~~~~fl~~~G-~VVVKP~dGnqGrGVtv  349 (547)
T TIGR03103       278 RCRESLSELTSAVAMSLCDDKRLTRRLVSEAGLQVPEQQLAGNGEAVEAFLAEHG-AVVVKPVRGEQGKGISV  349 (547)
T ss_pred             EEECHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCC-CEEECCCCCCCCCCEEE
T ss_conf             8612025788899988740499999999973998999745699899999998739-99977687888861587


No 393
>PRK00509 argininosuccinate synthase; Provisional
Probab=22.76  E-value=39  Score=12.15  Aligned_cols=33  Identities=30%  Similarity=0.435  Sum_probs=22.4

Q ss_pred             CCCCCCCHHHH--HHHHHC-C---------CCCCCHHHHHHHHHH
Q ss_conf             45777728999--999856-9---------768897889999999
Q gi|254780289|r  113 ADRSTDDPVRM--YLREMG-S---------IELLSREGEIAIAKR  145 (682)
Q Consensus       113 e~~rtdDPVRM--YLREMG-~---------V~LLTREgEIeIAKR  145 (682)
                      .+|+-+|-||.  +.+-++ .         -.+.||++||+.|+.
T Consensus       117 ~TGkGNDQvRFe~~~~aL~P~l~iiaP~Rd~~~~sR~~~i~ya~~  161 (398)
T PRK00509        117 CTGKGNDQVRFELAIAALAPDLKVIAPWREWDLMSREELIAYAEE  161 (398)
T ss_pred             CCCCCCCHHHHHHHHHHHCCCCEEEEEEECCCCCCHHHHHHHHHH
T ss_conf             556786089999999985999768611321341689999999998


No 394
>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=22.73  E-value=39  Score=12.14  Aligned_cols=30  Identities=30%  Similarity=0.355  Sum_probs=18.7

Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHH
Q ss_conf             999998776088999789998709998999999
Q gi|254780289|r  534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV  566 (682)
Q Consensus       534 ~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~  566 (682)
                      +.++.|+-   +.=++.|||+.||+|..-|..=
T Consensus         4 ~~Ar~LY~---qg~~~~eIA~~Lg~~~~tVysW   33 (58)
T pfam06056         4 RQARTLYW---QGYRPAEIAQELGLKARTVYSW   33 (58)
T ss_pred             HHHHHHHH---CCCCHHHHHHHHCCCCCHHHHH
T ss_conf             99999999---6898999999978993145658


No 395
>COG4473 EcsB Predicted ABC-type exoprotein transport system, permease component [Intracellular trafficking and secretion]
Probab=22.71  E-value=39  Score=12.14  Aligned_cols=30  Identities=30%  Similarity=0.402  Sum_probs=25.7

Q ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf             772899999985697688978899999999
Q gi|254780289|r  117 TDDPVRMYLREMGSIELLSREGEIAIAKRI  146 (682)
Q Consensus       117 tdDPVRMYLREMG~V~LLTREgEIeIAKRI  146 (682)
                      +.-|||-||+|--+|-||..|.|+.-=+|=
T Consensus        72 ~~g~vrT~LkeaDkVFLL~~E~~m~~y~r~  101 (379)
T COG4473          72 SIGSVRTFLKEADKVFLLPKEEEMDQYLRQ  101 (379)
T ss_pred             HHHHHHHHHHCCCEEEEECCHHHHHHHHHH
T ss_conf             986388898377878871448899999999


No 396
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=22.69  E-value=39  Score=12.14  Aligned_cols=21  Identities=29%  Similarity=0.583  Sum_probs=11.9

Q ss_pred             HHHHHHHHHHHHHHHCCHHHH
Q ss_conf             999999999999983296777
Q gi|254780289|r  653 RERIRQIEAKAIRKLKHPSRS  673 (682)
Q Consensus       653 ~er~rqi~~~a~~~l~~~~~~  673 (682)
                      .-|||||=..|++=++|..|.
T Consensus        33 eyRlkei~q~A~Kfm~hskR~   53 (65)
T smart00803       33 EYRIKEIVQEALKFMRHSKRT   53 (65)
T ss_pred             HHHHHHHHHHHHHHHHHHCCC
T ss_conf             999999999999999975767


No 397
>KOG0464 consensus
Probab=22.69  E-value=33  Score=12.68  Aligned_cols=26  Identities=19%  Similarity=0.307  Sum_probs=18.6

Q ss_pred             CCCCHHHHHHHHHHHHHCCCEEECCC
Q ss_conf             35998889999999984797783278
Q gi|254780289|r   56 DEVSSEQMEDTVAMLSNMGINVVDGD   81 (682)
Q Consensus        56 d~~~~e~ie~i~~~L~~~GI~Vve~~   81 (682)
                      ++-+.+.+-+++..=.+.||.|...+
T Consensus        69 ~vddgdtvtdfla~erergitiqsaa   94 (753)
T KOG0464          69 DVDDGDTVTDFLAIERERGITIQSAA   94 (753)
T ss_pred             CCCCCCHHHHHHHHHHHCCCEEEEEE
T ss_conf             56788537788888886483665404


No 398
>PRK02793 hypothetical protein; Provisional
Probab=22.66  E-value=39  Score=12.13  Aligned_cols=49  Identities=16%  Similarity=0.184  Sum_probs=38.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             9999999999862100577887899999999999999999999999712
Q gi|254780289|r  316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG  364 (682)
Q Consensus       316 kl~~eL~e~~~~lkl~~k~iE~L~~~l~~~~k~Ir~~Er~L~rl~~k~~  364 (682)
                      .+...|.++-..+-|--..|+.|.+.+......|..+.+.+..++.+.+
T Consensus         5 ~le~Ri~~LE~rlAfQe~tIe~LN~~v~~Qq~~i~~L~~ql~~L~~rLk   53 (72)
T PRK02793          5 SLEARLAELESRLAFQEITIEELNLTVTAHEMEMAKLRDHLRLLTEKLK   53 (72)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             8999999999999968999999999999999999999999999999998


No 399
>TIGR02485 CobZ_N-term precorrin 3B synthase CobZ; InterPro: IPR012831   Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase . In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase .    There are at least two distinct cobalamin biosynthetic pathways in bacteria :  Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway ; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis ; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii shermanii.     Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) . There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans.   This entry represents CobZ, which is essential for cobalamin biosynthesis  and is complemented by precorrin 3B synthase CobG (1.3.99.1 from EC). The enzyme has been shown to contain flavin, haem and Fe-S cluster cofactors, and is believed to require dioxygen as a substrate. In Rhodobacter capsulatus, CobZ is found as a N-terminal domain, whereas in other species it exists as a separate protein. The C-terminal portion is homologous to the 2-component signal transduction system protein CitB (IPR012830 from INTERPRO)..
Probab=22.59  E-value=39  Score=12.12  Aligned_cols=44  Identities=27%  Similarity=0.428  Sum_probs=31.2

Q ss_pred             CCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCC-CCCCCCCEEEEEEC
Q ss_conf             89997899987099989999999860898755363-58899860475623
Q gi|254780289|r  545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP-IGDEDTSHLGDFIE  593 (682)
Q Consensus       545 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~-~~~~~~~~~~~~~~  593 (682)
                      .-||++|||..|+++++-....+..-.     +.| +|.=+.++|-|.-.
T Consensus       327 ~Adtl~eLA~~lgidp~~l~~tld~~n-----aaprvGqfdhttlddCht  371 (467)
T TIGR02485       327 KADTLEELAAKLGIDPDALAETLDAYN-----AAPRVGQFDHTTLDDCHT  371 (467)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHCCC-----CCCCCCCCCCCCHHCCCC
T ss_conf             888879999985888889998650678-----787666555531000013


No 400
>TIGR03653 arch_L6P archaeal ribosomal protein L6P. Members of this protein family are the archaeal ribosomal protein L6P. The top-scoring proteins not selected by this model are eukaryotic cytosolic ribosomal protein L9. Bacterial ribosomal protein L6 scores lower and is described by a distinct model.
Probab=22.43  E-value=37  Score=12.33  Aligned_cols=32  Identities=25%  Similarity=0.421  Sum_probs=15.1

Q ss_pred             HCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHCC
Q ss_conf             6678999999999999983296777875665179
Q gi|254780289|r  649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG  682 (682)
Q Consensus       649 ~~~~~er~rqi~~~a~~~l~~~~~~~~l~~~~~~  682 (682)
                      -|..+|.|-|.-|. +|+++. .+.+-.|-|+||
T Consensus       133 ~G~DKq~VGq~AA~-Ir~~~k-~k~kd~R~f~dG  164 (170)
T TIGR03653       133 TGIDKEDVGQTAAN-IEQATR-IKGRDPRVFQDG  164 (170)
T ss_pred             EECCHHHHHHHHHH-HHHHCC-CCCCCCCEEECC
T ss_conf             97789998699987-466255-689977684156


No 401
>pfam10566 Glyco_hydro_97 Glycoside hydrolase 97. This is the 97th family of glycosidases, in this case bacterial. The central part of the GH97 family protein sequences represents a typical and complete (beta/alpha)8-barrel or catalytic TIM-barrel type domain. The N- and C-terminal parts of the sequences, mainly consisting of beta-strands, most probably form two additional non-catalytic domains with as yet unknown functions. The non-catalytic domains of glycosidases from the alpha-galactosidase and alpha-glucosidase superfamilies are also predominantly composed of beta-strands, and at least some of these domains are involved in oligomerisation and carbohydrate binding. In all known glycosidases with the (beta-alpha)8-barrel fold, the amino acid residues at the active site are located on the C-termini of the beta-strands.
Probab=22.42  E-value=39  Score=12.10  Aligned_cols=40  Identities=33%  Similarity=0.240  Sum_probs=21.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHH---------HCCCCCCH--H-HHHHHHHHHHH
Q ss_conf             46899987555789998875---------22356777--8-87544367999
Q gi|254780289|r  443 IAKKEMVEANLRLVISVAKK---------YTNRGLQF--L-DLIQEGNIGLM  482 (682)
Q Consensus       443 ~AK~~l~~anlr~v~~~~~~---------~~~~~~~~--~-~~~~~~~~~l~  482 (682)
                      +..++||....+.+---|+.         |.-+|+.-  . =+-+||..|.=
T Consensus       402 ~d~Q~~v~~y~~i~~~AA~~~L~V~fHg~~kPtG~~RTYPN~~t~Egv~G~E  453 (643)
T pfam10566       402 RDDQEMVRWVYEALEKAAKYKLLVDFHGEYKPTGLSRTYPNLLTQEGVRGNE  453 (643)
T ss_pred             CCCHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCCCHHHHHHHCCEE
T ss_conf             6528999999999999987794699268716986530275366665533232


No 402
>pfam02002 TFIIE_alpha TFIIE alpha subunit. The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF. This family consists of the conserved amino terminal region of eukaryotic TFIIE-alpha and proteins from archaebacteria that are presumed to be TFIIE-alpha subunits.
Probab=22.36  E-value=40  Score=12.09  Aligned_cols=27  Identities=30%  Similarity=0.362  Sum_probs=22.8

Q ss_pred             CCCCHHHHHHHCCCCHHHHHHHHHHHC
Q ss_conf             899978999870999899999998608
Q gi|254780289|r  545 REPTPEEIAKKLAMPVEGVRKVLKITK  571 (682)
Q Consensus       545 ~~~~~~~~a~~~~~~~~~~~~~~~~~~  571 (682)
                      ..-|.++||+.+|+....|++++-...
T Consensus        26 ~~v~dedLa~~l~~~~n~vRkiL~~L~   52 (105)
T pfam02002        26 GEVTEEDLAELLGIDLNELRKLLYRLY   52 (105)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             883899999997898889999999998


No 403
>PRK08359 transcription factor; Validated
Probab=22.36  E-value=40  Score=12.09  Aligned_cols=23  Identities=22%  Similarity=0.450  Sum_probs=12.5

Q ss_pred             CCCCHHHHHHHCCCCHHHHHHHH
Q ss_conf             89997899987099989999999
Q gi|254780289|r  545 REPTPEEIAKKLAMPVEGVRKVL  567 (682)
Q Consensus       545 ~~~~~~~~a~~~~~~~~~~~~~~  567 (682)
                      +.-|-+|||..+++.+.-++++-
T Consensus        95 ~GlSqeeLA~ki~ek~nvI~kiE  117 (175)
T PRK08359         95 SGLSYEELSHKVGLSVNDLRRIA  117 (175)
T ss_pred             CCCCHHHHHHHHCCHHHHHHHHH
T ss_conf             59999999999722299999998


No 404
>PRK08217 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
Probab=22.29  E-value=40  Score=12.08  Aligned_cols=96  Identities=19%  Similarity=0.173  Sum_probs=51.7

Q ss_pred             HHHHHHHHHH----HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCE
Q ss_conf             4689998755----578999887522356777887544367999988743854573120102898999999999722870
Q gi|254780289|r  443 IAKKEMVEAN----LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT  518 (682)
Q Consensus       443 ~AK~~l~~an----lr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~  518 (682)
                      .+-..|.+.+    .-.+.|++ .+.+.|..------.|-.||+|+.-+.=...|.|..+-+-.||.-.++..+      
T Consensus       132 ~~~~~m~~~~~~g~Ii~isS~~-~~~~~~~~~Y~asKaal~~ltk~lA~el~~~gIrVN~I~PG~i~T~~~~~~------  204 (253)
T PRK08217        132 EAAAKMIESGSKGVIINISSIA-RAGNMGQTNYSASKAGVAAMTVTWAKELARYGIRVAAIAPGVIETEMTAAM------  204 (253)
T ss_pred             HHHHHHHHHCCCEEEEEECCHH-CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEEECCCCCCCCCCC------
T ss_conf             9999999848972799963311-138888616899999999999999999532195999997388987331117------


Q ss_pred             EECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHC
Q ss_conf             46142058898999999999877608899978999870
Q gi|254780289|r  519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL  556 (682)
Q Consensus       519 ~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~  556 (682)
                         +-.   ...+     -.-..-+||-.+|+|+|...
T Consensus       205 ---~~~---~~~~-----~~~~~pl~R~g~p~dva~~v  231 (253)
T PRK08217        205 ---KPE---ALER-----LEKMIPVGRLGEPEEIAHTV  231 (253)
T ss_pred             ---CHH---HHHH-----HHHCCCCCCCCCHHHHHHHH
T ss_conf             ---999---9999-----98579999984999999999


No 405
>TIGR02617 tnaA_trp_ase tryptophanase; InterPro: IPR013440    Proteins in this entry belong to the beta-eliminating lyase family and are thought to act as tryptophanases (4.1.99.1 from EC) (also known as L-tryptophan indole-lyases). The genes encoding these proteins are, as a rule, found with a tryptophanase leader peptide TnaC (IPR013439 from INTERPRO) encoded upstream. ; GO: 0009034 tryptophanase activity, 0006568 tryptophan metabolic process.
Probab=22.25  E-value=40  Score=12.07  Aligned_cols=19  Identities=42%  Similarity=0.499  Sum_probs=14.1

Q ss_pred             HHHHHHHHHHHHHHHHCCC
Q ss_conf             9875557899988752235
Q gi|254780289|r  448 MVEANLRLVISVAKKYTNR  466 (682)
Q Consensus       448 l~~anlr~v~~~~~~~~~~  466 (682)
                      .--|||+=|.+|||+|---
T Consensus       201 vSlANlKAvY~IAk~yDIP  219 (468)
T TIGR02617       201 VSLANLKAVYEIAKKYDIP  219 (468)
T ss_pred             HHHHHHHHHHHHHHHCCCC
T ss_conf             6788889999998645998


No 406
>PRK03501 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional
Probab=22.21  E-value=40  Score=12.07  Aligned_cols=32  Identities=19%  Similarity=0.192  Sum_probs=23.9

Q ss_pred             CCCCHHHHHHHHHHHHHCCCEEECCCCCCCCC
Q ss_conf             35998889999999984797783278410000
Q gi|254780289|r   56 DEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE   87 (682)
Q Consensus        56 d~~~~e~ie~i~~~L~~~GI~Vve~~~~~~~~   87 (682)
                      +.-..|..+.++..++++|+.++|..+++|..
T Consensus        12 ~~~~~e~~~~~~~~~~~~g~~~vdd~~~aDli   43 (264)
T PRK03501         12 DKELVEKVKPLKKIAEENGFTVVDDPKNANII   43 (264)
T ss_pred             CHHHHHHHHHHHHHHHHCCCEEECCCCCCCEE
T ss_conf             87899999999999998798884898898999


No 407
>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=22.21  E-value=40  Score=12.07  Aligned_cols=23  Identities=26%  Similarity=0.271  Sum_probs=18.8

Q ss_pred             CHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf             97899987099989999999860
Q gi|254780289|r  548 TPEEIAKKLAMPVEGVRKVLKIT  570 (682)
Q Consensus       548 ~~~~~a~~~~~~~~~~~~~~~~~  570 (682)
                      |+.|+|+.+|+|+..++---+..
T Consensus         2 tIgelA~~~gvs~~tlRyYe~~G   24 (113)
T cd01109           2 TIKEVAEKTGLSADTLRYYEKEG   24 (113)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHCC
T ss_conf             78899999895999999999838


No 408
>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=22.15  E-value=40  Score=12.06  Aligned_cols=18  Identities=22%  Similarity=0.268  Sum_probs=7.2

Q ss_pred             CHHHHHHHCCCCHHHHHH
Q ss_conf             978999870999899999
Q gi|254780289|r  548 TPEEIAKKLAMPVEGVRK  565 (682)
Q Consensus       548 ~~~~~a~~~~~~~~~~~~  565 (682)
                      |..+||+..|+|..-|.+
T Consensus        36 si~~lA~~~~vS~atv~R   53 (106)
T pfam01418        36 SIAELAKAAGVSEASVVR   53 (106)
T ss_pred             CHHHHHHHHCCCHHHHHH
T ss_conf             399999896998999999


No 409
>pfam07455 Psu Phage polarity suppression protein (Psu). This family contains a number of phage polarity suppression proteins (Psu) (approximately 190 residues long). The Psu protein of bacteriophage P4 causes suppression of transcriptional polarity in Escherichia coli by overcoming Rho termination factor activity.
Probab=22.05  E-value=38  Score=12.27  Aligned_cols=73  Identities=14%  Similarity=0.193  Sum_probs=35.3

Q ss_pred             HHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCC-------HHHHHHHHHHHCCC
Q ss_conf             89899999999972287046142058898999999999877608899978999870999-------89999999860898
Q gi|254780289|r  501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP-------VEGVRKVLKITKEP  573 (682)
Q Consensus       501 ~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~-------~~~~~~~~~~~~~~  573 (682)
                      -|=|-|+-.|+|.-|        |.+..++ +....+.|.|.+|-+-+..---+.||++       ..-+...+.+.++.
T Consensus        60 kWeiNqaAgryI~SH--------e~vq~is-ir~~L~~FMQ~hG~~L~aaLAPeLmg~~~q~~~~~~~aldra~~yLReA  130 (188)
T pfam07455        60 KWEINQAAGRYIRSH--------EEVQHIS-IRDRLNDFMQQHGAELAAALAPELMGYSEQTAAVKRCAMQRSVDYLREA  130 (188)
T ss_pred             HHHHHHHHHHHHHHH--------HHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             999847888887889--------9999999-9999999999827999997659970853250888876789999999999


Q ss_pred             CCCCCCCCC
Q ss_conf             755363588
Q gi|254780289|r  574 ISLETPIGD  582 (682)
Q Consensus       574 ~sl~~~~~~  582 (682)
                      +|.-..+|+
T Consensus       131 L~~~la~g~  139 (188)
T pfam07455       131 LSVWLAAGE  139 (188)
T ss_pred             HHHHHHHCC
T ss_conf             999997178


No 410
>pfam04433 SWIRM SWIRM domain. This SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in chromosomal proteins. It contains a helix-turn helix motif and binds to DNA.
Probab=22.04  E-value=40  Score=12.04  Aligned_cols=33  Identities=15%  Similarity=0.286  Sum_probs=18.5

Q ss_pred             HCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHCCC
Q ss_conf             848867899975268435998889999999984797
Q gi|254780289|r   40 QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGI   75 (682)
Q Consensus        40 e~GylTydeIn~~LP~d~~~~e~ie~i~~~L~~~GI   75 (682)
                      ..+|||..+.-..++.   +...+-.|+.+|+..|+
T Consensus        49 p~~~Lt~t~~r~~~~~---D~~~i~ri~~FL~~~G~   81 (84)
T pfam04433        49 PGKYLTKTDARRLLKG---DVNKVSRVHDFLERWGL   81 (84)
T ss_pred             CCEEEEHHHHHHHHCC---CHHHHHHHHHHHHHCCC
T ss_conf             8704649999998458---89999999999998083


No 411
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=22.03  E-value=40  Score=12.04  Aligned_cols=19  Identities=11%  Similarity=-0.081  Sum_probs=6.9

Q ss_pred             HHHHHHHHHHCCCCCCCEE
Q ss_conf             6799998874385457312
Q gi|254780289|r  478 NIGLMKAAEKFDWCLGYKF  496 (682)
Q Consensus       478 ~~~l~~a~~~~~~~~g~~f  496 (682)
                      |..-++.+-+|=..+|+|=
T Consensus       166 ~~~~~~~a~~~L~~~Ghr~  184 (342)
T PRK10014        166 NMQAAQLLTEHLIRNGHQR  184 (342)
T ss_pred             HHHHHHHHHHHHHHCCCCE
T ss_conf             6999999999998759986


No 412
>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=21.93  E-value=40  Score=12.03  Aligned_cols=40  Identities=28%  Similarity=0.409  Sum_probs=28.9

Q ss_pred             HCCCHHHHHHH----HHHHCCCCCCC-CCHHHHHHHHCCCHHHHH
Q ss_conf             32998899999----99818798674-688999899667899999
Q gi|254780289|r  618 ASLTPREERVL----RMRFGIGMNTD-HTLEEVGKQFCVTRERIR  657 (682)
Q Consensus       618 ~~l~~re~~v~----~~r~g~~~~~~-~tl~e~~~~~~~~~er~r  657 (682)
                      ..|+.||..|+    |+-||.+-..+ -|..+++..-|+++-.|.
T Consensus        28 ~~lt~rq~kv~~aV~RkTyG~nK~~d~I~~sqi~~mtgi~~~~Vs   72 (100)
T pfam04492        28 ADLSGRQLKVLLAVIRKTYGWNKPMDRVTNEQIAELTGLSRTHVS   72 (100)
T ss_pred             CCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCHHHHH
T ss_conf             888788999999999986077850336229999999788854599


No 413
>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=21.91  E-value=40  Score=12.03  Aligned_cols=41  Identities=20%  Similarity=0.332  Sum_probs=29.2

Q ss_pred             CHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf             988999999981879867468899989966789999999999999832
Q gi|254780289|r  621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK  668 (682)
Q Consensus       621 ~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~  668 (682)
                      +.|...|..-.-    |  ....|++..||+|--+|++|=.+ .+|+.
T Consensus        59 ~~Rd~~I~~eFn----G--~N~~eLArkY~ls~~~i~~ii~~-~rk~~   99 (107)
T pfam08765        59 ALRDLEIYNEFN----G--NNHAELARKYGVSEQWIYKIIKR-VRKLE   99 (107)
T ss_pred             HHHHHHHHHHHC----C--CCHHHHHHHHCCCHHHHHHHHHH-HHHHH
T ss_conf             999999999807----9--87999999969889999999999-99999


No 414
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=21.82  E-value=40  Score=12.01  Aligned_cols=37  Identities=24%  Similarity=0.166  Sum_probs=26.5

Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf             99999987760889997899987099989999999860
Q gi|254780289|r  533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT  570 (682)
Q Consensus       533 ~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  570 (682)
                      .+.--..+|+.||. +..+||+.+|+|...|+.-++..
T Consensus         5 D~~Il~~L~~n~R~-s~~~iA~~lg~S~~tv~~Ri~~L   41 (108)
T smart00344        5 DRKILEELQKDARI-SLAELAKKVGLSPSTVHNRVKRL   41 (108)
T ss_pred             HHHHHHHHHHCCCC-CHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             99999999982899-99999999893999999999999


No 415
>cd02844 PAZ_CAF_like PAZ domain, CAF_like subfamily. CAF (for carpel factory) is a plant homolog of Dicer. CAF has been implicated in flower morphogenesis and in early Arabidopsis development and might function through posttranscriptional regulation of specific mRNA molecules. PAZ domains are named after the proteins Piwi, Argonaut, and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the Piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes.
Probab=21.32  E-value=41  Score=11.94  Aligned_cols=24  Identities=25%  Similarity=0.450  Sum_probs=19.3

Q ss_pred             HHHHHHCCCCCCCEEEHHHHHHHH
Q ss_conf             998874385457312010289899
Q gi|254780289|r  482 MKAAEKFDWCLGYKFSTYAMWWVK  505 (682)
Q Consensus       482 ~~a~~~~~~~~g~~f~tya~~~i~  505 (682)
                      |-|-..|+.+.|.+|+||+.++-.
T Consensus        53 ln~~S~f~~~~g~~~~SY~eYykk   76 (135)
T cd02844          53 LNANSSFPGKEGLGYATYAEYFKE   76 (135)
T ss_pred             CCCCCCCCCCCCCCCCCHHHHHHH
T ss_conf             898886876578771439999999


No 416
>PRK12429 3-hydroxybutyrate dehydrogenase; Provisional
Probab=21.31  E-value=41  Score=11.94  Aligned_cols=106  Identities=21%  Similarity=0.099  Sum_probs=50.9

Q ss_pred             HHHHHHHHHHH---HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHH-HHCCC
Q ss_conf             24689998755---578999887522356777887544367999988743854573120102898999999999-72287
Q gi|254780289|r  442 SIAKKEMVEAN---LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI-ADQSC  517 (682)
Q Consensus       442 ~~AK~~l~~an---lr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~-~~~~~  517 (682)
                      +.+-..|.+.+   .-.+.|++-.....|...-----.|..||.|+.-+---.+|.|.-+-+-=||.-.+.+.. .+.+.
T Consensus       121 ~~~~p~m~~~~~G~Iv~isS~~~~~~~~~~~~Y~asKaal~~lt~~lA~e~~~~gIrvN~V~PG~i~T~~~~~~~~~~~~  200 (258)
T PRK12429        121 KAALPHMKAQKWGRIINMASVHGLVGSAGKAAYVSAKHGLIGLTKVVALEGATHGVTVNAICPGYVDTPLVRKQIPDLAK  200 (258)
T ss_pred             HHHHHHHHHCCCCEEEEECCHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCEEEEEEEECCCCCCCHHHHHHHHHH
T ss_conf             67777664359928999877554668999758999999999999999998532097999997487987102213367897


Q ss_pred             EEECCCHHHHHHHHHHHHHHHHH---HHCCCCCCHHHHHHHC
Q ss_conf             04614205889899999999987---7608899978999870
Q gi|254780289|r  518 TIRIPVHMRDKIHKVVRTARRMS---NKIKREPTPEEIAKKL  556 (682)
Q Consensus       518 ~~r~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~a~~~  556 (682)
                      .-.++.         ....++..   .-+||-.+|+|+|...
T Consensus       201 ~~~~~~---------~~~~~~~~~~~~P~~R~g~p~dia~~v  233 (258)
T PRK12429        201 ERGISE---------EEVLEDVLLPLVPQKRFTTVEEIADLA  233 (258)
T ss_pred             HCCCCH---------HHHHHHHHHHCCCCCCCCCHHHHHHHH
T ss_conf             739997---------999999997279989984999999999


No 417
>TIGR00370 TIGR00370 conserved hypothetical protein TIGR00370; InterPro: IPR010016   This is an uncharacterised family of proteins of unknown function..
Probab=21.06  E-value=38  Score=12.19  Aligned_cols=23  Identities=26%  Similarity=0.313  Sum_probs=14.9

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             46889998996678999999999
Q gi|254780289|r  639 DHTLEEVGKQFCVTRERIRQIEA  661 (682)
Q Consensus       639 ~~tl~e~~~~~~~~~er~rqi~~  661 (682)
                      ..-|++|++.-++|-|+|=||++
T Consensus       105 GpDL~~VAk~~qlspe~vi~~Hs  127 (217)
T TIGR00370       105 GPDLEEVAKFNQLSPEEVIDLHS  127 (217)
T ss_pred             CCCHHHHHHHHCCCHHHEEEECC
T ss_conf             98989999771788457344047


No 418
>PRK07740 hypothetical protein; Provisional
Probab=21.06  E-value=25  Score=13.72  Aligned_cols=14  Identities=21%  Similarity=0.245  Sum_probs=6.0

Q ss_pred             CCHHHHHHHHCCCH
Q ss_conf             68899989966789
Q gi|254780289|r  640 HTLEEVGKQFCVTR  653 (682)
Q Consensus       640 ~tl~e~~~~~~~~~  653 (682)
                      ++|+.+...||++-
T Consensus       185 ~sL~~l~~~fgI~~  198 (240)
T PRK07740        185 PTLDDALACYGITC  198 (240)
T ss_pred             CCHHHHHHHCCCCC
T ss_conf             78999999769999


No 419
>COG0411 LivG ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]
Probab=21.05  E-value=23  Score=14.00  Aligned_cols=60  Identities=18%  Similarity=0.381  Sum_probs=39.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q ss_conf             222211268899999987653321124689998755578999887522356777887544367
Q gi|254780289|r  417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI  479 (682)
Q Consensus       417 e~~~gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~  479 (682)
                      |--.||+..|-.++...|......... -==|||+++.+|..++.+-.  .+.+-..|.+|.-
T Consensus       175 EPaAGln~~e~~~l~~~i~~i~~~~g~-tillIEHdM~~Vm~l~dri~--Vl~~G~~IAeG~P  234 (250)
T COG0411         175 EPAAGLNPEETEELAELIRELRDRGGV-TILLIEHDMKLVMGLADRIV--VLNYGEVIAEGTP  234 (250)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCC-EEEEEEECCHHHHHHCCEEE--ECCCCCCCCCCCH
T ss_conf             765798989999999999998854896-89999742078862266999--5018838441898


No 420
>TIGR02104 pulA_typeI pullulanase, type I; InterPro: IPR011840    Pullulan is an unusual, industrially important polysaccharide in which short alpha-1,4 chains (maltotriose) are connected in alpha-1,6 linkages. Enzymes that cleave alpha-1,6 linkages in pullulan and release maltotriose are called pullulanases although pullulan itself may not be the natural substrate. This family consists of pullulanases related to the entries in IPR011838 from INTERPRO and IPR011839 from INTERPRO but having a different domain architecture with shorter sequences. Members are called type I pullulanases ..
Probab=21.02  E-value=42  Score=11.89  Aligned_cols=20  Identities=20%  Similarity=0.189  Sum_probs=11.7

Q ss_pred             HHHHHHCCCEEECCCCCCCC
Q ss_conf             99998479778327841000
Q gi|254780289|r   67 VAMLSNMGINVVDGDDLEDE   86 (682)
Q Consensus        67 ~~~L~~~GI~Vve~~~~~~~   86 (682)
                      ++.|.+|||.=|+=.|..|-
T Consensus       188 l~y~keLGVTHVqLLP~fDf  207 (655)
T TIGR02104       188 LDYLKELGVTHVQLLPVFDF  207 (655)
T ss_pred             HHHHHHCCCCEEEECCCCCC
T ss_conf             35554336535654341122


No 421
>PRK02234 recU Holliday junction-specific endonuclease; Reviewed
Probab=20.99  E-value=42  Score=11.89  Aligned_cols=16  Identities=44%  Similarity=0.692  Sum_probs=5.9

Q ss_pred             HCCCCCCHHHHHHHHH
Q ss_conf             2235677788754436
Q gi|254780289|r  463 YTNRGLQFLDLIQEGN  478 (682)
Q Consensus       463 ~~~~~~~~~~~~~~~~  478 (682)
                      |.|||+.|.++|.+.|
T Consensus        25 y~nRGM~LE~~IN~tN   40 (199)
T PRK02234         25 YANRGMSLEKDINETN   40 (199)
T ss_pred             CCCCCCHHHHHHHHHH
T ss_conf             2446605999999999


No 422
>COG4809 Archaeal ADP-dependent phosphofructokinase/glucokinase [Carbohydrate transport and metabolism]
Probab=20.99  E-value=33  Score=12.71  Aligned_cols=116  Identities=16%  Similarity=0.239  Sum_probs=50.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             33332222211268899999987653321124689998755578999887522356777887544367999988743854
Q gi|254780289|r  412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC  491 (682)
Q Consensus       412 kL~~ie~~~gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~  491 (682)
                      .+..+...+||+..|+..+..-+-  +++                  +|++....+ ...|+|    .|+|+-.++|+..
T Consensus       288 ~il~~v~SvGldE~ElA~vl~vlG--~~e------------------La~~I~~~~-~~~avi----eg~~~L~~e~~~e  342 (466)
T COG4809         288 NILSIVYSVGLDEVELANVLNVLG--YRE------------------LADRIISKD-DIEAVI----EGAMILLDELGLE  342 (466)
T ss_pred             HHHHHHHHCCCCHHHHHHHHHHHC--HHH------------------HHHHHHCCC-CHHHHH----HHHHHHHHHCCCC
T ss_conf             998664404878999999998607--699------------------987664134-388999----9999999863950


Q ss_pred             CCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHH
Q ss_conf             57312010289899999999972287046142058898999999999877608899978999870999899
Q gi|254780289|r  492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG  562 (682)
Q Consensus       492 ~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~  562 (682)
                      |=+ |-||..+.   +|++  +++.  . -.-|..+.+.+-. ..-.-...+|+--.+.++-+-|.+|...
T Consensus       343 ~i~-vHT~~y~l---~i~~--~~np--l-~~Ee~~daL~Fs~-~lAa~~A~~GnIe~~~d~~~glkvp~~~  403 (466)
T COG4809         343 RIH-VHTYGYYL---AITK--RGNP--L-SGEELRDALLFST-LLAAAKAMLGNIERLDDLKEGLKVPISE  403 (466)
T ss_pred             EEE-EEEEEEEE---EEEC--CCCC--C-CHHHHHHHHHHHH-HHHHHHHHCCCCCCHHHHHHHCCCCCHH
T ss_conf             899-98755788---8864--8995--4-3899999888888-9999998607866635677650488102


No 423
>COG1904 UxaC Glucuronate isomerase [Carbohydrate transport and metabolism]
Probab=20.92  E-value=42  Score=11.88  Aligned_cols=95  Identities=14%  Similarity=0.155  Sum_probs=56.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHH---HHHHHHHHHHHHHHHCCCCCCCEEE
Q ss_conf             1126889999998765332112468999875557899988752235677788---7544367999988743854573120
Q gi|254780289|r  421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD---LIQEGNIGLMKAAEKFDWCLGYKFS  497 (682)
Q Consensus       421 gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~---~~~~~~~~l~~a~~~~~~~~g~~f~  497 (682)
                      .++..+...|..+...|+.-. ....++-+|++  .+-+||.|..+|+-++=   -...-|.   ++..||-+..||--+
T Consensus       244 ~~~~~~a~~if~k~l~G~~lt-~~E~~~f~a~~--l~~l~km~~~~gwVmQiH~ga~RN~n~---~~~~k~G~D~GfDi~  317 (463)
T COG1904         244 ELSEADADAIFDKRLAGEALS-TEEAEQFKAAM--LTELAKMSAEDGWVMQIHPGALRNHNP---RMFKKLGPDTGFDIP  317 (463)
T ss_pred             CCCHHHHHHHHHHHHCCCCCC-HHHHHHHHHHH--HHHHHHHHHHCCEEEEECCCCCCCCCH---HHHHHHCCCCCCCCC
T ss_conf             578899999999986478788-89999999999--999998644168268851461036788---999973898777887


Q ss_pred             HHHHHHHHHHHHHHHHHCCCEEECCC
Q ss_conf             10289899999999972287046142
Q gi|254780289|r  498 TYAMWWVKQAITRSIADQSCTIRIPV  523 (682)
Q Consensus       498 tya~~~i~~~i~~~~~~~~~~~r~~~  523 (682)
                      +=--  |-.+.++.+....-.=++|+
T Consensus       318 ~~~~--~a~~L~~LLd~~~~~~~L~k  341 (463)
T COG1904         318 NDTE--IAEGLKPLLDAFGEDNDLPK  341 (463)
T ss_pred             CCCH--HHHHHHHHHHHHCCCCCCCE
T ss_conf             8404--67889999875402578754


No 424
>pfam11503 DUF3215 Protein of unknown function (DUF3215). This family of proteins with unknown function appears to be restricted to Saccharomycetaceae.
Probab=20.90  E-value=26  Score=13.50  Aligned_cols=44  Identities=20%  Similarity=0.353  Sum_probs=34.7

Q ss_pred             HHCCCCCHHHHHHHCCCCCCCHHHHHHHHHH----HHHCCCEEECCCC
Q ss_conf             7848867899975268435998889999999----9847977832784
Q gi|254780289|r   39 RQRGYVTIEELNAFLPPDEVSSEQMEDTVAM----LSNMGINVVDGDD   82 (682)
Q Consensus        39 ke~GylTydeIn~~LP~d~~~~e~ie~i~~~----L~~~GI~Vve~~~   82 (682)
                      +--|-||||+=|..+-......+.+++|+..    |.+.|..|++...
T Consensus         9 ~aiGtlaFDen~nlv~stGigk~rveDI~~lS~~eld~eG~~v~~d~~   56 (77)
T pfam11503         9 RAVGTLAFDENYNVVDSTGVGKSRIEDIIRLSNAELDREGYAVYQDAQ   56 (77)
T ss_pred             CCEEEEEECCCCCEEEECCCCHHHHHHHHHHHHHHHCCCCEEEEECCC
T ss_conf             632589984899899702432566777887756443665337985696


No 425
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=20.85  E-value=42  Score=11.87  Aligned_cols=34  Identities=32%  Similarity=0.308  Sum_probs=26.0

Q ss_pred             CCCCCCHHHHHHHCCCCHHHHHHHHHHHC--CCCCCC
Q ss_conf             08899978999870999899999998608--987553
Q gi|254780289|r  543 IKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLE  577 (682)
Q Consensus       543 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~--~~~sl~  577 (682)
                      .| +-|.++||+.+|+....|+.+|....  ..++..
T Consensus        30 kg-e~tDeela~~l~i~~~~vrriL~~L~e~~li~~~   65 (176)
T COG1675          30 KG-ELTDEELAELLGIKKNEVRRILYALYEDGLISYR   65 (176)
T ss_pred             CC-CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEE
T ss_conf             27-7674899888676399999999999857926888


No 426
>cd05133 RasGAP_IQGAP1 IQGAP1 is a homodimeric protein that is widely expressed among vertebrate cell types from early embryogenesis. Mammalian IQGAP1 protein is the best characterized member of the IQGAP family, and contains several protein-interacting domains. Human IQGAP1 is most similar to mouse Iqgap1 (94% identity) and has 62% identity to human IQGAP2. IQGAP1 binds and cross-links actin filaments in vitro and has been implicated in Ca2+/calmodulin signaling, E-cadherin-dependent cell adhesion, cell motility, and invasion. Yeast IQGAP homologues have a role in the recruitment of actin filaments, are components of the spindle pole body, and are required for actomyosin ring assembly and cytokinesis. Furthermore, IQGAP1 over-expression has also been detected in gastric and colorectal carcinomas and gastric cancer cell lines.
Probab=20.71  E-value=42  Score=11.85  Aligned_cols=43  Identities=14%  Similarity=0.312  Sum_probs=25.3

Q ss_pred             HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCHHHHHHH
Q ss_conf             99999988999999987282389999999987311710367876
Q gi|254780289|r  142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII  185 (682)
Q Consensus       142 IAKRIE~G~~~i~~al~~~P~ti~~il~~~e~i~~ge~~LrdII  185 (682)
                      +...|+.....+...+-..|..++.+..++. -..|..-|++++
T Consensus        18 l~~Ei~s~~~~~~d~lr~N~~~~km~~~y~R-~~~g~~~Lk~iL   60 (360)
T cd05133          18 LQEEIKSKVDQIQEIVTGNPTVIKMVVSFNR-GARGQNALRQIL   60 (360)
T ss_pred             HHHHHHHCCCCHHHHHHCCCHHHHHHHHHHC-CCCCHHHHHHHH
T ss_conf             9999986037899997458099999999854-875359999999


No 427
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=20.55  E-value=43  Score=11.82  Aligned_cols=24  Identities=8%  Similarity=0.126  Sum_probs=14.8

Q ss_pred             CCCCHHHHHHHCCCCHHHHHHHHH
Q ss_conf             899978999870999899999998
Q gi|254780289|r  545 REPTPEEIAKKLAMPVEGVRKVLK  568 (682)
Q Consensus       545 ~~~~~~~~a~~~~~~~~~~~~~~~  568 (682)
                      +.-|-.++|+.+|++..-|...-+
T Consensus        17 ~glTQ~eLA~~~Gvs~~tVs~wE~   40 (135)
T PRK09706         17 LKLSQRALAKAVGVSHVSISQWER   40 (135)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHC
T ss_conf             599999999996988999999982


No 428
>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=20.53  E-value=43  Score=11.82  Aligned_cols=19  Identities=32%  Similarity=0.342  Sum_probs=7.5

Q ss_pred             CHHHHHHHCCCCHHHHHHH
Q ss_conf             9789998709998999999
Q gi|254780289|r  548 TPEEIAKKLAMPVEGVRKV  566 (682)
Q Consensus       548 ~~~~~a~~~~~~~~~~~~~  566 (682)
                      |.+|+++.|+++..+|.++
T Consensus        54 t~~el~~~L~~s~~~v~k~   72 (76)
T pfam06970        54 TNEELMELLNCSKQKVIKI   72 (76)
T ss_pred             EHHHHHHHHCCCHHHHHHH
T ss_conf             4999999978788899999


No 429
>TIGR01752 flav_long flavodoxin; InterPro: IPR010086   Flavodoxins are small redox-active proteins with a flavin mononucleotide (FMN) prosthetic group. They function as electron transfer agents in a variety of microbial metabolic processes, including nitrogen fixation by nitrogenase , sulphite reduction , and light-dependent NADP+ reduction during photosynthesis . This entry describes the long chain type, typical for nitrogen fixation but associated with pyruvate formate-lyase activation and cobalamin-dependent methionine synthase activity in Escherichia coli .; GO: 0010181 FMN binding, 0006118 electron transport.
Probab=20.52  E-value=39  Score=12.11  Aligned_cols=19  Identities=37%  Similarity=0.351  Sum_probs=9.8

Q ss_pred             HHHHHHCC-CCHHHHHHHHH
Q ss_conf             89998709-99899999998
Q gi|254780289|r  550 EEIAKKLA-MPVEGVRKVLK  568 (682)
Q Consensus       550 ~~~a~~~~-~~~~~~~~~~~  568 (682)
                      +.|+..|| -+..+|..+-+
T Consensus        18 e~I~~~lG~~~~~d~~ni~~   37 (176)
T TIGR01752        18 EKIAKELGKESDVDVFNIAK   37 (176)
T ss_pred             HHHHHHHCCCCCCCCCCCCC
T ss_conf             99999818886621013231


No 430
>KOG1389 consensus
Probab=20.40  E-value=43  Score=11.80  Aligned_cols=25  Identities=32%  Similarity=0.563  Sum_probs=14.0

Q ss_pred             HHCCCCHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             87099989999999860898755363588
Q gi|254780289|r  554 KKLAMPVEGVRKVLKITKEPISLETPIGD  582 (682)
Q Consensus       554 ~~~~~~~~~~~~~~~~~~~~~sl~~~~~~  582 (682)
                      +.|+++.+||    ....-.+-|-.|+|-
T Consensus       358 ~KL~ld~ekV----N~~GGaiAlGHPlGa  382 (435)
T KOG1389         358 NKLGLDPEKV----NVNGGAIALGHPLGA  382 (435)
T ss_pred             HHHCCCHHHC----CCCCCEEECCCCCCC
T ss_conf             8738988884----888862330687577


No 431
>TIGR00624 tag DNA-3-methyladenine glycosylase I; InterPro: IPR004597   One common form of damage to DNA occurs when alkyl groups become covalently linked to DNA, leading to the formation of mutagenic or toxic lesions. Alkylating agents are ubiquitous in the environment and can also exist endogenously; for example S-adenosylmethionine, a commonly used methyl donor in many cellualr pathways, can produce methylation damage. Given the prevalence of alkylating agents it is not surprising that all cellular organisms studied so far have developed repair systems to deal with DNA alkylation .   DNA-3-methyladenine glycosylase I (also known as TagI) is part of the broader helix-hairpin-helix DNA repair glycosylase supefamily. It specifically catalyses the release of 3-methylated adenine and, to a lesser extent, guanosine bases from DNA by hydrolysis of the deoxyribose N-glycosidic bond , . A phylogenomic study suggests that TagI evolved in, and is specific to, the bacteria .; GO: 0008725 DNA-3-methyladenine glycosylase I activity, 0006284 base-excision repair.
Probab=20.33  E-value=43  Score=11.79  Aligned_cols=31  Identities=19%  Similarity=0.253  Sum_probs=18.9

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCEEE-HHHHHHHHHHH
Q ss_conf             544367999988743854573120-10289899999
Q gi|254780289|r  474 IQEGNIGLMKAAEKFDWCLGYKFS-TYAMWWVKQAI  508 (682)
Q Consensus       474 ~~~~~~~l~~a~~~~~~~~g~~f~-tya~~~i~~~i  508 (682)
                      +.-....|-|+..    +|||||. |=-.|-..||.
T Consensus       141 ~t~ea~Amsk~LK----krGF~FVGpTicYalMQA~  172 (185)
T TIGR00624       141 ITSEAKAMSKELK----KRGFRFVGPTICYALMQAT  172 (185)
T ss_pred             CCHHHHHHHHHHH----HCCCCCCCHHHHHHHHHHH
T ss_conf             6767899999987----5688300168999988641


No 432
>TIGR02881 spore_V_K stage V sporulation protein K; InterPro: IPR014232   Proteins in this entry include the stage V sporulation protein K (SpoVK), a close homologue of the Rubisco expression protein CbbX (IPR000470 from INTERPRO), and are members of an ATPase family associated with various cellular activities. These proteins are strictly limited to bacterial endospore-forming species, but are not found universally among members of this group; they are missing from the Clostridium species..
Probab=20.06  E-value=44  Score=11.75  Aligned_cols=55  Identities=24%  Similarity=0.359  Sum_probs=40.9

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHH------CCCEEECCCHHHHH
Q ss_conf             77788754436799998874385457312010289899999999972------28704614205889
Q gi|254780289|r  468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD------QSCTIRIPVHMRDK  528 (682)
Q Consensus       468 ~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~------~~~~~r~~~~~~~~  528 (682)
                      +.|.|---+   -||.=+.+|=-.|-|+||.-|.|-+|+-+.+.-..      |+|.||   .|+|.
T Consensus       173 i~FPdY~~e---eL~~Ia~~m~~~ReY~Lt~~A~~~lr~~l~~~~~~~~~~~sNaR~vR---N~iE~  233 (261)
T TIGR02881       173 IDFPDYTVE---ELMEIAERMVKEREYKLTEEAKWKLREHLAKVDQLSSREFSNARYVR---NIIEK  233 (261)
T ss_pred             EECCCCCHH---HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHH---HHHHH
T ss_conf             418899888---99999999986464225788999999997412444210057620124---28899


No 433
>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=20.00  E-value=44  Score=11.74  Aligned_cols=23  Identities=22%  Similarity=0.245  Sum_probs=15.9

Q ss_pred             CHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf             97899987099989999999860
Q gi|254780289|r  548 TPEEIAKKLAMPVEGVRKVLKIT  570 (682)
Q Consensus       548 ~~~~~a~~~~~~~~~~~~~~~~~  570 (682)
                      |+.|+|+.+|+|+..++.--+..
T Consensus         2 ~Ige~A~~~gvs~~tlR~Ye~~G   24 (123)
T cd04770           2 KIGELAKAAGVSPDTIRYYERIG   24 (123)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHCC
T ss_conf             68999999895999999999818


Done!