Query gi|254780611|ref|YP_003065024.1| RNA polymerase factor sigma-32 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 302
No_of_seqs 184 out of 3786
Neff 8.1
Searched_HMMs 39220
Date Sun May 29 21:41:30 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780611.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR02997 Sig70-cyanoRpoD RNA 100.0 0 0 603.8 19.5 257 14-281 1-336 (336)
2 PRK06596 RNA polymerase factor 100.0 0 0 541.1 28.6 273 10-287 10-283 (284)
3 TIGR02392 rpoH_proteo alternat 100.0 0 0 543.4 23.4 272 14-285 1-278 (279)
4 TIGR02394 rpoS_proteo RNA poly 100.0 0 0 547.2 19.7 273 8-287 7-284 (292)
5 PRK05657 RNA polymerase sigma 100.0 0 0 530.0 25.4 265 12-287 54-320 (328)
6 PRK07500 rpoH2 RNA polymerase 100.0 0 0 526.7 27.4 278 12-289 4-282 (289)
7 PRK09210 RNA polymerase sigma 100.0 0 0 528.4 25.5 266 11-287 94-361 (368)
8 PRK07921 RNA polymerase sigma 100.0 0 0 520.7 26.1 272 4-286 12-312 (320)
9 PRK07405 RNA polymerase sigma 100.0 0 0 513.9 25.2 265 9-284 4-309 (318)
10 PRK05901 RNA polymerase sigma 100.0 0 0 508.2 24.7 267 10-287 104-390 (398)
11 PRK05949 RNA polymerase sigma 100.0 0 0 508.3 24.4 264 9-283 13-317 (327)
12 PRK07406 RNA polymerase sigma 100.0 0 0 509.1 23.6 265 12-287 73-378 (385)
13 PRK07598 RNA polymerase sigma 100.0 0 0 507.5 24.0 269 7-286 48-399 (410)
14 PRK05658 RNA polymerase sigma 100.0 0 0 502.0 23.2 254 23-287 354-612 (620)
15 TIGR02393 RpoD_Cterm RNA polym 100.0 0 0 502.9 16.5 229 49-287 1-233 (240)
16 COG0568 RpoD DNA-directed RNA 100.0 0 0 482.4 24.1 266 11-287 64-334 (342)
17 PRK08215 sporulation sigma fac 100.0 0 0 472.7 23.6 257 1-284 1-257 (257)
18 PRK08583 RNA polymerase sigma 100.0 0 0 466.4 23.9 251 20-285 1-254 (257)
19 PRK07408 RNA polymerase sigma 100.0 0 0 454.3 24.3 247 28-287 5-254 (256)
20 PRK05572 sporulation sigma fac 100.0 0 0 450.3 23.7 247 22-286 5-251 (251)
21 PRK06288 RNA polymerase sigma 100.0 0 0 435.8 25.6 250 25-287 4-259 (261)
22 PRK07122 RNA polymerase sigma 100.0 0 0 431.6 17.2 249 14-285 8-263 (263)
23 PRK05911 RNA polymerase sigma 100.0 0 0 415.8 25.2 244 30-286 5-255 (257)
24 PRK07670 RNA polymerase sigma 100.0 0 0 416.7 24.4 241 32-286 2-247 (250)
25 PRK05803 sporulation sigma fac 100.0 0 0 418.0 22.1 211 14-286 15-228 (228)
26 TIGR02980 SigBFG RNA polymeras 100.0 0 0 422.9 10.6 224 46-284 1-228 (229)
27 PRK08301 sporulation sigma fac 100.0 0 0 397.8 21.8 206 19-286 28-237 (239)
28 PRK06986 fliA flagellar biosyn 100.0 0 0 382.9 21.6 227 41-286 2-233 (234)
29 TIGR02885 spore_sigF RNA polym 100.0 0 0 384.4 9.0 231 37-284 1-231 (231)
30 COG1191 FliA DNA-directed RNA 100.0 0 0 350.5 22.6 241 26-286 3-246 (247)
31 PRK12427 flagellar biosynthesi 100.0 0 0 346.4 20.6 216 44-284 9-229 (229)
32 TIGR02479 FliA_WhiG RNA polyme 100.0 0 0 348.0 15.7 220 53-285 1-227 (227)
33 TIGR02941 Sigma_B RNA polymera 100.0 0 0 329.6 12.7 243 28-285 9-255 (256)
34 TIGR02846 spore_sigmaK RNA pol 100.0 8.8E-44 0 312.1 13.4 212 11-284 11-227 (228)
35 TIGR02850 spore_sigG RNA polym 100.0 1E-40 2.8E-45 291.6 18.2 252 5-283 2-253 (254)
36 TIGR02835 spore_sigmaE RNA pol 100.0 8.5E-31 2.2E-35 225.4 15.5 198 27-286 32-232 (234)
37 PRK08295 RNA polymerase factor 100.0 3.5E-28 8.8E-33 207.9 21.5 201 26-287 4-205 (209)
38 PRK06759 RNA polymerase factor 99.9 2.6E-24 6.6E-29 182.0 15.8 151 48-284 4-154 (154)
39 TIGR02937 sigma70-ECF RNA poly 99.9 5.1E-24 1.3E-28 180.1 15.2 162 48-284 1-162 (162)
40 PRK11922 RNA polymerase sigma 99.8 1.5E-17 3.8E-22 136.9 19.1 193 27-289 10-202 (231)
41 PRK12531 RNA polymerase sigma 99.8 2.5E-17 6.4E-22 135.3 19.2 184 29-287 9-192 (194)
42 PRK12534 RNA polymerase sigma 99.8 6.6E-17 1.7E-21 132.5 19.4 186 24-286 2-187 (187)
43 PRK12519 RNA polymerase sigma 99.8 5.5E-17 1.4E-21 133.1 18.7 185 28-289 10-194 (194)
44 PRK09652 RNA polymerase sigma 99.8 5.7E-17 1.5E-21 132.9 18.5 184 35-289 7-190 (192)
45 PRK11923 algU RNA polymerase s 99.8 6.8E-17 1.7E-21 132.4 18.3 191 28-289 1-191 (193)
46 PRK09641 RNA polymerase sigma 99.8 7.8E-17 2E-21 132.0 18.4 182 34-286 5-186 (187)
47 PRK12513 RNA polymerase sigma 99.8 1.5E-16 3.7E-21 130.2 19.6 180 35-290 14-193 (194)
48 PRK09646 RNA polymerase sigma 99.8 5.9E-17 1.5E-21 132.9 17.5 182 27-285 10-191 (194)
49 PRK13919 putative RNA polymera 99.8 9.2E-17 2.3E-21 131.6 17.8 176 35-286 11-186 (187)
50 PRK06811 RNA polymerase factor 99.8 3.7E-16 9.5E-21 127.5 19.6 174 34-287 3-179 (185)
51 PRK09648 RNA polymerase sigma 99.8 3.8E-16 9.8E-21 127.4 19.5 179 30-286 5-187 (187)
52 PRK05602 RNA polymerase sigma 99.7 4.5E-16 1.2E-20 126.9 18.4 177 32-289 5-181 (186)
53 PRK12543 RNA polymerase sigma 99.7 1.5E-15 3.7E-20 123.5 19.1 176 33-287 5-180 (190)
54 PRK11924 RNA polymerase sigma 99.7 9.8E-16 2.5E-20 124.7 18.1 178 36-290 2-179 (180)
55 PRK12514 RNA polymerase sigma 99.7 1.4E-15 3.6E-20 123.6 18.7 178 30-286 2-179 (179)
56 PRK12526 RNA polymerase sigma 99.7 2.3E-15 5.8E-20 122.2 19.6 186 28-287 19-204 (206)
57 PRK12524 RNA polymerase sigma 99.7 2.4E-15 6.2E-20 122.1 18.9 179 28-288 10-188 (196)
58 PRK12515 RNA polymerase sigma 99.7 2.5E-15 6.4E-20 122.0 18.7 175 34-288 9-183 (189)
59 PRK12537 RNA polymerase sigma 99.7 1.5E-15 3.7E-20 123.5 17.1 177 31-284 7-183 (184)
60 PRK12538 RNA polymerase sigma 99.7 3.3E-15 8.5E-20 121.1 18.8 175 32-287 48-222 (233)
61 PRK09643 RNA polymerase sigma 99.7 4.7E-15 1.2E-19 120.1 19.3 177 35-296 15-191 (197)
62 PRK09638 RNA polymerase sigma 99.7 2.4E-15 6.1E-20 122.1 16.8 174 32-286 4-177 (177)
63 PRK12512 RNA polymerase sigma 99.7 6E-15 1.5E-19 119.4 18.3 174 30-287 5-182 (184)
64 PRK08311 putative RNA polymera 99.7 1.6E-15 4.2E-20 123.2 14.4 89 36-125 7-97 (237)
65 PRK09647 RNA polymerase sigma 99.7 1.5E-14 3.9E-19 116.7 18.2 184 27-288 26-209 (222)
66 PRK12542 RNA polymerase sigma 99.7 9.5E-15 2.4E-19 118.1 16.2 171 40-286 2-172 (185)
67 PRK12539 RNA polymerase sigma 99.6 7.3E-14 1.9E-18 112.2 18.7 176 29-287 2-182 (184)
68 PRK09415 RNA polymerase factor 99.6 4.8E-14 1.2E-18 113.4 17.6 174 36-286 4-177 (177)
69 PRK12518 RNA polymerase sigma 99.6 3.9E-14 1E-18 114.0 16.6 171 37-287 1-171 (175)
70 PRK09640 RNA polymerase sigma 99.6 5.9E-14 1.5E-18 112.8 17.0 177 29-288 8-186 (188)
71 PRK12536 RNA polymerase sigma 99.6 1.5E-13 3.8E-18 110.1 18.3 173 32-286 3-176 (178)
72 PRK12544 RNA polymerase sigma 99.6 2.3E-13 5.9E-18 108.8 17.1 184 46-287 12-200 (207)
73 TIGR02859 spore_sigH RNA polym 99.6 9.8E-14 2.5E-18 111.3 14.6 190 36-289 8-198 (198)
74 PRK12522 RNA polymerase sigma 99.6 6.9E-13 1.8E-17 105.7 17.6 170 47-288 2-171 (173)
75 PRK12520 RNA polymerase sigma 99.6 6.3E-13 1.6E-17 105.9 16.5 184 52-294 6-190 (191)
76 PRK12532 RNA polymerase sigma 99.6 1.1E-12 2.9E-17 104.2 17.7 178 52-288 10-188 (195)
77 PRK12533 RNA polymerase sigma 99.6 9.1E-13 2.3E-17 104.9 17.2 186 44-301 17-202 (217)
78 PRK12535 RNA polymerase sigma 99.6 2.5E-12 6.5E-17 101.9 19.5 178 32-292 11-188 (195)
79 TIGR02984 Sig-70_plancto1 RNA 99.6 7.1E-13 1.8E-17 105.6 16.6 183 44-285 3-190 (190)
80 PRK09649 RNA polymerase sigma 99.5 1.2E-12 3E-17 104.1 17.1 176 29-287 6-181 (185)
81 pfam07638 Sigma70_ECF ECF sigm 99.5 1.1E-12 2.8E-17 104.3 16.9 175 35-285 5-184 (185)
82 PRK12545 RNA polymerase sigma 99.5 8.1E-13 2.1E-17 105.2 16.1 177 55-288 15-191 (201)
83 PRK09645 RNA polymerase sigma 99.5 2.2E-12 5.7E-17 102.2 16.2 165 44-287 3-167 (171)
84 PRK12517 RNA polymerase sigma 99.5 3.2E-12 8.1E-17 101.2 16.0 163 44-290 19-182 (188)
85 PRK09637 RNA polymerase sigma 99.5 5.5E-12 1.4E-16 99.6 15.6 157 50-289 3-159 (181)
86 PRK12516 RNA polymerase sigma 99.5 9.3E-12 2.4E-16 98.1 16.4 168 44-293 9-176 (190)
87 PRK09644 RNA polymerase sigma 99.5 7.7E-12 2E-16 98.6 16.0 157 50-287 3-159 (165)
88 PRK12541 RNA polymerase sigma 99.5 1.1E-11 2.8E-16 97.6 16.3 160 45-285 2-161 (161)
89 COG1595 RpoE DNA-directed RNA 99.5 2.7E-11 6.8E-16 95.0 18.1 170 43-288 10-179 (182)
90 PRK09642 RNA polymerase sigma 99.4 7.5E-12 1.9E-16 98.7 14.4 157 54-287 1-157 (160)
91 PRK12530 RNA polymerase sigma 99.4 2.3E-11 5.9E-16 95.5 16.6 173 54-288 15-188 (191)
92 PRK12546 RNA polymerase sigma 99.4 1.5E-11 3.9E-16 96.7 15.6 161 45-288 5-165 (188)
93 PRK09047 RNA polymerase factor 99.4 1.3E-11 3.2E-16 97.2 14.3 69 217-287 89-157 (161)
94 PRK07037 extracytoplasmic-func 99.4 3.2E-11 8E-16 94.6 16.0 166 45-287 9-174 (183)
95 PRK12547 RNA polymerase sigma 99.4 7.7E-11 2E-15 92.0 17.1 160 46-287 4-163 (164)
96 PRK09639 RNA polymerase sigma 99.4 7.3E-11 1.9E-15 92.1 16.7 161 47-287 2-162 (166)
97 PRK09651 RNA polymerase sigma 99.4 7.7E-11 2E-15 92.0 15.8 165 44-287 6-170 (172)
98 TIGR02948 SigW_bacill RNA poly 99.3 2.1E-11 5.4E-16 95.7 10.3 179 35-288 6-184 (187)
99 PRK12540 RNA polymerase sigma 99.3 3.1E-10 8E-15 87.9 16.0 160 47-288 4-163 (181)
100 PRK12527 RNA polymerase sigma 99.3 3.1E-10 7.8E-15 88.0 14.1 64 222-287 93-156 (159)
101 TIGR02952 Sig70_famx2 RNA poly 99.2 2.7E-10 6.8E-15 88.4 13.0 169 38-284 2-171 (171)
102 TIGR02985 Sig70_bacteroi1 RNA 99.2 4.4E-10 1.1E-14 86.9 14.0 166 49-284 2-167 (167)
103 PRK12523 RNA polymerase sigma 99.2 1.4E-09 3.6E-14 83.5 16.1 165 44-287 6-170 (172)
104 PRK12511 RNA polymerase sigma 99.2 4.4E-10 1.1E-14 86.9 13.4 158 50-289 7-164 (182)
105 PRK08241 RNA polymerase factor 99.1 5.6E-09 1.4E-13 79.5 15.1 191 35-285 10-205 (341)
106 pfam04542 Sigma70_r2 Sigma-70 99.1 2.4E-10 6.1E-15 88.7 7.3 70 53-122 1-70 (71)
107 PRK12528 RNA polymerase sigma 99.1 1.2E-08 3.2E-13 77.2 14.5 162 43-283 5-166 (167)
108 PRK12525 RNA polymerase sigma 99.0 4.1E-08 1E-12 73.7 15.6 164 44-286 4-168 (168)
109 TIGR02954 Sig70_famx3 RNA poly 99.0 4.2E-08 1.1E-12 73.7 14.9 166 34-286 3-172 (173)
110 pfam04545 Sigma70_r4 Sigma-70, 99.0 6.9E-10 1.8E-14 85.6 5.4 50 231-282 1-50 (50)
111 PRK12529 RNA polymerase sigma 98.9 1.7E-07 4.4E-12 69.6 16.1 165 44-284 9-175 (178)
112 PRK09636 RNA polymerase sigma 98.8 6.1E-07 1.6E-11 65.9 14.5 153 54-283 6-158 (289)
113 cd06171 Sigma70_r4 Sigma70, re 98.8 2.2E-08 5.6E-13 75.6 6.5 54 226-281 2-55 (55)
114 TIGR02999 Sig-70_X6 RNA polyme 98.7 2.4E-06 6E-11 62.0 15.8 159 35-271 5-180 (194)
115 TIGR02989 Sig-70_gvs1 RNA poly 98.7 1.1E-06 2.9E-11 64.1 13.5 156 52-285 5-160 (163)
116 TIGR02895 spore_sigI RNA polym 98.6 1.9E-07 4.9E-12 69.3 6.6 79 44-122 6-86 (225)
117 TIGR02939 RpoE_Sigma70 RNA pol 98.6 5.2E-06 1.3E-10 59.7 13.8 181 34-288 8-188 (192)
118 PRK09635 sigI RNA polymerase s 98.5 2E-05 5E-10 55.9 15.5 158 51-283 8-165 (290)
119 PRK06930 positive control sigm 98.5 9.7E-07 2.5E-11 64.6 8.0 64 225-290 105-168 (170)
120 TIGR02983 SigE-fam_strep RNA p 98.4 1.7E-07 4.4E-12 69.6 3.1 152 53-286 11-163 (165)
121 TIGR03001 Sig-70_gmx1 RNA poly 98.4 3.8E-06 9.7E-11 60.6 9.2 82 210-293 142-227 (249)
122 pfam08281 Sigma70_r4_2 Sigma-7 98.1 6.2E-06 1.6E-10 59.2 6.2 53 226-280 2-54 (54)
123 TIGR02957 SigX4 RNA polymerase 98.1 1.6E-05 4E-10 56.5 7.6 157 55-289 4-162 (287)
124 pfam00140 Sigma70_r1_2 Sigma-7 98.1 4E-06 1E-10 60.5 4.0 36 13-49 1-36 (37)
125 pfam04539 Sigma70_r3 Sigma-70 98.0 3.1E-06 7.9E-11 61.2 2.8 72 139-212 3-74 (78)
126 TIGR02233 Myxo_sigma_rel Myxoc 98.0 6.9E-05 1.8E-09 52.2 8.6 77 214-292 4-84 (106)
127 PRK05658 RNA polymerase sigma 97.9 0.0024 6.2E-08 41.8 18.5 65 12-79 100-168 (620)
128 PRK00118 putative DNA-binding 97.7 0.00011 2.8E-09 50.9 6.7 54 228-283 10-64 (105)
129 PRK03975 tfx putative transcri 97.7 0.0001 2.6E-09 51.1 6.2 49 234-285 4-52 (139)
130 pfam04297 UPF0122 Putative hel 97.7 0.0003 7.5E-09 48.0 8.4 55 227-283 9-64 (101)
131 TIGR02943 Sig70_famx1 RNA poly 97.7 0.0012 3.1E-08 43.8 11.1 158 75-287 30-188 (194)
132 TIGR02959 SigZ RNA polymerase 97.5 0.0004 1E-08 47.1 6.6 62 222-286 88-150 (170)
133 TIGR00721 tfx DNA-binding prot 97.5 0.00024 6E-09 48.6 5.1 47 234-283 6-52 (142)
134 TIGR02960 SigX5 RNA polymerase 97.4 0.0076 1.9E-07 38.6 12.1 74 206-288 118-191 (329)
135 TIGR02950 SigM_subfam RNA poly 97.3 0.001 2.6E-08 44.4 6.7 69 209-283 92-160 (162)
136 PRK09958 DNA-binding transcrip 97.2 0.0013 3.4E-08 43.6 6.4 47 232-281 141-187 (204)
137 pfam00196 GerE Bacterial regul 97.1 0.0014 3.6E-08 43.4 6.1 47 232-281 1-47 (58)
138 COG3413 Predicted DNA binding 97.1 0.0023 5.9E-08 42.0 6.8 52 234-285 155-211 (215)
139 PRK09483 response regulator; P 96.9 0.0029 7.5E-08 41.3 6.3 47 232-281 146-192 (216)
140 smart00421 HTH_LUXR helix_turn 96.9 0.0028 7.2E-08 41.4 6.1 46 233-281 2-47 (58)
141 PRK10840 transcriptional regul 96.9 0.0032 8.2E-08 41.0 6.2 45 234-281 150-194 (216)
142 PRK10403 transcriptional regul 96.8 0.0041 1E-07 40.3 6.4 47 233-282 152-198 (215)
143 PRK12469 RNA polymerase factor 96.8 0.047 1.2E-06 33.3 13.9 43 232-274 329-385 (475)
144 PRK10651 transcriptional regul 96.8 0.0044 1.1E-07 40.1 6.4 47 232-281 153-199 (216)
145 PRK09935 transcriptional regul 96.8 0.0044 1.1E-07 40.2 6.3 45 234-281 149-193 (210)
146 cd06170 LuxR_C_like C-terminal 96.8 0.0046 1.2E-07 40.0 6.4 44 235-281 1-44 (57)
147 pfam07374 DUF1492 Protein of u 96.8 0.0046 1.2E-07 40.0 6.3 57 222-280 42-99 (100)
148 TIGR03020 EpsA transcriptional 96.7 0.0052 1.3E-07 39.6 6.3 48 232-282 188-235 (247)
149 PRK10360 DNA-binding transcrip 96.7 0.0052 1.3E-07 39.7 6.2 45 233-280 136-180 (196)
150 PRK10188 DNA-binding transcrip 96.7 0.0067 1.7E-07 38.9 6.4 47 234-283 179-225 (240)
151 pfam04967 HTH_10 HTH DNA bindi 96.7 0.0079 2E-07 38.4 6.8 46 235-280 1-51 (53)
152 PRK11475 DNA-binding transcrip 96.7 0.0061 1.6E-07 39.2 6.1 46 233-281 133-178 (205)
153 COG2739 Uncharacterized protei 96.6 0.0095 2.4E-07 37.9 7.0 46 233-280 16-61 (105)
154 TIGR03541 reg_near_HchA LuxR f 96.6 0.0076 1.9E-07 38.5 6.4 46 234-282 171-216 (232)
155 PRK09390 fixJ response regulat 96.6 0.012 3.1E-07 37.2 7.5 50 229-281 136-185 (202)
156 PRK06704 RNA polymerase factor 96.6 0.067 1.7E-06 32.2 14.2 61 224-286 106-166 (228)
157 COG2197 CitB Response regulato 96.5 0.0084 2.1E-07 38.3 6.2 46 233-281 147-192 (211)
158 TIGR01637 phage_arpU phage tra 96.4 0.034 8.6E-07 34.2 8.8 64 224-287 73-136 (139)
159 COG4566 TtrR Response regulato 96.3 0.034 8.8E-07 34.2 8.3 57 224-283 132-188 (202)
160 pfam02001 DUF134 Protein of un 96.3 0.015 3.9E-07 36.5 6.5 51 234-286 36-86 (100)
161 PRK13870 transcriptional regul 96.3 0.016 4.2E-07 36.3 6.5 45 235-282 174-218 (234)
162 COG1356 tfx Transcriptional re 96.2 0.0033 8.4E-08 41.0 2.7 47 234-283 8-54 (143)
163 PRK10100 DNA-binding transcrip 96.1 0.021 5.3E-07 35.6 6.3 45 234-281 155-199 (216)
164 PRK09954 hypothetical protein; 96.0 0.015 3.8E-07 36.6 4.9 16 18-33 7-22 (362)
165 PRK05932 RNA polymerase factor 95.8 0.16 4.2E-06 29.6 15.9 43 232-274 315-371 (461)
166 PRK04217 hypothetical protein; 95.7 0.041 1.1E-06 33.6 6.5 58 235-294 43-100 (110)
167 PRK04841 transcriptional regul 95.5 0.041 1E-06 33.7 5.8 44 234-280 838-881 (903)
168 COG2390 DeoR Transcriptional r 95.5 0.026 6.6E-07 35.0 4.8 14 260-273 266-279 (321)
169 TIGR03209 P21_Cbot clostridium 94.9 0.012 3.1E-07 37.2 1.4 40 228-269 101-140 (142)
170 COG1342 Predicted DNA-binding 94.8 0.098 2.5E-06 31.1 6.0 50 235-286 34-83 (99)
171 COG2771 CsgD DNA-binding HTH d 94.6 0.14 3.5E-06 30.1 6.4 51 233-286 3-53 (65)
172 PRK13558 bacterio-opsin activa 94.3 0.35 8.9E-06 27.4 7.8 57 228-284 609-671 (674)
173 PRK09191 two-component respons 94.1 0.13 3.4E-06 30.2 5.3 136 52-288 5-140 (261)
174 COG1508 RpoN DNA-directed RNA 93.8 0.55 1.4E-05 26.1 10.2 57 232-288 296-373 (444)
175 pfam05263 DUF722 Protein of un 93.4 0.63 1.6E-05 25.7 7.8 54 220-273 67-120 (130)
176 PRK11564 stationary phase indu 93.1 0.39 1E-05 27.1 6.4 14 235-248 314-327 (426)
177 COG1510 Predicted transcriptio 93.0 0.16 4E-06 29.8 4.2 29 151-179 36-64 (177)
178 pfam01726 LexA_DNA_bind LexA D 93.0 0.3 7.6E-06 27.9 5.6 41 232-272 1-46 (65)
179 pfam01371 Trp_repressor Trp re 92.7 0.53 1.3E-05 26.2 6.5 44 234-278 26-74 (88)
180 COG3355 Predicted transcriptio 92.5 0.66 1.7E-05 25.6 6.8 47 230-280 20-66 (126)
181 TIGR02612 mob_myst_A mobile my 91.7 0.27 6.8E-06 28.2 4.0 52 121-188 19-71 (150)
182 PRK12423 LexA repressor; Provi 91.7 0.41 1E-05 27.0 5.0 33 144-176 13-46 (202)
183 smart00419 HTH_CRP helix_turn_ 91.5 0.29 7.5E-06 27.9 4.1 28 251-282 7-34 (48)
184 PRK01381 Trp operon repressor; 91.3 0.8 2E-05 25.0 6.1 55 234-289 32-95 (99)
185 smart00344 HTH_ASNC helix_turn 90.9 0.65 1.7E-05 25.6 5.4 28 152-180 14-41 (108)
186 TIGR02947 SigH_actino RNA poly 90.6 1.3 3.4E-05 23.5 14.9 177 33-287 5-182 (193)
187 pfam09862 DUF2089 Protein of u 90.5 0.86 2.2E-05 24.8 5.7 47 232-280 31-77 (113)
188 pfam04552 Sigma54_DBD Sigma-54 90.3 0.5 1.3E-05 26.4 4.4 25 152-176 45-69 (160)
189 PRK09863 putative frv operon r 90.3 0.35 8.8E-06 27.5 3.5 35 234-270 1-35 (585)
190 cd00092 HTH_CRP helix_turn_hel 90.3 0.43 1.1E-05 26.8 4.0 29 250-282 23-51 (67)
191 pfam12116 SpoIIID Stage III sp 89.8 0.64 1.6E-05 25.7 4.6 48 239-286 6-53 (82)
192 pfam00325 Crp Bacterial regula 89.8 0.44 1.1E-05 26.8 3.7 27 252-282 2-28 (32)
193 pfam08279 HTH_11 HTH domain. T 89.8 0.84 2.2E-05 24.9 5.2 40 240-283 3-42 (55)
194 COG2512 Predicted membrane-ass 89.7 0.63 1.6E-05 25.7 4.4 44 233-280 191-234 (258)
195 cd00569 HTH_Hin_like Helix-tur 89.5 0.77 2E-05 25.1 4.8 36 234-271 5-40 (42)
196 PRK11557 putative DNA-binding 89.5 1.6 4.2E-05 22.9 7.4 11 25-35 10-20 (282)
197 TIGR01321 TrpR trp operon repr 89.5 1.1 2.7E-05 24.2 5.5 52 235-287 34-94 (95)
198 PRK11161 fumarate/nitrate redu 89.4 0.55 1.4E-05 26.1 4.0 28 252-283 184-211 (235)
199 PRK11302 DNA-binding transcrip 89.2 1.7 4.4E-05 22.8 7.3 10 26-35 11-20 (284)
200 PRK11179 DNA-binding transcrip 89.2 1.2 3.2E-05 23.7 5.7 35 145-180 13-47 (153)
201 COG2973 TrpR Trp operon repres 89.0 1.8 4.5E-05 22.7 6.5 53 235-288 38-99 (103)
202 PRK11753 cAMP-regulatory prote 88.9 0.64 1.6E-05 25.7 4.0 27 252-282 168-194 (211)
203 COG1522 Lrp Transcriptional re 88.8 1.3 3.3E-05 23.7 5.5 28 152-180 19-46 (154)
204 PRK00215 LexA repressor; Valid 88.6 0.82 2.1E-05 24.9 4.4 27 149-175 16-43 (204)
205 PRK09391 fixK transcriptional 88.5 0.71 1.8E-05 25.4 4.0 29 251-283 172-200 (224)
206 PRK11534 DNA-binding transcrip 88.3 0.78 2E-05 25.1 4.1 18 75-99 51-68 (224)
207 pfam00392 GntR Bacterial regul 88.2 0.82 2.1E-05 25.0 4.2 39 240-282 11-50 (64)
208 TIGR03338 phnR_burk phosphonat 88.1 0.82 2.1E-05 25.0 4.1 28 35-64 38-67 (212)
209 PRK09392 ftrB transcriptional 88.0 0.79 2E-05 25.1 4.0 28 252-283 173-200 (236)
210 COG1654 BirA Biotin operon rep 87.9 2 5.1E-05 22.3 6.0 31 248-282 15-45 (79)
211 cd07377 WHTH_GntR Winged helix 87.9 0.96 2.4E-05 24.5 4.4 39 240-282 12-51 (66)
212 pfam06530 Phage_antitermQ Phag 87.6 2.2 5.5E-05 22.1 7.6 51 232-284 60-110 (126)
213 COG1802 GntR Transcriptional r 87.1 0.8 2E-05 25.0 3.6 33 63-102 44-80 (230)
214 TIGR02607 antidote_HigA addict 86.8 0.64 1.6E-05 25.7 3.0 28 247-274 15-42 (81)
215 smart00345 HTH_GNTR helix_turn 86.5 1.3 3.3E-05 23.7 4.4 39 240-282 7-46 (60)
216 PRK11169 leucine-responsive tr 86.3 2 5.2E-05 22.3 5.3 39 141-180 14-52 (164)
217 COG1476 Predicted transcriptio 86.0 1.1 2.7E-05 24.2 3.8 24 252-275 14-37 (68)
218 COG2522 Predicted transcriptio 86.0 1.5 3.9E-05 23.2 4.5 19 159-177 25-43 (119)
219 PRK11337 DNA-binding transcrip 85.8 2.7 6.9E-05 21.5 5.8 33 1-35 1-33 (293)
220 pfam09339 HTH_IclR IclR helix- 85.6 2.1 5.3E-05 22.2 5.1 33 241-273 7-39 (52)
221 PRK10225 DNA-binding transcrip 85.4 1.7 4.4E-05 22.8 4.6 13 48-62 52-64 (257)
222 PRK13413 mpi multiple promoter 85.2 2.3 5.8E-05 22.0 5.2 25 251-275 171-195 (200)
223 PRK11414 putative DNA-binding 85.2 1.2 3.1E-05 23.8 3.8 44 44-100 26-73 (221)
224 pfam01381 HTH_3 Helix-turn-hel 84.9 0.91 2.3E-05 24.6 3.0 25 251-275 8-32 (55)
225 PRK09943 DNA-binding transcrip 84.7 1.5 3.8E-05 23.2 4.0 13 20-32 12-24 (185)
226 pfam01047 MarR MarR family. Th 84.7 3 7.6E-05 21.2 5.5 37 235-272 1-37 (59)
227 PRK04158 transcriptional repre 84.3 3.1 8E-05 21.0 6.2 59 219-281 164-226 (256)
228 smart00347 HTH_MARR helix_turn 84.2 2.8 7.2E-05 21.4 5.2 19 158-176 26-44 (101)
229 PRK09706 transcriptional repre 84.0 1.1 2.9E-05 24.0 3.1 19 155-173 46-64 (135)
230 COG2909 MalT ATP-dependent tra 83.6 2.7 6.9E-05 21.5 5.0 43 235-280 832-874 (894)
231 TIGR03070 couple_hipB transcri 83.4 1.1 2.7E-05 24.2 2.8 25 251-275 14-38 (58)
232 smart00530 HTH_XRE Helix-turn- 83.4 1.2 3E-05 23.9 3.0 25 251-275 9-33 (56)
233 TIGR02787 codY_Gpos GTP-sensin 82.9 1.8 4.5E-05 22.7 3.8 57 220-280 166-226 (255)
234 COG5606 Uncharacterized conser 82.8 3.5 9E-05 20.7 5.3 46 250-295 39-90 (91)
235 PRK10411 DNA-binding transcrip 82.7 1.9 4.9E-05 22.5 3.9 11 74-84 38-48 (240)
236 PRK10434 srlR DNA-bindng trans 82.7 1.9 4.9E-05 22.5 3.9 11 74-84 39-49 (256)
237 PRK09464 pdhR transcriptional 82.6 2 5.1E-05 22.3 4.0 29 35-65 38-68 (254)
238 PRK13918 CRP/FNR family transc 82.6 2 5.2E-05 22.3 4.0 27 252-282 145-171 (201)
239 COG1349 GlpR Transcriptional r 82.5 1.8 4.7E-05 22.6 3.7 10 158-167 102-111 (253)
240 PRK10421 DNA-binding transcrip 82.5 2.1 5.2E-05 22.3 4.0 26 35-62 30-57 (253)
241 pfam10668 Phage_terminase Phag 82.1 1.6 4.2E-05 22.9 3.4 23 251-273 21-43 (60)
242 PRK09802 DNA-binding transcrip 81.8 1.7 4.4E-05 22.8 3.4 11 74-84 51-61 (269)
243 TIGR03337 phnR transcriptional 81.8 2.9 7.4E-05 21.3 4.5 14 159-172 104-117 (231)
244 PRK04424 fatty acid biosynthes 81.8 3.1 8E-05 21.1 4.7 16 158-173 23-38 (185)
245 pfam02796 HTH_7 Helix-turn-hel 81.8 2.4 6.1E-05 21.9 4.1 37 234-272 5-41 (45)
246 KOG0197 consensus 81.6 0.78 2E-05 25.1 1.6 49 14-65 286-345 (468)
247 PRK11402 DNA-binding transcrip 81.6 3 7.7E-05 21.2 4.6 12 161-172 115-126 (243)
248 PRK10906 DNA-binding transcrip 81.4 1.9 4.8E-05 22.5 3.5 11 74-84 39-49 (252)
249 pfam01022 HTH_5 Bacterial regu 81.1 3.6 9.2E-05 20.6 4.8 37 240-282 5-41 (47)
250 COG3093 VapI Plasmid maintenan 81.0 2.7 7E-05 21.4 4.2 19 158-176 25-43 (104)
251 PRK13509 transcriptional repre 80.8 2.6 6.6E-05 21.6 4.0 11 74-84 39-49 (251)
252 PRK13890 conjugal transfer pro 80.8 1.3 3.3E-05 23.7 2.4 24 152-175 43-66 (119)
253 pfam01418 HTH_6 Helix-turn-hel 80.4 4.4 0.00011 20.1 7.2 63 226-288 5-74 (106)
254 PRK04984 fatty acid metabolism 80.4 3.1 7.9E-05 21.1 4.3 56 35-96 35-92 (239)
255 pfam08006 DUF1700 Protein of u 80.3 4.4 0.00011 20.1 6.5 12 253-264 41-52 (181)
256 COG3415 Transposase and inacti 80.2 3.5 8.8E-05 20.8 4.5 24 158-181 23-46 (138)
257 cd00090 HTH_ARSR Arsenical Res 80.0 4.5 0.00011 20.0 5.0 40 237-282 7-46 (78)
258 PRK09764 DNA-binding transcrip 80.0 3.4 8.7E-05 20.8 4.4 14 159-172 108-121 (239)
259 COG2188 PhnF Transcriptional r 79.9 3.2 8.1E-05 21.0 4.2 19 158-176 109-128 (236)
260 TIGR02395 rpoN_sigma RNA polym 78.8 1.1 2.8E-05 24.1 1.6 57 233-289 332-409 (477)
261 PHA01976 helix-turn-helix prot 78.4 3.3 8.4E-05 20.9 3.9 24 251-274 14-37 (67)
262 PRK09726 DNA-binding transcrip 78.3 2.1 5.4E-05 22.2 2.9 35 251-285 24-62 (88)
263 pfam01710 Transposase_14 Trans 78.2 3.7 9.5E-05 20.6 4.1 30 253-286 72-101 (120)
264 pfam00356 LacI Bacterial regul 78.1 2 5.2E-05 22.3 2.8 20 254-273 1-20 (46)
265 smart00420 HTH_DEOR helix_turn 77.8 2.7 6.9E-05 21.5 3.3 22 251-272 13-34 (53)
266 PRK10079 putative transcriptio 76.8 5.2 0.00013 19.6 4.5 15 159-173 114-128 (241)
267 PRK03573 transcriptional regul 76.6 5.6 0.00014 19.4 7.2 23 158-180 48-70 (144)
268 smart00418 HTH_ARSR helix_turn 76.6 4.4 0.00011 20.0 4.2 30 249-282 7-36 (66)
269 TIGR01826 CofD_related conserv 76.5 1.6 4.1E-05 23.0 1.9 59 228-288 55-121 (331)
270 pfam08220 HTH_DeoR DeoR-like h 76.2 3.2 8E-05 21.0 3.3 21 251-271 13-33 (57)
271 pfam12298 Bot1p Eukaryotic mit 75.9 5.9 0.00015 19.2 5.8 19 27-45 15-33 (171)
272 smart00354 HTH_LACI helix_turn 75.7 2.8 7.1E-05 21.4 2.9 19 254-272 2-20 (70)
273 pfam02650 HTH_WhiA Sporulation 75.5 6 0.00015 19.2 7.7 38 232-270 141-180 (191)
274 TIGR01884 cas_HTH CRISPR locus 75.1 6.2 0.00016 19.1 5.3 52 227-282 159-210 (231)
275 TIGR01764 excise DNA binding d 74.8 2.7 6.9E-05 21.5 2.6 22 253-274 2-23 (49)
276 smart00346 HTH_ICLR helix_turn 74.7 6.3 0.00016 19.0 5.1 25 155-179 19-43 (91)
277 pfam04814 HNF-1_N Hepatocyte n 74.3 6.4 0.00016 19.0 6.1 57 219-276 96-152 (177)
278 pfam04645 DUF603 Protein of un 73.9 3.7 9.4E-05 20.6 3.2 20 159-178 22-41 (181)
279 cd00093 HTH_XRE Helix-turn-hel 73.9 2.8 7.2E-05 21.3 2.6 24 252-275 12-35 (58)
280 COG4465 CodY Pleiotropic trans 72.8 7 0.00018 18.7 7.0 60 219-282 167-230 (261)
281 TIGR00223 panD aspartate 1-dec 71.9 0.073 1.9E-06 32.0 -5.9 47 53-107 15-61 (127)
282 PRK00423 tfb transcription ini 71.2 7.6 0.00019 18.5 6.6 34 248-285 272-305 (310)
283 pfam01325 Fe_dep_repress Iron 70.6 7.8 0.0002 18.4 4.7 28 251-282 19-46 (58)
284 PRK03902 manganese transport t 70.5 7.8 0.0002 18.4 4.7 26 156-181 22-47 (142)
285 pfam08765 Mor Mor transcriptio 70.4 7.9 0.0002 18.4 5.7 36 237-276 60-95 (107)
286 COG2411 Uncharacterized conser 70.3 7.9 0.0002 18.4 7.1 50 230-282 133-184 (188)
287 PRK04140 hypothetical protein; 67.5 6.3 0.00016 19.1 3.2 21 158-178 140-160 (319)
288 cd04981 IgV_H Immunoglobulin ( 67.2 0.51 1.3E-05 26.3 -2.4 19 97-115 22-40 (117)
289 PRK11050 manganese transport r 66.9 6.3 0.00016 19.0 3.1 34 148-182 47-80 (155)
290 PRK10402 DNA-binding transcrip 66.7 9.3 0.00024 17.9 5.4 26 253-282 157-182 (213)
291 cd06571 Bac_DnaA_C C-terminal 66.2 9.6 0.00024 17.8 5.4 32 252-287 44-76 (90)
292 TIGR00738 rrf2_super rrf2 fami 66.1 9.2 0.00024 17.9 3.8 25 156-180 25-49 (133)
293 PRK09508 leuO leucine transcri 66.1 9.6 0.00025 17.8 5.8 35 91-125 103-142 (314)
294 TIGR01636 phage_rinA phage tra 66.0 9.6 0.00025 17.8 7.0 63 222-284 73-136 (138)
295 COG1321 TroR Mn-dependent tran 65.8 9.7 0.00025 17.8 4.4 28 154-181 22-49 (154)
296 COG3766 Predicted membrane pro 65.4 9.1 0.00023 18.0 3.7 63 26-93 29-91 (133)
297 pfam01978 TrmB Sugar-specific 64.9 10 0.00026 17.7 5.6 43 234-281 5-47 (68)
298 smart00550 Zalpha Z-DNA-bindin 63.9 11 0.00027 17.5 5.7 43 237-283 6-49 (68)
299 pfam04492 Phage_rep_O Bacterio 63.4 11 0.00027 17.5 6.7 49 228-280 22-78 (100)
300 pfam04218 CENP-B_N CENP-B N-te 62.9 11 0.00028 17.4 6.0 41 234-276 6-46 (53)
301 smart00529 HTH_DTXR Helix-turn 62.9 8.6 0.00022 18.1 3.2 23 159-181 2-24 (96)
302 TIGR02431 pcaR_pcaU beta-ketoa 62.4 11 0.00028 17.4 3.6 10 158-167 87-96 (252)
303 cd04762 HTH_MerR-trunc Helix-T 61.5 8.1 0.00021 18.3 2.8 22 254-275 2-23 (49)
304 pfam04963 Sigma54_CBD Sigma-54 61.1 12 0.0003 17.2 7.3 22 157-178 53-74 (195)
305 pfam08535 KorB KorB domain. Th 60.5 9.9 0.00025 17.7 3.1 22 159-180 6-27 (93)
306 PRK10046 dpiA two-component re 60.0 12 0.00031 17.1 4.4 22 250-271 175-196 (225)
307 PRK00876 nadE NAD synthetase; 59.5 13 0.00032 17.0 4.7 26 248-273 274-299 (325)
308 COG1318 Predicted transcriptio 58.2 12 0.0003 17.2 3.2 23 157-179 62-84 (182)
309 PRK10141 DNA-binding transcrip 57.9 13 0.00034 16.9 5.5 22 158-179 30-51 (106)
310 pfam02082 Rrf2 Transcriptional 57.6 13 0.00034 16.8 4.2 23 158-180 26-48 (82)
311 TIGR01074 rep ATP-dependent DN 57.4 14 0.00035 16.8 4.5 91 75-166 424-539 (677)
312 TIGR02463 MPGP_rel mannosyl-3- 57.2 6.1 0.00015 19.2 1.6 44 226-273 90-133 (224)
313 smart00342 HTH_ARAC helix_turn 56.8 14 0.00035 16.7 3.9 21 156-176 1-21 (84)
314 COG1959 Predicted transcriptio 56.1 14 0.00036 16.7 5.0 25 156-180 25-49 (150)
315 pfam11268 DUF3071 Protein of u 55.1 15 0.00038 16.6 4.2 40 234-278 55-94 (169)
316 pfam03444 DUF293 Domain of unk 55.1 15 0.00038 16.6 5.7 36 235-270 2-41 (79)
317 pfam07022 Phage_CI_repr Bacter 55.0 12 0.00032 17.0 2.9 23 253-275 13-35 (65)
318 pfam05043 Mga Mga helix-turn-h 54.2 15 0.00039 16.5 5.5 49 241-294 20-69 (87)
319 pfam00376 MerR MerR family reg 53.9 9.8 0.00025 17.7 2.2 22 254-275 1-22 (38)
320 PRK11511 DNA-binding transcrip 53.2 16 0.0004 16.4 4.3 35 141-175 10-44 (127)
321 PRK11014 transcriptional repre 53.0 16 0.00041 16.3 4.5 22 158-179 27-48 (141)
322 TIGR01610 phage_O_Nterm phage 52.9 16 0.00041 16.3 6.4 58 227-288 13-88 (104)
323 COG3283 TyrR Transcriptional r 52.6 16 0.00041 16.3 4.9 37 238-283 469-505 (511)
324 TIGR02899 spore_safA spore coa 52.4 8.6 0.00022 18.1 1.7 15 63-80 9-23 (44)
325 COG1405 SUA7 Transcription ini 51.8 17 0.00042 16.2 6.5 26 248-273 247-272 (285)
326 smart00803 TAF TATA box bindin 51.3 11 0.00028 17.4 2.1 25 267-291 34-58 (65)
327 PRK00082 hrcA heat-inducible t 51.2 17 0.00043 16.2 4.0 27 75-101 48-75 (339)
328 COG1481 Uncharacterized protei 50.9 17 0.00044 16.1 6.2 38 232-270 251-290 (308)
329 COG4742 Predicted transcriptio 50.3 18 0.00045 16.1 4.1 38 59-98 54-91 (260)
330 PRK10820 DNA-binding transcrip 50.3 18 0.00045 16.1 5.5 29 239-269 469-497 (513)
331 TIGR00370 TIGR00370 conserved 50.1 6.7 0.00017 18.8 0.9 51 226-276 78-129 (217)
332 PRK10430 DNA-binding transcrip 49.9 18 0.00045 16.0 4.3 22 250-271 176-197 (239)
333 COG3620 Predicted transcriptio 49.8 18 0.00045 16.0 3.9 22 91-122 41-62 (187)
334 COG2826 Tra8 Transposase and i 49.3 16 0.0004 16.4 2.6 12 99-111 105-116 (318)
335 pfam05732 RepL Firmicute plasm 49.2 18 0.00046 15.9 3.2 20 253-272 76-95 (165)
336 pfam00046 Homeobox Homeobox do 48.4 19 0.00048 15.9 3.3 35 235-269 7-44 (57)
337 pfam03811 Ins_element1 Inserti 48.4 19 0.00048 15.9 4.0 28 239-269 53-80 (88)
338 PRK13805 bifunctional acetalde 48.3 19 0.00048 15.9 6.4 58 46-107 699-771 (862)
339 PRK11512 DNA-binding transcrip 47.4 19 0.00049 15.8 7.5 23 158-180 56-78 (144)
340 pfam02969 TAF TATA box binding 47.2 14 0.00037 16.6 2.2 23 267-289 35-57 (66)
341 cd01392 HTH_LacI Helix-turn-he 46.9 13 0.00032 17.0 1.8 16 257-272 2-17 (52)
342 PRK13869 plasmid-partitioning 46.8 20 0.0005 15.7 3.6 12 75-86 155-166 (405)
343 KOG0915 consensus 46.7 19 0.00049 15.8 2.8 39 44-85 891-931 (1702)
344 pfam06971 Put_DNA-bind_N Putat 46.3 20 0.00051 15.7 3.2 19 253-271 28-46 (49)
345 PRK04184 DNA topoisomerase VI 45.8 14 0.00036 16.7 2.0 29 238-269 467-495 (533)
346 pfam08822 DUF1804 Protein of u 45.8 20 0.00052 15.6 5.1 19 86-108 22-40 (165)
347 pfam10078 DUF2316 Uncharacteri 45.5 21 0.00053 15.6 4.4 18 159-176 26-43 (89)
348 PRK09463 fadE acyl-CoA dehydro 45.4 21 0.00053 15.6 7.3 39 44-82 560-606 (761)
349 TIGR02844 spore_III_D sporulat 45.0 20 0.00051 15.7 2.6 25 247-271 14-38 (80)
350 COG4367 Uncharacterized protei 44.1 22 0.00055 15.4 6.7 24 155-178 22-45 (97)
351 PRK10371 DNA-binding transcrip 44.0 22 0.00056 15.4 4.8 26 251-276 206-231 (302)
352 PRK10870 transcriptional repre 43.4 22 0.00057 15.4 7.3 22 155-176 70-91 (176)
353 COG0122 AlkA 3-methyladenine D 43.3 15 0.00038 16.6 1.7 22 153-174 144-169 (285)
354 cd07285 PX_SNX9 The phosphoino 43.3 10 0.00026 17.6 1.0 16 94-109 7-25 (126)
355 COG4565 CitB Response regulato 43.1 23 0.00057 15.3 4.2 24 249-272 170-193 (224)
356 COG1497 Predicted transcriptio 42.8 23 0.00058 15.3 3.6 10 75-84 46-55 (260)
357 PRK08359 transcription factor; 42.1 23 0.0006 15.2 3.5 40 251-290 95-137 (175)
358 PRK10219 DNA-binding transcrip 42.0 23 0.0006 15.2 4.2 35 142-176 7-41 (107)
359 pfam09317 DUF1974 Domain of un 41.5 24 0.00061 15.2 7.4 67 13-82 60-135 (284)
360 COG3711 BglG Transcriptional a 40.9 24 0.00062 15.1 6.6 14 235-248 354-367 (491)
361 TIGR02702 SufR_cyano iron-sulf 40.5 25 0.00063 15.1 2.6 22 159-180 18-39 (215)
362 cd04790 HTH_Cfa-like_unk Helix 40.5 25 0.00063 15.1 6.6 28 72-101 12-39 (172)
363 COG1389 DNA topoisomerase VI, 40.3 19 0.00048 15.8 1.9 15 257-271 488-502 (538)
364 cd01107 HTH_BmrR Helix-Turn-He 40.3 22 0.00056 15.4 2.3 21 158-178 2-22 (108)
365 pfam11242 DUF2774 Protein of u 40.0 25 0.00064 15.0 2.8 28 246-273 7-34 (63)
366 pfam08280 HTH_Mga M protein tr 39.5 26 0.00065 15.0 4.7 45 238-287 6-50 (59)
367 cd04772 HTH_TioE_rpt1 First He 39.2 23 0.0006 15.2 2.3 20 159-178 3-22 (99)
368 COG4941 Predicted RNA polymera 38.8 26 0.00067 14.9 5.7 49 233-283 119-167 (415)
369 pfam00382 TFIIB Transcription 38.7 21 0.00053 15.6 1.9 19 249-267 51-69 (71)
370 COG2944 Predicted transcriptio 38.4 27 0.00068 14.9 5.6 44 228-275 37-80 (104)
371 KOG0723 consensus 37.8 27 0.00069 14.8 3.5 21 249-269 49-69 (112)
372 cd04781 HTH_MerR-like_sg6 Heli 37.6 26 0.00065 15.0 2.3 21 158-178 2-22 (120)
373 KOG3251 consensus 37.5 27 0.0007 14.8 3.4 24 255-278 166-189 (213)
374 cd04787 HTH_HMRTR_unk Helix-Tu 37.4 26 0.00067 14.9 2.3 21 158-178 2-22 (133)
375 cd00086 homeodomain Homeodomai 36.9 28 0.00071 14.7 3.3 36 235-270 7-45 (59)
376 cd07311 terB_like_1 tellurium 36.8 28 0.00071 14.7 5.5 30 234-275 104-133 (150)
377 COG1414 IclR Transcriptional r 36.7 28 0.00072 14.7 5.0 21 58-84 29-49 (246)
378 COG3888 Predicted transcriptio 36.7 28 0.00072 14.7 5.2 17 58-74 86-102 (321)
379 smart00422 HTH_MERR helix_turn 36.7 28 0.00071 14.7 2.3 21 158-178 2-22 (70)
380 COG0099 RpsM Ribosomal protein 36.1 12 0.00032 17.1 0.4 15 158-172 29-43 (121)
381 PRK13503 transcriptional activ 35.8 29 0.00074 14.6 4.8 18 155-172 186-203 (278)
382 COG1846 MarR Transcriptional r 35.1 30 0.00076 14.5 5.1 21 160-180 40-60 (126)
383 cd04782 HTH_BltR Helix-Turn-He 34.8 30 0.00076 14.5 2.2 21 158-178 2-22 (97)
384 smart00389 HOX Homeodomain. DN 34.5 30 0.00078 14.5 3.2 21 153-173 24-44 (56)
385 cd01108 HTH_CueR Helix-Turn-He 34.5 30 0.00078 14.5 2.3 21 158-178 2-22 (127)
386 KOG3716 consensus 34.5 30 0.00078 14.5 5.0 53 12-68 172-224 (764)
387 cd01110 HTH_SoxR Helix-Turn-He 34.3 31 0.00078 14.4 2.3 21 158-178 3-23 (139)
388 pfam06163 DUF977 Bacterial pro 34.3 31 0.00078 14.4 4.9 16 159-174 29-44 (127)
389 PRK11642 exoribonuclease R; Pr 34.1 31 0.00079 14.4 5.8 29 255-283 609-637 (813)
390 pfam01527 Transposase_8 Transp 34.1 31 0.00079 14.4 5.1 21 158-178 25-45 (75)
391 pfam06353 DUF1062 Protein of u 33.8 30 0.00077 14.5 2.1 21 256-276 107-127 (142)
392 cd04761 HTH_MerR-SF Helix-Turn 33.7 31 0.00078 14.4 2.1 20 159-178 3-22 (49)
393 cd04789 HTH_Cfa Helix-Turn-Hel 33.6 31 0.0008 14.4 2.2 21 158-178 3-23 (102)
394 pfam06970 RepA_N Replication i 32.9 32 0.00082 14.3 2.9 29 246-274 41-74 (76)
395 cd04768 HTH_BmrR-like Helix-Tu 32.7 32 0.00083 14.3 7.2 90 158-286 2-91 (96)
396 KOG0923 consensus 32.6 26 0.00066 14.9 1.6 24 32-56 47-70 (902)
397 PHA00542 putative Cro-like pro 32.4 33 0.00084 14.2 2.4 24 251-274 30-53 (82)
398 pfam00440 TetR_N Bacterial reg 32.1 33 0.00085 14.2 3.7 20 251-270 15-34 (47)
399 pfam06056 Terminase_5 Putative 32.1 33 0.00085 14.2 2.9 18 159-176 16-33 (58)
400 cd06898 PX_SNX10 The phosphoin 31.9 33 0.00085 14.2 2.2 11 136-146 43-53 (113)
401 TIGR00538 hemN oxygen-independ 31.9 26 0.00067 14.9 1.6 101 53-167 191-305 (462)
402 PRK06424 transcription factor; 31.6 34 0.00086 14.1 3.0 40 251-290 96-138 (144)
403 pfam02954 HTH_8 Bacterial regu 31.5 34 0.00087 14.1 3.4 17 254-270 20-36 (42)
404 PRK09775 hypothetical protein; 31.3 34 0.00087 14.1 3.3 16 12-27 162-177 (443)
405 cd04770 HTH_HMRTR Helix-Turn-H 31.2 34 0.00088 14.1 2.4 21 158-178 2-22 (123)
406 COG3877 Uncharacterized protei 31.2 34 0.00088 14.1 5.0 46 233-280 40-85 (122)
407 cd04773 HTH_TioE_rpt2 Second H 31.2 34 0.00088 14.1 2.2 21 158-178 2-22 (108)
408 KOG3973 consensus 31.1 32 0.00082 14.3 1.9 12 253-264 260-271 (465)
409 pfam00126 HTH_1 Bacterial regu 31.1 35 0.00088 14.1 4.2 34 253-290 14-47 (60)
410 PRK13752 putative transcriptio 31.0 33 0.00084 14.2 1.9 22 157-178 8-29 (144)
411 COG0853 PanD Aspartate 1-decar 30.4 2.3 5.7E-05 22.0 -4.1 46 54-107 15-60 (126)
412 pfam05066 RNA_pol_delta DNA-di 30.2 16 0.00042 16.3 0.3 51 159-209 37-87 (94)
413 PRK02234 recU Holliday junctio 29.9 32 0.00081 14.3 1.7 18 66-83 23-40 (199)
414 pfam11198 DUF2857 Protein of u 29.6 36 0.00093 13.9 5.1 19 158-176 89-107 (181)
415 cd07282 PX_SNX2 The phosphoino 29.1 31 0.00079 14.4 1.5 16 94-109 7-23 (124)
416 cd00592 HTH_MerR-like Helix-Tu 29.1 37 0.00095 13.9 2.2 21 158-178 2-22 (100)
417 TIGR03453 partition_RepA plasm 29.0 37 0.00095 13.9 2.8 11 75-85 138-148 (387)
418 TIGR02147 Fsuc_second hypothet 28.4 38 0.00097 13.8 2.1 117 151-288 137-258 (281)
419 KOG3099 consensus 28.0 39 0.00099 13.8 2.2 56 58-119 9-64 (340)
420 cd01520 RHOD_YbbB Member of th 28.0 39 0.00099 13.7 3.8 35 25-59 35-72 (128)
421 PRK13026 acyl-CoA dehydrogenas 27.9 39 0.001 13.7 6.7 35 44-78 560-600 (771)
422 pfam06322 Phage_NinH Phage Nin 27.9 39 0.001 13.7 2.3 19 254-272 18-36 (64)
423 pfam00183 HSP90 Hsp90 protein. 27.8 39 0.001 13.7 2.8 22 5-26 164-185 (529)
424 pfam06413 Neugrin Neugrin. Thi 27.7 39 0.001 13.7 4.7 29 73-107 11-47 (225)
425 TIGR02812 fadR_gamma fatty aci 27.7 39 0.001 13.7 1.9 14 83-96 127-140 (275)
426 pfam04760 IF2_N Translation in 27.6 17 0.00044 16.1 0.0 21 157-177 4-24 (52)
427 pfam11913 DUF3431 Protein of u 27.3 29 0.00074 14.6 1.1 40 259-298 158-198 (222)
428 PRK05472 redox-sensing transcr 27.1 40 0.001 13.6 3.6 11 70-80 63-73 (211)
429 cd04766 HTH_HspR Helix-Turn-He 26.9 41 0.001 13.6 2.2 21 158-178 3-23 (91)
430 COG3824 Predicted Zn-dependent 26.5 37 0.00095 13.9 1.6 22 255-276 114-135 (136)
431 COG1426 Predicted transcriptio 26.4 41 0.0011 13.6 1.8 65 15-87 3-77 (284)
432 cd06919 Asp_decarbox Aspartate 26.3 2.4 6.2E-05 21.8 -4.6 32 76-107 29-60 (111)
433 cd01980 Chlide_reductase_Y Chl 26.2 42 0.0011 13.5 5.0 32 255-286 244-275 (416)
434 cd04774 HTH_YfmP Helix-Turn-He 26.2 42 0.0011 13.5 6.7 92 158-288 2-96 (96)
435 PRK13626 transcriptional regul 26.1 42 0.0011 13.5 4.6 17 92-108 156-172 (551)
436 pfam11662 DUF3263 Protein of u 25.6 43 0.0011 13.5 5.7 44 234-277 2-47 (77)
437 pfam07037 DUF1323 Putative tra 25.6 43 0.0011 13.5 3.1 37 226-265 84-120 (122)
438 TIGR01326 OAH_OAS_sulfhy O-ace 25.5 43 0.0011 13.5 3.8 19 96-114 279-297 (434)
439 cd00383 trans_reg_C Effector d 25.4 43 0.0011 13.4 4.6 54 234-287 23-78 (95)
440 cd04783 HTH_MerR1 Helix-Turn-H 25.4 43 0.0011 13.4 2.2 21 158-178 2-22 (126)
441 KOG2165 consensus 25.2 43 0.0011 13.4 4.4 67 50-126 303-369 (765)
442 PRK09480 slmA nucleoid occlusi 25.2 43 0.0011 13.4 3.9 30 145-174 19-48 (194)
443 COG0789 SoxR Predicted transcr 25.2 44 0.0011 13.4 2.6 21 158-178 2-22 (124)
444 cd04397 RhoGAP_fLRG1 RhoGAP_fL 25.0 44 0.0011 13.4 4.0 182 72-296 2-212 (213)
445 pfam07900 DUF1670 Protein of u 25.0 44 0.0011 13.4 4.0 23 158-180 107-129 (220)
446 TIGR01368 CPSaseIIsmall carbam 24.8 25 0.00064 15.0 0.4 39 11-50 99-137 (383)
447 pfam07180 DUF1401 Protein of u 24.7 44 0.0011 13.4 2.8 14 66-79 32-45 (150)
448 COG1905 NuoE NADH:ubiquinone o 24.6 45 0.0011 13.4 4.1 61 101-178 5-65 (160)
449 PRK12435 ferrochelatase; Provi 24.5 45 0.0011 13.3 4.7 60 13-72 19-92 (316)
450 TIGR01968 minD_bact septum sit 24.5 45 0.0011 13.3 2.2 27 74-100 92-130 (272)
451 TIGR00014 arsC arsenate reduct 24.4 39 0.00098 13.8 1.3 42 147-188 29-71 (114)
452 PRK04570 cell division protein 24.3 45 0.0012 13.3 4.6 41 254-302 194-244 (244)
453 pfam04079 DUF387 Putative tran 24.2 45 0.0012 13.3 4.8 48 234-282 79-127 (159)
454 PRK09744 DNA-binding transcrip 24.1 46 0.0012 13.3 2.6 29 254-283 12-40 (75)
455 PRK08025 lipid A biosynthesis 24.0 46 0.0012 13.3 2.2 16 26-41 67-82 (305)
456 COG4753 Response regulator con 24.0 46 0.0012 13.3 6.4 45 251-295 387-439 (475)
457 cd01282 HTH_MerR-like_sg3 Heli 24.0 46 0.0012 13.3 2.4 20 159-178 3-22 (112)
458 cd04780 HTH_MerR-like_sg5 Heli 23.9 46 0.0012 13.3 2.3 21 158-178 2-22 (95)
459 PRK09514 zntR zinc-responsive 23.9 46 0.0012 13.3 7.5 21 158-178 3-23 (140)
460 cd04785 HTH_CadR-PbrR-like Hel 23.6 47 0.0012 13.2 2.3 21 158-178 2-22 (126)
461 cd04775 HTH_Cfa-like Helix-Tur 23.5 47 0.0012 13.2 2.2 21 158-178 3-23 (102)
462 COG1378 Predicted transcriptio 23.3 47 0.0012 13.2 3.4 110 14-129 3-141 (247)
463 cd01109 HTH_YyaN Helix-Turn-He 23.3 47 0.0012 13.2 2.4 21 158-178 2-22 (113)
464 PRK12681 cysB transcriptional 22.9 48 0.0012 13.1 4.1 16 159-174 207-222 (324)
465 TIGR01193 bacteriocin_ABC ABC- 22.8 41 0.001 13.6 1.2 68 2-70 323-400 (710)
466 cd07281 PX_SNX1 The phosphoino 22.5 49 0.0012 13.1 1.8 10 100-109 14-23 (124)
467 pfam09068 efhand_1 EF hand. Me 22.4 49 0.0013 13.1 3.6 20 83-105 2-21 (125)
468 cd04769 HTH_MerR2 Helix-Turn-H 22.4 49 0.0013 13.1 2.2 25 253-277 1-25 (116)
469 PRK10227 DNA-binding transcrip 22.3 49 0.0013 13.1 2.4 25 253-277 1-25 (135)
470 PRK12422 chromosomal replicati 22.2 50 0.0013 13.0 5.4 44 237-286 384-427 (455)
471 PHA01083 hypothetical protein 22.0 50 0.0013 13.0 2.7 19 256-274 18-36 (153)
472 PRK07248 hypothetical protein; 21.9 50 0.0013 13.0 3.3 55 20-74 34-88 (88)
473 cd06866 PX_SNX8_Mvp1p_like The 21.8 51 0.0013 13.0 1.7 24 15-38 78-101 (105)
474 pfam02261 Asp_decarbox Asparta 21.8 3.1 8E-05 21.0 -4.7 30 76-105 30-59 (116)
475 pfam08784 RPA_C Replication pr 21.3 52 0.0013 12.9 6.1 42 235-280 45-90 (103)
476 pfam00486 Trans_reg_C Transcri 21.3 52 0.0013 12.9 4.8 53 234-286 5-59 (77)
477 PRK11242 DNA-binding transcrip 21.2 52 0.0013 12.9 3.9 39 254-296 17-55 (292)
478 TIGR01958 nuoE_fam NADH-quinon 21.2 52 0.0013 12.9 3.0 60 108-182 1-63 (153)
479 COG4537 ComGC Competence prote 20.9 53 0.0013 12.9 2.8 46 26-84 34-83 (107)
480 pfam00988 CPSase_sm_chain Carb 20.6 53 0.0014 12.8 2.3 45 4-49 81-128 (131)
481 PRK02842 light-independent pro 20.5 54 0.0014 12.8 4.1 46 255-300 253-303 (425)
482 cd04786 HTH_MerR-like_sg7 Heli 20.5 54 0.0014 12.8 2.2 25 253-277 1-25 (131)
483 cd06862 PX_SNX9_18_like The ph 20.5 43 0.0011 13.4 0.9 38 15-52 80-117 (125)
484 pfam05930 Phage_AlpA Prophage 20.5 54 0.0014 12.8 3.0 23 253-275 4-26 (51)
485 COG4533 ABC-type uncharacteriz 20.2 54 0.0014 12.8 5.1 43 237-283 5-50 (564)
486 PRK08024 consensus 20.0 55 0.0014 12.7 1.9 67 221-287 56-123 (306)
No 1
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family.
Probab=100.00 E-value=0 Score=603.79 Aligned_cols=257 Identities=28% Similarity=0.522 Sum_probs=240.0
Q ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHHHHH----------------H----------------------------------
Q ss_conf 05999999840799999899999999999----------------8----------------------------------
Q gi|254780611|r 14 IGLSRYIHEIRKIPMLEKQEEYVLAKRYR----------------E---------------------------------- 43 (302)
Q Consensus 14 ~~~~~yl~~i~~~~~Lt~eee~~l~~~~~----------------~---------------------------------- 43 (302)
|+++.||++|||+||||+|||++|+++++ +
T Consensus 1 D~Vr~YL~eIGRvPLLt~eEEI~LArqVQry~~LLa~r~~~~~~~~~~~l~~~~~~l~~~~g~~ps~~ewA~~~~~~~~~ 80 (336)
T TIGR02997 1 DLVRLYLQEIGRVPLLTPEEEIELARQVQRYEALLAVRDKADEKVQMMALEELREELEEQLGREPSKEEWAAALGLSEAE 80 (336)
T ss_pred CCCHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHH
T ss_conf 92004445056678987688999989999999998875327889999999988999998508999878999871899889
Q ss_pred -----H--------------------CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf -----2--------------------859999999994307787565555799998889999998889989862185345
Q gi|254780611|r 44 -----H--------------------GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98 (302)
Q Consensus 44 -----~--------------------gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG 98 (302)
. -...|+++||.+||||||||||||.|||++|-||||||+|||.+|+|||||+||
T Consensus 81 l~~~l~G~~aWA~~a~l~leLk~~~r~G~RAK~kMi~ANLRLVVSvAKKYq~RglElLDLIQEG~lGL~RAVEKFDPtrG 160 (336)
T TIGR02997 81 LRQRLRGLQAWAEAAQLELELKLVLRQGQRAKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTRG 160 (336)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf 99998765788998422589999999789999999876022688999985136883356887634312211233577778
Q ss_pred CCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf 68999757789999998532024600110230035899999999788786624478882467788861898321100000
Q gi|254780611|r 99 FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178 (302)
Q Consensus 99 ~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~ 178 (302)
|||||||||||||+|+|+|.+++||||+|+|+++ +++|+|+....+....|+.|+.+|||++|++++++|++++.
T Consensus 161 YKFSTYAYWWIRQ~ITRAIA~qSRTIRLPiH~~E-----KLnkiKK~qReL~q~lGR~Ps~~EiAe~lel~~~qvR~~l~ 235 (336)
T TIGR02997 161 YKFSTYAYWWIRQGITRAIANQSRTIRLPIHITE-----KLNKIKKVQRELSQKLGRRPSEAEIAEALELEPEQVRELLQ 235 (336)
T ss_pred CCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCHHH-----HHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 8633012468756889998436883247410766-----66899899899999838897868999883889889999999
Q ss_pred CCCCCCCHHHHC-CCCCCCCCCHHCCCCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCC--CCCC
Q ss_conf 012234335520-2323453200000123-56870565566666667779999996219999999999982788--8889
Q gi|254780611|r 179 RLAGDESLNALI-NSSDKNSSQWQDWLVY-DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVT 254 (302)
Q Consensus 179 ~~~~~~SLd~~i-~~~d~~~~~~~d~l~~-~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~--~~~T 254 (302)
....++|||.++ +. ++++.++|.+++ +...|++.+. ...++..|..+|..|+|+|+.||.+|||.+ +++|
T Consensus 236 ~~~~p~SLd~~VrG~--e~dt~LgdLl~d~~~~~P~~~~~----~~~l~~dL~~lL~~L~p~e~~VL~LRfGL~~~~~~T 309 (336)
T TIGR02997 236 RARQPVSLDTRVRGD--EEDTELGDLLEDEDGESPEEQVE----QESLRQDLESLLAELTPRERQVLRLRFGLDDGEPLT 309 (336)
T ss_pred HHCCCCCCCCCCCCC--CCCCHHHHHCCCCCCCCCHHHHH----HHHHHHHHHHHHHHCCHHHHHHHHHHCCCCCCCCCC
T ss_conf 707874457732688--85422654326888998278999----999999999988637988999999857899897532
Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf 899999977899999999999999999
Q gi|254780611|r 255 LENLSSEFEVSRERVRQIEARAFKKVQ 281 (302)
Q Consensus 255 l~EIa~~lgiS~eRVrQI~~~AL~kLR 281 (302)
|.|||+.||||+|||||||.+||.|||
T Consensus 310 L~eiG~~l~lSRERVRQiE~~AL~kLR 336 (336)
T TIGR02997 310 LAEIGERLNLSRERVRQIEAKALRKLR 336 (336)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHCC
T ss_conf 789998838836888899999975349
No 2
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=100.00 E-value=0 Score=541.09 Aligned_cols=273 Identities=50% Similarity=0.800 Sum_probs=251.8
Q ss_pred CCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHH
Q ss_conf 58740599999984079999989999999999982859999999994307787565555799998889999998889989
Q gi|254780611|r 10 VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89 (302)
Q Consensus 10 ~~~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~A 89 (302)
-+.+++|+.||++|+++|+||+|||.+|+++|+++||.+|+++||++|||||++||++|.|+|++++|||||||||||+|
T Consensus 10 ~~~~~sl~~Yl~~i~~~plLt~eeE~~La~r~~~~gd~~A~~~Li~sNLRLVvsiAkky~~~gl~l~DLIQEGniGLikA 89 (284)
T PRK06596 10 PSPEGNLDAYIQAVNRIPMLTAEEEYMLAKRLREHGDLEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKA 89 (284)
T ss_pred CCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHH
T ss_conf 99997099999996578999999999999999977899999999998679999999846789999899999989999999
Q ss_pred HHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCC
Q ss_conf 86218534568999757789999998532024600110230035899999999788786624478882467788861898
Q gi|254780611|r 90 VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169 (302)
Q Consensus 90 i~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis 169 (302)
|+||||++|+||||||+|||||+|.+||.++||+||+|++..++++++++++++..+.. .+++++++||+.||++
T Consensus 90 vekFDp~kG~rFSTYA~wWIrq~I~r~i~~~~r~Vrip~~~~~rkl~~~lr~~~~~~~~-----~~~~~~~eiA~~l~~~ 164 (284)
T PRK06596 90 VKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKAQRKLFFNLRKAKKRLGW-----LNPEEVEMIAEELGVS 164 (284)
T ss_pred HHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHC-----CCCCCHHHHHHHHCCC
T ss_conf 97058998998186799999999999998745613788899999999999999998714-----5986299999997919
Q ss_pred CCCCCCCCCCCC-CCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHC
Q ss_conf 321100000012-2343355202323453200000123568705655666666677799999962199999999999827
Q gi|254780611|r 170 ESEVISMNCRLA-GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248 (302)
Q Consensus 170 ~~~v~~l~~~~~-~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~ 248 (302)
+++|..+..++. .+.|||.+++.+++...++.|++.+..+.+++.+.+..+....+..|..+++.|++||+.||.+||+
T Consensus 165 ~~~v~~~~~~l~~~~~SLd~~~~~~~~~~~~~~d~l~d~~~~~~~~~~~~~~~~~~~~~L~~al~~L~~REr~Il~~Ry~ 244 (284)
T PRK06596 165 EEEVREMESRLSGQDASLDAPIDDDDGESGAPQDYLEDKSSDPAAVLEEDNWEDQRRELLADALETLDERSRDIIEARWL 244 (284)
T ss_pred HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCC
T ss_conf 99999999985379820237888887775424665146789867899999999999999999986099999999999767
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 888889899999977899999999999999999999974
Q gi|254780611|r 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287 (302)
Q Consensus 249 ~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~ 287 (302)
.++++||+|||+.||||+||||||+++||.|||+.|+.-
T Consensus 245 ~d~~~TL~EIg~~lgiSrERVRQIe~kAL~KLR~~L~~~ 283 (284)
T PRK06596 245 DDDKSTLQELAAEYGVSAERIRQIEKNAMKKLKAAIEAA 283 (284)
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 999948999999979799999999999999999998802
No 3
>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=543.43 Aligned_cols=272 Identities=49% Similarity=0.803 Sum_probs=260.0
Q ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf 05999999840799999899999999999828599999999943077875655557999988899999988899898621
Q gi|254780611|r 14 IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93 (302)
Q Consensus 14 ~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kF 93 (302)
.+|+.||+.|+++|+||+|||..|+++|+++||..|..+||.||||||++||+.|.|||+|..|||||||||||+||.||
T Consensus 1 g~L~~Yi~~vn~~P~L~~EEE~~LA~r~r~~~Dl~AA~~Lv~SHLRfVv~iArgY~GYGL~~aDLIQEGNIGLMkAVkRF 80 (279)
T TIGR02392 1 GSLDAYIRAVNRIPMLTAEEEQELAKRLREEGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRF 80 (279)
T ss_pred CCHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHC
T ss_conf 97788999997178999889999999865423778999874662478755320367777442443422226655334421
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCC
Q ss_conf 85345689997577899999985320246001102300358999999997887866244788824677888618983211
Q gi|254780611|r 94 DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173 (302)
Q Consensus 94 Dp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v 173 (302)
||++|+|+.|||+||||.+|+.||..+||+|||.+|.+||+||||+|+.++.+..+.....++.++..||+.|||+.++|
T Consensus 81 dP~~GvRLvSfAvHWIkAeIHEyILrnWRlVKvATTkaQrKLFFNLRk~K~ki~~l~~gw~~~~e~~~~A~~L~V~~~eV 160 (279)
T TIGR02392 81 DPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRKLFFNLRKMKKKITRLQDGWLNPEEVEAIAEELGVSEEEV 160 (279)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHH
T ss_conf 78987220478889999998668997555988852776788876588899986310157989899999997638988899
Q ss_pred CCCCCCCCC-CCCHHHHCCCCCCCCC---CHHCCCCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHC
Q ss_conf 000000122-3433552023234532---000001235-68705655666666677799999962199999999999827
Q gi|254780611|r 174 ISMNCRLAG-DESLNALINSSDKNSS---QWQDWLVYD-HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248 (302)
Q Consensus 174 ~~l~~~~~~-~~SLd~~i~~~d~~~~---~~~d~l~~~-~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~ 248 (302)
.+|+.++++ +.|||.++.++++++. ...++|.|. ...|+..+.+..........|..+|..||+|+|.||..|++
T Consensus 161 ~eMe~RlsG~D~~L~~~~~~~~~~~~~~~~~~~yL~D~~~~~~~~~l~~~~~~~~~~~~L~~AL~~Ld~RsR~I~~~RwL 240 (279)
T TIGR02392 161 LEMESRLSGRDISLNASIDDDEDDGGSDFAPIAYLADKATSDPEATLEEEQWEELQTQKLANALESLDARSRRIIEARWL 240 (279)
T ss_pred HHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 88751455377334788765534563114578863047777888999998999999999999988522887999987302
Q ss_pred CCC-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 888-8898999999778999999999999999999999
Q gi|254780611|r 249 QEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285 (302)
Q Consensus 249 ~~~-~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~ 285 (302)
.|+ |.||+++|..+|||+|||||||++|++|||..|.
T Consensus 241 ~d~~~~TL~~LA~eygvSaERiRQiE~~Am~K~k~~~~ 278 (279)
T TIGR02392 241 DDDGKLTLHELAAEYGVSAERIRQIEKNAMKKLKAALA 278 (279)
T ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHC
T ss_conf 78899647899988487466799999999999999841
No 4
>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=547.16 Aligned_cols=273 Identities=30% Similarity=0.473 Sum_probs=242.9
Q ss_pred CCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH
Q ss_conf 45587405999999840799999899999999999828599999999943077875655557999988899999988899
Q gi|254780611|r 8 IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87 (302)
Q Consensus 8 ~~~~~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi 87 (302)
......|.+-.||++|+.-||||++||..++++.. .||.+||+++|++||||||+|||+|.|||+++-|||-|||||||
T Consensus 7 ~~~~~~D~~Q~YL~eIg~~PLLt~~EE~~~Arra~-~GD~eAR~~MIE~NLRLVV~IAk~Y~nRGlpLlDLIEEGNLGLm 85 (292)
T TIGR02394 7 TETRVADVTQLYLREIGFKPLLTAEEELAYARRAL-AGDFEARKKMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLM 85 (292)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHH-CCCHHHHHHHHHHHCHHHHHHHHHCCCCCCHHHHHHHHHHHHHH
T ss_conf 22233026888788860155889889999988865-07888988877640126767864404765145777765335665
Q ss_pred HHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCC---CCHHHHHHHH
Q ss_conf 8986218534568999757789999998532024600110230035899999999788786624478---8824677888
Q gi|254780611|r 88 QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL---KPEQVVAIAK 164 (302)
Q Consensus 88 ~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~---~~~~~~eiA~ 164 (302)
+|++||||+|||||||||+|||||+|-|+|++|+|+||+|+|+. |++ +.+=|..+++.......+ ++|+++|||.
T Consensus 86 ~AvEKFDPeRGFRFSTYATWWIRQtIERAIMNQaRTiRLPvHV~-kEL-Nv~LRa~r~L~~ns~~~~E~~~EpS~eeiA~ 163 (292)
T TIGR02394 86 HAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHVV-KEL-NVYLRAARQLEKNSAKLDEEEREPSVEEIAE 163 (292)
T ss_pred HHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEECCHHHH-HHH-HHHHHHHHHHHHHHHHCCCCCCCCCHHHHHH
T ss_conf 42104588999844301113665327865313544110531434-677-7999988876556763373357788789998
Q ss_pred HCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH
Q ss_conf 61898321100000012234335520232345320000012356870565566666667779999996219999999999
Q gi|254780611|r 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244 (302)
Q Consensus 165 ~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~ 244 (302)
.++-++++|..++......+|+|.|++.+ .+..++.|+++|+....|+... ...++...+..+|+.|++|+|.||.
T Consensus 164 ~~~kpvedv~~~L~Lne~~~S~D~Pl~~D-~n~~Sl~d~~ADe~~~~P~~~~---~~~~l~~~~~~~L~~Lne~~R~V~~ 239 (292)
T TIGR02394 164 LLDKPVEDVSKVLALNERIASLDAPLDED-SNSKSLLDTIADEQSIDPESLV---QNDDLKQLIEAWLAELNERQREVLA 239 (292)
T ss_pred HHCCCHHHHHHHHHHCCCCEEEECCCCCC-CCCHHHHHCCCCCCCCCHHHHH---HHHHHHHHHHHHHHHHCHHHHEEHH
T ss_conf 83898889999984179952530577877-4301210004788877807642---1899999999988610632112101
Q ss_pred HHHCC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 98278--88889899999977899999999999999999999974
Q gi|254780611|r 245 ARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287 (302)
Q Consensus 245 ~ry~~--~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~ 287 (302)
.|||. .|+.||.++|..+|+||||||||+..||.|||..|+++
T Consensus 240 rRFGL~g~E~~TLE~va~~~gLTRERvRQIQ~eaL~~Lr~~L~~~ 284 (292)
T TIGR02394 240 RRFGLRGYEKATLEEVAKELGLTRERVRQIQVEALKKLRRILERK 284 (292)
T ss_pred HHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 003766542666999998728810478998899999999999864
No 5
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=100.00 E-value=0 Score=529.99 Aligned_cols=265 Identities=30% Similarity=0.471 Sum_probs=235.2
Q ss_pred CCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 74059999998407999998999999999998285999999999430778756555579999888999999888998986
Q gi|254780611|r 12 GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91 (302)
Q Consensus 12 ~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~ 91 (302)
..|++..||++|+++||||+|||.+|+++++ .||.+|+++||++|||||++||++|.|+|++++|||||||||||+||+
T Consensus 54 ~~d~~~~YL~eI~~~pLLt~eEE~~La~~~~-~GD~~Ar~~LI~sNLRLVvsIAkkY~~~Gl~l~DLIQEGniGLikAve 132 (328)
T PRK05657 54 VLDATQLYLNEIGYSPLLTAEEEVYFARRAL-RGDFAARQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVE 132 (328)
T ss_pred CCCHHHHHHHHHCCCCCCCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 0556999999956789999999999999998-178999999999818999999985568998989999886899999999
Q ss_pred HCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCC
Q ss_conf 21853456899975778999999853202460011023003589999999978878662447888246778886189832
Q gi|254780611|r 92 KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171 (302)
Q Consensus 92 kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~ 171 (302)
||||++|+||||||+|||||+|.+||.+++|+||+|+++.. .++++.++...+....++.|++++||+.+|++++
T Consensus 133 KFDp~rG~RFSTYA~WWIRq~I~raI~~~~r~IRlP~~~~~-----~l~~i~ra~~~l~~~~gr~pt~eEIA~~lg~~~~ 207 (328)
T PRK05657 133 KFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVK-----ELNVYLRAARELEHKLDHEPSAEEIAELLDKPVD 207 (328)
T ss_pred HCCCCCCCCEEEEEHHHHHHHHHHHHHHCCCCCCCCCHHHH-----HHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHH
T ss_conf 71976699842300999999999999965777775611999-----9999999999999984899989999999695999
Q ss_pred CCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCC--
Q ss_conf 110000001223433552023234532000001235687056556666666777999999621999999999998278--
Q gi|254780611|r 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ-- 249 (302)
Q Consensus 172 ~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~-- 249 (302)
+|..+......+.|||+|++. +++.++.|.+.++...+++... +...++..+..++..|++||+.||.+|||.
T Consensus 208 ~v~~~l~~~~~~~SLD~pv~~--d~~~tl~d~l~D~~~~~pd~~~---~~~~l~~~l~~~L~~L~~REr~II~~RfGL~~ 282 (328)
T PRK05657 208 DVSRMLALNERITSLDAPLGG--DPEKSLLDILADDQENGPEDTT---QDDDLKQSIVKWLFELNDKQREVIERRFGLNG 282 (328)
T ss_pred HHHHHHHHCCCCCCCCCCCCC--CCCCHHHHHHCCCCCCCHHHHH---HHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCC
T ss_conf 999999745876344453589--9851178886277899999999---99999999999980699999999999808899
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 88889899999977899999999999999999999974
Q gi|254780611|r 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287 (302)
Q Consensus 250 ~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~ 287 (302)
++++||+|||+.||||+||||||+++||.|||+.|+++
T Consensus 283 ~e~~TL~EIg~~lgvSRERVRQIE~~AL~KLR~~l~~~ 320 (328)
T PRK05657 283 YEAATLEEVAREIGLTRERVRQIQVEALRRLREILQTQ 320 (328)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 89605999998969799999999999999987999986
No 6
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=100.00 E-value=0 Score=526.68 Aligned_cols=278 Identities=41% Similarity=0.677 Sum_probs=257.6
Q ss_pred CCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 74059999998407999998999999999998285999999999430778756555579999888999999888998986
Q gi|254780611|r 12 GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91 (302)
Q Consensus 12 ~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~ 91 (302)
..++-..||++|+++||||+|||.+|+.+|++.||.+||++||++|||||++||++|.|+|++++|||||||||||+||+
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 HCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCC
Q ss_conf 21853456899975778999999853202460011023003589999999978878662447888246778886189832
Q gi|254780611|r 92 KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171 (302)
Q Consensus 92 kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~ 171 (302)
||||++|++|||||+|||||+|.+||++++++||+|++..++.+++++++++..+.......++.|..++||+.+|++++
T Consensus 84 kFDp~rG~rFSTYA~wWIr~aI~r~i~~~~~~iR~p~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~eiA~~l~~~~~ 163 (289)
T PRK07500 84 RFDPDRDVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRARLAQSDEQLTKHEIHREIATALGVSLS 163 (289)
T ss_pred CCCCCCCCCEEEHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCHH
T ss_conf 36988899721101999999998877736651000038878999999999999999861545655439999988099999
Q ss_pred CCCCCCCCCC-CCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCC
Q ss_conf 1100000012-234335520232345320000012356870565566666667779999996219999999999982788
Q gi|254780611|r 172 EVISMNCRLA-GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250 (302)
Q Consensus 172 ~v~~l~~~~~-~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~ 250 (302)
++..+...+. .+.|||.++..+++......|.+.++.+.|++.+.+..+...++..|..++..|++||+.||.+||+.+
T Consensus 164 ~v~~~~~~~~~~~~SL~~~~~~d~~~~~~~~d~l~d~~~~p~~~~e~~~~~~~~~~~L~~~l~~L~eREr~Ii~~r~~~~ 243 (289)
T PRK07500 164 DVEMMDARLSGPDSSLNAPQSEEDEGRSERMDFLVDDSPLPDEIVESSIDGERRRQWLTQALQTLNERELFIIRERRLRE 243 (289)
T ss_pred HHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCC
T ss_conf 99999999737986666806787777401555404688983899999999999999999998549999999999976689
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 888989999997789999999999999999999997401
Q gi|254780611|r 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289 (302)
Q Consensus 251 ~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~~~ 289 (302)
+++||+|||+.||||+||||||+++||.|||+.|.++..
T Consensus 244 e~~TL~EIg~~lgvSreRVRQIe~kAL~KLR~~L~~~~~ 282 (289)
T PRK07500 244 DGATLEALGEELGISKERVRQIEARALEKLRRALLSQSP 282 (289)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCH
T ss_conf 985899999997979999999999999999999998477
No 7
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=0 Score=528.39 Aligned_cols=266 Identities=29% Similarity=0.457 Sum_probs=234.7
Q ss_pred CCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 87405999999840799999899999999999828599999999943077875655557999988899999988899898
Q gi|254780611|r 11 NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90 (302)
Q Consensus 11 ~~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai 90 (302)
.-++++..||++|+++||||+|||.+|+++++ .||.+|+++||++|||||++||++|.|+|+++.|||||||||||+||
T Consensus 94 ~~~d~v~~YL~eI~~~pLLt~eEE~~La~r~~-~GD~~Ar~~Li~aNLRLVVsIAkkY~~~Gl~l~DLIQEGNiGLmkAV 172 (368)
T PRK09210 94 KINDPVRMYLKEIGRVPLLTAEEEIELAKRIE-EGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAV 172 (368)
T ss_pred CCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf 55858999999956788999999999999988-15799999999983899999998666899898999998679999999
Q ss_pred HHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCC
Q ss_conf 62185345689997577899999985320246001102300358999999997887866244788824677888618983
Q gi|254780611|r 91 KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170 (302)
Q Consensus 91 ~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~ 170 (302)
+||||++|+||||||+|||||+|.+||.+++|+||+|+|+.+ .++++.+....+....++.|+.++||+.+|+++
T Consensus 173 eKFDp~rG~RFSTYA~WWIRqaI~raI~~q~r~IRiPvh~~e-----~~~kl~r~~r~L~q~lGrePt~eEIA~~lgi~~ 247 (368)
T PRK09210 173 EKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE-----TINKLIRVQRQLLQELGRDPTPEEIAEEMDMPP 247 (368)
T ss_pred HHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHH-----HHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCH
T ss_conf 972987799533466999999999999982785135424999-----999999999999998389998899998949989
Q ss_pred CCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCC
Q ss_conf 21100000012234335520232345320000012356870565566666667779999996219999999999982788
Q gi|254780611|r 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250 (302)
Q Consensus 171 ~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~ 250 (302)
++|..+......+.|||.|++.+ ++..+.|+++++....++. ..+...++..|..+|+.|++||+.||.+|||.+
T Consensus 248 e~V~~i~~~~~~~~SLd~pvg~e--~~s~l~d~i~D~~~~~p~e---~~~~~~l~~~l~~~L~~L~~REr~Il~~RfGL~ 322 (368)
T PRK09210 248 EKVREILKIAQEPVSLETPIGEE--DDSHLGDFIEDQDATSPAD---HAAYELLKEQLEEVLDTLTDREENVLRLRFGLD 322 (368)
T ss_pred HHHHHHHHHCCCCCCCCCCCCCC--CCCHHHHHHCCCCCCCHHH---HHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCC
T ss_conf 99999998538885668867887--7552875524899999899---999999999999998179999999999975999
Q ss_pred --CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf --8889899999977899999999999999999999974
Q gi|254780611|r 251 --NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287 (302)
Q Consensus 251 --~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~ 287 (302)
+++||.|||+.||||+||||||+.+||+|||+.-+.+
T Consensus 323 ~~~~~TLeEIg~~lgvSRERVRQIE~kAL~KLR~~~~~~ 361 (368)
T PRK09210 323 DGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 361 (368)
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHH
T ss_conf 689614999998969798999999999999976736878
No 8
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=100.00 E-value=0 Score=520.72 Aligned_cols=272 Identities=24% Similarity=0.402 Sum_probs=238.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHC---------------------------CHHHHHHHHHH
Q ss_conf 655745587405999999840799999899999999999828---------------------------59999999994
Q gi|254780611|r 4 KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG---------------------------DLSAAHRLVTS 56 (302)
Q Consensus 4 ~~~~~~~~~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~g---------------------------d~~Ar~~Li~~ 56 (302)
+++....-.+|++..||++|+++||||+|||++|+++++. | +.+|+++||++
T Consensus 12 ~~~~~~~p~~D~~~~Yl~ei~~~~lLt~eeE~~La~~i~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~A~~~lI~a 90 (320)
T PRK07921 12 SDLDAQSPAADLVRVYLNGIGKTALLTAADEVELAKRIEA-GLYAEHLLETRKRLGEARKRDLAAVVRDGEAARRHLLEA 90 (320)
T ss_pred HCCCCCCCCCCCHHHHHHHCCCCCCCCHHHHHHHHHHHHH-HHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 4489999898819999997188789899999999999997-377898875111001677889998776069999999998
Q ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHH
Q ss_conf 30778756555579999888999999888998986218534568999757789999998532024600110230035899
Q gi|254780611|r 57 HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136 (302)
Q Consensus 57 nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~ 136 (302)
|||||++||++|.|+|++++|||||||||||+||+||||++|+||||||+||||++|.+||.+++|+||+|+|..+
T Consensus 91 NLRLVvsIAk~Y~~~Gl~~~DLIQEGniGLirAvekFDp~rG~rFSTYA~wWIRq~I~r~i~~~~r~IRlP~~~~~---- 166 (320)
T PRK07921 91 NLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVE---- 166 (320)
T ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHH----
T ss_conf 1899999998565899998999998389999888516899998128777999999999999970862147188999----
Q ss_pred HHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHH
Q ss_conf 99999978878662447888246778886189832110000001223433552023234532000001235687056556
Q gi|254780611|r 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216 (302)
Q Consensus 137 ~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~ 216 (302)
.++++.+....+....++.|+.++||+.+|+++++|..+......++|||.+++. +++.++.|++.+....+++..
T Consensus 167 -~~~ki~~~~~~l~~~lGR~Pt~eEIA~~lgi~~~~v~~~l~~~~~~~SLD~~vg~--d~~~~l~d~i~D~~~~~~e~~- 242 (320)
T PRK07921 167 -QVNKLARIKREMHQHLGREATDEELAEESGIPEEKINDLLEHSRDPVSLDMPVGS--DEEAPLGDFIEDAEAMSAENA- 242 (320)
T ss_pred -HHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCC--CCCCCHHHHHHCCCCCCHHHH-
T ss_conf -9999999999999983899989999988199999999999972888366776688--875303324405678998999-
Q ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 6666667779999996219999999999982788--888989999997789999999999999999999997
Q gi|254780611|r 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286 (302)
Q Consensus 217 e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~--~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~ 286 (302)
.+...+...|..+++.|++||+.||.+|||.+ +++||+|||+.||||+||||||+.+||+|||+....
T Consensus 243 --~~~~~l~~~L~~~L~~L~eREr~IL~~RfGl~~~~~~TL~EIg~~lgvSrERVRQIE~~AL~KLR~~~~~ 312 (320)
T PRK07921 243 --VIAELLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRHGERA 312 (320)
T ss_pred --HHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHH
T ss_conf --9999999999999975999999999997489998974799999897969999999999999997072888
No 9
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=0 Score=513.91 Aligned_cols=265 Identities=25% Similarity=0.457 Sum_probs=233.9
Q ss_pred CCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH---------------------------------------HCCHHH
Q ss_conf 55874059999998407999998999999999998---------------------------------------285999
Q gi|254780611|r 9 IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------------------------HGDLSA 49 (302)
Q Consensus 9 ~~~~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~---------------------------------------~gd~~A 49 (302)
.-..+|++..||++|+++||||++||++|++++++ .++..|
T Consensus 4 ~~~~~d~~~~Yl~ei~~~~LLt~eeE~~la~~i~~~~~~~~~~~~l~~~~~~~~~~~~~a~a~~~~~~~l~~~~~~g~~A 83 (318)
T PRK07405 4 AKTATDLVRTYLREIGRVPLLTHEEEILYGKQVQRLMALQEIRESLAEELGREPSDLEWAKAAKLSEEELRRAIAEGEAA 83 (318)
T ss_pred CCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHHH
T ss_conf 87898759999998177679999999999999999988899999999871678746788876045689999987627999
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCC
Q ss_conf 99999943077875655557999988899999988899898621853456899975778999999853202460011023
Q gi|254780611|r 50 AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129 (302)
Q Consensus 50 r~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~ 129 (302)
+++||++|||||++||++|.|+|++++|||||||||||+||+||||++|+||||||+||||++|.+||.+++++||+|+|
T Consensus 84 ~~~lv~~NLRLVv~iAk~y~~~gl~~~DLIQEGniGLi~AvekFDp~rG~rFSTYA~wWIrq~I~r~i~~~~r~IRlP~~ 163 (318)
T PRK07405 84 KRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIH 163 (318)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEHHHHHHHHHHHHHHHCCCCCCCCHH
T ss_conf 99999981999999998665799798899998689999999970976598022200999999999999976985168778
Q ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCC
Q ss_conf 00358999999997887866244788824677888618983211000000122343355202323453200000123568
Q gi|254780611|r 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209 (302)
Q Consensus 130 ~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~ 209 (302)
..+ .++++.+....+....+++|++++||+.+|+++++|..+......+.|||.+++++ ++.++.|++.++.+
T Consensus 164 ~~~-----~~~ki~~~~~~L~~~lGr~Pt~~EIAe~lgi~~e~V~~~l~~~~~~~SLD~~v~d~--~~~~l~dll~D~~~ 236 (318)
T PRK07405 164 ITE-----KLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDN--QDTELGELLEDDGA 236 (318)
T ss_pred HHH-----HHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCC--CCCHHHHHHCCCCC
T ss_conf 999-----99999999999998718986489999885999999999999807886768888999--86405667547889
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 7056556666666777999999621999999999998278--88889899999977899999999999999999999
Q gi|254780611|r 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284 (302)
Q Consensus 210 ~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~--~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l 284 (302)
.|++... ...++..|..+++.|++||+.||.+|||. ++++||+|||+.||||+||||||+++||.|||+..
T Consensus 237 ~pe~~~~----~~~l~~~L~~~L~~L~eREr~II~lRfGl~~~~~~TL~EIg~~lgvSrERVRQIE~~AL~KLR~~~ 309 (318)
T PRK07405 237 SPEDFAT----QSSLRRDLERLMADLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKRK 309 (318)
T ss_pred CHHHHHH----HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 8799999----999999999999629998999999980778989747999998979599999999999999998728
No 10
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=100.00 E-value=0 Score=508.18 Aligned_cols=267 Identities=25% Similarity=0.424 Sum_probs=232.9
Q ss_pred CCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHC------------------CHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 587405999999840799999899999999999828------------------59999999994307787565555799
Q gi|254780611|r 10 VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG------------------DLSAAHRLVTSHLRLVVKIAMGYRGY 71 (302)
Q Consensus 10 ~~~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~g------------------d~~Ar~~Li~~nlrlV~~iA~~y~~~ 71 (302)
...+|.+..||++|+++||||++||.+|++++.. | +++||++||++|||||++||++|.|+
T Consensus 104 ~~tdd~v~~yl~~~g~~~ll~~~~e~~~a~~~~~-~~~~~~~~~~~~~~~~~~~~~~Ar~~Li~aNLRLVvsIAkkY~~~ 182 (398)
T PRK05901 104 TATADPVKAYLKQIGKVKLLNAEEEVELAKRIEA-GLYAEELLEKRDLRWIARDGKRAKNHLLEANLRLVVSLAKRYTNR 182 (398)
T ss_pred CCCCCCHHHHHHHCCCCCCCCHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 8889719999986275548887999999999984-045676676777777530539999999997069999999764689
Q ss_pred CCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 99888999999888998986218534568999757789999998532024600110230035899999999788786624
Q gi|254780611|r 72 GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151 (302)
Q Consensus 72 g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~ 151 (302)
|+++.|||||||||||+||+||||++|+||||||+|||||+|.++|.+++|+||+|+|+.. . ++++.+....+..
T Consensus 183 Gl~l~DLIQEGniGLirAvekFDp~rG~rFSTYA~wWIRqaI~rai~~~~r~IRiP~h~~e--~---~~k~~r~~~~l~~ 257 (398)
T PRK05901 183 GLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--T---INKLGRIERELLQ 257 (398)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHCCCEEECCHHHHH--H---HHHHHHHHHHHHH
T ss_conf 9898899998689999999971977799542114999999999999966873523323999--9---9999999999999
Q ss_pred CCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 47888246778886189832110000001223433552023234532000001235687056556666666777999999
Q gi|254780611|r 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231 (302)
Q Consensus 152 ~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~ 231 (302)
..++.|+.++||+.+|+++++|..+......++|||.+++. ++..++.|++.+.....|+. ..+...++..|..+
T Consensus 258 ~~gr~Pt~eEiA~~lg~~~~~v~~~~~~~~~~~SLd~~vg~--d~~~~l~d~i~D~~~~~p~~---~~~~~~l~~~l~~~ 332 (398)
T PRK05901 258 ELGREPTPEELAEEMDFTPEKVREIQKYAREPISLDKTIGD--EGDSQFGDFIEDSEAVSPVD---AVSFTLLQDQLQEV 332 (398)
T ss_pred HHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCC--CCCCCHHHHCCCCCCCCHHH---HHHHHHHHHHHHHH
T ss_conf 84899999999988199999999999972898556787789--98651866416999999999---99999999999999
Q ss_pred HHCCCHHHHHHHHHHHCC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 621999999999998278--88889899999977899999999999999999999974
Q gi|254780611|r 232 MSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287 (302)
Q Consensus 232 l~~L~~rEr~II~~ry~~--~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~ 287 (302)
|..|++||+.||.+|||. ++++||.|||+.||||+||||||+.+||.|||.....+
T Consensus 333 L~~L~~REr~Ii~~RyGL~~~~~~TL~eIg~~lgvSrERVRQIE~kAL~KLR~~~~~~ 390 (398)
T PRK05901 333 LETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTMRKLRHPSRSQ 390 (398)
T ss_pred HCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHH
T ss_conf 8389999999999975899989603999998979699999999999999967837887
No 11
>PRK05949 RNA polymerase sigma factor; Validated
Probab=100.00 E-value=0 Score=508.25 Aligned_cols=264 Identities=24% Similarity=0.451 Sum_probs=231.3
Q ss_pred CCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH---------------------------------------HCCHHH
Q ss_conf 55874059999998407999998999999999998---------------------------------------285999
Q gi|254780611|r 9 IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------------------------HGDLSA 49 (302)
Q Consensus 9 ~~~~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~---------------------------------------~gd~~A 49 (302)
+...+|++..||++|+++||||+|||++|+++++. ..+.+|
T Consensus 13 ~~~~~D~~~~YL~ei~~~pLLt~eeE~~La~~iq~~~~~~~~~~~l~~~~~~~~~~~ewa~~~~~~~~~l~~~~~~g~~A 92 (327)
T PRK05949 13 PTFTADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWADAVNLSETELKQALKQGKRA 92 (327)
T ss_pred CCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf 98998819999998278668899999999999999998899999999983789756889987266789999998758999
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCC
Q ss_conf 99999943077875655557999988899999988899898621853456899975778999999853202460011023
Q gi|254780611|r 50 AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129 (302)
Q Consensus 50 r~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~ 129 (302)
+++||++|||||++||++|.|+|++++|||||||||||+||+||||++|+||||||+||||++|.+||.+++++||+|+|
T Consensus 93 ~~~LI~sNLRLVvsIAkrY~~~Gl~~~DLIQEGniGLirAvekFDp~rG~RFSTYA~wWIRq~I~r~i~~~~r~IRlP~~ 172 (327)
T PRK05949 93 KQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIH 172 (327)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEHHHHHHHHHHHHHHHCCCCCCCCHH
T ss_conf 99999981999999998643699898999998589999999980965597134200999989999999982887446378
Q ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCC
Q ss_conf 00358999999997887866244788824677888618983211000000122343355202323453200000123568
Q gi|254780611|r 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209 (302)
Q Consensus 130 ~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~ 209 (302)
..+ .++++++....+....++.|+..+||+.+|+++++|..+......+.|||.++++ +++.++.|++.++.+
T Consensus 173 ~~~-----~~~ki~~~~~~l~~~lgr~pt~~EiA~~l~i~~~~v~~~l~~~~~~~SLD~~v~d--~~~~~l~dll~d~~~ 245 (327)
T PRK05949 173 ITE-----KLNKIKKTQRELSQKLGRSATPAEIAKALELEPSQIREYLSMARQPISLDVRVGD--NQDTELSELLEDEGV 245 (327)
T ss_pred HHH-----HHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCC--CCCCHHHHHHCCCCC
T ss_conf 999-----9999999999999981889988999989499999999999841887223674699--974026667336889
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 70565566666667779999996219999999999982788--888989999997789999999999999999999
Q gi|254780611|r 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302)
Q Consensus 210 ~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~--~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302)
.|++.+ ....++..|..+|..|++||+.||.+|||.+ +++||+|||+.||||+||||||+++||.|||+.
T Consensus 246 ~pe~~~----~~~~lr~~l~~~L~~L~~REr~Ii~~RfGl~~~~~~TL~EIg~~lgiSrERVRQIE~rAL~KLR~~ 317 (327)
T PRK05949 246 SPDQYI----TQELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGQRLNLSRERVRQLEHQALAHLRRR 317 (327)
T ss_pred CHHHHH----HHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHC
T ss_conf 999999----999999999999856999999999997189996985799999998959999999999999998625
No 12
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=0 Score=509.14 Aligned_cols=265 Identities=28% Similarity=0.463 Sum_probs=232.6
Q ss_pred CCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH---------------------------------------HCCHHHHHH
Q ss_conf 74059999998407999998999999999998---------------------------------------285999999
Q gi|254780611|r 12 GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------------------------HGDLSAAHR 52 (302)
Q Consensus 12 ~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~---------------------------------------~gd~~Ar~~ 52 (302)
-+|++..||++|+++||||++||++|+++++. ..+.+|+++
T Consensus 73 t~D~vr~YL~eIg~~~LLt~~eEi~La~~i~~~~~le~~~~~l~~~~~~~p~~~ewa~~~~~~~~~l~~~~~~g~~Ar~~ 152 (385)
T PRK07406 73 TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGHFPSVEEWAELVDMPLPKFRRRLMLGRRAKEK 152 (385)
T ss_pred CCCCHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHH
T ss_conf 88849999986277679999999999999999999999999988741665427999988088889999999879999999
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHH
Q ss_conf 99943077875655557999988899999988899898621853456899975778999999853202460011023003
Q gi|254780611|r 53 LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132 (302)
Q Consensus 53 Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~ 132 (302)
||++|||||++||++|.|+|++|+|||||||||||+||+||||++|+||||||+|||||+|.++|.+++|+||+|+|..
T Consensus 153 LI~aNLRLVVsIAkkY~~rGl~l~DLIQEGniGLirAvEKFDp~rG~RFSTYA~WWIRqaI~RaI~~~sr~IRlP~h~~- 231 (385)
T PRK07406 153 MVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLY- 231 (385)
T ss_pred HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEHHHHHHHHHHHHHHHHCCCEECCHHHHH-
T ss_conf 9999899999999865689989889999858999999998196548822110299999999999997386120208999-
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCH
Q ss_conf 58999999997887866244788824677888618983211000000122343355202323453200000123568705
Q gi|254780611|r 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212 (302)
Q Consensus 133 r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~ 212 (302)
..++++++....+....++.|+.++||+.++++++++..+......++|||.|++.++ +..+.|++.++...|+
T Consensus 232 ----e~l~ki~k~~~~L~~~lGr~Pt~eEIA~~l~i~~e~v~~~~~~~~~~vSLD~pvg~~~--ds~l~D~i~~d~~~pe 305 (385)
T PRK07406 232 ----ETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEE--DSRLGDFIEADGETPE 305 (385)
T ss_pred ----HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCC--CCCHHHHHHCCCCCHH
T ss_conf ----9999999999999987089986999999939999999999985489865458888765--3318889863599999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 65566666667779999996219999999999982788--8889899999977899999999999999999999974
Q gi|254780611|r 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287 (302)
Q Consensus 213 ~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~--~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~ 287 (302)
+.+ ....++..|..+|+.|++||+.||.+|||.+ .++||+|||+.||||+||||||+++||.|||..-..+
T Consensus 306 ~~~----~~~~lr~~L~~~L~~L~eREr~II~lRfGL~dg~~~TL~EIg~~lgISRERVRQIE~rAL~KLR~p~r~~ 378 (385)
T PRK07406 306 DDV----SKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNS 378 (385)
T ss_pred HHH----HHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHH
T ss_conf 999----9999999999998649999999999975899999646999998979599999999999999967717789
No 13
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=100.00 E-value=0 Score=507.48 Aligned_cols=269 Identities=28% Similarity=0.495 Sum_probs=234.5
Q ss_pred CCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH-------------------------------------------
Q ss_conf 7455874059999998407999998999999999998-------------------------------------------
Q gi|254780611|r 7 SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------------------------------- 43 (302)
Q Consensus 7 ~~~~~~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~------------------------------------------- 43 (302)
.-+...+|.+..||++|+++||||++||++|+++++.
T Consensus 48 ~~~~~s~D~vr~YL~eIgrvpLLt~eeEv~la~~ve~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~ 127 (410)
T PRK07598 48 SRNRRSTDLVRLYLQEIGRVPLLGRDEEVSEAQKVQRYMKLVVLANAAKEGDEVIKPYLRLIEVRDRLTAELGHRPSLER 127 (410)
T ss_pred CCCCCCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCHHH
T ss_conf 77999997199999982877789858999999999999999999876520220245667788899999987356851788
Q ss_pred --------------------------------------HCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf --------------------------------------285999999999430778756555579999888999999888
Q gi|254780611|r 44 --------------------------------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85 (302)
Q Consensus 44 --------------------------------------~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iG 85 (302)
.....||++||++|||||+||||+|.|+|++++|||||||||
T Consensus 128 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~el~~~~~~G~~Ar~kLI~aNLRLVVsIAkkY~~rGl~l~DLIQEGniG 207 (410)
T PRK07598 128 WAAIADISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLG 207 (410)
T ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHH
T ss_conf 87740331234556655445556664014699999999999999999999989999999986578998989999874899
Q ss_pred HHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q ss_conf 99898621853456899975778999999853202460011023003589999999978878662447888246778886
Q gi|254780611|r 86 LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165 (302)
Q Consensus 86 Li~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~ 165 (302)
||+||+||||++|+||||||+||||++|.++|.+++|+||+|+|..+ .++++++....+....++.|++++||+.
T Consensus 208 LirAVEKFDp~rG~RFSTYA~WWIRQaI~RaI~~~~r~IRlP~h~~e-----~l~ki~r~~r~L~q~lGR~Pt~eEIA~~ 282 (410)
T PRK07598 208 LERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITE-----KLNKIKKAQRKISQEKGRTPTIEDIAQE 282 (410)
T ss_pred HHHHHHHCCCCCCCEEEEEEHHHHHHHHHHHHHHHCCEECCCCHHHH-----HHHHHHHHHHHHHHHCCCCCCHHHHHHH
T ss_conf 99999970965597257621899999999999980880204602999-----9999999999999875999979999988
Q ss_pred CCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHH
Q ss_conf 18983211000000122343355202323453200000123568705655666666677799999962199999999999
Q gi|254780611|r 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245 (302)
Q Consensus 166 Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ 245 (302)
+|+++++|..+......++|||.+++. +++..+.|++.++...|++.+. ...++..|..+|..|++||+.||.+
T Consensus 283 lg~s~e~V~~~l~~~~~~vSLd~pvg~--d~d~~l~dll~~~~~~pee~~~----~~~l~~~L~~lL~~L~~REr~IL~l 356 (410)
T PRK07598 283 LEMTPTQVREVLLRVPRSVSLETKVGK--DKDTELGDLLETDDVSPEEMLM----RESLQRDLQQLLADLTSRERDVIRM 356 (410)
T ss_pred CCCCHHHHHHHHHHCCCCCCCCCCCCC--CCCCCHHHHHCCCCCCHHHHHH----HHHHHHHHHHHHHCCCHHHHHHHHH
T ss_conf 099999999999872788553678888--8864188874458999899999----9999999999983699999999999
Q ss_pred HHCC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 8278--8888989999997789999999999999999999997
Q gi|254780611|r 246 RRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286 (302)
Q Consensus 246 ry~~--~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~ 286 (302)
|||. ++++||.|||+.||||+||||||+++||.|||..-..
T Consensus 357 RfGL~dg~~~TL~EIG~~lgISRERVRQIE~kAL~KLR~p~r~ 399 (410)
T PRK07598 357 RFGLADGRTYSLAEIGRALDLSRERVRQIEAKALQKLRQPKRR 399 (410)
T ss_pred HCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHH
T ss_conf 6489997966899999897969999999999999996773778
No 14
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=0 Score=502.02 Aligned_cols=254 Identities=27% Similarity=0.438 Sum_probs=217.3
Q ss_pred HHCCCCCCHHHHHHHHHHHHHHCC---HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 407999998999999999998285---99999999943077875655557999988899999988899898621853456
Q gi|254780611|r 23 IRKIPMLEKQEEYVLAKRYREHGD---LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99 (302)
Q Consensus 23 i~~~~~Lt~eee~~l~~~~~~~gd---~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~ 99 (302)
|...-.+|..|=+.+.++++. |. ..|+..||++|||||+||||||.|||++|.|||||||||||+||+|||..|||
T Consensus 354 ie~~~gl~i~elK~i~r~I~~-Ge~~a~~AKkeMiEANLRLVISIAKKYtNRGLqFLDLIQEGNiGLMkAVdKFeyrrGy 432 (620)
T PRK05658 354 IEEETGLTIEELKEINRQISK-GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 432 (620)
T ss_pred HHHHHCCCHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCHHHHHHHHHCCCCCCC
T ss_conf 999849799999999999999-8777899999999861899999999831489987899874407999999862845597
Q ss_pred CHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf 89997577899999985320246001102300358999999997887866244788824677888618983211000000
Q gi|254780611|r 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179 (302)
Q Consensus 100 ~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~ 179 (302)
||||||+|||||+|.|+|.|++|+||||||+- ..++|+.+...++.+..|+.|+.+|||+.||+++++|+.+++.
T Consensus 433 KFSTYATWWIRQAITRaIaDqaRTIRiPVHmi-----etinkl~r~~r~l~qe~Grept~eEia~~~~~~~~kvr~vlki 507 (620)
T PRK05658 433 KFSTYATWWIRQAITRSIADQARTIRIPVHMI-----ETINKLNRISRQMLQEMGREPTPEELAERLGMPEDKVRKVLKI 507 (620)
T ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHH-----HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 13577999999999999986177401518899-----9999999999999998289999999998949899999999986
Q ss_pred CCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCC--CCCHHH
Q ss_conf 122343355202323453200000123568705655666666677799999962199999999999827888--889899
Q gi|254780611|r 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLEN 257 (302)
Q Consensus 180 ~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~--~~Tl~E 257 (302)
...++||+.|++.+ +++.++|++.|.....|. +......++..+..+|+.|+|||+.||++|||.+. .+||.|
T Consensus 508 ~~epiSle~pig~~--~ds~lgdfied~~~~~p~---~~~~~~~l~~~~~~vl~~Lt~rE~~vl~~RfGi~~~~~~TLee 582 (620)
T PRK05658 508 AKEPISLETPIGDD--EDSHLGDFIEDKNAELPI---DAATQESLREQTTDVLASLTPREAKVLRMRFGIDMNTDHTLEE 582 (620)
T ss_pred CCCCCCCCCCCCCC--CCCCCCCCCCCCCCCCHH---HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCHHH
T ss_conf 48980243887888--876400101689999879---9999999999999998479999999999957999999678999
Q ss_pred HHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999977899999999999999999999974
Q gi|254780611|r 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287 (302)
Q Consensus 258 Ia~~lgiS~eRVrQI~~~AL~kLR~~l~~~ 287 (302)
||..||||||||||||.+||+|||..-+++
T Consensus 583 vg~~f~vtRERiRQIEakalrklrhp~r~~ 612 (620)
T PRK05658 583 VGKQFDVTRERIRQIEAKALRKLRHPSRSR 612 (620)
T ss_pred HHHHHCCCHHHHHHHHHHHHHHHCCCCHHH
T ss_conf 998829768989999999999856872578
No 15
>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=502.91 Aligned_cols=229 Identities=29% Similarity=0.484 Sum_probs=207.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCC
Q ss_conf 99999994307787565555799998889999998889989862185345689997577899999985320246001102
Q gi|254780611|r 49 AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128 (302)
Q Consensus 49 Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~ 128 (302)
|+++||++|||||+||||||.|||++|.|||||||+|||+||+|||..|||||||||+|||||+|.|+|.||+|+|||||
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 CCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCC
Q ss_conf 30035899999999788786624478882467788861898321100000012234335520232345320000012356
Q gi|254780611|r 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208 (302)
Q Consensus 129 ~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~ 208 (302)
|+.+ .++|+.+....+.+..|+.|+.++||+.||++.++|..+......++||+.|+++ ++++.++|++.|..
T Consensus 81 Hm~E-----TINk~~~~~R~l~Q~~Gr~Pt~EelAe~~g~~~~Kv~~i~~~~~~PiSLe~piG~--e~dS~l~DFi~D~~ 153 (240)
T TIGR02393 81 HMVE-----TINKLIKAERKLLQELGREPTDEELAERMGLPVEKVREIKKIAQEPISLETPIGE--EEDSSLGDFIEDES 153 (240)
T ss_pred HHHH-----HHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCC--CCCCCCCCCCCCCC
T ss_conf 2667-----8889999989999872889987789987089989999999862488656667788--77774426525744
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHCCC---CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 8705655666666677799999962-19999999999982788---8889899999977899999999999999999999
Q gi|254780611|r 209 DGQEQVLIEKEERKNRRNMLTRSMS-VLNPRERRIFEARRLQE---NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284 (302)
Q Consensus 209 ~~~~~~~~e~~e~~~~~~~L~~~l~-~L~~rEr~II~~ry~~~---~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l 284 (302)
...|. +......+...|..+|. +|++||+.||.+|||.. .+.||.|||..||||||||||||.+||+|||..-
T Consensus 154 ~~~P~---~~~~~~~l~~~l~~vL~~~L~~rE~~Vl~~RyGL~d~~~~~TLEEVG~~f~VTRERIRQIE~KALRKLrhp~ 230 (240)
T TIGR02393 154 IESPE---DAAAKELLREQLEEVLENTLTERERKVLRMRYGLLDGEKPKTLEEVGKEFNVTRERIRQIESKALRKLRHPS 230 (240)
T ss_pred CCCHH---HHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHCCCHH
T ss_conf 46858---999999999999999860178889999987438998876533788876517871145688899988502843
Q ss_pred HHH
Q ss_conf 974
Q gi|254780611|r 285 QKQ 287 (302)
Q Consensus 285 ~~~ 287 (302)
+.+
T Consensus 231 r~~ 233 (240)
T TIGR02393 231 RSK 233 (240)
T ss_pred HHH
T ss_conf 667
No 16
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=100.00 E-value=0 Score=482.39 Aligned_cols=266 Identities=38% Similarity=0.576 Sum_probs=237.9
Q ss_pred CCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHC-CHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHH
Q ss_conf 87405999999840799999899999999999828-59999999994307787565555799998889999998889989
Q gi|254780611|r 11 NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG-DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89 (302)
Q Consensus 11 ~~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~g-d~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~A 89 (302)
.....+..|+..+...|+||++||..|+.++++.+ |..|+++||++|||||+|||++|.|+|++|.|||||||||||+|
T Consensus 64 ~~~~~~~~~~~~~~~~~~l~~~Ee~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkA 143 (342)
T COG0568 64 RPAGRLSFYIRAIEAAPLLTPEEEKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKA 143 (342)
T ss_pred HHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHCCCHHHHHH
T ss_conf 13456889998876400159789999999998588559999999999889999999986337986889885250999999
Q ss_pred HHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCC
Q ss_conf 86218534568999757789999998532024600110230035899999999788786624478882467788861898
Q gi|254780611|r 90 VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169 (302)
Q Consensus 90 i~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis 169 (302)
++||||++||+|||||+||||++|++||.++||+||+|+| +.+.+++++|++..+.+. .+++|+.++||+.||++
T Consensus 144 VekFdp~rG~kFsTYA~wWIrqaI~raI~~q~rtIRipvh--~~e~~nkl~r~~r~l~q~---~~r~p~~eeia~~l~~~ 218 (342)
T COG0568 144 VEKFDPEKGFKFSTYATWWIRQAITRAIADQARTIRIPVH--QVELINKLRRVKRELLQE---LGREPTPEEIAEELGVS 218 (342)
T ss_pred HHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHH--HHHHHHHHHHHHHHHHHH---HCCCCCHHHHHHHHCCC
T ss_conf 9962966687211099999999999999974234657699--999999999999999998---45899799999995999
Q ss_pred CCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHHC-CCHHHHHHHHHHH
Q ss_conf 3211000000122343355202323453200000123568-7056556666666777999999621-9999999999982
Q gi|254780611|r 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSV-LNPRERRIFEARR 247 (302)
Q Consensus 170 ~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~-~~~~~~~e~~e~~~~~~~L~~~l~~-L~~rEr~II~~ry 247 (302)
+++|..++.....+.|||.+++.++++ .++|++.++.. .|++.+... .....+...+.. |++||+.||.+||
T Consensus 219 ~~~V~~m~~~~~~~~SLd~~ig~ded~--~l~d~leD~~~~~p~~~~~~~----~~~~~~~~~L~~~Lt~rE~~Vi~~R~ 292 (342)
T COG0568 219 PDKVREMLKRASEPISLDTPIGDDEDS--ELGDFLEDDKSVSPEDAVERE----SLKEDLNEVLAEALTERERRVIRLRF 292 (342)
T ss_pred HHHHHHHHHHCCCCCCCCCCCCCCCCC--HHHHHHHCCCCCCHHHHHHHH----HHHHHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 999999998653676767848888520--788876426878989999988----89999999987159999999999995
Q ss_pred CC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 78--88889899999977899999999999999999999974
Q gi|254780611|r 248 LQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287 (302)
Q Consensus 248 ~~--~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~ 287 (302)
|. +++.||.|||+.+|||+||||||+.+||+|||....++
T Consensus 293 gl~~~~~~TLeevg~~~~vsrERvRQIE~kAl~KLr~~~~~~ 334 (342)
T COG0568 293 GLDDGEPKTLEELGEEFGISRERVRQIEAKALRKLRRHPERS 334 (342)
T ss_pred CCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 567999551999998959869999999999999998706322
No 17
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=100.00 E-value=0 Score=472.71 Aligned_cols=257 Identities=25% Similarity=0.362 Sum_probs=219.7
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHH
Q ss_conf 98665574558740599999984079999989999999999982859999999994307787565555799998889999
Q gi|254780611|r 1 MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80 (302)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQ 80 (302)
|.++++.+|.. +++|+|+||+|||.+|+++|+ +||.+|+++||++|||||++||++|.++|++++||||
T Consensus 1 ~~~~~~~~~~~----------~~~k~PlLt~EEe~~L~~~~~-~gD~~Ar~~LI~~nLrLV~~iA~ky~~~g~~~~DLiQ 69 (257)
T PRK08215 1 MTRNKVEICGV----------NTSKLPVLKNEEMKELFRRMQ-NGDTSAREKLINGNLRLVLSVIQRFNNRGEYVDDLFQ 69 (257)
T ss_pred CCCCEEEEECC----------CCCCCCCCCHHHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHH
T ss_conf 98650476266----------622489999999999999999-3889999999998789999999876589989889999
Q ss_pred HHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHH
Q ss_conf 99888998986218534568999757789999998532024600110230035899999999788786624478882467
Q gi|254780611|r 81 EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160 (302)
Q Consensus 81 eG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~ 160 (302)
|||+|||+||++|||++|++|||||+|||||+|.+|++++ ++||+|.+.. ...+++.+....+....+++|+++
T Consensus 70 eG~iGLi~AiekFDp~rG~rFsTYA~~wIr~~I~~~i~~~-~~irip~~~~-----~~~~k~~~~~~~l~~~~~r~pt~~ 143 (257)
T PRK08215 70 VGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDN-NPIRVSRSLR-----DIAYKALQVREKLIKENSKEPTVS 143 (257)
T ss_pred HHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHC-CCCEEEHHHH-----HHHHHHHHHHHHHHHHHCCCCCHH
T ss_conf 8799999999970976799543211999999999999967-9851009999-----999999999999999838999999
Q ss_pred HHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHH
Q ss_conf 78886189832110000001223433552023234532000001235687056556666666777999999621999999
Q gi|254780611|r 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240 (302)
Q Consensus 161 eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr 240 (302)
++|+.||++.+++......+..+.|||.++.+++++.....|.+.+.....+.. .+ ...|..+++.||+||+
T Consensus 144 eiA~~l~i~~~~v~~~l~~~~~~~SL~~~~~~d~~d~~~~~d~~~d~~~~~~~~-~~-------~~~l~~~l~~L~~REr 215 (257)
T PRK08215 144 EIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIFVMDQISDEKNKDEQW-LE-------EIALKEAMKRLNDREK 215 (257)
T ss_pred HHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCHHH-HH-------HHHHHHHHHCCCHHHH
T ss_conf 999880989999999998638986676855578997104422147976550899-99-------9999999964999999
Q ss_pred HHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999827888889899999977899999999999999999999
Q gi|254780611|r 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284 (302)
Q Consensus 241 ~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l 284 (302)
.||.+||+.+ +|+.|||+.||||++|||||+++||.|||+.|
T Consensus 216 ~Ii~~ry~~~--~Tl~eIa~~lGvSreRVrQie~~AL~kLR~~l 257 (257)
T PRK08215 216 MILNLRFFQG--KTQMEVADEIGISQAQVSRLEKAALKHMRKYI 257 (257)
T ss_pred HHHHHHHCCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHC
T ss_conf 9999994799--98999999989699999999999999998549
No 18
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=100.00 E-value=0 Score=466.37 Aligned_cols=251 Identities=21% Similarity=0.277 Sum_probs=214.6
Q ss_pred HHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 99840799999899999999999828599999999943077875655557999988899999988899898621853456
Q gi|254780611|r 20 IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99 (302)
Q Consensus 20 l~~i~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~ 99 (302)
|++|+++|+||+|||.+||++|+++||.+|+++||++|||||++||++|.++|++++|||||||||||+|++||||++|+
T Consensus 1 ~~~~~~~~~Lt~eee~~L~~~~~~~gd~~Ar~~Li~~nlrLV~~iA~~y~~~g~~~~DLiQeG~iGLi~AiekFDp~rG~ 80 (257)
T PRK08583 1 MKESSQPTKLTKEDVNQWIAEYQENQDEEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDYSFGR 80 (257)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf 98676899999999999999998819999999999984999999999862689886179999999999998706986588
Q ss_pred CHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf 89997577899999985320246001102300358999999997887866244788824677888618983211000000
Q gi|254780611|r 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179 (302)
Q Consensus 100 ~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~ 179 (302)
+|||||+|||||+|.+|+++++++||+|.+. ....+++++....+....++.|++++||+.||++.++|.+++..
T Consensus 81 rFsTYA~~wIr~~I~~~lr~~~~~ir~P~~~-----~~~~~ki~~~~~~l~~~~~r~pt~~eiA~~l~~s~e~v~~~l~~ 155 (257)
T PRK08583 81 SFEAFAVPTIIGEIKRYLRDKTWSVHVPRRI-----KELGPKIKKAVDELTDELQRSPKISEIADRLGVSEEEVLEAMEM 155 (257)
T ss_pred CCHHHHHHHHHHHHHHHHHHCCCCCCCCHHH-----HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 8398789999999999999648711354999-----99988899999999998089987999998959599999999997
Q ss_pred C--CCCCCHHHHCCCCCC-CCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHH
Q ss_conf 1--223433552023234-5320000012356870565566666667779999996219999999999982788888989
Q gi|254780611|r 180 L--AGDESLNALINSSDK-NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256 (302)
Q Consensus 180 ~--~~~~SLd~~i~~~d~-~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~ 256 (302)
. ....|||.++..+++ ...++.|.+.+ +++.. +....+..|..+++.|++||+.||.+||+.+ +|++
T Consensus 156 ~~~~~~~Sld~~~~~d~d~~~~~~~d~~~~----~e~~~----e~~e~~~~l~~~l~~L~erEr~Ii~lry~~~--~t~~ 225 (257)
T PRK08583 156 GKSYQALSVDHSIEADSDGSTVTLLDIVGQ----QEDGY----ELTEQRMILEKILPVLSDREKSIIQCTFIEN--LSQK 225 (257)
T ss_pred HCCCCCCCCCCCCCCCCCCCCCCHHHCCCC----CCCHH----HHHHHHHHHHHHHHCCCHHHHHHHHHHHCCC--CCHH
T ss_conf 516897027888877888771204330489----66247----8999999999999549999999999995799--9999
Q ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999778999999999999999999999
Q gi|254780611|r 257 NLSSEFEVSRERVRQIEARAFKKVQESIQ 285 (302)
Q Consensus 257 EIa~~lgiS~eRVrQI~~~AL~kLR~~l~ 285 (302)
|||+.||||++|||||+++||+|||+.+-
T Consensus 226 eIa~~lGiS~eRVrQi~~~Al~kLR~~~~ 254 (257)
T PRK08583 226 ETGERLGISQMHVSRLQRQAIKKLREAAF 254 (257)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHHHHC
T ss_conf 99999896999999999999999877750
No 19
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00 E-value=0 Score=454.33 Aligned_cols=247 Identities=21% Similarity=0.294 Sum_probs=214.6
Q ss_pred CCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCC-CCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH
Q ss_conf 99989999999999982859999999994307787565555799-99888999999888998986218534568999757
Q gi|254780611|r 28 MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY-GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106 (302)
Q Consensus 28 ~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~-g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~ 106 (302)
-=++|||.+||++|+++||.+||++||++|||||++||++|.++ |.+++||||+||||||+|+++|||++|++|||||+
T Consensus 5 ~~~keee~eL~~~y~~~gd~~ar~~LI~~nlrLV~~iA~ry~~~~~~~~~DLiQeG~iGLi~AvekFDp~kG~rFsTYA~ 84 (256)
T PRK07408 5 ESLKSETMELLRAYQQTPSIALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLEQVGYLGLIRAIERFDPSKGHAFSSFAV 84 (256)
T ss_pred CHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH
T ss_conf 11579999999999884999999999998099999999986157999878999999999999999739733898899999
Q ss_pred HHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCC--CCCC
Q ss_conf 78999999853202460011023003589999999978878662447888246778886189832110000001--2234
Q gi|254780611|r 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL--AGDE 184 (302)
Q Consensus 107 ~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~--~~~~ 184 (302)
|||||+|.+||++++++||+|++. ....+++++....+....+++|+.++||+.||++++++..+.... ..+.
T Consensus 85 ~wIr~~I~~~lr~~~~~iRiP~~~-----~~~~~ki~~~~~~l~~~~gr~pt~~EiA~~l~is~~~v~~~~~~~~~~~~~ 159 (256)
T PRK07408 85 PYIRGEIQHYLRDKSPTVRIPRRW-----LELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRMPL 159 (256)
T ss_pred HHHHHHHHHHHHHHCCCEECCHHH-----HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCE
T ss_conf 999999999999808974136999-----999999999999999987899989999989596999999999987278873
Q ss_pred CHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCC
Q ss_conf 33552023234532000001235687056556666666777999999621999999999998278888898999999778
Q gi|254780611|r 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264 (302)
Q Consensus 185 SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgi 264 (302)
|||.++..++++..++.|.+++.......... ..+..|..+|..||+||+.||.+||+.+ +|++|||+.|||
T Consensus 160 SLd~~~~~~~d~~~~l~d~l~d~~~~~~~~~~------e~~~~L~~~l~~L~eREr~Il~~ry~~~--~tl~EIa~~lgv 231 (256)
T PRK07408 160 SLDAPVSQDEDGSTSLGDLLPDPRYRSFQLAQ------EDRIRLQQALAQLEERTREVLEFVFLHD--LTQKEAAERLGI 231 (256)
T ss_pred ECCCCCCCCCCCCCHHHHHCCCCCCCHHHHHH------HHHHHHHHHHHCCCHHHHHHHHHHHCCC--CCHHHHHHHHCC
T ss_conf 05664779998761177755899975388999------9999999998569999999999996379--989999989798
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999999999974
Q gi|254780611|r 265 SRERVRQIEARAFKKVQESIQKQ 287 (302)
Q Consensus 265 S~eRVrQI~~~AL~kLR~~l~~~ 287 (302)
|++|||||+++||.|||+.|+++
T Consensus 232 S~~rVsqi~~~AL~kLR~~L~~~ 254 (256)
T PRK07408 232 SPVTVSRRVKKGLQQLKKLLQPQ 254 (256)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 99999999999999999972133
No 20
>PRK05572 sporulation sigma factor SigF; Validated
Probab=100.00 E-value=0 Score=450.28 Aligned_cols=247 Identities=21% Similarity=0.327 Sum_probs=209.8
Q ss_pred HHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCH
Q ss_conf 84079999989999999999982859999999994307787565555799998889999998889989862185345689
Q gi|254780611|r 22 EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101 (302)
Q Consensus 22 ~i~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~F 101 (302)
+--|.|+||+|||.+|+++++ +||.+|+++||++|||||++||++|.|+|++++||||+||+|||+|++||||++|++|
T Consensus 5 ~~~~~~~Ls~eee~~L~~~~~-~Gd~~Ar~~Li~~nlrLV~siA~ry~~~g~~~~DLiQeG~iGLi~A~ekFDp~~G~rF 83 (251)
T PRK05572 5 NEVKKEQLKDEENKELIKKAQ-DGDKEARDKLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKF 83 (251)
T ss_pred CCCCCCCCCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCH
T ss_conf 124689999999999999998-0799999999998599999999877589999889999999999999622598989840
Q ss_pred HHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 99757789999998532024600110230035899999999788786624478882467788861898321100000012
Q gi|254780611|r 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181 (302)
Q Consensus 102 sTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~ 181 (302)
||||+|||+|+|.+||++++ +||+|.+.. ...+++.+....+....++.|++++||+.+|++.+++........
T Consensus 84 sTYA~~wIr~~I~~~ir~~~-~irvp~~~~-----~~~~ki~~~~~~l~~~~~r~ps~~eia~~lg~~~~~v~~~~~~~~ 157 (251)
T PRK05572 84 STYAVPMIIGEIQRFLRDDG-IIKVSRSLK-----ELANKIRKDKEELSKELGRAPTIEELAEYLGVTPEEVVLAQEASR 157 (251)
T ss_pred HHHHHHHHHHHHHHHHHHCC-CCCCCHHHH-----HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHC
T ss_conf 22009999999999998578-766868899-----999889999999999878899899999997939999999998817
Q ss_pred CCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHH
Q ss_conf 23433552023234532000001235687056556666666777999999621999999999998278888898999999
Q gi|254780611|r 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261 (302)
Q Consensus 182 ~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~ 261 (302)
...|++.++..++++...+.|.+.++. .++.. ..+..|..++..||+||+.||.+||+.+ +|++|||+.
T Consensus 158 ~~~sl~~~~~~~d~~~~~l~d~~~~~~--~~~~~-------~~~~~L~~~l~~L~~rEr~Vi~~ry~~~--~tl~EIa~~ 226 (251)
T PRK05572 158 SPQSIHETVHENDGDPITLLDQIADQS--EEDDW-------FDKIALKEAIRELDERERLIIYLRYFKD--KTQSEVAKR 226 (251)
T ss_pred CCCCCCCCCCCCCCCHHHHHHHCCCCC--HHHHH-------HHHHHHHHHHHCCCHHHHHHHHHHHCCC--CCHHHHHHH
T ss_conf 987534666678997156654126873--46899-------9999999999728999999999981789--889999999
Q ss_pred HCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 7789999999999999999999997
Q gi|254780611|r 262 FEVSRERVRQIEARAFKKVQESIQK 286 (302)
Q Consensus 262 lgiS~eRVrQI~~~AL~kLR~~l~~ 286 (302)
||||++|||||+++||.|||+.|++
T Consensus 227 lgiS~eRVrQI~~~Al~kLR~~L~e 251 (251)
T PRK05572 227 LGISQVQVSRLEKKILKQMKEKLDE 251 (251)
T ss_pred HCCCHHHHHHHHHHHHHHHHHHHCC
T ss_conf 7979999999999999999998529
No 21
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=100.00 E-value=0 Score=435.77 Aligned_cols=250 Identities=23% Similarity=0.313 Sum_probs=213.0
Q ss_pred CCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHC---CCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCH
Q ss_conf 799999899999999999828599999999943077875655557---99998889999998889989862185345689
Q gi|254780611|r 25 KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101 (302)
Q Consensus 25 ~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~---~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~F 101 (302)
+.+.||+|||.+||++|+++||.+||++||++|||||++||++|. ++|++++||||+||||||+|++||||++|++|
T Consensus 4 ~~~~~s~eee~eL~~~~~~~gd~~ar~~LI~~nlrLV~~iA~~~~~~~~~~~~~~DLiQeG~iGLi~AvekFDp~rG~rF 83 (261)
T PRK06288 4 KNRKYAQQDETELWKSYKETGDAKIREYLILKYSPLVKYVAGRVAVGMPQNVEFDDLVSYGVFGLLDAIEKFDPEREIKF 83 (261)
T ss_pred CCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf 62223869999999999881999999999998599999999998457999999999999999999999996599878883
Q ss_pred HHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 99757789999998532024600110230035899999999788786624478882467788861898321100000012
Q gi|254780611|r 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181 (302)
Q Consensus 102 sTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~ 181 (302)
||||+|||||+|.++++... .+|.+ +....+++++....+....+++|+.++||+.||++++++..+...+.
T Consensus 84 sTYA~~wIr~aI~~~lR~~~---~~pr~-----~~~~~~ki~~~~~~l~~~~gr~pt~~eia~~lg~~~~~v~~~~~~~~ 155 (261)
T PRK06288 84 ETYAITRIRGAIFDELRSID---WIPRS-----VRQKARQVERAIAMLEAKLGRTPTDDEIAKELGISLEEYHSLLSKVS 155 (261)
T ss_pred HHHHHHHHHHHHHHHHHHHH---HCCHH-----HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf 98799999999999999860---03199-----99999999999999999868999878888781999999999999972
Q ss_pred --CCCCHHHHCCCC-CCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHH
Q ss_conf --234335520232-34532000001235687056556666666777999999621999999999998278888898999
Q gi|254780611|r 182 --GDESLNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258 (302)
Q Consensus 182 --~~~SLd~~i~~~-d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EI 258 (302)
...|||.++..+ +++..++.|.+.++....++... +...++..|..++..||+||+.||.+||+.+ +||+||
T Consensus 156 ~~~~~SLd~~~~~~~~~~~~~~~d~l~d~~~~~p~~~~---e~~~~~~~l~~~l~~L~erEr~Il~lry~e~--~Tl~eI 230 (261)
T PRK06288 156 GTSVVSLNDLLFLGDENDEVSLMDTLEDPAAMNPDEII---EKEEIKRVIVEAINTLPEREKKVITLYYYED--LTLKEI 230 (261)
T ss_pred CCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCHHHHH---HHHHHHHHHHHHHHCCCHHHHHHHHHHCCCC--CCHHHH
T ss_conf 69974767776579998643087870588989999999---9999999999998708999999999980799--889999
Q ss_pred HHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99977899999999999999999999974
Q gi|254780611|r 259 SSEFEVSRERVRQIEARAFKKVQESIQKQ 287 (302)
Q Consensus 259 a~~lgiS~eRVrQI~~~AL~kLR~~l~~~ 287 (302)
|+.||||++|||||+++||+|||+.|.+.
T Consensus 231 a~~lgiS~eRVrQie~~AL~kLR~~L~~~ 259 (261)
T PRK06288 231 GEVLGVTESRISQIHTKAVLQLRAKLAKV 259 (261)
T ss_pred HHHHCCCHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 99979789999999999999999999861
No 22
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00 E-value=0 Score=431.58 Aligned_cols=249 Identities=20% Similarity=0.261 Sum_probs=206.7
Q ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHHHHH--HHCC---HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHH
Q ss_conf 05999999840799999899999999999--8285---999999999430778756555579999888999999888998
Q gi|254780611|r 14 IGLSRYIHEIRKIPMLEKQEEYVLAKRYR--EHGD---LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88 (302)
Q Consensus 14 ~~~~~yl~~i~~~~~Lt~eee~~l~~~~~--~~gd---~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~ 88 (302)
-.+..|+.+++++|. +++.+. ..|+ +.||++||++|||||++||++|.|+|++++||||+|++|||+
T Consensus 8 ~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~aR~~lI~~nLrLV~~iA~ry~~rGl~~~DLiQeG~iGLi~ 79 (263)
T PRK07122 8 GGSARRPDEYADVPE--------MFRELAGLPAGSPEFQRQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVN 79 (263)
T ss_pred CCCCCCCCCHHHHHH--------HHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHH
T ss_conf 999998430335999--------999998568999899999999999909999999987216898888999999999999
Q ss_pred HHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCC
Q ss_conf 98621853456899975778999999853202460011023003589999999978878662447888246778886189
Q gi|254780611|r 89 AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168 (302)
Q Consensus 89 Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgi 168 (302)
|++||||++|++|||||+|||||+|.+|+++++++||+|.+.. ....++.+....+....+++|+.++||+.||+
T Consensus 80 A~ekFDp~rG~rFsTYA~~wIrgaI~r~lr~~~~~IRlP~~~~-----~~~~ki~~~~~~l~~~~gr~Pt~~EiA~~lg~ 154 (263)
T PRK07122 80 AVNRFDVEAGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRRLK-----ELHLRLGRATAELSQRLGRAPTASELAAELGM 154 (263)
T ss_pred HHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHH-----HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCC
T ss_conf 9997198779985999999999999999998287546579999-----99899999999999986889999999989693
Q ss_pred CCCCCCCCCCC--CCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 83211000000--1223433552023234532000001235687056556666666777999999621999999999998
Q gi|254780611|r 169 SESEVISMNCR--LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246 (302)
Q Consensus 169 s~~~v~~l~~~--~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~r 246 (302)
+.++|.+.... ...+.|||.++.+++++...+.|.+.+.++ .+ +....+..|..+++.||+||+.||.+|
T Consensus 155 ~~~~v~~~l~~~~~~~~~SlD~~~~~~~~~~~~l~d~~~d~~~----~~----e~~~~~~~L~~~l~~L~eREr~Vi~lr 226 (263)
T PRK07122 155 DREEVVEGLVAGSSYNTLSIDSGGGSGDDDARAIADTLGDVDA----GL----DHIENREALRPLLAALPERERTVLVLR 226 (263)
T ss_pred CHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCH----HH----HHHHHHHHHHHHHHCCCHHHHHHHHHH
T ss_conf 9999999998733589877878888888652035464169764----28----999999999999975999999999999
Q ss_pred HCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 278888898999999778999999999999999999999
Q gi|254780611|r 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285 (302)
Q Consensus 247 y~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~ 285 (302)
|+ +++|++|||+.||||++|||||+++||.|||+.|+
T Consensus 227 y~--e~~Tl~EIa~~lGiSreRVrQIe~~AL~KLR~~Le 263 (263)
T PRK07122 227 FF--ESMTQTQIAERVGISQMHVSRLLAKSLARLRDQLE 263 (263)
T ss_pred HC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHC
T ss_conf 56--99989999999897999999999999999999749
No 23
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=100.00 E-value=0 Score=415.83 Aligned_cols=244 Identities=20% Similarity=0.270 Sum_probs=202.6
Q ss_pred CHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCC---CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH
Q ss_conf 98999999999998285999999999430778756555579---999888999999888998986218534568999757
Q gi|254780611|r 30 EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106 (302)
Q Consensus 30 t~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~---~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~ 106 (302)
.+++-.+||++|+++||.+||++||++|||||++||++|.+ +|++++||||+||||||+||+||||++|++|||||+
T Consensus 5 ~~~~~~~lw~~y~~~~d~~ar~~LI~~nLrLV~~iA~r~~~~~p~~v~~~DLiQeG~iGLi~AiekFDp~kG~rFsTYA~ 84 (257)
T PRK05911 5 KTQNIAETWQLYWETQEIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYAL 84 (257)
T ss_pred CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH
T ss_conf 06789999999988399999999999839999999999864699999889999999999999998329866999488769
Q ss_pred HHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCC--CCC
Q ss_conf 789999998532024600110230035899999999788786624478882467788861898321100000012--234
Q gi|254780611|r 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDE 184 (302)
Q Consensus 107 ~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~--~~~ 184 (302)
|||||+|.++++++.+ +|.+. ....+++.+....+....++.|+..+||+.||++.+++..+..... ...
T Consensus 85 ~wIr~aI~~~lr~~~~---lpr~~-----~~~~~ki~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~ 156 (257)
T PRK05911 85 FLIKAAIIDDLRKQDW---VPRSV-----HQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALIL 156 (257)
T ss_pred HHHHHHHHHHHHHCCC---CCHHH-----HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCEE
T ss_conf 9989999999987162---55799-----999999999999999986889999999988397999999999853552223
Q ss_pred CHHHHCCCC--CCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHH
Q ss_conf 335520232--345320000012356870565566666667779999996219999999999982788888989999997
Q gi|254780611|r 185 SLNALINSS--DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262 (302)
Q Consensus 185 SLd~~i~~~--d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~l 262 (302)
|++...... ++.+..+.|.++++...++.. ..+.......|..++..||+||+.||.+||+.+ +||+|||+.|
T Consensus 157 sl~~~~~~~~d~~~~~~l~d~i~d~~~~~~~~---~~~~~~~~~~L~~al~~L~erEr~Ii~lry~e~--~Tl~EIg~~l 231 (257)
T PRK05911 157 SLNEEFPSQSDDEAGLALEERIADERAETGYD---VVDKKEFSSILANAILALEEKERKVMALYYYEE--LVLKEIGKIL 231 (257)
T ss_pred CCCCCCCCCCCCCCCCCHHHHCCCCCCCCHHH---HHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCC--CCHHHHHHHH
T ss_conf 05788887888876530777467988899899---999999999999998658999999999874898--7899999897
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 789999999999999999999997
Q gi|254780611|r 263 EVSRERVRQIEARAFKKVQESIQK 286 (302)
Q Consensus 263 giS~eRVrQI~~~AL~kLR~~l~~ 286 (302)
|||++|||||+++||.|||+.|..
T Consensus 232 gvS~eRVrQi~~~AL~kLR~~L~a 255 (257)
T PRK05911 232 GVSESRVSQIHSKALLKLRAALSA 255 (257)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 988999999999999999999986
No 24
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=0 Score=416.72 Aligned_cols=241 Identities=21% Similarity=0.303 Sum_probs=203.2
Q ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCC---CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHH
Q ss_conf 999999999998285999999999430778756555579---99988899999988899898621853456899975778
Q gi|254780611|r 32 QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108 (302)
Q Consensus 32 eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~---~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~w 108 (302)
.||.+||++|+++||.+|+++||++|||||+++|++|.+ +|++++||||+|+||||+|++||||++|++|||||+||
T Consensus 2 ~ee~~l~~~~~~~gD~~Ar~~LV~~nl~LV~~ia~r~~~~~~~~v~~eDLiQeG~iGLi~AiekFDp~~G~rFsTYA~~w 81 (250)
T PRK07670 2 YEDQKLWDRWKEERDPEAADDLIRRYMPLVTYHVQRISAGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFR 81 (250)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHH
T ss_conf 78999999998859999999999981999999999997048999988899999999999999960986699907721999
Q ss_pred HHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCC--CCCCCCH
Q ss_conf 99999985320246001102300358999999997887866244788824677888618983211000000--1223433
Q gi|254780611|r 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR--LAGDESL 186 (302)
Q Consensus 109 Ir~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~--~~~~~SL 186 (302)
|||+|.+++++.++ +|.+ +....+++++....+....++.|+.++||+.||++++++..+... .....||
T Consensus 82 Ir~aI~~~lr~~~~---lpr~-----~~~~~~ki~~~~~~l~~~~gr~ps~~eia~~lg~s~~~v~~~~~~~~~~~~~Sl 153 (250)
T PRK07670 82 IRGAIIDGLRKEDW---LPRS-----SREKTKKVEAAIEKLEQRYMRNVTPSEVAAELGMSEEEVVTTMNEGFFANLLSI 153 (250)
T ss_pred HHHHHHHHHHHCCC---CHHH-----HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCCCC
T ss_conf 99999999874254---0099-----999999999999999998389998889987719999999999998754798036
Q ss_pred HHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCH
Q ss_conf 55202323453200000123568705655666666677799999962199999999999827888889899999977899
Q gi|254780611|r 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266 (302)
Q Consensus 187 d~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~ 266 (302)
|.+..+++++. ...+.+.++...+++ +..+...+...|..+++.||+||+.||.+||+ +++|++|||+.||||+
T Consensus 154 d~~~~~~~~~~-~~~~~~~d~~~~~pe---~~~~~~~~~~~L~~~l~~L~~rEr~Vl~l~y~--e~~Tl~eIa~~lgvS~ 227 (250)
T PRK07670 154 DEKLHDQDDGE-NVQVMIRDDKAVTPE---EKLVKEELIEQLAEKIKELNEKEQLVISLFYK--EELTLTEIGQVLNLST 227 (250)
T ss_pred CCCCCCCCCCC-HHHHHHHCCCCCCHH---HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCC--CCCCHHHHHHHHCCCH
T ss_conf 77777888850-477888524679999---99999999999999985589999999999748--9868999999989799
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999999997
Q gi|254780611|r 267 ERVRQIEARAFKKVQESIQK 286 (302)
Q Consensus 267 eRVrQI~~~AL~kLR~~l~~ 286 (302)
+|||||+++||+|||+.|++
T Consensus 228 erVrQi~~~AL~kLr~~l~k 247 (250)
T PRK07670 228 SRISQIHSKALFKLKKLLEK 247 (250)
T ss_pred HHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999999999999998
No 25
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=100.00 E-value=0 Score=417.95 Aligned_cols=211 Identities=26% Similarity=0.385 Sum_probs=172.7
Q ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf 05999999840799999899999999999828599999999943077875655557999988899999988899898621
Q gi|254780611|r 14 IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93 (302)
Q Consensus 14 ~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kF 93 (302)
.-|..||++|+++|+||+|||.+|+++|++ ||.+|+++||++|||||++||++|.|+|++++|||||||+|||+||++|
T Consensus 15 ~~l~syl~~i~~~~~Ls~eEE~~La~~~~~-GD~~Ar~~LI~~NLRLVvsIAkky~~~g~~l~DLIQEGniGLi~AvekF 93 (228)
T PRK05803 15 LFLVSYVKNNSFPQPLSEEEERKYLELMKQ-GDEEARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIDSF 93 (228)
T ss_pred HHHHHHHHCCCCCCCCCHHHHHHHHHHHHC-CCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 999999974788999999999999999984-6899999999987799999996277999898999999999999999984
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCC
Q ss_conf 85345689997577899999985320246001102300358999999997887866244788824677888618983211
Q gi|254780611|r 94 DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173 (302)
Q Consensus 94 Dp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v 173 (302)
||++|++|||||+|||+++|..++++..+ .+.
T Consensus 94 Dp~rG~rFSTYA~~wIr~~I~~~lr~~kk-------------------~~~----------------------------- 125 (228)
T PRK05803 94 DAGKGTKLATYAARCIENEILMHLRNLKK-------------------TKG----------------------------- 125 (228)
T ss_pred CCCCCCCCHHCCHHHHHHHHHHHHHHHHH-------------------HCC-----------------------------
T ss_conf 89989970520099999999999999887-------------------535-----------------------------
Q ss_pred CCCCCCCCCCCCHHHHCCCC-CCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCC--C
Q ss_conf 00000012234335520232-34532000001235687056556666666777999999621999999999998278--8
Q gi|254780611|r 174 ISMNCRLAGDESLNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--E 250 (302)
Q Consensus 174 ~~l~~~~~~~~SLd~~i~~~-d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~--~ 250 (302)
.+|++.+++.+ +++..++.|.+.++.+..++.+ +.......|..++..|++||+.||.+|||. +
T Consensus 126 ---------~~sl~~~i~~d~e~~e~~l~d~l~~~~~~~~e~~----~~~~~~~~l~~~l~~L~~REr~II~~RfGL~~~ 192 (228)
T PRK05803 126 ---------EVSLQDPIGVDKEGNEISLIDILKSESDDVIEMV----ELSMEVEKLYKKIDILDPREKEVIEMRYGLGDG 192 (228)
T ss_pred ---------CCCCCCCCCCCCCCCCCHHHHHCCCCCCCHHHHH----HHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCC
T ss_conf ---------5012374466878983224343168899879999----999989999999851898899999998647899
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 888989999997789999999999999999999997
Q gi|254780611|r 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286 (302)
Q Consensus 251 ~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~ 286 (302)
+++||.|||+.||||+||||||+++||+|||+.|.+
T Consensus 193 ~~~Tl~eIg~~lgiSrERVRQIe~~Al~KLrk~L~r 228 (228)
T PRK05803 193 KEKTQREIAKALGISRSYVSRIEKKALKKLFKELVR 228 (228)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCC
T ss_conf 971599999998979999999999999999998559
No 26
>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=422.92 Aligned_cols=224 Identities=28% Similarity=0.380 Sum_probs=203.1
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCH
Q ss_conf 59999999994307787565555799998-88999999888998986218534568999757789999998532024600
Q gi|254780611|r 46 DLSAAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124 (302)
Q Consensus 46 d~~Ar~~Li~~nlrlV~~iA~~y~~~g~~-~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~I 124 (302)
|.+||++||++||+||.+||+||.|||-+ +|||+|.||||||+||+||||++|++|+|||+|.|-|+|+||+||++|.|
T Consensus 1 ~~~~R~~Lv~~nlpLv~~~A~RF~~RGe~~~EDL~QVG~iGL~kAidrFD~~~g~~F~tyAVPtI~GEIkR~fRD~~W~v 80 (229)
T TIGR02980 1 DKEAREKLVELNLPLVESIARRFRSRGEPHLEDLVQVGTIGLVKAIDRFDPSYGVKFSTYAVPTIMGEIKRFFRDDTWAV 80 (229)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCEEEEEEEEEECCCCEE
T ss_conf 96788999996127999999985137887431157888888887775301111698664104602332313342487326
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCC--CCCHHHHCC-CCCCCCCCHH
Q ss_conf 1102300358999999997887866244788824677888618983211000000122--343355202-3234532000
Q gi|254780611|r 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG--DESLNALIN-SSDKNSSQWQ 201 (302)
Q Consensus 125 RiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~--~~SLd~~i~-~~d~~~~~~~ 201 (302)
|||... ..--.+++++.+.+....++.|++.|||+.|++++++|...+.+... +.|||+++. .+|++..++.
T Consensus 81 rVPRrl-----kEl~~~~~~a~eeL~~~lgR~Pt~~EiAe~L~~s~EEv~~aleA~~~Y~~~Sld~~~~a~~dg~~~~L~ 155 (229)
T TIGR02980 81 RVPRRL-----KELRLKINKATEELTQRLGRSPTVAEIAEELGVSEEEVVEALEAGNSYSALSLDATIEADDDGDPIALL 155 (229)
T ss_pred ECCHHH-----HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHH
T ss_conf 605138-----988999999999999982889887899988588999999999865417861120004558888424566
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf 00123568705655666666677799999962199999999999827888889899999977899999999999999999
Q gi|254780611|r 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281 (302)
Q Consensus 202 d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR 281 (302)
|.+.+.++..+.. ..+..|+.+|..||||||.||.+||+.+ +||.|||+.||||++.||+|+++||+|||
T Consensus 156 D~lG~~D~~~e~~--------~~~~aLk~~l~~LpeRER~il~lRFf~~--~TQ~eiA~~lGiSQMhVSRl~~~~L~~LR 225 (229)
T TIGR02980 156 DTLGDEDDALETV--------EDRLALKPLLAALPERERRILLLRFFED--KTQSEIAERLGISQMHVSRLLRRALKRLR 225 (229)
T ss_pred HHHCCCCCHHHHH--------HHHHHHHHHHHHCCHHHCEEEEEEEECC--CCHHHHHHHCCCCHHHHHHHHHHHHHHHH
T ss_conf 4440224326789--------9999999998507902707610001069--77899997818436788999999999999
Q ss_pred HHH
Q ss_conf 999
Q gi|254780611|r 282 ESI 284 (302)
Q Consensus 282 ~~l 284 (302)
+.+
T Consensus 226 ~~l 228 (229)
T TIGR02980 226 EQL 228 (229)
T ss_pred HHC
T ss_conf 860
No 27
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=100.00 E-value=0 Score=397.79 Aligned_cols=206 Identities=30% Similarity=0.449 Sum_probs=160.6
Q ss_pred HHHHHHCC-CCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 99984079-99998999999999998285999999999430778756555579999888999999888998986218534
Q gi|254780611|r 19 YIHEIRKI-PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97 (302)
Q Consensus 19 yl~~i~~~-~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~k 97 (302)
|+..-..+ |+||+|||.+|+++++ .||.+|+++||++|||||++||++|.++|++++|||||||||||+||++|||++
T Consensus 28 ~~~~~~~~pp~Ls~eeE~~l~~~~~-~GD~~Ar~~LI~~NLRLVv~IAkky~~~G~~l~DLIqEGniGLikAvekFDp~k 106 (239)
T PRK08301 28 YIGGSEALPPPLSKEEEEVLLNKLP-KGDEAVRSILIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEK 106 (239)
T ss_pred EECCCCCCCCCCCHHHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf 7478987999989999999999998-346999999999878999999975768997989999985899999999649888
Q ss_pred CCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCC
Q ss_conf 56899975778999999853202460011023003589999999978878662447888246778886189832110000
Q gi|254780611|r 98 GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177 (302)
Q Consensus 98 G~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~ 177 (302)
|++|||||+|||+++|.+|++++++. +.+
T Consensus 107 G~rFSTYA~~~I~~eI~~~lr~~~~~-r~e-------------------------------------------------- 135 (239)
T PRK08301 107 KIKLATYASRCIENEILMYLRRNNKV-RSE-------------------------------------------------- 135 (239)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHH-HCC--------------------------------------------------
T ss_conf 99716301999999999999970424-224--------------------------------------------------
Q ss_pred CCCCCCCCHHHHCCC-CCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCC--CCCCC
Q ss_conf 001223433552023-234532000001235687056556666666777999999621999999999998278--88889
Q gi|254780611|r 178 CRLAGDESLNALINS-SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVT 254 (302)
Q Consensus 178 ~~~~~~~SLd~~i~~-~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~--~~~~T 254 (302)
+|++.|++. .+++...+.|.+..+.+...+ ..+....+..|..+++.|++||+.||.+|||. ++++|
T Consensus 136 ------vsl~epl~~d~d~~e~~l~D~l~~d~d~~~~----~~e~~~~~~~L~~al~~L~eREr~Ii~lRfGL~~~~~~T 205 (239)
T PRK08301 136 ------VSFDEPLNIDWDGNELLLSDVLGTDNDIIYK----DIEDEVDKKLLLKALKKLNDREKQIMELRFGLAGGEEKT 205 (239)
T ss_pred ------CHHCCCCCCCCCCCHHHHHHCCCCCCCHHHH----HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCC
T ss_conf ------0001536877665622430114898750667----899999999999999648999999999995788998406
Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 89999997789999999999999999999997
Q gi|254780611|r 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286 (302)
Q Consensus 255 l~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~ 286 (302)
++|||+.||||++|||||+++||+|||+.|.+
T Consensus 206 l~EIa~~lgISrerVrQIe~~AL~KLR~~l~k 237 (239)
T PRK08301 206 QKEVADMLGISQSYISRLEKRIIKRLKKEINK 237 (239)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999998978999999999999999999985
No 28
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=100.00 E-value=0 Score=382.92 Aligned_cols=227 Identities=21% Similarity=0.292 Sum_probs=182.8
Q ss_pred HHHHCCHHHHHHHHHHHHHHHHHHHHHHCCC---CCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 9982859999999994307787565555799---9988899999988899898621853456899975778999999853
Q gi|254780611|r 41 YREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117 (302)
Q Consensus 41 ~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~---g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i 117 (302)
|.+ ..++||++||.+|||||++||++|.++ |++++|||||||+|||+|++||||++|++|||||+|||||+|.+++
T Consensus 2 ~~~-~g~~Ar~~Lv~~nl~LV~~iA~r~~~r~~~~v~~~DLiQeG~iGLi~AvekFDp~~G~rFsTYA~~~Ir~aI~~~~ 80 (234)
T PRK06986 2 YTA-QGKMSQDSLVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEASRRYDGEQGASFETYAGQRIRGAMLDEL 80 (234)
T ss_pred CCH-HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 617-6899999999981999999999997338999988999999999999999981886699969999999999999999
Q ss_pred HCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCC--CCCCCHHHHCCCCCC
Q ss_conf 202460011023003589999999978878662447888246778886189832110000001--223433552023234
Q gi|254780611|r 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL--AGDESLNALINSSDK 195 (302)
Q Consensus 118 ~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~--~~~~SLd~~i~~~d~ 195 (302)
++..+ +|.+ +....+++.+....+....+++|+.++||+.+|++.+++..+.... ....|+|.....++
T Consensus 81 r~~~~---~~r~-----~~~~~~~i~~~~~~l~~~~~r~pt~~eia~~l~~s~e~v~~~~~~~~~~~~~sld~~~~~~~- 151 (234)
T PRK06986 81 RSGDW---VPRS-----VRRNAREVADAIRELEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDDLGESGE- 151 (234)
T ss_pred HHCCC---CCHH-----HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC-
T ss_conf 85456---6499-----99999999999999999878799899999895949999999999850577868776776643-
Q ss_pred CCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 53200000123568705655666666677799999962199999999999827888889899999977899999999999
Q gi|254780611|r 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275 (302)
Q Consensus 196 ~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~ 275 (302)
...+....+.+. +.+..+...++..|..+|+.||+||+.||.+||+ +++|++|||+.||||++|||||+++
T Consensus 152 ---~~~~~~~~~~~~----~~~~~~~~~~~~~l~~~l~~L~~rEr~Ii~l~y~--~~~tl~eIa~~lgiS~eRVrQie~~ 222 (234)
T PRK06986 152 ---LLTDEDQSEHED----PLQQLEDEELREALVEAIEKLPEREQLVLSLYYD--EELNLKEIGAVLGVSESRVSQIHSQ 222 (234)
T ss_pred ---CCCCCCCCCCCC----HHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCC--CCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf ---111222457899----9999999999999999998099999999998738--9989999999979789999999999
Q ss_pred HHHHHHHHHHH
Q ss_conf 99999999997
Q gi|254780611|r 276 AFKKVQESIQK 286 (302)
Q Consensus 276 AL~kLR~~l~~ 286 (302)
||.|||+.|.+
T Consensus 223 AL~kLR~~L~e 233 (234)
T PRK06986 223 AIKRLRARLGE 233 (234)
T ss_pred HHHHHHHHHHC
T ss_conf 99999998753
No 29
>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=0 Score=384.40 Aligned_cols=231 Identities=23% Similarity=0.358 Sum_probs=202.8
Q ss_pred HHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 99999982859999999994307787565555799998889999998889989862185345689997577899999985
Q gi|254780611|r 37 LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116 (302)
Q Consensus 37 l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~ 116 (302)
|+...+ +||++|+|+||+.|++||.+|.+||.|||-++|||+|.|||||+|||+|||-+-.+||||||+|.|-|+|+||
T Consensus 1 Li~~a~-~GDk~A~dkLi~~N~~LV~siv~rF~nRGYe~eDlFQIGciGLvKAidkFD~~y~VKFSTYAVPmI~GEIkRF 79 (231)
T TIGR02885 1 LIKLAK-EGDKEARDKLIEENLRLVSSIVKRFLNRGYEYEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRF 79 (231)
T ss_pred CCHHHH-HHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHH
T ss_conf 904567-4048999999872334689999985206887000022211556665542176777015521222022122231
Q ss_pred HHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCC
Q ss_conf 32024600110230035899999999788786624478882467788861898321100000012234335520232345
Q gi|254780611|r 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196 (302)
Q Consensus 117 i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~ 196 (302)
|||++ +|||.++. |.+-. ++...-+.+....+|.||++|+|+.+|+++|+|...........||...++.+|++
T Consensus 80 LRDDG-~ikVSRSl--K~la~---k~~~~kE~L~~~l~R~PTi~Elae~lg~~~EEiv~A~Es~~~~~sly~tvh~dDGd 153 (231)
T TIGR02885 80 LRDDG-IIKVSRSL--KELAR---KIRYEKEELTKKLGREPTINELAEALGVSPEEIVMALESARSLQSLYDTVHEDDGD 153 (231)
T ss_pred HCCCC-CEEEEHHH--HHHHH---HHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHCCEEECCCCC
T ss_conf 02688-55751527--89999---99877999999838998889998875878878664420257610110011417946
Q ss_pred CCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 32000001235687056556666666777999999621999999999998278888898999999778999999999999
Q gi|254780611|r 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276 (302)
Q Consensus 197 ~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~A 276 (302)
...+.|-+.+..... ..+.+ +-.|+++|+.|++|||.||.+||+-| +|+-|||+.||||+-.||+||+++
T Consensus 154 Pi~LlD~i~d~~~~~-~~~~~-------ki~Lke~i~~Ld~rer~ii~LRYFKD--kTQ~eVA~~LGISQVQVSRlEkk~ 223 (231)
T TIGR02885 154 PILLLDQIADKGSED-SDLLE-------KIALKEAISKLDERERQIIMLRYFKD--KTQTEVAKMLGISQVQVSRLEKKV 223 (231)
T ss_pred HHHHHHHHCCCCCCH-HHHHH-------HHHHHHHHHHCCCCCCEEEEEECCCC--CHHHHHHHHCCCCCCHHHHHHHHH
T ss_conf 446766521257713-68999-------89999998612522678977410140--017999977185700122789999
Q ss_pred HHHHHHHH
Q ss_conf 99999999
Q gi|254780611|r 277 FKKVQESI 284 (302)
Q Consensus 277 L~kLR~~l 284 (302)
|++||+.|
T Consensus 224 L~~~k~~l 231 (231)
T TIGR02885 224 LKKMKEKL 231 (231)
T ss_pred HHHHHHHC
T ss_conf 99987409
No 30
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=100.00 E-value=0 Score=350.50 Aligned_cols=241 Identities=24% Similarity=0.378 Sum_probs=204.8
Q ss_pred CCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHHHHHHHCCCCCCCCHHHH
Q ss_conf 999998999999999998285999999999430778756555579999-8889999998889989862185345689997
Q gi|254780611|r 26 IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATY 104 (302)
Q Consensus 26 ~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~-~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTY 104 (302)
-|.++.++...+...++ +||.+++ +||+.|++||.+||++|.+++- ++|||+|.|+|||++|+++|||++|.+|+||
T Consensus 3 ~~~~~~~e~~~~~~~~~-~g~~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~ty 80 (247)
T COG1191 3 PQPLSKEEEEKLLEYYA-EGDEEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTY 80 (247)
T ss_pred CCCCCHHHHHHHHHHHH-HCCHHHH-HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHH
T ss_conf 76224689999999998-4589999-999997899999999998059985438999789999999997493128614888
Q ss_pred HHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCC--C
Q ss_conf 57789999998532024600110230035899999999788786624478882467788861898321100000012--2
Q gi|254780611|r 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--G 182 (302)
Q Consensus 105 A~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~--~ 182 (302)
|+++|+|+|.+|+|++. +|++| |.+....+++....+.+..+++++|++.|||+.||++.+++........ .
T Consensus 81 A~~~I~Gei~d~LR~~~-~v~vp-----R~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~ 154 (247)
T COG1191 81 AVRRIRGEILDYLRKND-SVKVP-----RSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQ 154 (247)
T ss_pred HHHHHHHHHHHHHHHCC-CCCCC-----HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCC
T ss_conf 99999999999998478-74676-----8998887788999999999847998689999896989999999998730124
Q ss_pred CCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHH
Q ss_conf 34335520232345320000012356870565566666667779999996219999999999982788888989999997
Q gi|254780611|r 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262 (302)
Q Consensus 183 ~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~l 262 (302)
..|+|..+...+++. ..+....+. ...+.......|.+++..|++||+.|+.+||..+ +|++|||+.|
T Consensus 155 ~~sld~~~~~~~d~~-------~~~~~~~~~---~~~~~~~~~~~l~~~i~~L~EREk~Vl~l~y~ee--lt~kEI~~~L 222 (247)
T COG1191 155 LLSLDEDVLKDDDDD-------VDDQIENPD---DGVEKEELLEILKEAIEPLPEREKLVLVLRYKEE--LTQKEIAEVL 222 (247)
T ss_pred CCCCCCCCCCCCCCC-------HHHCCCCCH---HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHC--CCHHHHHHHH
T ss_conf 541100001356520-------220235603---5778899999999998766899999999999701--5799999994
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 789999999999999999999997
Q gi|254780611|r 263 EVSRERVRQIEARAFKKVQESIQK 286 (302)
Q Consensus 263 giS~eRVrQI~~~AL~kLR~~l~~ 286 (302)
|||.+|||||+++||.|||+.|..
T Consensus 223 gISes~VSql~kkai~kLr~~l~~ 246 (247)
T COG1191 223 GISESRVSRLHKKAIKKLRKELNK 246 (247)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHCC
T ss_conf 914989999999999999998604
No 31
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=100.00 E-value=0 Score=346.41 Aligned_cols=216 Identities=16% Similarity=0.232 Sum_probs=176.3
Q ss_pred HCCHHHHHHHHHHHHHHHHHHHHHHCCCC---CCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf 28599999999943077875655557999---988899999988899898621853456899975778999999853202
Q gi|254780611|r 44 HGDLSAAHRLVTSHLRLVVKIAMGYRGYG---LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120 (302)
Q Consensus 44 ~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g---~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~ 120 (302)
+-...++++||++||+||.+||++|.+++ ++++||+|+|+||||+|++||||++| +|+|||+|||||+|.+++|+.
T Consensus 9 ~~~~~~k~~lV~~~L~LV~~ia~r~~~~~~~~vd~dDLiq~G~iGLi~Ai~rFD~~~g-~F~tYA~~rIrGaI~d~lR~~ 87 (229)
T PRK12427 9 TLTAAEEGKYLNAYLPLVKRIVRQLSFQADSVIGKEDMQQIALMGLLEALRRYGHPDG-QFAAYAVHRIRGSILDQLREH 87 (229)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCC-CHHHHHHHHHHHHHHHHHHHH
T ss_conf 6899999999999599999999999742877798888999999999999984499898-859999999999999999872
Q ss_pred CCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCC--CCCCCCHHHHCCCCCCCCC
Q ss_conf 46001102300358999999997887866244788824677888618983211000000--1223433552023234532
Q gi|254780611|r 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR--LAGDESLNALINSSDKNSS 198 (302)
Q Consensus 121 ~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~--~~~~~SLd~~i~~~d~~~~ 198 (302)
.+. | |.+....+++.++...+....+++|+.+|||+.||++.+++.++... .....|||.++..+..++
T Consensus 88 ~~~---p-----R~~r~~~~ki~~a~~~l~~~lgr~Pt~~EiA~~l~is~~~v~~~~~~~~~~~~~sld~~~~~e~~~~- 158 (229)
T PRK12427 88 DWR---P-----RRLRQKTHKTNEAIRQIAKRLGHEPNFEEISAELNLTADEYQEYLLLENAGAMESLDEILALEAHND- 158 (229)
T ss_pred CCC---C-----HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC-
T ss_conf 137---5-----9999999999999999999858899999999891999999999999873668757233445788765-
Q ss_pred CHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 00000123568705655666666677799999962199999999999827888889899999977899999999999999
Q gi|254780611|r 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278 (302)
Q Consensus 199 ~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~ 278 (302)
.+ + ....++ .......|..+|+.||+|||.||.+||+. ++||+|||+.||||++||||||++||.
T Consensus 159 ----~~-~-~~~~~e-------~~~~~~~L~~al~~L~erEr~Vi~l~y~e--~ltlkEIa~~LgvS~~RVsQi~~kal~ 223 (229)
T PRK12427 159 ----IL-Q-SRDLEE-------NIIIEDNLKQAISQLDEREQMILHLYYQQ--ELSMKEIAQVLDLTEARICQLNKKLVQ 223 (229)
T ss_pred ----CC-C-CCCHHH-------HHHHHHHHHHHHHHCCHHHHHHHHHHCCC--CCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf ----45-6-766467-------89999999999971999999999998058--998999999979889999999999999
Q ss_pred HHHHHH
Q ss_conf 999999
Q gi|254780611|r 279 KVQESI 284 (302)
Q Consensus 279 kLR~~l 284 (302)
|||..+
T Consensus 224 kLR~~f 229 (229)
T PRK12427 224 KIKSFF 229 (229)
T ss_pred HHHHHC
T ss_conf 988439
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=0 Score=347.98 Aligned_cols=220 Identities=23% Similarity=0.358 Sum_probs=191.8
Q ss_pred HHHHHHHHHHHHHHHHCC---CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCC
Q ss_conf 999430778756555579---99988899999988899898621853456899975778999999853202460011023
Q gi|254780611|r 53 LVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129 (302)
Q Consensus 53 Li~~nlrlV~~iA~~y~~---~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~ 129 (302)
||.+|++||..+|.+-.. ..+++|||||.|++|||.|++||||++|++|.|||..||||+|.+++|..-| +|
T Consensus 1 l~~~Y~pLVk~~a~rl~~~~P~~v~~~DL~q~G~~GL~dA~~ryd~~~g~~F~TyA~~RIRGAmlDELR~~DW---~P-- 75 (227)
T TIGR02479 1 LIKKYLPLVKRIAGRLVVQLPSSVELDDLIQAGMIGLLDAIERYDPSKGVKFETYAVQRIRGAMLDELRKLDW---VP-- 75 (227)
T ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHCCCCHHHHHHHHHHCCC---CC--
T ss_conf 9001268999988664310488234875898889999999983188888944100011130205788753066---78--
Q ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCC--CCCCHHHHCCCCCCC--CCCHHCCCC
Q ss_conf 0035899999999788786624478882467788861898321100000012--234335520232345--320000012
Q gi|254780611|r 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKN--SSQWQDWLV 205 (302)
Q Consensus 130 ~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~--~~~SLd~~i~~~d~~--~~~~~d~l~ 205 (302)
|.+..+.+++..++..+..++++.|+.+|||+.||++.++|.++...+. ..+|||+...+++++ ...+.|.+.
T Consensus 76 ---Rs~R~~~~~~~~a~~~Le~~LgR~P~~~EiA~~Lg~~~~e~~~~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~~~~ 152 (227)
T TIGR02479 76 ---RSLRQKARKLEEAIEELEARLGREPTEEEIAEELGMDLKEVRQALNEINAESLVSLDELLESGDDGGAEGSLIDLIE 152 (227)
T ss_pred ---HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHEEC
T ss_conf ---36899986899999999998698988889999839999899999999889987648999841463223453231001
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 35687056556666666777999999621999999999998278888898999999778999999999999999999999
Q gi|254780611|r 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285 (302)
Q Consensus 206 ~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~ 285 (302)
+++..+|... .+...++..|..+|+.||+|||.||.+||-.+ +||+|||+.||||.+||||||++|+.|||..|.
T Consensus 153 ~~~~~~P~~~---~~~~~L~~~l~~ai~~L~eRE~LVl~LYY~eE--LnLKEIg~VL~lsESRvSQiHs~A~~~Lr~~L~ 227 (227)
T TIGR02479 153 DDKSEDPEEE---LEREELREALAEAIEKLSEREKLVLSLYYYEE--LNLKEIGEVLGLSESRVSQIHSQALKKLRAKLS 227 (227)
T ss_pred CCCCCCHHHH---HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCC
T ss_conf 4357681358---99999999999997406855788888864127--668899988378705799999999999987539
No 33
>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=100.00 E-value=0 Score=329.61 Aligned_cols=243 Identities=23% Similarity=0.327 Sum_probs=216.6
Q ss_pred CCCHHHHHHHHHHHHHH-CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH
Q ss_conf 99989999999999982-85999999999430778756555579999888999999888998986218534568999757
Q gi|254780611|r 28 MLEKQEEYVLAKRYREH-GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106 (302)
Q Consensus 28 ~Lt~eee~~l~~~~~~~-gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~ 106 (302)
-+|+|+-..++.-+|++ .+.+|.++||.+|-.||.|||+||+..+--.+||||.||+|||-||.||||+-|.+|.+||+
T Consensus 9 n~~~e~v~~wI~e~Q~nP~n~eaQeklV~hY~~Lv~SiAykYSKg~~~HEDlvQVGM~GLlgAirRyD~s~g~~FE~Fai 88 (256)
T TIGR02941 9 NLTKEDVIQWIKEFQKNPKNEEAQEKLVKHYQDLVESIAYKYSKGSAIHEDLVQVGMVGLLGAIRRYDYSYGKAFEAFAI 88 (256)
T ss_pred CCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf 57887899999996369983257899999998999988754048788333045676899999986511000456566236
Q ss_pred HHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCC--CCCCC
Q ss_conf 7899999985320246001102300358999999997887866244788824677888618983211000000--12234
Q gi|254780611|r 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR--LAGDE 184 (302)
Q Consensus 107 ~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~--~~~~~ 184 (302)
|.|-|+|.+||||+.|.|+||+ ++..---|+++.++.++.++.+.|++.|||+.||+|+++|.+.+.. .....
T Consensus 89 PTiiGEIKrylRDKTWsvHVPR-----RIKelGpkIkk~~dELT~~lqrSP~i~EIA~~lg~SEEEVLE~Me~g~sY~al 163 (256)
T TIGR02941 89 PTIIGEIKRYLRDKTWSVHVPR-----RIKELGPKIKKAVDELTDELQRSPKIAEIADRLGVSEEEVLEIMEMGQSYKAL 163 (256)
T ss_pred CCHHHHHHHHHCCCCCCCCCCC-----CHHCCCCCCHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHCCCCCCEE
T ss_conf 6100101121115643001574-----11003772014556644442148706546412177488898776147774333
Q ss_pred CHHHHCCCC-CCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHC
Q ss_conf 335520232-3453200000123568705655666666677799999962199999999999827888889899999977
Q gi|254780611|r 185 SLNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263 (302)
Q Consensus 185 SLd~~i~~~-d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lg 263 (302)
|+|..+..+ |+.+....|.+...+++.+.+ | .|..|...|..|++||+.||..-|..+ ++++|+|+.||
T Consensus 164 SvD~~iEadsDGStVa~ld~vG~~edgYd~t-----E---~Rm~LekIlpiLserE~~ii~c~f~en--lsQKeTGErlG 233 (256)
T TIGR02941 164 SVDDKIEADSDGSTVALLDLVGEVEDGYDQT-----E---KRMVLEKILPILSEREKEIIECTFIEN--LSQKETGERLG 233 (256)
T ss_pred ECCCCCCCCCCCCCCHHHHHHCCCCCCHHHH-----H---HHHHHHHHHHHCCHHHHHHHHHHHHCC--CCCCHHHHHCC
T ss_conf 2253000368885111111216766654578-----8---888888741000544567666553147--87300232224
Q ss_pred CCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 8999999999999999999999
Q gi|254780611|r 264 VSRERVRQIEARAFKKVQESIQ 285 (302)
Q Consensus 264 iS~eRVrQI~~~AL~kLR~~l~ 285 (302)
||++.||+|+.+||+|||++..
T Consensus 234 iSQMHVSRl~R~ai~KL~eAa~ 255 (256)
T TIGR02941 234 ISQMHVSRLQRRAIKKLKEAAF 255 (256)
T ss_pred HHHHHHHHHHHHHHHHHHHHHC
T ss_conf 0355677888999999999722
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=100.00 E-value=8.8e-44 Score=312.14 Aligned_cols=212 Identities=29% Similarity=0.411 Sum_probs=183.9
Q ss_pred CCCHHHHHHHHHHHCCC-CCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHH
Q ss_conf 87405999999840799-99989999999999982859999999994307787565555799998889999998889989
Q gi|254780611|r 11 NGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89 (302)
Q Consensus 11 ~~~~~~~~yl~~i~~~~-~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~A 89 (302)
.+---|.-|+..-+.+| ||+++||..++.+++ .||..||+.||++|||||.+|.|||.+.|-++||||+.|+||||+|
T Consensus 11 ~~~lfL~gY~~n~~~FP~PLs~~eE~~YL~~l~-~GD~~Ar~~LiErNLRLVAHiVKKf~~~G~~~dDLISIGTiGLIKA 89 (228)
T TIGR02846 11 KSLLFLVGYVTNNASFPQPLSEEEEKKYLERLK-EGDEEARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKA 89 (228)
T ss_pred HHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHH-HHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCHHCCCCHHEECC
T ss_conf 999998777506888978898668999999987-3159999997763330002156511788741000010022010001
Q ss_pred HHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCC
Q ss_conf 86218534568999757789999998532024600110230035899999999788786624478882467788861898
Q gi|254780611|r 90 VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169 (302)
Q Consensus 90 i~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis 169 (302)
|+.|+|+||.+..|||.-+|-.+|.-++|...
T Consensus 90 idsf~~~KGt~LATYAArCiENEILM~lR~~K------------------------------------------------ 121 (228)
T TIGR02846 90 IDSFDPEKGTRLATYAARCIENEILMHLRALK------------------------------------------------ 121 (228)
T ss_pred EECCCCCCCCHHHHHHHHHHHHHHHHHHHHCC------------------------------------------------
T ss_conf 10224787731566786653478999997436------------------------------------------------
Q ss_pred CCCCCCCCCCCCCCCCHHHHCCCC-CCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH-HCCCHHHHHHHHHHH
Q ss_conf 321100000012234335520232-345320000012356870565566666667779999996-219999999999982
Q gi|254780611|r 170 ESEVISMNCRLAGDESLNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARR 247 (302)
Q Consensus 170 ~~~v~~l~~~~~~~~SLd~~i~~~-d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l-~~L~~rEr~II~~ry 247 (302)
.....+||.+|++.+ +++..++.|.+..+.+...+.+.... ....|..-+ +.|.+||+.||..||
T Consensus 122 ---------K~k~eV~L~DPIG~DKEGNEIsL~DiL~~~~d~v~e~v~~~~----~~~~l~~~~~~~L~~rE~~vi~~Ry 188 (228)
T TIGR02846 122 ---------KTKGEVSLQDPIGVDKEGNEISLIDILGSDEDSVIEQVEKKL----EIKKLYKKLNSVLKGREREVIEMRY 188 (228)
T ss_pred ---------CCCCCEEECCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf ---------747833210788867676423000001688731688888644----5999999999874088899998743
Q ss_pred CCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 788--8889899999977899999999999999999999
Q gi|254780611|r 248 LQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284 (302)
Q Consensus 248 ~~~--~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l 284 (302)
|.. ..+||+|||..|||||+.||+||++||.||-+.+
T Consensus 189 GL~~~~~~tQREIA~~LgISRSYVSRIEK~Al~Kl~~~~ 227 (228)
T TIGR02846 189 GLKDGREKTQREIAKILGISRSYVSRIEKKALKKLYKEL 227 (228)
T ss_pred CCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHC
T ss_conf 668889541789987708650045488899999998633
No 35
>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=100.00 E-value=1e-40 Score=291.63 Aligned_cols=252 Identities=23% Similarity=0.329 Sum_probs=219.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q ss_conf 55745587405999999840799999899999999999828599999999943077875655557999988899999988
Q gi|254780611|r 5 NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84 (302)
Q Consensus 5 ~~~~~~~~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~i 84 (302)
++.+|+.+.. +.|.|+.++..+|+.+.+ .|+..||+.||.+|||||.++..+|.|||...|||+|.|||
T Consensus 2 kvei~Gv~t~----------klPvl~~~~~~~l~~~~~-~G~~~ar~~l~~~nlrlvlsviqrf~nrGe~~ddlfqvGCi 70 (254)
T TIGR02850 2 KVEICGVNTS----------KLPVLKNEEMRELFVRMK-SGDKSAREKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 70 (254)
T ss_pred CEEECCCCCC----------CCCCCCHHHHHHHHHHHH-CCHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 2241265500----------055435478999999985-12078999987522688888888751145403456763257
Q ss_pred HHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHH
Q ss_conf 89989862185345689997577899999985320246001102300358999999997887866244788824677888
Q gi|254780611|r 85 GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164 (302)
Q Consensus 85 GLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~ 164 (302)
||++|+++||-+..++|||||+|.|-|+|.+|++|+. .||+... +..-..++-.-.+.+.....+.|++.+||+
T Consensus 71 Gl~k~idnfdl~~nv~fstyavPmiiGeirrylrdn~-~irvsrs-----lrd~ay~alqvr~~l~~~~~~eP~~~~ia~ 144 (254)
T TIGR02850 71 GLIKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRS-----LRDIAYKALQVRDKLVSKNSKEPTVSEIAK 144 (254)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCC-CEEEHHH-----HHHHHHHHHHHHHHHHHHHCCCCCHHHHHH
T ss_conf 7777655310111320011346678898899852487-4130355-----889999999999999853125875889998
Q ss_pred HCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH
Q ss_conf 61898321100000012234335520232345320000012356870565566666667779999996219999999999
Q gi|254780611|r 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244 (302)
Q Consensus 165 ~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~ 244 (302)
.|+++.+++.-.+..++.++||..|+..++++.....|.+.++.......+. ...|.+++..|++||+.|+.
T Consensus 145 ~l~~~~~~~v~aldaiq~PvslfeP~y~d~Gd~i~vmdq~~d~~~~d~~W~~--------~~~l~~~~~~l~~re~~il~ 216 (254)
T TIGR02850 145 ELDVPKEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDEKNKDEQWLE--------EIALKEALKRLNEREKLILK 216 (254)
T ss_pred HHCCCHHHHHHHHHHHCCCHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHH
T ss_conf 7347557877656642164234310013799748874010020345699998--------88999999987667887777
Q ss_pred HHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 982788888989999997789999999999999999999
Q gi|254780611|r 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302)
Q Consensus 245 ~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302)
.||+.+ .|+-|+|++.|+|+..|+++++.|+.+|++.
T Consensus 217 ~rff~G--~tqmeva~eiGisqaqvsrlek~a~~~~~k~ 253 (254)
T TIGR02850 217 LRFFEG--KTQMEVAEEIGISQAQVSRLEKAALKHMRKY 253 (254)
T ss_pred HHHHCC--CHHHHHHHHHCCHHHHHHHHHHHHHHHHHHC
T ss_conf 553146--3133456540301688888889999997512
No 36
>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=99.97 E-value=8.5e-31 Score=225.36 Aligned_cols=198 Identities=31% Similarity=0.469 Sum_probs=165.0
Q ss_pred CCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH
Q ss_conf 99998999999999998285999999999430778756555579999888999999888998986218534568999757
Q gi|254780611|r 27 PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106 (302)
Q Consensus 27 ~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~ 106 (302)
|+||.|||..|..++. .||..++..||+.|||||+.||++|.|.|+.++||++.|.|||++|+..|||++-.++.|||.
T Consensus 32 PPl~~eee~~l~~~l~-~Gd~~~~~~liernlrlvvyia~kf~ntG~~~edl~s~GtiGlikav~tf~P~k~iklatyas 110 (234)
T TIGR02835 32 PPLTKEEEEALLEKLE-KGDEAAKSILIERNLRLVVYIARKFENTGINIEDLVSIGTIGLIKAVNTFNPEKKIKLATYAS 110 (234)
T ss_pred CCCCHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf 9887157999999987-547999999886222431121012202562110222221478887765227301103556776
Q ss_pred HHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCH
Q ss_conf 78999999853202460011023003589999999978878662447888246778886189832110000001223433
Q gi|254780611|r 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186 (302)
Q Consensus 107 ~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SL 186 (302)
.+|..+|.-|++.+.+. ...+|+
T Consensus 111 ~Cieneilmylrr~~~~---------------------------------------------------------~~evsf 133 (234)
T TIGR02835 111 RCIENEILMYLRRNNKI---------------------------------------------------------RSEVSF 133 (234)
T ss_pred HHHHHHHHHHHHHHCCC---------------------------------------------------------CCEEEE
T ss_conf 76788899988751121---------------------------------------------------------000000
Q ss_pred HHHCCC-CCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCC--CCCCHHHHHHHHC
Q ss_conf 552023-2345320000012356870565566666667779999996219999999999982788--8889899999977
Q gi|254780611|r 187 NALINS-SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFE 263 (302)
Q Consensus 187 d~~i~~-~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~--~~~Tl~EIa~~lg 263 (302)
+.|... .|++..-+.|.+..+.+. +....+....+..|..++..|+.||+.|+.+|||.. ...|++++|+.+|
T Consensus 134 ~ePln~dW~Gnelllsd~lGt~~~~----~~~~~e~~v~~~ll~~al~~l~~re~~i~~lrfGl~~~~e~tqk~vad~lG 209 (234)
T TIGR02835 134 DEPLNVDWDGNELLLSDVLGTDSDI----VYKVLEEEVDRELLKKALKKLNDREKKIMELRFGLAGGTEKTQKEVADLLG 209 (234)
T ss_pred CCCCCCCCCCCHHHHHHHHCCCHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHH
T ss_conf 2554656676211434441474268----899999999999999999987676787667630436772146788898862
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 89999999999999999999997
Q gi|254780611|r 264 VSRERVRQIEARAFKKVQESIQK 286 (302)
Q Consensus 264 iS~eRVrQI~~~AL~kLR~~l~~ 286 (302)
+|+..|++++++.+++|++.+.+
T Consensus 210 isqsyisrlek~i~krl~ke~~~ 232 (234)
T TIGR02835 210 ISQSYISRLEKRILKRLKKEINR 232 (234)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 46899999999999999999873
No 37
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=99.97 E-value=3.5e-28 Score=207.92 Aligned_cols=201 Identities=19% Similarity=0.265 Sum_probs=152.2
Q ss_pred CCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHH
Q ss_conf 99999899999999999828599999999943077875655557999988899999988899898621853456899975
Q gi|254780611|r 26 IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105 (302)
Q Consensus 26 ~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA 105 (302)
++ |+..++.+|+.+++ .||.+|.+.|+..|.++|.++|++|.+.+.+.+||+|||+|++++|+.+|||++|.+|+||+
T Consensus 4 ~~-~~~~~d~~Li~~~~-~GD~~Af~~L~~~y~~~v~~~~~~~~~~~~d~EDlvQe~~i~l~kai~~f~~~k~~~F~t~~ 81 (209)
T PRK08295 4 YN-LRDKEDEELVELAQ-SGDTEALEYLIEKYKNFVRAKARSYFLIGAEREDIVQEGMIGLYKAIRDYDEDKLSSFKSFA 81 (209)
T ss_pred CC-CCHHHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHH
T ss_conf 89-87201999999999-16799999999998999999999982898779999999999999999856865487289999
Q ss_pred HHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf 77899999985320246001102300358999999997887866244788824677888618983211000000122343
Q gi|254780611|r 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185 (302)
Q Consensus 106 ~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~S 185 (302)
.+||+..|.++++...+--+.| .....|
T Consensus 82 ~~~i~~~i~~~ir~~~r~k~~~----------------------------------------------------~~~~~s 109 (209)
T PRK08295 82 ELCITRQIITAIKTANRQKHIP----------------------------------------------------LNSYVS 109 (209)
T ss_pred HHHHHHHHHHHHHHHHCCCCCC----------------------------------------------------CCHHHC
T ss_conf 9999999999999983304545----------------------------------------------------202414
Q ss_pred HHHHCCCCCCCCCCHHCCCCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCC
Q ss_conf 35520232345320000012356-87056556666666777999999621999999999998278888898999999778
Q gi|254780611|r 186 LNALINSSDKNSSQWQDWLVYDH-DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264 (302)
Q Consensus 186 Ld~~i~~~d~~~~~~~d~l~~~~-~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgi 264 (302)
||.++...+ ++....+.+.+.. ++|++.+...+.. ...+..+...|+++++.|+.++ + +++|++|||+.||+
T Consensus 110 ld~~~~~~~-~~~~~~~~~~~~~~~~pe~~~~~~e~~---~~i~~~i~~~l~~~e~~V~~~~-~--eg~s~~EIA~~l~i 182 (209)
T PRK08295 110 LDKPIYDEE-SDRTLLDVISGAKVTDPEELIISKEEL---EIIEEKILELLSDLEKEVLELY-L--DGKSYQEIAEELNR 182 (209)
T ss_pred CCCCCCCCC-CHHHHHHHCCCCCCCCHHHHHHHHHHH---HHHHHHHHHCCCHHHHHHHHHH-H--CCCCHHHHHHHHCC
T ss_conf 566645554-203565430467789999999999999---9999999846918999999999-8--69999999999892
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999999999974
Q gi|254780611|r 265 SRERVRQIEARAFKKVQESIQKQ 287 (302)
Q Consensus 265 S~eRVrQI~~~AL~kLR~~l~~~ 287 (302)
|...|+....+|.+|||+.|+++
T Consensus 183 s~~tV~~~l~RarkkLr~~L~~~ 205 (209)
T PRK08295 183 HVKSIDNALQRVKRKLEKYLEIR 205 (209)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 99999999999999999998744
No 38
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=99.93 E-value=2.6e-24 Score=182.01 Aligned_cols=151 Identities=21% Similarity=0.284 Sum_probs=118.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHC
Q ss_conf 99999999430778756555579999888999999888998986218534568999757789999998532024600110
Q gi|254780611|r 48 SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127 (302)
Q Consensus 48 ~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP 127 (302)
.+.+.+|+.|-++|.+++++|.-+ -++||++|+|+|||++|+++|||+|| +|||||+.+||+.+.+.+++..+.-
T Consensus 4 ~sFee~~~~Y~pmI~~~lkkl~i~-~d~dd~~Q~g~i~Lw~a~~~yd~~kg-~fstya~~~ir~~~ld~lrKe~~~~--- 78 (154)
T PRK06759 4 ATFTEAVVLYEGLIVNQIKKLGIY-QDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYILERLKKEFAVQ--- 78 (154)
T ss_pred CCHHHHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHHHHHCCCCCC-CHHHHHHHHHHHHHHHHHHHCCCCC---
T ss_conf 559999999878999999993673-33899999999999999997694347-6699999999999999998631433---
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCC
Q ss_conf 23003589999999978878662447888246778886189832110000001223433552023234532000001235
Q gi|254780611|r 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207 (302)
Q Consensus 128 ~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~ 207 (302)
... .. .+.. + |.+
T Consensus 79 -----------------------e~~------------------------------~~----~~~~-e------d~~--- 91 (154)
T PRK06759 79 -----------------------EKC------------------------------VC----VGEY-E------DHF--- 91 (154)
T ss_pred -----------------------CCC------------------------------CC----CCCC-H------HHH---
T ss_conf -----------------------433------------------------------35----5652-2------555---
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 68705655666666677799999962199999999999827888889899999977899999999999999999999
Q gi|254780611|r 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284 (302)
Q Consensus 208 ~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l 284 (302)
...+....+..+++.|++||+.||.++|+.| +|.+|||+.+|||..+|+++.++||.|||..+
T Consensus 92 ------------~~~d~~~~l~~~l~~L~~re~~ii~~~~~~g--~t~~EIA~~~gis~~~Vk~~~r~Al~KLR~~~ 154 (154)
T PRK06759 92 ------------HFEDVEMKVKDFMSVLDEKEKYIIFERFFVG--KTMGEIALETEMTYYQVRWIYRQALEKMRNSV 154 (154)
T ss_pred ------------HHCHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHCC
T ss_conf ------------1011889999999849999999999999969--98999999989899999999999999987339
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=99.92 E-value=5.1e-24 Score=180.06 Aligned_cols=162 Identities=24% Similarity=0.320 Sum_probs=129.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHC
Q ss_conf 99999999430778756555579999888999999888998986218534568999757789999998532024600110
Q gi|254780611|r 48 SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127 (302)
Q Consensus 48 ~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP 127 (302)
+|.+.|+..|.++|.++|++|.+...+.+||+|+|+++|++++++|||. |..|.||+++|+++.+.++++++.+..+.+
T Consensus 1 ~a~~~l~~~~~~~~~~~a~~~~~~~~~aeDl~Qe~~~~~~~~~~~~~~~-~~~f~~wl~~~~~n~~~d~~R~~~~~~~~~ 79 (162)
T TIGR02937 1 EAFEELVERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE-GGSFKAWLFRIARNLILDYLRRKRRRVRRL 79 (162)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9788999999999999999971787579999999999999878624878-765389999999999999999866442001
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCC
Q ss_conf 23003589999999978878662447888246778886189832110000001223433552023234532000001235
Q gi|254780611|r 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207 (302)
Q Consensus 128 ~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~ 207 (302)
.. ... +. ...... +
T Consensus 80 ~~---------------~~~-------------------------------------~~------------~~~~~~-~- 93 (162)
T TIGR02937 80 RV---------------ELD-------------------------------------ED------------DELEEL-E- 93 (162)
T ss_pred HH---------------HHC-------------------------------------CH------------HHHHHH-C-
T ss_conf 45---------------412-------------------------------------21------------344321-3-
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 68705655666666677799999962199999999999827888889899999977899999999999999999999
Q gi|254780611|r 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284 (302)
Q Consensus 208 ~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l 284 (302)
.+. +.+ .+ ......|..+|..||+++|.||.++|+.+ +|++|||+.||||..+|++...+|++|||+.+
T Consensus 94 ~~~----~~~-~~-~~~~~~l~~al~~Lp~~~r~~~~l~~~~~--~s~~eIA~~lg~s~~~v~~~~~ra~~~L~~~l 162 (162)
T TIGR02937 94 DPS----PEE-LE-EEEREALREALEKLPEREREVLVLRYLEG--LSYKEIAEILGISEGTVKSRLKRARKKLRELL 162 (162)
T ss_pred CCC----HHH-HH-HHHHHHHHHHHHHCCHHHHHHHHHHHHHC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHC
T ss_conf 578----778-99-99999999998747998999999999718--99889999868999999999999999998529
No 40
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=1.5e-17 Score=136.87 Aligned_cols=193 Identities=19% Similarity=0.246 Sum_probs=139.3
Q ss_pred CCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH
Q ss_conf 99998999999999998285999999999430778756555579999888999999888998986218534568999757
Q gi|254780611|r 27 PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106 (302)
Q Consensus 27 ~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~ 106 (302)
+.++..++.+|+.+++ .||.+|-..|+..|.+.|..+|.++.+...+-+|++|+-.+-+.+...+|++.. +|.||-+
T Consensus 10 ~~~~~~~D~eLi~~~~-~GD~~Af~~L~~ry~~~ly~~a~~~~~~~~dAEDlvQevFlk~~~~l~~f~~~~--~f~tWL~ 86 (231)
T PRK11922 10 TPLSAADDAELVARVL-AGDEAAFEQLMRRHNRRLYRLARAILRDDAEAEDVVQEAYLRAFRALARFRGDA--SLSTWLS 86 (231)
T ss_pred CCCCCCCHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCC--CHHHHHH
T ss_conf 9999975999999999-565999999999999999999999929999999999999999998753057756--5999999
Q ss_pred HHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCH
Q ss_conf 78999999853202460011023003589999999978878662447888246778886189832110000001223433
Q gi|254780611|r 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186 (302)
Q Consensus 107 ~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SL 186 (302)
--.+..+.+++++..+ ..... ... ....
T Consensus 87 ~Ia~N~~ld~lRk~~~----------------------~~~~~-~~~-----------------------------~~~~ 114 (231)
T PRK11922 87 RIVLNEALGRLRRRRR----------------------DVIEL-RLA-----------------------------TESE 114 (231)
T ss_pred HHHHHHHHHHHHHHHC----------------------CCCCC-CCC-----------------------------CCCC
T ss_conf 9999999999998741----------------------22311-000-----------------------------1233
Q ss_pred HHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCH
Q ss_conf 55202323453200000123568705655666666677799999962199999999999827888889899999977899
Q gi|254780611|r 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266 (302)
Q Consensus 187 d~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~ 266 (302)
++. .......+...++++ .....+....|..+|+.||+++|.|+.++|+.+ +|.+|||+.||+|.
T Consensus 115 -------~~~--~~~~~~~~~~~~pe~----~~~~~E~~~~l~~al~~Lp~~~R~v~~L~~~eg--lS~~EIA~~Lgis~ 179 (231)
T PRK11922 115 -------EGE--EIEFPDADPAEDPED----AAARREIRALLERAIDALPDAFRAVFVLRVVEE--LSVEETAQALGLPE 179 (231)
T ss_pred -------CCH--HHCCCCCCCCCCHHH----HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCH
T ss_conf -------210--100233567899999----999999999999999809999999999999939--99999999989399
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 99999999999999999997401
Q gi|254780611|r 267 ERVRQIEARAFKKVQESIQKQVE 289 (302)
Q Consensus 267 eRVrQI~~~AL~kLR~~l~~~~~ 289 (302)
..|+..-.+|.++||+.|.++..
T Consensus 180 ~TVKsrL~RArk~LRe~La~~~~ 202 (231)
T PRK11922 180 ETVKTRLHRARRLLRESLAREIG 202 (231)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999999999999999872
No 41
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=2.5e-17 Score=135.33 Aligned_cols=184 Identities=18% Similarity=0.209 Sum_probs=134.5
Q ss_pred CCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHH
Q ss_conf 99899999999999828599999999943077875655557999988899999988899898621853456899975778
Q gi|254780611|r 29 LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108 (302)
Q Consensus 29 Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~w 108 (302)
.+.+|+.+|+.+++ .||.+|-..|+..|-+.|...|.++.+..-+-+|++|+..+-+.+.+..||+.++ .|+||.+--
T Consensus 9 ~~~~~~~eLi~r~~-~GD~~Af~~Ly~~y~~~l~~~~~~~~~d~~~AeDlvQe~Flk~~~~~~~~~~~~s-~f~tWl~~I 86 (194)
T PRK12531 9 FGRQEWLECMEKVK-SRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYTI 86 (194)
T ss_pred CCCHHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCC-CHHHHHHHH
T ss_conf 35166999999999-5889999999999999999999999399999999999999999998886676536-099999999
Q ss_pred HHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHH
Q ss_conf 99999985320246001102300358999999997887866244788824677888618983211000000122343355
Q gi|254780611|r 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188 (302)
Q Consensus 109 Ir~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~ 188 (302)
.+..+.++++++.+ ... .+.. +.
T Consensus 87 a~N~~~d~lRk~~~----------------------~~~-------------------~~~~----------------~~ 109 (194)
T PRK12531 87 IRNLCFDLLRKQKG----------------------KDL-------------------HIHA----------------DD 109 (194)
T ss_pred HHHHHHHHHHHHCC----------------------CCC-------------------CCCH----------------HH
T ss_conf 99999999997404----------------------343-------------------4321----------------11
Q ss_pred HCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHH
Q ss_conf 20232345320000012356870565566666667779999996219999999999982788888989999997789999
Q gi|254780611|r 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268 (302)
Q Consensus 189 ~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eR 268 (302)
... .+.... +. . +...++ ...+...+..+|+.||+++|.|+.++|+.+ +|.+|||+.||+|...
T Consensus 110 ~~~-~~~~~~---~~-~-~~~~~e--------~~~~~~~~~~~l~~Lp~~~R~vi~L~~~e~--~s~~EIAe~l~is~~T 173 (194)
T PRK12531 110 IWP-SDYYPP---DL-V-DHYSPE--------QDMLKEQVMKFLDRLPKAQRDVLQAVYLEE--LPHQQVAEMFDIPLGT 173 (194)
T ss_pred CCC-CCCCCC---CC-C-CCCCHH--------HHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHH
T ss_conf 142-224783---00-0-125879--------999999999999869999999999998869--9999999998929999
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999999999999974
Q gi|254780611|r 269 VRQIEARAFKKVQESIQKQ 287 (302)
Q Consensus 269 VrQI~~~AL~kLR~~l~~~ 287 (302)
|.-.-.+|+++||+.|+.+
T Consensus 174 VKsrl~rA~k~LR~~Le~e 192 (194)
T PRK12531 174 VKSRLRLAVEKLRHSMDAE 192 (194)
T ss_pred HHHHHHHHHHHHHHHHHHC
T ss_conf 9999999999999998657
No 42
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=99.79 E-value=6.6e-17 Score=132.53 Aligned_cols=186 Identities=16% Similarity=0.204 Sum_probs=138.0
Q ss_pred HCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHH
Q ss_conf 07999998999999999998285999999999430778756555579999888999999888998986218534568999
Q gi|254780611|r 24 RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103 (302)
Q Consensus 24 ~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsT 103 (302)
+..|--..+|+.+|+.+++ .||..|-+.|+..|-+.|.++|.++.+..-+-+|++|+..+-+.+.+.+|||+++ +|+|
T Consensus 2 ~~~p~~~~de~~~Li~~~~-~GD~~Af~~Ly~~y~~~l~~~~~~~~~~~~~AeDv~Qe~Fl~vw~~~~~~~~~~~-~~~t 79 (187)
T PRK12534 2 SAIPGHDDDETGRLLTATA-GGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLT 79 (187)
T ss_pred CCCCCCCCHHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCC-CHHH
T ss_conf 9999999628999999999-3689999999999999999999998699999999999999999987533687522-1899
Q ss_pred HHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf 75778999999853202460011023003589999999978878662447888246778886189832110000001223
Q gi|254780611|r 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183 (302)
Q Consensus 104 YA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~ 183 (302)
|.+--.+....+++|.+.+. .+ .
T Consensus 80 Wl~~IarN~~~d~lR~~~~~------------------------------~~---------------------------~ 102 (187)
T PRK12534 80 WLAMIARNKAIDHLRANAPQ------------------------------RR---------------------------N 102 (187)
T ss_pred HHHHHHHHHHHHHHHHCCCC------------------------------CC---------------------------C
T ss_conf 99999999999999962441------------------------------35---------------------------7
Q ss_pred CCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHC
Q ss_conf 43355202323453200000123568705655666666677799999962199999999999827888889899999977
Q gi|254780611|r 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263 (302)
Q Consensus 184 ~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lg 263 (302)
.+++. ... +...+..+. +..+.......|..+|..||+.++.||.++|+.+ +|.+|||+.||
T Consensus 103 ~~~~~------~~~------~~~~~~~~~----e~~~~~~~~~~l~~al~~L~~~~r~vi~l~~~eg--~s~~EIA~~l~ 164 (187)
T PRK12534 103 VALDD------AGE------LRAADASPL----ERTERASTRRRIDHCLAELEPPRSELIRTAFFEG--ITYEELAARTD 164 (187)
T ss_pred CCCCC------CCC------CCCCCCCHH----HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHC
T ss_conf 77341------100------135689827----7899999999999999868998999999999849--99999999989
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 89999999999999999999997
Q gi|254780611|r 264 VSRERVRQIEARAFKKVQESIQK 286 (302)
Q Consensus 264 iS~eRVrQI~~~AL~kLR~~l~~ 286 (302)
+|...|.-.-.+|+++||+.|++
T Consensus 165 i~~gTVksrl~ra~~~Lr~~Lek 187 (187)
T PRK12534 165 TPIGTVKSWIRRGLAKLKACLER 187 (187)
T ss_pred CCHHHHHHHHHHHHHHHHHHHCC
T ss_conf 19999999999999999998667
No 43
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=5.5e-17 Score=133.07 Aligned_cols=185 Identities=16% Similarity=0.233 Sum_probs=134.6
Q ss_pred CCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHH
Q ss_conf 99989999999999982859999999994307787565555799998889999998889989862185345689997577
Q gi|254780611|r 28 MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107 (302)
Q Consensus 28 ~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~ 107 (302)
-+|...+.+|+.+++ .||..|-..|+..|-+.|..+|.++.+...+-+|++|+..+.+.+.+. |++.+| .|.||.+.
T Consensus 10 ~m~~~tD~eLi~~~~-~GD~~Af~~L~~ry~~~l~~~a~~~~~~~~~AeDlvQe~fl~~~~~~~-~~~~~~-~~~~wL~~ 86 (194)
T PRK12519 10 SLSSRSDAELFSALK-AGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRKSS-YDPKRG-SLSSYLLT 86 (194)
T ss_pred CCCCCCHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH-CCCCCC-CHHHHHHH
T ss_conf 999960999999999-385999999999999999999999939999999999999999998633-166624-29999999
Q ss_pred HHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHH
Q ss_conf 89999998532024600110230035899999999788786624478882467788861898321100000012234335
Q gi|254780611|r 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187 (302)
Q Consensus 108 wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd 187 (302)
..+..+.++++.+.+.. .. .+...
T Consensus 87 ia~n~~~d~~R~~~~~~----------------------~~----------~~~~~------------------------ 110 (194)
T PRK12519 87 LTRSRAIDRLRSRRSRQ----------------------RL----------LERWQ------------------------ 110 (194)
T ss_pred HHHHHHHHHHHHHHCCC----------------------CH----------HHHHH------------------------
T ss_conf 99999999999863201----------------------22----------44444------------------------
Q ss_pred HHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHH
Q ss_conf 52023234532000001235687056556666666777999999621999999999998278888898999999778999
Q gi|254780611|r 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267 (302)
Q Consensus 188 ~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~e 267 (302)
..... + ...+.+.+ ..........|..+|..||+++|.|+.++|+.+ +|.+|||+.||+|..
T Consensus 111 ~~~~~--~----------~~~~~~~~----~~~~~e~~~~l~~al~~Lp~~~R~v~~L~~~eg--~s~~EIA~~lgis~~ 172 (194)
T PRK12519 111 QELLG--E----------ASEDTPLE----QASLAERSQRVQTALAQLPESQRQVLELAYYEG--LSQSEIAKRLGIPLG 172 (194)
T ss_pred HHHCC--C----------CCCCCHHH----HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHH
T ss_conf 54114--6----------77898588----998999999999999819988756889999819--999999999894999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9999999999999999997401
Q gi|254780611|r 268 RVRQIEARAFKKVQESIQKQVE 289 (302)
Q Consensus 268 RVrQI~~~AL~kLR~~l~~~~~ 289 (302)
.|...-.+|+++||+.|++.++
T Consensus 173 tVk~rl~rA~~~Lr~~L~e~le 194 (194)
T PRK12519 173 TVKARARQGLLKLRELLQDLLE 194 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHC
T ss_conf 9999999999999999898739
No 44
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=99.78 E-value=5.7e-17 Score=132.95 Aligned_cols=184 Identities=15% Similarity=0.110 Sum_probs=130.6
Q ss_pred HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf 99999999828599999999943077875655557999988899999988899898621853456899975778999999
Q gi|254780611|r 35 YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114 (302)
Q Consensus 35 ~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~ 114 (302)
.+|+.+++ .||.+|-+.|+..|.+.|.++|.++.+...+.+|++|+..+.+++.+.+|++. ..|.+|.+.-.+..+.
T Consensus 7 ~~Li~~~~-~Gd~~A~~~L~~~y~~~l~~~~~~~~~~~~~aeDv~Qe~fl~l~~~~~~~~~~--~~~~~wL~~iarn~~~ 83 (192)
T PRK09652 7 QELVERVQ-QGDRAAFELLVRKYQPRLYRLLSRLVRDPADAEDLAQETFIKAYRALPSFRGG--AAFYTWLYRIAVNTAI 83 (192)
T ss_pred HHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCC--HHHHHHHHHHHHHHHH
T ss_conf 99999998-38899999999999999999999996999999998759999988711345771--1799999999999999
Q ss_pred HHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCC
Q ss_conf 85320246001102300358999999997887866244788824677888618983211000000122343355202323
Q gi|254780611|r 115 EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194 (302)
Q Consensus 115 ~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d 194 (302)
++++.+.+. ... . +.+.....
T Consensus 84 d~~r~~~r~----------------------~~~--------~---------------------------~~~~~~~~-- 104 (192)
T PRK09652 84 NYLRKQGRR----------------------PPE--------S---------------------------DLDAEDAE-- 104 (192)
T ss_pred HHHHHHHCC----------------------CCC--------C---------------------------CCCHHHHH--
T ss_conf 999997165----------------------665--------5---------------------------40023454--
Q ss_pred CCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 45320000012356870565566666667779999996219999999999982788888989999997789999999999
Q gi|254780611|r 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274 (302)
Q Consensus 195 ~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~ 274 (302)
.......+++.+.++..+ ........|..++..||++++.|+.++|+.+ +|.+|||+.||+|...|+..-.
T Consensus 105 ---~~~~~~~~~~~~~~e~~~----~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~~--~s~~EIA~~lgis~~tVk~~l~ 175 (192)
T PRK09652 105 ---YFEDADALREISSPEEEL----LSQELEQRVRRAIESLPEELRTAITLREIEG--LSYEEIAEIMGCPIGTVRSRIF 175 (192)
T ss_pred ---HHCCCCCCCCCCCHHHHH----HHHHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHH
T ss_conf ---300000355557679999----9999999999999839999998888999729--9999999998939999999999
Q ss_pred HHHHHHHHHHHHHHC
Q ss_conf 999999999997401
Q gi|254780611|r 275 RAFKKVQESIQKQVE 289 (302)
Q Consensus 275 ~AL~kLR~~l~~~~~ 289 (302)
+|+++||+.|+.-++
T Consensus 176 Ra~~~Lr~~L~~~~~ 190 (192)
T PRK09652 176 RAREALRAKLQPLLD 190 (192)
T ss_pred HHHHHHHHHHHHHHH
T ss_conf 999999999898771
No 45
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=99.78 E-value=6.8e-17 Score=132.43 Aligned_cols=191 Identities=19% Similarity=0.241 Sum_probs=135.5
Q ss_pred CCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHH
Q ss_conf 99989999999999982859999999994307787565555799998889999998889989862185345689997577
Q gi|254780611|r 28 MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107 (302)
Q Consensus 28 ~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~ 107 (302)
++|.+++.+|+.+++ .||..|-+.|+..|-+.|..+|.+|.+..-+-+|++|+..+.+.+.+.+|++. .+|.||.+-
T Consensus 1 m~t~~~D~~Li~~~~-~GD~~Af~~L~~~y~~~l~~~~~~~~~d~~~AeDi~Qe~f~~~~~~~~~~~~~--~~f~~WL~~ 77 (193)
T PRK11923 1 MLTQEEDQQLVERVQ-RGDKRAFDLLVLKYQHKILGLIVRFVHDTHEAQDVAQEAFIKAYRALGNFRGD--SAFYTWLYR 77 (193)
T ss_pred CCCCCCHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCCC--HHHHHHHHH
T ss_conf 998710999999999-48699999999999999999999990999999999999999998613212650--468999999
Q ss_pred HHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHH
Q ss_conf 89999998532024600110230035899999999788786624478882467788861898321100000012234335
Q gi|254780611|r 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187 (302)
Q Consensus 108 wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd 187 (302)
-.+....++++...+ +++. . .+.. -+
T Consensus 78 Ia~n~~~~~~~~~~r--------------------------------r~~~-~------~~~~---------------~~ 103 (193)
T PRK11923 78 IAINTAKNHLVSRGR--------------------------------RPPD-S------DVSS---------------ED 103 (193)
T ss_pred HHHHHHHHHHHHHHC--------------------------------CCCC-C------CCCH---------------HH
T ss_conf 999999999999865--------------------------------5753-3------3453---------------46
Q ss_pred HHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHH
Q ss_conf 52023234532000001235687056556666666777999999621999999999998278888898999999778999
Q gi|254780611|r 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267 (302)
Q Consensus 188 ~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~e 267 (302)
......+ +. ..+...|+..+ ........|..+|..||+++|.|+.++|+.| +|.+|||+.||+|..
T Consensus 104 ~~~~~~~-------~~-~~~~~~~e~~~----~~~e~~~~i~~~l~~Lp~~~R~v~~L~~~eg--ls~~EIA~~l~is~~ 169 (193)
T PRK11923 104 AEFYDGD-------HA-LKDIESPERAL----LRDEIEATVHRTIQQLPEDLRTALTLREFDG--LSYEDIASVMQCPVG 169 (193)
T ss_pred HHHCCCC-------CC-CCCCCCHHHHH----HHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHH
T ss_conf 6522554-------32-23448888999----9999999999999817898999999999949--999999999892999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9999999999999999997401
Q gi|254780611|r 268 RVRQIEARAFKKVQESIQKQVE 289 (302)
Q Consensus 268 RVrQI~~~AL~kLR~~l~~~~~ 289 (302)
.|+..-.+|.++||+.|++-++
T Consensus 170 tVk~rl~RAr~~Lr~~L~~ll~ 191 (193)
T PRK11923 170 TVRSRIFRAREAIDKALQPLLQ 191 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999999999999999899873
No 46
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=99.78 E-value=7.8e-17 Score=132.02 Aligned_cols=182 Identities=13% Similarity=0.158 Sum_probs=130.7
Q ss_pred HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHH
Q ss_conf 99999999982859999999994307787565555799998889999998889989862185345689997577899999
Q gi|254780611|r 34 EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113 (302)
Q Consensus 34 e~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I 113 (302)
-.+|+++++ .||.+|-+.|+..|-+.|..+|.++.+...+-+|++|+..+.+.+.+++|+|.. +|.||.+--.+..+
T Consensus 5 i~~Li~~~~-~GD~~Af~~L~~~y~~~l~~~~~~~~~~~~~AeD~vQe~flk~~~~~~~~~~~~--~~~~WL~~Ia~N~~ 81 (187)
T PRK09641 5 IKKRIKQVK-KGDQNAFADIVDLYKDKIYQLCYRMLGNRHEAEDIAQEAFIRAYVNIDSFDINR--KFSTWLYRIATNLT 81 (187)
T ss_pred HHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCC--CHHHHHHHHHHHHH
T ss_conf 999999999-388999999999999999999999909999999999999999998461257413--49999999999999
Q ss_pred HHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCC
Q ss_conf 98532024600110230035899999999788786624478882467788861898321100000012234335520232
Q gi|254780611|r 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193 (302)
Q Consensus 114 ~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~ 193 (302)
.++++++.+.+. ++......
T Consensus 82 ~d~~Rk~~~~~~------------------------------------------------------------~~~~~~~~ 101 (187)
T PRK09641 82 IDRLRKKKPDYY------------------------------------------------------------LDAEVAGT 101 (187)
T ss_pred HHHHHHHCCCCC------------------------------------------------------------HHHHHCCC
T ss_conf 999997265343------------------------------------------------------------12654031
Q ss_pred CCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 34532000001235687056556666666777999999621999999999998278888898999999778999999999
Q gi|254780611|r 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273 (302)
Q Consensus 194 d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~ 273 (302)
+.....+.++++...+++.+. .......+..+++.||+++|.|+.++|+.+ +|.+|||+.+|+|...|+..-
T Consensus 102 --~~~~~~~~~~~~~~~~~~~~~----~~e~~~~l~~al~~Lp~~~r~v~~L~~~~~--~s~~EIA~~l~is~~tVk~~l 173 (187)
T PRK09641 102 --EGLTMYSQLAADEALPEDQVE----SLELQETIQEEILQLPDKYRTVIVLKYIEE--LSLKEISEILDLPVGTVKTRI 173 (187)
T ss_pred --CCCHHHHHCCCCCCCHHHHHH----HHHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHH
T ss_conf --000044303566798478999----999999999999828988889999999829--989999999893999999999
Q ss_pred HHHHHHHHHHHHH
Q ss_conf 9999999999997
Q gi|254780611|r 274 ARAFKKVQESIQK 286 (302)
Q Consensus 274 ~~AL~kLR~~l~~ 286 (302)
.+|+++||+.|+.
T Consensus 174 ~RAr~~Lr~~Lk~ 186 (187)
T PRK09641 174 HRGREALRKQLRH 186 (187)
T ss_pred HHHHHHHHHHHHC
T ss_conf 9999999998666
No 47
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=99.77 E-value=1.5e-16 Score=130.23 Aligned_cols=180 Identities=19% Similarity=0.240 Sum_probs=131.3
Q ss_pred HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf 99999999828599999999943077875655557999988899999988899898621853456899975778999999
Q gi|254780611|r 35 YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114 (302)
Q Consensus 35 ~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~ 114 (302)
.+|+.+++ .||..|-..|+..|-+.|..++.++.+..-.-+|++|+..+-+.+.+.+|++. .+|.||.+.-.+..+.
T Consensus 14 ~eL~~~~~-~GD~~Af~~L~~~y~~~l~~~~~~~~~d~~~AeDl~Qevfl~~~~~~~~~~~~--~~~~~wL~~ia~n~~~ 90 (194)
T PRK12513 14 EALMLRYR-AGDAAAFEALYARHRTGLYRFLLRLARDPALADDIFQETWLRVIRARSQWQPR--ARFRTWLYQIARNRLI 90 (194)
T ss_pred HHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHHH
T ss_conf 99999999-46299999999999999999999996999999999989999999887616975--4599999999999999
Q ss_pred HHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCC
Q ss_conf 85320246001102300358999999997887866244788824677888618983211000000122343355202323
Q gi|254780611|r 115 EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194 (302)
Q Consensus 115 ~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d 194 (302)
++++++.+ .. ..+ .+.+.
T Consensus 91 ~~~R~~~~----------------------~~-------~~~---------------------------~~~~~------ 108 (194)
T PRK12513 91 DHWRKHGA----------------------RQ-------APS---------------------------LDADE------ 108 (194)
T ss_pred HHHHHHHC----------------------CC-------CCC---------------------------CCHHH------
T ss_conf 99998744----------------------37-------753---------------------------11036------
Q ss_pred CCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 45320000012356870565566666667779999996219999999999982788888989999997789999999999
Q gi|254780611|r 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274 (302)
Q Consensus 195 ~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~ 274 (302)
......+..+.++..+ ........|..++..||+++|.|+.++|+.+ +|.+|||+.||+|...|+..-.
T Consensus 109 -----~~~~~~~~~~~~e~~~----~~~e~~~~l~~~l~~Lp~~~r~il~L~~~~g--~s~~EIA~~l~is~~tVk~~l~ 177 (194)
T PRK12513 109 -----LAHALADDGAGPEQQL----SLFRDRRRLQAALETLPDEQREVFLLREHGD--LSLEEIAQLTGVPLETVKSRLR 177 (194)
T ss_pred -----HHHCCCCCCCCHHHHH----HHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHH
T ss_conf -----6503677889999999----9999999999999729989999999999849--9999999998949999999999
Q ss_pred HHHHHHHHHHHHHHCC
Q ss_conf 9999999999974012
Q gi|254780611|r 275 RAFKKVQESIQKQVEL 290 (302)
Q Consensus 275 ~AL~kLR~~l~~~~~~ 290 (302)
+|+++||+.|.+++.+
T Consensus 178 rA~~~Lr~~L~~e~~~ 193 (194)
T PRK12513 178 YALQKLRELLAEEVAV 193 (194)
T ss_pred HHHHHHHHHHHHHHCC
T ss_conf 9999999999885355
No 48
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=99.77 E-value=5.9e-17 Score=132.86 Aligned_cols=182 Identities=16% Similarity=0.209 Sum_probs=126.6
Q ss_pred CCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH
Q ss_conf 99998999999999998285999999999430778756555579999888999999888998986218534568999757
Q gi|254780611|r 27 PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106 (302)
Q Consensus 27 ~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~ 106 (302)
|+....++.+|+.+++ .||.+|-..|+..|-+.|...|.+|.+...+-+|++|+-.+-+.+.+.+|||++| .|.||.+
T Consensus 10 ~~~~~~d~~~Li~~~~-~GD~~Af~~Ly~~y~~~l~~~~~~~~~d~~~AeDivQevFl~~~~~~~~~~~~~~-~~~~WL~ 87 (194)
T PRK09646 10 PPAPSPDLDALLRRVA-RGDQDAFAELYDRTASRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SALAWLL 87 (194)
T ss_pred CCCCCCCHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCC-CHHHHHH
T ss_conf 6437966999999999-3679999999999999999999999299999999999999999997521475426-5999999
Q ss_pred HHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCH
Q ss_conf 78999999853202460011023003589999999978878662447888246778886189832110000001223433
Q gi|254780611|r 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186 (302)
Q Consensus 107 ~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SL 186 (302)
-..+....+ .+|+.+..... .. .. ...+.
T Consensus 88 ~Ia~n~~~d----------------------~~R~~~~~~~~--------~~--------------------~~-~~~~~ 116 (194)
T PRK09646 88 TLAHRRAVD----------------------RVRSEQAASQR--------EV--------------------RY-GARNV 116 (194)
T ss_pred HHHHHHHHH----------------------HHHHHHHHHHH--------HH--------------------HH-CCCCC
T ss_conf 999999999----------------------99998741324--------43--------------------20-00236
Q ss_pred HHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCH
Q ss_conf 55202323453200000123568705655666666677799999962199999999999827888889899999977899
Q gi|254780611|r 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266 (302)
Q Consensus 187 d~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~ 266 (302)
+ . . .+... +..+.......|..+|..||+++|.||.++|+.+ +|.+|||+.||+|.
T Consensus 117 ~-------~---------~--~~~~~----e~~~~~~~~~~l~~~l~~Lp~~~R~vi~L~~~~g--~s~~EIA~~Lgis~ 172 (194)
T PRK09646 117 D-------P---------A--FDQVA----EEVEARLERERVRGCLDALTDTQREAITLAYYGG--LTYREVAERLAVPL 172 (194)
T ss_pred C-------C---------C--CCCCH----HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCH
T ss_conf 8-------8---------7--55314----7899899999999999867815789999999939--99999999989199
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999999999999999
Q gi|254780611|r 267 ERVRQIEARAFKKVQESIQ 285 (302)
Q Consensus 267 eRVrQI~~~AL~kLR~~l~ 285 (302)
..|+.-..+|+++||+.|.
T Consensus 173 ~TVk~rl~rA~~~LR~~LG 191 (194)
T PRK09646 173 GTVKTRMRDGLRRLRDCLG 191 (194)
T ss_pred HHHHHHHHHHHHHHHHHHC
T ss_conf 9999999999999999837
No 49
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=99.77 E-value=9.2e-17 Score=131.57 Aligned_cols=176 Identities=22% Similarity=0.237 Sum_probs=125.8
Q ss_pred HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf 99999999828599999999943077875655557999988899999988899898621853456899975778999999
Q gi|254780611|r 35 YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114 (302)
Q Consensus 35 ~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~ 114 (302)
.+|+.+++ .||.+|-..|+..|-+.|.++|.++.+....-+|++|+..+.+.+.+.+|||.+| .|.||-+-+.+....
T Consensus 11 ~eLi~~~~-~GD~~Af~~L~~ry~~~l~~~~~~~~~d~~~AEDivQe~flki~~~~~~~~~~~~-~~~~wL~~ia~n~~~ 88 (187)
T PRK13919 11 EALLALVA-RGDEEAFRALFRRYAGSFLALARRMGLDGAAAEDVVQEAMIRVWQKAKEFDPRRG-SARAFLLTLGHHAAV 88 (187)
T ss_pred HHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCC-CHHHHHHHHHHHHHH
T ss_conf 99999999-4779999999999999999999999099999999999999999999987687646-499999999999999
Q ss_pred HHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCC
Q ss_conf 85320246001102300358999999997887866244788824677888618983211000000122343355202323
Q gi|254780611|r 115 EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194 (302)
Q Consensus 115 ~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d 194 (302)
++++++.+- | . ... ..++. .....+
T Consensus 89 d~~Rk~~~~---~---------------------~-~~~-~~~~~----------------------~~~~~~------- 113 (187)
T PRK13919 89 DEVRRRAAR---P---------------------L-PLE-PDPER----------------------EEEAFD------- 113 (187)
T ss_pred HHHHHHHCC---C---------------------C-CCC-CCCHH----------------------HHHHCC-------
T ss_conf 999976267---7---------------------8-777-66101----------------------133204-------
Q ss_pred CCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 45320000012356870565566666667779999996219999999999982788888989999997789999999999
Q gi|254780611|r 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274 (302)
Q Consensus 195 ~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~ 274 (302)
.++.....+ .......|..+|..|||++|.||.++|+.+ +|.+|||+.||+|...|.-.-.
T Consensus 114 ---------~~~~~~~~e--------~~~~~~~l~~al~~L~~~~r~vi~L~~~~g--~s~~EIA~~L~is~~TVk~~l~ 174 (187)
T PRK13919 114 ---------LPGPGLDEE--------GHLDRTRLGRALKALSPEERRVIEVLYYQG--YTHREAARLLGLPLGTLKTWAR 174 (187)
T ss_pred ---------CCCCCCCHH--------HHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHH
T ss_conf ---------688640278--------789999999999849999999999999859--9999999998939999999999
Q ss_pred HHHHHHHHHHHH
Q ss_conf 999999999997
Q gi|254780611|r 275 RAFKKVQESIQK 286 (302)
Q Consensus 275 ~AL~kLR~~l~~ 286 (302)
+|+++||+.|++
T Consensus 175 rA~k~Lr~~Lke 186 (187)
T PRK13919 175 RALSKLKEVLRE 186 (187)
T ss_pred HHHHHHHHHHCC
T ss_conf 999999998459
No 50
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=99.76 E-value=3.7e-16 Score=127.52 Aligned_cols=174 Identities=18% Similarity=0.253 Sum_probs=125.2
Q ss_pred HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCC---CCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHH
Q ss_conf 999999999828599999999943077875655557999---98889999998889989862185345689997577899
Q gi|254780611|r 34 EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG---LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110 (302)
Q Consensus 34 e~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g---~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr 110 (302)
+.+|+.+++ .||.+|-+.|+..|-++|.++|.++.++. .+.+|++|+..+-+.+.+.+||+++| +|.||.+-=.+
T Consensus 3 d~~Li~~~~-~GD~~Af~~l~~~y~~~v~~~~~~~l~~~~~~~~aeD~vQevFi~~~~~~~~~~~~~~-~f~~WL~~Ia~ 80 (185)
T PRK06811 3 EDNFIKELK-KKNEKALEFIIDTYGNLIKKIVHKVLGTDQYKQLIEECVNDIFLSIWNNIDKFDEEKG-SFKNWIAAISK 80 (185)
T ss_pred HHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCHHCCCCCC-CHHHHHHHHHH
T ss_conf 999999998-2789999999999999999999999677688989999999999999983700388645-29999999999
Q ss_pred HHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHC
Q ss_conf 99998532024600110230035899999999788786624478882467788861898321100000012234335520
Q gi|254780611|r 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190 (302)
Q Consensus 111 ~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i 190 (302)
..+.+++++..+ ... .+.+...
T Consensus 81 n~~~d~~Rk~~r----------------------~~~------------------------------------~~~~~~~ 102 (185)
T PRK06811 81 YKAIDYKRKLTK----------------------NNN------------------------------------IDSDEFI 102 (185)
T ss_pred HHHHHHHHHHCC----------------------CCC------------------------------------CCHHHHC
T ss_conf 999999997426----------------------566------------------------------------6456521
Q ss_pred CCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHH
Q ss_conf 23234532000001235687056556666666777999999621999999999998278888898999999778999999
Q gi|254780611|r 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270 (302)
Q Consensus 191 ~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVr 270 (302)
......+++... .......|..++..||+++|.|+.++|+.+ +|.+|||+.||+|...|.
T Consensus 103 --------------~~~~~~~e~~~~----~~e~~~~l~~~l~~L~~~~r~v~~l~~~~~--~s~~EIA~~l~is~~tVk 162 (185)
T PRK06811 103 --------------LISEESIENEII----LKENKEEIIKLINDLKKLDREIFIKRYLLG--ESIEEIAKKLGLTRSAID 162 (185)
T ss_pred --------------CCCCCCHHHHHH----HHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHH
T ss_conf --------------355588788999----999999999998489999999999999949--999999999892999999
Q ss_pred HHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999974
Q gi|254780611|r 271 QIEARAFKKVQESIQKQ 287 (302)
Q Consensus 271 QI~~~AL~kLR~~l~~~ 287 (302)
..-.+|+++||+.|+.-
T Consensus 163 ~rl~Rar~~Lr~~L~~~ 179 (185)
T PRK06811 163 NRLSRGRKKLKNKLNIL 179 (185)
T ss_pred HHHHHHHHHHHHHHHHH
T ss_conf 99999999999998898
No 51
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=99.76 E-value=3.8e-16 Score=127.42 Aligned_cols=179 Identities=17% Similarity=0.238 Sum_probs=127.0
Q ss_pred CHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCC----CCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHH
Q ss_conf 989999999999982859999999994307787565555799----9988899999988899898621853456899975
Q gi|254780611|r 30 EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY----GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105 (302)
Q Consensus 30 t~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~----g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA 105 (302)
+.+|-.+|+.+++ .||.+|-+.|+..|.+.|...|.+..++ ..+-+|++||..+.+++++.+|++ .|..|.||.
T Consensus 5 ~~~~l~~Li~~a~-~GD~~Af~~L~~~~~~~v~r~~~~~l~~~~~~~~dAeDl~Qe~fl~~~~~l~~f~~-~~~~f~~Wl 82 (187)
T PRK09648 5 AGEELDALVAEAV-AGDRRALREVLETIHPLVVRYCRARLGTVERSGLSADDVAQEVCLAVITALPRYRD-QGRPFLAFV 82 (187)
T ss_pred CHHHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCC-CCCCHHHHH
T ss_conf 2178999999998-45899999999999999999999997144587643999999999999983766266-778499999
Q ss_pred HHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf 77899999985320246001102300358999999997887866244788824677888618983211000000122343
Q gi|254780611|r 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185 (302)
Q Consensus 106 ~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~S 185 (302)
+--.+..+.++. |+.+.. ...|.
T Consensus 83 ~~Ia~n~~~d~~----------------------R~~~r~--------~~~~~--------------------------- 105 (187)
T PRK09648 83 YGIAAHKVADAH----------------------RAAGRD--------KAYPT--------------------------- 105 (187)
T ss_pred HHHHHHHHHHHH----------------------HHHHCC--------CCCCC---------------------------
T ss_conf 999999999999----------------------987467--------64321---------------------------
Q ss_pred HHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCC
Q ss_conf 35520232345320000012356870565566666667779999996219999999999982788888989999997789
Q gi|254780611|r 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265 (302)
Q Consensus 186 Ld~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS 265 (302)
+. +. + ..++.++|++..... .....|..+|..||+++|.|+.++|+.+ +|.+|||+.||+|
T Consensus 106 -~~-~~----------~-~~~~~~~pe~~~~~~----e~~~~l~~~l~~Lp~~~R~vl~L~~~~g--~s~~EIA~~lg~s 166 (187)
T PRK09648 106 -EE-VP----------E-RPSDEAGPEQRALEA----ESSARMRELLEILPEKQREILILRVVVG--LSAEETAEAVGST 166 (187)
T ss_pred -CC-CC----------C-CCCCCCCHHHHHHHH----HHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCC
T ss_conf -12-33----------3-478778858999989----9999999999839999999999999849--9999999998939
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999999999999999997
Q gi|254780611|r 266 RERVRQIEARAFKKVQESIQK 286 (302)
Q Consensus 266 ~eRVrQI~~~AL~kLR~~l~~ 286 (302)
...|+....+|+++||+.|++
T Consensus 167 ~~tVk~~l~RA~~~Lr~~lE~ 187 (187)
T PRK09648 167 PGAVRVAQHRALSRLRAEIEQ 187 (187)
T ss_pred HHHHHHHHHHHHHHHHHHHCC
T ss_conf 999999999999999998659
No 52
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=99.75 E-value=4.5e-16 Score=126.92 Aligned_cols=177 Identities=18% Similarity=0.228 Sum_probs=127.5
Q ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHH
Q ss_conf 99999999999828599999999943077875655557999988899999988899898621853456899975778999
Q gi|254780611|r 32 QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111 (302)
Q Consensus 32 eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~ 111 (302)
+.+.+|+.+++ .||.+|-+.|+..|.+.|..+|.++.+...+-+|++|+..+.+.+.+.+|+|..+ +|.||.+--.+.
T Consensus 5 ~sD~eLi~~~~-~Gd~~Af~~L~~~y~~~l~~~~~~~~~d~~~AeDivQe~fl~~~~~~~~~~~~~~-~~~~wL~~ia~n 82 (186)
T PRK05602 5 DPDAELMARVG-AGDASAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWNQAPSWRPGEA-RFDTWLHRVVLN 82 (186)
T ss_pred CCHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCCH-HHHHHHHHHHHH
T ss_conf 42999999999-2889999999999999999999999299999999999999999987222588620-399999999999
Q ss_pred HHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCC
Q ss_conf 99985320246001102300358999999997887866244788824677888618983211000000122343355202
Q gi|254780611|r 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191 (302)
Q Consensus 112 ~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~ 191 (302)
.+.++ +|+-+ .. + ... +..
T Consensus 83 ~~~d~----------------------~Rk~~-~~----------~------------~~~-------------~~~--- 101 (186)
T PRK05602 83 LCYDR----------------------LRRRR-EV----------P------------VED-------------APE--- 101 (186)
T ss_pred HHHHH----------------------HHHHH-CC----------C------------CCC-------------CCC---
T ss_conf 99999----------------------98714-15----------7------------322-------------200---
Q ss_pred CCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 32345320000012356870565566666667779999996219999999999982788888989999997789999999
Q gi|254780611|r 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271 (302)
Q Consensus 192 ~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQ 271 (302)
..+..+.+++.. ........|..+|..||+++|.|+.++|+.+ +|.+|||+.||+|...|+.
T Consensus 102 ------------~~~~~~~~~~~~----~~~e~~~~l~~al~~Lp~~~R~v~~L~~~~g--~s~~EIA~~l~is~~tVk~ 163 (186)
T PRK05602 102 ------------VPDPAPGPDERL----EARQRARRVEQALAALPERQREAIVLQYYQG--LSNIEAARVMGLSVDALES 163 (186)
T ss_pred ------------CCCCCCCHHHHH----HHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHH
T ss_conf ------------034689877899----9999999999999759987889999998638--9999999998939999999
Q ss_pred HHHHHHHHHHHHHHHHHC
Q ss_conf 999999999999997401
Q gi|254780611|r 272 IEARAFKKVQESIQKQVE 289 (302)
Q Consensus 272 I~~~AL~kLR~~l~~~~~ 289 (302)
.-.+|+++||+.|++--+
T Consensus 164 ~l~RAr~~Lr~~L~e~~~ 181 (186)
T PRK05602 164 LLARARRALRAQLAELPP 181 (186)
T ss_pred HHHHHHHHHHHHHHCCCC
T ss_conf 999999999999766797
No 53
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=99.73 E-value=1.5e-15 Score=123.53 Aligned_cols=176 Identities=17% Similarity=0.189 Sum_probs=125.5
Q ss_pred HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHH
Q ss_conf 99999999998285999999999430778756555579999888999999888998986218534568999757789999
Q gi|254780611|r 33 EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112 (302)
Q Consensus 33 ee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~ 112 (302)
.+.+|+.+++ .||..|-..|+..|.+.|..+|.++.+..-+-+|++|+-.+-+.+.+.+||+.+ .|.+|.+--.+..
T Consensus 5 d~~~Li~~~~-~Gd~~Af~~Ly~~y~~~l~~~~~~~~~d~~~AeD~vQe~Flk~~~~~~~~~~~~--~~~~WL~~ia~n~ 81 (190)
T PRK12543 5 DYKHLIQLTL-SGNKEAYSELYDVTIQEVYKTVHFLIEDKTDVDDVVQEVYIQLYESLRKYDSEK--PFRPWLIGLVIKQ 81 (190)
T ss_pred CHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCC--CHHHHHHHHHHHH
T ss_conf 8999999999-566999999999999999999999909999999999999999999998718888--6899999999999
Q ss_pred HHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCC
Q ss_conf 99853202460011023003589999999978878662447888246778886189832110000001223433552023
Q gi|254780611|r 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192 (302)
Q Consensus 113 I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~ 192 (302)
+.++.+..+ ...... .......
T Consensus 82 ~~~~~r~~~----------------------~~~~~~-------------------------------~~~~~~~----- 103 (190)
T PRK12543 82 IHSYRRKRW----------------------MRLRIF-------------------------------KKAEEQR----- 103 (190)
T ss_pred HHHHHHHHH----------------------HHCCCC-------------------------------CCHHHHC-----
T ss_conf 999999875----------------------003412-------------------------------2001001-----
Q ss_pred CCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 23453200000123568705655666666677799999962199999999999827888889899999977899999999
Q gi|254780611|r 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272 (302)
Q Consensus 193 ~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI 272 (302)
......+++.+... .....|..++..||+++|.|+.++|+.+ +|.+|||+.||+|...|+--
T Consensus 104 ------------~~~~~~~~~~~~~~----~~~~~l~~~l~~Lp~~~R~vi~L~~~~g--~s~~EIA~~l~is~~tVk~r 165 (190)
T PRK12543 104 ------------KPVQIDFSNDLLSK----ISNQKLIELIHKLPYKLKQVIILRYLHD--YSQEEVAQILHIPIGTVKSR 165 (190)
T ss_pred ------------CCCCCCHHHHHHHH----HHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHH
T ss_conf ------------55568826899999----9999999999849999999999999859--99999999989399999999
Q ss_pred HHHHHHHHHHHHHHH
Q ss_conf 999999999999974
Q gi|254780611|r 273 EARAFKKVQESIQKQ 287 (302)
Q Consensus 273 ~~~AL~kLR~~l~~~ 287 (302)
-.+|+++||+.|+.+
T Consensus 166 l~rA~k~LR~kle~~ 180 (190)
T PRK12543 166 IHAALKKLRQKEQIE 180 (190)
T ss_pred HHHHHHHHHHHHHHH
T ss_conf 999999999999999
No 54
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=99.73 E-value=9.8e-16 Score=124.69 Aligned_cols=178 Identities=17% Similarity=0.194 Sum_probs=130.3
Q ss_pred HHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf 99999998285999999999430778756555579999888999999888998986218534568999757789999998
Q gi|254780611|r 36 VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE 115 (302)
Q Consensus 36 ~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~ 115 (302)
+|....+ .||..|-+.|+..|-++|..+|.++.+..-+.+|++|+..+.+++.++.|++.. .|.+|.+.-.+..+.+
T Consensus 2 ~l~~~a~-~Gd~~Af~~ly~~y~~~l~~~~~~~~~d~~~AeDi~Qe~fi~l~~~~~~~~~~~--~~~~wL~~iarn~~~d 78 (180)
T PRK11924 2 QLPAVAA-SGDKEAFSELFLPHAPDLLRYARRQLGNRALAEDAVQEAFLRAWRKADLFNGKG--SARTWLLTIARNKCYD 78 (180)
T ss_pred HHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCC--CHHHHHHHHHHHHHHH
T ss_conf 8889999-559999999999999999999999929999999999999999988632235434--7999999999999999
Q ss_pred HHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCC
Q ss_conf 53202460011023003589999999978878662447888246778886189832110000001223433552023234
Q gi|254780611|r 116 YILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195 (302)
Q Consensus 116 ~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~ 195 (302)
+++++.+..+ . .+ ..+...
T Consensus 79 ~~rk~~~~~~--------------------------~---~~---------------------------~~~~~~----- 97 (180)
T PRK11924 79 MLRRRRRERK--------------------------E---AA---------------------------EDEDLA----- 97 (180)
T ss_pred HHHHHHHHCC--------------------------C---CC---------------------------CHHHCC-----
T ss_conf 9999720102--------------------------2---33---------------------------110013-----
Q ss_pred CCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 53200000123568705655666666677799999962199999999999827888889899999977899999999999
Q gi|254780611|r 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275 (302)
Q Consensus 196 ~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~ 275 (302)
...+..+++++.+ +.......|..++..||++++.|+.++|+.+ ++.+|||+.||+|...|++...+
T Consensus 98 -------~~~~~~~~~e~~~----~~~~~~~~l~~~l~~L~~~~r~il~l~~~~g--~s~~eIA~~lgis~~tv~~~l~R 164 (180)
T PRK11924 98 -------PLSAEFETPEAAL----LAKDDLARIDRCLDALPEKQREVFLLRYVEG--LSYQEIADQLGVPLGTVKSRLRR 164 (180)
T ss_pred -------CCCCCCCCHHHHH----HHHHHHHHHHHHHHHCCHHHHHHHHHHHHHC--CCHHHHHHHHCCCHHHHHHHHHH
T ss_conf -------3344669858999----9999999999999859999999999999968--59999999989499999999999
Q ss_pred HHHHHHHHHHHHHCC
Q ss_conf 999999999974012
Q gi|254780611|r 276 AFKKVQESIQKQVEL 290 (302)
Q Consensus 276 AL~kLR~~l~~~~~~ 290 (302)
|.++||+.|++++..
T Consensus 165 a~~~Lr~~Le~~~~~ 179 (180)
T PRK11924 165 ARQKLRECLEAQWSA 179 (180)
T ss_pred HHHHHHHHHHHHHCC
T ss_conf 999999999986546
No 55
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=99.73 E-value=1.4e-15 Score=123.65 Aligned_cols=178 Identities=14% Similarity=0.169 Sum_probs=127.9
Q ss_pred CHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHH
Q ss_conf 98999999999998285999999999430778756555579999888999999888998986218534568999757789
Q gi|254780611|r 30 EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109 (302)
Q Consensus 30 t~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wI 109 (302)
.|+++.+|+.+++ .||..|-+.|+..|-+.|..+|.++.+..-+-+|++|+..+-+.+.+++|+++. ..|.||.+--.
T Consensus 2 ~p~d~~~Li~~~~-~GD~~Af~~L~~~y~~~l~~~a~~~~~d~~~AeDi~Qe~fl~~~~~~~~~~~~~-~~~~~wL~~ia 79 (179)
T PRK12514 2 QPDDIEKLIVRVS-LGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSG-LSPMTWLITIA 79 (179)
T ss_pred CCCCHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCC-CCHHHHHHHHH
T ss_conf 9710999999999-658999999999999999999999909999999999999999998875157665-53999999999
Q ss_pred HHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHH
Q ss_conf 99999853202460011023003589999999978878662447888246778886189832110000001223433552
Q gi|254780611|r 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189 (302)
Q Consensus 110 r~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~ 189 (302)
+....+++ |+-+ ... ..++..
T Consensus 80 rN~~id~~----------------------R~~~----------~~~---------------------------~~~~~~ 100 (179)
T PRK12514 80 RNHAIDRL----------------------RARK----------AVA---------------------------VDIDEA 100 (179)
T ss_pred HHHHHHHH----------------------HHCC----------CCC---------------------------CCHHHH
T ss_conf 99999999----------------------8637----------777---------------------------874567
Q ss_pred CCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHH
Q ss_conf 02323453200000123568705655666666677799999962199999999999827888889899999977899999
Q gi|254780611|r 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269 (302)
Q Consensus 190 i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRV 269 (302)
. + +.+..++++....... ....|..++..||++++.|+.++|+.+ +|.+|||+.||+|...|
T Consensus 101 ~-----------~-~~~~~~~~e~~~~~~~----~~~~l~~~l~~Lp~~~r~~~~l~~~eg--~s~~EIA~~l~is~~tV 162 (179)
T PRK12514 101 H-----------D-LADPSPGPEAEVIAGD----EGQRIDACLEELEKDRAAAVRRAYLEG--LSYKELAERHDVPLNTM 162 (179)
T ss_pred H-----------H-HCCCCCCHHHHHHHHH----HHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHH
T ss_conf 6-----------5-1246898699999889----999999999875599999999996069--98999999889099999
Q ss_pred HHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999997
Q gi|254780611|r 270 RQIEARAFKKVQESIQK 286 (302)
Q Consensus 270 rQI~~~AL~kLR~~l~~ 286 (302)
+..-.+|+++||+.|++
T Consensus 163 k~~l~rA~~~Lr~~L~k 179 (179)
T PRK12514 163 RTWLRRSLLKLRECLSR 179 (179)
T ss_pred HHHHHHHHHHHHHHHCC
T ss_conf 99999999999998576
No 56
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=99.73 E-value=2.3e-15 Score=122.25 Aligned_cols=186 Identities=13% Similarity=0.157 Sum_probs=130.1
Q ss_pred CCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHH
Q ss_conf 99989999999999982859999999994307787565555799998889999998889989862185345689997577
Q gi|254780611|r 28 MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107 (302)
Q Consensus 28 ~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~ 107 (302)
-+..+....|+.+++ .||..|-..|+..+-+.|...|.++.+..-.-+|++|+-.+-+.+.+..|+|++| +|+||.+-
T Consensus 19 ~~p~~~~~~Lv~~A~-~GD~~AF~~Ly~~y~~~l~~~~~r~l~d~~~AEDvvQetFlkvw~~~~~~~~~~~-~f~tWL~~ 96 (206)
T PRK12526 19 QVPTELSQWLILVAI-SRDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYT 96 (206)
T ss_pred CCCHHHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCC-HHHHHHHH
T ss_conf 673689999999999-6589999999999999999999999199999999999999999983876586425-29999999
Q ss_pred HHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHH
Q ss_conf 89999998532024600110230035899999999788786624478882467788861898321100000012234335
Q gi|254780611|r 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187 (302)
Q Consensus 108 wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd 187 (302)
=.+..+.+++++. +..-.. .+. +++ ..+.
T Consensus 97 IarN~~~d~lRk~----------------------~~~~~~------------------~~~-~d~----------~~~~ 125 (206)
T PRK12526 97 VMRNAAFDMLRKI----------------------KAKKEQ------------------NLG-DDI----------WPIE 125 (206)
T ss_pred HHHHHHHHHHHHH----------------------HCCCCC------------------CCC-CHH----------CHHH
T ss_conf 9999999999865----------------------312222------------------321-000----------0044
Q ss_pred HHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHH
Q ss_conf 52023234532000001235687056556666666777999999621999999999998278888898999999778999
Q gi|254780611|r 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267 (302)
Q Consensus 188 ~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~e 267 (302)
+.... ...+++..... .....|..+|..||+++|.||.++|+.+ +|.+|||+.||+|..
T Consensus 126 --------------~~~~~-~~~~~~~~~~~----~~~~~l~~~l~~LP~~~R~vi~L~~~eg--ls~~EIA~~l~is~~ 184 (206)
T PRK12526 126 --------------QALAE-SQSESEEFSDH----LMDKQILSYIEKLPEAQQTVVKGVYFQE--LSQEQLAQQLNVPLG 184 (206)
T ss_pred --------------HCCCC-CCCCHHHHHHH----HHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHH
T ss_conf --------------30145-78835789989----9999999999868999888989999859--999999999893999
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999999974
Q gi|254780611|r 268 RVRQIEARAFKKVQESIQKQ 287 (302)
Q Consensus 268 RVrQI~~~AL~kLR~~l~~~ 287 (302)
.|..--.+|+++||+.|.++
T Consensus 185 TVksrl~rAlk~LR~~L~e~ 204 (206)
T PRK12526 185 TVKSRLRLALAKLKVQMGEQ 204 (206)
T ss_pred HHHHHHHHHHHHHHHHHHCC
T ss_conf 99999999999999987303
No 57
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=99.72 E-value=2.4e-15 Score=122.06 Aligned_cols=179 Identities=17% Similarity=0.231 Sum_probs=127.9
Q ss_pred CCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHH
Q ss_conf 99989999999999982859999999994307787565555799998889999998889989862185345689997577
Q gi|254780611|r 28 MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107 (302)
Q Consensus 28 ~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~ 107 (302)
-+|.+ +|+.+++ .||.+|-..|+..|-+.|..+|.++.+...+-+|++|+..+-+.+.+.+|.+.++ +|+||.+-
T Consensus 10 ~~sD~---~Lv~~~~-~GD~~Af~~L~~ry~~~l~~~a~~~l~d~~~AEDlvQe~Fl~~~~~~~~~~~~~~-~~~tWL~~ 84 (196)
T PRK12524 10 DVSDE---ALLVLFA-NGDPAAARALTLRLAPRALAVATRVLGNRAEAEDVTQEAMLRLWRIAPDWRQGEA-RVSTWLYR 84 (196)
T ss_pred CCCHH---HHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCC-HHHHHHHH
T ss_conf 89999---9999999-2889999999999999999999999199999999999999999997466156520-79999999
Q ss_pred HHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHH
Q ss_conf 89999998532024600110230035899999999788786624478882467788861898321100000012234335
Q gi|254780611|r 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187 (302)
Q Consensus 108 wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd 187 (302)
-.+..+.++ +|+.+.. . ..++
T Consensus 85 Ia~N~~~d~----------------------~R~~~~~---------~----------------------------~~~~ 105 (196)
T PRK12524 85 VVCNLCTDR----------------------LRRQRRA---------S----------------------------VDLD 105 (196)
T ss_pred HHHHHHHHH----------------------HHHHHCC---------C----------------------------CCCC
T ss_conf 999999999----------------------9985056---------7----------------------------7611
Q ss_pred HHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHH
Q ss_conf 52023234532000001235687056556666666777999999621999999999998278888898999999778999
Q gi|254780611|r 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267 (302)
Q Consensus 188 ~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~e 267 (302)
. . . ...+..+.+++.+. .......|..+|..||+++|.||.++|+.+ +|.+|||+.||+|..
T Consensus 106 ~------~--~----~~~~~~~~~e~~~~----~~~~~~~l~~al~~Lp~~~R~vi~L~~~eg--~s~~EIA~~lgis~~ 167 (196)
T PRK12524 106 D------A--P----EPADAAPGAEEALQ----EGDRMRALDAALAALPERQRQAVVLRHIEG--LSNPEIAEVMQIGVE 167 (196)
T ss_pred C------C--C----CCCCCCCCHHHHHH----HHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHH
T ss_conf 2------4--3----32456898879999----899999999999859999999989999808--999999999892999
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999999999999999740
Q gi|254780611|r 268 RVRQIEARAFKKVQESIQKQV 288 (302)
Q Consensus 268 RVrQI~~~AL~kLR~~l~~~~ 288 (302)
.|+....+|+++||+.|..+-
T Consensus 168 tVk~~l~Rark~Lr~~L~~~r 188 (196)
T PRK12524 168 AVESLTARGKRALAALLAGQR 188 (196)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
T ss_conf 999999999999999987179
No 58
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=99.72 E-value=2.5e-15 Score=121.98 Aligned_cols=175 Identities=19% Similarity=0.247 Sum_probs=125.9
Q ss_pred HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHH
Q ss_conf 99999999982859999999994307787565555799998889999998889989862185345689997577899999
Q gi|254780611|r 34 EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113 (302)
Q Consensus 34 e~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I 113 (302)
+.+|+.+++ +||.+|-+.|+..|-+.+...|.+|.+..-+-+|++|+..+.+++.+.+|++. ..|.||.+.-.+...
T Consensus 9 D~~Lv~~~~-~gd~~Af~~L~~ry~~~l~~~~~~~~~~~~~AeDivQe~Fl~~~~~~~~~~~~--~~~~~WL~~Iarn~~ 85 (189)
T PRK12515 9 DEMLLARIA-QGDRTAMHTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIARFKA 85 (189)
T ss_pred HHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCC--CHHHHHHHHHHHHHH
T ss_conf 999999999-37799999999999999999999992999999999999999999865102530--229999999999999
Q ss_pred HHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCC
Q ss_conf 98532024600110230035899999999788786624478882467788861898321100000012234335520232
Q gi|254780611|r 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193 (302)
Q Consensus 114 ~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~ 193 (302)
.++ +++-+. .... ..+ .
T Consensus 86 ~~~----------------------~r~~~~-------~~~~--------------~~~-----------------~--- 102 (189)
T PRK12515 86 LSA----------------------LRQRKD-------EEID--------------DEA-----------------A--- 102 (189)
T ss_pred HHH----------------------HHHCCC-------CCCC--------------HHH-----------------H---
T ss_conf 999----------------------985133-------6665--------------456-----------------7---
Q ss_pred CCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 34532000001235687056556666666777999999621999999999998278888898999999778999999999
Q gi|254780611|r 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273 (302)
Q Consensus 194 d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~ 273 (302)
. .+.+....++... +.......|..+|..||+++|.||.++|+.+ +|.+|||+.||+|...|+-.-
T Consensus 103 ----~----~~~~~~~~~e~~~----~~~~~~~~l~~~l~~L~~~~R~vi~l~~~e~--~s~~EIA~~lgis~~tV~~~l 168 (189)
T PRK12515 103 ----A----AIEDGSDTPEVAL----QKKDTSAILRACIAKLSPAHREIIDLVYYHE--KSVEEVGEIVGIPESTVKTRM 168 (189)
T ss_pred ----H----HCCCCCCCHHHHH----HHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHH
T ss_conf ----6----3367789988999----8999999999998759999999999999849--999999999892999999999
Q ss_pred HHHHHHHHHHHHHHH
Q ss_conf 999999999999740
Q gi|254780611|r 274 ARAFKKVQESIQKQV 288 (302)
Q Consensus 274 ~~AL~kLR~~l~~~~ 288 (302)
.+|+++||+.|++.-
T Consensus 169 ~RAr~~Lr~~L~~~g 183 (189)
T PRK12515 169 FYARKKLAELLKAAG 183 (189)
T ss_pred HHHHHHHHHHHHHHC
T ss_conf 999999999999728
No 59
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=99.71 E-value=1.5e-15 Score=123.53 Aligned_cols=177 Identities=11% Similarity=0.116 Sum_probs=122.8
Q ss_pred HHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHH
Q ss_conf 89999999999982859999999994307787565555799998889999998889989862185345689997577899
Q gi|254780611|r 31 KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110 (302)
Q Consensus 31 ~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr 110 (302)
+-++.+|+++.+ .||.+|-+.|+..|-+.|..+|.++.+....-+|++|+..+-+.+.+.+|||.+| .|.||.+--.+
T Consensus 7 p~d~e~ll~~~~-~GD~~Af~~Ly~~y~~~l~~~~~~~~~d~~~AeDivQe~Fl~~~~~~~~~~~~~~-~~~~WL~~Iar 84 (184)
T PRK12537 7 PFDYEACLQACA-RGERRALQRLYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTKAASFDAARG-SARGWIYSVTR 84 (184)
T ss_pred CCCHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCCCCC-CHHHHHHHHHH
T ss_conf 999999999999-5889999999999999999999999299999999999999999986041684426-39999999999
Q ss_pred HHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHC
Q ss_conf 99998532024600110230035899999999788786624478882467788861898321100000012234335520
Q gi|254780611|r 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190 (302)
Q Consensus 111 ~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i 190 (302)
....++++++.+-+ ...+. ..+. .
T Consensus 85 n~~~~~lR~~~r~~-----------------------------~~~~~--------------------------~~~~-~ 108 (184)
T PRK12537 85 HLALNTLRDTRREV-----------------------------VLDDD--------------------------ASEQ-A 108 (184)
T ss_pred HHHHHHHHHHCCCC-----------------------------CCCCH--------------------------HHHH-C
T ss_conf 99999999850656-----------------------------66510--------------------------0210-1
Q ss_pred CCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHH
Q ss_conf 23234532000001235687056556666666777999999621999999999998278888898999999778999999
Q gi|254780611|r 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270 (302)
Q Consensus 191 ~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVr 270 (302)
. .. ......+ ..+.......|..+|..||+.++.||.++|+.+ +|.+|||+.||+|...|+
T Consensus 109 ~---~~----------~~~~~~~----~~~~~~~~~~l~~~l~~L~~~~r~~i~l~~~eg--~s~~EIA~~l~is~~TVk 169 (184)
T PRK12537 109 T---AQ----------GWQEIID----DFDLWVNSGKIHRCLEQLEPARRNCILHAYVDG--CSHAEIAQRLGAPLGTVK 169 (184)
T ss_pred C---CC----------CCCCCCC----HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHH
T ss_conf 3---46----------7777556----798999999999999809998999999988439--999999999892999999
Q ss_pred HHHHHHHHHHHHHH
Q ss_conf 99999999999999
Q gi|254780611|r 271 QIEARAFKKVQESI 284 (302)
Q Consensus 271 QI~~~AL~kLR~~l 284 (302)
..-.+|+++||+.|
T Consensus 170 ~rl~rA~~~LR~~L 183 (184)
T PRK12537 170 AWIKRSLKALRECM 183 (184)
T ss_pred HHHHHHHHHHHHHC
T ss_conf 99999999999872
No 60
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=99.71 E-value=3.3e-15 Score=121.14 Aligned_cols=175 Identities=15% Similarity=0.232 Sum_probs=128.0
Q ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHH
Q ss_conf 99999999999828599999999943077875655557999988899999988899898621853456899975778999
Q gi|254780611|r 32 QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111 (302)
Q Consensus 32 eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~ 111 (302)
++..+|..+++ .||.+|-..|+..|.+.|...|.++.+..-+-+|++||-.+-+.+.+.+|++.++ +|+||-+--.+.
T Consensus 48 d~D~eLv~R~~-~GD~~AF~~Ly~ry~~~l~~~a~r~l~d~~dAEDvvQEvFlk~w~~~~~f~~g~s-~f~tWL~~IA~N 125 (233)
T PRK12538 48 DEDEELLDRLA-TDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSN 125 (233)
T ss_pred CCHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCCC-HHHHHHHHHHHH
T ss_conf 97899999999-6029999999999999999999999599999999999999999998844777867-399999999999
Q ss_pred HHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCC
Q ss_conf 99985320246001102300358999999997887866244788824677888618983211000000122343355202
Q gi|254780611|r 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191 (302)
Q Consensus 112 ~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~ 191 (302)
...++ .|+.+ ...+ .++..
T Consensus 126 ~~id~----------------------~Rk~r------------~~~~------------------------d~~~e--- 144 (233)
T PRK12538 126 RCIDL----------------------RRKPR------------TENV------------------------DAVPE--- 144 (233)
T ss_pred HHHHH----------------------HHHHC------------CCCC------------------------CCCCC---
T ss_conf 99999----------------------97414------------5652------------------------23444---
Q ss_pred CCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 32345320000012356870565566666667779999996219999999999982788888989999997789999999
Q gi|254780611|r 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271 (302)
Q Consensus 192 ~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQ 271 (302)
..+..+++.+. .+.......|..+|..||+++|.||.++|+.+ +|.+|||+.||+|...|..
T Consensus 145 ------------~~d~~~~~~~~----l~~~e~~~~L~~aL~~Lp~~~R~vl~L~~~eg--ls~~EIA~~Lgis~~TVKs 206 (233)
T PRK12538 145 ------------VADGKPDAVSV----IERNELSDLLEAAMQRLPEQQRIAVILSYHEN--MSNGEIAEVMDTTVAAVES 206 (233)
T ss_pred ------------CCCCCCCHHHH----HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHH
T ss_conf ------------45689888789----99999999999999759999999999999849--9999999998929999999
Q ss_pred HHHHHHHHHHHHHHHH
Q ss_conf 9999999999999974
Q gi|254780611|r 272 IEARAFKKVQESIQKQ 287 (302)
Q Consensus 272 I~~~AL~kLR~~l~~~ 287 (302)
.-.+|+++||+.|++.
T Consensus 207 rL~RAr~~LR~~L~r~ 222 (233)
T PRK12538 207 LLKRGRQQLRDLLRRH 222 (233)
T ss_pred HHHHHHHHHHHHHHHH
T ss_conf 9999999999999987
No 61
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=99.71 E-value=4.7e-15 Score=120.13 Aligned_cols=177 Identities=15% Similarity=0.142 Sum_probs=128.6
Q ss_pred HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf 99999999828599999999943077875655557999988899999988899898621853456899975778999999
Q gi|254780611|r 35 YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114 (302)
Q Consensus 35 ~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~ 114 (302)
.+|+.+++ .||..|-+.|+..|-+.|..+|.++.+...+-+|++|+-.+-+++.+.+|++. .+|.||.+.-.+....
T Consensus 15 ~eLi~~~~-~GD~~Af~~L~~ry~~~l~~~a~~~~~~~~~AeDvvQe~flk~~~~~~~~~~~--~~f~~WL~~Ia~N~~~ 91 (197)
T PRK09643 15 AELLAAHV-AGDRYAFGELFRRHHRQLWRLARRTSGTREDAADALQDAMLSAHRGAGSFRGD--AAVSSWLHRIVVNACL 91 (197)
T ss_pred HHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCC--CHHHHHHHHHHHHHHH
T ss_conf 99999999-27799999999999999999999991999999999999999999988633886--3499999999999999
Q ss_pred HHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCC
Q ss_conf 85320246001102300358999999997887866244788824677888618983211000000122343355202323
Q gi|254780611|r 115 EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194 (302)
Q Consensus 115 ~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d 194 (302)
++ +|+.+.. + ..+++...
T Consensus 92 d~----------------------~Rk~~~~-----------~-------------------------~~~~~~~~---- 109 (197)
T PRK09643 92 DR----------------------LRRAKAR-----------P-------------------------TVPLEDVY---- 109 (197)
T ss_pred HH----------------------HHHHCCC-----------C-------------------------CCCCCCCC----
T ss_conf 99----------------------9985146-----------7-------------------------78866567----
Q ss_pred CCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 45320000012356870565566666667779999996219999999999982788888989999997789999999999
Q gi|254780611|r 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274 (302)
Q Consensus 195 ~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~ 274 (302)
+.+++...+ .+....|..+|..||+++|.||.++|+.+ +|.+|||+.||+|...|+....
T Consensus 110 --------------~~~~~~~~~----~e~~~~l~~al~~Lp~~~R~vl~L~~~eg--~s~~EIA~~lgis~~tVKsrl~ 169 (197)
T PRK09643 110 --------------PVADRETAR----VETAIAVQRALMRLPVEQRAALVAVDMQG--YSVADTARMLGVAEGTVKSRCA 169 (197)
T ss_pred --------------CCCCCHHHH----HHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHH
T ss_conf --------------786520313----89999999999769998879999999819--9999999998939999999999
Q ss_pred HHHHHHHHHHHHHHCCCCCCCC
Q ss_conf 9999999999974012246776
Q gi|254780611|r 275 RAFKKVQESIQKQVELSSSPPL 296 (302)
Q Consensus 275 ~AL~kLR~~l~~~~~~~~~~~~ 296 (302)
+|+++||+.|..--....++|.
T Consensus 170 RAr~~Lr~~L~~l~~~g~~~~~ 191 (197)
T PRK09643 170 RGRARLAELLGYLRAGGNASPG 191 (197)
T ss_pred HHHHHHHHHHHHHHCCCCCCCC
T ss_conf 9999999999988457899998
No 62
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=99.70 E-value=2.4e-15 Score=122.12 Aligned_cols=174 Identities=14% Similarity=0.186 Sum_probs=122.5
Q ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHH
Q ss_conf 99999999999828599999999943077875655557999988899999988899898621853456899975778999
Q gi|254780611|r 32 QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111 (302)
Q Consensus 32 eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~ 111 (302)
-++.+|+.+++ .||.+|-+.|+..|-+.|...|.++.+..-.-+|++|+..+-+.+.+.+|+|. ..|.||.+--.+.
T Consensus 4 ~~d~~Li~~~~-~GD~~Af~~L~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~~~~~~~~~~~~--~~~~~wL~~ia~n 80 (177)
T PRK09638 4 MEEKELIRRAK-KGNDAALTKLLQQHYNFLYGYVLKLTLNPDLAEDLVQETMLKAIENIHQFQGR--SKFSTWLISIASR 80 (177)
T ss_pred CCHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--HHHHHHHHHHHHH
T ss_conf 77999999999-47799999999999999999999991999999999999999999988770650--0799999999999
Q ss_pred HHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCC
Q ss_conf 99985320246001102300358999999997887866244788824677888618983211000000122343355202
Q gi|254780611|r 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191 (302)
Q Consensus 112 ~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~ 191 (302)
.+.++++++. ... . ..+ ...+.+..
T Consensus 81 ~~~d~~Rk~~----------------------r~~-------~----~~~----------------------~~~~~~~~ 105 (177)
T PRK09638 81 LYLDHLRKRK----------------------REE-------L----REE----------------------AATEETLR 105 (177)
T ss_pred HHHHHHHHHC----------------------CCC-------C----CCC----------------------CCCCCCCC
T ss_conf 9999999860----------------------301-------1----000----------------------23333556
Q ss_pred CCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 32345320000012356870565566666667779999996219999999999982788888989999997789999999
Q gi|254780611|r 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271 (302)
Q Consensus 192 ~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQ 271 (302)
. .+++......+ ...+..+|..||+++|.|+.++|+.| +|.+|||+.||+|...|+.
T Consensus 106 ----------------~-~~~~~~~~~~~----~~~l~~~l~~Lp~~~r~v~~L~~~eg--~s~~EIA~~l~is~~tVk~ 162 (177)
T PRK09638 106 ----------------K-EKWETAISGHE----WSELLDLLMKLPPELRAPFILKHYYG--YTYEEIAKMLGIPEGTVKS 162 (177)
T ss_pred ----------------C-CCCCHHHHHHH----HHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHH
T ss_conf ----------------6-76114653799----99999999759998989999999919--9999999998939999999
Q ss_pred HHHHHHHHHHHHHHH
Q ss_conf 999999999999997
Q gi|254780611|r 272 IEARAFKKVQESIQK 286 (302)
Q Consensus 272 I~~~AL~kLR~~l~~ 286 (302)
.-.+|+++||+.|.+
T Consensus 163 ~l~rA~~~Lr~~L~~ 177 (177)
T PRK09638 163 RVHHGLKKIRKELGQ 177 (177)
T ss_pred HHHHHHHHHHHHHCC
T ss_conf 999999999998582
No 63
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=99.70 E-value=6e-15 Score=119.44 Aligned_cols=174 Identities=16% Similarity=0.203 Sum_probs=124.2
Q ss_pred CHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCC-C---CCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHH
Q ss_conf 989999999999982859999999994307787565555799-9---988899999988899898621853456899975
Q gi|254780611|r 30 EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY-G---LPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105 (302)
Q Consensus 30 t~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~-g---~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA 105 (302)
+.+|..+|+.+++ .||.+|-..|+..+.+.|.++|.++.++ | .+-+|++|+-.+-+.+...+|+|. ..|.||.
T Consensus 5 ~~~e~~~Li~~~~-~GD~~Af~~L~~~~~~~l~~~~~~~l~~~~~~~~dAeDlvQevfl~~~~~~~~~~~~--~~f~~WL 81 (184)
T PRK12512 5 REDEWTDLMRSAN-AGDAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWL 81 (184)
T ss_pred CHHHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCC--CCHHHHH
T ss_conf 5287999999998-278999999999999999999999988468998899999999999999872314888--8589999
Q ss_pred HHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf 77899999985320246001102300358999999997887866244788824677888618983211000000122343
Q gi|254780611|r 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185 (302)
Q Consensus 106 ~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~S 185 (302)
+.=.+..+.++++++.+-.. .+
T Consensus 82 ~~Iarn~~~d~~Rk~~~~~~----------------------------------------------------------~~ 103 (184)
T PRK12512 82 FAIARNKLIDALRRRGRRVF----------------------------------------------------------VD 103 (184)
T ss_pred HHHHHHHHHHHHHHHCCCCC----------------------------------------------------------CC
T ss_conf 99999999999997437778----------------------------------------------------------98
Q ss_pred HHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCC
Q ss_conf 35520232345320000012356870565566666667779999996219999999999982788888989999997789
Q gi|254780611|r 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265 (302)
Q Consensus 186 Ld~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS 265 (302)
++... +.++. .+.+ +.. ....+..+|..||+++|.||.++|+.+ +|.+|||+.||+|
T Consensus 104 ~~~~~-----------~~~~~-~~~~-~~~--------~~~~l~~~L~~Lp~~~R~vi~L~~~~g--~s~~EIA~~lgis 160 (184)
T PRK12512 104 IDDFA-----------ETLPS-EPAA-ETL--------PAGDVGRHLETLPPRQRDVVQSIAVEG--ASIKETAAKLSMS 160 (184)
T ss_pred HHHHH-----------HCCCC-CCCC-CHH--------HHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCC
T ss_conf 34442-----------21678-8876-426--------899999999689999999999998559--7999999998919
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999999999999999974
Q gi|254780611|r 266 RERVRQIEARAFKKVQESIQKQ 287 (302)
Q Consensus 266 ~eRVrQI~~~AL~kLR~~l~~~ 287 (302)
...|+....+|+++||+.|+++
T Consensus 161 ~~tVk~~l~RA~~~Lr~~l~~e 182 (184)
T PRK12512 161 EGAVRVALHRGLAALAAKFRSE 182 (184)
T ss_pred HHHHHHHHHHHHHHHHHHHHHC
T ss_conf 9999999999999999998608
No 64
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=99.69 E-value=1.6e-15 Score=123.20 Aligned_cols=89 Identities=19% Similarity=0.311 Sum_probs=79.8
Q ss_pred HHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCC--HHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHH
Q ss_conf 999999982859999999994307787565555799998--889999998889989862185345689997577899999
Q gi|254780611|r 36 VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP--ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113 (302)
Q Consensus 36 ~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~--~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I 113 (302)
.++.+++ .||..||+.||+.|++||.+++.++.++-++ -||+++.|.+|+.+||++|||++|+.|.|||...|++.+
T Consensus 7 ~~l~~i~-~Gd~~~re~lI~~y~pfI~k~~s~~~~r~~~~e~DDe~SIgliAfneAI~~y~~~kg~~F~~fA~~vIk~rl 85 (237)
T PRK08311 7 DILEKIQ-NGDEELREELIEEYKPFILKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELVIKRRL 85 (237)
T ss_pred HHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHH
T ss_conf 9999988-678999999999927899999999967778988782998999999999986283359865999999999999
Q ss_pred HHHHHCCCCCHH
Q ss_conf 985320246001
Q gi|254780611|r 114 QEYILRSWSLVK 125 (302)
Q Consensus 114 ~~~i~~~~~~IR 125 (302)
.+|+|++.+.-.
T Consensus 86 iDy~Rke~k~~~ 97 (237)
T PRK08311 86 IDYIRKEKKHSK 97 (237)
T ss_pred HHHHHHHCCCCC
T ss_conf 999997404445
No 65
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=99.68 E-value=1.5e-14 Score=116.72 Aligned_cols=184 Identities=14% Similarity=0.206 Sum_probs=129.4
Q ss_pred CCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH
Q ss_conf 99998999999999998285999999999430778756555579999888999999888998986218534568999757
Q gi|254780611|r 27 PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106 (302)
Q Consensus 27 ~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~ 106 (302)
.+..+--+..++.+..+.||..|-+.|+..|.+.|...|.++.+..-+-+||+||-.+-+.+.+.+|+|+ +|+||-+
T Consensus 26 ~~~~~~~~~~~~~~~~~~~d~~AF~eLv~rh~~~vy~~a~r~~gn~~dAEDlvQEtFlka~r~l~~f~~~---sf~tWL~ 102 (222)
T PRK09647 26 EPSDELTGTAVFDATGDKATMPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQPG---TFEGWLH 102 (222)
T ss_pred CCCCCCCCHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC---CHHHHHH
T ss_conf 9865444448887414524589999999999999999999985999899999999999999862224773---0899999
Q ss_pred HHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCH
Q ss_conf 78999999853202460011023003589999999978878662447888246778886189832110000001223433
Q gi|254780611|r 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186 (302)
Q Consensus 107 ~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SL 186 (302)
-=.+....++ +|+-+. . +. .++
T Consensus 103 rIA~N~~iD~----------------------~Rr~~r-~--------~~---------------------------~~~ 124 (222)
T PRK09647 103 RITTNLFLDM----------------------VRRRQR-I--------RM---------------------------EAL 124 (222)
T ss_pred HHHHHHHHHH----------------------HHHCCC-C--------CC---------------------------CCC
T ss_conf 9999999999----------------------981124-6--------65---------------------------556
Q ss_pred HHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCH
Q ss_conf 55202323453200000123568705655666666677799999962199999999999827888889899999977899
Q gi|254780611|r 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266 (302)
Q Consensus 187 d~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~ 266 (302)
.. + .+.++...+.+++.... ......|..+|..|++++|.||.++|+.+ +|.+|||+.||+|.
T Consensus 125 ~e------~-----~e~~~~~~~~pe~~~~~----~~~~~~L~~al~~Lp~~qR~vl~Lr~~eg--lS~~EIAe~Lgis~ 187 (222)
T PRK09647 125 PE------D-----YDRVPADEPNPEQIYHD----ARLDPDLQAALDSLPPEFRAAVVLCDIEG--LSYEEIAATLGVKL 187 (222)
T ss_pred CC------H-----HHHCCCCCCCHHHHHHH----HHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCH
T ss_conf 11------3-----44256678997899999----99999999999829999988998799639--99999999989399
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999999999999999740
Q gi|254780611|r 267 ERVRQIEARAFKKVQESIQKQV 288 (302)
Q Consensus 267 eRVrQI~~~AL~kLR~~l~~~~ 288 (302)
..|+-.-.+|+++||+.|+...
T Consensus 188 gTVKsrl~RAr~~LR~~Lea~~ 209 (222)
T PRK09647 188 GTVRSRIHRGRQALRAYLAAHA 209 (222)
T ss_pred HHHHHHHHHHHHHHHHHHHHCC
T ss_conf 9999999999999999987109
No 66
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=99.67 E-value=9.5e-15 Score=118.11 Aligned_cols=171 Identities=21% Similarity=0.216 Sum_probs=121.7
Q ss_pred HHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf 99982859999999994307787565555799998889999998889989862185345689997577899999985320
Q gi|254780611|r 40 RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119 (302)
Q Consensus 40 ~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~ 119 (302)
|++ +||.+|-+.|+..|-+.|.++|.++.+..-+-+|++|+-.|-+.+.+++|++..+.+|+||.+.-.+....+++++
T Consensus 2 rv~-~GD~~afe~Ly~~y~~~ly~~a~~~~~d~~~AEDivQe~Flk~~~~~~~~~~~~~~~~~~wL~rIa~N~~id~~Rk 80 (185)
T PRK12542 2 KVT-NNDYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRK 80 (185)
T ss_pred CCC-CCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 641-3489999999999999999999999499999999999999999998887166552679999999999999999997
Q ss_pred CCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCC
Q ss_conf 24600110230035899999999788786624478882467788861898321100000012234335520232345320
Q gi|254780611|r 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199 (302)
Q Consensus 120 ~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~ 199 (302)
+. ... . ...+. .. .+ +..
T Consensus 81 ~k----------------------~~~--------~--~~~~~--------------~~-----~~----~~~------- 98 (185)
T PRK12542 81 NK----------------------RHE--------T--FLEEY--------------ER-----ES----IEA------- 98 (185)
T ss_pred HC----------------------CCC--------C--CHHHH--------------HC-----CC----CCC-------
T ss_conf 32----------------------434--------4--20132--------------10-----23----356-------
Q ss_pred HHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 00001235687056556666666777999999621999999999998278888898999999778999999999999999
Q gi|254780611|r 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279 (302)
Q Consensus 200 ~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~k 279 (302)
. ...+++ ..........|..++..||+++|.|+.++|+.+ +|.+|||+.||+|...|+..-.+|+++
T Consensus 99 -----~--~~~~e~----~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g--ls~~EIA~~L~is~~tVk~rl~RArk~ 165 (185)
T PRK12542 99 -----V--DENIEE----WEKRKMSEVQIDTLLKELNESNRQVFKYKVFYN--LTYQEISSVMGITEANVRKQFERARKR 165 (185)
T ss_pred -----C--CCCHHH----HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf -----7--877437----999998999999999829998889976799839--999999999892999999999999999
Q ss_pred HHHHHHH
Q ss_conf 9999997
Q gi|254780611|r 280 VQESIQK 286 (302)
Q Consensus 280 LR~~l~~ 286 (302)
||+.|..
T Consensus 166 Lr~~Lgg 172 (185)
T PRK12542 166 VQNMIGG 172 (185)
T ss_pred HHHHHCC
T ss_conf 9998767
No 67
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=99.64 E-value=7.3e-14 Score=112.19 Aligned_cols=176 Identities=17% Similarity=0.224 Sum_probs=120.9
Q ss_pred CCHHHH-HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHC----CCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHH
Q ss_conf 998999-99999999828599999999943077875655557----9999888999999888998986218534568999
Q gi|254780611|r 29 LEKQEE-YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR----GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103 (302)
Q Consensus 29 Lt~eee-~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~----~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsT 103 (302)
.+++.+ ..|+.+++ .||..|-..|+..+-+.+..+++.+. +...+-+|++|+..+-+.+...+||+.. +|.|
T Consensus 2 ~~~~~~~~~Lv~~~~-~GD~~Af~~L~~r~~~~l~~~~~~~l~r~~~~~~dAeDlvQe~fl~~~~~~~~~~~~~--~~~~ 78 (184)
T PRK12539 2 MSKENELKALMLASL-DGDAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTP 78 (184)
T ss_pred CCCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCC--CHHH
T ss_conf 997799999999998-0889999999999899999999999998439998999999999999998377559998--5799
Q ss_pred HHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf 75778999999853202460011023003589999999978878662447888246778886189832110000001223
Q gi|254780611|r 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183 (302)
Q Consensus 104 YA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~ 183 (302)
|.+.=.+..+.++++ +-+.... .
T Consensus 79 WL~~Ia~n~~~d~~R----------------------~~~~~~~-------------------~---------------- 101 (184)
T PRK12539 79 WVYAIARYKLIDHLR----------------------RTRASLA-------------------D---------------- 101 (184)
T ss_pred HHHHHHHHHHHHHHH----------------------HCCCCCC-------------------C----------------
T ss_conf 999999999999998----------------------5145534-------------------4----------------
Q ss_pred CCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHC
Q ss_conf 43355202323453200000123568705655666666677799999962199999999999827888889899999977
Q gi|254780611|r 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263 (302)
Q Consensus 184 ~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lg 263 (302)
.+++. .++ ....+. . ... + ....|..+|..||++.+.|+.++|+.+ +|.+|||+.||
T Consensus 102 ~~~~~----~~~-------~~~~~~--~-~~~----e---~~~~l~~~l~~Lp~~~r~v~~L~~~eg--~s~~EIA~~lg 158 (184)
T PRK12539 102 VPIDD----ADE-------LVAHDD--A-AAV----E---STLDLGRLLARLPEKMRLAIQAVKLDG--LSVAEAATRSG 158 (184)
T ss_pred CCCCC----CCC-------CCCCCC--H-HHH----H---HHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHC
T ss_conf 88443----444-------567851--3-318----8---999999999849999999999999949--99999999989
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 899999999999999999999974
Q gi|254780611|r 264 VSRERVRQIEARAFKKVQESIQKQ 287 (302)
Q Consensus 264 iS~eRVrQI~~~AL~kLR~~l~~~ 287 (302)
+|...|.-.-.+|+++||+.|.++
T Consensus 159 is~~tVks~l~Rark~Lr~~L~~e 182 (184)
T PRK12539 159 MSESAVKVSVHRGLKALAALIGRE 182 (184)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 199999999999999999998650
No 68
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=99.64 E-value=4.8e-14 Score=113.39 Aligned_cols=174 Identities=7% Similarity=0.133 Sum_probs=124.4
Q ss_pred HHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf 99999998285999999999430778756555579999888999999888998986218534568999757789999998
Q gi|254780611|r 36 VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE 115 (302)
Q Consensus 36 ~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~ 115 (302)
+|+.++.-.||.+|-+.|+..|-..|..+|.++.+..-+-+|++|+-.+-+++.+.+|++. ..|.||.+--.+..+.+
T Consensus 4 ~~i~~~~~e~~e~Af~~L~~~y~~~v~~~~~~~~~d~~~AeD~~Qe~fl~~~~~~~~~~~~--~~~~~Wl~~ia~N~~~d 81 (177)
T PRK09415 4 LTIEAFEIEDKEDLIDEIMNKYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGK--SNLKTWLYRIAINHCKD 81 (177)
T ss_pred HHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHHHH
T ss_conf 9999998769299999999999999999999990999999999999999999987455885--54999999999999999
Q ss_pred HHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCC
Q ss_conf 53202460011023003589999999978878662447888246778886189832110000001223433552023234
Q gi|254780611|r 116 YILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195 (302)
Q Consensus 116 ~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~ 195 (302)
+++. .+... .. +. +...
T Consensus 82 ~~R~----------------------~~~~~-----~~---~~----------------------------~~~~----- 98 (177)
T PRK09415 82 YLKS----------------------WHNKK-----VI---VT----------------------------EDIF----- 98 (177)
T ss_pred HHHH----------------------HHCCC-----CC---CC----------------------------HHHH-----
T ss_conf 9999----------------------87135-----56---30----------------------------3566-----
Q ss_pred CCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 53200000123568705655666666677799999962199999999999827888889899999977899999999999
Q gi|254780611|r 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275 (302)
Q Consensus 196 ~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~ 275 (302)
+.+....+.+++.. ........|..++..||+++|.|+.++|+.+ +|.+|||+.||+|...|+....+
T Consensus 99 ------~~~~~~~~~~~~~~----~~~~~~~~l~~~l~~L~~~~r~ii~l~~~~~--~s~~EIA~~l~is~~tV~~rl~R 166 (177)
T PRK09415 99 ------TYMESQKESVEEEV----IQNAEDERLASAVMSLPIKYREVIYLFYYEE--LSIKEIATVTGVNENTIKTRLKK 166 (177)
T ss_pred ------HHCCCCCCCHHHHH----HHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHH
T ss_conf ------40255579989999----9999999999999769999999999999809--98999999889299999999999
Q ss_pred HHHHHHHHHHH
Q ss_conf 99999999997
Q gi|254780611|r 276 AFKKVQESIQK 286 (302)
Q Consensus 276 AL~kLR~~l~~ 286 (302)
|.++||+.|++
T Consensus 167 ark~Lr~~Lee 177 (177)
T PRK09415 167 AKELLKKGLEE 177 (177)
T ss_pred HHHHHHHHHCC
T ss_conf 99999988368
No 69
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=99.64 E-value=3.9e-14 Score=113.98 Aligned_cols=171 Identities=14% Similarity=0.192 Sum_probs=119.6
Q ss_pred HHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 99999982859999999994307787565555799998889999998889989862185345689997577899999985
Q gi|254780611|r 37 LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116 (302)
Q Consensus 37 l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~ 116 (302)
|+++++ .||..|-+.|+..|.+.|..++.++.+. ..-+|++|+..+.+.+.+.+|++. + .|.||.+--.+..+.++
T Consensus 1 Li~~~~-~Gd~~Af~~ly~~y~~~l~~~~~~~~~~-~~AEDi~Qd~fik~~~~~~~~~~~-~-~~~~wl~~ia~N~~~d~ 76 (175)
T PRK12518 1 LIQRCQ-RGDRQAFRQLYRRYQQKVRSTLYQLCGR-ELLDDLVQEVFLRVWKGLPKLRNP-A-YFSTWLYRITWNVATDA 76 (175)
T ss_pred CHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCH-HHHHHHHHHHHHHHHHCCCCCCCC-C-HHHHHHHHHHHHHHHHH
T ss_conf 989898-6589999999999999999999997799-889999999999998711127982-3-59999999999999999
Q ss_pred HHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCC
Q ss_conf 32024600110230035899999999788786624478882467788861898321100000012234335520232345
Q gi|254780611|r 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196 (302)
Q Consensus 117 i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~ 196 (302)
+++. ++... ..+. ....+ .
T Consensus 77 ~Rk~----------------------~r~~~-------~~~~------------------------~~~~~-------~- 95 (175)
T PRK12518 77 RRQF----------------------AKRPS-------RIQQ------------------------DSSLD-------Q- 95 (175)
T ss_pred HHHH----------------------HCCCC-------CCCC------------------------CCCCC-------C-
T ss_conf 9998----------------------70243-------2332------------------------10002-------4-
Q ss_pred CCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 32000001235687056556666666777999999621999999999998278888898999999778999999999999
Q gi|254780611|r 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276 (302)
Q Consensus 197 ~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~A 276 (302)
....+++++ ... ......+..+++.||+++|.|+.++|+.+ +|.+|||+.+|+|...|+..-.+|
T Consensus 96 --------~~~~~~~~~-~~~----~~~~~~l~~~l~~Lp~~~r~vi~l~~~~~--~s~~EIA~~l~is~~tVk~~l~Ra 160 (175)
T PRK12518 96 --------PSRPSDEPD-LMQ----LHYQDLVQQGLATLSLEHRAVLVLHDLED--LPQKEIAEILNIPVGTVKSRLFYA 160 (175)
T ss_pred --------CCCCCCCHH-HHH----HHHHHHHHHHHHCCCHHHHHHHHHHHHHC--CCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf --------567889769-999----99999999999769999999999999929--999999999895999999999999
Q ss_pred HHHHHHHHHHH
Q ss_conf 99999999974
Q gi|254780611|r 277 FKKVQESIQKQ 287 (302)
Q Consensus 277 L~kLR~~l~~~ 287 (302)
+++||+.|+++
T Consensus 161 ~k~Lr~~L~~e 171 (175)
T PRK12518 161 RRQLRKFLQQQ 171 (175)
T ss_pred HHHHHHHHHHC
T ss_conf 99999999986
No 70
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=99.63 E-value=5.9e-14 Score=112.81 Aligned_cols=177 Identities=16% Similarity=0.229 Sum_probs=123.6
Q ss_pred CCHHHHHHHHHHHHH--HCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH
Q ss_conf 998999999999998--285999999999430778756555579999888999999888998986218534568999757
Q gi|254780611|r 29 LEKQEEYVLAKRYRE--HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106 (302)
Q Consensus 29 Lt~eee~~l~~~~~~--~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~ 106 (302)
||.+| |..+++. .||.+|-+.|+..|-+.|.+.|.++.+...+-+|++|+..+-+.+.+.+|++. .+|.||.+
T Consensus 8 l~D~e---Lv~~~~~g~~gD~~AF~~L~~~y~~~v~~~~~~~~~~~~dAEDl~Qe~flk~~~~l~~~~~~--~~f~~WL~ 82 (188)
T PRK09640 8 LNDEE---LVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGK--SKFKTWLY 82 (188)
T ss_pred CCHHH---HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHH
T ss_conf 99999---99999827963899999999999999999999990999999999999999999988765898--87899999
Q ss_pred HHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCH
Q ss_conf 78999999853202460011023003589999999978878662447888246778886189832110000001223433
Q gi|254780611|r 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186 (302)
Q Consensus 107 ~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SL 186 (302)
-=.+....++++++ +... .. ....++
T Consensus 83 ~Ia~N~~~d~~Rk~----------------------~r~~--------~~------------------------~~~~~~ 108 (188)
T PRK09640 83 SITYNECITQYRKE----------------------RRKR--------RL------------------------MDALSL 108 (188)
T ss_pred HHHHHHHHHHHHHH----------------------CCCC--------CC------------------------CCCCCC
T ss_conf 99999999999986----------------------1545--------55------------------------430002
Q ss_pred HHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCH
Q ss_conf 55202323453200000123568705655666666677799999962199999999999827888889899999977899
Q gi|254780611|r 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266 (302)
Q Consensus 187 d~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~ 266 (302)
+. +. + +.+... ........|..++..|++.+|.||.++|+.+ +|.+|||+.+|+|.
T Consensus 109 ~~-~~---~---------~~~~~~---------~~~e~~~~l~~~l~~L~~~~R~vl~L~~~~~--ls~~EIA~~l~is~ 164 (188)
T PRK09640 109 DP-LE---E---------ASEEKA---------PKPEERGGLDRWLVHVNPIDREILVLRFVAE--LEFQEIADIMHMGL 164 (188)
T ss_pred CC-CC---C---------CCCCCC---------HHHHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCH
T ss_conf 44-45---6---------863100---------2489999999999848999999999999929--99999999989299
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999999999999999740
Q gi|254780611|r 267 ERVRQIEARAFKKVQESIQKQV 288 (302)
Q Consensus 267 eRVrQI~~~AL~kLR~~l~~~~ 288 (302)
..|...-.+|+++||+.|+.=.
T Consensus 165 ~tVksrl~RAr~~Lr~~L~~~~ 186 (188)
T PRK09640 165 SATKMRYKRALDKLREKFAGLA 186 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHCCC
T ss_conf 9999999999999999864514
No 71
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=99.62 E-value=1.5e-13 Score=110.07 Aligned_cols=173 Identities=16% Similarity=0.175 Sum_probs=119.5
Q ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCC-CCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHH
Q ss_conf 99999999999828599999999943077875655557999-98889999998889989862185345689997577899
Q gi|254780611|r 32 QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG-LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110 (302)
Q Consensus 32 eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g-~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr 110 (302)
.+-.+|+.+++ .||.+|-+.|+..+-+.|...+.++.+.. -+-+|++|+..+-+.+...+|+|.. +|.||.+--.+
T Consensus 3 ~~l~~Ll~~~~-~GD~~Af~~l~~~y~~~l~~~~~~~l~~~~~~AEDl~Qe~fl~~~~~~~~~~~~~--~~~~WL~~Ia~ 79 (178)
T PRK12536 3 SRLKALLLRGL-AGDAAAYRQFLTELARHLRAFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRPDQ--PLTAWVQAIAR 79 (178)
T ss_pred HHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCC--CHHHHHHHHHH
T ss_conf 88999999998-1569999999999999999999999099876899999999999999787669999--68999999999
Q ss_pred HHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHC
Q ss_conf 99998532024600110230035899999999788786624478882467788861898321100000012234335520
Q gi|254780611|r 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190 (302)
Q Consensus 111 ~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i 190 (302)
..+.+++++.+ ... ... ..++...
T Consensus 80 n~~~d~~R~~~----------------------r~~------~~~----------------------------~~~~~~~ 103 (178)
T PRK12536 80 YKLADFLRRRA----------------------RRE------ALH----------------------------DPLDDEA 103 (178)
T ss_pred HHHHHHHHHHH----------------------CCC------CCC----------------------------CCCHHHH
T ss_conf 99999999874----------------------645------445----------------------------7511232
Q ss_pred CCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHH
Q ss_conf 23234532000001235687056556666666777999999621999999999998278888898999999778999999
Q gi|254780611|r 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270 (302)
Q Consensus 191 ~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVr 270 (302)
+........+. .....|..+|..||+++|.||.++|+.+ +|.+|||+.||+|...|+
T Consensus 104 -----------~~~~~~~~~~~----------~~~~~l~~~l~~Lp~~~R~~~~l~~~eg--~s~~EIA~~lgis~~tVk 160 (178)
T PRK12536 104 -----------ELFATSDDEAA----------EARRDLGKLLEQLPDRQRLPIVHVKLEG--LSVEETAQLTGLSESAVK 160 (178)
T ss_pred -----------HCCCCCCCCHH----------HHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHH
T ss_conf -----------02478863589----------9999999999869998999999998859--999999999892999999
Q ss_pred HHHHHHHHHHHHHHHH
Q ss_conf 9999999999999997
Q gi|254780611|r 271 QIEARAFKKVQESIQK 286 (302)
Q Consensus 271 QI~~~AL~kLR~~l~~ 286 (302)
..-.+|+++||+.|+.
T Consensus 161 ~rl~Ra~k~Lr~~L~g 176 (178)
T PRK12536 161 VGIHRGLKALAAKIRG 176 (178)
T ss_pred HHHHHHHHHHHHHHCC
T ss_conf 9999999999998079
No 72
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=99.59 E-value=2.3e-13 Score=108.81 Aligned_cols=184 Identities=13% Similarity=0.148 Sum_probs=120.4
Q ss_pred CHHHHHH-----HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf 5999999-----99943077875655557999988899999988899898621853456899975778999999853202
Q gi|254780611|r 46 DLSAAHR-----LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120 (302)
Q Consensus 46 d~~Ar~~-----Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~ 120 (302)
..+|.+. ||+.|-+=....|.++.+..-.-+|++||..+-..+.+++|++. .+|+|+.+-=.+..+.+++|++
T Consensus 12 ~~~~~~~~~~~~l~e~y~~~L~r~A~r~l~d~~~AEDlvQEtFlka~~~l~~F~g~--s~f~tWL~~Ia~N~~iD~lRk~ 89 (207)
T PRK12544 12 SSDAVNVLQDPVFLEDLRAQMLKFAKLQLRDNHLAEDAVQEALFSAYQNADSFAGR--AAFKTWVFAILKNKIIDLLRQK 89 (207)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHHHHHHHHH
T ss_conf 28887611589999999999999999994999999999999999999817743888--8609899999999999999985
Q ss_pred CCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCH
Q ss_conf 46001102300358999999997887866244788824677888618983211000000122343355202323453200
Q gi|254780611|r 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200 (302)
Q Consensus 121 ~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~ 200 (302)
.+...++. . . ..+.. ...++..++ +.+...
T Consensus 90 ~r~~~~~~--------------------~---~-~~~~~-----------------------~~~~~~~~d---~~g~~~ 119 (207)
T PRK12544 90 KRHVSASQ--------------------L---E-DGDEG-----------------------EALIEALFD---ESGHWQ 119 (207)
T ss_pred CCCCCCCC--------------------C---C-CCCCH-----------------------HHHHHHHHC---CCCCCC
T ss_conf 16565210--------------------1---3-45410-----------------------134666511---123433
Q ss_pred HCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 00012356870565566666667779999996219999999999982788888989999997789999999999999999
Q gi|254780611|r 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280 (302)
Q Consensus 201 ~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kL 280 (302)
.+..+...+.| .+..+.......+..+|..||+++|.|+.++|+.| ++.+|||+.||+|...|...-.+|.++|
T Consensus 120 ~~e~p~~~~~p----ee~l~~~e~~~~l~~aL~~Lp~~~R~vl~Lr~~eg--lS~~EIAe~Lgis~~tVks~L~RAR~~L 193 (207)
T PRK12544 120 KDERPQKWDQP----EEGVEQEQFWRIFDACLDALPAKYARVFMMREFIE--LETPEICHNEDLTVSNLNVMLYRSRLRL 193 (207)
T ss_pred CCCCCCCCCCH----HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf 33465333898----99999999999999999839999999999999819--9999999997979999999999999999
Q ss_pred HHHHHHH
Q ss_conf 9999974
Q gi|254780611|r 281 QESIQKQ 287 (302)
Q Consensus 281 R~~l~~~ 287 (302)
|+.|+++
T Consensus 194 r~~Le~~ 200 (207)
T PRK12544 194 RECLENH 200 (207)
T ss_pred HHHHHHH
T ss_conf 9999984
No 73
>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=99.59 E-value=9.8e-14 Score=111.32 Aligned_cols=190 Identities=18% Similarity=0.255 Sum_probs=142.1
Q ss_pred HHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf 99999998285999999999430778756555579999888999999888998986218534568999757789999998
Q gi|254780611|r 36 VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE 115 (302)
Q Consensus 36 ~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~ 115 (302)
++....+ .||..|.+-||..+-.||..-|+.|---|-+-+|++|||+|||.+|+..|++++=..|.+||-.+|...|..
T Consensus 8 ~~~~~~~-~G~~~a~~~~i~~y~~fv~ak~~~yfl~Gad~edi~qeGmiGlyka~rd~~~~~l~sf~afaelC~trqiit 86 (198)
T TIGR02859 8 EIVELAR-EGDEKALEYLIEKYKNFVKAKARSYFLVGADKEDIIQEGMIGLYKAIRDYKEDKLSSFKAFAELCVTRQIIT 86 (198)
T ss_pred HHHHHHH-CCHHHHHHHHHHHHHHHHHHHHHHHEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999997-011889999999999998775311013206456566611689999997531567899999999999999999
Q ss_pred HHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCC
Q ss_conf 53202460011023003589999999978878662447888246778886189832110000001223433552023234
Q gi|254780611|r 116 YILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195 (302)
Q Consensus 116 ~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~ 195 (302)
+|.--.|--++| +..-+||+.|+... +
T Consensus 87 aiktatrqkhiP----------------------------------------------------ln~y~sl~kPiy~~-~ 113 (198)
T TIGR02859 87 AIKTATRQKHIP----------------------------------------------------LNSYVSLNKPIYDE-E 113 (198)
T ss_pred HHHHHHHHCCCC----------------------------------------------------CHHHEECCCCCCCC-C
T ss_conf 988765202465----------------------------------------------------20000025652545-2
Q ss_pred CCCCHHCCCCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 5320000012356-870565566666667779999996219999999999982788888989999997789999999999
Q gi|254780611|r 196 NSSQWQDWLVYDH-DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274 (302)
Q Consensus 196 ~~~~~~d~l~~~~-~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~ 274 (302)
.+.++.|.+.... .+|++.+...++.......+... |+.-|..|+..|. ++.+.+||+..|+-..--| .
T Consensus 114 sdrtl~d~~~~~~~~dP~~l~i~~e~~~~~~~~~~~~---ls~le~~vl~~yl---~G~~yqei~~~l~r~~ksi----d 183 (198)
T TIGR02859 114 SDRTLLDVVSEAKVADPEELIISKEEYEKIESKLEEL---LSDLELKVLVLYL---DGKSYQEIAEDLNRHVKSI----D 183 (198)
T ss_pred CHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHH---CCCHHHHHHHHHHHHHHHH----H
T ss_conf 0147999885443225277763168899999999999---9999999999984---5740788998864566789----9
Q ss_pred HHHHHHHHHHHHHHC
Q ss_conf 999999999997401
Q gi|254780611|r 275 RAFKKVQESIQKQVE 289 (302)
Q Consensus 275 ~AL~kLR~~l~~~~~ 289 (302)
.||.+.+..|++-++
T Consensus 184 nalqrvkrkle~~l~ 198 (198)
T TIGR02859 184 NALQRVKRKLEKYLE 198 (198)
T ss_pred HHHHHHHHHHHHHCC
T ss_conf 999999999976309
No 74
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=99.57 E-value=6.9e-13 Score=105.67 Aligned_cols=170 Identities=11% Similarity=0.117 Sum_probs=117.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHH
Q ss_conf 99999999943077875655557999988899999988899898621853456899975778999999853202460011
Q gi|254780611|r 47 LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126 (302)
Q Consensus 47 ~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRi 126 (302)
.+|-+.|+..|-+.|..+|.++.+...+-+|++|+..+-+.+.+++|++.. .|.||.+--.+..+.++++++.+
T Consensus 2 Eeafe~L~~~y~~~l~~~~~~~~~~~~~AeDl~Qe~flk~~~~~~~~~~~~--~~~~WL~~Ia~N~~~d~~Rk~~r---- 75 (173)
T PRK12522 2 EEKVEELIDIYKDQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVE--NYKKWITTICVRTFYDFYRKKKR---- 75 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCC--CHHHHHHHHHHHHHHHHHHHHCC----
T ss_conf 799999999999999999999919999999999999999999777668854--48999999999999999998634----
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCC
Q ss_conf 02300358999999997887866244788824677888618983211000000122343355202323453200000123
Q gi|254780611|r 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206 (302)
Q Consensus 127 P~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~ 206 (302)
....... ..+ ..+.. +....
T Consensus 76 ------------------~~~~~~~---------------------------------~~~----~~~~~-----~~~~~ 95 (173)
T PRK12522 76 ------------------WKDRILD---------------------------------LFH----KEDGG-----EIEFA 95 (173)
T ss_pred ------------------CCCCCCC---------------------------------CCC----HHHHH-----CCCCC
T ss_conf ------------------1211101---------------------------------000----10000-----12356
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 56870565566666667779999996219999999999982788888989999997789999999999999999999997
Q gi|254780611|r 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286 (302)
Q Consensus 207 ~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~ 286 (302)
+...+++.... ......|..++..||+++|.|+.++|+.+ +|.+|||+.||+|...|+-.-.+|.++||+.|+.
T Consensus 96 ~~~~~~~~~~~----~~~~~~l~~~l~~L~~~~R~vi~L~~~~~--~s~~EIA~~l~is~~tVksrl~rAr~~Lr~~Le~ 169 (173)
T PRK12522 96 DDVNISEEFIQ----KVEAEMIREVIQLLNEKYKTVLVLYYYEQ--YSYKEMSEILNIPIGTVKYRLNYAKKQMREHLEG 169 (173)
T ss_pred CCCCCHHHHHH----HHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf 77885299999----99999999999819999999999999839--9999999998939999999999999999998756
Q ss_pred HH
Q ss_conf 40
Q gi|254780611|r 287 QV 288 (302)
Q Consensus 287 ~~ 288 (302)
-+
T Consensus 170 ~~ 171 (173)
T PRK12522 170 FV 171 (173)
T ss_pred CC
T ss_conf 51
No 75
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=99.56 E-value=6.3e-13 Score=105.94 Aligned_cols=184 Identities=15% Similarity=0.207 Sum_probs=123.4
Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCH
Q ss_conf 99994307787565555799998889999998889989862185345689997577899999985320246001102300
Q gi|254780611|r 52 RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131 (302)
Q Consensus 52 ~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~ 131 (302)
.+++.+-+.+...|.+|.+..-.-+|++|+-.+.+++..++|++. .+|.||.+-=.+..+.++++++.+-++++...
T Consensus 6 ~~le~~r~~L~r~A~~~v~d~~~AEDvvQetfl~~~~~~~~f~~~--~~~~tWL~~IarN~~id~lR~~~r~~~~~~~~- 82 (191)
T PRK12520 6 AQLEALRPYLLRFARLQLRDEAWAEDAVSETLLAALEKPERFAGQ--SQLKTYLVGILKHKIIDALRSGRREVRLSLDE- 82 (191)
T ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC-
T ss_conf 999999999999999994999999999999999999817642765--45598999999999999999836755554334-
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCC
Q ss_conf 35899999999788786624478882467788861898321100000012234335520232345320000012356870
Q gi|254780611|r 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211 (302)
Q Consensus 132 ~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~ 211 (302)
... .+. ..++......++. ..+ .+.+..+|
T Consensus 83 -------------------~~~---~~~------------------------~~~~~~~~~~~~~---~~~-~p~~~~~P 112 (191)
T PRK12520 83 -------------------GDE---QSD------------------------DDLFDALFTADGH---YRE-PPSDWGDP 112 (191)
T ss_pred -------------------CCC---CCH------------------------HHHHHHHHCCCCC---CCC-CCCCCCCH
T ss_conf -------------------565---540------------------------4677776223443---235-87665999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH-HCC
Q ss_conf 5655666666677799999962199999999999827888889899999977899999999999999999999974-012
Q gi|254780611|r 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ-VEL 290 (302)
Q Consensus 212 ~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~-~~~ 290 (302)
+.. .........+..+|+.||+++|.|+.++|+.+ +|..|||+.+|+|...|+..-.+|.++||+.|++. +--
T Consensus 113 e~~----l~~~e~~~~l~~aL~~Lp~~~R~v~~Lr~~~~--ls~~EIA~~l~~s~~tVk~~l~RAR~~Lr~~Le~~~~~~ 186 (191)
T PRK12520 113 EAT----LQRRQFFEVLQACVERLPARTGRVFMMREWLE--LETEEICKELQITATNLWVMLYRARLRLRECLELHWFGN 186 (191)
T ss_pred HHH----HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 999----99999999999999877499999999999938--999999999894999999999999999999998862789
Q ss_pred CCCC
Q ss_conf 2467
Q gi|254780611|r 291 SSSP 294 (302)
Q Consensus 291 ~~~~ 294 (302)
+.+|
T Consensus 187 ~~~~ 190 (191)
T PRK12520 187 QPAP 190 (191)
T ss_pred CCCC
T ss_conf 9999
No 76
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=99.56 E-value=1.1e-12 Score=104.25 Aligned_cols=178 Identities=13% Similarity=0.126 Sum_probs=111.4
Q ss_pred HHHHHHHHHHHHHHH-HHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCC
Q ss_conf 999943077875655-5579999888999999888998986218534568999757789999998532024600110230
Q gi|254780611|r 52 RLVTSHLRLVVKIAM-GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130 (302)
Q Consensus 52 ~Li~~nlrlV~~iA~-~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~ 130 (302)
.|++..-+|+ ..|. +..+..-.-+|++|+..+-.+++++.|++ +.+|+|+.+-=.+..+.+++|+.++..++....
T Consensus 10 ~l~~~r~~L~-~fa~~~L~~~~d~AEDlvQEtflka~~~~~~f~~--~s~f~tWL~~IarN~~id~lR~~~r~~~~~~~~ 86 (195)
T PRK12532 10 ELIESRKLLL-HFARLQLPDHPDLAEDLVQETLLSAYSAGDSFQG--RALVNSWLFAILKNKIIDALRQIGRQRKVFTAL 86 (195)
T ss_pred HHHHHHHHHH-HHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf 9999899999-9999980898757999999999999986874589--887888999999999999999862766767532
Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCC
Q ss_conf 03589999999978878662447888246778886189832110000001223433552023234532000001235687
Q gi|254780611|r 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210 (302)
Q Consensus 131 ~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~ 210 (302)
. .+.. ..+.+..+.. ++.. ..+..+.+..+
T Consensus 87 ------------------------~----~e~~-------------------d~~~~~~~~~--~~~~-~~~~~p~~~~~ 116 (195)
T PRK12532 87 ------------------------D----DELL-------------------DEAFESHFSQ--NGHW-TPEGQPQHWNT 116 (195)
T ss_pred ------------------------C----HHHH-------------------HHHHHHHHCC--CCCC-CCCCCCCCCCC
T ss_conf ------------------------0----2333-------------------2566654201--3445-75446555499
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 056556666666777999999621999999999998278888898999999778999999999999999999999740
Q gi|254780611|r 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288 (302)
Q Consensus 211 ~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~~ 288 (302)
|++ ..........|..+|..||++.|.|+.++|+.| +|.+|||+.+|+|...|+....+|-++||+.|+++-
T Consensus 117 pe~----~~~~~e~~~~l~~~l~~Lp~~~R~vl~L~~~eg--ls~~EIA~~lgis~~tVks~l~RAR~~Lr~~Le~k~ 188 (195)
T PRK12532 117 PEK----SLNNNEFQKILQSCLYNLPENTARVFTLKEILG--FSSDEIQQMCGISTSNYHTIMHRARESLRQCLQIKW 188 (195)
T ss_pred HHH----HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 999----999899999999999859999989999999819--999999999895999999999999999999998827
No 77
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=99.56 E-value=9.1e-13 Score=104.86 Aligned_cols=186 Identities=13% Similarity=0.136 Sum_probs=122.2
Q ss_pred HCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 28599999999943077875655557999988899999988899898621853456899975778999999853202460
Q gi|254780611|r 44 HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123 (302)
Q Consensus 44 ~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~ 123 (302)
.|+.+|-+.||..|.+.|..+|.++.+..-+-+|++|+..+-..+.+.+|+.+ .+.||.+...+....+
T Consensus 17 A~r~eaF~~Lv~rh~~~lyr~a~r~~gn~~dAEDlvQEtFlra~r~l~~frg~---~~~tWL~rIa~N~~~~-------- 85 (217)
T PRK12533 17 AARGERFRALVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSCRGD---NARPWLLAIVRHTWYS-------- 85 (217)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCC---CHHHHHHHHHHHHHHH--------
T ss_conf 21899999999999999999999996999999999999999999867762344---2489999999999999--------
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCC
Q ss_conf 01102300358999999997887866244788824677888618983211000000122343355202323453200000
Q gi|254780611|r 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203 (302)
Q Consensus 124 IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~ 203 (302)
.+++-+... ... ....... . ... +.
T Consensus 86 --------------~~Rrr~~~~-----~~~-------------------------------~~~~~~~--~--~~~-~~ 110 (217)
T PRK12533 86 --------------EWRRRANAH-----EVA-------------------------------YPDTLDD--A--DSP-DD 110 (217)
T ss_pred --------------HHHHHHCCC-----CCC-------------------------------CCCCCCC--C--CCC-CC
T ss_conf --------------999741123-----344-------------------------------2111344--3--234-33
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 12356870565566666667779999996219999999999982788888989999997789999999999999999999
Q gi|254780611|r 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302)
Q Consensus 204 l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302)
.......++..+ ........|..+|..||+.+|.||.++|+.+ +|..|||+.|||+...|.--..+|-++||+.
T Consensus 111 ~~~~~~~pe~~~----~~~e~~~~l~~AL~~Lp~~~R~vl~Lr~~eg--lS~~EIAeiLgip~gTVKSRL~RAR~~Lr~~ 184 (217)
T PRK12533 111 WQPAVEDPLALL----LRGEDVRLVNAALAKLPVEYREVLVLRELED--MSYREIAAIADVPVGTVMSRLARARRRLAAL 184 (217)
T ss_pred CCCCCCCHHHHH----HHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_conf 467879999999----9889999999999809998868999999809--9999999998949999999999999999997
Q ss_pred HHHHHCCCCCCCCCCCCC
Q ss_conf 997401224677645899
Q gi|254780611|r 284 IQKQVELSSSPPLLQKPR 301 (302)
Q Consensus 284 l~~~~~~~~~~~~~~~~~ 301 (302)
|..-...+..+|.=-.||
T Consensus 185 L~~~~~~~~~~~~~~~~~ 202 (217)
T PRK12533 185 LGGAAQAAPGPRAGGRAR 202 (217)
T ss_pred CCCCCCCCCCCCCCCCCC
T ss_conf 223455678999998777
No 78
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=99.56 E-value=2.5e-12 Score=101.88 Aligned_cols=178 Identities=16% Similarity=0.144 Sum_probs=118.6
Q ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHH
Q ss_conf 99999999999828599999999943077875655557999988899999988899898621853456899975778999
Q gi|254780611|r 32 QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111 (302)
Q Consensus 32 eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~ 111 (302)
.+-.+|+.+++ .||..|-..|+..|-..|..++.+..+. -.-+|++|+-.+-+++.+.+|++. -+|.||.+.=.+.
T Consensus 11 a~~~~Lv~~a~-~GD~~Af~~L~~r~~~~v~r~~~~l~~~-~~AeDl~QEtflk~~~~l~~f~~~--~~f~tWL~~Ia~n 86 (195)
T PRK12535 11 AHVTELALAAG-RGDRAALTEFIRATQDDVWRLLAHLGGH-DIADDLTQETYLRVMSALPRFAAR--SSARTWLLSLARR 86 (195)
T ss_pred HHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCH-HHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHH
T ss_conf 88999999998-2209999999999999999999893799-779999999999999988770788--8799999999999
Q ss_pred HHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCC
Q ss_conf 99985320246001102300358999999997887866244788824677888618983211000000122343355202
Q gi|254780611|r 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191 (302)
Q Consensus 112 ~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~ 191 (302)
...+ .+|+-.. ++.. .. ...+
T Consensus 87 ~~~d----------------------~~R~~~~----------~~~~----------~~-------------~~~~---- 107 (195)
T PRK12535 87 VWVD----------------------NIRHDMA----------RPRK----------SA-------------VEYE---- 107 (195)
T ss_pred HHHH----------------------HHHHHHC----------CCCC----------CC-------------CCCC----
T ss_conf 9999----------------------9998851----------6665----------53-------------3322----
Q ss_pred CCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 32345320000012356870565566666667779999996219999999999982788888989999997789999999
Q gi|254780611|r 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271 (302)
Q Consensus 192 ~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQ 271 (302)
+. ...+. .+.....+ ...+..+|..||+.+|.||.++|+.+ +|.+|||+.||+|...|+-
T Consensus 108 ---~~-------~~~d~-~~~~~~~~-------~~~l~~~l~~Lp~~~R~~l~L~~~~g--~s~~EIA~ilgi~~gTVKs 167 (195)
T PRK12535 108 ---DT-------GATDA-TNAGIWSE-------WIDVRTLIDALPPERREALILTQVLG--YTYEEAAKIADVRVGTIRS 167 (195)
T ss_pred ---CC-------CCCCC-CCCHHHHH-------HHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHH
T ss_conf ---35-------66777-64035777-------99999999849998879999999829--9899999998939999999
Q ss_pred HHHHHHHHHHHHHHHHHCCCC
Q ss_conf 999999999999997401224
Q gi|254780611|r 272 IEARAFKKVQESIQKQVELSS 292 (302)
Q Consensus 272 I~~~AL~kLR~~l~~~~~~~~ 292 (302)
-..+|.++||+.|..-.+...
T Consensus 168 Rl~RAr~~Lr~~L~~~~~~~~ 188 (195)
T PRK12535 168 RVARARADLVAATATGDSSAE 188 (195)
T ss_pred HHHHHHHHHHHHHHCCCCCCC
T ss_conf 999999999999756897655
No 79
>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=99.55 E-value=7.1e-13 Score=105.60 Aligned_cols=183 Identities=20% Similarity=0.303 Sum_probs=129.2
Q ss_pred HCCHHHHHHHHHHHHHHHHHHHHH-----HCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 285999999999430778756555-----579999888999999888998986218534568999757789999998532
Q gi|254780611|r 44 HGDLSAAHRLVTSHLRLVVKIAMG-----YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118 (302)
Q Consensus 44 ~gd~~Ar~~Li~~nlrlV~~iA~~-----y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~ 118 (302)
.||.+|..+|+..|-.++.-+|.- ++++ ++-.|++||.+ |.|...||-=+|-.=.=|+.| -|+=..+.|.
T Consensus 3 ~GD~eAl~~L~~~Y~~yLr~La~~~L~~~L~~r-~dpSD~VQe~~---l~A~~~~~~fRG~t~~Ef~~W-LR~IL~~~l~ 77 (190)
T TIGR02984 3 AGDQEALGELLDRYRNYLRLLARVQLDRRLRRR-VDPSDVVQETL---LEAHRDFDQFRGKTEGEFAGW-LRQILANVLA 77 (190)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCHHHHHHHHH---HHHHHHHHHHCCCCHHHHHHH-HHHHHHHHHH
T ss_conf 872778988999862499999999760884001-57545899999---999988875328985789999-9999999999
Q ss_pred CCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCC
Q ss_conf 02460011023003589999999978878662447888246778886189832110000001223433552023234532
Q gi|254780611|r 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198 (302)
Q Consensus 119 ~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~ 198 (302)
+ . ++.++. -..++. ..-+||+..-...++.+.
T Consensus 78 ~------------------~---~~~h~~-~qkRD~--------------------------rrE~~l~~~~~~~~~Ss~ 109 (190)
T TIGR02984 78 D------------------A---LRRHLG-AQKRDI--------------------------RREQSLDAGAARVDESSV 109 (190)
T ss_pred H------------------H---HHHHHH-HHCCCC--------------------------HHCCCCCCCCCCHHHHHH
T ss_conf 9------------------9---998866-420262--------------------------010120124576588799
Q ss_pred CHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 00000123568705655666666677799999962199999999999827888889899999977899999999999999
Q gi|254780611|r 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278 (302)
Q Consensus 199 ~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~ 278 (302)
.+...+.++.+.|.......+ ....|..+|+.|||..|+||.+||+++ +++.|||+.||.|..-|+-+-.+||+
T Consensus 110 ~L~~~Laa~~~sPS~~a~r~E----~~~~L~~AL~~L~e~~REvi~LR~~EG--LS~~EvA~~Md~~~~av~~l~~Ral~ 183 (190)
T TIGR02984 110 RLEAQLAADGPSPSQAAARRE----SAVRLAQALAKLPEDYREVILLRHLEG--LSFAEVAERMDRSEGAVSMLWVRALA 183 (190)
T ss_pred HHHHHHCCCCCCCHHHHHHHH----HHHHHHHHHHHCCHHHHHHHHHHHHHC--CCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 999975189998558999977----999999999647922589999987603--55589998707975898758999999
Q ss_pred HHHHHHH
Q ss_conf 9999999
Q gi|254780611|r 279 KVQESIQ 285 (302)
Q Consensus 279 kLR~~l~ 285 (302)
|||+.+.
T Consensus 184 ~Lr~~l~ 190 (190)
T TIGR02984 184 RLRQILE 190 (190)
T ss_pred HHHHHCC
T ss_conf 9987509
No 80
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=99.55 E-value=1.2e-12 Score=104.07 Aligned_cols=176 Identities=12% Similarity=0.147 Sum_probs=117.4
Q ss_pred CCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHH
Q ss_conf 99899999999999828599999999943077875655557999988899999988899898621853456899975778
Q gi|254780611|r 29 LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108 (302)
Q Consensus 29 Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~w 108 (302)
.+.++-.+|..+++ .||.+|-+.||..|-+-|...+. |.+..-+-+|++||-.+-..+++.+|++. .+|+|+-+-=
T Consensus 6 ~dd~~l~aLv~~a~-~GD~~Af~~L~~~~~~~v~r~~~-~l~d~~~AeDl~QEtFlka~~~l~~f~~~--s~f~tWL~~I 81 (185)
T PRK09649 6 SDDEAVTALALSAA-KGNGRALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAI 81 (185)
T ss_pred CCHHHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHH-HHCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHH
T ss_conf 46099999999999-44799999999999999999999-93899899999999999999988762887--6189999999
Q ss_pred HHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHH
Q ss_conf 99999985320246001102300358999999997887866244788824677888618983211000000122343355
Q gi|254780611|r 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188 (302)
Q Consensus 109 Ir~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~ 188 (302)
.+....+ .+|+.+.. +... .+..++.
T Consensus 82 A~N~~~d----------------------~~Rk~~~~----------~~~~------~~~~~e~---------------- 107 (185)
T PRK09649 82 ARHVVAD----------------------HIRHVRSR----------PRTT------RGARPEH---------------- 107 (185)
T ss_pred HHHHHHH----------------------HHHHHHCC----------CCCC------CCCCHHH----------------
T ss_conf 9999999----------------------99987437----------7643------4457231----------------
Q ss_pred HCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHH
Q ss_conf 20232345320000012356870565566666667779999996219999999999982788888989999997789999
Q gi|254780611|r 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268 (302)
Q Consensus 189 ~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eR 268 (302)
..+... ...... ....+..+|..||+.+|.||.++|+.+ +|.+|||+.+|+|...
T Consensus 108 ---------------~~~~~~-~~~~~e-------~~~~l~~al~~Lp~~~R~vl~L~~~eg--ls~~EIA~~lg~~~gT 162 (185)
T PRK09649 108 ---------------LIDGDR-HARGFE-------DLVEVTTMIADLTTDQREALLLTQLLG--LSYADAAAVCGCPVGT 162 (185)
T ss_pred ---------------CCCCCC-CCCCHH-------HHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHH
T ss_conf ---------------158431-102378-------899999999849999999999899729--9999999998939999
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999999999999974
Q gi|254780611|r 269 VRQIEARAFKKVQESIQKQ 287 (302)
Q Consensus 269 VrQI~~~AL~kLR~~l~~~ 287 (302)
|+---.+|.++|+..|++.
T Consensus 163 VKsRl~RAR~~L~a~le~~ 181 (185)
T PRK09649 163 IRSRVARARDALLADAEPD 181 (185)
T ss_pred HHHHHHHHHHHHHHHCCCC
T ss_conf 9999999999999766855
No 81
>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=99.54 E-value=1.1e-12 Score=104.29 Aligned_cols=175 Identities=14% Similarity=0.142 Sum_probs=115.0
Q ss_pred HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCC-----CHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHH
Q ss_conf 999999998285999999999430778756555579999-----888999999888998986218534568999757789
Q gi|254780611|r 35 YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL-----PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109 (302)
Q Consensus 35 ~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~-----~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wI 109 (302)
.+|+.+++ .||..|-+.|+..+-.-+..+|.++.+..- +-+|++|+..+=|.+..+.++.+....|.||++.|+
T Consensus 5 teLi~~~k-~GD~~Af~~L~~~y~~~l~r~a~~~l~~~~~~ed~~~~~lvqe~Flrl~~~~~~~~~~~~~~f~~~l~~i~ 83 (185)
T pfam07638 5 TQLLQQVK-DGDAAATEQLLPLVYDELRRLAGSKLQNERRGHTLQPTALVHEAFVRLVDTEDFPDWSGRGHFFAAAAEAM 83 (185)
T ss_pred HHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHH
T ss_conf 99999998-67799999999999999999999996353210167789999999999984020236775689999999999
Q ss_pred HHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHH
Q ss_conf 99999853202460011023003589999999978878662447888246778886189832110000001223433552
Q gi|254780611|r 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189 (302)
Q Consensus 110 r~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~ 189 (302)
+..+.++++.+.+ . . ..+... ..+++..
T Consensus 84 ~~~~id~~R~~~~----------------------~-~----~~~~~~-------------------------~~~~~~~ 111 (185)
T pfam07638 84 RRILIDHARRRQR----------------------Q-K----RGGDVQ-------------------------RRELDEV 111 (185)
T ss_pred HHHHHHHHHHHHH----------------------H-H----CCCCCH-------------------------HCCHHHH
T ss_conf 9999999998886----------------------6-1----266410-------------------------1010110
Q ss_pred CCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHH
Q ss_conf 02323453200000123568705655666666677799999962199999999999827888889899999977899999
Q gi|254780611|r 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269 (302)
Q Consensus 190 i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRV 269 (302)
... ...+.+ +... .+. .+...+..|||+++.|+.++|+.+ +|.+|||+.||||...|
T Consensus 112 ~~~-------------~~~~~~-~~~~------~l~-~~~~~l~~Lpp~~r~v~~L~~~eg--lS~~EIAe~Lgis~~TV 168 (185)
T pfam07638 112 VDN-------------GDSPNP-DLLL------DLD-EALEQLFSLSPRQARLVELRFFAG--LSNDEIAERLGVSERTV 168 (185)
T ss_pred CCC-------------CCCCCH-HHHH------HHH-HHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHH
T ss_conf 014-------------568987-8899------999-999998648998888988899759--99999999979699899
Q ss_pred HHHHHHHHHHHHHHHH
Q ss_conf 9999999999999999
Q gi|254780611|r 270 RQIEARAFKKVQESIQ 285 (302)
Q Consensus 270 rQI~~~AL~kLR~~l~ 285 (302)
..--.+|..+||+.|+
T Consensus 169 k~rl~~Ar~~Lr~~l~ 184 (185)
T pfam07638 169 ERNWALARAWLHRELR 184 (185)
T ss_pred HHHHHHHHHHHHHHHC
T ss_conf 9999999999998824
No 82
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=99.54 E-value=8.1e-13 Score=105.20 Aligned_cols=177 Identities=10% Similarity=0.153 Sum_probs=112.8
Q ss_pred HHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHH
Q ss_conf 94307787565555799998889999998889989862185345689997577899999985320246001102300358
Q gi|254780611|r 55 TSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134 (302)
Q Consensus 55 ~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~ 134 (302)
..+=+-....|.++.+..-.-+|++||..+...+++.+|++. .+|+|+.+-=.+..+.+++|+..+.+.+..
T Consensus 15 ~~~r~~L~r~A~~~l~d~~~AEDlvQEtflka~~~~~~F~g~--ss~~TWL~~Ia~N~~id~lRkr~r~~~~~~------ 86 (201)
T PRK12545 15 AQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQ--SAHKTWVFGILRNKLIDTLRARRRTINLSA------ 86 (201)
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCC--CHHHHHHHHHHHHHHHHHHHHHCCCCCCCC------
T ss_conf 999999999999990999899999999999999854045875--238999999999999999996157788553------
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHH
Q ss_conf 99999999788786624478882467788861898321100000012234335520232345320000012356870565
Q gi|254780611|r 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214 (302)
Q Consensus 135 l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~ 214 (302)
+ . ........++..... ++ +.+.....+.+.+.
T Consensus 87 ---------------------------~----d----------~~~d~e~~~d~~~~~--d~----g~w~~~~~p~~~~~ 119 (201)
T PRK12545 87 ---------------------------L----D----------AELDGESLLDRELFK--DN----GHWAAHAKPRPWPK 119 (201)
T ss_pred ---------------------------C----C----------CCCCCCCCCHHHHHC--CC----CCCCCCCCCCCCCC
T ss_conf ---------------------------4----4----------454632111055403--44----54323357888999
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 56666666777999999621999999999998278888898999999778999999999999999999999740
Q gi|254780611|r 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288 (302)
Q Consensus 215 ~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~~ 288 (302)
+....+.......+..+|..||++.|.||.+|++.+ ++..|||+.||+|...|.-.-.+|-.+||+.|+++-
T Consensus 120 Pe~~l~~~e~~~~l~~aL~~LP~~~R~v~~Lr~~eg--ls~~EIA~~L~is~~tVksrL~RAR~~LR~~L~ek~ 191 (201)
T PRK12545 120 PETILQQQQFWTLFETCLDHLPEQIGRVFMMREFLD--FEIDDICTELTLTANHCSVLLYRARTRLRTCLSEKG 191 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 899999999999999999959999988989999928--989999999896999999999999999999999818
No 83
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=99.51 E-value=2.2e-12 Score=102.24 Aligned_cols=165 Identities=10% Similarity=0.123 Sum_probs=115.1
Q ss_pred HCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 28599999999943077875655557999988899999988899898621853456899975778999999853202460
Q gi|254780611|r 44 HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123 (302)
Q Consensus 44 ~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~ 123 (302)
.||.+|-+.|+..|-+.|...|.++.+....-+|++|+-.+-+++.++.|+.. +..|.||.+--.+..+.+++
T Consensus 3 ~gD~~af~~Ly~~~~~~l~~~~~~~~~d~~~AeDivQe~F~k~~~~~~~~~~~-~~~~~~wL~~Ia~n~~~d~~------ 75 (171)
T PRK09645 3 DAEAALMRALYDEHAAALWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADP-TRSARAWLFTVARNLVIDER------ 75 (171)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHHHHHHHHHHH------
T ss_conf 63999999999999999999999990999999999999999999858870664-14199999999999999999------
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCC
Q ss_conf 01102300358999999997887866244788824677888618983211000000122343355202323453200000
Q gi|254780611|r 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203 (302)
Q Consensus 124 IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~ 203 (302)
|+.+... .... ......
T Consensus 76 ----------------R~~~~~~-----~~~~---------------------------~~~~~~--------------- 92 (171)
T PRK09645 76 ----------------RSARARP-----VEGS---------------------------PDVLGV--------------- 92 (171)
T ss_pred ----------------HHHHCCC-----CCCC---------------------------CCHHHH---------------
T ss_conf ----------------9875475-----4344---------------------------423320---------------
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 12356870565566666667779999996219999999999982788888989999997789999999999999999999
Q gi|254780611|r 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302)
Q Consensus 204 l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302)
. ....++.... ......|..+|..||++++.|+.++|+.+ +|.+|||+.||+|...|+..-.+|+++||+.
T Consensus 93 -~--~~~~~~~~~~----~~~~~~l~~ai~~L~~~~r~v~~l~~~~g--~s~~EIA~~l~is~~tVk~~l~ra~~~Lr~~ 163 (171)
T PRK09645 93 -P--EQSTPDEVDA----ALDRLLIADALAQLSPEHRAVLVRSYYRG--WSTAQIAADLGIPEGTVKSRLHYAVRALRLT 163 (171)
T ss_pred -C--CCCCCCHHHH----HHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_conf -2--5688316889----99999999999759999887989999869--9999999998929999999999999999999
Q ss_pred HHHH
Q ss_conf 9974
Q gi|254780611|r 284 IQKQ 287 (302)
Q Consensus 284 l~~~ 287 (302)
|++.
T Consensus 164 L~~~ 167 (171)
T PRK09645 164 LQEM 167 (171)
T ss_pred HHHC
T ss_conf 9970
No 84
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=99.50 E-value=3.2e-12 Score=101.22 Aligned_cols=163 Identities=15% Similarity=0.175 Sum_probs=115.1
Q ss_pred HCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 28599999999943077875655557999988899999988899898621853456899975778999999853202460
Q gi|254780611|r 44 HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123 (302)
Q Consensus 44 ~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~ 123 (302)
.||++|-+.|+..|-+.|.+.|.++.+...+-+|++|+..+-+++.+.+|++.. .|.||.+- |. +++
T Consensus 19 ~~~~~AFe~L~~~y~~~ly~~a~~~~~d~~~AeDl~QEtFlk~~~~~~~~~~~~--~~~tWL~~-----I~---~~~--- 85 (188)
T PRK12517 19 LSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEK--AAKAWLIT-----IL---RRE--- 85 (188)
T ss_pred HCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCC--CHHHHHHH-----HH---HHH---
T ss_conf 135999999999999999999999949999999999999999999887647963--18999999-----99---999---
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCC
Q ss_conf 01102300358999999997887866244788824677888618983211000000122343355202323453200000
Q gi|254780611|r 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203 (302)
Q Consensus 124 IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~ 203 (302)
+.++.++.. . .. ..++...
T Consensus 86 --------------~~~r~~r~~-------~---~~------------------------~~~~~~~------------- 104 (188)
T PRK12517 86 --------------NARRFERKQ-------F---DL------------------------VDIEDDS------------- 104 (188)
T ss_pred --------------HHHHHHHCC-------C---CC------------------------CCCCCCC-------------
T ss_conf --------------889998615-------7---75------------------------6522000-------------
Q ss_pred CCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf 1235-687056556666666777999999621999999999998278888898999999778999999999999999999
Q gi|254780611|r 204 LVYD-HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282 (302)
Q Consensus 204 l~~~-~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~ 282 (302)
+.+. ...+++ ......|..+|..||+++|.||.++|+.+ +|.+|||+.||||...|+..-.+|.++||+
T Consensus 105 ~~~~~~~~~e~--------~~~~~~l~~~l~~Lp~~~R~vi~L~~~eg--~s~~EIA~~Lgis~~tVksrl~RAr~~Lr~ 174 (188)
T PRK12517 105 IEDDLSSSSEE--------EMEQYWLRRQIAKLDPEYREPLLLQVIGG--FSGEEIAEILDLNKNTVMTRLFRARNQLKE 174 (188)
T ss_pred CCCCCCCCCHH--------HHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf 24666788168--------99999999999769999999999999839--999999999893999999999999999999
Q ss_pred HHHHHHCC
Q ss_conf 99974012
Q gi|254780611|r 283 SIQKQVEL 290 (302)
Q Consensus 283 ~l~~~~~~ 290 (302)
.|++.-+.
T Consensus 175 ~Le~~~e~ 182 (188)
T PRK12517 175 ALEKPDEV 182 (188)
T ss_pred HHCCHHHH
T ss_conf 97420275
No 85
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=99.47 E-value=5.5e-12 Score=99.63 Aligned_cols=157 Identities=8% Similarity=0.100 Sum_probs=112.9
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCC
Q ss_conf 99999943077875655557999988899999988899898621853456899975778999999853202460011023
Q gi|254780611|r 50 AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129 (302)
Q Consensus 50 r~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~ 129 (302)
.+.|...|-+.|...|.++.+..-+-+|++|+..+-+.+...+|++. ..|.||.+--.+..+.++++++.+.
T Consensus 3 ~E~Ly~~y~~~l~~~~~~~~~d~~~AEDivQe~flk~~~~~~~~~~~--~~~~~WL~~IarN~~id~~Rk~~r~------ 74 (181)
T PRK09637 3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDG--SSIKSWLYQIANNTIIDFYRKKNRS------ 74 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCC--CCHHHHHHHHHHHHHHHHHHHHCCC------
T ss_conf 99999999999999999995999999999999999999852205882--3499999999999999999861555------
Q ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCC
Q ss_conf 00358999999997887866244788824677888618983211000000122343355202323453200000123568
Q gi|254780611|r 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209 (302)
Q Consensus 130 ~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~ 209 (302)
. ..+. +. ... +.+
T Consensus 75 -----------------------~-~~~~----------------------------~~-~~~--------------~~~ 87 (181)
T PRK09637 75 -----------------------E-ELPD----------------------------DL-LFE--------------DEE 87 (181)
T ss_pred -----------------------C-CCCH----------------------------HH-CCC--------------CCC
T ss_conf -----------------------6-7742----------------------------22-146--------------798
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 70565566666667779999996219999999999982788888989999997789999999999999999999997401
Q gi|254780611|r 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289 (302)
Q Consensus 210 ~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~~~ 289 (302)
+++. ........|..+|+.||+++|.|+.++|+.+ +|.+|||+.||+|...|+..-.+|.++||+.|+....
T Consensus 88 -~~~~-----~~~e~~~~l~~~l~~Lp~~~R~v~~L~~~eg--~s~~EIA~~L~is~~tVksrl~RAr~~Lr~~LE~~~~ 159 (181)
T PRK09637 88 -REEN-----AKKELAPCLRPFIDALPEKYAEALRLTELEG--LSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEGCCD 159 (181)
T ss_pred -CCHH-----HHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf -3224-----9999999999999769999989979998859--9999999998949999999999999999999971278
No 86
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=99.47 E-value=9.3e-12 Score=98.12 Aligned_cols=168 Identities=10% Similarity=0.085 Sum_probs=117.5
Q ss_pred HCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 28599999999943077875655557999988899999988899898621853456899975778999999853202460
Q gi|254780611|r 44 HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123 (302)
Q Consensus 44 ~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~ 123 (302)
.++..+-++|+.++++-+...|.++.+..-+-+|++|+.++=+.+..++|++. ..|.||.+--.+..+.++++++++
T Consensus 9 ~~~~~~F~~l~~~~~p~L~~~a~~l~~~~~dAEDlvQetflk~~~~~~~~~~~--~~~~aWL~~IarN~~~d~~Rk~~r- 85 (190)
T PRK12516 9 VEGTPPFKRELLASLPSLRAFAVSLIGQHDRADDLVQDTIMKAWAKQESFEVG--TNMKAWLFTILRNEFYTQMRKRGR- 85 (190)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHHHHHHHHCCC-
T ss_conf 99872099999998999999999990999999999999999999998635656--779999999999999999996168-
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCC
Q ss_conf 01102300358999999997887866244788824677888618983211000000122343355202323453200000
Q gi|254780611|r 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203 (302)
Q Consensus 124 IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~ 203 (302)
.. ... ...+... ..
T Consensus 86 ---------------------~~----------~~~-----------------d~~~~e~------~~------------ 99 (190)
T PRK12516 86 ---------------------EV----------QDT-----------------DGMFSEQ------LA------------ 99 (190)
T ss_pred ---------------------CC----------CCC-----------------CCCCCCC------CC------------
T ss_conf ---------------------66----------653-----------------2223333------46------------
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 12356870565566666667779999996219999999999982788888989999997789999999999999999999
Q gi|254780611|r 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302)
Q Consensus 204 l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302)
..+... ...+ ...+..+|..||+++|.|+.++|+.+ +|.+|||+.||||...|+.--.+|.++||+.
T Consensus 100 ---~~~~~~----~~~~----~~~l~~al~~Lp~~~R~vl~L~~~eg--ls~~EIAe~Lgis~~TVksrl~RAr~~Lr~~ 166 (190)
T PRK12516 100 ---VHPSQY----GTLD----LQDFRAALDQLPDDQREAIILIGASG--FAYEEAAEICGCAVGTIKSRVSRARARLQEI 166 (190)
T ss_pred ---CCCCCC----CHHH----HHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_conf ---895420----2077----99999999819999989999899829--9999999998949999999999999999999
Q ss_pred HHHHHCCCCC
Q ss_conf 9974012246
Q gi|254780611|r 284 IQKQVELSSS 293 (302)
Q Consensus 284 l~~~~~~~~~ 293 (302)
|+.+-+....
T Consensus 167 L~~~g~~~~g 176 (190)
T PRK12516 167 LQIEGEADYG 176 (190)
T ss_pred HHHCCCCCCC
T ss_conf 9845998789
No 87
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=99.46 E-value=7.7e-12 Score=98.64 Aligned_cols=157 Identities=11% Similarity=0.147 Sum_probs=110.1
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCC
Q ss_conf 99999943077875655557999988899999988899898621853456899975778999999853202460011023
Q gi|254780611|r 50 AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129 (302)
Q Consensus 50 r~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~ 129 (302)
-+.|+..|-+-|...|.++.+....-+|++|+..+-+.+.+..||++ +|.||.+.-.+..+.++++++.+...
T Consensus 3 ~E~ly~~y~~~l~~~~~~~~~d~~~AeDl~Qe~flk~~~~~~~~~~~---~~~~WL~~Ia~n~~~d~~Rk~~r~~~---- 75 (165)
T PRK09644 3 IEEIYKMYINDVYRYLFSLTKSHHLAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYHTFIDFVRKEKKVVF---- 75 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCC---CHHHHHHHHHHHHHHHHHHHHCCCCC----
T ss_conf 99999999999999999990999999999999999999988766813---18999999999999999997447577----
Q ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCC
Q ss_conf 00358999999997887866244788824677888618983211000000122343355202323453200000123568
Q gi|254780611|r 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209 (302)
Q Consensus 130 ~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~ 209 (302)
++.+ .++. +. ..
T Consensus 76 --------------------------------------~~~~-------------~~~~---------------~~--~~ 87 (165)
T PRK09644 76 --------------------------------------VGTD-------------EIET---------------IQ--AE 87 (165)
T ss_pred --------------------------------------CCHH-------------HHCC---------------CC--CC
T ss_conf --------------------------------------6521-------------1001---------------13--58
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 705655666666677799999962199999999999827888889899999977899999999999999999999974
Q gi|254780611|r 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287 (302)
Q Consensus 210 ~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~ 287 (302)
.+++.. ........|..+|..||++++.|+.++|+.+ +|.+|||+.||+|...|+..-.+|.++||+.|+++
T Consensus 88 ~~~~~~----~~~e~~~~l~~~l~~Lp~~~r~v~~L~~~~~--~s~~EIA~~l~is~~tVk~rl~RAr~~Lr~~L~~e 159 (165)
T PRK09644 88 STEEYA----VAKNSYEKLIQIIHTLPVIEAQAILLCDVHE--LTYEEAASVLDLKENTYKSHLFRGRKRLKALLKEE 159 (165)
T ss_pred CHHHHH----HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 801499----9899999999998729999999999999988--89999999989399999999999999999999987
No 88
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=99.46 E-value=1.1e-11 Score=97.63 Aligned_cols=160 Identities=11% Similarity=0.142 Sum_probs=108.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCH
Q ss_conf 85999999999430778756555579999888999999888998986218534568999757789999998532024600
Q gi|254780611|r 45 GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124 (302)
Q Consensus 45 gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~I 124 (302)
++++|-+.|+..|-+.|...|.++.+..-.-+|++|+..+-+++.++.|. |-.|.||.+--.+....+++
T Consensus 2 ~~r~afe~ly~~~~~~l~~~~~~~~~d~~~AeDl~QetFlk~~~~~~~~~---~~~~~~WL~~Ia~N~~~d~~------- 71 (161)
T PRK12541 2 KRKQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYK---GEEIRPWLFTIAYNAFIDWY------- 71 (161)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCC---CCCHHHHHHHHHHHHHHHHH-------
T ss_conf 63999999999999999999999939999999999999999998361316---67568999999999999999-------
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCC
Q ss_conf 11023003589999999978878662447888246778886189832110000001223433552023234532000001
Q gi|254780611|r 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204 (302)
Q Consensus 125 RiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l 204 (302)
|+.+.. .. . +++. ..
T Consensus 72 ---------------Rk~~~~--------~~-~---------------------------~~~~--------------~~ 86 (161)
T PRK12541 72 ---------------RKEKKY--------KT-T---------------------------TVEE--------------FH 86 (161)
T ss_pred ---------------HHHHCC--------CC-C---------------------------CHHH--------------HC
T ss_conf ---------------986044--------65-5---------------------------2555--------------40
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 23568705655666666677799999962199999999999827888889899999977899999999999999999999
Q gi|254780611|r 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284 (302)
Q Consensus 205 ~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l 284 (302)
..+.+.+++...... ....+..++..||+++|.|+.++|+.| +|.+|||+.||+|...|+-.-.+|.++||+.+
T Consensus 87 ~~~~~~~~~~~~~~~----~~~~~~~~l~~Lp~~~R~v~~L~~~~g--~s~~EIA~~lgis~~tVk~~l~RArk~Lr~l~ 160 (161)
T PRK12541 87 LPNVPSTEHEYFVKH----EIASWLDSLSSLPLERRNVLLLRDYYG--FSYKEIAEMTGLSLAKVKIELHRGRKETKSIK 160 (161)
T ss_pred CCCCCCCHHHHHHHH----HHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 468999627789999----999999999819999999999899749--99999999989399999999999999998762
Q ss_pred H
Q ss_conf 9
Q gi|254780611|r 285 Q 285 (302)
Q Consensus 285 ~ 285 (302)
+
T Consensus 161 E 161 (161)
T PRK12541 161 E 161 (161)
T ss_pred C
T ss_conf 9
No 89
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=99.45 E-value=2.7e-11 Score=95.04 Aligned_cols=170 Identities=16% Similarity=0.183 Sum_probs=121.6
Q ss_pred HHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 82859999999994307787565555799998889999998889989862185345689997577899999985320246
Q gi|254780611|r 43 EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122 (302)
Q Consensus 43 ~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~ 122 (302)
..|+..+-..++..+.+-+...|.++.+..-+-+||+||.++.+++++..| +. +..|.||.+--++....+++++..+
T Consensus 10 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~-~~~~~~wl~~Ia~n~~iD~~R~~~r 87 (182)
T COG1595 10 LRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RG-RSSFKAWLYRIARNLAIDRLRKRKR 87 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCHHC-CC-CCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 875178899999999999999999996884309999999999999733311-67-8878999999999999999997610
Q ss_pred CHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHC
Q ss_conf 00110230035899999999788786624478882467788861898321100000012234335520232345320000
Q gi|254780611|r 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202 (302)
Q Consensus 123 ~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d 202 (302)
......... . . .
T Consensus 88 ----------------------~~~~~~~~~------------------------~-----~------~----------- 99 (182)
T COG1595 88 ----------------------RRARVEEAD------------------------L-----L------P----------- 99 (182)
T ss_pred ----------------------HCCHHHHCC------------------------C-----C------C-----------
T ss_conf ----------------------132001000------------------------2-----4------5-----------
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf 01235687056556666666777999999621999999999998278888898999999778999999999999999999
Q gi|254780611|r 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282 (302)
Q Consensus 203 ~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~ 282 (302)
......++.. +..........+..++..||++++.++.++|+.| +|..|||+.+|||...|.....+|+.+|++
T Consensus 100 --~~~~~~~~~~--~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~~~g--ls~~EIA~~l~i~~~tVks~l~ra~~~l~~ 173 (182)
T COG1595 100 --EEADPAPDLA--ELLLAEEELERLRRALARLPPRQREAFLLRYLEG--LSYEEIAEILGISVGTVKSRLHRARKKLRE 173 (182)
T ss_pred --CCCCCCCHHH--HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf --4345670267--8887678999999999839999999999999859--999999989599999999999999999999
Q ss_pred HHHHHH
Q ss_conf 999740
Q gi|254780611|r 283 SIQKQV 288 (302)
Q Consensus 283 ~l~~~~ 288 (302)
.|....
T Consensus 174 ~l~~~~ 179 (182)
T COG1595 174 QLEEAG 179 (182)
T ss_pred HHHHHC
T ss_conf 875501
No 90
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=99.44 E-value=7.5e-12 Score=98.74 Aligned_cols=157 Identities=13% Similarity=0.179 Sum_probs=106.4
Q ss_pred HHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHH
Q ss_conf 99430778756555579999888999999888998986218534568999757789999998532024600110230035
Q gi|254780611|r 54 VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133 (302)
Q Consensus 54 i~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r 133 (302)
|+.|-+.|.++|.++.+..-+-+|++|+-.+-+.+++.+|+.. | |+||-+-=.+....++++++.+
T Consensus 1 v~~Y~~~ly~~~~~~~~n~~dAeDi~QevFik~~~~~~~~~~~-~--~~~WL~~Ia~N~~~d~~Rk~~r----------- 66 (160)
T PRK09642 1 MQTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFR-G--LKTWMARIATNHAIDYKRKKAR----------- 66 (160)
T ss_pred CCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCC-C--HHHHHHHHHHHHHHHHHHHHHC-----------
T ss_conf 9467899999999990999999999999999999845033624-4--9999999999999999998724-----------
Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHH
Q ss_conf 89999999978878662447888246778886189832110000001223433552023234532000001235687056
Q gi|254780611|r 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213 (302)
Q Consensus 134 ~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~ 213 (302)
. .. ..++... .++ ......++++
T Consensus 67 -----------~-----------~~------------------------~~~~~~~---~~~--------~~~~~~~~e~ 89 (160)
T PRK09642 67 -----------E-----------NE------------------------ELSLCKE---TEE--------NIKSSHNIED 89 (160)
T ss_pred -----------C-----------CC------------------------CCCCCHH---HHH--------CCCCCCCHHH
T ss_conf -----------5-----------53------------------------1220001---121--------1567799899
Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 55666666677799999962199999999999827888889899999977899999999999999999999974
Q gi|254780611|r 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287 (302)
Q Consensus 214 ~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~ 287 (302)
.+. .+.....+..+|..||++.|.|+.++|+.+ +|.+|||+.||+|...|...-.+|.++||+.++++
T Consensus 90 ~~~----~~e~~~~l~~~l~~Lp~~~R~v~~L~~~e~--~s~~EIA~~l~is~~tVk~~l~RArk~Lkk~lkee 157 (160)
T PRK09642 90 LLL----TKEQKLLIAQKLRELPENYRDVVLAHYLEE--KSYQEIALQENIEVKTVEMKLYRARKWIKKHWKEE 157 (160)
T ss_pred HHH----HHHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 999----899999999999979999999979999829--99999999989199999999999999999999875
No 91
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=99.43 E-value=2.3e-11 Score=95.46 Aligned_cols=173 Identities=16% Similarity=0.184 Sum_probs=110.1
Q ss_pred HHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHH
Q ss_conf 99430778756555579999888999999888998986218534568999757789999998532024600110230035
Q gi|254780611|r 54 VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133 (302)
Q Consensus 54 i~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r 133 (302)
++.+-+=+...|.++.+..-+-+|++||-.+-..+.++.|++. .+|+|+.+-=.+..+.+++|++.|.+...
T Consensus 15 ~e~yr~~L~~fa~~~l~d~~~AEDlvQEtFlka~~~~~~f~~~--~~f~tWL~~Ia~N~~id~lRk~~r~~~~~------ 86 (191)
T PRK12530 15 LEEIRLQMLKFATLQLKDADLAEDVVQEAFTSALKNIDSFKGQ--SALKTWIFAILKNKIIDYIRQRKRFVNES------ 86 (191)
T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHHHHHHHHHCCCCCCC------
T ss_conf 9999999999999993999999999999999999868863787--72999999999999999999846667721------
Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCC-CCCCCCH
Q ss_conf 899999999788786624478882467788861898321100000012234335520232345320000012-3568705
Q gi|254780611|r 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV-YDHDGQE 212 (302)
Q Consensus 134 ~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~-~~~~~~~ 212 (302)
++. .++. +.++ . |+.+....+... ....+++
T Consensus 87 ---------------------------~~~------~~~~---------~~~~---~---d~~~~~~~~~~~~~~~~~~e 118 (191)
T PRK12530 87 ---------------------------ELI------EEES---------PNSF---F---DEKGHWKPETYEPSELQDVE 118 (191)
T ss_pred ---------------------------CCC------CCCC---------CHHH---H---CCCCCCCCCCCCCCCCCCHH
T ss_conf ---------------------------001------2224---------1001---0---11122343336830216899
Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 6556666666777999999621999999999998278888898999999778999999999999999999999740
Q gi|254780611|r 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288 (302)
Q Consensus 213 ~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~~ 288 (302)
+..........+..+|..||++++.|+.++|+.+ +|.+|||+.||+|...|.....+|..+||+.|+++-
T Consensus 119 ----~~~~~~e~~~~l~~~l~~LP~~~R~v~~Lr~~~~--ls~~EIA~~l~is~~tVksrL~RAR~~Lr~~L~~~~ 188 (191)
T PRK12530 119 ----QTVYSEEFWLIFEICLNKLPAQQARVFMMREFLE--LSSEQICQECHITTSNLHVLLYRARLQLQACLSKKW 188 (191)
T ss_pred ----HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf ----9999999999999999869999999999999929--999999999896999999999999999999999845
No 92
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=99.43 E-value=1.5e-11 Score=96.66 Aligned_cols=161 Identities=13% Similarity=0.132 Sum_probs=109.4
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCH
Q ss_conf 85999999999430778756555579999888999999888998986218534568999757789999998532024600
Q gi|254780611|r 45 GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124 (302)
Q Consensus 45 gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~I 124 (302)
.+.+.++.|++ |.+-+...|.++.+..-+-+|++|+..+-+.+.+.+|++. .+|.||.+--++..+.++
T Consensus 5 ~~~~~~~~l~e-H~p~L~~fa~r~~~~~~~AEDlvQEtflk~~~~l~~~~~~--~~~~tWL~~IarN~~~d~-------- 73 (188)
T PRK12546 5 KHRDPRDELVE-HLPALRAFAISLTRNVAAADDLVQDTVVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSD-------- 73 (188)
T ss_pred CCHHHHHHHHH-HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHHHHH--------
T ss_conf 30629999999-9999999999991999999999999999999978764765--313889999999999999--------
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCC
Q ss_conf 11023003589999999978878662447888246778886189832110000001223433552023234532000001
Q gi|254780611|r 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204 (302)
Q Consensus 125 RiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l 204 (302)
.|+.+... . ..+.... + ..
T Consensus 74 --------------~Rk~~r~~--------~-----------------------------~~~~~~~---~-------~~ 92 (188)
T PRK12546 74 --------------RRKHKREV--------E-----------------------------DPEGVHA---A-------SL 92 (188)
T ss_pred --------------HHHHCCCC--------C-----------------------------CCCCCCC---C-------CC
T ss_conf --------------99744777--------7-----------------------------6421112---3-------34
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 23568705655666666677799999962199999999999827888889899999977899999999999999999999
Q gi|254780611|r 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284 (302)
Q Consensus 205 ~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l 284 (302)
. ..+..+. . .....+..+|..||+++|.|+.++|+.| +|.+|||+.||||...|.---.+|.++||+.|
T Consensus 93 ~-~~~~~~~----~----~~~~~l~~aL~~LP~~~R~vl~L~~~eg--ls~~EIAe~Lgis~gTVKsRL~RAR~~Lr~~L 161 (188)
T PRK12546 93 A-VKPAHDG----R----LAMSDFRAAFAQLPDEQREALILVGASG--FSYEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred C-CCCCCHH----H----HHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 6-8987006----8----9999999999869999988958799829--89999999989399999999999999999987
Q ss_pred HHHH
Q ss_conf 9740
Q gi|254780611|r 285 QKQV 288 (302)
Q Consensus 285 ~~~~ 288 (302)
+.+.
T Consensus 162 e~~~ 165 (188)
T PRK12546 162 QLEE 165 (188)
T ss_pred HCCC
T ss_conf 2721
No 93
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=99.42 E-value=1.3e-11 Score=97.22 Aligned_cols=69 Identities=16% Similarity=0.311 Sum_probs=60.5
Q ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 66666677799999962199999999999827888889899999977899999999999999999999974
Q gi|254780611|r 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287 (302)
Q Consensus 217 e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~ 287 (302)
+..+.......|..+|..||+++|.|+.++|+.+ +|..|||+.||+|...|.-.-.+|+++||+.|+++
T Consensus 89 ~~~~~~e~~~~l~~ai~~Lp~~qR~vl~L~~~eg--ls~~EIA~~l~is~~tVk~~l~RAr~~Lr~~Le~~ 157 (161)
T PRK09047 89 DRLERAQVLQLIEEAIQKLPARQREAFLLRYWED--MDVAETAAAMGCSEGSVKTHCSRATHTLAKALEAK 157 (161)
T ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 9999999999999999819999999989999987--79999999989699999999999999999999986
No 94
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=99.41 E-value=3.2e-11 Score=94.56 Aligned_cols=166 Identities=18% Similarity=0.222 Sum_probs=116.5
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCH
Q ss_conf 85999999999430778756555579999888999999888998986218534568999757789999998532024600
Q gi|254780611|r 45 GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124 (302)
Q Consensus 45 gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~I 124 (302)
-+..|...|...|-.-+...|.++.+...+-+|++|+..+-|.++...|++.. .+ +|.+.-++....++++++.
T Consensus 9 ~~e~al~elf~~~~~~L~~~a~r~~~~~~~AEDivQe~Flkl~~~~~~~~~~~--~~-awL~~iarN~~id~lRr~~--- 82 (183)
T PRK07037 9 ACDGALLDVFVDNRSMLVKIARGIVGCASRAEDVVQDAFVKLVEAPNQDAVKQ--PV-AYLFQMVRNLAIDHCRRQS--- 82 (183)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCC--HH-HHHHHHHHHHHHHHHHHHH---
T ss_conf 60899999999999999999999979998899999999999997454344136--99-9999999999999999777---
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCC
Q ss_conf 11023003589999999978878662447888246778886189832110000001223433552023234532000001
Q gi|254780611|r 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204 (302)
Q Consensus 125 RiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l 204 (302)
.... ... . +++.. .+
T Consensus 83 -------------------~~~~-----~~~-----------------------------~--------~~~~~----~~ 97 (183)
T PRK07037 83 -------------------LENK-----YHG-----------------------------D--------EDDGL----DV 97 (183)
T ss_pred -------------------HHHH-----CCC-----------------------------C--------HHHHC----CC
T ss_conf -------------------6650-----134-----------------------------2--------44421----26
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 23568705655666666677799999962199999999999827888889899999977899999999999999999999
Q gi|254780611|r 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284 (302)
Q Consensus 205 ~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l 284 (302)
++..+.|++.+...+ ....|..+|..||+++|.|+.++++.| +|.+|||+.||||...|.-.-.+|+++||+.|
T Consensus 98 ~~~~~~pe~~~~~~e----~~~~l~~ai~~LP~~~R~v~~L~~~eg--~s~~EIAe~LgiS~~tVk~~l~rAl~~LR~~L 171 (183)
T PRK07037 98 PSPEASPEAALINRD----TLRHVADALDELPARTRAAFEMVRLRG--ETLQDIARELNVSQTLVNFMIRDALRHCRKCL 171 (183)
T ss_pred CCCCCCHHHHHHHHH----HHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 788999899999999----999999999819999999989898739--89999999989299999999999999999999
Q ss_pred HHH
Q ss_conf 974
Q gi|254780611|r 285 QKQ 287 (302)
Q Consensus 285 ~~~ 287 (302)
+.=
T Consensus 172 e~~ 174 (183)
T PRK07037 172 DAC 174 (183)
T ss_pred HHH
T ss_conf 876
No 95
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=99.39 E-value=7.7e-11 Score=91.96 Aligned_cols=160 Identities=12% Similarity=0.139 Sum_probs=111.0
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHH
Q ss_conf 59999999994307787565555799998889999998889989862185345689997577899999985320246001
Q gi|254780611|r 46 DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125 (302)
Q Consensus 46 d~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IR 125 (302)
..++-++|+..+.+-+...|.++.+..-+-+|++|+..+=+.+...+|++. ..|.||.+--.+..+.+++
T Consensus 4 ~~~~F~~l~~~~~p~L~~~a~~l~~~~~~AeDlvQe~flk~~~~~~~~~~~--~~~~~Wl~~IarN~~~d~~-------- 73 (164)
T PRK12547 4 TSKNFKQELLAALPSLRAFAVSLSSKHDKADDLVQDTLMKAWAKQDSFQPG--TNLKAWLFTILRNEFYSQM-------- 73 (164)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHHHHHH--------
T ss_conf 799999999998999999999994999999999999999999988876998--8699999999999999999--------
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCC
Q ss_conf 10230035899999999788786624478882467788861898321100000012234335520232345320000012
Q gi|254780611|r 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205 (302)
Q Consensus 126 iP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~ 205 (302)
|+-+... . . . ...+. . . .
T Consensus 74 --------------Rk~~r~~--------~--~------------~-----~~~~~------~------~--------~- 91 (164)
T PRK12547 74 --------------RKRGREV--------Q--D------------S-----DGVFT------A------R--------L- 91 (164)
T ss_pred --------------HHHCCCC--------C--C------------C-----CCCCC------C------C--------C-
T ss_conf --------------9727877--------6--5------------2-----10110------1------2--------5-
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 35687056556666666777999999621999999999998278888898999999778999999999999999999999
Q gi|254780611|r 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285 (302)
Q Consensus 206 ~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~ 285 (302)
...+..+ ...+ ...+..++..||+.+|.|+.++|+.| +|.+|||+.+|+|...|+.-..+|.++||+.|+
T Consensus 92 ~~~~~~~----~~~~----~~~l~~al~~Lp~~~r~v~~L~~~~g--~s~~EIA~~lgis~~tVksrl~rAr~~Lr~~Lk 161 (164)
T PRK12547 92 AVHPAQY----GSLD----LQDFRKALNLLPADQREAIILIGASG--FSYEEAAEICGCAVGTIKSRVSRARNRLQELLK 161 (164)
T ss_pred CCCCHHH----HHHH----HHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 6894024----3689----99999999858999999999899849--999999999893999999999999999999987
Q ss_pred HH
Q ss_conf 74
Q gi|254780611|r 286 KQ 287 (302)
Q Consensus 286 ~~ 287 (302)
+.
T Consensus 162 ~~ 163 (164)
T PRK12547 162 ID 163 (164)
T ss_pred HC
T ss_conf 67
No 96
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=99.39 E-value=7.3e-11 Score=92.14 Aligned_cols=161 Identities=12% Similarity=0.103 Sum_probs=108.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHH
Q ss_conf 99999999943077875655557999988899999988899898621853456899975778999999853202460011
Q gi|254780611|r 47 LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126 (302)
Q Consensus 47 ~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRi 126 (302)
.+|-+.|+..|-+.|...|.++.+....-+|++|+..+-+++. .|++ ...|.||.+--.+..+.++++++.
T Consensus 2 eeAF~~ly~~y~~~l~~~~~~~~~d~~~AeDl~Qe~flk~~~~--~~~~--~~~~~~wL~~ia~n~~~d~~R~~~----- 72 (166)
T PRK09639 2 EETFEDLFKQYYQDVVQQIIYIVKDRTQAEDLAQEVFLRLLRS--DWKG--IENEKGWLIKSARNVAYNYFRSEK----- 72 (166)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHC--CCCC--CCCHHHHHHHHHHHHHHHHHHHHH-----
T ss_conf 8999999999999999999999299999999999999999872--6354--467899999999999999999884-----
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCC
Q ss_conf 02300358999999997887866244788824677888618983211000000122343355202323453200000123
Q gi|254780611|r 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206 (302)
Q Consensus 127 P~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~ 206 (302)
....... ...+ ... ..
T Consensus 73 -----------------~~~~~~~---------------------------------~~~~-------~~~-------~~ 88 (166)
T PRK09639 73 -----------------RHRARIL---------------------------------GEFQ-------WQE-------EQ 88 (166)
T ss_pred -----------------HHHHHHC---------------------------------CCHH-------CCC-------CC
T ss_conf -----------------0201000---------------------------------0100-------013-------45
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 56870565566666667779999996219999999999982788888989999997789999999999999999999997
Q gi|254780611|r 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286 (302)
Q Consensus 207 ~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~ 286 (302)
...++++.... ......+..++..||++++.|+.++| .| +|.+|||+.||+|...|+..-.+|+++||+.|++
T Consensus 89 ~~~~~e~~~~~----~~~~~~l~~~l~~Lp~~~r~v~~l~~-~g--~s~~EIA~~l~is~~tVk~~l~RA~~~Lr~~le~ 161 (166)
T PRK09639 89 IDSSPEEIWIR----KEEITKVQEVLAKMTERDRTVLLLRF-SG--YSYKEIAQALGIDESSVGTTLHRAKKKFRKIYEQ 161 (166)
T ss_pred CCCCHHHHHHH----HHHHHHHHHHHHHCCHHHHHHHHHHH-HC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 57997899998----99999999998839999999999999-38--9999999998919999999999999999999998
Q ss_pred H
Q ss_conf 4
Q gi|254780611|r 287 Q 287 (302)
Q Consensus 287 ~ 287 (302)
.
T Consensus 162 ~ 162 (166)
T PRK09639 162 M 162 (166)
T ss_pred H
T ss_conf 7
No 97
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=99.37 E-value=7.7e-11 Score=91.99 Aligned_cols=165 Identities=13% Similarity=0.097 Sum_probs=118.1
Q ss_pred HCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 28599999999943077875655557999988899999988899898621853456899975778999999853202460
Q gi|254780611|r 44 HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123 (302)
Q Consensus 44 ~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~ 123 (302)
.+|.-|-+.|...|-+-+...+.++.+...+-+|++|+..+-+.+. +++.+-+ .+.+|-+++.+.-+.++++++..
T Consensus 6 ~~~~~AFe~Ly~~~~~~l~~~~~~~~~~~~~AeDivQe~Flr~~~~-~~~~~~~--~~~a~L~~iarn~~id~~Rr~~~- 81 (172)
T PRK09651 6 TTASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRNAL- 81 (172)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHC-CCCCCCC--CHHHHHHHHHHHHHHHHHHHHHH-
T ss_conf 5586699999999999999999999598868999999999999863-8523346--88999999999999999999888-
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCC
Q ss_conf 01102300358999999997887866244788824677888618983211000000122343355202323453200000
Q gi|254780611|r 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203 (302)
Q Consensus 124 IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~ 203 (302)
.... .+.++. ..
T Consensus 82 -------------------~~~~------------~~~~~~-------------------------~~------------ 93 (172)
T PRK09651 82 -------------------EKAY------------LEMLAL-------------------------MP------------ 93 (172)
T ss_pred -------------------HHHH------------HHHHHH-------------------------CC------------
T ss_conf -------------------8878------------888874-------------------------75------------
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 12356870565566666667779999996219999999999982788888989999997789999999999999999999
Q gi|254780611|r 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302)
Q Consensus 204 l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302)
....+.|+... ........|..+|+.||++.|.|+.++++.| +|.+|||+.||||...|..--.+||+.++..
T Consensus 94 -~~~~~~~e~~~----~~~e~~~~l~~~l~~Lp~~~R~v~~L~~~eg--ls~~EIA~~lgiS~~tVk~~l~rAlk~c~~~ 166 (172)
T PRK09651 94 -EGGAPSPEERE----SQLETLQLLDSMLDGLNGKTREAFLLSQLDG--LTYSEIAHKLGVSISSVKKYVAKAVEHCLLF 166 (172)
T ss_pred -CCCCCCHHHHH----HHHHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_conf -54599988999----9999999999998709999999999998839--9999999998939999999999999999999
Q ss_pred HHHH
Q ss_conf 9974
Q gi|254780611|r 284 IQKQ 287 (302)
Q Consensus 284 l~~~ 287 (302)
+.++
T Consensus 167 ~~~~ 170 (172)
T PRK09651 167 RLEY 170 (172)
T ss_pred HHHC
T ss_conf 9873
No 98
>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=99.32 E-value=2.1e-11 Score=95.74 Aligned_cols=179 Identities=18% Similarity=0.277 Sum_probs=131.6
Q ss_pred HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf 99999999828599999999943077875655557999988899999988899898621853456899975778999999
Q gi|254780611|r 35 YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114 (302)
Q Consensus 35 ~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~ 114 (302)
+.+++.++ .||..|--.||.-|--=|..+|.|..|+..+-+|.-||+.|==---|+.||+++ ||||+-+
T Consensus 6 Kk~ik~v~-~GD~~AfAdlVdlYKDKiY~l~YRMlGN~HEA~D~AQEAF~RAY~~IDtyd~~~--KFSTWLy-------- 74 (187)
T TIGR02948 6 KKRIKEVK-KGDENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYVNIDTYDIER--KFSTWLY-------- 74 (187)
T ss_pred HHHHHHHH-HCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCC--CHHHHHH--------
T ss_conf 88999986-021788899999964247777776506743055688888888654114316664--3147899--------
Q ss_pred HHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCC
Q ss_conf 85320246001102300358999999997887866244788824677888618983211000000122343355202323
Q gi|254780611|r 115 EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194 (302)
Q Consensus 115 ~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d 194 (302)
||.+... ...+|| +.| +.-|++++.+.|
T Consensus 75 ----------RIATNl~----IDrlRK----------rKP----------------------------D~yLd~~V~G~d 102 (187)
T TIGR02948 75 ----------RIATNLT----IDRLRK----------RKP----------------------------DFYLDDEVAGTD 102 (187)
T ss_pred ----------HHHHHHH----HHHHHC----------CCC----------------------------CCCCCCCCCCCC
T ss_conf ----------9998778----865413----------488----------------------------864367557867
Q ss_pred CCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 45320000012356870565566666667779999996219999999999982788888989999997789999999999
Q gi|254780611|r 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274 (302)
Q Consensus 195 ~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~ 274 (302)
+ .+....++.+...+++.+..- +++..+++.+..||++=|.||.+.|..+ +||+||++.||+.-.+|.
T Consensus 103 G--LT~~sQlaa~~~~~~d~V~~l----E~~~~iQ~~I~~LP~KYR~~ivLKY~ed--LSL~EIS~IL~lPVgTVK---- 170 (187)
T TIGR02948 103 G--LTMESQLAADEASPEDEVVSL----ELRDTIQEEIEALPEKYRSVIVLKYMED--LSLKEISEILDLPVGTVK---- 170 (187)
T ss_pred C--CHHHHCCCCCCCCCHHHHHHH----HHHHHHHHHHHHCCHHHCEEHHHHHHHH--HHHHHHHHHHCCCCCCEE----
T ss_conf 7--400100110124621465553----5678999999743433512224544444--218889998578943100----
Q ss_pred HHHHHHHHHHHHHH
Q ss_conf 99999999999740
Q gi|254780611|r 275 RAFKKVQESIQKQV 288 (302)
Q Consensus 275 ~AL~kLR~~l~~~~ 288 (302)
--|.+=|++|++++
T Consensus 171 TRiHRGREALRk~l 184 (187)
T TIGR02948 171 TRIHRGREALRKQL 184 (187)
T ss_pred CCCCCCHHHHHHHH
T ss_conf 24302458999873
No 99
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=99.31 E-value=3.1e-10 Score=87.90 Aligned_cols=160 Identities=12% Similarity=0.154 Sum_probs=107.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHH
Q ss_conf 99999999943077875655557999988899999988899898621853456899975778999999853202460011
Q gi|254780611|r 47 LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126 (302)
Q Consensus 47 ~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRi 126 (302)
.+|-++++....+=+...|.++.+..-+-+|++|+.++-+.+.+++|++. .+|.||.+-=.+....++
T Consensus 4 ~~~f~~~~l~~~P~L~~fa~~l~~n~~dAEDlvQEtflk~~~~~~~~~~~--~~~~tWL~~IarN~~~~~---------- 71 (181)
T PRK12540 4 TDSLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPG--SNLPAWLFTILRNLFRSD---------- 71 (181)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHHHHH----------
T ss_conf 08899999998799999999993999999999999999999849875987--624899999999999999----------
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCC
Q ss_conf 02300358999999997887866244788824677888618983211000000122343355202323453200000123
Q gi|254780611|r 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206 (302)
Q Consensus 127 P~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~ 206 (302)
.|+-+.... . .. .+... .+ .
T Consensus 72 ------------~Rk~~r~~~----------~-----------------~~------~~~~~--------------~~-~ 91 (181)
T PRK12540 72 ------------YRKRRREVE----------D-----------------AD------GSYAK--------------TL-K 91 (181)
T ss_pred ------------HHHHCCCCC----------C-----------------CC------CCCCC--------------CC-C
T ss_conf ------------998357666----------4-----------------32------11000--------------14-6
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 56870565566666667779999996219999999999982788888989999997789999999999999999999997
Q gi|254780611|r 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286 (302)
Q Consensus 207 ~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~ 286 (302)
..+..+ ... ....|..+|..||+.+|.||.++|..+ +|.+|||+.||+|...|.---.+|.++||+.|+.
T Consensus 92 ~~~~~~----~~~----~~~~l~~al~~Lp~~~R~vl~L~~~eg--ls~~EIA~iL~is~gTVKsRL~RAr~kLr~~L~~ 161 (181)
T PRK12540 92 SQPGQN----AHL----EFEEFRAALEKLPQDQREALILVGASG--FSYEDAAAICGCAVGTIKSRVNRARSKLSALLYV 161 (181)
T ss_pred CCCCHH----HHH----HHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 899735----677----899999999819999989988799809--9999999998949999999999999999999874
Q ss_pred HH
Q ss_conf 40
Q gi|254780611|r 287 QV 288 (302)
Q Consensus 287 ~~ 288 (302)
.-
T Consensus 162 ~g 163 (181)
T PRK12540 162 DG 163 (181)
T ss_pred CC
T ss_conf 65
No 100
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=99.27 E-value=3.1e-10 Score=87.95 Aligned_cols=64 Identities=22% Similarity=0.359 Sum_probs=57.0
Q ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 677799999962199999999999827888889899999977899999999999999999999974
Q gi|254780611|r 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287 (302)
Q Consensus 222 ~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~ 287 (302)
......|..+++.|||+.|.|+.++|+.+ +|.+|||+.||||...|..--.+|+++||..|++.
T Consensus 93 ~e~~~~l~~al~~Lp~~~R~v~~L~~~eg--ls~~EIA~~lgis~~tVk~~l~rA~k~Lr~~L~~~ 156 (159)
T PRK12527 93 GQRLALLQRALAELPPICRESFLLRKLEG--LSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQW 156 (159)
T ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999999869999989998898739--79999999989199999999999999999999977
No 101
>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=99.25 E-value=2.7e-10 Score=88.38 Aligned_cols=169 Identities=15% Similarity=0.217 Sum_probs=120.0
Q ss_pred HHHHHHHCCHHHHHHHHHHHHHHH-HHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 999998285999999999430778-7565555799998889999998889989862185345689997577899999985
Q gi|254780611|r 38 AKRYREHGDLSAAHRLVTSHLRLV-VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116 (302)
Q Consensus 38 ~~~~~~~gd~~Ar~~Li~~nlrlV-~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~ 116 (302)
.++.+ .+|.+|--.|-+.|-.=| ..|+.|- |.-..-|||+|+=.+-.|.-|..|.......|+..-+-=-+.-|.||
T Consensus 2 l~~a~-~~e~~Afa~lye~Y~~~vYrYI~yrv-g~~~tAEDL~s~vF~~~L~~i~~f~~~~~t~f~~WLf~iA~N~v~Dy 79 (171)
T TIGR02952 2 LERAQ-EKEEDAFARLYETYSDKVYRYIYYRV-GDKYTAEDLTSEVFLRVLRKIDSFKEQKNTDFEAWLFTIARNVVADY 79 (171)
T ss_pred CHHHH-HHHHHHHHHHHHHHHHHHHHHHEEEE-CCEEEHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf 03577-67699999998987256662101312-88531146478999999731221012578772247899999999988
Q ss_pred HHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCC
Q ss_conf 32024600110230035899999999788786624478882467788861898321100000012234335520232345
Q gi|254780611|r 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196 (302)
Q Consensus 117 i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~ 196 (302)
++...|- | ..|+|...
T Consensus 80 fr~~~r~---------------------------------~-------------------------~~~~~~~~------ 95 (171)
T TIGR02952 80 FRKSKRR---------------------------------P-------------------------LLSLDVVK------ 95 (171)
T ss_pred HHCCCCC---------------------------------C-------------------------CCCHHHHH------
T ss_conf 5113455---------------------------------2-------------------------10099989------
Q ss_pred CCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 32000001235687056556666666777999999621999999999998278888898999999778999999999999
Q gi|254780611|r 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276 (302)
Q Consensus 197 ~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~A 276 (302)
.+.+.++.|++.+ +.......|..++..|+|.||+||.+||+.+ +..+|||+.||.+..-|-+|+-+|
T Consensus 96 ------~l~~~e~~P~e~~----~~~~~n~~L~~a~~~L~p~qq~viaLrF~~~--L~~~EvA~ilGk~~gavk~Lq~rA 163 (171)
T TIGR02952 96 ------ELLSAEPSPEEAV----LKELANEKLLEAVKKLTPKQQEVIALRFAQN--LPIAEVARILGKTEGAVKALQFRA 163 (171)
T ss_pred ------HHHHCCCCHHHHH----HHHHHHHHHHHHHHHCCHHHHHHHHHHHCCC--CCHHHHHHHHCCCCCHHHHHHHHH
T ss_conf ------8873489817899----9888899999999610832312033321168--838789987268974689999999
Q ss_pred HHHHHHHH
Q ss_conf 99999999
Q gi|254780611|r 277 FKKVQESI 284 (302)
Q Consensus 277 L~kLR~~l 284 (302)
+++|+..|
T Consensus 164 v~~L~r~l 171 (171)
T TIGR02952 164 VKKLARQL 171 (171)
T ss_pred HHHHHHHC
T ss_conf 99987309
No 102
>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=99.25 E-value=4.4e-10 Score=86.95 Aligned_cols=166 Identities=14% Similarity=0.214 Sum_probs=121.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCC
Q ss_conf 99999994307787565555799998889999998889989862185345689997577899999985320246001102
Q gi|254780611|r 49 AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128 (302)
Q Consensus 49 Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~ 128 (302)
|=+.|...|-+-+...|.+|.+..-.-+|++|+-.+.|.+--+.+++.. .|.+|-.-.+|..+.+||+.+. |+
T Consensus 2 aF~~ly~~Yy~~l~~fA~~yv~~~e~AEdIVqdvF~~lWe~r~~l~~~~--~~~~YL~~~v~N~~ln~Lr~~~--~~--- 74 (167)
T TIGR02985 2 AFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRESLEESE--SIKAYLFTIVKNRCLNYLRHKQ--VE--- 74 (167)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCC--CCCHHHHHHHHHHHHHHHHHHH--HH---
T ss_conf 4889999987999999999836899999999999999973145256213--5217999999998998998899--99---
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCC
Q ss_conf 30035899999999788786624478882467788861898321100000012234335520232345320000012356
Q gi|254780611|r 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208 (302)
Q Consensus 129 ~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~ 208 (302)
.+....+. ... ...++.. +...+
T Consensus 75 -----------~~~~~~~~---~~~-----------------------------~~~~~~~--------------~~~l~ 97 (167)
T TIGR02985 75 -----------EKYQEELS---EIE-----------------------------EDEIELR--------------LQSLE 97 (167)
T ss_pred -----------HHHHHHHH---HHH-----------------------------HHHHHHH--------------HHHCC
T ss_conf -----------99999999---865-----------------------------5678763--------------10036
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 8705655666666677799999962199999999999827888889899999977899999999999999999999
Q gi|254780611|r 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284 (302)
Q Consensus 209 ~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l 284 (302)
+.+++.+ ..+++...+..+|+.||++-|.|..+-+. +++|-+|||+.||||..+|--=-.+||+.||+.|
T Consensus 98 ~~~~~~~----~~~El~~~i~~~~~~LPe~~R~iF~lsr~--eg~s~~EIA~~L~iS~~TVe~hi~~ALk~LR~~L 167 (167)
T TIGR02985 98 ADPEEDI----YSKELEEIIEEAIEKLPEQCREIFILSRF--EGLSNKEIAEELGISVKTVEYHITKALKFLRKEL 167 (167)
T ss_pred CCCHHHH----HHHHHHHHHHHHHHHCCHHHHHHHHHHHH--HCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHC
T ss_conf 8974578----79999999999987568989999999886--1798678998848988899999999999998739
No 103
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=99.24 E-value=1.4e-09 Score=83.53 Aligned_cols=165 Identities=13% Similarity=0.113 Sum_probs=111.2
Q ss_pred HCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 28599999999943077875655557999988899999988899898621853456899975778999999853202460
Q gi|254780611|r 44 HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123 (302)
Q Consensus 44 ~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~ 123 (302)
+.+.++-+.|...|-.-|...+.++.+..-.-+|++|+..+=|++. ..|+.. ..|.+|-+--.+.-+.++++.+
T Consensus 6 ~p~~~~~~~Ly~~~~~~L~~~~~r~~~~~e~AEDivQd~Flrl~~~-~~~~~~--~~~~a~Lf~iarNl~~D~~Rr~--- 79 (172)
T PRK12523 6 SPHSELVGALYRDHRGWLLAWLRRNLACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRRA--- 79 (172)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHC-CCCCCC--CCHHHHHHHHHHHHHHHHHHHH---
T ss_conf 9739999999999999999999999498868999999999999827-765673--4599999999999999999989---
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCC
Q ss_conf 01102300358999999997887866244788824677888618983211000000122343355202323453200000
Q gi|254780611|r 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203 (302)
Q Consensus 124 IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~ 203 (302)
...... ..+++. ..
T Consensus 80 -------------------~~~~~~----------~~~~~~-------------------------~~------------ 93 (172)
T PRK12523 80 -------------------ALEQAY----------LAELAL-------------------------VP------------ 93 (172)
T ss_pred -------------------HHHHHH----------HHHHHC-------------------------CC------------
T ss_conf -------------------988500----------888862-------------------------66------------
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 12356870565566666667779999996219999999999982788888989999997789999999999999999999
Q gi|254780611|r 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302)
Q Consensus 204 l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302)
..+.+.+++..... .....|..+|..||+++|.|+.++++.| +|.+|||+.||||...|+.--.+||+++|..
T Consensus 94 -~~~~~~~e~~~~~~----e~~~~l~~al~~Lp~~~R~v~~L~~~eG--ls~~EIA~~LgiS~~tVk~~l~rAl~~~~~~ 166 (172)
T PRK12523 94 -EAEQPSPEEQHLIL----EDLKAIDRLLGKLSSKARAAFLYNRLDG--MGHAEIAERLGVSVSRVRQYLAQGLRQCYIA 166 (172)
T ss_pred -CCCCCCHHHHHHHH----HHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_conf -54689979999999----9999999998649999999999999939--9999999998939999999999999999998
Q ss_pred HHHH
Q ss_conf 9974
Q gi|254780611|r 284 IQKQ 287 (302)
Q Consensus 284 l~~~ 287 (302)
|...
T Consensus 167 l~~~ 170 (172)
T PRK12523 167 LYGE 170 (172)
T ss_pred HHCC
T ss_conf 6079
No 104
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=99.23 E-value=4.4e-10 Score=86.94 Aligned_cols=158 Identities=9% Similarity=0.091 Sum_probs=102.8
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCC
Q ss_conf 99999943077875655557999988899999988899898621853456899975778999999853202460011023
Q gi|254780611|r 50 AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129 (302)
Q Consensus 50 r~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~ 129 (302)
|..|+.. ++=....|.++.+...+-+|++|+..+=+++...+|++. ..|.||.+--++....++++.+.
T Consensus 7 ~~~~~~~-~P~L~rfa~~l~~d~~dAEDlvQetflk~~~~~~~~~~~--~~~~~WL~~IarN~~id~~Rr~~-------- 75 (182)
T PRK12511 7 RFDVIDQ-LVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSG--GNLRTWLMSILHNAFIDELRRRR-------- 75 (182)
T ss_pred HHHHHHH-HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHHHHHHHHCC--------
T ss_conf 9999998-999999999992999999999999999999998866886--64999999999999999998433--------
Q ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCC
Q ss_conf 00358999999997887866244788824677888618983211000000122343355202323453200000123568
Q gi|254780611|r 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209 (302)
Q Consensus 130 ~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~ 209 (302)
. ..... ...+ ... + ...+
T Consensus 76 --------------~----------~~~~~------------------------~~~~---~~~-~----------~~~~ 93 (182)
T PRK12511 76 --------------A----------EARRA------------------------DELV---VEA-D----------ASAP 93 (182)
T ss_pred --------------C----------CCCCC------------------------CCCC---CCC-C----------CCCC
T ss_conf --------------4----------43433------------------------3101---235-5----------5689
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 70565566666667779999996219999999999982788888989999997789999999999999999999997401
Q gi|254780611|r 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289 (302)
Q Consensus 210 ~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~~~ 289 (302)
.+++. ......+..+|..||+++|.|+.++|+.+ +|.+|||+.||||...|.....+|.++||+.|+....
T Consensus 94 ~~~e~-------~~~~~~l~~al~~Lp~~~R~vl~L~~~eg--ls~~EIAe~Lgis~gTVKsrl~RAr~~LR~~le~~g~ 164 (182)
T PRK12511 94 AGQEH-------AVRLAQIRDAFFDLPEEQRAALHLVAIEG--LSYQEAANVLGIPIGTLMSRIGRARAALRAFEEGTGP 164 (182)
T ss_pred CCHHH-------HHHHHHHHHHHHCCCHHHHHHEEEEEECC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 63568-------99999999999869998950112410079--9999999998939999999999999999998631288
No 105
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=99.13 E-value=5.6e-09 Score=79.53 Aligned_cols=191 Identities=15% Similarity=0.150 Sum_probs=120.1
Q ss_pred HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf 99999999828599999999943077875655557999988899999988899898621853456899975778999999
Q gi|254780611|r 35 YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114 (302)
Q Consensus 35 ~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~ 114 (302)
..|..+.+ .||.+|-..|++.|-+-+...+.+..|..-+-+|++||..+-..++.++|++. ..|.||-+--......
T Consensus 10 ~~~~a~a~-~GD~~Af~~Lv~~~r~~L~~~cyRmlGs~~dAED~vQEt~lrawr~~~~f~~~--~~~rtWL~rIatn~cL 86 (341)
T PRK08241 10 VAGLAAAA-DGDRDAFLALAEPHRRELLAHCYRMLGSLHDAEDLVQETLLRAWRSYDRFEGR--SSLRTWLYRIATNVCL 86 (341)
T ss_pred HHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCC--CCCCEEEHHHHHHHHH
T ss_conf 99999997-47999999999999999999999980999899999999999998513222655--6641310198999999
Q ss_pred HHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCC
Q ss_conf 85320246001102300358999999997887866244788824677888618983211000000122343355202323
Q gi|254780611|r 115 EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194 (302)
Q Consensus 115 ~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d 194 (302)
+.++...| .. ...+ .+ ++. .. ....+ . .
T Consensus 87 d~Lr~r~R---------------------R~--~~~~-l~-~~~------------~~------------~~~~~-~--~ 114 (341)
T PRK08241 87 DALEGRAR---------------------RP--LPTG-LG-PPS------------AD------------PSAAL-V--E 114 (341)
T ss_pred HHHHHHHC---------------------CC--CCCC-CC-CCC------------CC------------CCCCC-C--C
T ss_conf 99987424---------------------46--7444-56-665------------66------------54455-5--5
Q ss_pred CCCCCHHC-----CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHH
Q ss_conf 45320000-----0123568705655666666677799999962199999999999827888889899999977899999
Q gi|254780611|r 195 KNSSQWQD-----WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269 (302)
Q Consensus 195 ~~~~~~~d-----~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRV 269 (302)
.....+.+ .+.+...+|++..... +.....+..+|+.|+++||.|+.+|-..+ .+..|||+.||+|..-|
T Consensus 115 ~~~~~WleP~Pd~~~~~~~~dP~~~~~~r---Esv~lA~laaLq~Lpp~QRavlvLRdV~g--~s~~EiAe~Lg~S~aAV 189 (341)
T PRK08241 115 RPEVPWLEPLPDALLDPAAADPAAIVVAR---ESVRLAFVAALQHLPPRQRAVLLLRDVLG--WSAAEVAEALGTSTAAV 189 (341)
T ss_pred CCCCCCCCCCCCCCCCCCCCCHHHHHHHH---HHHHHHHHHHHHHCCHHHHEEEEHHHHCC--CCHHHHHHHHCCCHHHH
T ss_conf 55666546677534566779988998887---78999999999839997902001297529--98899999978999999
Q ss_pred HHHHHHHHHHHHHHHH
Q ss_conf 9999999999999999
Q gi|254780611|r 270 RQIEARAFKKVQESIQ 285 (302)
Q Consensus 270 rQI~~~AL~kLR~~l~ 285 (302)
++.-++|=..|++..-
T Consensus 190 ks~L~RARa~L~~~~p 205 (341)
T PRK08241 190 NSALQRARATLAERRP 205 (341)
T ss_pred HHHHHHHHHHHHHHCC
T ss_conf 9999999999986477
No 106
>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=99.11 E-value=2.4e-10 Score=88.69 Aligned_cols=70 Identities=36% Similarity=0.576 Sum_probs=66.0
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 9994307787565555799998889999998889989862185345689997577899999985320246
Q gi|254780611|r 53 LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122 (302)
Q Consensus 53 Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~ 122 (302)
|++.|.++|.++|.+|.+.+.+.+|++|++.+++++++++|||++|.+|+||++.+++..+.++++++.+
T Consensus 1 L~~~y~~~l~~~~~~~~~~~~~aeDl~Qe~f~~~~~~~~~~~~~~~~~f~~wl~~i~~n~~~d~~Rk~~r 70 (71)
T pfam04542 1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLLRAVERFDPERGVSFSTWLYTIIRNAIIDALRKQRR 70 (71)
T ss_pred CHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 9998999999999988398602999999999999999875796136609989999999999999997399
No 107
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=99.07 E-value=1.2e-08 Score=77.21 Aligned_cols=162 Identities=12% Similarity=0.080 Sum_probs=108.6
Q ss_pred HHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 82859999999994307787565555799998889999998889989862185345689997577899999985320246
Q gi|254780611|r 43 EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122 (302)
Q Consensus 43 ~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~ 122 (302)
+.||..|.++|...|-+.+...+.++.|..-.-+|++|+-.+-|+.+-+..+.+ ...+|-+-+.+.-+.++++++.
T Consensus 5 ~~~~~~~~e~ly~~~~~~L~~~~~r~~g~~~~AEDivQd~Flrl~~~~~~~~~~---~~~ayL~~iA~n~~id~~R~~~- 80 (167)
T PRK12528 5 DSAHAATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQII---EPRAFLTTIAKRVLCNHYRRQD- 80 (167)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCC---CHHHHHHHHHHHHHHHHHHHHH-
T ss_conf 655789999999999999999999993988579999999999999656544656---7999999999999999999999-
Q ss_pred CHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHC
Q ss_conf 00110230035899999999788786624478882467788861898321100000012234335520232345320000
Q gi|254780611|r 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202 (302)
Q Consensus 123 ~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d 202 (302)
...... +.+. . ..
T Consensus 81 ---------------------~~~~~~----------~~~~------------------------~-~~----------- 93 (167)
T PRK12528 81 ---------------------LERAYL----------EALA------------------------Q-LP----------- 93 (167)
T ss_pred ---------------------HHHHHH----------HHHH------------------------C-CC-----------
T ss_conf ---------------------899899----------8876------------------------3-65-----------
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf 01235687056556666666777999999621999999999998278888898999999778999999999999999999
Q gi|254780611|r 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282 (302)
Q Consensus 203 ~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~ 282 (302)
....+.+++..... .....|..+++.||++.|.|+.++.+.| +|.+|||+.||||...|..--.+|+.+-.-
T Consensus 94 --~~~~~~~e~~~~~~----e~~~~l~~~l~~LP~~~R~vf~L~r~~g--ls~~EIA~~LgiS~~tVk~~l~rA~~~c~~ 165 (167)
T PRK12528 94 --ERVAPSEEERAIIL----ETLVELDRLLDGLPPLVKRAFLLAQVDG--LGYGEIATELGISLATVKRYLNKAAMRCYF 165 (167)
T ss_pred --CCCCCCHHHHHHHH----HHHHHHHHHHHCCCHHHHHHHHHHHHHC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf --32469857899999----9999999998709999999999999829--899999999797999999999999999997
Q ss_pred H
Q ss_conf 9
Q gi|254780611|r 283 S 283 (302)
Q Consensus 283 ~ 283 (302)
+
T Consensus 166 ~ 166 (167)
T PRK12528 166 A 166 (167)
T ss_pred H
T ss_conf 6
No 108
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=99.02 E-value=4.1e-08 Score=73.74 Aligned_cols=164 Identities=15% Similarity=0.102 Sum_probs=97.4
Q ss_pred HCCHHHH-HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 2859999-999994307787565555799998889999998889989862185345689997577899999985320246
Q gi|254780611|r 44 HGDLSAA-HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122 (302)
Q Consensus 44 ~gd~~Ar-~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~ 122 (302)
.+++.+. .+|...|-+-...-+.+..+..-.-+|++|+-.+=+...-+..+. ..+-+|-+-..+.-+.++
T Consensus 4 ~~~~~~~l~~Lf~~~y~~L~~~~~r~lg~~~~AeDivQe~Flr~~~~~~~~~~---~~~~a~L~~iArnl~~d~------ 74 (168)
T PRK12525 4 GSIKNTLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEG------ 74 (168)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCC---CCHHHHHHHHHHHHHHHH------
T ss_conf 31898999999999999999999999498857999999999999867774554---588999999999999999------
Q ss_pred CHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHC
Q ss_conf 00110230035899999999788786624478882467788861898321100000012234335520232345320000
Q gi|254780611|r 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202 (302)
Q Consensus 123 ~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d 202 (302)
+|+-+.... .+. ++. ...+
T Consensus 75 ----------------~Rr~~~~~~----------~~~------------------------~~~----~~~~------- 93 (168)
T PRK12525 75 ----------------WRRQDLERA----------YLQ------------------------SLA----EAPE------- 93 (168)
T ss_pred ----------------HHHHHHHHH----------HHH------------------------HHH----CCCC-------
T ss_conf ----------------999999998----------888------------------------885----1666-------
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf 01235687056556666666777999999621999999999998278888898999999778999999999999999999
Q gi|254780611|r 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282 (302)
Q Consensus 203 ~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~ 282 (302)
...+.|++..... .....+..+|+.||++.|.|+.++++.| +|.+|||+.||||...|..--.+||+..++
T Consensus 94 ---~~~~~pe~~~~~~----e~~~~l~~al~~LP~~~R~vflL~~~eG--lsy~EIAe~LgIS~~tV~~~l~rAl~~c~~ 164 (168)
T PRK12525 94 ---AVQPSPEEQWMVI----ETLLAIDRLLDGLSGKARAAFLMSQLEG--LTYVEIGERLGVSLSRIHQYMVEAFKCCYQ 164 (168)
T ss_pred ---CCCCCHHHHHHHH----HHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf ---5689867899999----9999999998639999999999999929--999999999897999999999999999999
Q ss_pred HHHH
Q ss_conf 9997
Q gi|254780611|r 283 SIQK 286 (302)
Q Consensus 283 ~l~~ 286 (302)
.|+.
T Consensus 165 ~lq~ 168 (168)
T PRK12525 165 GFQE 168 (168)
T ss_pred HHHC
T ss_conf 8409
No 109
>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=99.00 E-value=4.2e-08 Score=73.72 Aligned_cols=166 Identities=14% Similarity=0.207 Sum_probs=111.3
Q ss_pred HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHH
Q ss_conf 99999999982859999999994307787565555799998889999998889989862185345689997577899999
Q gi|254780611|r 34 EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113 (302)
Q Consensus 34 e~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I 113 (302)
+..|+.+.. .||..|=..||..|-----++|-.|.+.--|-.|.|||...==-.+|++-.-. .+ |.|.- +|==|
T Consensus 3 ~~~Lv~~a~-~Gn~~aF~~Li~~~ke~LYk~Af~Yvkne~DALd~i~EtvyKAY~sI~kLk~~-~Y-F~TW~---trILI 76 (173)
T TIGR02954 3 DIELVKKAI-RGNKEAFESLIKKNKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIEKLKHP-EY-FNTWL---TRILI 76 (173)
T ss_pred HHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCCC-CC-CHHHH---HHHHH
T ss_conf 368999987-24934789999984366857665440673405899999999999989983361-00-02567---89999
Q ss_pred H---HHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHC
Q ss_conf 9---8532024600110230035899999999788786624478882467788861898321100000012234335520
Q gi|254780611|r 114 Q---EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190 (302)
Q Consensus 114 ~---~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i 190 (302)
+ ..|.++.++| -++.+.
T Consensus 77 n~ci~lL~K~kk~i------------------------------------------------------------~~~~~~ 96 (173)
T TIGR02954 77 NECIDLLKKKKKVI------------------------------------------------------------LFDKNT 96 (173)
T ss_pred HHHHHHHHCCCCEE------------------------------------------------------------ECCCCC
T ss_conf 99999984389753------------------------------------------------------------068871
Q ss_pred CCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHH-
Q ss_conf 2323453200000123568705655666666677799999962199999999999827888889899999977899999-
Q gi|254780611|r 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV- 269 (302)
Q Consensus 191 ~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRV- 269 (302)
..... .. +.. ..+..+. ..|-.|++.|+++++.+|.++|+.| +|-.|||+.|+.+..+|
T Consensus 97 ~~~~~---------~~-~~~----~~~~lef----~dLy~Ai~~L~~~~~t~IIL~Yy~D--L~I~eIa~vM~~P~gTvK 156 (173)
T TIGR02954 97 KIEKK---------EC-EVD----ADERLEF----EDLYKAIDTLNDKYKTAIILRYYHD--LKIKEIAEVMNKPEGTVK 156 (173)
T ss_pred CHHHH---------HC-CCC----HHHHHCH----HHHHHHHHHHHHHHHHHHHHHHCCC--CCHHHHHHHCCCCCCCHH
T ss_conf 01223---------21-668----6886258----6899999731145440264332179--984259985168985178
Q ss_pred HHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999997
Q gi|254780611|r 270 RQIEARAFKKVQESIQK 286 (302)
Q Consensus 270 rQI~~~AL~kLR~~l~~ 286 (302)
++| .||+.+||+.|++
T Consensus 157 tyl-~Ra~~~lk~~l~~ 172 (173)
T TIGR02954 157 TYL-RRAKKKLKKELEE 172 (173)
T ss_pred HHH-HHHHHHHHHHHCC
T ss_conf 999-9999998886236
No 110
>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=98.99 E-value=6.9e-10 Score=85.62 Aligned_cols=50 Identities=42% Similarity=0.678 Sum_probs=47.0
Q ss_pred HHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf 9621999999999998278888898999999778999999999999999999
Q gi|254780611|r 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282 (302)
Q Consensus 231 ~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~ 282 (302)
||+.|||+++.||.++|+.+ +|+.|||+.||+|.++|+|++.+||.+||+
T Consensus 1 Al~~L~~~~r~ii~l~y~~~--~t~~EIA~~lgis~~~V~~~~~ral~~LR~ 50 (50)
T pfam04545 1 ALASLPPREREVLVLRFGEG--LTLEEIGERLGISRERVRQIEKRALRKLRK 50 (50)
T ss_pred CHHHCCHHHHHHHHHHCCCC--CHHHHHHHHHCCCHHHHHHHHHHHHHHHCC
T ss_conf 97668999999999870688--249999999897999999999999998629
No 111
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=98.94 E-value=1.7e-07 Score=69.59 Aligned_cols=165 Identities=13% Similarity=0.118 Sum_probs=102.0
Q ss_pred HCCHHHHHHHHHHHHHHH-HHHHHHHCCCC-CCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 285999999999430778-75655557999-9888999999888998986218534568999757789999998532024
Q gi|254780611|r 44 HGDLSAAHRLVTSHLRLV-VKIAMGYRGYG-LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121 (302)
Q Consensus 44 ~gd~~Ar~~Li~~nlrlV-~~iA~~y~~~g-~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~ 121 (302)
.||..|-+.|...|-+.+ ..+.++..+.| -.-+||+|+-.+=|+.+-+...++---.|.+|-+---+.-..+
T Consensus 9 ~~D~~a~~~Ly~~h~~~L~~~l~~Rl~~~~~~~AeDl~QDvFlrl~~~~~~~~~~~i~~p~a~L~rIA~Nl~id------ 82 (178)
T PRK12529 9 SADRDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVS------ 82 (178)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHH------
T ss_conf 44799999999999999999999982899835469999999999997344456432334899999999999999------
Q ss_pred CCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHH
Q ss_conf 60011023003589999999978878662447888246778886189832110000001223433552023234532000
Q gi|254780611|r 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201 (302)
Q Consensus 122 ~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~ 201 (302)
..|+-...... .+.+ .
T Consensus 83 ----------------~~Rr~~~~~~~----------le~~------------------------~-------------- 98 (178)
T PRK12529 83 ----------------WRRRQSLELAW----------LEAL------------------------A-------------- 98 (178)
T ss_pred ----------------HHHHHHHHHHH----------HHHH------------------------H--------------
T ss_conf ----------------99988889878----------9988------------------------6--------------
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf 00123568705655666666677799999962199999999999827888889899999977899999999999999999
Q gi|254780611|r 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281 (302)
Q Consensus 202 d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR 281 (302)
+......+.++...... +....|..+|..||++.|.|+.++++.| +|.+|||+.||||...|.+--.+|+..=-
T Consensus 99 ~~~~~~~pspE~~~~~~----e~l~~l~~al~~Lp~r~R~vF~L~r~eG--ls~~EIAe~LgiS~~tV~~~l~rAl~~C~ 172 (178)
T PRK12529 99 TLPEPLHPSPEQQSVIL----ETLHEIDALLDTLRPRVKQAFLMATLDG--MKQKDIAQALDIALPTVKKYIHQAYVTCL 172 (178)
T ss_pred CCCCCCCCCHHHHHHHH----HHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 47866689989999999----9999999998569978889987998829--99999999989599999999999999999
Q ss_pred HHH
Q ss_conf 999
Q gi|254780611|r 282 ESI 284 (302)
Q Consensus 282 ~~l 284 (302)
..|
T Consensus 173 ~~~ 175 (178)
T PRK12529 173 SLM 175 (178)
T ss_pred HHC
T ss_conf 867
No 112
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=98.78 E-value=6.1e-07 Score=65.90 Aligned_cols=153 Identities=18% Similarity=0.182 Sum_probs=92.0
Q ss_pred HHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHH
Q ss_conf 99430778756555579999888999999888998986218534568999757789999998532024600110230035
Q gi|254780611|r 54 VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133 (302)
Q Consensus 54 i~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r 133 (302)
.+.+=+....+|.+..|...+-+|++||..+-+..+ |+...-.|.||.+-....-..+.
T Consensus 6 fe~~R~~L~~~AyRmlGs~~DAEDvvQEt~lr~~~~----~~~~~~~~~aWL~rI~~n~~ld~----------------- 64 (289)
T PRK09636 6 FEPLRPHLLSVAYRMLGSVADAEDIVQEAWLRWNNA----DRAEIRDPRAFLTRVVTRLCLDR----------------- 64 (289)
T ss_pred HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCC----CCCCCCCHHHHHHHHHHHHHHHH-----------------
T ss_conf 998799999999998099978999999999998506----84223478999999999999999-----------------
Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHH
Q ss_conf 89999999978878662447888246778886189832110000001223433552023234532000001235687056
Q gi|254780611|r 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213 (302)
Q Consensus 134 ~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~ 213 (302)
+|+.+...+...+. -|..| +.+...++++
T Consensus 65 -----LR~ar~rre~~~g~--------------------------------wlpep--------------~~~~~~~p~~ 93 (289)
T PRK09636 65 -----LRSARHRRETYVGP--------------------------------WLPEP--------------VVEDSDDPLE 93 (289)
T ss_pred -----HHHHHCCCCCCCCC--------------------------------CCCCC--------------CCCCCCCCHH
T ss_conf -----98540165546787--------------------------------78876--------------6788899356
Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 5566666667779999996219999999999982788888989999997789999999999999999999
Q gi|254780611|r 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302)
Q Consensus 214 ~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302)
.... .......+..+|+.|||+||.|+.+|...+ ++..|||+.||+|...|+|+..+|=++|+..
T Consensus 94 ~~~~---~e~~~~al~~~L~~L~p~qRav~vLrdv~g--~s~~EIA~iLg~s~~avR~~l~RAR~~l~~~ 158 (289)
T PRK09636 94 AVVA---AEDLSLALMLALERLSPLERAAFLLHDVFG--VPFDEIASTLGRSEAACRQLASRARKHVRAA 158 (289)
T ss_pred HHHH---HHHHHHHHHHHHHHCCHHHHHHHHHHHHHC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_conf 7887---788999999999739998962540498609--9999999998179999999999999987344
No 113
>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=98.76 E-value=2.2e-08 Score=75.57 Aligned_cols=54 Identities=30% Similarity=0.398 Sum_probs=50.7
Q ss_pred HHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf 99999962199999999999827888889899999977899999999999999999
Q gi|254780611|r 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281 (302)
Q Consensus 226 ~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR 281 (302)
+.|..+|+.||+++|.||.++|+.+ +|++|||+.||+|...|++...+|+++||
T Consensus 2 ~~l~~al~~L~~~~r~vl~l~y~~~--~s~~EIa~~lgis~~tVk~~l~rA~~~Lr 55 (55)
T cd06171 2 ERLEEALDKLPEREREVILLRFGEG--LSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHCC
T ss_conf 8999999839999989899999809--99999999989599999999999998758
No 114
>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=98.72 E-value=2.4e-06 Score=62.00 Aligned_cols=159 Identities=19% Similarity=0.285 Sum_probs=98.3
Q ss_pred HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHC-----CCCCC----------HHHHHHHHHHHHH--HHHHHCCCCC
Q ss_conf 99999999828599999999943077875655557-----99998----------8899999988899--8986218534
Q gi|254780611|r 35 YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR-----GYGLP----------ISEVVSEGNIGLM--QAVKKFDPER 97 (302)
Q Consensus 35 ~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~-----~~g~~----------~~DLiQeG~iGLi--~Ai~kFDp~k 97 (302)
.+|+..|+ +||..|++.|+..-.---..||.++. +.++. --+||.|.++=|. ..-..|+ +|
T Consensus 5 t~ll~~~~-~Gd~~A~~~L~~~~Y~~LR~~A~~~~~~~~~~~~Lq~~~~~~ci~stT~LV~EAylrL~~t~~~~~~~-~r 82 (194)
T TIGR02999 5 TELLQQWQ-NGDQAARDQLFPALYQELRRIARRELRRERSGQTLQVEVLAVCIDSTTALVHEAYLRLVDTQDEQEWS-DR 82 (194)
T ss_pred HHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCHHHHHHHHHHHHHCCCCHHHHC-CH
T ss_conf 99999883-64588999999999999999999999851036652044677510466788998766421232023222-50
Q ss_pred CCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCC
Q ss_conf 56899975778999999853202460011023003589999999978878662447888246778886189832110000
Q gi|254780611|r 98 GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177 (302)
Q Consensus 98 G~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~ 177 (302)
+. |=+-|. ..|.+-+-|+. |+- .. . .++|...
T Consensus 83 ~H-F~~~AA----~aMRrIL~D~A------------------R~~-~~--~--KRGg~~~-------------------- 114 (194)
T TIGR02999 83 RH-FFAAAA----KAMRRILVDHA------------------RRR-RA--Q--KRGGGAV-------------------- 114 (194)
T ss_pred HH-HHHHHH----HHHHHHHHHHH------------------HHH-HH--H--CCCCCCC--------------------
T ss_conf 88-999999----99999999999------------------999-87--4--1367763--------------------
Q ss_pred CCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHH
Q ss_conf 00122343355202323453200000123568705655666666677799999962199999999999827888889899
Q gi|254780611|r 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257 (302)
Q Consensus 178 ~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~E 257 (302)
..+++..- ++-.++..+ +..++-..|. .|...+||...|+.+|||.| +|.+|
T Consensus 115 -----~~~l~~~~--------------~~~~~~~~~------~L~~Ld~aL~-~L~~~~Pr~a~~veLr~F~G--l~~~E 166 (194)
T TIGR02999 115 -----RVSLDEVL--------------PDAEADADE------ELLDLDDALD-KLAQVDPRQAEVVELRFFAG--LTVEE 166 (194)
T ss_pred -----CCCCCCCC--------------CCCCCCCHH------HHHHHHHHHH-HHHHCCHHHHHHHHHHHHCC--CCHHH
T ss_conf -----35520000--------------135777403------5999999998-77400678899885311048--89899
Q ss_pred HHHHHCCCHHHHHH
Q ss_conf 99997789999999
Q gi|254780611|r 258 LSSEFEVSRERVRQ 271 (302)
Q Consensus 258 Ia~~lgiS~eRVrQ 271 (302)
||+.||||..+|.+
T Consensus 167 ~A~~L~~S~~Tv~R 180 (194)
T TIGR02999 167 IAELLGVSVRTVER 180 (194)
T ss_pred HHHHHCCCHHHHHH
T ss_conf 99986888878998
No 115
>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=98.69 E-value=1.1e-06 Score=64.11 Aligned_cols=156 Identities=17% Similarity=0.238 Sum_probs=93.2
Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCH
Q ss_conf 99994307787565555799998889999998889989862185345689997577899999985320246001102300
Q gi|254780611|r 52 RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131 (302)
Q Consensus 52 ~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~ 131 (302)
.|+..|-+-|...+..-...--+-||++||-++-+++-.+.|||+.+ |.-+|.-==|-.+..+.++.+|.
T Consensus 5 ~ll~~h~~~~rafv~~L~~~~~dadDv~QEt~v~~~~k~~~f~~~~~--F~aWa~~iArn~vl~~~r~~~R~-------- 74 (163)
T TIGR02989 5 RLLTRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGTD--FGAWARGIARNKVLNHRRKLGRD-------- 74 (163)
T ss_pred HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCCCCC--CHHHHHHHHHHHHHHHHHHCCCC--------
T ss_conf 99999989999999997179565888999999999860775178989--76789999999999998730244--------
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCC
Q ss_conf 35899999999788786624478882467788861898321100000012234335520232345320000012356870
Q gi|254780611|r 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211 (302)
Q Consensus 132 ~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~ 211 (302)
+ ..+..+..+ =.+.||..+ +.+
T Consensus 75 -~----------~~l~~f~D~-----l~e~lA~~~--------------------~~~---------------------- 96 (163)
T TIGR02989 75 -R----------ERLVVFDDE-----LLEALAAEL--------------------EEA---------------------- 96 (163)
T ss_pred -C----------HHHHHHHHH-----HHHHHHHHH--------------------HHH----------------------
T ss_conf -1----------277762599-----999999987--------------------555----------------------
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 56556666666777999999621999999999998278888898999999778999999999999999999999
Q gi|254780611|r 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285 (302)
Q Consensus 212 ~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~ 285 (302)
.+..........|..++.+||+++|.+|.++|..| .++.+||+.+|.|...|.| +|.+||..|.
T Consensus 97 ----~~~~~~~~~~~AL~~C~~~L~~~~R~Ll~~rY~~G--~~~~~~A~~~g~~~~A~~~----~L~R~R~~L~ 160 (163)
T TIGR02989 97 ----EEADRSEDELQALEGCLEKLPERQRELLQLRYQRG--VSLEALAEQLGRTVNAVYK----ALSRLRVRLR 160 (163)
T ss_pred ----HCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHCCC--CCHHHHHHHHCCHHHHHHH----HHHHHHHHHH
T ss_conf ----22788178999999878635978899999982279--7878999884713899999----9999999975
No 116
>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=98.56 E-value=1.9e-07 Score=69.26 Aligned_cols=79 Identities=16% Similarity=0.272 Sum_probs=68.7
Q ss_pred HCCHHHHHHHHHHHHHHHHHHHHHHCCCCC--CHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 285999999999430778756555579999--888999999888998986218534568999757789999998532024
Q gi|254780611|r 44 HGDLSAAHRLVTSHLRLVVKIAMGYRGYGL--PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121 (302)
Q Consensus 44 ~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~--~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~ 121 (302)
.|..+-+++||+-|-+|.++++.+..+|=+ .-||=.+.|.+++-+||++||++||..|-+||.-=|+-.+.||+|.+.
T Consensus 6 ~~~~~l~e~LI~~Y~PFI~k~vs~~~~ryId~~~DDE~SIGL~AFnEAI~sY~~~KG~sFL~FA~l~IkRr~IDy~R~n~ 85 (225)
T TIGR02895 6 KGNEELREELIRQYKPFIAKLVSSVCKRYIDTKEDDELSIGLIAFNEAIESYDLNKGKSFLSFAKLIIKRRVIDYIRKNQ 85 (225)
T ss_pred CCCHHHHHHHHHHHCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 88068999998851468999999986330688888325588999998998731435621699999988999888887411
Q ss_pred C
Q ss_conf 6
Q gi|254780611|r 122 S 122 (302)
Q Consensus 122 ~ 122 (302)
+
T Consensus 86 k 86 (225)
T TIGR02895 86 K 86 (225)
T ss_pred H
T ss_conf 1
No 117
>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=98.55 E-value=5.2e-06 Score=59.67 Aligned_cols=181 Identities=21% Similarity=0.280 Sum_probs=123.5
Q ss_pred HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHH
Q ss_conf 99999999982859999999994307787565555799998889999998889989862185345689997577899999
Q gi|254780611|r 34 EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113 (302)
Q Consensus 34 e~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I 113 (302)
-..|.+|.| .||+.|-+-||..|.+=|+++..||....-+.+|.-||..|==-+|+-.|--+ ..|=|+-+
T Consensus 8 D~~Lv~RVQ-rG~k~AF~lLV~KYQ~kv~~Lv~Ryv~~~~e~~DVAQe~FvkAYRAl~~FRGd--saFYTWLy------- 77 (192)
T TIGR02939 8 DLELVERVQ-RGEKQAFDLLVRKYQHKVVSLVGRYVRDSEEVEDVAQEAFVKAYRALASFRGD--SAFYTWLY------- 77 (192)
T ss_pred HHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHHHCCHHCCCCHHHHHHHHHHHHHCCCCCC--HHHHHHHH-------
T ss_conf 289988873-32235677788999999999998761481003401477899999751235551--36789999-------
Q ss_pred HHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCC
Q ss_conf 98532024600110230035899999999788786624478882467788861898321100000012234335520232
Q gi|254780611|r 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193 (302)
Q Consensus 114 ~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~ 193 (302)
||. ++.+|+++- .++-++|+.. |+..+
T Consensus 78 -----------RIa-----------vNTAKNyLV---aq~Rr~p~~d------g~~~e---------------------- 104 (192)
T TIGR02939 78 -----------RIA-----------VNTAKNYLV---AQGRRPPTSD------GVEAE---------------------- 104 (192)
T ss_pred -----------HHH-----------HHHHHHHHH---HCCCCCCCCC------CCCCH----------------------
T ss_conf -----------999-----------988777664---2479887445------67604----------------------
Q ss_pred CCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 34532000001235687056556666666777999999621999999999998278888898999999778999999999
Q gi|254780611|r 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273 (302)
Q Consensus 194 d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~ 273 (302)
|-+....+|.|- +-+.||..++ ...+...+..++.-|||.=|.-|.+|=+ +|+|..|||..|.+--.+||=-.
T Consensus 105 dAE~F~~a~~Lr-~~~tPE~~ll----~~el~~~v~~a~~aLPE~Lr~Ai~LREl--eGLSYe~IA~~MdCPvGTVRSRI 177 (192)
T TIGR02939 105 DAEQFEEADALR-DIDTPERLLL----SRELEQTVNKALEALPEDLRTAITLREL--EGLSYEDIAEIMDCPVGTVRSRI 177 (192)
T ss_pred HHHCCCCCCCCC-CCCCHHHHHH----HHHHHHHHHHHHHHCCHHHHHHHHHHHC--CCCCHHHHHHHCCCCCCCCCCHH
T ss_conf 331200267665-5666167999----9999999999986172678745446512--68787888733069988621146
Q ss_pred HHHHHHHHHHHHHHH
Q ss_conf 999999999999740
Q gi|254780611|r 274 ARAFKKVQESIQKQV 288 (302)
Q Consensus 274 ~~AL~kLR~~l~~~~ 288 (302)
-+| |+++.+.+
T Consensus 178 FRA----REAi~~~l 188 (192)
T TIGR02939 178 FRA----REAIAKRL 188 (192)
T ss_pred HHH----HHHHHHHH
T ss_conf 775----89999862
No 118
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=98.50 E-value=2e-05 Score=55.85 Aligned_cols=158 Identities=15% Similarity=0.105 Sum_probs=92.1
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCC
Q ss_conf 99999430778756555579999888999999888998986218534568999757789999998532024600110230
Q gi|254780611|r 51 HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130 (302)
Q Consensus 51 ~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~ 130 (302)
-...+.|=+....+|.+..|...+-+|++||..+-+.++-... . -.+.+|-+-....-.
T Consensus 8 ~~~fe~hR~~L~~~ayRmlGs~~dAED~VQEa~lr~~~~~~~~---~-~~~~awL~ri~tn~c----------------- 66 (290)
T PRK09635 8 SAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGD---I-DDERGWLIVVTSRLC----------------- 66 (290)
T ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCC---C-CCHHHHHHHHHHHHH-----------------
T ss_conf 9999998999999999980898789999999999997477312---3-578889999999999-----------------
Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCC
Q ss_conf 03589999999978878662447888246778886189832110000001223433552023234532000001235687
Q gi|254780611|r 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210 (302)
Q Consensus 131 ~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~ 210 (302)
.+.+++.+..-+. |.. .+ ..+ .. +. .....+
T Consensus 67 -----ld~LR~~r~rre~--------~~~------~~----------------~~~-----~~--------~~-~~~~~d 97 (290)
T PRK09635 67 -----LDHIKSASTRRER--------PQD------IA----------------AWH-----DG--------DA-SVSSVD 97 (290)
T ss_pred -----HHHHHHHHHCCCC--------CCC------CC----------------CCC-----CC--------CC-CCCCCC
T ss_conf -----9998766522678--------766------67----------------778-----76--------77-788898
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 0565566666667779999996219999999999982788888989999997789999999999999999999
Q gi|254780611|r 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302)
Q Consensus 211 ~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302)
|.+.. ...+.....+..+|+.|+|.||.++.++-..+ ++..|||+.||.|..-|||+-.+|=++|+..
T Consensus 98 p~~~~---~~~~~v~~All~~Le~L~P~eRaa~vLrdvfg--~~~~EIA~~Lg~s~~a~Rqll~RAR~~l~~~ 165 (290)
T PRK09635 98 PADRV---TLDDEVRLALLIMLERLGPAERVVFVLHEIFG--LPYQQIATTIGSQASTCRQLAHRARRKINES 165 (290)
T ss_pred HHHHH---HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_conf 28898---87778999999998629986854552698608--9889999996899899999999999987323
No 119
>PRK06930 positive control sigma-like factor; Validated
Probab=98.46 E-value=9.7e-07 Score=64.56 Aligned_cols=64 Identities=19% Similarity=0.342 Sum_probs=57.2
Q ss_pred HHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 799999962199999999999827888889899999977899999999999999999999974012
Q gi|254780611|r 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290 (302)
Q Consensus 225 ~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~~~~ 290 (302)
+..|..+|+.|++||+.|..+.++.+ +|..|||+.||||...|...-++|..||++.+++.+.+
T Consensus 105 ~~~iedALs~Lt~rErevfll~~~~g--lsy~EIA~~L~Is~~tV~~~l~RA~~Ki~~~~~~~Lf~ 168 (170)
T PRK06930 105 KIRIEDALSVLTEREKEVYLMHRGYG--LSYSEIAAYLNIKKSTVQSMIERAEKKIAKQINESLFC 168 (170)
T ss_pred HHHHHHHHHHCCHHHHHHHHHHHHHC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf 98899999856988889998897618--88999999979889999999999999999985405312
No 120
>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=98.41 E-value=1.7e-07 Score=69.57 Aligned_cols=152 Identities=14% Similarity=0.252 Sum_probs=94.6
Q ss_pred HHHHHHHHHHHHHHHHC-CCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCH
Q ss_conf 99943077875655557-99998889999998889989862185345689997577899999985320246001102300
Q gi|254780611|r 53 LVTSHLRLVVKIAMGYR-GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131 (302)
Q Consensus 53 Li~~nlrlV~~iA~~y~-~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~ 131 (302)
.+..+-+=-...|.... |...+-+||+|+..+-+-.+=+++ .+.+. -.. |+|+.+.+--...|
T Consensus 11 f~~~r~~~L~r~A~lLt~GD~~~AEDLvQ~Al~~~y~rW~Ri-~~~~~-~~a----YvR~vl~n~~~s~w---------- 74 (165)
T TIGR02983 11 FVAARYPRLLRTAYLLTAGDPHEAEDLVQEALVRTYVRWDRI-RDADA-PDA----YVRRVLVNLAISRW---------- 74 (165)
T ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCC-CCCCC-CHH----HHHHHHHHHHHHHH----------
T ss_conf 999999999999999827887569999999999998862215-88254-057----89999999999999----------
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCC
Q ss_conf 35899999999788786624478882467788861898321100000012234335520232345320000012356870
Q gi|254780611|r 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211 (302)
Q Consensus 132 ~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~ 211 (302)
|+-+-.......+.|.. ...+
T Consensus 75 --------RrR~~~~e~~~~~~Pd~---------------------------------------------------~ga~ 95 (165)
T TIGR02983 75 --------RRRRVRLELPTEELPDA---------------------------------------------------AGAP 95 (165)
T ss_pred --------HHHHHHHHCCCCCCCCC---------------------------------------------------CCCC
T ss_conf --------98876442146686488---------------------------------------------------8898
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 565566666667779999996219999999999982788888989999997789999999999999999999997
Q gi|254780611|r 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286 (302)
Q Consensus 212 ~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~ 286 (302)
+. . .....+..|.++|..||+|+|.||.+||+.| +|=.|||+.||||...|+==-.+||.+||+.+..
T Consensus 96 d~-~----~~~~~r~~l~~AL~~LP~rQR~vvVLRY~eD--lSe~~~A~~LG~SvGTVKS~~sRal~~LR~~~~~ 163 (165)
T TIGR02983 96 DP-A----ADVALRAALARALRRLPARQRAVVVLRYYED--LSEAEVAEVLGISVGTVKSRLSRALARLRELLEE 163 (165)
T ss_pred CC-C----CCHHHHHHHHHHHHHCCHHCCEEEEEECCCC--CCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCC
T ss_conf 75-3----1122699999999735641236723204578--9868999881999322899899999998873257
No 121
>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=98.37 E-value=3.8e-06 Score=60.59 Aligned_cols=82 Identities=21% Similarity=0.414 Sum_probs=68.8
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHH----HHHHHHHHHHHHH
Q ss_conf 705655666666677799999962199999999999827888889899999977899999999----9999999999999
Q gi|254780611|r 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI----EARAFKKVQESIQ 285 (302)
Q Consensus 210 ~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI----~~~AL~kLR~~l~ 285 (302)
++|=.+....-....+..+.+|+..||++||.+++++|+++ +|+.+||..+++++++|++= ..+.++..|..|+
T Consensus 142 DpEl~llr~~~r~~f~~Al~~Al~~L~~rER~LLRLHfv~~--Ls~~r~g~my~~~~STvsR~~~~ARe~lle~Tr~~La 219 (249)
T TIGR03001 142 DPELDLLRERYRQEFRAALREALAALSERERTLLRLHFVEG--LSMDRLGAMYQVHRSTVSRWVAQARERLLERTRRRLA 219 (249)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 17899999999999999999987328986876555688203--3299998774577507899999999999999999999
Q ss_pred HHHCCCCC
Q ss_conf 74012246
Q gi|254780611|r 286 KQVELSSS 293 (302)
Q Consensus 286 ~~~~~~~~ 293 (302)
..+.++++
T Consensus 220 ~RL~L~~~ 227 (249)
T TIGR03001 220 ERLKLSSR 227 (249)
T ss_pred HHHCCCCH
T ss_conf 97488805
No 122
>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=98.15 E-value=6.2e-06 Score=59.20 Aligned_cols=53 Identities=28% Similarity=0.451 Sum_probs=48.1
Q ss_pred HHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 9999996219999999999982788888989999997789999999999999999
Q gi|254780611|r 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280 (302)
Q Consensus 226 ~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kL 280 (302)
..|..+++.||++++.|+.++|+.+ +|.+|||+.||+|...|+..-.+|+++|
T Consensus 2 ~~l~~ai~~Lp~~~r~~~~l~~~~~--~s~~eIA~~lg~s~~tVk~~l~RA~~~L 54 (54)
T pfam08281 2 EALLRALEELPPRQREVFLLRYLEG--LSYAEIAELLGISEGTVKSRLSRARKKL 54 (54)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHC--CCHHHHHHHHCCCHHHHHHHHHHHHHCC
T ss_conf 8999999859999998968799878--5999999998949999999999999719
No 123
>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=98.10 E-value=1.6e-05 Score=56.49 Aligned_cols=157 Identities=17% Similarity=0.149 Sum_probs=92.5
Q ss_pred HHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHH
Q ss_conf 94307787565555799998889999998889989862185345689997577899999985320246001102300358
Q gi|254780611|r 55 TSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134 (302)
Q Consensus 55 ~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~ 134 (302)
+.|=+|=.+||.|--|.-.+-||++||-.+=+-.| +.=.++.--.|-+ ++-+ +.
T Consensus 4 ~~~rplLF~~AYRmLGSv~dAED~VQEtfLrw~~~-d~~~i~~~~AyL~---------------------~~~T----r~ 57 (287)
T TIGR02957 4 EALRPLLFSVAYRMLGSVADAEDIVQETFLRWQEA-DRAQIENPKAYLV---------------------KVVT----RR 57 (287)
T ss_pred HHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHC-CHHCCCCCCCHHH---------------------HHHH----HH
T ss_conf 56723789999997304756877899998978711-4404268640556---------------------8789----74
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHH
Q ss_conf 99999999788786624478882467788861898321100000012234335520232345320000012356870565
Q gi|254780611|r 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214 (302)
Q Consensus 135 l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~ 214 (302)
-.+.++.++..-+...|-...+|.+ .....+|.+.
T Consensus 58 cid~LrSAr~rRE~YvG~WLPEPl~---------------------------------------------~~s~~dP~e~ 92 (287)
T TIGR02957 58 CIDVLRSARARRESYVGPWLPEPLL---------------------------------------------TTSSADPAES 92 (287)
T ss_pred HHHHHHHCCCCCCCCCCCCCCCCCC---------------------------------------------CCCCCCHHHH
T ss_conf 5788885022146310788988888---------------------------------------------8885553889
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHH--HCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 56666666777999999621999999999998--2788888989999997789999999999999999999997401
Q gi|254780611|r 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289 (302)
Q Consensus 215 ~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~r--y~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~~~ 289 (302)
.+ ..+.+.....-.|+.|+|-||-|..+| |..+ .+|||+.+|.|..-+|||.+||=+|||..=+++..
T Consensus 93 ~E---~~eslS~A~L~lLErL~P~ERAVF~LREVF~y~----Y~EIA~~v~kS~ancRQl~~RAr~~lr~~~r~R~~ 162 (287)
T TIGR02957 93 VE---LAESLSMAYLLLLERLSPLERAVFLLREVFDYD----YEEIASIVGKSEANCRQLVSRARRHLRAARRPRFE 162 (287)
T ss_pred HH---HHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCC----CHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf 98---875377999998730797899999999874588----26789760689579999999999999752888751
No 124
>pfam00140 Sigma70_r1_2 Sigma-70 factor, region 1.2.
Probab=98.07 E-value=4e-06 Score=60.49 Aligned_cols=36 Identities=36% Similarity=0.574 Sum_probs=32.8
Q ss_pred CHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHH
Q ss_conf 4059999998407999998999999999998285999
Q gi|254780611|r 13 EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSA 49 (302)
Q Consensus 13 ~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~gd~~A 49 (302)
+|++..||++|+++||||++||++|++++++ |+..|
T Consensus 1 ~D~v~~YL~eIg~~pLLt~eEEi~LA~~i~~-g~~~~ 36 (37)
T pfam00140 1 SDSVRLYLREIGRVPLLTAEEEVELARRIEA-GDELA 36 (37)
T ss_pred CCHHHHHHHHHCCCCCCCHHHHHHHHHHHHH-CCHHH
T ss_conf 9709999998377678998999999999981-63731
No 125
>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=98.02 E-value=3.1e-06 Score=61.18 Aligned_cols=72 Identities=18% Similarity=0.179 Sum_probs=58.8
Q ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCH
Q ss_conf 99997887866244788824677888618983211000000122343355202323453200000123568705
Q gi|254780611|r 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212 (302)
Q Consensus 139 ~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~ 212 (302)
++|++++...+...+++.|+.+|||..||+++++|..++.....++|||.+++.+ ++.++.|++.+.....+
T Consensus 3 i~ki~ka~~~L~q~lgR~Pt~eEiA~~l~~s~~~v~~~~~~~~~~~SLd~p~~~~--~~~~l~d~i~D~~~~~P 74 (78)
T pfam04539 3 LNKIKRAQRELEQELGREPTPEEIAEELGISEEKVREVLEAAREPVSLDLPVGEE--EDGELGDLLEDDDAESP 74 (78)
T ss_pred HHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCEEEECCCCCC--CCCCHHHHCCCCCCCCH
T ss_conf 7999999999999988899999999996949999999998758986610676889--98628662059999881
No 126
>TIGR02233 Myxo_sigma_rel Myxococcus probable DNA-binding regulatory protein.
Probab=97.96 E-value=6.9e-05 Score=52.19 Aligned_cols=77 Identities=18% Similarity=0.418 Sum_probs=63.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHH----HHHHHHHHHHHHHHHHHHHC
Q ss_conf 55666666677799999962199999999999827888889899999977899999----99999999999999997401
Q gi|254780611|r 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV----RQIEARAFKKVQESIQKQVE 289 (302)
Q Consensus 214 ~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRV----rQI~~~AL~kLR~~l~~~~~ 289 (302)
.+.....+....+.+..|+..|+++||.|++++|+.+ .|+..||..+|++++.| .+.....+++-|+.|.+.+.
T Consensus 4 ~~lr~~~R~~~~~al~~Ala~L~~~eR~lLRLH~~~g--LsldR~~~lY~~hrStvaR~v~~are~Ll~~Tr~~LaeRL~ 81 (106)
T TIGR02233 4 AYLREEARQHLSAALSEALAALSERERTLLRLHHVEG--LSLDRLGTLYGVHRSTVARWVAGARELLLERTRQELAERLR 81 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 6788999999999999997528963335666776236--55899998847886169999999999999998998767407
Q ss_pred CCC
Q ss_conf 224
Q gi|254780611|r 290 LSS 292 (302)
Q Consensus 290 ~~~ 292 (302)
.++
T Consensus 82 L~~ 84 (106)
T TIGR02233 82 LTS 84 (106)
T ss_pred CCH
T ss_conf 886
No 127
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=97.91 E-value=0.0024 Score=41.84 Aligned_cols=65 Identities=18% Similarity=0.294 Sum_probs=43.2
Q ss_pred CCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHH----HHHHHHCCCCCCHHHHH
Q ss_conf 740599999984079999989999999999982859999999994307787----56555579999888999
Q gi|254780611|r 12 GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV----KIAMGYRGYGLPISEVV 79 (302)
Q Consensus 12 ~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~----~iA~~y~~~g~~~~DLi 79 (302)
.+|-+.-||++.|.+||||.|+|+++++++- .|-.....-|..+ ++++ ..+.+..+..+.+.|+|
T Consensus 100 TdDPVRMYLREMG~V~LLTREGEIeIAKRIE-~G~~~~~~ai~~~--P~~i~~il~~~e~l~~ge~rl~diI 168 (620)
T PRK05658 100 TDDPVRMYLREMGTVELLTREGEIEIAKRIE-DGENIMIAALCES--PLTIDAILEWYDRLENEEIRLRELI 168 (620)
T ss_pred CCCCHHHHHHHCCCCCCCCCHHHHHHHHHHH-HHHHHHHHHHHCC--HHHHHHHHHHHHHHHCCCEEHHHHH
T ss_conf 8980999999728876788074999999999-9999999999629--6999999999999982871399998
No 128
>PRK00118 putative DNA-binding protein; Validated
Probab=97.74 E-value=0.00011 Score=50.85 Aligned_cols=54 Identities=28% Similarity=0.360 Sum_probs=46.0
Q ss_pred HHHHH-HCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99996-219999999999982788888989999997789999999999999999999
Q gi|254780611|r 228 LTRSM-SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302)
Q Consensus 228 L~~~l-~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302)
|-..- ..|+++++.++.+||..| +||.|||+.+||||..|+-.-++|...|.+.
T Consensus 10 L~D~Yg~LLT~kQ~~~~~lyy~~D--lSl~EIAe~~~iSRQaV~D~ikr~~~~L~~y 64 (105)
T PRK00118 10 LFDFYQSLLTEKQRNYMELYYLDD--YSLGEIAEEFNVSRQAVYDNIKRTEKLLEDY 64 (105)
T ss_pred HHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_conf 999989875599999999998854--9999998996985999999999999999999
No 129
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=97.71 E-value=0.0001 Score=51.06 Aligned_cols=49 Identities=20% Similarity=0.367 Sum_probs=44.1
Q ss_pred CCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 1999999999998278888898999999778999999999999999999999
Q gi|254780611|r 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285 (302)
Q Consensus 234 ~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~ 285 (302)
.|++|+..||.+|- .++|+.|||+.||.|+.-|+-||++|+..++++-+
T Consensus 4 ~Lt~~q~~vL~lR~---~G~tQ~eIA~~lgTSraNvs~iEk~A~eNIekAre 52 (139)
T PRK03975 4 FLTERQIEVLRLRK---RGLTQQEIADILGTSRANISIIEKRARENIEKARN 52 (139)
T ss_pred HHHHHHHHHHHHHH---CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 56899999999998---28979999999773288999999999999999999
No 130
>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=97.70 E-value=0.0003 Score=47.97 Aligned_cols=55 Identities=27% Similarity=0.384 Sum_probs=46.1
Q ss_pred HHHHHH-HCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 999996-219999999999982788888989999997789999999999999999999
Q gi|254780611|r 227 MLTRSM-SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302)
Q Consensus 227 ~L~~~l-~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302)
.|-.+- ..|+++++.++.++|..| .||.|||+.+||||..|.-.-++|.+.|.+.
T Consensus 9 ~L~DfYg~LLT~KQ~~~~~lyy~eD--lSL~EIAe~~~iSRQaV~D~ikR~~~~L~~y 64 (101)
T pfam04297 9 YLFDFYQSLLTDKQKNYFELYYLDD--LSLSEIAEEFNVSRQAVYDNIKRTEKMLESY 64 (101)
T ss_pred HHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_conf 9999989876599999999998763--9899999881985999999999999999999
No 131
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family; InterPro: IPR014289 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This group of sigma factors are part of the larger sigma-70 family. From homology, tree building, bidirectional best hits and their one-to-a-genome distribution, they appear to represent a conserved family..
Probab=97.66 E-value=0.0012 Score=43.83 Aligned_cols=158 Identities=18% Similarity=0.260 Sum_probs=103.6
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCC-CCHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 889999998889989862185345689997577899999985320246001102-3003589999999978878662447
Q gi|254780611|r 75 ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFFNLRRLKGHLQAITDNN 153 (302)
Q Consensus 75 ~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~-~~~~r~l~~~~rk~~~~~~~~~~~~ 153 (302)
-||.|||.-+|-..|.++|.- + ...-||-.==.|..|.+.||...|.+++.. +. ++ ++
T Consensus 30 AEDaVQEtLl~Al~~~~~F~G-~-s~lkTWl~~ILknKiID~LR~~~R~~~v~laT~---------------~d---~e- 88 (194)
T TIGR02943 30 AEDAVQETLLAALEHADSFAG-R-SALKTWLFAILKNKIIDVLRAKGREVKVALATD---------------LD---DE- 88 (194)
T ss_pred HHHHHHHHHHHHHHCCCCCHH-H-HHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECC---------------HH---HH-
T ss_conf 889999999998735776014-8-999999999999999999834675454332010---------------22---01-
Q ss_pred CCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 88824677888618983211000000122343355202323453200000123568705655666666677799999962
Q gi|254780611|r 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233 (302)
Q Consensus 154 ~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~ 233 (302)
+. ......|+... . -+.+-....+.+-..|....+.+.--.+++.++.
T Consensus 89 ------------~~-------------dE~d~~~~lF~---~----~GHW~~~~~P~~W~~Pe~~l~~~~Fw~vfeaCl~ 136 (194)
T TIGR02943 89 ------------LD-------------DEADEFDALFT---Q----NGHWAEHEKPREWSTPEKQLENKEFWEVFEACLD 136 (194)
T ss_pred ------------CC-------------CCHHHHHHCCC---C----CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf ------------26-------------71023243168---5----7661446789998521688875568999999998
Q ss_pred CCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 199999999999827888889899999977899999999999999999999974
Q gi|254780611|r 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287 (302)
Q Consensus 234 ~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~ 287 (302)
.||++...|-.+|=..| +...||=..++||..-++=|--||=.+||+-|+.+
T Consensus 137 ~LP~~~ARVF~MRE~L~--~~~~eIC~~l~is~~N~~VlLyRAR~~LR~CL~~~ 188 (194)
T TIGR02943 137 RLPEQTARVFMMREVLG--FESEEICQELEISASNCHVLLYRARLSLRECLSAN 188 (194)
T ss_pred HHHHHHCCHHHHHHHHC--CCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 61676401355565424--86688753003137679999999999999998633
No 132
>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=97.48 E-value=0.0004 Score=47.11 Aligned_cols=62 Identities=16% Similarity=0.247 Sum_probs=49.0
Q ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHH-HHHHHHHHHHHHHHHHH
Q ss_conf 677799999962199999999999827888889899999977899999-99999999999999997
Q gi|254780611|r 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV-RQIEARAFKKVQESIQK 286 (302)
Q Consensus 222 ~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRV-rQI~~~AL~kLR~~l~~ 286 (302)
+.+..-|..+|..||+..+.-|.+.=+ +|.|++|+|+.||+|-..+ |++ +||=.+||+.|..
T Consensus 88 ~e~~~Cl~~~i~~LP~~~r~a~~L~el--~G~sQ~e~A~kLGlSlSGaKSRV-QRGR~~Lk~~L~~ 150 (170)
T TIGR02959 88 KELSQCLRPMIKELPDEYREAIRLTEL--EGLSQKEIAEKLGLSLSGAKSRV-QRGRKKLKELLED 150 (170)
T ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHC--CCCCHHHHHHHCCCCCCCHHHHH-HHHHHHHHHHHHC
T ss_conf 568888899887569867889888750--79982799876175335156788-9999999987742
No 133
>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=97.45 E-value=0.00024 Score=48.62 Aligned_cols=47 Identities=21% Similarity=0.446 Sum_probs=43.3
Q ss_pred CCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 19999999999982788888989999997789999999999999999999
Q gi|254780611|r 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302)
Q Consensus 234 ~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302)
-|++++..||.+|- .|++|.+||+.|+-||.-||=||++|+.++.++
T Consensus 6 FLTe~Q~kVL~lR~---kGl~Q~eIAk~LkTtRaNvS~iEkrA~EnIeKa 52 (142)
T TIGR00721 6 FLTERQIKVLELRE---KGLKQKEIAKILKTTRANVSIIEKRALENIEKA 52 (142)
T ss_pred CCHHHHHHHHHHHH---CCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
T ss_conf 34065689999863---388878898772672013789888744323776
No 134
>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=97.38 E-value=0.0076 Score=38.56 Aligned_cols=74 Identities=14% Similarity=0.242 Sum_probs=53.6
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 35687056556666666777999999621999999999998278888898999999778999999999999999999999
Q gi|254780611|r 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285 (302)
Q Consensus 206 ~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~ 285 (302)
+...+|+.....+ +-.+-....+|+.||||+|-||.+|=..+ ..=.|+|+.||.|-.-| +.||++=|..|.
T Consensus 118 p~aa~P~~~~~~~---EsvrLAF~AAlQ~LpPrQRAvL~LRdvlG--w~A~E~A~~L~~s~ASV----nSaLQRARAtL~ 188 (329)
T TIGR02960 118 PAAADPEAAAVAR---ESVRLAFVAALQLLPPRQRAVLLLRDVLG--WKAAEVAELLGTSVASV----NSALQRARATLA 188 (329)
T ss_pred CCCCCHHHHHHHH---HHHHHHHHHHHHCCCCHHHHHHHHHHHHC--CCHHHHHHHHCCCHHHH----HHHHHHHHHHHH
T ss_conf 8888711233211---46899999998748814578999898835--55568998743832678----658888788665
Q ss_pred HHH
Q ss_conf 740
Q gi|254780611|r 286 KQV 288 (302)
Q Consensus 286 ~~~ 288 (302)
...
T Consensus 189 ~~~ 191 (329)
T TIGR02960 189 ESE 191 (329)
T ss_pred HCC
T ss_conf 317
No 135
>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=97.28 E-value=0.001 Score=44.35 Aligned_cols=69 Identities=22% Similarity=0.309 Sum_probs=50.9
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 870565566666667779999996219999999999982788888989999997789999999999999999999
Q gi|254780611|r 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302)
Q Consensus 209 ~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302)
..|+..+..+ ...+.|...|+.|++..|.||.+|.+.+ .|.+|||+.+|+|-..|-=.--||=++|++.
T Consensus 92 ~~pE~~~~~K----~~~e~~~~~l~~Lpe~yr~vl~Lr~~~e--fSYkEia~~~n~sl~~vK~~LfRaR~eLk~~ 160 (162)
T TIGR02950 92 ESPEHELLIK----EELEELTKHLSSLPENYRTVLLLREFKE--FSYKEIAELLNLSLAKVKSELFRARKELKKL 160 (162)
T ss_pred CCHHHHHHHH----HHHHHHHHHHHHCHHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_conf 4108999999----9999999998527087656567543126--6888999984560221004444877999874
No 136
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=97.18 E-value=0.0013 Score=43.57 Aligned_cols=47 Identities=13% Similarity=0.241 Sum_probs=41.0
Q ss_pred HHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf 62199999999999827888889899999977899999999999999999
Q gi|254780611|r 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281 (302)
Q Consensus 232 l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR 281 (302)
+..|++||++|+.+.- +++|-+|||+.|++|..+|+--..+.++||.
T Consensus 141 ~~~Lt~RE~eVL~ll~---~G~snkeIA~~L~iS~~TV~~h~~~i~~KL~ 187 (204)
T PRK09958 141 LDSLSKQEISVMRYIL---DGKDNNDIAEKMFISNKTVSTYKSRLMEKLE 187 (204)
T ss_pred CCCCCHHHHHHHHHHH---CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
T ss_conf 2568999999999998---6999999998978899999999999999848
No 137
>pfam00196 GerE Bacterial regulatory proteins, luxR family.
Probab=97.12 E-value=0.0014 Score=43.39 Aligned_cols=47 Identities=17% Similarity=0.354 Sum_probs=40.1
Q ss_pred HHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf 62199999999999827888889899999977899999999999999999
Q gi|254780611|r 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281 (302)
Q Consensus 232 l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR 281 (302)
++.|++||++|+.+.- +++|-+|||+.||||...|+.-..++..||.
T Consensus 1 l~~LT~RE~~il~~l~---~G~s~~eIA~~L~is~~TV~~h~~~i~~Kl~ 47 (58)
T pfam00196 1 LDSLSPREREVLRLLA---AGKSNKEIADILGISEKTVKVHRSNIMRKLN 47 (58)
T ss_pred CCCCCHHHHHHHHHHH---HCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
T ss_conf 9977999999999998---0799999999978889999999999999809
No 138
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=97.08 E-value=0.0023 Score=41.99 Aligned_cols=52 Identities=23% Similarity=0.307 Sum_probs=42.5
Q ss_pred CCCHHHHHHHHHHH--C-CCCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 19999999999982--7-8888--898999999778999999999999999999999
Q gi|254780611|r 234 VLNPRERRIFEARR--L-QENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285 (302)
Q Consensus 234 ~L~~rEr~II~~ry--~-~~~~--~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~ 285 (302)
.|+|||+.||..=| | .+.| .|++|+|+.||||+..+.|.-.+|.+||=..+-
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~~~~ 211 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLIEAYF 211 (215)
T ss_pred CCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 699999999999998589888765899999999599888999999999999999975
No 139
>PRK09483 response regulator; Provisional
Probab=96.95 E-value=0.0029 Score=41.31 Aligned_cols=47 Identities=21% Similarity=0.333 Sum_probs=40.3
Q ss_pred HHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf 62199999999999827888889899999977899999999999999999
Q gi|254780611|r 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281 (302)
Q Consensus 232 l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR 281 (302)
+..|++||++|+.+.- +++|-+|||+.|++|..+|+--..+.++||.
T Consensus 146 ~~~LT~RE~eVl~ll~---~G~snkeIA~~L~iS~~TV~~h~~~i~~KL~ 192 (216)
T PRK09483 146 FASLSERELQIMLMIT---KGQKVNEISEQLNLSPKTVNSYRYRMFSKLN 192 (216)
T ss_pred CCCCCHHHHHHHHHHH---CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
T ss_conf 4568999999999998---7999999999969899999999999999809
No 140
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=96.92 E-value=0.0028 Score=41.42 Aligned_cols=46 Identities=20% Similarity=0.380 Sum_probs=39.5
Q ss_pred HCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf 2199999999999827888889899999977899999999999999999
Q gi|254780611|r 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281 (302)
Q Consensus 233 ~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR 281 (302)
..|++||..|+.+-- .++|.+|||+.||+|...|+.-..++.+||.
T Consensus 2 ~~LT~rE~~il~~l~---~G~s~~eIA~~L~is~~TV~~~~~~i~~Kl~ 47 (58)
T smart00421 2 ASLTPREREVLRLLA---EGLTNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCCCHHHHHHHHHHH---HCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
T ss_conf 761899999999998---1799999998989789899999999999848
No 141
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=96.90 E-value=0.0032 Score=41.03 Aligned_cols=45 Identities=13% Similarity=0.250 Sum_probs=39.7
Q ss_pred CCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf 199999999999827888889899999977899999999999999999
Q gi|254780611|r 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281 (302)
Q Consensus 234 ~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR 281 (302)
.|++||++|+.+.- +++|-+|||+.|++|..+|+--.++.++||.
T Consensus 150 ~LT~RE~eVL~lla---~G~snkeIA~~L~iS~~TV~~h~~~i~~KLg 194 (216)
T PRK10840 150 RLSPKESEVLRLFA---EGFLVTEIAKKLNRSIKTISSQKKSAMMKLG 194 (216)
T ss_pred CCCHHHHHHHHHHH---CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
T ss_conf 99989999999998---6999999998969899999999999999829
No 142
>PRK10403 transcriptional regulator NarP; Provisional
Probab=96.84 E-value=0.0041 Score=40.34 Aligned_cols=47 Identities=19% Similarity=0.288 Sum_probs=39.6
Q ss_pred HCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf 21999999999998278888898999999778999999999999999999
Q gi|254780611|r 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282 (302)
Q Consensus 233 ~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~ 282 (302)
..|++||++|+.+.- .++|-+|||+.|+||..+|+--.++.++||.-
T Consensus 152 ~~LT~RE~eVL~lla---~G~snkeIA~~L~iS~~TV~~h~~~I~~KLgv 198 (215)
T PRK10403 152 SVLTERELDVLHELA---QGLSNKQIASVLNISEQTVKVHIRNLLRKLNV 198 (215)
T ss_pred CCCCHHHHHHHHHHH---CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
T ss_conf 568999999999998---69999999999798299999999999998689
No 143
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=96.82 E-value=0.047 Score=33.27 Aligned_cols=43 Identities=14% Similarity=0.223 Sum_probs=30.0
Q ss_pred HHCCCHHHHHHHHH---------HHC-CC----CCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 62199999999999---------827-88----888989999997789999999999
Q gi|254780611|r 232 MSVLNPRERRIFEA---------RRL-QE----NPVTLENLSSEFEVSRERVRQIEA 274 (302)
Q Consensus 232 l~~L~~rEr~II~~---------ry~-~~----~~~Tl~EIa~~lgiS~eRVrQI~~ 274 (302)
+..|..|.+.++.- -|+ .| .|+|+++||+.+|++.++||++-+
T Consensus 329 i~~i~~R~~Tl~~v~~~Iv~~Q~~Ff~~G~~~lkPL~lkdiA~~lglheSTVSRav~ 385 (475)
T PRK12469 329 IRNAQQRFDTIQRVAECIVARQRDFFRYGEIALKPLVLRDVAEELGLHESTVSRATG 385 (475)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCCCHHHHHHC
T ss_conf 999999999999999999999999984785003673499999981998203768862
No 144
>PRK10651 transcriptional regulator NarL; Provisional
Probab=96.82 E-value=0.0044 Score=40.15 Aligned_cols=47 Identities=19% Similarity=0.374 Sum_probs=39.6
Q ss_pred HHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf 62199999999999827888889899999977899999999999999999
Q gi|254780611|r 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281 (302)
Q Consensus 232 l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR 281 (302)
+..|++||++|+.+.- .++|-+|||+.|++|..+|+--.++.++||.
T Consensus 153 ~~~LT~RE~eVL~ll~---~G~snkeIA~~L~iS~~TV~~h~~~i~~KLg 199 (216)
T PRK10651 153 VNQLTPRERDILKLIA---QGLSNKMIARRLDITESTVKVHVKHMLKKMK 199 (216)
T ss_pred CCCCCHHHHHHHHHHH---CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
T ss_conf 2348989999999998---5999999999969789999999999999848
No 145
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=96.81 E-value=0.0044 Score=40.15 Aligned_cols=45 Identities=13% Similarity=0.254 Sum_probs=39.6
Q ss_pred CCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf 199999999999827888889899999977899999999999999999
Q gi|254780611|r 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281 (302)
Q Consensus 234 ~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR 281 (302)
.|++||++|+.+.- +++|-+|||+.|++|..+|+--.++.++||.
T Consensus 149 ~Lt~RE~eVL~ll~---~G~snkeIA~~L~iS~~TV~~h~~~I~~KL~ 193 (210)
T PRK09935 149 PLSNREVTVLRYLA---NGLSNKEIAEQLLLSNKTISAHKSNIYGKLG 193 (210)
T ss_pred CCCHHHHHHHHHHH---CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
T ss_conf 99989999999998---6999999998949889999999999999819
No 146
>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=96.80 E-value=0.0046 Score=39.98 Aligned_cols=44 Identities=20% Similarity=0.335 Sum_probs=37.6
Q ss_pred CCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf 99999999999827888889899999977899999999999999999
Q gi|254780611|r 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281 (302)
Q Consensus 235 L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR 281 (302)
|++||.+|+.+.- .++|-+|||+.||+|...|+--.+++.+||.
T Consensus 1 LT~rE~~il~~~~---~G~s~~eIA~~L~is~~TV~~~~~~i~~Kl~ 44 (57)
T cd06170 1 LTPREREVLRLLA---EGKTNKEIADILGISEKTVKTHLRNIMRKLG 44 (57)
T ss_pred CCHHHHHHHHHHH---CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
T ss_conf 9889999999998---0799999999989789999999999999868
No 147
>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=96.79 E-value=0.0046 Score=39.98 Aligned_cols=57 Identities=23% Similarity=0.297 Sum_probs=48.8
Q ss_pred HHHHHHHHHHHHCC-CHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 67779999996219-999999999982788888989999997789999999999999999
Q gi|254780611|r 222 KNRRNMLTRSMSVL-NPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280 (302)
Q Consensus 222 ~~~~~~L~~~l~~L-~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kL 280 (302)
...+..|.+.++.| ++.+|.|++++|+.. ++--++++.|++|+..+-.+.++|++.|
T Consensus 42 ik~r~El~rlI~~l~np~~RtvL~m~Yid~--~~~~~v~e~l~~Sr~Tyyr~~r~Ai~~L 99 (100)
T pfam07374 42 IKRKLELGRLIDKLENPDSRTILRMVYIDK--MTVWQVCDKLNCSRTTYYRKLRVAIKEL 99 (100)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHEEEEECC--CCHHHHHHHHCCCHHHHHHHHHHHHHHC
T ss_conf 999999999998457802213111434434--7499999997666678999999999852
No 148
>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=96.74 E-value=0.0052 Score=39.62 Aligned_cols=48 Identities=23% Similarity=0.296 Sum_probs=40.6
Q ss_pred HHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf 621999999999998278888898999999778999999999999999999
Q gi|254780611|r 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282 (302)
Q Consensus 232 l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~ 282 (302)
+..|++||++|+.+-- +++|-+|||..||||..+|..=-+++++||.-
T Consensus 188 ~glLT~RE~EVL~~va---~G~sn~eIA~~L~iS~~TVk~H~~~i~~KL~v 235 (247)
T TIGR03020 188 AGLITAREAEILAWVR---DGKTNEEIAAILGISSLTVKNHLQHIFKKLDV 235 (247)
T ss_pred CCCCCHHHHHHHHHHH---CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCC
T ss_conf 7899989999999998---79999999999497999999999999998099
No 149
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=96.74 E-value=0.0052 Score=39.65 Aligned_cols=45 Identities=22% Similarity=0.352 Sum_probs=39.0
Q ss_pred HCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 219999999999982788888989999997789999999999999999
Q gi|254780611|r 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280 (302)
Q Consensus 233 ~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kL 280 (302)
..|++||++|+.+.- +++|.+|||+.|+||..+|+-=.++.++||
T Consensus 136 ~~LT~RE~eVL~lia---~G~snkeIA~~L~IS~~TVk~h~~~i~~KL 180 (196)
T PRK10360 136 DPLTKRERQVAEKLA---QGMAVKEIAAELGLSPKTVHVHRANLMEKL 180 (196)
T ss_pred CCCCHHHHHHHHHHH---CCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
T ss_conf 899979999999998---799999999996999999999999999981
No 150
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=96.68 E-value=0.0067 Score=38.92 Aligned_cols=47 Identities=17% Similarity=0.189 Sum_probs=40.1
Q ss_pred CCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 19999999999982788888989999997789999999999999999999
Q gi|254780611|r 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302)
Q Consensus 234 ~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302)
.|++||++||..-= +++|-.|||.+||||...|..=.++|.+||-..
T Consensus 179 ~LT~RE~E~L~W~A---~GKTs~EIa~IL~ISe~TV~fHl~na~~KL~a~ 225 (240)
T PRK10188 179 NFSKREKEILKWTA---EGKTSAEIAMILSISENTVNFHQKNMQKKFNAP 225 (240)
T ss_pred CCCHHHHHHHHHHH---CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
T ss_conf 89989999999997---799999999883999999999999999995899
No 151
>pfam04967 HTH_10 HTH DNA binding domain.
Probab=96.67 E-value=0.0079 Score=38.43 Aligned_cols=46 Identities=30% Similarity=0.416 Sum_probs=36.8
Q ss_pred CCHHHHHHHHHHH--C-CCCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 9999999999982--7-8888--8989999997789999999999999999
Q gi|254780611|r 235 LNPRERRIFEARR--L-QENP--VTLENLSSEFEVSRERVRQIEARAFKKV 280 (302)
Q Consensus 235 L~~rEr~II~~ry--~-~~~~--~Tl~EIa~~lgiS~eRVrQI~~~AL~kL 280 (302)
|++||+.|+..=| | .+.| .|+.|||+.||||+..++..-.+|..|+
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 152
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=96.65 E-value=0.0061 Score=39.19 Aligned_cols=46 Identities=17% Similarity=0.335 Sum_probs=39.7
Q ss_pred HCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf 2199999999999827888889899999977899999999999999999
Q gi|254780611|r 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281 (302)
Q Consensus 233 ~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR 281 (302)
..|++||++|+++.- +++|.+|||+.|++|..+|+-=..++++||-
T Consensus 133 ~~Lt~rE~eVl~l~a---~G~s~~eIA~~L~~S~kTv~thr~~~m~KLg 178 (205)
T PRK11475 133 RMLSPTEREILRFMS---RGYSMPQIAEQLERNIKTIRAHKFNVMSKLG 178 (205)
T ss_pred CCCCHHHHHHHHHHH---CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
T ss_conf 889858999999997---6999999999978888899999999999829
No 153
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=96.64 E-value=0.0095 Score=37.91 Aligned_cols=46 Identities=26% Similarity=0.429 Sum_probs=39.9
Q ss_pred HCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 219999999999982788888989999997789999999999999999
Q gi|254780611|r 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280 (302)
Q Consensus 233 ~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kL 280 (302)
+.|+++++..+.++|..| .|+.|||+.++||++.|.+-.++.-..|
T Consensus 16 sLLT~KQ~~Y~~lyy~dD--lSl~EIAee~~VSRqAIyDnIKr~~~~L 61 (105)
T COG2739 16 SLLTKKQKNYLELYYLDD--LSLSEIAEEFNVSRQAIYDNIKRTEKIL 61 (105)
T ss_pred HHHHHHHHHHHHHHHHHH--CCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf 998688999999999811--6699999995750999999999999999
No 154
>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=96.62 E-value=0.0076 Score=38.55 Aligned_cols=46 Identities=20% Similarity=0.203 Sum_probs=39.4
Q ss_pred CCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf 1999999999998278888898999999778999999999999999999
Q gi|254780611|r 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282 (302)
Q Consensus 234 ~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~ 282 (302)
.|++||+++|..-- +++|-.|||.+||||...|..--++|.+||-.
T Consensus 171 ~LT~RE~E~L~w~A---~Gkt~~eIa~iL~iSe~TV~~hl~~a~~KLga 216 (232)
T TIGR03541 171 VLSEREREVLAWTA---LGRRQADIAAILGISERTVENHLRSARRKLGV 216 (232)
T ss_pred CCCHHHHHHHHHHH---CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
T ss_conf 98989999999998---79999999999698999999999999998489
No 155
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=96.62 E-value=0.012 Score=37.15 Aligned_cols=50 Identities=18% Similarity=0.343 Sum_probs=39.7
Q ss_pred HHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf 99962199999999999827888889899999977899999999999999999
Q gi|254780611|r 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281 (302)
Q Consensus 229 ~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR 281 (302)
...+..|++||++|+.+-- +++|-+|||..|++|..+|.-=..+.++||.
T Consensus 136 ~~~~~~LT~RE~eVL~ll~---~G~snkeIA~~L~iS~~TV~~h~~~I~~KL~ 185 (202)
T PRK09390 136 RARIASLSERERQVMDGLV---AGLSNKVIARDLDISPRTVEVYRANVMTKMQ 185 (202)
T ss_pred HHHHCCCCHHHHHHHHHHH---CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
T ss_conf 7400669989999999998---3896899999979878899999999999968
No 156
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=96.59 E-value=0.067 Score=32.23 Aligned_cols=61 Identities=15% Similarity=0.240 Sum_probs=43.9
Q ss_pred HHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 779999996219999999999982788888989999997789999999999999999999997
Q gi|254780611|r 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286 (302)
Q Consensus 224 ~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~ 286 (302)
..+.+...++.|++++-.|+.++-..+ .|+.|||+.+++|...|.-.-.++-.+|+..-++
T Consensus 106 ~~em~~~l~~~L~p~Q~vIfLLkDVF~--ys~~eiAe~~s~sEGaVKasLfRsR~RLK~~~ee 166 (228)
T PRK06704 106 LHEMVGKVLSSLNVQQSAILLLKDVFQ--YSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEE 166 (228)
T ss_pred HHHHHHHHHHHCCHHHHHHHHHHHHHH--HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCHH
T ss_conf 999999998325888899999999987--5599999995566349999999999998733853
No 157
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=96.53 E-value=0.0084 Score=38.27 Aligned_cols=46 Identities=17% Similarity=0.372 Sum_probs=40.0
Q ss_pred HCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf 2199999999999827888889899999977899999999999999999
Q gi|254780611|r 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281 (302)
Q Consensus 233 ~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR 281 (302)
..|++||+.|+++.- +++|-+|||+.|++|..+|+-=..+.++||.
T Consensus 147 ~~LT~RE~eVl~lla---~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~ 192 (211)
T COG2197 147 ELLTPRELEVLRLLA---EGLSNKEIAEELNLSEKTVKTHVSNILRKLG 192 (211)
T ss_pred CCCCHHHHHHHHHHH---CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
T ss_conf 789989999999998---7998899999978789899999999999839
No 158
>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=96.45 E-value=0.034 Score=34.20 Aligned_cols=64 Identities=19% Similarity=0.299 Sum_probs=52.9
Q ss_pred HHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 7799999962199999999999827888889899999977899999999999999999999974
Q gi|254780611|r 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287 (302)
Q Consensus 224 ~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~ 287 (302)
....+..++..||+.+|.||...|...+...=-+|-..+|+|..+--.++.+|+-+|-..|..-
T Consensus 73 ~~~~v~~~~~~L~~~~R~Il~~~Y~~~~~~~D~~i~~el~~s~~~Yy~~K~rA~l~lA~~l~~~ 136 (139)
T TIGR01637 73 IVNAVSKAINQLDEISRQILYDKYLEEDKKSDYQIMNELGYSHSQYYRIKKRALLRLAEALKIG 136 (139)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHCHHHHCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999999984088889999999710455303788888743777899999999999999985221
No 159
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=96.33 E-value=0.034 Score=34.16 Aligned_cols=57 Identities=19% Similarity=0.370 Sum_probs=41.7
Q ss_pred HHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 779999996219999999999982788888989999997789999999999999999999
Q gi|254780611|r 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302)
Q Consensus 224 ~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302)
....+...+.+|++|||+|+..-- .+..-++||..||||.-+|--=..+.+.||+..
T Consensus 132 ~~~~~~~~l~tLT~RERqVl~~vV---~G~~NKqIA~dLgiS~rTVe~HRanvM~Km~a~ 188 (202)
T COG4566 132 RQAAIRARLATLTPRERQVLDLVV---RGLMNKQIAFDLGISERTVELHRANVMEKMQAR 188 (202)
T ss_pred HHHHHHHHHHHCCHHHHHHHHHHH---CCCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHC
T ss_conf 899999999866988999999998---376308999983986645999999999997333
No 160
>pfam02001 DUF134 Protein of unknown function DUF134. This family of archaeal proteins has no known function.
Probab=96.32 E-value=0.015 Score=36.54 Aligned_cols=51 Identities=18% Similarity=0.217 Sum_probs=43.8
Q ss_pred CCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 19999999999982788888989999997789999999999999999999997
Q gi|254780611|r 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286 (302)
Q Consensus 234 ~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~ 286 (302)
.|+..|-+.|++-.+ +++|+.|-|+.||||+.++.+|-..|-+|+-.+|-.
T Consensus 36 ~L~~dE~EAiRL~D~--egl~QeeaA~~MgVSR~Tf~ril~~ARkKvA~aLv~ 86 (100)
T pfam02001 36 IITLDEFEAIRLVDY--EDYTQEEAAKLMGISRRTVWRLLTSARKKIADALVE 86 (100)
T ss_pred EECHHHHHHHHHHHH--CCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf 734999999998736--079899999884976999999999999999999867
No 161
>PRK13870 transcriptional regulator TraR; Provisional
Probab=96.28 E-value=0.016 Score=36.32 Aligned_cols=45 Identities=22% Similarity=0.248 Sum_probs=38.3
Q ss_pred CCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf 999999999998278888898999999778999999999999999999
Q gi|254780611|r 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282 (302)
Q Consensus 235 L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~ 282 (302)
|++||+++|.-- -+++|-.|||.+||||...|.-=-++|.+||-.
T Consensus 174 LT~RE~E~L~W~---A~GKT~~EIA~ILgISe~TV~fHl~na~~KL~a 218 (234)
T PRK13870 174 LDPKEATYLRWI---AVGMTMEEIADVEGVKYNSVRVKLREAMKRFDV 218 (234)
T ss_pred CCHHHHHHHHHH---HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
T ss_conf 997999999999---789989999999798899999999999999589
No 162
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=96.24 E-value=0.0033 Score=40.96 Aligned_cols=47 Identities=19% Similarity=0.404 Sum_probs=40.7
Q ss_pred CCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 19999999999982788888989999997789999999999999999999
Q gi|254780611|r 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302)
Q Consensus 234 ~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302)
.|++++-.|+.+|- .+.|++|||++||-|+.-||-|+++|+..+.++
T Consensus 8 flte~qikvl~lRe---kG~tQ~eIA~~L~TTraNvSaIEkrA~enIeka 54 (143)
T COG1356 8 FLTEQQIKVLVLRE---KGLTQSEIARILKTTRANVSAIEKRALENIEKA 54 (143)
T ss_pred EEEHHHEEEEEHHH---CCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHH
T ss_conf 10023023565264---056489999997545101799999999989999
No 163
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=96.12 E-value=0.021 Score=35.62 Aligned_cols=45 Identities=22% Similarity=0.330 Sum_probs=37.8
Q ss_pred CCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf 199999999999827888889899999977899999999999999999
Q gi|254780611|r 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281 (302)
Q Consensus 234 ~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR 281 (302)
.|++||++|+.+-- .++|-+|||+.|.||..+|.-=-.+.++||-
T Consensus 155 ~LT~RE~eIL~lla---~G~sNkEIA~~L~iSe~TVk~H~~~I~~KL~ 199 (216)
T PRK10100 155 LLTHREKEILNKLR---IGASNNEIARSLFISENTVKTHLYNLFKKIA 199 (216)
T ss_pred CCCHHHHHHHHHHH---CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
T ss_conf 99989999999998---7999999998949889899999999999809
No 164
>PRK09954 hypothetical protein; Provisional
Probab=95.95 E-value=0.015 Score=36.58 Aligned_cols=16 Identities=19% Similarity=0.565 Sum_probs=8.4
Q ss_pred HHHHHHHCCCCCCHHH
Q ss_conf 9999840799999899
Q gi|254780611|r 18 RYIHEIRKIPMLEKQE 33 (302)
Q Consensus 18 ~yl~~i~~~~~Lt~ee 33 (302)
+-|+-|.+-|+.|-+|
T Consensus 7 ~il~~i~~~p~i~q~e 22 (362)
T PRK09954 7 EILAILRRNPLIQQNE 22 (362)
T ss_pred HHHHHHHHCCCCCHHH
T ss_conf 9999998789958999
No 165
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=95.82 E-value=0.16 Score=29.62 Aligned_cols=43 Identities=9% Similarity=0.359 Sum_probs=29.6
Q ss_pred HHCCCHHHHHHHHH---------HHC-CC----CCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 62199999999999---------827-88----888989999997789999999999
Q gi|254780611|r 232 MSVLNPRERRIFEA---------RRL-QE----NPVTLENLSSEFEVSRERVRQIEA 274 (302)
Q Consensus 232 l~~L~~rEr~II~~---------ry~-~~----~~~Tl~EIa~~lgiS~eRVrQI~~ 274 (302)
+..|..|...++.- -|+ .| .|+|+++||+.+|++.++||++-+
T Consensus 315 i~~i~~R~~Tl~~v~~~Iv~~Q~~Ff~~G~~~lkPL~lkdiA~~lglheSTVSRav~ 371 (461)
T PRK05932 315 IKSLEQRKETLLKVATCIVEQQRDFFEHGEEALKPLVLKDIAEALGMHESTISRATT 371 (461)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHCCCCHHHHHHHHH
T ss_conf 999999999999999999998799996795446676399999873998125889871
No 166
>PRK04217 hypothetical protein; Provisional
Probab=95.73 E-value=0.041 Score=33.62 Aligned_cols=58 Identities=24% Similarity=0.197 Sum_probs=45.3
Q ss_pred CCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 999999999998278888898999999778999999999999999999999740122467
Q gi|254780611|r 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294 (302)
Q Consensus 235 L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~~~~~~~~ 294 (302)
|+-.|-..|++-.+ +++|+.|-|+.||||+.++.+|-..|-+|+-.+|-.--.+...|
T Consensus 43 LtvdE~EaiRL~D~--egl~qeeaA~~M~VSR~Tf~ril~~AR~KvA~aLv~Gkal~I~~ 100 (110)
T PRK04217 43 MTYEEFEALRLVDY--EGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGRELIILP 100 (110)
T ss_pred ECHHHHHHHHHHHH--CCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEC
T ss_conf 11999999998736--07989999988497699999999999999999986797489974
No 167
>PRK04841 transcriptional regulator MalT; Provisional
Probab=95.54 E-value=0.041 Score=33.68 Aligned_cols=44 Identities=16% Similarity=0.288 Sum_probs=35.3
Q ss_pred CCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 19999999999982788888989999997789999999999999999
Q gi|254780611|r 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280 (302)
Q Consensus 234 ~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kL 280 (302)
.|++||.+|+.+-- .++|-+|||+.|+||..+|.-=-++...||
T Consensus 838 ~LT~RE~eVL~lLa---~GlSNkeIA~~L~IS~~TVK~HlrnIy~KL 881 (903)
T PRK04841 838 PLTQREWQVLGLIY---SGYSNEQIAGELDVAATTIKTHIRNLYQKL 881 (903)
T ss_pred CCCHHHHHHHHHHH---CCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
T ss_conf 97999999999997---689999999881998769999999998565
No 168
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=95.53 E-value=0.026 Score=34.97 Aligned_cols=14 Identities=29% Similarity=0.358 Sum_probs=6.3
Q ss_pred HHHCCCHHHHHHHH
Q ss_conf 99778999999999
Q gi|254780611|r 260 SEFEVSRERVRQIE 273 (302)
Q Consensus 260 ~~lgiS~eRVrQI~ 273 (302)
..+|++-+..+++.
T Consensus 266 r~igl~L~~l~~ip 279 (321)
T COG2390 266 RVIGLSLDDLRQIP 279 (321)
T ss_pred CEECCCHHHHHCCC
T ss_conf 16437788973278
No 169
>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=94.86 E-value=0.012 Score=37.18 Aligned_cols=40 Identities=15% Similarity=0.404 Sum_probs=33.7
Q ss_pred HHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHH
Q ss_conf 999962199999999999827888889899999977899999
Q gi|254780611|r 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269 (302)
Q Consensus 228 L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRV 269 (302)
....++.||++|+.||.++|+.+ +.--|||+.|.+||+-|
T Consensus 101 F~DLISiL~~~QKkIIYmKFf~~--~kdieIak~L~ISRQsV 140 (142)
T TIGR03209 101 FNDLISILPNKQKKIIYMKFFED--MKEIDIAKKLHISRQSV 140 (142)
T ss_pred HHHHHHHCCCCHHEEEHHHHHHH--HHHHHHHHHHCCHHHHH
T ss_conf 98899857940010115899877--77857999953028751
No 170
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=94.83 E-value=0.098 Score=31.13 Aligned_cols=50 Identities=20% Similarity=0.244 Sum_probs=41.7
Q ss_pred CCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999999982788888989999997789999999999999999999997
Q gi|254780611|r 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286 (302)
Q Consensus 235 L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~ 286 (302)
|+-.|-+.|++....+ +|+.|-|..||||+..+-.+-+.|.+|.-.+|-+
T Consensus 34 lt~eElEAlRLvD~~~--l~QeeAA~rMgISr~Tfwr~l~sAR~KvA~aLve 83 (99)
T COG1342 34 LTIEELEALRLVDYEG--LTQEEAALRMGISRQTFWRLLTSARKKVADALVE 83 (99)
T ss_pred ECHHHHHHHHHHHHHH--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf 2299988999886861--0578999984642999999999999999999855
No 171
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=94.64 E-value=0.14 Score=30.12 Aligned_cols=51 Identities=20% Similarity=0.280 Sum_probs=40.8
Q ss_pred HCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 219999999999982788888989999997789999999999999999999997
Q gi|254780611|r 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286 (302)
Q Consensus 233 ~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~ 286 (302)
..|++||..|+.+.- .++|..|||..+|+|...|..-..++..||.-.-+.
T Consensus 3 ~~Lt~rE~~~~~l~~---~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~~~~r~ 53 (65)
T COG2771 3 ADLTPREREILRLVA---QGKSNKEIARILGISEETVKTHLRNIYRKLGVKNRV 53 (65)
T ss_pred CCCCHHHHHHHHHHH---CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHH
T ss_conf 113888999999998---699899999998779999999999999997758699
No 172
>PRK13558 bacterio-opsin activator; Provisional
Probab=94.28 E-value=0.35 Score=27.43 Aligned_cols=57 Identities=14% Similarity=0.167 Sum_probs=43.2
Q ss_pred HHHHH-HCCCHHHHHHHHHHHC---CCCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 99996-2199999999999827---8888--89899999977899999999999999999999
Q gi|254780611|r 228 LTRSM-SVLNPRERRIFEARRL---QENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284 (302)
Q Consensus 228 L~~~l-~~L~~rEr~II~~ry~---~~~~--~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l 284 (302)
+..++ +.|++|++.+|+.=|. .+-| .|=+|||+.||||+....|=...|-+||=..+
T Consensus 609 ~~~aL~e~LTDRQ~eaLqtAY~sGyFEwPR~sTGeElAesLgIS~pTfhqHLRaaerKL~~a~ 671 (674)
T PRK13558 609 FREELRNDLTDRQLTALQKAYVSGYFEWPRRAEGKQLAESMDIVPSTYHQHLQAAKQKLVGAF 671 (674)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 999998760498999999998647577887787899998709883889999999999999987
No 173
>PRK09191 two-component response regulator; Provisional
Probab=94.07 E-value=0.13 Score=30.22 Aligned_cols=136 Identities=17% Similarity=0.203 Sum_probs=84.9
Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCH
Q ss_conf 99994307787565555799998889999998889989862185345689997577899999985320246001102300
Q gi|254780611|r 52 RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131 (302)
Q Consensus 52 ~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~ 131 (302)
.-|..||++.+.-|+-..|.--.=|.++..---+|+..-..||..-+.|..-|..+
T Consensus 5 ~~ia~~LPyLRRYARALTGsQ~~GD~yV~a~LEallad~~~~~~~~~~Rv~Ly~~f------------------------ 60 (261)
T PRK09191 5 QRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEASSPRVGLYRLF------------------------ 60 (261)
T ss_pred HHHHHHCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCHHCCCCCCHHHHHHHHH------------------------
T ss_conf 98887583999999986178201899999999999809220267775589999999------------------------
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCC
Q ss_conf 35899999999788786624478882467788861898321100000012234335520232345320000012356870
Q gi|254780611|r 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211 (302)
Q Consensus 132 ~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~ 211 (302)
.++... . + .+... . ....
T Consensus 61 --------~~iw~s-------~-------------~--------------------~~~~~--~------------~~~~ 78 (261)
T PRK09191 61 --------HRIWSS-------A-------------G--------------------ANDPE--P------------ESPF 78 (261)
T ss_pred --------HHHHHH-------C-------------C--------------------CCCCC--C------------CCCC
T ss_conf --------999972-------5-------------9--------------------99888--8------------7630
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 56556666666777999999621999999999998278888898999999778999999999999999999999740
Q gi|254780611|r 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288 (302)
Q Consensus 212 ~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~~ 288 (302)
. .....+|..|+++.|+.+.+.=+++ .+..|+|+.||++.+.|.++-..|-..+++.+...+
T Consensus 79 -----~--------~~~~~~L~~ltp~~RqAlLL~alEg--Fs~~eaA~Il~v~~~e~~~l~~~A~~ei~~~~~~rI 140 (261)
T PRK09191 79 -----E--------ARAERRLSAITPLPRQAFLLTALEG--FSEEEAAEILGVDPAEVAALLDDASREIARQVATSV 140 (261)
T ss_pred -----H--------HHHHHHHHHCCCHHHHHHHHHHHHC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCE
T ss_conf -----0--------6899998748930349999898828--988999999789999999999999999973747887
No 174
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=93.81 E-value=0.55 Score=26.11 Aligned_cols=57 Identities=11% Similarity=0.272 Sum_probs=35.2
Q ss_pred HHCCCHHHHHHHH-------HH--HC-CC----CCCCHHHHHHHHCCCHHHHHHHHHH-------HHHHHHHHHHHHH
Q ss_conf 6219999999999-------98--27-88----8889899999977899999999999-------9999999999740
Q gi|254780611|r 232 MSVLNPRERRIFE-------AR--RL-QE----NPVTLENLSSEFEVSRERVRQIEAR-------AFKKVQESIQKQV 288 (302)
Q Consensus 232 l~~L~~rEr~II~-------~r--y~-~~----~~~Tl~EIa~~lgiS~eRVrQI~~~-------AL~kLR~~l~~~~ 288 (302)
++.|.-|++.++. .= |+ .+ .|+||++||+.+|++.++||+.-.. .+-.||-.+...+
T Consensus 296 iksL~qR~~TLlkV~~~Iv~~Q~~Ff~~g~~~l~PL~LrdvA~~i~~HESTISRai~nKy~~tprG~feLk~FFs~~i 373 (444)
T COG1508 296 IKSLEQREETLLKVAEEIVEYQKAFFEGGEEALKPLVLRDVADEIGMHESTISRAITNKYLATPRGLFELKYFFSSSL 373 (444)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCEEEHHHHHHHHC
T ss_conf 999999999999999999999999983785457763199999883712888999982541048863344898877741
No 175
>pfam05263 DUF722 Protein of unknown function (DUF722). This family contains several bacteriophage proteins of unknown function.
Probab=93.42 E-value=0.63 Score=25.71 Aligned_cols=54 Identities=26% Similarity=0.421 Sum_probs=44.0
Q ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 666777999999621999999999998278888898999999778999999999
Q gi|254780611|r 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273 (302)
Q Consensus 220 e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~ 273 (302)
.....+..|..+...|.+.++.||.+||..-+++|--.||..++||.-.++.+.
T Consensus 67 ~l~~qk~~id~~~~~~~~~~k~ii~lrY~~r~~~sW~~Va~~l~i~er~~~~~~ 120 (130)
T pfam05263 67 KLKRQKEILDNFYKVLTEEEKRIIELRYKGRNGMTWYQVAQELDISEKKAKRIY 120 (130)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 999999999999998518999999998676467549999999651199999999
No 176
>PRK11564 stationary phase inducible protein CsiE; Provisional
Probab=93.12 E-value=0.39 Score=27.08 Aligned_cols=14 Identities=7% Similarity=-0.045 Sum_probs=6.4
Q ss_pred CCHHHHHHHHHHHC
Q ss_conf 99999999999827
Q gi|254780611|r 235 LNPRERRIFEARRL 248 (302)
Q Consensus 235 L~~rEr~II~~ry~ 248 (302)
+|+.|---|.++||
T Consensus 314 ~~edEi~yiaihfg 327 (426)
T PRK11564 314 FSDEETGLVAVIFG 327 (426)
T ss_pred CCHHHHHHHHHHHH
T ss_conf 88899999999999
No 177
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=93.05 E-value=0.16 Score=29.78 Aligned_cols=29 Identities=28% Similarity=0.153 Sum_probs=20.4
Q ss_pred CCCCCCHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf 44788824677888618983211000000
Q gi|254780611|r 151 DNNLKPEQVVAIAKKLNVSESEVISMNCR 179 (302)
Q Consensus 151 ~~~~~~~~~~eiA~~Lgis~~~v~~l~~~ 179 (302)
--...|-++.||++.+|+|...+-...+.
T Consensus 36 yls~~Pmtl~Ei~E~lg~Sks~vS~~lkk 64 (177)
T COG1510 36 YLSRKPLTLDEIAEALGMSKSNVSMGLKK 64 (177)
T ss_pred EECCCCCCHHHHHHHHCCCCCHHHHHHHH
T ss_conf 00699966999999977780128899999
No 178
>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=92.99 E-value=0.3 Score=27.90 Aligned_cols=41 Identities=15% Similarity=0.300 Sum_probs=29.5
Q ss_pred HHCCCHHHHHHHHHH--HC--CCCCCCHHHHHHHHCC-CHHHHHHH
Q ss_conf 621999999999998--27--8888898999999778-99999999
Q gi|254780611|r 232 MSVLNPRERRIFEAR--RL--QENPVTLENLSSEFEV-SRERVRQI 272 (302)
Q Consensus 232 l~~L~~rEr~II~~r--y~--~~~~~Tl~EIa~~lgi-S~eRVrQI 272 (302)
|..|++|++.|+..- |. .+-+-|++|||+.+|+ |...|.+.
T Consensus 1 M~~LT~rQ~~il~~I~~~~~~~G~~Pt~rEI~~~~g~~S~s~v~~~ 46 (65)
T pfam01726 1 MKPLTERQREVLDFIKASIEETGYPPSRREIAQALGLRSPNAAEEH 46 (65)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCHHHHHHH
T ss_conf 9633799999999999999982889879999999389980999999
No 179
>pfam01371 Trp_repressor Trp repressor protein. This protein binds to tryptophan and represses transcription of the Trp operon.
Probab=92.69 E-value=0.53 Score=26.23 Aligned_cols=44 Identities=20% Similarity=0.358 Sum_probs=32.3
Q ss_pred CCCHHHHHHHHHHH-----CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 19999999999982-----7888889899999977899999999999999
Q gi|254780611|r 234 VLNPRERRIFEARR-----LQENPVTLENLSSEFEVSRERVRQIEARAFK 278 (302)
Q Consensus 234 ~L~~rEr~II~~ry-----~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~ 278 (302)
.+++.|..-+..|+ +...++|++||++.+|+|-..|++. ++.|+
T Consensus 26 l~T~~E~~ala~R~~va~~LL~~~~syreI~~~~g~S~aTItRv-sr~Lk 74 (88)
T pfam01371 26 LLTPDEREALAQRLRIAKELLRGELSQREIAQELGASIATITRG-SNCLK 74 (88)
T ss_pred HCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH-HHHHH
T ss_conf 39999999999999999999978998999999859852314788-99987
No 180
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=92.46 E-value=0.66 Score=25.60 Aligned_cols=47 Identities=19% Similarity=0.362 Sum_probs=21.6
Q ss_pred HHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 996219999999999982788888989999997789999999999999999
Q gi|254780611|r 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280 (302)
Q Consensus 230 ~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kL 280 (302)
.++-.|++.+-.|+..---.+.|+|-.+||+.+|.|+.+| .+||++|
T Consensus 20 ~c~~GLs~~Dv~v~~~LL~~~~~~tvdelae~lnr~rStv----~rsl~~L 66 (126)
T COG3355 20 KCVYGLSELDVEVYKALLEENGPLTVDELAEILNRSRSTV----YRSLQNL 66 (126)
T ss_pred HHHHCCCHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHH----HHHHHHH
T ss_conf 9993896889999999986469957999999978319999----9999999
No 181
>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=91.71 E-value=0.27 Score=28.23 Aligned_cols=52 Identities=19% Similarity=0.211 Sum_probs=32.0
Q ss_pred CCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCC-CCCCCCHHH
Q ss_conf 46001102300358999999997887866244788824677888618983211000000-122343355
Q gi|254780611|r 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR-LAGDESLNA 188 (302)
Q Consensus 121 ~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~-~~~~~SLd~ 188 (302)
...++.|.. ..+|.+++++. -+..++|..|||.+..|..+.+. +.+.+.|..
T Consensus 19 ~g~~~~P~~-------GWvR~~R~ALG---------ms~~QLA~RlGV~p~Rv~~~E~~E~~G~VTL~t 71 (150)
T TIGR02612 19 AGALKTPKK-------GWVRAIRKALG---------MSGAQLAARLGVTPQRVEAIEKSELSGAVTLKT 71 (150)
T ss_pred CCCCCCCCC-------CCHHHHHHHHC---------CCHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHH
T ss_conf 245387688-------61688987725---------157887665289737799988887555355888
No 182
>PRK12423 LexA repressor; Provisional
Probab=91.68 E-value=0.41 Score=27.00 Aligned_cols=33 Identities=12% Similarity=0.166 Sum_probs=18.4
Q ss_pred HHHHHHHCCCCCCHHHHHHHHHCCCCC-CCCCCC
Q ss_conf 887866244788824677888618983-211000
Q gi|254780611|r 144 GHLQAITDNNLKPEQVVAIAKKLNVSE-SEVISM 176 (302)
Q Consensus 144 ~~~~~~~~~~~~~~~~~eiA~~Lgis~-~~v~~l 176 (302)
..+.....+.+.+|++.|||+.+|++. ..|...
T Consensus 13 ~fI~~~~~~~G~~Pt~rEI~~~~g~~S~~~v~~h 46 (202)
T PRK12423 13 AFIRERIAQAGQPPSLAEIAQAFGFASRSVARKH 46 (202)
T ss_pred HHHHHHHHHCCCCCCHHHHHHHHCCCCCHHHHHH
T ss_conf 9999999962989889999998299986789999
No 183
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=91.47 E-value=0.29 Score=27.94 Aligned_cols=28 Identities=21% Similarity=0.476 Sum_probs=22.9
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf 88898999999778999999999999999999
Q gi|254780611|r 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282 (302)
Q Consensus 251 ~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~ 282 (302)
-++|.+|||+.+|+|+|.|+++ |.+|++
T Consensus 7 l~lt~~~iA~~lG~tretvsR~----l~~l~~ 34 (48)
T smart00419 7 LPLTRQEIAELLGLTRETVSRT----LKRLEK 34 (48)
T ss_pred ECCCHHHHHHHHCCCHHHHHHH----HHHHHH
T ss_conf 3379999999979979999999----999998
No 184
>PRK01381 Trp operon repressor; Provisional
Probab=91.29 E-value=0.8 Score=25.02 Aligned_cols=55 Identities=18% Similarity=0.334 Sum_probs=38.2
Q ss_pred CCCHHHHHHHHHHH-----CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH----HHHHHHHHHHC
Q ss_conf 19999999999982-----7888889899999977899999999999999----99999997401
Q gi|254780611|r 234 VLNPRERRIFEARR-----LQENPVTLENLSSEFEVSRERVRQIEARAFK----KVQESIQKQVE 289 (302)
Q Consensus 234 ~L~~rEr~II~~ry-----~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~----kLR~~l~~~~~ 289 (302)
.|++.|+.-|..|+ +....+|++|||+.+|||-..|.+= +++|+ ..+..|++.+.
T Consensus 32 lLTp~Er~al~~R~~I~~~Ll~ge~sQReIa~~lgvsiAtITRG-Sn~LK~~~~~~k~~l~~~l~ 95 (99)
T PRK01381 32 LLTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATITRG-SNSLKTAPPEFKEWLEQLLL 95 (99)
T ss_pred HCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCEECCCC-HHHHHCCCHHHHHHHHHHHH
T ss_conf 78999999999999999999948764999999849740200002-69885399999999999860
No 185
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=90.88 E-value=0.65 Score=25.63 Aligned_cols=28 Identities=29% Similarity=0.329 Sum_probs=17.1
Q ss_pred CCCCCHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf 47888246778886189832110000001
Q gi|254780611|r 152 NNLKPEQVVAIAKKLNVSESEVISMNCRL 180 (302)
Q Consensus 152 ~~~~~~~~~eiA~~Lgis~~~v~~l~~~~ 180 (302)
.+++. +..+||+.+|+|+..+..-.+.+
T Consensus 14 ~n~R~-s~~~iA~~lg~S~~tv~~Ri~~L 41 (108)
T smart00344 14 KDARI-SLAELAKKVGLSPSTVHNRVKRL 41 (108)
T ss_pred HCCCC-CHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 82899-99999999893999999999999
No 186
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family; InterPro: IPR014293 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This group of sigma factors are members of the sigma-70 family (IPR014284 from INTERPRO). They and appear by homology, tree building, bidirectional best hits and (with one exception, a paralog in Thermobifida fusca strain YX) their one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor (see IPR014295 from INTERPRO) in an apparent operon.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=90.59 E-value=1.3 Score=23.51 Aligned_cols=177 Identities=15% Similarity=0.150 Sum_probs=89.8
Q ss_pred HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHH-H
Q ss_conf 999999999982859999999994307787565555799998889999998889989862185345689997577899-9
Q gi|254780611|r 33 EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK-A 111 (302)
Q Consensus 33 ee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr-~ 111 (302)
.+.....++. ..-..-.++|-.+-||+ .+..-+-+||+||.+.--..+...|.|.-. +..+-+--+- .
T Consensus 5 ~~~~~~~rfe-rdal~~~dqly~aalrm--------~rnPadaed~vqe~y~kaf~~f~~~~~Gtn--l~aWlyriltnt 73 (193)
T TIGR02947 5 TEEQRAQRFE-RDALEYLDQLYGAALRM--------TRNPADAEDLVQEAYVKAFSAFKQFKPGTN--LKAWLYRILTNT 73 (193)
T ss_pred HHHHHHHHHH-HHHHHHHHHHHHHHHHH--------HCCCCCHHHHHHHHHHHHHHHHHHHCCCCH--HHHHHHHHHHHH
T ss_conf 2689998776-77999999999999876--------238654788999999999998874137742--899999999999
Q ss_pred HHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCC
Q ss_conf 99985320246001102300358999999997887866244788824677888618983211000000122343355202
Q gi|254780611|r 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191 (302)
Q Consensus 112 ~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~ 191 (302)
.|..|-..+ |-|..... ..-+.=+||.. ..+.|- .+.
T Consensus 74 yin~yrk~q----r~P~~~~~----------------------~~~~dWq~a~~---------------~~h~s~--Glr 110 (193)
T TIGR02947 74 YINSYRKKQ----REPAQSDS----------------------DEIEDWQLAKA---------------ASHTSS--GLR 110 (193)
T ss_pred HHHHHHHHH----CCCCCCCC----------------------CHHHHHHHHHH---------------HHHHHC--CCH
T ss_conf 999888752----27655652----------------------01468888765---------------311001--204
Q ss_pred CCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 32345320000012356870565566666667779999996219999999999982788888989999997789999999
Q gi|254780611|r 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271 (302)
Q Consensus 192 ~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQ 271 (302)
....+..|.+++ ..+..++..|++.=+.++.+ -.-++...+||++++|..-..|--
T Consensus 111 ---sae~eald~lPd-------------------~~~~~al~~~~~efr~~v~~--adveGf~ykei~~im~tP~Gtvms 166 (193)
T TIGR02947 111 ---SAEVEALDALPD-------------------DDIKAALQELPEEFRLAVYF--ADVEGFAYKEIAEIMGTPIGTVMS 166 (193)
T ss_pred ---HHHHHHHHCCCH-------------------HHHHHHHHHHHHHHHHHHHH--HHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf ---777888752884-------------------89999998737999898887--620353157799885474779999
Q ss_pred HHHHHHHHHHHHHHHH
Q ss_conf 9999999999999974
Q gi|254780611|r 272 IEARAFKKVQESIQKQ 287 (302)
Q Consensus 272 I~~~AL~kLR~~l~~~ 287 (302)
--.++-+.||..|..-
T Consensus 167 rl~r~rk~l~~~l~d~ 182 (193)
T TIGR02947 167 RLHRGRKQLRDLLADV 182 (193)
T ss_pred HHHHHHHHHHHHHHHH
T ss_conf 9899999999999988
No 187
>pfam09862 DUF2089 Protein of unknown function(DUF2089). This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=90.49 E-value=0.86 Score=24.82 Aligned_cols=47 Identities=15% Similarity=0.162 Sum_probs=34.6
Q ss_pred HHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 6219999999999982788888989999997789999999999999999
Q gi|254780611|r 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280 (302)
Q Consensus 232 l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kL 280 (302)
+..|++.+..-|..+.... -+++++++.+|||..+||-.-.+.+.+|
T Consensus 31 f~~L~~E~l~Fi~~fi~~~--Gnlke~~~~lgiSYpTvR~rLd~ii~~l 77 (113)
T pfam09862 31 FCRLTPEQLEFVELFIKCR--GNIKEVEKELGISYPTVRNRLDEIIAAL 77 (113)
T ss_pred HHCCCHHHHHHHHHHHHHC--CCHHHHHHHHCCCCHHHHHHHHHHHHHC
T ss_conf 5238999999999999916--8899999997888188999999999980
No 188
>pfam04552 Sigma54_DBD Sigma-54, DNA binding domain. This DNA binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore this region contains a putative helix-turn-helix motif. At the C-terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins.
Probab=90.33 E-value=0.5 Score=26.37 Aligned_cols=25 Identities=28% Similarity=0.407 Sum_probs=19.9
Q ss_pred CCCCCHHHHHHHHHCCCCCCCCCCC
Q ss_conf 4788824677888618983211000
Q gi|254780611|r 152 NNLKPEQVVAIAKKLNVSESEVISM 176 (302)
Q Consensus 152 ~~~~~~~~~eiA~~Lgis~~~v~~l 176 (302)
....|-+..+||+.+|+.+.+|-..
T Consensus 45 ~~l~PLtlk~iA~~l~lh~STVSRa 69 (160)
T pfam04552 45 EALRPLTLREVAEALGMHESTVSRA 69 (160)
T ss_pred CCCCCCCHHHHHHHCCCCCCHHHHH
T ss_conf 3575761999998809981069999
No 189
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=90.30 E-value=0.35 Score=27.46 Aligned_cols=35 Identities=29% Similarity=0.436 Sum_probs=0.0
Q ss_pred CCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHH
Q ss_conf 1999999999998278888898999999778999999
Q gi|254780611|r 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270 (302)
Q Consensus 234 ~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVr 270 (302)
.|+.|+.+++.+ +.++++|..|+|+.||||.=+||
T Consensus 1 Mln~Rq~~il~l--L~~~~lt~~eLA~~L~VS~RTIR 35 (585)
T PRK09863 1 MLNERELKIVDL--LEQQDRSGGELAQQLGVSRRTIV 35 (585)
T ss_pred CCCHHHHHHHHH--HHCCCCCHHHHHHHCCCCCHHHH
T ss_conf 966799999999--97599998999987499711789
No 190
>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=90.29 E-value=0.43 Score=26.83 Aligned_cols=29 Identities=24% Similarity=0.494 Sum_probs=23.4
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf 888898999999778999999999999999999
Q gi|254780611|r 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282 (302)
Q Consensus 250 ~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~ 282 (302)
+-++|.+|||+.+|+|+|.|+++ |.+|++
T Consensus 23 ~l~ltr~eiA~~lG~t~eTVsR~----l~~l~~ 51 (67)
T cd00092 23 QLPLTRQEIADYLGLTRETVSRT----LKELEE 51 (67)
T ss_pred ECCCCHHHHHHHHCCCHHHHHHH----HHHHHH
T ss_conf 61779999999978909999999----999998
No 191
>pfam12116 SpoIIID Stage III sporulation protein D. This stage III sporulation protein is a small DNA-binding family that is essential for gene expression of the mother-cell compartment during sporulation. The domain is found in bacteria and viruses, and is about 40 amino acids in length. It has a conserved RGG sequence motif.
Probab=89.82 E-value=0.64 Score=25.68 Aligned_cols=48 Identities=25% Similarity=0.302 Sum_probs=30.7
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999982788888989999997789999999999999999999997
Q gi|254780611|r 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286 (302)
Q Consensus 239 Er~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~ 286 (302)
||.|-...|..+...|.++.|+.||||++.|..=-..-|.++-..|..
T Consensus 6 eR~~~i~~YIi~~~aTVR~tAk~FGvSKSTVHkDvTeRL~~inp~La~ 53 (82)
T pfam12116 6 ERVLEIANYIIENKATVRQAAKVFGVSKSTVHKDVTERLPKINPQLAK 53 (82)
T ss_pred HHHHHHHHHHHHCCHHHHHHHHHHCCCHHHHHHHHHHHHHHCCHHHHH
T ss_conf 999999999996262899999996960988988799999873999999
No 192
>pfam00325 Crp Bacterial regulatory proteins, crp family.
Probab=89.77 E-value=0.44 Score=26.79 Aligned_cols=27 Identities=22% Similarity=0.589 Sum_probs=22.6
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf 8898999999778999999999999999999
Q gi|254780611|r 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282 (302)
Q Consensus 252 ~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~ 282 (302)
++|-++||+-+|+|.|.|+++ |.+||+
T Consensus 2 pmsrqdIadylGlt~ETVsR~----l~~L~~ 28 (32)
T pfam00325 2 PMSRQEIADYLGLTRETVSRL----LKRLRE 28 (32)
T ss_pred CCCHHHHHHHHCCHHHHHHHH----HHHHHH
T ss_conf 865889999847259999999----999998
No 193
>pfam08279 HTH_11 HTH domain. This family includes helix-turn-helix domains in a wide variety of proteins.
Probab=89.77 E-value=0.84 Score=24.87 Aligned_cols=40 Identities=25% Similarity=0.408 Sum_probs=27.5
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99999982788888989999997789999999999999999999
Q gi|254780611|r 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302)
Q Consensus 240 r~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302)
..|+....-.+.+.|-.++|+.||||+..|+ +-++.|++.
T Consensus 3 ~~il~~L~~~~~~vt~~~La~~l~VSr~TV~----rdi~~L~~~ 42 (55)
T pfam08279 3 LQILELLLQAREPISGQELAEKLGVSRRTIR----RDIKALEAL 42 (55)
T ss_pred HHHHHHHHHCCCCCCHHHHHHHHCCCHHHHH----HHHHHHHHC
T ss_conf 9999999976999189999999698899999----999999988
No 194
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=89.67 E-value=0.63 Score=25.72 Aligned_cols=44 Identities=23% Similarity=0.381 Sum_probs=34.6
Q ss_pred HCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 219999999999982788888989999997789999999999999999
Q gi|254780611|r 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280 (302)
Q Consensus 233 ~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kL 280 (302)
..|++.|+.||.+--..+...+|+|+.+.+|.|+..|+++ |++|
T Consensus 191 ~~L~~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~----L~~L 234 (258)
T COG2512 191 YDLNEDEKEILDLIRERGGRITQAELRRALGLSKTTVSRI----LRRL 234 (258)
T ss_pred CCCCHHHHHHHHHHHHHCCEEEHHHHHHHHCCCHHHHHHH----HHHH
T ss_conf 7899789999999998589786999888609976779999----9999
No 195
>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=89.55 E-value=0.77 Score=25.14 Aligned_cols=36 Identities=14% Similarity=0.161 Sum_probs=26.6
Q ss_pred CCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 19999999999982788888989999997789999999
Q gi|254780611|r 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271 (302)
Q Consensus 234 ~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQ 271 (302)
.|++.+..-+...+- .+.|..+||+.||||+..|-+
T Consensus 5 ~lt~~q~~~ar~l~~--~G~~~~~iA~~~GVsr~Tiyr 40 (42)
T cd00569 5 KLTPEQIEEARRLLA--AGESVAEIARRLGVSRSTLYR 40 (42)
T ss_pred CCCHHHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHH
T ss_conf 699999999999999--789899999997979999986
No 196
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=89.49 E-value=1.6 Score=22.93 Aligned_cols=11 Identities=18% Similarity=0.389 Sum_probs=5.6
Q ss_pred CCCCCCHHHHH
Q ss_conf 79999989999
Q gi|254780611|r 25 KIPMLEKQEEY 35 (302)
Q Consensus 25 ~~~~Lt~eee~ 35 (302)
++|-||+.|.+
T Consensus 10 ~~~~Lt~~Ek~ 20 (282)
T PRK11557 10 RYPGLAQSDRK 20 (282)
T ss_pred HHHHCCHHHHH
T ss_conf 88544999999
No 197
>TIGR01321 TrpR trp operon repressor; InterPro: IPR013335 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan . The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit. This entry represents Trp repressors found in proteobacterial and chlamydial species.; GO: 0016564 transcription repressor activity, 0006355 regulation of transcription DNA-dependent.
Probab=89.46 E-value=1.1 Score=24.16 Aligned_cols=52 Identities=21% Similarity=0.336 Sum_probs=33.8
Q ss_pred CCHHHHHHHHHHH-----CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH----HHHHHHHHH
Q ss_conf 9999999999982-----7888889899999977899999999999999----999999974
Q gi|254780611|r 235 LNPRERRIFEARR-----LQENPVTLENLSSEFEVSRERVRQIEARAFK----KVQESIQKQ 287 (302)
Q Consensus 235 L~~rEr~II~~ry-----~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~----kLR~~l~~~ 287 (302)
|++-|++-+-.|+ +.+..+|++||+..||+|-..|-+= +.+|+ .+|+.|++.
T Consensus 34 Lt~~Er~dl~~R~~I~~~LL~~~~~QREi~~~lG~SiA~ITRG-Sn~Lk~~D~~~~~fL~~~ 94 (95)
T TIGR01321 34 LTADEREDLGSRVRIVEELLEGEMSQREIAEKLGVSIATITRG-SNALKALDPEFKQFLKKK 94 (95)
T ss_pred CCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHH-HHHHCCCCHHHHHHHHHH
T ss_conf 6863799998799999999614897478888637616678787-887516987889998842
No 198
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=89.41 E-value=0.55 Score=26.10 Aligned_cols=28 Identities=18% Similarity=0.322 Sum_probs=23.2
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 88989999997789999999999999999999
Q gi|254780611|r 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302)
Q Consensus 252 ~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302)
++|.+|||..+|+|+|+|+ +.|++|++.
T Consensus 184 ~lt~~dLA~~lG~trEtVs----R~L~~L~~~ 211 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETIS----RLLGRFQKS 211 (235)
T ss_pred CCCHHHHHHHHCCCHHHHH----HHHHHHHHC
T ss_conf 3789999988789899999----999999978
No 199
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=89.20 E-value=1.7 Score=22.80 Aligned_cols=10 Identities=30% Similarity=0.351 Sum_probs=4.9
Q ss_pred CCCCCHHHHH
Q ss_conf 9999989999
Q gi|254780611|r 26 IPMLEKQEEY 35 (302)
Q Consensus 26 ~~~Lt~eee~ 35 (302)
+|-||+.|.+
T Consensus 11 ~~~Lt~~Ek~ 20 (284)
T PRK11302 11 LEHLSKSERK 20 (284)
T ss_pred HHHCCHHHHH
T ss_conf 8645999999
No 200
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=89.17 E-value=1.2 Score=23.74 Aligned_cols=35 Identities=14% Similarity=0.154 Sum_probs=21.7
Q ss_pred HHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf 878662447888246778886189832110000001
Q gi|254780611|r 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180 (302)
Q Consensus 145 ~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~ 180 (302)
.+-.....+++. +..+||+.+|+|+..+..-.+.+
T Consensus 13 ~IL~~Lq~d~R~-s~~eiA~~lglS~stv~~Ri~rL 47 (153)
T PRK11179 13 GILEALMENART-PYAELAKQFGVSPGTIHVRVEKM 47 (153)
T ss_pred HHHHHHHHCCCC-CHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 999999984899-99999999892999999999999
No 201
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=89.01 E-value=1.8 Score=22.71 Aligned_cols=53 Identities=19% Similarity=0.355 Sum_probs=34.4
Q ss_pred CCHHHHHHHHHHH-----CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH----HHHHHHHHHH
Q ss_conf 9999999999982-----7888889899999977899999999999999----9999999740
Q gi|254780611|r 235 LNPRERRIFEARR-----LQENPVTLENLSSEFEVSRERVRQIEARAFK----KVQESIQKQV 288 (302)
Q Consensus 235 L~~rEr~II~~ry-----~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~----kLR~~l~~~~ 288 (302)
|++.||+-+-.|+ +.+..+|++||+..||+|-..|-+= +.+|+ .++..|++++
T Consensus 38 LTpdEReal~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITRG-SN~LK~~~~~~k~~L~~~l 99 (103)
T COG2973 38 LTPDEREALGTRVRIVEELLRGELSQREIAQKLGVSIATITRG-SNSLKTADPEFKQWLEKVL 99 (103)
T ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHCCC-HHHHCCCCHHHHHHHHHHH
T ss_conf 6876899999999999999956353999999858625655044-4442359878999999973
No 202
>PRK11753 cAMP-regulatory protein; Provisional
Probab=88.88 E-value=0.64 Score=25.66 Aligned_cols=27 Identities=26% Similarity=0.384 Sum_probs=22.5
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf 8898999999778999999999999999999
Q gi|254780611|r 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282 (302)
Q Consensus 252 ~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~ 282 (302)
++|.+|||..+|+|++.|+ ++|++|++
T Consensus 168 ~lt~~eLA~~lG~sretvs----R~L~~L~~ 194 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVG----RVLKMLED 194 (211)
T ss_pred CCCHHHHHHHHCCCHHHHH----HHHHHHHH
T ss_conf 4699999988699899999----99999998
No 203
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=88.81 E-value=1.3 Score=23.65 Aligned_cols=28 Identities=21% Similarity=0.291 Sum_probs=17.3
Q ss_pred CCCCCHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf 47888246778886189832110000001
Q gi|254780611|r 152 NNLKPEQVVAIAKKLNVSESEVISMNCRL 180 (302)
Q Consensus 152 ~~~~~~~~~eiA~~Lgis~~~v~~l~~~~ 180 (302)
.+++ -+..+||+.+|+|+..+......+
T Consensus 19 ~d~r-~~~~eia~~lglS~~~v~~Ri~~L 46 (154)
T COG1522 19 EDAR-ISNAELAERVGLSPSTVLRRIKRL 46 (154)
T ss_pred HCCC-CCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 7276-579999999797989999999999
No 204
>PRK00215 LexA repressor; Validated
Probab=88.55 E-value=0.82 Score=24.95 Aligned_cols=27 Identities=22% Similarity=0.169 Sum_probs=12.0
Q ss_pred HHCCCCCCHHHHHHHHHCCCC-CCCCCC
Q ss_conf 624478882467788861898-321100
Q gi|254780611|r 149 ITDNNLKPEQVVAIAKKLNVS-ESEVIS 175 (302)
Q Consensus 149 ~~~~~~~~~~~~eiA~~Lgis-~~~v~~ 175 (302)
....++.+|++.|||..+|++ ...|..
T Consensus 16 ~~~~~g~~Ps~rEI~~~~g~~S~~tV~~ 43 (204)
T PRK00215 16 RIEETGYPPSRREIADALGLRSPSAVHE 43 (204)
T ss_pred HHHHHCCCCCHHHHHHHHCCCCCHHHHH
T ss_conf 9997488998999999809998189999
No 205
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=88.54 E-value=0.71 Score=25.38 Aligned_cols=29 Identities=17% Similarity=0.403 Sum_probs=23.7
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 888989999997789999999999999999999
Q gi|254780611|r 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302)
Q Consensus 251 ~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302)
-++|.+|||..+|+|+|.|+ ++|.+|++.
T Consensus 172 l~lT~~dLA~~lG~trETVs----R~L~~L~~e 200 (224)
T PRK09391 172 LPMSRRDIADYLGLTIETVS----RALSQLKDR 200 (224)
T ss_pred CCCCHHHHHHHHCCCHHHHH----HHHHHHHHC
T ss_conf 15799999988799799999----999999988
No 206
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=88.25 E-value=0.78 Score=25.11 Aligned_cols=18 Identities=22% Similarity=0.523 Sum_probs=8.1
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 8899999988899898621853456
Q gi|254780611|r 75 ISEVVSEGNIGLMQAVKKFDPERGF 99 (302)
Q Consensus 75 ~~DLiQeG~iGLi~Ai~kFDp~kG~ 99 (302)
+--|-++|.+ .+-|.+|+
T Consensus 51 L~rL~~eGLV-------~~~p~rG~ 68 (224)
T PRK11534 51 LSQLVAERLV-------TVVNQKGY 68 (224)
T ss_pred HHHHHHCCCE-------EEECCCEE
T ss_conf 9999987998-------87479736
No 207
>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=88.15 E-value=0.82 Score=24.97 Aligned_cols=39 Identities=28% Similarity=0.491 Sum_probs=29.3
Q ss_pred HHHHHHHHCCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf 99999982788888-98999999778999999999999999999
Q gi|254780611|r 240 RRIFEARRLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQE 282 (302)
Q Consensus 240 r~II~~ry~~~~~~-Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~ 282 (302)
..|+...|--++.+ |.+++|+.+|||+..|| +|+..|..
T Consensus 11 ~~I~~g~~~~G~~LPs~~~La~~~~vSr~tvr----~Al~~L~~ 50 (64)
T pfam00392 11 EDILSGRLRPGDKLPSERELAAEFGVSRTTVR----EALRRLEA 50 (64)
T ss_pred HHHHCCCCCCCCCCHHHHHHHHHHCCCHHHHH----HHHHHHHH
T ss_conf 99984999992998479999999796999999----99999998
No 208
>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=88.07 E-value=0.82 Score=24.96 Aligned_cols=28 Identities=21% Similarity=-0.024 Sum_probs=10.5
Q ss_pred HHHHHHHHH--HCCHHHHHHHHHHHHHHHHHH
Q ss_conf 999999998--285999999999430778756
Q gi|254780611|r 35 YVLAKRYRE--HGDLSAAHRLVTSHLRLVVKI 64 (302)
Q Consensus 35 ~~l~~~~~~--~gd~~Ar~~Li~~nlrlV~~i 64 (302)
.+|+.++.- +.=.+|..+|. ..+||...
T Consensus 38 ~~La~~~gVSRtpvREAL~~L~--~eGlv~~~ 67 (212)
T TIGR03338 38 SDIAARLGVSRGPVREAFRALE--EAGLVRNE 67 (212)
T ss_pred HHHHHHHCCCHHHHHHHHHHHH--HCCCHHEE
T ss_conf 9999988969499999999999--86963311
No 209
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=88.04 E-value=0.79 Score=25.07 Aligned_cols=28 Identities=25% Similarity=0.401 Sum_probs=23.2
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 88989999997789999999999999999999
Q gi|254780611|r 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302)
Q Consensus 252 ~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302)
++|.++||..+|+|+|.|+ ++|.+|++.
T Consensus 173 ~~t~~~lA~~lG~tretvs----R~L~~L~~~ 200 (236)
T PRK09392 173 PYEKRTLASYLGMTPENLS----RAFAALASH 200 (236)
T ss_pred CCCHHHHHHHHCCCHHHHH----HHHHHHHHC
T ss_conf 4789999998789899999----999999979
No 210
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=87.92 E-value=2 Score=22.35 Aligned_cols=31 Identities=32% Similarity=0.432 Sum_probs=24.0
Q ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf 78888898999999778999999999999999999
Q gi|254780611|r 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282 (302)
Q Consensus 248 ~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~ 282 (302)
..+...+..+||+.||+||..| .+.+++||+
T Consensus 15 ~~~~~~SGe~La~~LgiSRtaV----wK~Iq~Lr~ 45 (79)
T COG1654 15 LTGNFVSGEKLAEELGISRTAV----WKHIQQLRE 45 (79)
T ss_pred CCCCCCCHHHHHHHHCCCHHHH----HHHHHHHHH
T ss_conf 3799666899999978659999----999999998
No 211
>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=87.92 E-value=0.96 Score=24.50 Aligned_cols=39 Identities=23% Similarity=0.387 Sum_probs=29.4
Q ss_pred HHHHHHHHCCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf 99999982788888-98999999778999999999999999999
Q gi|254780611|r 240 RRIFEARRLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQE 282 (302)
Q Consensus 240 r~II~~ry~~~~~~-Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~ 282 (302)
..|....|--++.+ |.+++|+.+|||+..|| +|+..|..
T Consensus 12 ~~I~~g~~~~G~~LPs~~~La~~~~vSr~tvr----~Al~~L~~ 51 (66)
T cd07377 12 EAILSGELKPGDRLPSERELAEELGVSRTTVR----EALRELEA 51 (66)
T ss_pred HHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHH----HHHHHHHH
T ss_conf 99985999991999279999999798889999----99999998
No 212
>pfam06530 Phage_antitermQ Phage antitermination protein Q. This family consists of several phage antitermination protein Q and related bacterial sequences. Antiterminator proteins control gene expression by recognising control signals near the promoter and preventing transcriptional termination which would otherwise occur at sites that may be a long way downstream.
Probab=87.62 E-value=2.2 Score=22.13 Aligned_cols=51 Identities=10% Similarity=0.195 Sum_probs=42.5
Q ss_pred HHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 62199999999999827888889899999977899999999999999999999
Q gi|254780611|r 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284 (302)
Q Consensus 232 l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l 284 (302)
|..-++.+..+|..||..+ .|...||..+++|...||+.-++|-.-+...|
T Consensus 60 L~~~~~~~~~ll~~yYv~g--~S~r~IA~~~~~s~~~irk~lq~Aegfi~g~L 110 (126)
T pfam06530 60 LMYIDPKLFGLLLSYYVHG--SSKRAIARRYGCSVTRIRKRLCKAEGFIDGCL 110 (126)
T ss_pred HHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 9873989999999999748--66999999968881199999998463887759
No 213
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=87.12 E-value=0.8 Score=25.02 Aligned_cols=33 Identities=24% Similarity=0.409 Sum_probs=16.6
Q ss_pred HHHHHHCCCCCC----HHHHHHHHHHHHHHHHHHCCCCCCCCHH
Q ss_conf 565555799998----8899999988899898621853456899
Q gi|254780611|r 63 KIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGFRLA 102 (302)
Q Consensus 63 ~iA~~y~~~g~~----~~DLiQeG~iGLi~Ai~kFDp~kG~~Fs 102 (302)
.+|..|.-.-.| +--|.++|.+ .+.|++|+.++
T Consensus 44 ~La~~~gvSrtPVReAL~rL~~eGlv-------~~~p~rG~~V~ 80 (230)
T COG1802 44 ELAEELGVSRTPVREALRRLEAEGLV-------EIEPNRGAFVA 80 (230)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCE-------EECCCCCEEEC
T ss_conf 99999888907999999999889794-------77799832662
No 214
>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=86.84 E-value=0.64 Score=25.69 Aligned_cols=28 Identities=21% Similarity=0.290 Sum_probs=21.5
Q ss_pred HCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 2788888989999997789999999999
Q gi|254780611|r 247 RLQENPVTLENLSSEFEVSRERVRQIEA 274 (302)
Q Consensus 247 y~~~~~~Tl~EIa~~lgiS~eRVrQI~~ 274 (302)
|+..=++|..++|+.||||+.+|++|-.
T Consensus 15 fL~PLg~s~~~LA~~LgVsr~~~sriv~ 42 (81)
T TIGR02607 15 FLEPLGLSVRALAKALGVSRSTLSRIVN 42 (81)
T ss_pred HHHCCCHHHHHHHHHCCCCHHHHHHHHH
T ss_conf 5210470689999870999788888874
No 215
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=86.49 E-value=1.3 Score=23.66 Aligned_cols=39 Identities=21% Similarity=0.357 Sum_probs=29.0
Q ss_pred HHHHHHHHCCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf 99999982788888-98999999778999999999999999999
Q gi|254780611|r 240 RRIFEARRLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQE 282 (302)
Q Consensus 240 r~II~~ry~~~~~~-Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~ 282 (302)
..|....|--++.+ |.+++|+.||||+..|+ +|+..|..
T Consensus 7 ~~I~~g~~~~G~~LPs~~~la~~~~vSr~tvr----~A~~~L~~ 46 (60)
T smart00345 7 EDIVSGELRPGDKLPSERELAAQLGVSRTTVR----EALSRLEA 46 (60)
T ss_pred HHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHH----HHHHHHHH
T ss_conf 99983999983988109999999894999999----99999998
No 216
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=86.30 E-value=2 Score=22.32 Aligned_cols=39 Identities=15% Similarity=0.243 Sum_probs=22.9
Q ss_pred HHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf 9978878662447888246778886189832110000001
Q gi|254780611|r 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180 (302)
Q Consensus 141 k~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~ 180 (302)
.+...+-.....+++.+ ..+||+.+|+|+..+..-.+.+
T Consensus 14 ~~D~~IL~~Lq~daR~s-~~eLA~~vglS~stv~~RikrL 52 (164)
T PRK11169 14 RIDRNILNELQKDGRIS-NVELSKRVGLSPTPCLERVRRL 52 (164)
T ss_pred HHHHHHHHHHHHCCCCC-HHHHHHHHCCCHHHHHHHHHHH
T ss_conf 99999999999848999-9999999892999999999999
No 217
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=86.03 E-value=1.1 Score=24.21 Aligned_cols=24 Identities=33% Similarity=0.360 Sum_probs=20.9
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 889899999977899999999999
Q gi|254780611|r 252 PVTLENLSSEFEVSRERVRQIEAR 275 (302)
Q Consensus 252 ~~Tl~EIa~~lgiS~eRVrQI~~~ 275 (302)
++|+.+.|+.+|||++.|-.||+.
T Consensus 14 ~ltQ~elA~~vgVsRQTi~~iEkg 37 (68)
T COG1476 14 GLTQEELAKLVGVSRQTIIAIEKG 37 (68)
T ss_pred CCCHHHHHHHCCCCHHHHHHHHCC
T ss_conf 858999999919579999999917
No 218
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=85.96 E-value=1.5 Score=23.15 Aligned_cols=19 Identities=26% Similarity=0.237 Sum_probs=12.7
Q ss_pred HHHHHHHCCCCCCCCCCCC
Q ss_conf 6778886189832110000
Q gi|254780611|r 159 VVAIAKKLNVSESEVISMN 177 (302)
Q Consensus 159 ~~eiA~~Lgis~~~v~~l~ 177 (302)
..++|+.||++..-|-.++
T Consensus 25 q~~iA~LLGltqaAVS~Yl 43 (119)
T COG2522 25 QYRIAKLLGLTQAAVSQYL 43 (119)
T ss_pred HHHHHHHHCCCHHHHHHHH
T ss_conf 9999999688899999997
No 219
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=85.77 E-value=2.7 Score=21.49 Aligned_cols=33 Identities=21% Similarity=0.320 Sum_probs=17.5
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHCCCCCCHHHHH
Q ss_conf 98665574558740599999984079999989999
Q gi|254780611|r 1 MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEY 35 (302)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~yl~~i~~~~~Lt~eee~ 35 (302)
|+.+..-.-.-+.-+|-..++.- +|-||+.|.+
T Consensus 1 ~~~~~~~~~~~~~~~l~~~Ir~~--~~~Lt~sEk~ 33 (293)
T PRK11337 1 MSQSEFDSALPNGIGLAPYIRMK--QEGMTENESR 33 (293)
T ss_pred CCCCCCCCCCCCCCCHHHHHHHH--HHHCCHHHHH
T ss_conf 97200576699877899999997--7644999999
No 220
>pfam09339 HTH_IclR IclR helix-turn-helix domain.
Probab=85.63 E-value=2.1 Score=22.24 Aligned_cols=33 Identities=12% Similarity=0.206 Sum_probs=25.3
Q ss_pred HHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 999998278888898999999778999999999
Q gi|254780611|r 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273 (302)
Q Consensus 241 ~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~ 273 (302)
.||...-..+.++|+.|||+.+|+++..|.++-
T Consensus 7 ~iL~~~~~~~~~~~l~eia~~~gl~kstv~RlL 39 (52)
T pfam09339 7 AILEALAEAPGGLSLTEIARRTGLPKSTAHRLL 39 (52)
T ss_pred HHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 999998628999899999999891999999999
No 221
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=85.45 E-value=1.7 Score=22.78 Aligned_cols=13 Identities=31% Similarity=-0.002 Sum_probs=5.1
Q ss_pred HHHHHHHHHHHHHHH
Q ss_conf 999999994307787
Q gi|254780611|r 48 SAAHRLVTSHLRLVV 62 (302)
Q Consensus 48 ~Ar~~Li~~nlrlV~ 62 (302)
+|...|- ..+||.
T Consensus 52 EAL~~Le--~~GLV~ 64 (257)
T PRK10225 52 EALIMLE--IKGLVE 64 (257)
T ss_pred HHHHHHH--HCCCEE
T ss_conf 9999999--889979
No 222
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=85.25 E-value=2.3 Score=21.98 Aligned_cols=25 Identities=16% Similarity=0.260 Sum_probs=20.9
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 8889899999977899999999999
Q gi|254780611|r 251 NPVTLENLSSEFEVSRERVRQIEAR 275 (302)
Q Consensus 251 ~~~Tl~EIa~~lgiS~eRVrQI~~~ 275 (302)
+++|..+||+.+|||+..|.++.+.
T Consensus 171 ~g~s~~~iak~~gvsrsTvyR~lK~ 195 (200)
T PRK13413 171 KGTTKSEIAKKLKVSRTTLARFLKT 195 (200)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 8899999999989299999999974
No 223
>PRK11414 putative DNA-binding transcriptional regulator; Provisional
Probab=85.16 E-value=1.2 Score=23.77 Aligned_cols=44 Identities=25% Similarity=0.356 Sum_probs=17.9
Q ss_pred HCCHHHHHHHHHHHHHHHHHHHHHHCCCCCC----HHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf 2859999999994307787565555799998----88999999888998986218534568
Q gi|254780611|r 44 HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGFR 100 (302)
Q Consensus 44 ~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~----~~DLiQeG~iGLi~Ai~kFDp~kG~~ 100 (302)
.|....-++|.+. .+|.+|.-.-.| +--|.++|.+ ...|.+|+.
T Consensus 26 ~G~l~PG~~L~e~------~La~~lgVSRtPVREAL~rL~~eGLv-------~~~p~rG~~ 73 (221)
T PRK11414 26 IGALKPGARLITK------NLAEQLGMSITPVREALLRLVSVNAL-------SVAPAQAFT 73 (221)
T ss_pred CCCCCCCCCCCHH------HHHHHHCCCHHHHHHHHHHHHHCCCE-------EEECCCCEE
T ss_conf 3998995971899------99999799906899999999988895-------650487337
No 224
>pfam01381 HTH_3 Helix-turn-helix. This large family of DNA binding helix-turn helix proteins includes Cro and CI.
Probab=84.89 E-value=0.91 Score=24.64 Aligned_cols=25 Identities=28% Similarity=0.405 Sum_probs=22.1
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 8889899999977899999999999
Q gi|254780611|r 251 NPVTLENLSSEFEVSRERVRQIEAR 275 (302)
Q Consensus 251 ~~~Tl~EIa~~lgiS~eRVrQI~~~ 275 (302)
.++|++++|+.+|||+..|+++|+.
T Consensus 8 ~g~tq~~lA~~~gis~~~is~~E~g 32 (55)
T pfam01381 8 LGLSQEELAEKLGVSRSTISKIENG 32 (55)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHCC
T ss_conf 2998999999989699999999879
No 225
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=84.74 E-value=1.5 Score=23.20 Aligned_cols=13 Identities=31% Similarity=0.462 Sum_probs=4.4
Q ss_pred HHHHHCCCCCCHH
Q ss_conf 9984079999989
Q gi|254780611|r 20 IHEIRKIPMLEKQ 32 (302)
Q Consensus 20 l~~i~~~~~Lt~e 32 (302)
|+.+++-.-||-+
T Consensus 12 Ir~lR~~~glTL~ 24 (185)
T PRK09943 12 LSEIRQQQGLSQR 24 (185)
T ss_pred HHHHHHHCCCCHH
T ss_conf 9999998599899
No 226
>pfam01047 MarR MarR family. The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.
Probab=84.67 E-value=3 Score=21.21 Aligned_cols=37 Identities=22% Similarity=0.358 Sum_probs=27.1
Q ss_pred CCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 99999999999827888889899999977899999999
Q gi|254780611|r 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272 (302)
Q Consensus 235 L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI 272 (302)
|+.-|..||..-+- ..+.|+.+||+.+++++..|+++
T Consensus 1 lT~~Q~~vL~~l~~-~~~~s~~~la~~~~~~~~~vs~~ 37 (59)
T pfam01047 1 LTLTQFHILRILYE-HGPLTVSELAEKLGVDRSTVTRV 37 (59)
T ss_pred CCHHHHHHHHHHHH-CCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 98999999999994-69929999999988586549999
No 227
>PRK04158 transcriptional repressor CodY; Validated
Probab=84.29 E-value=3.1 Score=21.05 Aligned_cols=59 Identities=14% Similarity=0.257 Sum_probs=43.3
Q ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHC--C-CCC-CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf 666677799999962199999999999827--8-888-89899999977899999999999999999
Q gi|254780611|r 219 EERKNRRNMLTRSMSVLNPRERRIFEARRL--Q-ENP-VTLENLSSEFEVSRERVRQIEARAFKKVQ 281 (302)
Q Consensus 219 ~e~~~~~~~L~~~l~~L~~rEr~II~~ry~--~-~~~-~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR 281 (302)
++....+..++-|+..|+--|.+-|.+-|- . .++ ++-..||++.||||+=| -.||+||-
T Consensus 164 EeeaRkka~VqmAi~tLSYSEleAv~hIf~EL~G~EGlLVASkIADrvGITRSVI----VNALRKlE 226 (256)
T PRK04158 164 EEEARKKAAVQMAINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVI----VNALRKLE 226 (256)
T ss_pred HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCEEEEHHHHHHHCCCHHHH----HHHHHHHH
T ss_conf 9999999999999986378789999999996289755275433344308715677----87777653
No 228
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=84.17 E-value=2.8 Score=21.35 Aligned_cols=19 Identities=42% Similarity=0.518 Sum_probs=8.2
Q ss_pred HHHHHHHHCCCCCCCCCCC
Q ss_conf 4677888618983211000
Q gi|254780611|r 158 QVVAIAKKLNVSESEVISM 176 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v~~l 176 (302)
+..+||..++++...+-.+
T Consensus 26 t~~~la~~l~~~~~~vs~~ 44 (101)
T smart00347 26 SVSELAKRLGVSPSTVTRV 44 (101)
T ss_pred CHHHHHHHHCCCHHHHHHH
T ss_conf 9999999989688799999
No 229
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=83.98 E-value=1.1 Score=24.01 Aligned_cols=19 Identities=21% Similarity=0.281 Sum_probs=10.1
Q ss_pred CCHHHHHHHHHCCCCCCCC
Q ss_conf 8824677888618983211
Q gi|254780611|r 155 KPEQVVAIAKKLNVSESEV 173 (302)
Q Consensus 155 ~~~~~~eiA~~Lgis~~~v 173 (302)
....+..||+.||+++..+
T Consensus 46 ~~~~L~~LA~~L~vs~~wL 64 (135)
T PRK09706 46 AGKNLFALAQALQCSPTWL 64 (135)
T ss_pred CHHHHHHHHHHHCCCHHHH
T ss_conf 9999999999989099998
No 230
>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]
Probab=83.65 E-value=2.7 Score=21.47 Aligned_cols=43 Identities=19% Similarity=0.277 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 9999999999982788888989999997789999999999999999
Q gi|254780611|r 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280 (302)
Q Consensus 235 L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kL 280 (302)
|+.||+.|+.+-| .+.|-+|||..+.||-.+|--=-.+.-.||
T Consensus 832 Ls~RE~eVL~Lia---~G~SN~eIa~~L~isl~TVKtH~rniy~KL 874 (894)
T COG2909 832 LSQRELEVLGLIA---QGLSNEEIAQELFISLTTVKTHIRNIYQKL 874 (894)
T ss_pred CCHHHHHHHHHHH---CCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 6388999999998---257778999998898988999999999884
No 231
>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=83.43 E-value=1.1 Score=24.21 Aligned_cols=25 Identities=24% Similarity=0.185 Sum_probs=21.8
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 8889899999977899999999999
Q gi|254780611|r 251 NPVTLENLSSEFEVSRERVRQIEAR 275 (302)
Q Consensus 251 ~~~Tl~EIa~~lgiS~eRVrQI~~~ 275 (302)
-++|+.++|+..|||+..|++||+-
T Consensus 14 ~glTQ~~LA~~aGvs~~~Is~iE~G 38 (58)
T TIGR03070 14 LGLTQADLADLAGVGLRFIRDIEKG 38 (58)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHCC
T ss_conf 4998999998819989999999789
No 232
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=83.38 E-value=1.2 Score=23.92 Aligned_cols=25 Identities=32% Similarity=0.452 Sum_probs=21.5
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 8889899999977899999999999
Q gi|254780611|r 251 NPVTLENLSSEFEVSRERVRQIEAR 275 (302)
Q Consensus 251 ~~~Tl~EIa~~lgiS~eRVrQI~~~ 275 (302)
.++|++++|+.+|||+..|++++..
T Consensus 9 ~glsq~~lA~~~gis~~~is~~E~g 33 (56)
T smart00530 9 KGLTQEELAEKLGVSRSTLSRIENG 33 (56)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHCC
T ss_conf 2999999999989599999999979
No 233
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY; InterPro: IPR014154 This entry represents pleiotropic repressors in Bacillus subtilis, CodY, and other Firmicutes (low-GC Gram-positive bacteria) that respond to intracellular levels of GTP and branched chain amino acids. All have a C-terminal helix-turn-helix DNA-binding region..
Probab=82.86 E-value=1.8 Score=22.73 Aligned_cols=57 Identities=14% Similarity=0.243 Sum_probs=43.6
Q ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHC---CCCC-CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 66677799999962199999999999827---8888-8989999997789999999999999999
Q gi|254780611|r 220 ERKNRRNMLTRSMSVLNPRERRIFEARRL---QENP-VTLENLSSEFEVSRERVRQIEARAFKKV 280 (302)
Q Consensus 220 e~~~~~~~L~~~l~~L~~rEr~II~~ry~---~~~~-~Tl~EIa~~lgiS~eRVrQI~~~AL~kL 280 (302)
+....+..++-|+++|+==|-.-+.+=|. ++|+ ++--.||++.||||+=| -.||+||
T Consensus 166 ee~R~~a~VqmAi~TLSYSEL~AV~aIf~ELdG~EG~LvAS~IAD~vGITRSVI----VNALRKl 226 (255)
T TIGR02787 166 EEARKKAAVQMAINTLSYSELEAVEAIFEELDGNEGLLVASKIADRVGITRSVI----VNALRKL 226 (255)
T ss_pred HHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCHHHH----HHHHHHH
T ss_conf 999999999999872028899999999842289966277530207126603355----4543444
No 234
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=82.83 E-value=3.5 Score=20.72 Aligned_cols=46 Identities=15% Similarity=0.374 Sum_probs=33.1
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHH-----HHHHHHHHHHHHHHH-HCCCCCCC
Q ss_conf 88889899999977899999999-----999999999999974-01224677
Q gi|254780611|r 250 ENPVTLENLSSEFEVSRERVRQI-----EARAFKKVQESIQKQ-VELSSSPP 295 (302)
Q Consensus 250 ~~~~Tl~EIa~~lgiS~eRVrQI-----~~~AL~kLR~~l~~~-~~~~~~~~ 295 (302)
...+++++||+.|||++.||+-+ +.-.+.||...|..- .+....||
T Consensus 39 q~~l~Q~qiae~lgV~qprvS~l~~gk~~~fs~dkLvtml~~~g~ei~~rp~ 90 (91)
T COG5606 39 QAALSQAQIAELLGVTQPRVSDLARGKIQDFSIDKLVTMLARAGQEIDVRPP 90 (91)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf 9787799999983888731889983614576699999999975985521289
No 235
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=82.70 E-value=1.9 Score=22.49 Aligned_cols=11 Identities=27% Similarity=0.652 Sum_probs=5.5
Q ss_pred CHHHHHHHHHH
Q ss_conf 88899999988
Q gi|254780611|r 74 PISEVVSEGNI 84 (302)
Q Consensus 74 ~~~DLiQeG~i 84 (302)
++..|-++|.+
T Consensus 38 DL~~Le~~G~l 48 (240)
T PRK10411 38 DLNELQTQGKI 48 (240)
T ss_pred HHHHHHHCCCE
T ss_conf 29989778988
No 236
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=82.69 E-value=1.9 Score=22.49 Aligned_cols=11 Identities=9% Similarity=0.253 Sum_probs=4.7
Q ss_pred CHHHHHHHHHH
Q ss_conf 88899999988
Q gi|254780611|r 74 PISEVVSEGNI 84 (302)
Q Consensus 74 ~~~DLiQeG~i 84 (302)
++.+|-++|.+
T Consensus 39 DL~~Le~~G~l 49 (256)
T PRK10434 39 DLVILEHAGTV 49 (256)
T ss_pred HHHHHHHCCCE
T ss_conf 49999878988
No 237
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=82.61 E-value=2 Score=22.34 Aligned_cols=29 Identities=24% Similarity=0.197 Sum_probs=13.7
Q ss_pred HHHHHHHHH--HCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999998--2859999999994307787565
Q gi|254780611|r 35 YVLAKRYRE--HGDLSAAHRLVTSHLRLVVKIA 65 (302)
Q Consensus 35 ~~l~~~~~~--~gd~~Ar~~Li~~nlrlV~~iA 65 (302)
.+|+..+.- .-=.+|...|. ..+||....
T Consensus 38 ~eLA~~lgVSR~~VREAL~~L~--~~GlV~~r~ 68 (254)
T PRK09464 38 RELAKQFDVSRPSLREAIQRLE--AKGLLLRRQ 68 (254)
T ss_pred HHHHHHHCCCCHHHHHHHHHHH--HCCCEEEEC
T ss_conf 9999986899559999999999--889989717
No 238
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=82.59 E-value=2 Score=22.31 Aligned_cols=27 Identities=19% Similarity=0.288 Sum_probs=21.8
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf 8898999999778999999999999999999
Q gi|254780611|r 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282 (302)
Q Consensus 252 ~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~ 282 (302)
++|.+|||..+|.|+|.|+++ |.+|++
T Consensus 145 ~lT~~eLA~~iGttREtVsR~----L~~l~~ 171 (201)
T PRK13918 145 YATHDELAAAVGSVRETVTKV----VGELSR 171 (201)
T ss_pred CCCHHHHHHHHCCCHHHHHHH----HHHHHH
T ss_conf 579999998859868999999----999998
No 239
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=82.51 E-value=1.8 Score=22.61 Aligned_cols=10 Identities=30% Similarity=0.494 Sum_probs=4.7
Q ss_pred HHHHHHHHCC
Q ss_conf 4677888618
Q gi|254780611|r 158 QVVAIAKKLN 167 (302)
Q Consensus 158 ~~~eiA~~Lg 167 (302)
+..++|..|.
T Consensus 102 T~~~la~~L~ 111 (253)
T COG1349 102 TTLALARALP 111 (253)
T ss_pred HHHHHHHHCC
T ss_conf 4999999717
No 240
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=82.45 E-value=2.1 Score=22.29 Aligned_cols=26 Identities=19% Similarity=0.124 Sum_probs=10.5
Q ss_pred HHHHHHHHH--HCCHHHHHHHHHHHHHHHH
Q ss_conf 999999998--2859999999994307787
Q gi|254780611|r 35 YVLAKRYRE--HGDLSAAHRLVTSHLRLVV 62 (302)
Q Consensus 35 ~~l~~~~~~--~gd~~Ar~~Li~~nlrlV~ 62 (302)
.+|+..+.- .-=.+|...|-. .+||.
T Consensus 30 ~eLae~~GVSRt~VREAL~~L~~--eGlV~ 57 (253)
T PRK10421 30 RQLAMQLGVSRNSLREALAKLVS--EGVLL 57 (253)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHH--CCCEE
T ss_conf 99999979698999999999998--89879
No 241
>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=82.08 E-value=1.6 Score=22.94 Aligned_cols=23 Identities=17% Similarity=0.507 Sum_probs=19.0
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 88898999999778999999999
Q gi|254780611|r 251 NPVTLENLSSEFEVSRERVRQIE 273 (302)
Q Consensus 251 ~~~Tl~EIa~~lgiS~eRVrQI~ 273 (302)
..+++++||+.||||...||.=.
T Consensus 21 G~~~l~~IA~~L~vs~~~IrkWK 43 (60)
T pfam10668 21 GTMKLKDIANKLNVSESQIRKWK 43 (60)
T ss_pred CCEEHHHHHHHHCCCHHHHHHCC
T ss_conf 96449999999687988876031
No 242
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=81.83 E-value=1.7 Score=22.76 Aligned_cols=11 Identities=9% Similarity=0.123 Sum_probs=5.0
Q ss_pred CHHHHHHHHHH
Q ss_conf 88899999988
Q gi|254780611|r 74 PISEVVSEGNI 84 (302)
Q Consensus 74 ~~~DLiQeG~i 84 (302)
++..|-+.|.+
T Consensus 51 DL~~Le~~g~l 61 (269)
T PRK09802 51 DLAFLEKQGIA 61 (269)
T ss_pred HHHHHHHCCCE
T ss_conf 09999878986
No 243
>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=81.82 E-value=2.9 Score=21.30 Aligned_cols=14 Identities=14% Similarity=0.188 Sum_probs=10.3
Q ss_pred HHHHHHHCCCCCCC
Q ss_conf 67788861898321
Q gi|254780611|r 159 VVAIAKKLNVSESE 172 (302)
Q Consensus 159 ~~eiA~~Lgis~~~ 172 (302)
..++|+.|++++.+
T Consensus 104 ~~~~a~~l~~~~~~ 117 (231)
T TIGR03337 104 PARMAELLQLQPFD 117 (231)
T ss_pred CHHHHHHCCCCCCC
T ss_conf 99999861989998
No 244
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=81.77 E-value=3.1 Score=21.05 Aligned_cols=16 Identities=25% Similarity=0.279 Sum_probs=7.5
Q ss_pred HHHHHHHHCCCCCCCC
Q ss_conf 4677888618983211
Q gi|254780611|r 158 QVVAIAKKLNVSESEV 173 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v 173 (302)
+++++|+.+++|..++
T Consensus 23 TDeeLa~~f~VSiqTI 38 (185)
T PRK04424 23 TDEELAEKFGVSIQTI 38 (185)
T ss_pred CHHHHHHHCCCEEEEE
T ss_conf 7799998609577788
No 245
>pfam02796 HTH_7 Helix-turn-helix domain of resolvase.
Probab=81.77 E-value=2.4 Score=21.86 Aligned_cols=37 Identities=19% Similarity=0.268 Sum_probs=24.2
Q ss_pred CCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 199999999999827888889899999977899999999
Q gi|254780611|r 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272 (302)
Q Consensus 234 ~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI 272 (302)
.|++.+..-+...+ +++.+-++||+.+|||++.|=+.
T Consensus 5 kl~~~~~~~v~~L~--~~G~~i~~IA~~~~vsrsTvYRy 41 (45)
T pfam02796 5 KLNEEDINEVITLL--EEGISIKQIAKIFGISRSTVYRY 41 (45)
T ss_pred CCCHHHHHHHHHHH--HCCCCHHHHHHHHCCHHHHHHHH
T ss_conf 03899999999999--87994999999986008888764
No 246
>KOG0197 consensus
Probab=81.61 E-value=0.78 Score=25.08 Aligned_cols=49 Identities=35% Similarity=0.410 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHHHHHH-----------HCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 059999998407999998999999999998-----------2859999999994307787565
Q gi|254780611|r 14 IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-----------HGDLSAAHRLVTSHLRLVVKIA 65 (302)
Q Consensus 14 ~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~-----------~gd~~Ar~~Li~~nlrlV~~iA 65 (302)
-+|..||+. ..-..|.-.+....+..+.+ |.|.+|||.||..++ |++||
T Consensus 286 GsLl~yLr~-~~~~~l~~~~Ll~~a~qIaeGM~YLes~~~IHRDLAARNiLV~~~~--~vKIs 345 (468)
T KOG0197 286 GSLLDYLRT-REGGLLNLPQLLDFAAQIAEGMAYLESKNYIHRDLAARNILVDEDL--VVKIS 345 (468)
T ss_pred CCHHHHHHH-CCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHEEECCCC--EEEEC
T ss_conf 829998532-2777666689999999998788889867812200346655645686--69874
No 247
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=81.56 E-value=3 Score=21.17 Aligned_cols=12 Identities=25% Similarity=0.495 Sum_probs=8.6
Q ss_pred HHHHHCCCCCCC
Q ss_conf 788861898321
Q gi|254780611|r 161 AIAKKLNVSESE 172 (302)
Q Consensus 161 eiA~~Lgis~~~ 172 (302)
++|+.|++.+.+
T Consensus 115 ~~a~~L~i~~~~ 126 (243)
T PRK11402 115 PFCEKLNIPGNS 126 (243)
T ss_pred HHHHHCCCCCCC
T ss_conf 999973989998
No 248
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=81.45 E-value=1.9 Score=22.55 Aligned_cols=11 Identities=18% Similarity=0.359 Sum_probs=5.4
Q ss_pred CHHHHHHHHHH
Q ss_conf 88899999988
Q gi|254780611|r 74 PISEVVSEGNI 84 (302)
Q Consensus 74 ~~~DLiQeG~i 84 (302)
++.+|-++|.+
T Consensus 39 DL~~Le~~G~l 49 (252)
T PRK10906 39 DLNELAEQNLI 49 (252)
T ss_pred HHHHHHHCCCE
T ss_conf 29999878988
No 249
>pfam01022 HTH_5 Bacterial regulatory protein, arsR family. Members of this family contains a DNA binding 'helix-turn-helix' motif. This family includes other proteins which are not included in the Prosite definition.
Probab=81.13 E-value=3.6 Score=20.65 Aligned_cols=37 Identities=24% Similarity=0.345 Sum_probs=26.2
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf 9999998278888898999999778999999999999999999
Q gi|254780611|r 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282 (302)
Q Consensus 240 r~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~ 282 (302)
..||.+ +.+.++|..||++.+|+|+..|+|= |+.|++
T Consensus 5 l~Il~~--L~~~~~~v~el~~~l~~sq~~vS~H----L~~L~~ 41 (47)
T pfam01022 5 LKILYL--LSEGELCVCELAEILGLSQSTVSHH----LKKLRE 41 (47)
T ss_pred HHHHHH--HHCCCCCHHHHHHHHCCCHHHHHHH----HHHHHH
T ss_conf 999999--9808996999999989588699999----999989
No 250
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=81.01 E-value=2.7 Score=21.44 Aligned_cols=19 Identities=16% Similarity=0.340 Sum_probs=12.4
Q ss_pred HHHHHHHHCCCCCCCCCCC
Q ss_conf 4677888618983211000
Q gi|254780611|r 158 QVVAIAKKLNVSESEVISM 176 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v~~l 176 (302)
+..++|+.||++...+-.+
T Consensus 25 t~~~lA~~lgV~r~~is~l 43 (104)
T COG3093 25 TQTELAEALGVTRNTISEL 43 (104)
T ss_pred CHHHHHHHHCCCHHHHHHH
T ss_conf 8999999939989999999
No 251
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=80.83 E-value=2.6 Score=21.62 Aligned_cols=11 Identities=18% Similarity=0.453 Sum_probs=5.8
Q ss_pred CHHHHHHHHHH
Q ss_conf 88899999988
Q gi|254780611|r 74 PISEVVSEGNI 84 (302)
Q Consensus 74 ~~~DLiQeG~i 84 (302)
++.+|-++|.+
T Consensus 39 DL~~Le~~g~l 49 (251)
T PRK13509 39 DINKLDESGKL 49 (251)
T ss_pred HHHHHHHCCCE
T ss_conf 39999878978
No 252
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=80.81 E-value=1.3 Score=23.66 Aligned_cols=24 Identities=17% Similarity=0.148 Sum_probs=13.5
Q ss_pred CCCCCHHHHHHHHHCCCCCCCCCC
Q ss_conf 478882467788861898321100
Q gi|254780611|r 152 NNLKPEQVVAIAKKLNVSESEVIS 175 (302)
Q Consensus 152 ~~~~~~~~~eiA~~Lgis~~~v~~ 175 (302)
.+|.-.+.+.||..|+++.....+
T Consensus 43 ~NPSL~tLe~IA~AL~VPL~~Lle 66 (119)
T PRK13890 43 ANPSLKVMEDIAQALETPLPLLLE 66 (119)
T ss_pred CCCCHHHHHHHHHHHCCCHHHHHH
T ss_conf 898799999999998797799876
No 253
>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=80.36 E-value=4.4 Score=20.09 Aligned_cols=63 Identities=14% Similarity=0.207 Sum_probs=39.7
Q ss_pred HHHHHHHHCCCHHHHHHHHHHHCCC---CCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHHHHH
Q ss_conf 9999996219999999999982788---8889899999977899999999999----9999999999740
Q gi|254780611|r 226 NMLTRSMSVLNPRERRIFEARRLQE---NPVTLENLSSEFEVSRERVRQIEAR----AFKKVQESIQKQV 288 (302)
Q Consensus 226 ~~L~~~l~~L~~rEr~II~~ry~~~---~~~Tl~EIa~~lgiS~eRVrQI~~~----AL~kLR~~l~~~~ 288 (302)
..|......|++.|+.|..+-.-.- ..+|.+++|+..|||...|-+.-++ ...-||-.|...+
T Consensus 5 ~rI~~~~~~lt~~e~~ia~yil~~~~~~~~~si~~lA~~~~vS~atv~Rf~kklG~~Gf~efk~~La~~~ 74 (106)
T pfam01418 5 EKIQSLYSKLTKSEKKIADYILASPDNAIHLSIAELAKAAGVSEASVVRFCRKLGFSGFSDLKVALAGEL 74 (106)
T ss_pred HHHHHHHHHCCHHHHHHHHHHHHCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf 9999989764999999999999299999883399999896998999999999958998999999999986
No 254
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=80.35 E-value=3.1 Score=21.09 Aligned_cols=56 Identities=11% Similarity=0.119 Sum_probs=25.3
Q ss_pred HHHHHHHHH--HCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 999999998--28599999999943077875655557999988899999988899898621853
Q gi|254780611|r 35 YVLAKRYRE--HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96 (302)
Q Consensus 35 ~~l~~~~~~--~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~ 96 (302)
.+|+..+-- .-=++|.+.|.. .+||.. -.|+|--..|...-+.+.++..+-++|++
T Consensus 35 reLa~~~gVsR~tvReal~~L~~--~G~v~~----~~G~gt~V~~~~e~sgl~iL~tl~~ld~~ 92 (239)
T PRK04984 35 RELSELIGVTRTTLREVLQRLAR--DGWLTI----QHGKPTKVNNFWETSGLNILETLARLDHE 92 (239)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHH--CCCEEE----ECCCCCEECCCCCCCCHHHHHHHHHHCCC
T ss_conf 99999979888999999999998--898888----55999755860101314799999984544
No 255
>pfam08006 DUF1700 Protein of unknown function (DUF1700). This family contains many hypothetical bacterial proteins and two putative membrane proteins.
Probab=80.33 E-value=4.4 Score=20.08 Aligned_cols=12 Identities=17% Similarity=0.147 Sum_probs=4.2
Q ss_pred CCHHHHHHHHCC
Q ss_conf 898999999778
Q gi|254780611|r 253 VTLENLSSEFEV 264 (302)
Q Consensus 253 ~Tl~EIa~~lgi 264 (302)
+|-.||.+.||-
T Consensus 41 ~se~ei~~~LG~ 52 (181)
T pfam08006 41 KSEEEIIKELGN 52 (181)
T ss_pred CCHHHHHHHHCC
T ss_conf 999999988299
No 256
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=80.23 E-value=3.5 Score=20.77 Aligned_cols=24 Identities=29% Similarity=0.200 Sum_probs=18.6
Q ss_pred HHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 467788861898321100000012
Q gi|254780611|r 158 QVVAIAKKLNVSESEVISMNCRLA 181 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v~~l~~~~~ 181 (302)
+..++|+.+|++...+.....+..
T Consensus 23 S~re~Ak~~gvs~sTvy~wv~r~~ 46 (138)
T COG3415 23 SCREAAKRFGVSISTVYRWVRRYR 46 (138)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHC
T ss_conf 499999996922999999998733
No 257
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=79.99 E-value=4.5 Score=20.02 Aligned_cols=40 Identities=33% Similarity=0.560 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf 9999999998278888898999999778999999999999999999
Q gi|254780611|r 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282 (302)
Q Consensus 237 ~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~ 282 (302)
+.-..|+.. +.+.++|..||++.+|+|+..|++- |++|++
T Consensus 7 ~~r~~Il~~--L~~~~~~~~eia~~l~is~~~vs~h----L~~L~~ 46 (78)
T cd00090 7 PTRLRILRL--LLEGPLTVSELAERLGLSQSTVSRH----LKKLEE 46 (78)
T ss_pred HHHHHHHHH--HHHCCCCHHHHHHHHCCCHHHHHHH----HHHHHH
T ss_conf 999999999--9848906999987778487899999----999998
No 258
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=79.95 E-value=3.4 Score=20.82 Aligned_cols=14 Identities=7% Similarity=0.233 Sum_probs=10.2
Q ss_pred HHHHHHHCCCCCCC
Q ss_conf 67788861898321
Q gi|254780611|r 159 VVAIAKKLNVSESE 172 (302)
Q Consensus 159 ~~eiA~~Lgis~~~ 172 (302)
..++|+.|++...+
T Consensus 108 ~~~~a~~l~l~~~~ 121 (239)
T PRK09764 108 DDFLQQQLQITAQD 121 (239)
T ss_pred CHHHHHHCCCCCCC
T ss_conf 98999860899998
No 259
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=79.91 E-value=3.2 Score=21.01 Aligned_cols=19 Identities=21% Similarity=0.300 Sum_probs=11.8
Q ss_pred HHHHHHHHCCCCCCC-CCCC
Q ss_conf 467788861898321-1000
Q gi|254780611|r 158 QVVAIAKKLNVSESE-VISM 176 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~-v~~l 176 (302)
...++|+.|++.+.+ |..+
T Consensus 109 a~~~~a~~L~l~~~~~v~~i 128 (236)
T COG2188 109 ASPEVAELLGLPPGEPVYRL 128 (236)
T ss_pred CCHHHHHHCCCCCCCEEEEE
T ss_conf 99899986298999869999
No 260
>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=78.85 E-value=1.1 Score=24.07 Aligned_cols=57 Identities=16% Similarity=0.281 Sum_probs=35.7
Q ss_pred HCCCHHHHHH-------HHH--HHCCC-----CCCCHHHHHHHHCCCHHHHHHHHHH-------HHHHHHHHHHHHHC
Q ss_conf 2199999999-------999--82788-----8889899999977899999999999-------99999999997401
Q gi|254780611|r 233 SVLNPRERRI-------FEA--RRLQE-----NPVTLENLSSEFEVSRERVRQIEAR-------AFKKVQESIQKQVE 289 (302)
Q Consensus 233 ~~L~~rEr~I-------I~~--ry~~~-----~~~Tl~EIa~~lgiS~eRVrQI~~~-------AL~kLR~~l~~~~~ 289 (302)
..|+-|+..+ +.+ =||.+ .|+||+|||+.+|++.++||+.-+. .+=.||..+.+.+.
T Consensus 332 ~~l~~R~~TL~~v~~~Iv~~Q~~FF~~g~~~LkPL~L~~vA~el~~heSTiSRai~~KYl~T~~G~f~Lk~FFS~~v~ 409 (477)
T TIGR02395 332 KALEQREETLLRVAEAIVERQKDFFEGGPAALKPLTLREVAEELGLHESTISRAINNKYLQTPRGVFELKYFFSSGVS 409 (477)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCCCCCCHHHHHHHHCCCCCCEEEEECCCEEECCCCCHHHHHHCCHHHC
T ss_conf 999998999999999999999998414520068863899998858898724633177357607640336543120120
No 261
>PHA01976 helix-turn-helix protein
Probab=78.44 E-value=3.3 Score=20.93 Aligned_cols=24 Identities=21% Similarity=0.182 Sum_probs=15.6
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 888989999997789999999999
Q gi|254780611|r 251 NPVTLENLSSEFEVSRERVRQIEA 274 (302)
Q Consensus 251 ~~~Tl~EIa~~lgiS~eRVrQI~~ 274 (302)
.++|+.|+|+.+|||+..|+.-|.
T Consensus 14 ~g~sQ~eLA~~lGVs~~~is~wE~ 37 (67)
T PHA01976 14 RAWSAPELSRRAGVRHSLIYDFEA 37 (67)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHC
T ss_conf 699999999994998999999987
No 262
>PRK09726 DNA-binding transcriptional regulator HipB; Provisional
Probab=78.26 E-value=2.1 Score=22.19 Aligned_cols=35 Identities=14% Similarity=0.248 Sum_probs=26.1
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH----HHHHHHHHH
Q ss_conf 88898999999778999999999999----999999999
Q gi|254780611|r 251 NPVTLENLSSEFEVSRERVRQIEARA----FKKVQESIQ 285 (302)
Q Consensus 251 ~~~Tl~EIa~~lgiS~eRVrQI~~~A----L~kLR~~l~ 285 (302)
.++|+.++|+.+||++.+|+.+|... |..|=+.|.
T Consensus 24 ~gLsQ~~lA~~vGi~Q~TiS~~E~~p~~~~leTLFkiL~ 62 (88)
T PRK09726 24 NGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQ 62 (88)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHH
T ss_conf 598799999981974999999975998786999999999
No 263
>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=78.21 E-value=3.7 Score=20.56 Aligned_cols=30 Identities=23% Similarity=0.352 Sum_probs=23.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 8989999997789999999999999999999997
Q gi|254780611|r 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286 (302)
Q Consensus 253 ~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~ 286 (302)
.||.|+|+.||||...|+ .||++|.=..++
T Consensus 72 ~tl~E~A~~~gVs~~tI~----~aLkrlgiT~KK 101 (120)
T pfam01710 72 AYLKERAKKFGVTPSSIH----YALKKMKITRKK 101 (120)
T ss_pred CHHHHHHHHCCCCHHHHH----HHHHHHCCCCCC
T ss_conf 209999998398799999----999990873048
No 264
>pfam00356 LacI Bacterial regulatory proteins, lacI family.
Probab=78.08 E-value=2 Score=22.32 Aligned_cols=20 Identities=20% Similarity=0.311 Sum_probs=16.4
Q ss_pred CHHHHHHHHCCCHHHHHHHH
Q ss_conf 98999999778999999999
Q gi|254780611|r 254 TLENLSSEFEVSRERVRQIE 273 (302)
Q Consensus 254 Tl~EIa~~lgiS~eRVrQI~ 273 (302)
|+++||+..|||...||+.-
T Consensus 1 Ti~DIA~~agVS~~TVSr~l 20 (46)
T pfam00356 1 TIKDVARLAGVSKATVSRVL 20 (46)
T ss_pred CHHHHHHHHCCCHHHHHHHH
T ss_conf 99999999897999999998
No 265
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=77.84 E-value=2.7 Score=21.51 Aligned_cols=22 Identities=27% Similarity=0.365 Sum_probs=18.4
Q ss_pred CCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 8889899999977899999999
Q gi|254780611|r 251 NPVTLENLSSEFEVSRERVRQI 272 (302)
Q Consensus 251 ~~~Tl~EIa~~lgiS~eRVrQI 272 (302)
...|..++++.||||.++||+=
T Consensus 13 ~~~~i~~La~~~~VS~~TiRRD 34 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRD 34 (53)
T ss_pred CCEEHHHHHHHHCCCHHHHHHH
T ss_conf 9797999999989799999996
No 266
>PRK10079 putative transcriptional regulator; Provisional
Probab=76.82 E-value=5.2 Score=19.60 Aligned_cols=15 Identities=27% Similarity=0.333 Sum_probs=10.9
Q ss_pred HHHHHHHCCCCCCCC
Q ss_conf 677888618983211
Q gi|254780611|r 159 VVAIAKKLNVSESEV 173 (302)
Q Consensus 159 ~~eiA~~Lgis~~~v 173 (302)
.+++|+.|++.+.+-
T Consensus 114 ~~~va~~L~l~~~~~ 128 (241)
T PRK10079 114 SGHVADALGITEGEN 128 (241)
T ss_pred CHHHHHHHCCCCCCC
T ss_conf 989999739899996
No 267
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=76.64 E-value=5.6 Score=19.37 Aligned_cols=23 Identities=13% Similarity=0.317 Sum_probs=15.3
Q ss_pred HHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf 46778886189832110000001
Q gi|254780611|r 158 QVVAIAKKLNVSESEVISMNCRL 180 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v~~l~~~~ 180 (302)
+-.++|+.++++...+-.+...+
T Consensus 48 tq~eLa~~l~v~~~t~tr~ld~L 70 (144)
T PRK03573 48 SQIQLAKAIGIEQPSLVRTLDQL 70 (144)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 99999999798783699999999
No 268
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=76.62 E-value=4.4 Score=20.05 Aligned_cols=30 Identities=23% Similarity=0.362 Sum_probs=21.6
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf 8888898999999778999999999999999999
Q gi|254780611|r 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282 (302)
Q Consensus 249 ~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~ 282 (302)
.+.++|..||++.+|+|+..|++ -|+.|++
T Consensus 7 ~~~~~~~~ela~~l~is~~tvs~----HL~~L~~ 36 (66)
T smart00418 7 AEGELCVCELAEILGLSQSTVSH----HLKKLRE 36 (66)
T ss_pred HCCCCCHHHHHHHHCCCHHHHHH----HHHHHHH
T ss_conf 73996699999998829888879----9999998
No 269
>TIGR01826 CofD_related conserved hypothetical protein; InterPro: IPR010119 This entry represents a subfamily of conserved hypothetical proteins that forms a sister group to the family of CofD, (IPR010115 from INTERPRO), LPPG:Fo 2-phospho-L-lactate transferase, an enzyme of cytochrome F420 biosynthesis..
Probab=76.45 E-value=1.6 Score=23.00 Aligned_cols=59 Identities=10% Similarity=0.120 Sum_probs=42.4
Q ss_pred HHHHHHCC---C---HHHHHHHHHHHCCCCCCCHHHHHHHH--CCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99996219---9---99999999982788888989999997--78999999999999999999999740
Q gi|254780611|r 228 LTRSMSVL---N---PRERRIFEARRLQENPVTLENLSSEF--EVSRERVRQIEARAFKKVQESIQKQV 288 (302)
Q Consensus 228 L~~~l~~L---~---~rEr~II~~ry~~~~~~Tl~EIa~~l--giS~eRVrQI~~~AL~kLR~~l~~~~ 288 (302)
|.++|..| + +.=.+++++||..+..++=.-+|..| ++|...+|-. .|++.|++.|+=+-
T Consensus 55 ~RNcl~ALs~~ePhG~~~~~LfqYRF~~~~~L~GH~lGNL~LaAL~~~~~~~~--~Ai~~l~~~L~v~G 121 (331)
T TIGR01826 55 IRNCLAALSDSEPHGSLLSKLFQYRFGGGGELSGHSLGNLILAALSEITGSFL--EAINLLSKILKVKG 121 (331)
T ss_pred HHHHHHHHCCCCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCHH--HHHHHHHHHHCCCC
T ss_conf 89999983279886168999987414778854575268999987422167889--99999998735655
No 270
>pfam08220 HTH_DeoR DeoR-like helix-turn-helix domain.
Probab=76.20 E-value=3.2 Score=21.04 Aligned_cols=21 Identities=24% Similarity=0.428 Sum_probs=17.8
Q ss_pred CCCCHHHHHHHHCCCHHHHHH
Q ss_conf 888989999997789999999
Q gi|254780611|r 251 NPVTLENLSSEFEVSRERVRQ 271 (302)
Q Consensus 251 ~~~Tl~EIa~~lgiS~eRVrQ 271 (302)
...+..|+++.||||.+.||+
T Consensus 13 ~~v~i~~La~~f~VS~~TiRR 33 (57)
T pfam08220 13 GTLSVEELAELLGVSEMTIRR 33 (57)
T ss_pred CCEEHHHHHHHHCCCHHHHHH
T ss_conf 979799999998959999999
No 271
>pfam12298 Bot1p Eukaryotic mitochondrial regulator protein. This family of proteins is found in eukaryotes. Proteins in this family are typically between 168 and 381 amino acids in length. Bot1p localizes to the mitochondria in live cells and cofractionates with purified mitochondrial ribosomes. Bot1p has a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery. Observations also indicate that in fission yeast, alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms.
Probab=75.92 E-value=5.9 Score=19.24 Aligned_cols=19 Identities=11% Similarity=0.240 Sum_probs=9.9
Q ss_pred CCCCHHHHHHHHHHHHHHC
Q ss_conf 9999899999999999828
Q gi|254780611|r 27 PMLEKQEEYVLAKRYREHG 45 (302)
Q Consensus 27 ~~Lt~eee~~l~~~~~~~g 45 (302)
++|+.+--...++++...|
T Consensus 15 ~vlse~lr~~I~~~v~~~g 33 (171)
T pfam12298 15 PVISEELREKIYEDVTVDG 33 (171)
T ss_pred CCCCHHHHHHHHHHHHHCC
T ss_conf 7689999999999998658
No 272
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=75.66 E-value=2.8 Score=21.42 Aligned_cols=19 Identities=21% Similarity=0.377 Sum_probs=11.4
Q ss_pred CHHHHHHHHCCCHHHHHHH
Q ss_conf 9899999977899999999
Q gi|254780611|r 254 TLENLSSEFEVSRERVRQI 272 (302)
Q Consensus 254 Tl~EIa~~lgiS~eRVrQI 272 (302)
|++|||+..|||...||+.
T Consensus 2 Ti~dvA~~aGVS~sTVSr~ 20 (70)
T smart00354 2 TIKDVARLAGVSKATVSRV 20 (70)
T ss_pred CHHHHHHHHCCCHHHHHHH
T ss_conf 8999999989599999999
No 273
>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=75.52 E-value=6 Score=19.17 Aligned_cols=38 Identities=18% Similarity=0.302 Sum_probs=30.8
Q ss_pred HHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHC--CCHHHHH
Q ss_conf 62199999999999827888889899999977--8999999
Q gi|254780611|r 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFE--VSRERVR 270 (302)
Q Consensus 232 l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lg--iS~eRVr 270 (302)
++.||+..+.+..+|-- ....||+|+|+.+. ||++.|.
T Consensus 141 l~~Lp~~l~~~a~lRl~-~Pd~SL~ELgell~p~isKSgvn 180 (191)
T pfam02650 141 LDNLPEKLREIAQLRLE-NPDASLKELGELLDPPITKSGVN 180 (191)
T ss_pred CCCCCHHHHHHHHHHHH-CCCCCHHHHHHHHCCCCCHHHHH
T ss_conf 12199999999999996-96567999998837997889998
No 274
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein; InterPro: IPR010163 Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity..
Probab=75.07 E-value=6.2 Score=19.10 Aligned_cols=52 Identities=15% Similarity=0.302 Sum_probs=36.5
Q ss_pred HHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf 99999621999999999998278888898999999778999999999999999999
Q gi|254780611|r 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282 (302)
Q Consensus 227 ~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~ 282 (302)
.+.-....++.++-.||..-.-......-+.||+.+|+|...++ +-|..|++
T Consensus 159 ~~~~~~~~~s~~~~~vL~~L~~~~Ge~~v~~iA~~lg~s~~T~~----~~~~~Lek 210 (231)
T TIGR01884 159 ELVPLLAGLSREELKVLEALKAEKGEKSVKNIAKKLGKSLSTIS----RHLAELEK 210 (231)
T ss_pred CCCCCCCCCCHHHHHHHHHHHCCCCEECHHHHHHHHCCCHHHHH----HHHHHHHH
T ss_conf 22244678889999999998507880528779988578887999----99998874
No 275
>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=74.76 E-value=2.7 Score=21.49 Aligned_cols=22 Identities=23% Similarity=0.315 Sum_probs=15.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 8989999997789999999999
Q gi|254780611|r 253 VTLENLSSEFEVSRERVRQIEA 274 (302)
Q Consensus 253 ~Tl~EIa~~lgiS~eRVrQI~~ 274 (302)
+|-+|+|+.||||+..|.++-.
T Consensus 2 lTv~EaA~yLgv~~~t~~~l~~ 23 (49)
T TIGR01764 2 LTVEEAAEYLGVSKSTVYRLIE 23 (49)
T ss_pred CCHHHHHHHCCCCHHHHHHHHH
T ss_conf 8778899771999057899997
No 276
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=74.69 E-value=6.3 Score=19.03 Aligned_cols=25 Identities=16% Similarity=0.171 Sum_probs=14.4
Q ss_pred CCHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf 8824677888618983211000000
Q gi|254780611|r 155 KPEQVVAIAKKLNVSESEVISMNCR 179 (302)
Q Consensus 155 ~~~~~~eiA~~Lgis~~~v~~l~~~ 179 (302)
.+-++.+||+.+|++...+..+...
T Consensus 19 ~~~sl~eia~~~~l~ksT~~RlL~t 43 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLNT 43 (91)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 9989999999989099999999999
No 277
>pfam04814 HNF-1_N Hepatocyte nuclear factor 1 (HNF-1), N terminus. This family consists of the N terminus of homeobox-containing transcription factor HNF-1. This region contains a dimerization sequence and an acidic region that may be involved in transcription activation. Mutations and the common Ala/Val 98 polymorphism in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3).
Probab=74.28 E-value=6.4 Score=18.97 Aligned_cols=57 Identities=12% Similarity=0.185 Sum_probs=41.1
Q ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 6666777999999621999999999998278888898999999778999999999999
Q gi|254780611|r 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276 (302)
Q Consensus 219 ~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~A 276 (302)
++....+..+...+..=+-+-...|..| +......++++++.-|+++.+++|--.+.
T Consensus 96 EEaa~qra~Ve~ll~~d~~~v~~~Ik~~-m~~h~ipQ~~vv~~TGlnQS~lSq~LnkG 152 (177)
T pfam04814 96 EEAAHQRAEVDRLLREDPWRVAKMIKSY-MQQHNIPQREVVDATGLNQSHLSQHLNKG 152 (177)
T ss_pred HHHHHHHHHHHHHHHHCHHHHHHHHHHH-HHHCCCCHHHHHHHCCCCHHHHHHHHHCC
T ss_conf 5888889999999972849999999999-98768846678761065599999999668
No 278
>pfam04645 DUF603 Protein of unknown function, DUF603. This family includes several uncharacterized proteins from Borrelia species.
Probab=73.90 E-value=3.7 Score=20.59 Aligned_cols=20 Identities=40% Similarity=0.366 Sum_probs=10.5
Q ss_pred HHHHHHHCCCCCCCCCCCCC
Q ss_conf 67788861898321100000
Q gi|254780611|r 159 VVAIAKKLNVSESEVISMNC 178 (302)
Q Consensus 159 ~~eiA~~Lgis~~~v~~l~~ 178 (302)
..+||..|||+..-|-.+-+
T Consensus 22 D~eIA~~LGVsr~nV~kmRq 41 (181)
T pfam04645 22 DAEIAKELGVSRVNVWRMRQ 41 (181)
T ss_pred HHHHHHHHCCHHHHHHHHHH
T ss_conf 79999997830999999999
No 279
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=73.88 E-value=2.8 Score=21.35 Aligned_cols=24 Identities=33% Similarity=0.477 Sum_probs=20.7
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 889899999977899999999999
Q gi|254780611|r 252 PVTLENLSSEFEVSRERVRQIEAR 275 (302)
Q Consensus 252 ~~Tl~EIa~~lgiS~eRVrQI~~~ 275 (302)
++|+.++|+.+|+|+..|+++++.
T Consensus 12 ~ls~~~lA~~~gis~~~l~~~e~g 35 (58)
T cd00093 12 GLTQEELAEKLGVSRSTISRIENG 35 (58)
T ss_pred CCCHHHHHHHCCCCHHHHHHHHCC
T ss_conf 999999957149999999999879
No 280
>COG4465 CodY Pleiotropic transcriptional repressor [Transcription]
Probab=72.81 E-value=7 Score=18.74 Aligned_cols=60 Identities=17% Similarity=0.279 Sum_probs=42.7
Q ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHC---CCCC-CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf 666677799999962199999999999827---8888-898999999778999999999999999999
Q gi|254780611|r 219 EERKNRRNMLTRSMSVLNPRERRIFEARRL---QENP-VTLENLSSEFEVSRERVRQIEARAFKKVQE 282 (302)
Q Consensus 219 ~e~~~~~~~L~~~l~~L~~rEr~II~~ry~---~~~~-~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~ 282 (302)
++....+..+.-+++.|+--|-.-+.+-|. +.++ ++-.-||++.||||+-| -.||+||-.
T Consensus 167 E~e~R~~t~V~mAi~tLSYSEleAve~I~eELdG~EG~lvASkiADrvGITRSVI----VNALRKlES 230 (261)
T COG4465 167 EEEARKRTVVQMAISTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVI----VNALRKLES 230 (261)
T ss_pred HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCEEEEHHHHHHHCCHHHHH----HHHHHHHHH
T ss_conf 9999888899999854249899999999986288665363024556517339999----999987654
No 281
>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=71.92 E-value=0.073 Score=31.96 Aligned_cols=47 Identities=17% Similarity=0.290 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHH
Q ss_conf 9994307787565555799998889999998889989862185345689997577
Q gi|254780611|r 53 LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107 (302)
Q Consensus 53 Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~ 107 (302)
...+||.+|=||+ ++ +||+...-|==-.+++=+|-+-|.|||||+..
T Consensus 15 vT~AnLnY~GSit-------ID-eDl~daag~lenekv~IvnvnNG~RfsTY~I~ 61 (127)
T TIGR00223 15 VTEANLNYVGSIT-------ID-EDLLDAAGLLENEKVDIVNVNNGKRFSTYVIA 61 (127)
T ss_pred EEECCCCEEEEEE-------HH-HHHHHHHHCCCCCEEEEEECCCCCCEEEEEEC
T ss_conf 6323674365332-------54-67999851289984899866899712346651
No 282
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=71.24 E-value=7.6 Score=18.50 Aligned_cols=34 Identities=21% Similarity=0.308 Sum_probs=25.2
Q ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 78888898999999778999999999999999999999
Q gi|254780611|r 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285 (302)
Q Consensus 248 ~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~ 285 (302)
+.+.+.|+++||+..|||..+||.. +++|-+.|.
T Consensus 272 ~~~~~~t~~~Ia~v~~vsevTIr~~----ykel~~~l~ 305 (310)
T PRK00423 272 LEGERRTQREVAEVAGVTEVTVRNR----YKELAEKLD 305 (310)
T ss_pred HHCCCCCHHHHHHHHCCCHHHHHHH----HHHHHHHHC
T ss_conf 9488989999998969889999999----999999848
No 283
>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=70.62 E-value=7.8 Score=18.42 Aligned_cols=28 Identities=25% Similarity=0.415 Sum_probs=20.6
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf 88898999999778999999999999999999
Q gi|254780611|r 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282 (302)
Q Consensus 251 ~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~ 282 (302)
.+.+-.+||+.||||+..|++ +++||.+
T Consensus 19 ~~v~~~~iA~~L~Vs~~SVt~----mlkkL~~ 46 (58)
T pfam01325 19 GVVKTKDLAERLNVSPSTVSE----MLKKLEK 46 (58)
T ss_pred CCEEHHHHHHHHCCCCHHHHH----HHHHHHH
T ss_conf 961299999995999252999----9999998
No 284
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=70.52 E-value=7.8 Score=18.40 Aligned_cols=26 Identities=35% Similarity=0.344 Sum_probs=20.1
Q ss_pred CHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 82467788861898321100000012
Q gi|254780611|r 156 PEQVVAIAKKLNVSESEVISMNCRLA 181 (302)
Q Consensus 156 ~~~~~eiA~~Lgis~~~v~~l~~~~~ 181 (302)
...+.+||+.||+++..|..+.+.+.
T Consensus 22 ~vr~~dIA~~L~Vs~~SVs~mikkL~ 47 (142)
T PRK03902 22 YARVSDIAEALSVHPSSVTKMVQKLD 47 (142)
T ss_pred CCCHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 71299999997899533999999999
No 285
>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=70.42 E-value=7.9 Score=18.39 Aligned_cols=36 Identities=22% Similarity=0.322 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 9999999998278888898999999778999999999999
Q gi|254780611|r 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276 (302)
Q Consensus 237 ~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~A 276 (302)
.|++.|..- | ++.+..|+|..+|+|..+|++|-++.
T Consensus 60 ~Rd~~I~~e-F---nG~N~~eLArkY~ls~~~i~~ii~~~ 95 (107)
T pfam08765 60 LRDLEIYNE-F---NGNNHAELARKYGVSEQWIYKIIKRV 95 (107)
T ss_pred HHHHHHHHH-H---CCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 999999998-0---79879999999698899999999999
No 286
>COG2411 Uncharacterized conserved protein [Function unknown]
Probab=70.34 E-value=7.9 Score=18.38 Aligned_cols=50 Identities=22% Similarity=0.439 Sum_probs=36.2
Q ss_pred HHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCC--CHHHHHHHHHHHHHHHHH
Q ss_conf 99621999999999998278888898999999778--999999999999999999
Q gi|254780611|r 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV--SRERVRQIEARAFKKVQE 282 (302)
Q Consensus 230 ~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgi--S~eRVrQI~~~AL~kLR~ 282 (302)
+.+..|+++++.|+...- .+ -|++..|..+|= -+-+|||.-.+|..-|.+
T Consensus 133 e~l~~Ls~~~~~iL~~~~-~~--gslRkaA~klgg~~kr~~ir~vLrKay~~L~~ 184 (188)
T COG2411 133 EHLDNLSERDKRILELFV-EE--GSLRKAAKKLGGLEKRGRIRRVLRKAYHELKK 184 (188)
T ss_pred HHCCCCCHHHHHHHHHHH-HC--CCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
T ss_conf 743258988999999999-75--92999999955841203899999999999986
No 287
>PRK04140 hypothetical protein; Provisional
Probab=67.45 E-value=6.3 Score=19.05 Aligned_cols=21 Identities=19% Similarity=0.249 Sum_probs=16.6
Q ss_pred HHHHHHHHCCCCCCCCCCCCC
Q ss_conf 467788861898321100000
Q gi|254780611|r 158 QVVAIAKKLNVSESEVISMNC 178 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v~~l~~ 178 (302)
++-++|..||+|...+..+..
T Consensus 140 SlG~LA~~LGVSRrtv~~YE~ 160 (319)
T PRK04140 140 SLGELASELGVSRRTISKYEN 160 (319)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
T ss_conf 888999984986999999970
No 288
>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=67.19 E-value=0.51 Score=26.33 Aligned_cols=19 Identities=26% Similarity=0.763 Sum_probs=15.5
Q ss_pred CCCCHHHHHHHHHHHHHHH
Q ss_conf 4568999757789999998
Q gi|254780611|r 97 RGFRLATYSMWWIKAAMQE 115 (302)
Q Consensus 97 kG~~FsTYA~~wIr~~I~~ 115 (302)
-|+.|++|+.+||||+=-+
T Consensus 22 SGftf~~y~m~WVRQaPGk 40 (117)
T cd04981 22 SGFTFTSYGVNWVRQAPGK 40 (117)
T ss_pred CCCCHHHCEEEEEEECCCC
T ss_conf 0669666916899858999
No 289
>PRK11050 manganese transport regulator MntR; Provisional
Probab=66.87 E-value=6.3 Score=19.03 Aligned_cols=34 Identities=32% Similarity=0.317 Sum_probs=23.7
Q ss_pred HHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCC
Q ss_conf 66244788824677888618983211000000122
Q gi|254780611|r 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182 (302)
Q Consensus 148 ~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~ 182 (302)
.+....|. ..+.+||..||+++..|..+.+.+..
T Consensus 47 ~L~~~~G~-aR~~DIA~~LgVs~pSVt~mlkrL~~ 80 (155)
T PRK11050 47 DLIAEVGE-ARQVDIAARLGVSQPTVAKMLKRLAR 80 (155)
T ss_pred HHHHCCCC-EEHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf 99982695-64999998909993319999999987
No 290
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=66.69 E-value=9.3 Score=17.89 Aligned_cols=26 Identities=8% Similarity=0.051 Sum_probs=20.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf 898999999778999999999999999999
Q gi|254780611|r 253 VTLENLSSEFEVSRERVRQIEARAFKKVQE 282 (302)
Q Consensus 253 ~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~ 282 (302)
.+..|||..+|+|++.|.++ |.++++
T Consensus 157 ~~~~elA~~lG~Sretl~R~----L~~f~~ 182 (213)
T PRK10402 157 EKHTQAAEYLGVSYRHLLYV----LAQFCQ 182 (213)
T ss_pred CCHHHHHHHHCCCHHHHHHH----HHHHHH
T ss_conf 67999999979889999999----999998
No 291
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.
Probab=66.16 E-value=9.6 Score=17.82 Aligned_cols=32 Identities=19% Similarity=0.392 Sum_probs=24.9
Q ss_pred CCCHHHHHHHHC-CCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 889899999977-899999999999999999999974
Q gi|254780611|r 252 PVTLENLSSEFE-VSRERVRQIEARAFKKVQESIQKQ 287 (302)
Q Consensus 252 ~~Tl~EIa~~lg-iS~eRVrQI~~~AL~kLR~~l~~~ 287 (302)
++|+.+||..|| -+...|. .|++|+.+.++..
T Consensus 44 ~~s~~~Ig~~fg~rdHsTV~----~a~~kv~~~~~~d 76 (90)
T cd06571 44 GLSLPEIGRAFGGRDHSTVL----HAVRKIEELLEED 76 (90)
T ss_pred CCCHHHHHHHHCCCCHHHHH----HHHHHHHHHHHHC
T ss_conf 88999999995899714999----9999999999839
No 292
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator); InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulphovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis strain PCC 6803 hypothetical protein slr0846. These are small proteins of 12 to 18 kD which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators..
Probab=66.15 E-value=9.2 Score=17.92 Aligned_cols=25 Identities=28% Similarity=0.286 Sum_probs=15.7
Q ss_pred CHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf 8246778886189832110000001
Q gi|254780611|r 156 PEQVVAIAKKLNVSESEVISMNCRL 180 (302)
Q Consensus 156 ~~~~~eiA~~Lgis~~~v~~l~~~~ 180 (302)
+-++++||+..+||+.=..+++..+
T Consensus 25 ~v~~~~ia~~~~Is~~yL~K~l~~L 49 (133)
T TIGR00738 25 PVSVKEIAERQGISRSYLEKVLRTL 49 (133)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 6078999988489987999999988
No 293
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=66.05 E-value=9.6 Score=17.81 Aligned_cols=35 Identities=14% Similarity=0.134 Sum_probs=15.2
Q ss_pred HHCCCCCCCC-----HHHHHHHHHHHHHHHHHHCCCCCHH
Q ss_conf 6218534568-----9997577899999985320246001
Q gi|254780611|r 91 KKFDPERGFR-----LATYSMWWIKAAMQEYILRSWSLVK 125 (302)
Q Consensus 91 ~kFDp~kG~~-----FsTYA~~wIr~~I~~~i~~~~~~IR 125 (302)
..|||...-+ .+.|...++--.+...++...--|+
T Consensus 103 ~~f~p~~~~~~~~i~~~~~~~~~llp~ll~~~~~~~P~v~ 142 (314)
T PRK09508 103 SGFEPESSERVFNLCICSPLDNRLASQIYNRIEQIAPNIH 142 (314)
T ss_pred CCCCCCCCCCEEEEEECCHHHHHHHHHHHHHHHHHCCCCE
T ss_conf 1368100473699996307899999999999998689977
No 294
>TIGR01636 phage_rinA phage transcriptional regulator, RinA family; InterPro: IPR006523 These sequences represent a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors . .
Probab=66.02 E-value=9.6 Score=17.80 Aligned_cols=63 Identities=16% Similarity=0.357 Sum_probs=52.4
Q ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHCCCC-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 677799999962199999999999827888-889899999977899999999999999999999
Q gi|254780611|r 222 KNRRNMLTRSMSVLNPRERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284 (302)
Q Consensus 222 ~~~~~~L~~~l~~L~~rEr~II~~ry~~~~-~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l 284 (302)
......+..++..+++.++.++..+|.... ++++-.++..+.++.....++....+..+-+.+
T Consensus 73 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 136 (138)
T TIGR01636 73 LEFKDAIENVLNELDDEDRELIEELYWDKKPPLTLVGLASDLNISDSTAYRLKKKIILALAEEL 136 (138)
T ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 8889999998851132578999988630366325666776653004677888888999888763
No 295
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=65.83 E-value=9.7 Score=17.78 Aligned_cols=28 Identities=32% Similarity=0.281 Sum_probs=20.6
Q ss_pred CCCHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 8882467788861898321100000012
Q gi|254780611|r 154 LKPEQVVAIAKKLNVSESEVISMNCRLA 181 (302)
Q Consensus 154 ~~~~~~~eiA~~Lgis~~~v~~l~~~~~ 181 (302)
..+....+||+.|+|++..|..+.+.+.
T Consensus 22 ~~~~~~~diA~~L~Vsp~sVt~ml~rL~ 49 (154)
T COG1321 22 KGFARTKDIAERLKVSPPSVTEMLKRLE 49 (154)
T ss_pred CCCCCHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 6875199999985899278999999998
No 296
>COG3766 Predicted membrane protein [Function unknown]
Probab=65.36 E-value=9.1 Score=17.98 Aligned_cols=63 Identities=21% Similarity=0.300 Sum_probs=45.9
Q ss_pred CCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf 99999899999999999828599999999943077875655557999988899999988899898621
Q gi|254780611|r 26 IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93 (302)
Q Consensus 26 ~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kF 93 (302)
|..+||-+|.+| +| +|+..|-=-+--.=+++|..+|..-+. ..++-|.+.-|.+|++-=+--|
T Consensus 29 y~~vTpyke~el---Ik-~GN~AaAlA~~G~llG~~~plassi~~-s~sl~~~~~Wg~~~~vvqLl~f 91 (133)
T COG3766 29 YEKVTPYKEWEL---IK-EGNTAAALALGGALLGYVIPLASSISH-SVSLPDYLAWGAIALVVQLLVF 91 (133)
T ss_pred HHHHCCCHHHHH---HH-CCCHHHHHHHCCHHHHHHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHH
T ss_conf 997376247999---98-356899999434178769998999986-0343899999999999999999
No 297
>pfam01978 TrmB Sugar-specific transcriptional regulator TrmB. One member of this family, TrmB, has been shown to be a sugar-specific transcriptional regulator of the trehalose/maltose ABC transporter in Thermococcus litoralis.
Probab=64.93 E-value=10 Score=17.67 Aligned_cols=43 Identities=21% Similarity=0.368 Sum_probs=30.2
Q ss_pred CCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf 199999999999827888889899999977899999999999999999
Q gi|254780611|r 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281 (302)
Q Consensus 234 ~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR 281 (302)
.|++.|-.|...-- ...+.|-.|||+..|+++.+|-. +|++|.
T Consensus 5 Gls~~E~~vY~~Ll-~~g~~t~~eia~~~~i~r~~vY~----~L~~L~ 47 (68)
T pfam01978 5 GLSEYEAKVYLALL-KLGPATADEIAEESGVPRSKVYE----VLRSLE 47 (68)
T ss_pred CCCHHHHHHHHHHH-HCCCCCHHHHHHHHCCCHHHHHH----HHHHHH
T ss_conf 98999999999999-81998899999995988989999----999999
No 298
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=63.91 E-value=11 Score=17.54 Aligned_cols=43 Identities=16% Similarity=0.259 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHCCCCC-CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999998278888-8989999997789999999999999999999
Q gi|254780611|r 237 PRERRIFEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302)
Q Consensus 237 ~rEr~II~~ry~~~~~-~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302)
+-|+.|+.+.+..+++ .|-..||+.+||++-.| .++|-+|.+.
T Consensus 6 ~~eqkil~~L~~~g~~~~tA~~lak~lg~~Kk~v----N~~LY~L~k~ 49 (68)
T smart00550 6 SLEEKILEFLENSGDETSTALQLAKNLGLPKKEV----NRVLYSLEKK 49 (68)
T ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHHCCCHHHH----HHHHHHHHHC
T ss_conf 7999999999974886403999999949989999----9999999974
No 299
>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=63.35 E-value=11 Score=17.48 Aligned_cols=49 Identities=24% Similarity=0.250 Sum_probs=34.6
Q ss_pred HHHHH-HCCCHHHHHHH----HHHHCCCCC---CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 99996-21999999999----998278888---8989999997789999999999999999
Q gi|254780611|r 228 LTRSM-SVLNPRERRIF----EARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKV 280 (302)
Q Consensus 228 L~~~l-~~L~~rEr~II----~~ry~~~~~---~Tl~EIa~~lgiS~eRVrQI~~~AL~kL 280 (302)
+...+ ..|+.||..|+ +.-||.+.+ .|..+|++.-|+++..|+ +|+..|
T Consensus 22 ldal~~~~lt~rq~kv~~aV~RkTyG~nK~~d~I~~sqi~~mtgi~~~~Vs----~a~~~L 78 (100)
T pfam04492 22 LEALCRADLSGRQLKVLLAVIRKTYGWNKPMDRVTNEQIAELTGLSRTHVS----EAKKSL 78 (100)
T ss_pred HHHHHHCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCHHHHH----HHHHHH
T ss_conf 999980888788999999999986077850336229999999788854599----999999
No 300
>pfam04218 CENP-B_N CENP-B N-terminal DNA-binding domain. Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure.
Probab=62.89 E-value=11 Score=17.42 Aligned_cols=41 Identities=27% Similarity=0.326 Sum_probs=28.6
Q ss_pred CCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 1999999999998278888898999999778999999999999
Q gi|254780611|r 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276 (302)
Q Consensus 234 ~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~A 276 (302)
.|+-.|+.=|.-+. +++.+-.++|..+||....||.|.+.-
T Consensus 6 ~LTl~eKi~iI~~~--e~G~s~~~lar~~gi~~STl~~I~Knk 46 (53)
T pfam04218 6 SLTLREKIEVIQRS--EEGESKASLARRFNVPRSTLRDILKNK 46 (53)
T ss_pred EECHHHHHHHHHHH--HCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 41699999999999--858968899999698797999999809
No 301
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=62.88 E-value=8.6 Score=18.12 Aligned_cols=23 Identities=39% Similarity=0.446 Sum_probs=18.0
Q ss_pred HHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 67788861898321100000012
Q gi|254780611|r 159 VVAIAKKLNVSESEVISMNCRLA 181 (302)
Q Consensus 159 ~~eiA~~Lgis~~~v~~l~~~~~ 181 (302)
+.+||+.||+++..|..+.+.+.
T Consensus 2 ~~diA~~L~vs~~sVs~~l~~L~ 24 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLE 24 (96)
T ss_pred HHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 78899884999167999999999
No 302
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; InterPro: IPR012794 Members of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.; GO: 0003677 DNA binding, 0016563 transcription activator activity, 0045941 positive regulation of transcription, 0046278 protocatechuate metabolic process.
Probab=62.42 E-value=11 Score=17.44 Aligned_cols=10 Identities=0% Similarity=0.089 Sum_probs=3.9
Q ss_pred HHHHHHHHCC
Q ss_conf 4677888618
Q gi|254780611|r 158 QVVAIAKKLN 167 (302)
Q Consensus 158 ~~~eiA~~Lg 167 (302)
-.+++++.++
T Consensus 87 ~l~~ls~~~~ 96 (252)
T TIGR02431 87 LLERLSAQTH 96 (252)
T ss_pred HHHHHHHHHC
T ss_conf 9999998537
No 303
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=61.49 E-value=8.1 Score=18.29 Aligned_cols=22 Identities=18% Similarity=0.166 Sum_probs=11.5
Q ss_pred CHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 9899999977899999999999
Q gi|254780611|r 254 TLENLSSEFEVSRERVRQIEAR 275 (302)
Q Consensus 254 Tl~EIa~~lgiS~eRVrQI~~~ 275 (302)
|-+|+|+.||||...|+.=.++
T Consensus 2 t~~e~A~~lgVs~~TlrrW~~~ 23 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CHHHHHHHHCCCHHHHHHHHHC
T ss_conf 8899999979899999999987
No 304
>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=61.06 E-value=12 Score=17.21 Aligned_cols=22 Identities=27% Similarity=0.274 Sum_probs=11.5
Q ss_pred HHHHHHHHHCCCCCCCCCCCCC
Q ss_conf 2467788861898321100000
Q gi|254780611|r 157 EQVVAIAKKLNVSESEVISMNC 178 (302)
Q Consensus 157 ~~~~eiA~~Lgis~~~v~~l~~ 178 (302)
.+.+++|..++++.+++.....
T Consensus 53 ~~~~eia~~~~~~~~~ie~~l~ 74 (195)
T pfam04963 53 ASLEEIAESLGVELDEVEAVLA 74 (195)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
T ss_conf 7999999880878999999999
No 305
>pfam08535 KorB KorB domain. This family consists of several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon. This domain includes the DNA-binding HTH motif.
Probab=60.53 E-value=9.9 Score=17.72 Aligned_cols=22 Identities=41% Similarity=0.238 Sum_probs=14.5
Q ss_pred HHHHHHHCCCCCCCCCCCCCCC
Q ss_conf 6778886189832110000001
Q gi|254780611|r 159 VVAIAKKLNVSESEVISMNCRL 180 (302)
Q Consensus 159 ~~eiA~~Lgis~~~v~~l~~~~ 180 (302)
-.+||+.||-+..-|-.....+
T Consensus 6 k~~IAk~LGks~s~VS~hlaL~ 27 (93)
T pfam08535 6 QAEIAKKLGKSKSFVSQHLALL 27 (93)
T ss_pred HHHHHHHHCCCHHHHHHHHHHH
T ss_conf 9999999788988999999983
No 306
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=60.01 E-value=12 Score=17.09 Aligned_cols=22 Identities=23% Similarity=0.323 Sum_probs=18.9
Q ss_pred CCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 8888989999997789999999
Q gi|254780611|r 250 ENPVTLENLSSEFEVSRERVRQ 271 (302)
Q Consensus 250 ~~~~Tl~EIa~~lgiS~eRVrQ 271 (302)
+.+.|-.|+|+.+|+|+-.+|+
T Consensus 175 ~~~~ta~eva~~~giSrvTaRR 196 (225)
T PRK10046 175 GVQHTAETVAQALTISRTTARR 196 (225)
T ss_pred CCCCCHHHHHHHHCCCHHHHHH
T ss_conf 9986899999985851999999
No 307
>PRK00876 nadE NAD synthetase; Reviewed
Probab=59.52 E-value=13 Score=17.04 Aligned_cols=26 Identities=19% Similarity=0.290 Sum_probs=21.3
Q ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 78888898999999778999999999
Q gi|254780611|r 248 LQENPVTLENLSSEFEVSRERVRQIE 273 (302)
Q Consensus 248 ~~~~~~Tl~EIa~~lgiS~eRVrQI~ 273 (302)
+.+++++..+|++.+|+|.+.|.++-
T Consensus 274 ~~~~~~~~~~~~~~~g~~~e~v~~v~ 299 (325)
T PRK00876 274 AQNHGVPAEVVAAALGLTPEQVERVW 299 (325)
T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 87649999999988398999999999
No 308
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=58.24 E-value=12 Score=17.19 Aligned_cols=23 Identities=22% Similarity=0.151 Sum_probs=19.0
Q ss_pred HHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf 24677888618983211000000
Q gi|254780611|r 157 EQVVAIAKKLNVSESEVISMNCR 179 (302)
Q Consensus 157 ~~~~eiA~~Lgis~~~v~~l~~~ 179 (302)
-++.+||..+|.++.+++...+.
T Consensus 62 ~Ti~EIAeelG~TeqTir~hlkg 84 (182)
T COG1318 62 MTISEIAEELGRTEQTVRNHLKG 84 (182)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHC
T ss_conf 74999999968779999999751
No 309
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=57.94 E-value=13 Score=16.86 Aligned_cols=22 Identities=14% Similarity=0.138 Sum_probs=13.4
Q ss_pred HHHHHHHHCCCCCCCCCCCCCC
Q ss_conf 4677888618983211000000
Q gi|254780611|r 158 QVVAIAKKLNVSESEVISMNCR 179 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v~~l~~~ 179 (302)
.+.+|++.+|++...+-..+..
T Consensus 30 cV~eL~~~l~~sQs~vS~HL~~ 51 (106)
T PRK10141 30 CVCDLCTALDQSQPKISRHLAL 51 (106)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
T ss_conf 6999998869988899999999
No 310
>pfam02082 Rrf2 Transcriptional regulator. This family is related to pfam001022 and other transcription regulation families (personal obs: Yeats C).
Probab=57.63 E-value=13 Score=16.83 Aligned_cols=23 Identities=22% Similarity=0.247 Sum_probs=10.7
Q ss_pred HHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf 46778886189832110000001
Q gi|254780611|r 158 QVVAIAKKLNVSESEVISMNCRL 180 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v~~l~~~~ 180 (302)
+..+||+.+++++.-+..+.+.+
T Consensus 26 s~~~iA~~~~i~~~~l~kil~~L 48 (82)
T pfam02082 26 TSEEIAERQNISPVYLRKILAKL 48 (82)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 59999987890999999999981
No 311
>TIGR01074 rep ATP-dependent DNA helicase Rep; InterPro: IPR005752 RepA hexameric DNA helicase contain ATP-binding domains similar to those seen in monomeric helicases but which are arranged in a ring. There is compelling evidence to suggest that a single ssDNA molecule passes through the centre of the hexameric ring. Activity of the enzyme is based upon two separate but coupled activities, ssDNA translocation and duplex destabilisation, and is driven by energy derived from the continuous ATP-binding and hydrolysis events that take place in the active-site cleft. The resulting conformational changes that accompany these events underpin the coupling process and allow the helicase to translocate along the DNA, destabilizing the duplex and separating the two strands in an active process ; GO: 0004003 ATP-dependent DNA helicase activity, 0006268 DNA unwinding during replication, 0005737 cytoplasm.
Probab=57.45 E-value=14 Score=16.81 Aligned_cols=91 Identities=13% Similarity=0.224 Sum_probs=37.6
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCC-----CC-CHHHHHHHHHHHHHHHHHHCC-CCCHH---------------HCCCCHH
Q ss_conf 88999999888998986218534-----56-899975778999999853202-46001---------------1023003
Q gi|254780611|r 75 ISEVVSEGNIGLMQAVKKFDPER-----GF-RLATYSMWWIKAAMQEYILRS-WSLVK---------------IGTTANQ 132 (302)
Q Consensus 75 ~~DLiQeG~iGLi~Ai~kFDp~k-----G~-~FsTYA~~wIr~~I~~~i~~~-~~~IR---------------iP~~~~~ 132 (302)
+..+-++=.+-|..|++.+...+ ++ ...+|. .||+.-...+-+.. ...|| -+.+..-
T Consensus 424 L~~~A~~~~~Slf~A~~~~gl~~~L~~r~~~~L~~F~-~wl~~i~~~~~~~e~~~~vr~l~~~i~YE~~L~~~~~~~k~~ 502 (677)
T TIGR01074 424 LGEYAAEKNKSLFEASFELGLLQTLSGRAYEKLQRFT-DWLVEIRRQAERSEPIEAVRSLVEDIDYENWLYENSESPKAA 502 (677)
T ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCHHH
T ss_conf 9999974079788998776489851365788899999-999999998740385899999998613778988525781146
Q ss_pred HHHHHHHHHHHHHHHH-HHCCCCCCH--HHHHHHHHC
Q ss_conf 5899999999788786-624478882--467788861
Q gi|254780611|r 133 KRLFFNLRRLKGHLQA-ITDNNLKPE--QVVAIAKKL 166 (302)
Q Consensus 133 r~l~~~~rk~~~~~~~-~~~~~~~~~--~~~eiA~~L 166 (302)
..-..|+..+-..+.. +.+.....+ ++.+++..|
T Consensus 503 e~r~~NV~~L~~W~~~~L~~~e~~~~~m~l~~~v~~l 539 (677)
T TIGR01074 503 EMRMKNVEDLFSWLKEMLEGDEEDGPEMNLEQVVQRL 539 (677)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHH
T ss_conf 7768669999999999841788885234689999999
No 312
>TIGR02463 MPGP_rel mannosyl-3-phosphoglycerate phosphatase homolog; InterPro: IPR012815 This family consists of members of the HAD superfamily, subfamily IIB. All members are closely related to mannosyl-3-phosphoglycerate phosphatase, the second enzyme in a two-step pathway for biosynthesis of mannosylglycerate, a compatible solute present in some thermophiles and in Dehalococcoides ethenogenes. However, members of this family are separable in a neighbour-joining tree constructed from a multiple sequence alignment and are found only in mesophiles that lack the companion mannosyl-3-phosphoglycerate synthase (IPR012812 from INTERPRO). Members of this family are likely to act on a compound related to yet distinct from mannosyl-3-phosphoglycerate.; GO: 0050531 mannosyl-3-phosphoglycerate phosphatase activity, 0005737 cytoplasm.
Probab=57.22 E-value=6.1 Score=19.15 Aligned_cols=44 Identities=11% Similarity=0.133 Sum_probs=28.8
Q ss_pred HHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 999999621999999999998278888898999999778999999999
Q gi|254780611|r 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273 (302)
Q Consensus 226 ~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~ 273 (302)
..|...|..|.+.+.. .++-++| +|-+||++..|+|++.+++.+
T Consensus 90 ~~l~~~L~~l~~~~~f--~l~~l~d--~~daei~ElTGL~~~~~~la~ 133 (224)
T TIGR02463 90 EILRLVLEELSEELSF--KLTPLDD--LSDAEIAELTGLSGEQLALAQ 133 (224)
T ss_pred HHHHHHHHHHHHHHCC--CCCCCCC--CCHHHHHHHCCCCHHHHHHHH
T ss_conf 7899999999886258--8778786--445667553077787999986
No 313
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=56.78 E-value=14 Score=16.74 Aligned_cols=21 Identities=19% Similarity=0.332 Sum_probs=14.9
Q ss_pred CHHHHHHHHHCCCCCCCCCCC
Q ss_conf 824677888618983211000
Q gi|254780611|r 156 PEQVVAIAKKLNVSESEVISM 176 (302)
Q Consensus 156 ~~~~~eiA~~Lgis~~~v~~l 176 (302)
|.+++++|+.+++++..+...
T Consensus 1 plsl~~lA~~~~~S~~~l~~~ 21 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRL 21 (84)
T ss_pred CCCHHHHHHHHCCCHHHHHHH
T ss_conf 989999999889099999999
No 314
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=56.07 E-value=14 Score=16.66 Aligned_cols=25 Identities=24% Similarity=0.320 Sum_probs=15.9
Q ss_pred CHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf 8246778886189832110000001
Q gi|254780611|r 156 PEQVVAIAKKLNVSESEVISMNCRL 180 (302)
Q Consensus 156 ~~~~~eiA~~Lgis~~~v~~l~~~~ 180 (302)
+.++.+||+..|+++.-+..+...+
T Consensus 25 ~~s~~~IA~~~~is~~~L~kil~~L 49 (150)
T COG1959 25 PVSSAEIAERQGISPSYLEKILSKL 49 (150)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 4649999999891999999999999
No 315
>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=55.06 E-value=15 Score=16.55 Aligned_cols=40 Identities=30% Similarity=0.440 Sum_probs=23.7
Q ss_pred CCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 199999999999827888889899999977899999999999999
Q gi|254780611|r 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278 (302)
Q Consensus 234 ~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~ 278 (302)
.|++|| |+.|.= .+.|..|||+..|++-++|++-..-.|.
T Consensus 55 ~lspre---IQarIR--aGas~eevA~~~g~~~~rVerfa~PVl~ 94 (169)
T pfam11268 55 TLSPRE---IQARIR--AGASAEEVAEAAGVPEERVERFEGPVLA 94 (169)
T ss_pred CCCHHH---HHHHHH--CCCCHHHHHHHHCCCHHHHHHCCCHHHH
T ss_conf 889899---999988--7999999999959999998742233889
No 316
>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=55.05 E-value=15 Score=16.55 Aligned_cols=36 Identities=25% Similarity=0.350 Sum_probs=19.7
Q ss_pred CCHHHHHHHHH----HHCCCCCCCHHHHHHHHCCCHHHHH
Q ss_conf 99999999999----8278888898999999778999999
Q gi|254780611|r 235 LNPRERRIFEA----RRLQENPVTLENLSSEFEVSRERVR 270 (302)
Q Consensus 235 L~~rEr~II~~----ry~~~~~~Tl~EIa~~lgiS~eRVr 270 (302)
|+++++.|+.. |--.+++..=++||+.++.|...||
T Consensus 2 LT~~Qr~IL~aLI~lY~~~~~pVks~~IAe~l~~spgTIR 41 (79)
T pfam03444 2 LTPVQKEILQALINLYRKKGRAVKGEEIADIIGRNPGTVR 41 (79)
T ss_pred CCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHH
T ss_conf 7789999999999999972998667999999878908899
No 317
>pfam07022 Phage_CI_repr Bacteriophage CI repressor helix-turn-helix domain. This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic.
Probab=55.04 E-value=12 Score=17.05 Aligned_cols=23 Identities=17% Similarity=0.228 Sum_probs=14.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 89899999977899999999999
Q gi|254780611|r 253 VTLENLSSEFEVSRERVRQIEAR 275 (302)
Q Consensus 253 ~Tl~EIa~~lgiS~eRVrQI~~~ 275 (302)
.|..|+|+.|||++..|+.-.++
T Consensus 13 ~t~~eLA~~LgI~~stis~w~~R 35 (65)
T pfam07022 13 KSRSELADHLGVSKSTLSTWYKR 35 (65)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHC
T ss_conf 86999999969888889999986
No 318
>pfam05043 Mga Mga helix-turn-helix domain. M regulator protein trans-acting positive regulator (Mga) is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions. This domain is found in the centre of the Mga proteins. This family also contains a number of bacterial RofA transcriptional regulators that seem to be largely restricted to streptococci. These proteins have been shown to regulate the expression of important bacterial adhesins. This is presumably a DNA-binding domain.
Probab=54.20 E-value=15 Score=16.46 Aligned_cols=49 Identities=14% Similarity=0.304 Sum_probs=34.1
Q ss_pred HHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH-HHCCCCCC
Q ss_conf 9999982788888989999997789999999999999999999997-40122467
Q gi|254780611|r 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK-QVELSSSP 294 (302)
Q Consensus 241 ~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~-~~~~~~~~ 294 (302)
.++..-| .++..|+.+.|+.+.||+..+. +-++++++.|++ .+.+...|
T Consensus 20 ~il~~lf-~~~~~s~~~~a~~l~iS~sTl~----R~ik~l~~~L~~~~l~i~~~~ 69 (87)
T pfam05043 20 QLLKFLF-FHEFFSLTSLAQKLFISESTLY----RLIKKLNKLLKEFDLSITKKP 69 (87)
T ss_pred HHHHHHH-CCCCCCHHHHHHHHCCCHHHHH----HHHHHHHHHHHHCCEEEEECC
T ss_conf 9999998-1899989999999788999999----999999999998596887078
No 319
>pfam00376 MerR MerR family regulatory protein.
Probab=53.86 E-value=9.8 Score=17.74 Aligned_cols=22 Identities=23% Similarity=0.253 Sum_probs=14.1
Q ss_pred CHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 9899999977899999999999
Q gi|254780611|r 254 TLENLSSEFEVSRERVRQIEAR 275 (302)
Q Consensus 254 Tl~EIa~~lgiS~eRVrQI~~~ 275 (302)
|..|+|+.+|||...||.-+++
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~ 22 (38)
T pfam00376 1 TIGEVAKLLGVSPRTLRYYEKI 22 (38)
T ss_pred CHHHHHHHHCCCHHHHHHHHHC
T ss_conf 9899999988799999999986
No 320
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=53.23 E-value=16 Score=16.36 Aligned_cols=35 Identities=17% Similarity=0.187 Sum_probs=24.3
Q ss_pred HHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCC
Q ss_conf 99788786624478882467788861898321100
Q gi|254780611|r 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175 (302)
Q Consensus 141 k~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~ 175 (302)
.+++.++.+......+.++++||+..|+++..+..
T Consensus 10 ~I~~i~~yI~~n~~~~lsl~~lA~~~~~S~~~l~r 44 (127)
T PRK11511 10 TIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQR 44 (127)
T ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHH
T ss_conf 99999999998658999999999998959999999
No 321
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=53.01 E-value=16 Score=16.34 Aligned_cols=22 Identities=9% Similarity=0.265 Sum_probs=11.0
Q ss_pred HHHHHHHHCCCCCCCCCCCCCC
Q ss_conf 4677888618983211000000
Q gi|254780611|r 158 QVVAIAKKLNVSESEVISMNCR 179 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v~~l~~~ 179 (302)
++.+||+..+++..-+..+.+.
T Consensus 27 ~~~eIae~~~Ip~~~L~KIl~~ 48 (141)
T PRK11014 27 SISEVTEVYGVSRNHMVKIINQ 48 (141)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
T ss_conf 4999999879499999999999
No 322
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain; InterPro: IPR006497 This set of protein sequences, defined by an N-terminal domain, represent phage lambda replication protein O and other homologous phage and prophage proteins. ; GO: 0006260 DNA replication.
Probab=52.90 E-value=16 Score=16.33 Aligned_cols=58 Identities=22% Similarity=0.253 Sum_probs=39.6
Q ss_pred HHHHHH--HCCCHHHHHHHH----HHHCCCCC---CCHHHHHHHHC-------CCHHHHHHHHHHHHHHH--HHHHHHHH
Q ss_conf 999996--219999999999----98278888---89899999977-------89999999999999999--99999740
Q gi|254780611|r 227 MLTRSM--SVLNPRERRIFE----ARRLQENP---VTLENLSSEFE-------VSRERVRQIEARAFKKV--QESIQKQV 288 (302)
Q Consensus 227 ~L~~~l--~~L~~rEr~II~----~ry~~~~~---~Tl~EIa~~lg-------iS~eRVrQI~~~AL~kL--R~~l~~~~ 288 (302)
.|.+++ -.|+.||-.|+. .-||.+.+ .|-.+||+..+ +++.+|+ +|+..| |+.|-++-
T Consensus 13 ~L~e~~~~~~L~~Ref~v~~Ai~R~T~Gyn~~~~rvt~~~ia~lt~Pdeakaal~~~~vs----~A~~~L~~~~ilf~~g 88 (104)
T TIGR01610 13 ELLEALAGADLSGREFRVLLAILRLTYGYNKEADRVTASEIAELTKPDEAKAALERKRVS----EAIKSLVRRRILFRQG 88 (104)
T ss_pred HHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHH----HHHHHHHHHHHHHHCC
T ss_conf 788874148784357999999998741566603566688888532831355521344788----9999988754422137
No 323
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=52.61 E-value=16 Score=16.30 Aligned_cols=37 Identities=16% Similarity=0.151 Sum_probs=27.5
Q ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999982788888989999997789999999999999999999
Q gi|254780611|r 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302)
Q Consensus 238 rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302)
=|+.|+...|-.. -|-+.+|++||||.- .+-.|||++
T Consensus 469 fE~~VL~rly~~y--PStRkLAkRLgvSHT-------aIAnKLRqy 505 (511)
T COG3283 469 FERSVLTRLYRSY--PSTRKLAKRLGVSHT-------AIANKLRQY 505 (511)
T ss_pred HHHHHHHHHHHHC--CCHHHHHHHHCCCHH-------HHHHHHHHH
T ss_conf 9999999999859--748899998587379-------999899982
No 324
>TIGR02899 spore_safA spore coat assembly protein SafA; InterPro: IPR014248 This entry represents a domain of about 40 residues long which is found in a variety of enzymes involved in bacterial cell wall degradation , and which may have a general peptidoglycan binding function. Proteins containing this domain include SafA of Bacillus subtilis, which is a protein found at the interface of the spore cortex and spore coat, and which is dependent on SpoVID for its localization. This domain is generally found towards the N-terminus of these proteins. The C-terminal region of these proteins are more variable and may contain blocks of 12-residue and 13-residue repeats, tandem LysM domains (IPR002482 from INTERPRO), or an SCP-like domain (IPR014258 from INTERPRO)..
Probab=52.38 E-value=8.6 Score=18.12 Aligned_cols=15 Identities=40% Similarity=0.769 Sum_probs=6.7
Q ss_pred HHHHHHCCCCCCHHHHHH
Q ss_conf 565555799998889999
Q gi|254780611|r 63 KIAMGYRGYGLPISEVVS 80 (302)
Q Consensus 63 ~iA~~y~~~g~~~~DLiQ 80 (302)
+||+|| |++|+.|++
T Consensus 9 kiA~ky---gV~~~~Li~ 23 (44)
T TIGR02899 9 KIAKKY---GVDLDELIQ 23 (44)
T ss_pred HHHHHH---CCCHHHHHH
T ss_conf 778771---787678864
No 325
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=51.76 E-value=17 Score=16.21 Aligned_cols=26 Identities=15% Similarity=0.095 Sum_probs=21.2
Q ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 78888898999999778999999999
Q gi|254780611|r 248 LQENPVTLENLSSEFEVSRERVRQIE 273 (302)
Q Consensus 248 ~~~~~~Tl~EIa~~lgiS~eRVrQI~ 273 (302)
+.+.+.|++|||...|||...||.--
T Consensus 247 l~~~~~tq~eva~v~~vtevTIrnry 272 (285)
T COG1405 247 LLGERRTQKEVAKVAGVTEVTIRNRY 272 (285)
T ss_pred HHCCCHHHHHHHHHHCCEEEHHHHHH
T ss_conf 71870279999988387220799889
No 326
>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=51.28 E-value=11 Score=17.44 Aligned_cols=25 Identities=24% Similarity=0.320 Sum_probs=14.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 9999999999999999999740122
Q gi|254780611|r 267 ERVRQIEARAFKKVQESIQKQVELS 291 (302)
Q Consensus 267 eRVrQI~~~AL~kLR~~l~~~~~~~ 291 (302)
-|++||-+.|++=+|..-+.++...
T Consensus 34 yRlkei~q~A~Kfm~hskR~~Lt~~ 58 (65)
T smart00803 34 YRIKEIVQEALKFMRHSKRTTLTTS 58 (65)
T ss_pred HHHHHHHHHHHHHHHHHCCCCCCHH
T ss_conf 9999999999999997576757699
No 327
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=51.24 E-value=17 Score=16.16 Aligned_cols=27 Identities=11% Similarity=0.368 Sum_probs=11.4
Q ss_pred HHHHHHHHHHHH-HHHHHHCCCCCCCCH
Q ss_conf 889999998889-989862185345689
Q gi|254780611|r 75 ISEVVSEGNIGL-MQAVKKFDPERGFRL 101 (302)
Q Consensus 75 ~~DLiQeG~iGL-i~Ai~kFDp~kG~~F 101 (302)
+.||-++|.+-= ...+-|-=.++||||
T Consensus 48 Ma~LE~~G~L~qpHTSAGRIPT~kGYR~ 75 (339)
T PRK00082 48 MADLEELGLLEKPHTSSGRIPTDKGYRY 75 (339)
T ss_pred HHHHHHCCCCCCCCCCCCCCCCHHHHHH
T ss_conf 9999978783679899987856789999
No 328
>COG1481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.85 E-value=17 Score=16.12 Aligned_cols=38 Identities=24% Similarity=0.211 Sum_probs=29.6
Q ss_pred HHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCC--CHHHHH
Q ss_conf 621999999999998278888898999999778--999999
Q gi|254780611|r 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEV--SRERVR 270 (302)
Q Consensus 232 l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgi--S~eRVr 270 (302)
+..||++.+.+-.+|-- ....||+|+|+.+.. |+.-|.
T Consensus 251 l~~lpe~l~e~a~LRl~-hpd~SLeeLg~~l~~~iSKSGvn 290 (308)
T COG1481 251 LEKLPEKLREAALLRLE-HPDASLEELGELLEPPISKSGVN 290 (308)
T ss_pred HHHCCHHHHHHHHHHHC-CHHHHHHHHHHHHCCCCCHHHHH
T ss_conf 31179889999999733-80510999999855843688888
No 329
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=50.34 E-value=18 Score=16.06 Aligned_cols=38 Identities=18% Similarity=0.267 Sum_probs=22.7
Q ss_pred HHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 7787565555799998889999998889989862185345
Q gi|254780611|r 59 RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98 (302)
Q Consensus 59 rlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG 98 (302)
+||+.--+.|.= -+...+|-+-+-+|+..++=|+-+..
T Consensus 54 ~LV~~~~~~Y~L--S~~G~iiv~km~~ll~tl~v~e~n~d 91 (260)
T COG4742 54 GLVVQEGDRYSL--SSLGKIIVEKMEPLLDTLEVFEENYD 91 (260)
T ss_pred CCEEECCCEEEE--CCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 987851999873--40089999999999999999973146
No 330
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=50.33 E-value=18 Score=16.06 Aligned_cols=29 Identities=17% Similarity=0.228 Sum_probs=19.2
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHH
Q ss_conf 9999999827888889899999977899999
Q gi|254780611|r 239 ERRIFEARRLQENPVTLENLSSEFEVSRERV 269 (302)
Q Consensus 239 Er~II~~ry~~~~~~Tl~EIa~~lgiS~eRV 269 (302)
|+.+|..-+-.. .+.++.|+.||||+..+
T Consensus 469 Er~~l~~l~~~~--~~~~kaAk~LGISrttL 497 (513)
T PRK10820 469 ERSVLTQLYRNY--PSTRKLAKRLGVSHTAI 497 (513)
T ss_pred HHHHHHHHHHHC--CCHHHHHHHHCCCHHHH
T ss_conf 999999999878--89999999979989999
No 331
>TIGR00370 TIGR00370 conserved hypothetical protein TIGR00370; InterPro: IPR010016 This is an uncharacterised family of proteins of unknown function..
Probab=50.07 E-value=6.7 Score=18.85 Aligned_cols=51 Identities=20% Similarity=0.156 Sum_probs=33.4
Q ss_pred HHHHHHHHCCCHHHHHH-HHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 99999962199999999-9998278888898999999778999999999999
Q gi|254780611|r 226 NMLTRSMSVLNPRERRI-FEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276 (302)
Q Consensus 226 ~~L~~~l~~L~~rEr~I-I~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~A 276 (302)
+.|.+.-+.++...|.| |=--||++.+.-|.++|+.-++|.++|=|||+..
T Consensus 78 erlaeiae~~e~~~R~iEIPV~YGGe~GpDL~~VAk~~qlspe~vi~~Hs~~ 129 (217)
T TIGR00370 78 ERLAEIAEALEVESRFIEIPVVYGGERGPDLEEVAKFNQLSPEEVIDLHSEG 129 (217)
T ss_pred HHHHHHHHHHCCCCCEEEEEEEECCCCCCCHHHHHHHHCCCHHHEEEECCCC
T ss_conf 8998887651458877873047578889898999977178845734404796
No 332
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=49.93 E-value=18 Score=16.02 Aligned_cols=22 Identities=23% Similarity=0.447 Sum_probs=18.8
Q ss_pred CCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 8888989999997789999999
Q gi|254780611|r 250 ENPVTLENLSSEFEVSRERVRQ 271 (302)
Q Consensus 250 ~~~~Tl~EIa~~lgiS~eRVrQ 271 (302)
+.+.|-.|||+.+|+|+-.+|+
T Consensus 176 ~~~~sa~eva~~~giSRvTaRR 197 (239)
T PRK10430 176 DYEFSTDELANEVNISRVSCRK 197 (239)
T ss_pred CCCCCHHHHHHHHCCCHHHHHH
T ss_conf 9984699999885852988999
No 333
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=49.85 E-value=18 Score=16.02 Aligned_cols=22 Identities=32% Similarity=0.370 Sum_probs=13.9
Q ss_pred HHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 62185345689997577899999985320246
Q gi|254780611|r 91 KKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122 (302)
Q Consensus 91 ~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~ 122 (302)
-++|| ++||+ ..|.+++.+...
T Consensus 41 G~vdP----rlSt~------k~Il~aL~e~e~ 62 (187)
T COG3620 41 GKVDP----RLSTV------KRILEALEEAEK 62 (187)
T ss_pred CCCCC----CHHHH------HHHHHHHHHHHC
T ss_conf 88793----08999------999999998546
No 334
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=49.26 E-value=16 Score=16.39 Aligned_cols=12 Identities=17% Similarity=0.487 Sum_probs=6.2
Q ss_pred CCHHHHHHHHHHH
Q ss_conf 6899975778999
Q gi|254780611|r 99 FRLATYSMWWIKA 111 (302)
Q Consensus 99 ~~FsTYA~~wIr~ 111 (302)
+.|+|- +.||.+
T Consensus 105 i~~eTI-Yr~ly~ 116 (318)
T COG2826 105 ISFETI-YRWLYQ 116 (318)
T ss_pred CCHHHH-HHHHHH
T ss_conf 669999-999860
No 335
>pfam05732 RepL Firmicute plasmid replication protein (RepL). This family consists of Firmicute RepL proteins which are involved in plasmid replication.
Probab=49.20 E-value=18 Score=15.95 Aligned_cols=20 Identities=35% Similarity=0.421 Sum_probs=15.7
Q ss_pred CCHHHHHHHHCCCHHHHHHH
Q ss_conf 89899999977899999999
Q gi|254780611|r 253 VTLENLSSEFEVSRERVRQI 272 (302)
Q Consensus 253 ~Tl~EIa~~lgiS~eRVrQI 272 (302)
.|.++||+..|+|.+.|++.
T Consensus 76 ~T~R~lae~~gvs~~TV~~t 95 (165)
T pfam05732 76 MTQREIAEETGISLETVRQT 95 (165)
T ss_pred EEHHHHHHHHCCCHHHHHHH
T ss_conf 87899999839529999999
No 336
>pfam00046 Homeobox Homeobox domain.
Probab=48.44 E-value=19 Score=15.87 Aligned_cols=35 Identities=14% Similarity=0.228 Sum_probs=15.3
Q ss_pred CCHHHHHHHHHHHCCCCC---CCHHHHHHHHCCCHHHH
Q ss_conf 999999999998278888---89899999977899999
Q gi|254780611|r 235 LNPRERRIFEARRLQENP---VTLENLSSEFEVSRERV 269 (302)
Q Consensus 235 L~~rEr~II~~ry~~~~~---~Tl~EIa~~lgiS~eRV 269 (302)
.++.+..+|...|-.+.. ....+||..+|+|...|
T Consensus 7 ft~~Q~~~Le~~F~~~~~P~~~~~~~LA~~l~l~~~~V 44 (57)
T pfam00046 7 FTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQV 44 (57)
T ss_pred CCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCHHHH
T ss_conf 99999999999998579999899999999839998997
No 337
>pfam03811 Ins_element1 Insertion element protein.
Probab=48.44 E-value=19 Score=15.87 Aligned_cols=28 Identities=11% Similarity=0.163 Sum_probs=20.8
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHH
Q ss_conf 9999999827888889899999977899999
Q gi|254780611|r 239 ERRIFEARRLQENPVTLENLSSEFEVSRERV 269 (302)
Q Consensus 239 Er~II~~ry~~~~~~Tl~EIa~~lgiS~eRV 269 (302)
...|+.+.+ ++...+++|..|+||...|
T Consensus 53 keqiv~m~~---nG~GiRdtaRvl~Is~nTV 80 (88)
T pfam03811 53 KEQIVDMAM---NGAGCRYTARTLKIGINTV 80 (88)
T ss_pred HHHHHHHHH---CCCCHHHHHHHHCCCHHHH
T ss_conf 899999976---7985404478737568999
No 338
>PRK13805 bifunctional acetaldehyde-CoA/alcohol dehydrogenase; Provisional
Probab=48.34 E-value=19 Score=15.86 Aligned_cols=58 Identities=17% Similarity=0.321 Sum_probs=30.5
Q ss_pred CHHHHHHHH-----------HHHHHHHHHHHHHHCC-CCCCHHHHHHHHHHHHHHHHHHCC---CCCCCCHHHHHHH
Q ss_conf 599999999-----------9430778756555579-999888999999888998986218---5345689997577
Q gi|254780611|r 46 DLSAAHRLV-----------TSHLRLVVKIAMGYRG-YGLPISEVVSEGNIGLMQAVKKFD---PERGFRLATYSMW 107 (302)
Q Consensus 46 d~~Ar~~Li-----------~~nlrlV~~iA~~y~~-~g~~~~DLiQeG~iGLi~Ai~kFD---p~kG~~FsTYA~~ 107 (302)
|.+||+.+- .+.|++|+++|+...+ .+++. -.+|-=|+-.+-+|+ |.|-..|+-|.++
T Consensus 699 d~eARe~M~~As~~AG~AF~na~lG~~HamaH~lG~~~~ipH----G~aNAilLP~Vi~fNa~~p~k~~~~p~y~~~ 771 (862)
T PRK13805 699 DPEAREKMHNAATIAGMAFANAFLGICHSMAHKLGAEFHIPH----GRANAILIPHVIRYNATDPTKQAAFPQYEYP 771 (862)
T ss_pred CHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCH----HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf 899999999999999999968517887886247514868655----8899999899999745575322333212333
No 339
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=47.41 E-value=19 Score=15.77 Aligned_cols=23 Identities=30% Similarity=0.287 Sum_probs=15.2
Q ss_pred HHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf 46778886189832110000001
Q gi|254780611|r 158 QVVAIAKKLNVSESEVISMNCRL 180 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v~~l~~~~ 180 (302)
+..++|+.++++...+-.+...+
T Consensus 56 t~~eLa~~l~id~~tvt~~ldrL 78 (144)
T PRK11512 56 TPVELKKVLSVDLGALTRMLDRL 78 (144)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 99999999788887899999999
No 340
>pfam02969 TAF TATA box binding protein associated factor (TAF). TAF proteins adopt a histone-like fold.
Probab=47.20 E-value=14 Score=16.64 Aligned_cols=23 Identities=22% Similarity=0.286 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 99999999999999999997401
Q gi|254780611|r 267 ERVRQIEARAFKKVQESIQKQVE 289 (302)
Q Consensus 267 eRVrQI~~~AL~kLR~~l~~~~~ 289 (302)
-|+++|-+.|++=+|..-+.++-
T Consensus 35 yRl~eiiqeA~KFMrhskR~~Lt 57 (66)
T pfam02969 35 YRLKEIVQDAAKFMRHSKRQKLT 57 (66)
T ss_pred HHHHHHHHHHHHHHHHHCCCCCC
T ss_conf 99999999999999986757787
No 341
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=46.86 E-value=13 Score=17.03 Aligned_cols=16 Identities=19% Similarity=0.293 Sum_probs=8.7
Q ss_pred HHHHHHCCCHHHHHHH
Q ss_conf 9999977899999999
Q gi|254780611|r 257 NLSSEFEVSRERVRQI 272 (302)
Q Consensus 257 EIa~~lgiS~eRVrQI 272 (302)
+||+..|||...||+.
T Consensus 2 diA~~~gvS~~TVSr~ 17 (52)
T cd01392 2 DIARAAGVSVATVSRV 17 (52)
T ss_pred HHHHHHCCCHHHHHHH
T ss_conf 2888878599999999
No 342
>PRK13869 plasmid-partitioning protein RepA; Provisional
Probab=46.83 E-value=20 Score=15.71 Aligned_cols=12 Identities=0% Similarity=0.149 Sum_probs=5.4
Q ss_pred HHHHHHHHHHHH
Q ss_conf 889999998889
Q gi|254780611|r 75 ISEVVSEGNIGL 86 (302)
Q Consensus 75 ~~DLiQeG~iGL 86 (302)
+-||=-.|++..
T Consensus 155 lIDLDPQgnlS~ 166 (405)
T PRK13869 155 AVDLDPQASLSA 166 (405)
T ss_pred EEECCHHHHHHH
T ss_conf 996456178889
No 343
>KOG0915 consensus
Probab=46.71 E-value=19 Score=15.82 Aligned_cols=39 Identities=31% Similarity=0.271 Sum_probs=17.7
Q ss_pred HCCHHHHHHHHHHHHHHHHHHHH--HHCCCCCCHHHHHHHHHHH
Q ss_conf 28599999999943077875655--5579999888999999888
Q gi|254780611|r 44 HGDLSAAHRLVTSHLRLVVKIAM--GYRGYGLPISEVVSEGNIG 85 (302)
Q Consensus 44 ~gd~~Ar~~Li~~nlrlV~~iA~--~y~~~g~~~~DLiQeG~iG 85 (302)
-||..-++.||.+ ||-..+. |-.+.-..--.|+|+|++|
T Consensus 891 lgd~~~k~~LV~s---L~~tl~~Gkr~~~~vs~eTelFq~G~Lg 931 (1702)
T KOG0915 891 LGDSSLKKSLVDS---LVNTLTGGKRKAIKVSEETELFQEGTLG 931 (1702)
T ss_pred CCCCHHHHHHHHH---HHHHHHCCCCCCCEECCCHHHCCCCCCC
T ss_conf 0775137999999---9998742663241214531100477678
No 344
>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=46.28 E-value=20 Score=15.66 Aligned_cols=19 Identities=21% Similarity=0.445 Sum_probs=13.1
Q ss_pred CCHHHHHHHHCCCHHHHHH
Q ss_conf 8989999997789999999
Q gi|254780611|r 253 VTLENLSSEFEVSRERVRQ 271 (302)
Q Consensus 253 ~Tl~EIa~~lgiS~eRVrQ 271 (302)
.+=+|+|+.+||+...||+
T Consensus 28 vSS~eLa~~~gv~~aqiRK 46 (49)
T pfam06971 28 VSSKELSEAIGIDAAQIRK 46 (49)
T ss_pred ECHHHHHHHHCCCHHHHHC
T ss_conf 9799999997939999614
No 345
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=45.82 E-value=14 Score=16.68 Aligned_cols=29 Identities=17% Similarity=0.119 Sum_probs=13.1
Q ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHH
Q ss_conf 99999999827888889899999977899999
Q gi|254780611|r 238 RERRIFEARRLQENPVTLENLSSEFEVSRERV 269 (302)
Q Consensus 238 rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRV 269 (302)
+++..+...|+-+ =-+.+++.+|....-+
T Consensus 467 ~~k~~~~~kyipe---vA~~l~~i~~~~~~~~ 495 (533)
T PRK04184 467 RKKYKTIEKYLPE---IARKLAEITGKPVEDI 495 (533)
T ss_pred HHHHHHHHHHHHH---HHHHHHHHHCCCCCCH
T ss_conf 9999999998899---9999999858994105
No 346
>pfam08822 DUF1804 Protein of unknown function (DUF1804). This family of bacterial protein is uncharacterized.
Probab=45.82 E-value=20 Score=15.61 Aligned_cols=19 Identities=32% Similarity=0.356 Sum_probs=11.7
Q ss_pred HHHHHHHCCCCCCCCHHHHHHHH
Q ss_conf 99898621853456899975778
Q gi|254780611|r 86 LMQAVKKFDPERGFRLATYSMWW 108 (302)
Q Consensus 86 Li~Ai~kFDp~kG~~FsTYA~~w 108 (302)
|=.|+.++ |+.|+|=..|-
T Consensus 22 Le~aA~~~----gV~~~TArrWK 40 (165)
T pfam08822 22 LEVAAAKA----GVSYSTARRWK 40 (165)
T ss_pred HHHHHHHC----CCCHHHHHHHH
T ss_conf 99999880----99888899999
No 347
>pfam10078 DUF2316 Uncharacterized protein conserved in bacteria (DUF2316). Members of this family of hypothetical bacterial proteins have no known function.
Probab=45.51 E-value=21 Score=15.58 Aligned_cols=18 Identities=28% Similarity=0.464 Sum_probs=8.6
Q ss_pred HHHHHHHCCCCCCCCCCC
Q ss_conf 677888618983211000
Q gi|254780611|r 159 VVAIAKKLNVSESEVISM 176 (302)
Q Consensus 159 ~~eiA~~Lgis~~~v~~l 176 (302)
++++|+.|++++.++...
T Consensus 26 ~~~iA~dL~~s~~~ve~v 43 (89)
T pfam10078 26 IEQVAKDLNTTPEKVEAL 43 (89)
T ss_pred HHHHHHHHCCCHHHHHHH
T ss_conf 999998949999999999
No 348
>PRK09463 fadE acyl-CoA dehydrogenase; Reviewed
Probab=45.35 E-value=21 Score=15.56 Aligned_cols=39 Identities=28% Similarity=0.397 Sum_probs=21.9
Q ss_pred HCCHHHHHHH------HHHHHHHHHHHHHHHCCCCCCHHH--HHHHH
Q ss_conf 2859999999------994307787565555799998889--99999
Q gi|254780611|r 44 HGDLSAAHRL------VTSHLRLVVKIAMGYRGYGLPISE--VVSEG 82 (302)
Q Consensus 44 ~gd~~Ar~~L------i~~nlrlV~~iA~~y~~~g~~~~D--LiQeG 82 (302)
.|+...+++| |.++|.|.-.+-|+|...|-+-+| |++.+
T Consensus 560 GG~LKrkE~lSaRLgDvLS~LYlasA~LKryed~Gr~~~Dlplv~wa 606 (761)
T PRK09463 560 GGSLKRRERLSARLGDILSQLYLASAVLKRYEDEGRPEEDLPLVHWA 606 (761)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf 14566888862477999999999999999998559975566999999
No 349
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID; InterPro: IPR014208 Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation ..
Probab=45.01 E-value=20 Score=15.71 Aligned_cols=25 Identities=24% Similarity=0.357 Sum_probs=15.6
Q ss_pred HCCCCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 2788888989999997789999999
Q gi|254780611|r 247 RLQENPVTLENLSSEFEVSRERVRQ 271 (302)
Q Consensus 247 y~~~~~~Tl~EIa~~lgiS~eRVrQ 271 (302)
|.-....|.+++|..||||+..|..
T Consensus 14 ~i~~~~~t~r~~a~~fGvskst~hk 38 (80)
T TIGR02844 14 YIVETKATVRETAKVFGVSKSTVHK 38 (80)
T ss_pred HHHHHHHHHHHHHHHHCCHHHHHHH
T ss_conf 9997689999999883432567766
No 350
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.08 E-value=22 Score=15.44 Aligned_cols=24 Identities=25% Similarity=0.145 Sum_probs=15.5
Q ss_pred CCHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf 882467788861898321100000
Q gi|254780611|r 155 KPEQVVAIAKKLNVSESEVISMNC 178 (302)
Q Consensus 155 ~~~~~~eiA~~Lgis~~~v~~l~~ 178 (302)
.+-++++||.+||+++.++..+++
T Consensus 22 ~~LS~~~iA~~Ln~t~~~lekil~ 45 (97)
T COG4367 22 CPLSDEEIATALNWTEVKLEKILQ 45 (97)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 645299999995887999999998
No 351
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=44.01 E-value=22 Score=15.43 Aligned_cols=26 Identities=12% Similarity=0.249 Sum_probs=13.5
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 88898999999778999999999999
Q gi|254780611|r 251 NPVTLENLSSEFEVSRERVRQIEARA 276 (302)
Q Consensus 251 ~~~Tl~EIa~~lgiS~eRVrQI~~~A 276 (302)
++.|+.+||+.+|+|+...+++=++.
T Consensus 206 e~IsL~diA~~~~lS~~y~sr~FKk~ 231 (302)
T PRK10371 206 QALTINDVAEHVKLNANYAMGIFQRV 231 (302)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 99999999989795999999999999
No 352
>PRK10870 transcriptional repressor MprA; Provisional
Probab=43.43 E-value=22 Score=15.37 Aligned_cols=22 Identities=14% Similarity=0.140 Sum_probs=13.3
Q ss_pred CCHHHHHHHHHCCCCCCCCCCC
Q ss_conf 8824677888618983211000
Q gi|254780611|r 155 KPEQVVAIAKKLNVSESEVISM 176 (302)
Q Consensus 155 ~~~~~~eiA~~Lgis~~~v~~l 176 (302)
.+-+..+||+.++++...+-.+
T Consensus 70 ~~l~PseLa~~l~~s~a~iTr~ 91 (176)
T PRK10870 70 HSIQPSELSCALGSSRTNATRI 91 (176)
T ss_pred CCCCHHHHHHHHCCCHHHHHHH
T ss_conf 9859899999977871019999
No 353
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=43.29 E-value=15 Score=16.57 Aligned_cols=22 Identities=23% Similarity=0.225 Sum_probs=9.7
Q ss_pred CCCCHHHHHHHHH----CCCCCCCCC
Q ss_conf 7888246778886----189832110
Q gi|254780611|r 153 NLKPEQVVAIAKK----LNVSESEVI 174 (302)
Q Consensus 153 ~~~~~~~~eiA~~----Lgis~~~v~ 174 (302)
.++|+++.++... .|++..+..
T Consensus 144 fptpe~l~~~~~~~l~~~g~s~~Ka~ 169 (285)
T COG0122 144 FPTPEQLAAADEEALRRCGLSGRKAE 169 (285)
T ss_pred CCCHHHHHHCCHHHHHHHCCCHHHHH
T ss_conf 98999998479999988378577899
No 354
>cd07285 PX_SNX9 The phosphoinositide binding Phox Homology domain of Sorting Nexin 9. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX9, also known as SH3PX1, is a cytosolic protein that interacts with proteins associated with clathrin-coated pits such as Cdc-42-associated tyrosine kinase 2 (ACK2). It contains an N-terminal Src Homology 3 (SH3) domain, a PX domain, and a C-terminal Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane curvature. T
Probab=43.28 E-value=10 Score=17.60 Aligned_cols=16 Identities=25% Similarity=0.708 Sum_probs=8.0
Q ss_pred CCCCCCCH---HHHHHHHH
Q ss_conf 85345689---99757789
Q gi|254780611|r 94 DPERGFRL---ATYSMWWI 109 (302)
Q Consensus 94 Dp~kG~~F---sTYA~~wI 109 (302)
||.|..+| .||-+|-|
T Consensus 7 dP~k~~~~~G~~sYi~Y~v 25 (126)
T cd07285 7 DPRKGSKMYGLKSYIEYQL 25 (126)
T ss_pred CCCCCCCCCCCCCEEEEEE
T ss_conf 9652357678533689998
No 355
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=43.09 E-value=23 Score=15.34 Aligned_cols=24 Identities=25% Similarity=0.422 Sum_probs=19.8
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 888889899999977899999999
Q gi|254780611|r 249 QENPVTLENLSSEFEVSRERVRQI 272 (302)
Q Consensus 249 ~~~~~Tl~EIa~~lgiS~eRVrQI 272 (302)
.+.+.|-.|+|+.+|+|+-.+|+-
T Consensus 170 ~~~~~Taeela~~~giSRvTaRRY 193 (224)
T COG4565 170 PDQELTAEELAQALGISRVTARRY 193 (224)
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 577647999998837219999999
No 356
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=42.84 E-value=23 Score=15.31 Aligned_cols=10 Identities=60% Similarity=0.807 Sum_probs=6.3
Q ss_pred HHHHHHHHHH
Q ss_conf 8899999988
Q gi|254780611|r 75 ISEVVSEGNI 84 (302)
Q Consensus 75 ~~DLiQeG~i 84 (302)
+-+|+.||.+
T Consensus 46 iK~Lv~eG~i 55 (260)
T COG1497 46 IKELVKEGLI 55 (260)
T ss_pred HHHHHHCCCE
T ss_conf 9999866466
No 357
>PRK08359 transcription factor; Validated
Probab=42.05 E-value=23 Score=15.23 Aligned_cols=40 Identities=15% Similarity=0.316 Sum_probs=30.8
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHH---HHHHHHHHHHHCC
Q ss_conf 888989999997789999999999999---9999999974012
Q gi|254780611|r 251 NPVTLENLSSEFEVSRERVRQIEARAF---KKVQESIQKQVEL 290 (302)
Q Consensus 251 ~~~Tl~EIa~~lgiS~eRVrQI~~~AL---~kLR~~l~~~~~~ 290 (302)
.++|++|+|..++++..-|+.|+.-=+ ..+.+.|++-+.+
T Consensus 95 ~GlSqeeLA~ki~ek~nvI~kiE~G~l~P~~~~akKLEk~L~I 137 (175)
T PRK08359 95 SGLSYEELSHKVGLSVNDLRRIAHGEYTPTIEEARKLERFFKI 137 (175)
T ss_pred CCCCHHHHHHHHCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCE
T ss_conf 5999999999972229999999838879998999999998490
No 358
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=41.96 E-value=23 Score=15.22 Aligned_cols=35 Identities=20% Similarity=0.185 Sum_probs=23.4
Q ss_pred HHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCC
Q ss_conf 97887866244788824677888618983211000
Q gi|254780611|r 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176 (302)
Q Consensus 142 ~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l 176 (302)
++..++.+.++...+.++++||+..|+|+..+..+
T Consensus 7 i~~~~~yI~~h~~~~i~l~~lA~~~~~S~~~l~r~ 41 (107)
T PRK10219 7 IQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRM 41 (107)
T ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 99999999986699999999998989399999999
No 359
>pfam09317 DUF1974 Domain of unknown function (DUF1974). Members of this family of functionally uncharacterized domains are predominantly found in various prokaryotic acyl-coenzyme a dehydrogenases.
Probab=41.49 E-value=24 Score=15.18 Aligned_cols=67 Identities=24% Similarity=0.342 Sum_probs=39.8
Q ss_pred CHHHHHHHHHHHCCCC-CCHHHHHHHHHHHHHHCCHHHHHHH------HHHHHHHHHHHHHHHCCCCCCHHHH--HHHH
Q ss_conf 4059999998407999-9989999999999982859999999------9943077875655557999988899--9999
Q gi|254780611|r 13 EIGLSRYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRL------VTSHLRLVVKIAMGYRGYGLPISEV--VSEG 82 (302)
Q Consensus 13 ~~~~~~yl~~i~~~~~-Lt~eee~~l~~~~~~~gd~~Ar~~L------i~~nlrlV~~iA~~y~~~g~~~~DL--iQeG 82 (302)
+.....|.+.++++.- +.---...++ --.|+...+++| |.++|.|.-.+-|+|...|-+-+|+ ++.+
T Consensus 60 ~~~~~~yyr~l~r~Sa~fAl~aD~am~---~LGG~LKrkE~lSaRlgDvLS~LYlasA~LKryed~g~~~~dlpl~~wa 135 (284)
T pfam09317 60 DGETKRYYRQLNRLSAALALLADVAML---VLGGDLKRKERLSARLGDVLSQLYLASAVLKRYEDEGRPEEDLPLVHWA 135 (284)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf 940189999999999999999998999---9727888999986576899999999999999999759975356999999
No 360
>COG3711 BglG Transcriptional antiterminator [Transcription]
Probab=40.95 E-value=24 Score=15.12 Aligned_cols=14 Identities=14% Similarity=-0.076 Sum_probs=6.1
Q ss_pred CCHHHHHHHHHHHC
Q ss_conf 99999999999827
Q gi|254780611|r 235 LNPRERRIFEARRL 248 (302)
Q Consensus 235 L~~rEr~II~~ry~ 248 (302)
+|+.|---|.++||
T Consensus 354 i~edEiafIalHf~ 367 (491)
T COG3711 354 LPEDEIAFIALHFG 367 (491)
T ss_pred CCHHHHHHHHHHHH
T ss_conf 98899999999999
No 361
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR; InterPro: IPR014075 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly . The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen . This entry represents members of the SufR cyanobacterial protein family of transcriptional regulators that control the SUF system. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus..
Probab=40.54 E-value=25 Score=15.08 Aligned_cols=22 Identities=27% Similarity=0.274 Sum_probs=12.5
Q ss_pred HHHHHHHCCCCCCCCCCCCCCC
Q ss_conf 6778886189832110000001
Q gi|254780611|r 159 VVAIAKKLNVSESEVISMNCRL 180 (302)
Q Consensus 159 ~~eiA~~Lgis~~~v~~l~~~~ 180 (302)
..+||+.|+||+.-|+..++-+
T Consensus 18 A~~lA~~L~iSpQAvRrHLKDL 39 (215)
T TIGR02702 18 ALALAEELAISPQAVRRHLKDL 39 (215)
T ss_pred HHHHHHHHCCCHHHHHHHHHHH
T ss_conf 9999997278867887654332
No 362
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=40.50 E-value=25 Score=15.08 Aligned_cols=28 Identities=32% Similarity=0.553 Sum_probs=12.2
Q ss_pred CCCHHHHHHHHHHHHHHHHHHCCCCCCCCH
Q ss_conf 998889999998889989862185345689
Q gi|254780611|r 72 GLPISEVVSEGNIGLMQAVKKFDPERGFRL 101 (302)
Q Consensus 72 g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~F 101 (302)
|++..-|-=---+||+....+ .+-|++.
T Consensus 12 gvs~~TLRyYe~~GLl~P~~r--~~nGYR~ 39 (172)
T cd04790 12 GLSRSTLLYYERIGLLSPSAR--SESNYRL 39 (172)
T ss_pred CCCHHHHHHHHHCCCCCCCCC--CCCCCCC
T ss_conf 949889999998879899884--9998707
No 363
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=40.34 E-value=19 Score=15.83 Aligned_cols=15 Identities=27% Similarity=0.465 Sum_probs=6.2
Q ss_pred HHHHHHCCCHHHHHH
Q ss_conf 999997789999999
Q gi|254780611|r 257 NLSSEFEVSRERVRQ 271 (302)
Q Consensus 257 EIa~~lgiS~eRVrQ 271 (302)
.+|..++.-..-++.
T Consensus 488 ~la~il~~~~~~i~~ 502 (538)
T COG1389 488 KLAEILEKPEEDIRE 502 (538)
T ss_pred HHHHHHCCCCHHHHH
T ss_conf 999985688413558
No 364
>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=40.32 E-value=22 Score=15.39 Aligned_cols=21 Identities=19% Similarity=0.067 Sum_probs=16.4
Q ss_pred HHHHHHHHCCCCCCCCCCCCC
Q ss_conf 467788861898321100000
Q gi|254780611|r 158 QVVAIAKKLNVSESEVISMNC 178 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v~~l~~ 178 (302)
++-++|+.+|+++..++-+..
T Consensus 2 tIgevAk~~gvs~~TlRyYE~ 22 (108)
T cd01107 2 TIGEFAKLSNLSIKALRYYDK 22 (108)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
T ss_conf 789999998959999999998
No 365
>pfam11242 DUF2774 Protein of unknown function (DUF2774). This is a viral family of proteins with unknown function.
Probab=40.03 E-value=25 Score=15.03 Aligned_cols=28 Identities=11% Similarity=0.313 Sum_probs=19.8
Q ss_pred HHCCCCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 8278888898999999778999999999
Q gi|254780611|r 246 RRLQENPVTLENLSSEFEVSRERVRQIE 273 (302)
Q Consensus 246 ry~~~~~~Tl~EIa~~lgiS~eRVrQI~ 273 (302)
+|+.+.++++-|||+.+|++..-|-.+-
T Consensus 7 h~lhE~g~~FveIAk~~~i~a~dva~~w 34 (63)
T pfam11242 7 HFLHESGLGFVEIAKKYDIRAKDVAKLW 34 (63)
T ss_pred HHHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 7798715669999999598878899999
No 366
>pfam08280 HTH_Mga M protein trans-acting positive regulator (MGA) HTH domain. Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions.
Probab=39.46 E-value=26 Score=14.97 Aligned_cols=45 Identities=16% Similarity=0.336 Sum_probs=27.2
Q ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999827888889899999977899999999999999999999974
Q gi|254780611|r 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287 (302)
Q Consensus 238 rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~ 287 (302)
|+..++.+-+= ...+++.|+|+.+|+|.-.++ .-+..|+..+...
T Consensus 6 rk~~Ll~lL~~-~~~~~l~el~~~l~ls~~tl~----~~i~~L~~~f~~~ 50 (59)
T pfam08280 6 RKLKLLELLTE-NKSITLDELAKQLGLSELTLK----SYIHELNELFPDE 50 (59)
T ss_pred HHHHHHHHHHC-CCCEEHHHHHHHCCCCHHHHH----HHHHHHHHHCCCC
T ss_conf 99999999980-883649999988099799999----9999999873764
No 367
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=39.18 E-value=23 Score=15.21 Aligned_cols=20 Identities=20% Similarity=0.336 Sum_probs=16.3
Q ss_pred HHHHHHHCCCCCCCCCCCCC
Q ss_conf 67788861898321100000
Q gi|254780611|r 159 VVAIAKKLNVSESEVISMNC 178 (302)
Q Consensus 159 ~~eiA~~Lgis~~~v~~l~~ 178 (302)
+.|+|+..|++++.++-+..
T Consensus 3 i~ElA~~~Gvs~~tiR~YE~ 22 (99)
T cd04772 3 TVDLARAIGLSPQTVRNYES 22 (99)
T ss_pred HHHHHHHHCCCHHHHHHHHH
T ss_conf 89999998969999999999
No 368
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=38.79 E-value=26 Score=14.90 Aligned_cols=49 Identities=20% Similarity=0.318 Sum_probs=41.0
Q ss_pred HCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 219999999999982788888989999997789999999999999999999
Q gi|254780611|r 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302)
Q Consensus 233 ~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302)
-.|++..|--+.+|-..+ +|-.|||..|=|+...+-|-.-+|-.+++..
T Consensus 119 Pal~~~~riALtLR~v~G--Ls~~eIArAFLv~e~am~QRivRAK~ri~~a 167 (415)
T COG4941 119 PALPPEQRIALTLRLVGG--LSTAEIARAFLVPEAAMAQRIVRAKARIREA 167 (415)
T ss_pred CCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCCHHHHHHHHHHHHHHHHC
T ss_conf 889722478899999828--7599999998078078999999999999853
No 369
>pfam00382 TFIIB Transcription factor TFIIB repeat.
Probab=38.67 E-value=21 Score=15.59 Aligned_cols=19 Identities=37% Similarity=0.370 Sum_probs=15.6
Q ss_pred CCCCCCHHHHHHHHCCCHH
Q ss_conf 8888898999999778999
Q gi|254780611|r 249 QENPVTLENLSSEFEVSRE 267 (302)
Q Consensus 249 ~~~~~Tl~EIa~~lgiS~e 267 (302)
.+.|.|++||++..|||.-
T Consensus 51 ~~~~rt~~eia~v~~vs~~ 69 (71)
T pfam00382 51 EEVKRTLKEISSVAQVSEK 69 (71)
T ss_pred CCCCCCHHHHHHHHCCCCC
T ss_conf 0899899999999689878
No 370
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=38.37 E-value=27 Score=14.86 Aligned_cols=44 Identities=18% Similarity=0.183 Sum_probs=33.7
Q ss_pred HHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 999962199999999999827888889899999977899999999999
Q gi|254780611|r 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275 (302)
Q Consensus 228 L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~ 275 (302)
.......|++-|-..|+-.++ +|+.+-|..||+|...|+.=|+.
T Consensus 37 ~l~~~~~ls~~eIk~iRe~~~----lSq~vFA~~L~vs~~Tv~~WEqG 80 (104)
T COG2944 37 CLLKVKTLSPTEIKAIREKLG----LSQPVFARYLGVSVSTVRKWEQG 80 (104)
T ss_pred HHCCCCCCCHHHHHHHHHHHC----CCHHHHHHHHCCCHHHHHHHHCC
T ss_conf 523678998899999999828----88999999988879999999817
No 371
>KOG0723 consensus
Probab=37.81 E-value=27 Score=14.80 Aligned_cols=21 Identities=10% Similarity=-0.043 Sum_probs=10.9
Q ss_pred CCCCCCHHHHHHHHCCCHHHH
Q ss_conf 888889899999977899999
Q gi|254780611|r 249 QENPVTLENLSSEFEVSRERV 269 (302)
Q Consensus 249 ~~~~~Tl~EIa~~lgiS~eRV 269 (302)
.+..||-+|-+.+||||..-.
T Consensus 49 F~~kMsr~EA~lIL~v~~s~~ 69 (112)
T KOG0723 49 FEPKMSRREAALILGVTPSLD 69 (112)
T ss_pred CCCCCCHHHHHHHHCCCCCCC
T ss_conf 553215688998827875456
No 372
>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=37.59 E-value=26 Score=14.96 Aligned_cols=21 Identities=10% Similarity=0.186 Sum_probs=16.4
Q ss_pred HHHHHHHHCCCCCCCCCCCCC
Q ss_conf 467788861898321100000
Q gi|254780611|r 158 QVVAIAKKLNVSESEVISMNC 178 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v~~l~~ 178 (302)
++-|+|+..|++...++-+..
T Consensus 2 tIgelA~~~gvs~~TiRyYE~ 22 (120)
T cd04781 2 DIAEVARQSGLPASTLRYYEE 22 (120)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
T ss_conf 689999998868898989996
No 373
>KOG3251 consensus
Probab=37.52 E-value=27 Score=14.77 Aligned_cols=24 Identities=21% Similarity=0.372 Sum_probs=21.4
Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 899999977899999999999999
Q gi|254780611|r 255 LENLSSEFEVSRERVRQIEARAFK 278 (302)
Q Consensus 255 l~EIa~~lgiS~eRVrQI~~~AL~ 278 (302)
...++..+|+|...+++|+++...
T Consensus 166 i~~~~ntLGlSn~ti~lIeRR~~~ 189 (213)
T KOG3251 166 ILDILNTLGLSNQTIRLIERRVRE 189 (213)
T ss_pred HHHHHHHCCCCHHHHHHHHHHHHH
T ss_conf 999998608709899999999876
No 374
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=37.41 E-value=26 Score=14.91 Aligned_cols=21 Identities=19% Similarity=0.146 Sum_probs=15.9
Q ss_pred HHHHHHHHCCCCCCCCCCCCC
Q ss_conf 467788861898321100000
Q gi|254780611|r 158 QVVAIAKKLNVSESEVISMNC 178 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v~~l~~ 178 (302)
++-|+|+..|+++..++-+..
T Consensus 2 ~Ige~A~~~gvs~~TlRyYe~ 22 (133)
T cd04787 2 KVKELANAAGVTPDTVRFYTR 22 (133)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
T ss_conf 689999998978999999998
No 375
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=36.94 E-value=28 Score=14.71 Aligned_cols=36 Identities=17% Similarity=0.278 Sum_probs=16.4
Q ss_pred CCHHHHHHHHHHHCCCC---CCCHHHHHHHHCCCHHHHH
Q ss_conf 99999999999827888---8898999999778999999
Q gi|254780611|r 235 LNPRERRIFEARRLQEN---PVTLENLSSEFEVSRERVR 270 (302)
Q Consensus 235 L~~rEr~II~~ry~~~~---~~Tl~EIa~~lgiS~eRVr 270 (302)
+++.+..+|...|..+. ..+..+||..+|+|...|+
T Consensus 7 ~~~~~~~~L~~~F~~~~~P~~~~~~~La~~~~l~~~qV~ 45 (59)
T cd00086 7 FTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVK 45 (59)
T ss_pred CCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCHHHHH
T ss_conf 999999999999963799999999999999792999999
No 376
>cd07311 terB_like_1 tellurium resistance terB-like protein, subgroup 1. This family includes several uncharacterized bacterial proteins. The prototype of this CD is tellurite resistance protein from Nostoc punctiforme that belongs to COG3793. Its precise biological function and its mechanism responsible for tellurium resistance still remains rather poorly understood.
Probab=36.80 E-value=28 Score=14.70 Aligned_cols=30 Identities=23% Similarity=0.344 Sum_probs=22.6
Q ss_pred CCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 199999999999827888889899999977899999999999
Q gi|254780611|r 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275 (302)
Q Consensus 234 ~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~ 275 (302)
.+++.|+..| +.+|..||||.+.|-||+.-
T Consensus 104 ~~~~~E~~~i------------~~~a~~LGI~ed~V~~leel 133 (150)
T cd07311 104 ELSPGEVAAV------------RKAASLLGISEDEVQKLEEI 133 (150)
T ss_pred CCCHHHHHHH------------HHHHHHHCCCHHHHHHHHHH
T ss_conf 7488899999------------99999929979999999999
No 377
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=36.72 E-value=28 Score=14.69 Aligned_cols=21 Identities=19% Similarity=0.233 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHHH
Q ss_conf 077875655557999988899999988
Q gi|254780611|r 58 LRLVVKIAMGYRGYGLPISEVVSEGNI 84 (302)
Q Consensus 58 lrlV~~iA~~y~~~g~~~~DLiQeG~i 84 (302)
+++=.+-++++ +..|+..|.+
T Consensus 29 ~glpksT~~Rl------L~tL~~~G~v 49 (246)
T COG1414 29 LGLPKSTVHRL------LQTLVELGYV 49 (246)
T ss_pred HCCCHHHHHHH------HHHHHHCCCE
T ss_conf 79198899999------9999978988
No 378
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=36.70 E-value=28 Score=14.69 Aligned_cols=17 Identities=6% Similarity=0.098 Sum_probs=11.0
Q ss_pred HHHHHHHHHHHCCCCCC
Q ss_conf 07787565555799998
Q gi|254780611|r 58 LRLVVKIAMGYRGYGLP 74 (302)
Q Consensus 58 lrlV~~iA~~y~~~g~~ 74 (302)
...+.+.||+|.+++++
T Consensus 86 Yp~~i~aaKnl~e~ki~ 102 (321)
T COG3888 86 YPFFISAAKNLEERKIS 102 (321)
T ss_pred CHHHHHHHHHHHHCCCE
T ss_conf 12575898766443640
No 379
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=36.67 E-value=28 Score=14.72 Aligned_cols=21 Identities=19% Similarity=0.082 Sum_probs=16.5
Q ss_pred HHHHHHHHCCCCCCCCCCCCC
Q ss_conf 467788861898321100000
Q gi|254780611|r 158 QVVAIAKKLNVSESEVISMNC 178 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v~~l~~ 178 (302)
++.|+|+.+|++...++-+..
T Consensus 2 tI~e~a~~~gvs~~tlR~ye~ 22 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
T ss_conf 788999998969999999998
No 380
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=36.15 E-value=12 Score=17.07 Aligned_cols=15 Identities=20% Similarity=0.330 Sum_probs=8.8
Q ss_pred HHHHHHHHCCCCCCC
Q ss_conf 467788861898321
Q gi|254780611|r 158 QVVAIAKKLNVSESE 172 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~ 172 (302)
...+|++++|+++..
T Consensus 29 ~a~~I~~~~gi~~~~ 43 (121)
T COG0099 29 RAKEICKKAGIDPDK 43 (121)
T ss_pred HHHHHHHHCCCCHHH
T ss_conf 999999991988667
No 381
>PRK13503 transcriptional activator RhaS; Provisional
Probab=35.80 E-value=29 Score=14.60 Aligned_cols=18 Identities=17% Similarity=0.163 Sum_probs=8.2
Q ss_pred CCHHHHHHHHHCCCCCCC
Q ss_conf 882467788861898321
Q gi|254780611|r 155 KPEQVVAIAKKLNVSESE 172 (302)
Q Consensus 155 ~~~~~~eiA~~Lgis~~~ 172 (302)
.+.+++++|+.+++++..
T Consensus 186 ~~isl~~lA~~~~lS~~~ 203 (278)
T PRK13503 186 EEVNWEAVADQFSLSLRT 203 (278)
T ss_pred CCCCHHHHHHHHCCCHHH
T ss_conf 999999999897959999
No 382
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=35.05 E-value=30 Score=14.52 Aligned_cols=21 Identities=29% Similarity=0.396 Sum_probs=15.2
Q ss_pred HHHHHHCCCCCCCCCCCCCCC
Q ss_conf 778886189832110000001
Q gi|254780611|r 160 VAIAKKLNVSESEVISMNCRL 180 (302)
Q Consensus 160 ~eiA~~Lgis~~~v~~l~~~~ 180 (302)
.++|+.++++...+-.+...+
T Consensus 40 ~~la~~l~~~~~~vt~~l~~L 60 (126)
T COG1846 40 KELAERLGLDRSTVTRLLKRL 60 (126)
T ss_pred HHHHHHHCCCHHHHHHHHHHH
T ss_conf 999999787888899999999
No 383
>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=34.77 E-value=30 Score=14.52 Aligned_cols=21 Identities=14% Similarity=0.137 Sum_probs=16.0
Q ss_pred HHHHHHHHCCCCCCCCCCCCC
Q ss_conf 467788861898321100000
Q gi|254780611|r 158 QVVAIAKKLNVSESEVISMNC 178 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v~~l~~ 178 (302)
++-++|+.+|++...++-+..
T Consensus 2 ~Ige~Ak~~gvs~~TLRyYe~ 22 (97)
T cd04782 2 TTGEFAKLCGISKQTLFHYDK 22 (97)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
T ss_conf 789999998969999999996
No 384
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=34.53 E-value=30 Score=14.46 Aligned_cols=21 Identities=33% Similarity=0.347 Sum_probs=9.7
Q ss_pred CCCCHHHHHHHHHCCCCCCCC
Q ss_conf 788824677888618983211
Q gi|254780611|r 153 NLKPEQVVAIAKKLNVSESEV 173 (302)
Q Consensus 153 ~~~~~~~~eiA~~Lgis~~~v 173 (302)
.|+..+..+||..+|++...|
T Consensus 24 ~P~~~~~~~La~~l~l~~~~I 44 (56)
T smart00389 24 YPSREEREELAAKLGLSERQV 44 (56)
T ss_pred CCCHHHHHHHHHHHCCCHHHH
T ss_conf 999899999999969499999
No 385
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=34.50 E-value=30 Score=14.46 Aligned_cols=21 Identities=14% Similarity=0.017 Sum_probs=16.3
Q ss_pred HHHHHHHHCCCCCCCCCCCCC
Q ss_conf 467788861898321100000
Q gi|254780611|r 158 QVVAIAKKLNVSESEVISMNC 178 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v~~l~~ 178 (302)
++-++|+..|+++..++-+..
T Consensus 2 ~Ige~Ak~~gvs~~tlRyYe~ 22 (127)
T cd01108 2 NIGEAAKLTGLSAKMIRYYEE 22 (127)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
T ss_conf 789999998959999999998
No 386
>KOG3716 consensus
Probab=34.50 E-value=30 Score=14.46 Aligned_cols=53 Identities=19% Similarity=0.197 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 740599999984079999989999999999982859999999994307787565555
Q gi|254780611|r 12 GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68 (302)
Q Consensus 12 ~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y 68 (302)
=+|.++.||..+. |+|+.||=..+....++=-...++ ..+.+|.|-...+..|
T Consensus 172 v~DTV~rYL~Smk--pilseEe~~~l~~la~eF~~~~g~--~LQ~yl~lksw~s~NY 224 (764)
T KOG3716 172 VKDTVTRYLDSMK--PILSEEEFDRLEELAEEFLSTEGR--RLQRYLWLKSWWSDNY 224 (764)
T ss_pred HHHHHHHHHHHCC--CCCCHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHCH
T ss_conf 7779999998315--225877799999999999975637--7889999999987232
No 387
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.
Probab=34.32 E-value=31 Score=14.44 Aligned_cols=21 Identities=24% Similarity=0.159 Sum_probs=16.5
Q ss_pred HHHHHHHHCCCCCCCCCCCCC
Q ss_conf 467788861898321100000
Q gi|254780611|r 158 QVVAIAKKLNVSESEVISMNC 178 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v~~l~~ 178 (302)
++-++|+..|++.+.++-+..
T Consensus 3 tIgelA~~~gvs~~tiRyYE~ 23 (139)
T cd01110 3 SVGEVAKRSGVAVSALHFYEQ 23 (139)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
T ss_conf 789999998878899999998
No 388
>pfam06163 DUF977 Bacterial protein of unknown function (DUF977). This family consists of several hypothetical bacterial proteins from Escherichia coli and Salmonella typhi. The function of this family is unknown.
Probab=34.31 E-value=31 Score=14.44 Aligned_cols=16 Identities=0% Similarity=-0.078 Sum_probs=6.4
Q ss_pred HHHHHHHCCCCCCCCC
Q ss_conf 6778886189832110
Q gi|254780611|r 159 VVAIAKKLNVSESEVI 174 (302)
Q Consensus 159 ~~eiA~~Lgis~~~v~ 174 (302)
..++....|++...+.
T Consensus 29 ~~qL~~~tG~~~~s~~ 44 (127)
T pfam06163 29 TNQLEAITGAHRTTAE 44 (127)
T ss_pred HHHHHHHHCCCHHHHH
T ss_conf 9999998783399999
No 389
>PRK11642 exoribonuclease R; Provisional
Probab=34.10 E-value=31 Score=14.42 Aligned_cols=29 Identities=7% Similarity=0.101 Sum_probs=15.3
Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 89999997789999999999999999999
Q gi|254780611|r 255 LENLSSEFEVSRERVRQIEARAFKKVQES 283 (302)
Q Consensus 255 l~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302)
+.++|+....+.-+..+.+..+..-++..
T Consensus 609 l~~~~~~~S~~ERrA~~AeRd~~~~~~~~ 637 (813)
T PRK11642 609 MLQLGQHCSMAERRADEATRDVADWLKCD 637 (813)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999986798999999999999999999
No 390
>pfam01527 Transposase_8 Transposase. Transposase proteins are necessary for efficient DNA transposition. This family consists of various E. coli insertion elements and other bacterial transposases some of which are members of the IS3 family.
Probab=34.08 E-value=31 Score=14.42 Aligned_cols=21 Identities=19% Similarity=0.224 Sum_probs=11.6
Q ss_pred HHHHHHHHCCCCCCCCCCCCC
Q ss_conf 467788861898321100000
Q gi|254780611|r 158 QVVAIAKKLNVSESEVISMNC 178 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v~~l~~ 178 (302)
++.+||..+|+++..+.....
T Consensus 25 sv~~var~~gi~~~~l~~W~k 45 (75)
T pfam01527 25 SVSELAREHGVSPATLYKWRK 45 (75)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
T ss_conf 499999998959999999999
No 391
>pfam06353 DUF1062 Protein of unknown function (DUF1062). This family consists of several hypothetical bacterial proteins of unknown function.
Probab=33.75 E-value=30 Score=14.47 Aligned_cols=21 Identities=24% Similarity=0.441 Sum_probs=17.6
Q ss_pred HHHHHHHCCCHHHHHHHHHHH
Q ss_conf 999999778999999999999
Q gi|254780611|r 256 ENLSSEFEVSRERVRQIEARA 276 (302)
Q Consensus 256 ~EIa~~lgiS~eRVrQI~~~A 276 (302)
+=||+.||+|+.+|.++....
T Consensus 107 ~Lla~~L~lSrs~l~~l~~~G 127 (142)
T pfam06353 107 RLLAEELGLSRSRLQRLIDQG 127 (142)
T ss_pred HHHHHHHCCCHHHHHHHHHCC
T ss_conf 999988186899999999889
No 392
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=33.73 E-value=31 Score=14.44 Aligned_cols=20 Identities=25% Similarity=0.142 Sum_probs=11.2
Q ss_pred HHHHHHHCCCCCCCCCCCCC
Q ss_conf 67788861898321100000
Q gi|254780611|r 159 VVAIAKKLNVSESEVISMNC 178 (302)
Q Consensus 159 ~~eiA~~Lgis~~~v~~l~~ 178 (302)
+.++|+.+|+++..++-...
T Consensus 3 I~eva~~~gvs~~tlR~ye~ 22 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYER 22 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHH
T ss_conf 88999998939999999999
No 393
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=33.61 E-value=31 Score=14.37 Aligned_cols=21 Identities=19% Similarity=0.308 Sum_probs=16.5
Q ss_pred HHHHHHHHCCCCCCCCCCCCC
Q ss_conf 467788861898321100000
Q gi|254780611|r 158 QVVAIAKKLNVSESEVISMNC 178 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v~~l~~ 178 (302)
++.|+|+..|+++..++-+.+
T Consensus 3 ~Ige~A~~~gvs~~TlRyYe~ 23 (102)
T cd04789 3 TISELAEKAGISRSTLLYYEK 23 (102)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
T ss_conf 099999998979999999998
No 394
>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=32.90 E-value=32 Score=14.29 Aligned_cols=29 Identities=24% Similarity=0.334 Sum_probs=21.6
Q ss_pred HHCCCCC-----CCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 8278888-----8989999997789999999999
Q gi|254780611|r 246 RRLQENP-----VTLENLSSEFEVSRERVRQIEA 274 (302)
Q Consensus 246 ry~~~~~-----~Tl~EIa~~lgiS~eRVrQI~~ 274 (302)
-|.++++ .|..|+++.||+|+..|..+.+
T Consensus 41 ~WiD~~g~vY~ift~~el~~~L~~s~~~v~k~~k 74 (76)
T pfam06970 41 NWIDEEGNVYFIFTNEELMELLNCSKQKVIKIKK 74 (76)
T ss_pred CCCCCCCCEEEEEEHHHHHHHHCCCHHHHHHHHH
T ss_conf 8897999999996499999997878889999996
No 395
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=32.72 E-value=32 Score=14.27 Aligned_cols=90 Identities=13% Similarity=0.109 Sum_probs=48.0
Q ss_pred HHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCH
Q ss_conf 46778886189832110000001223433552023234532000001235687056556666666777999999621999
Q gi|254780611|r 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~ 237 (302)
++-++|+.+|+++..++-+... -|-.|....+++.-.+ +.+ .+.
T Consensus 2 tIge~Ak~~gvs~~tlRyYe~~-----GLl~p~~~~~ngyR~Y---------~~~--------------~~~-------- 45 (96)
T cd04768 2 TIGEFAKLAGVSIRTLRHYDDI-----GLFKPAKIAENGYRYY---------SYA--------------QLY-------- 45 (96)
T ss_pred CHHHHHHHHCCCHHHHHHHHHC-----CCCCCCCCCCCCCEEC---------CHH--------------HHH--------
T ss_conf 7899999988699999999843-----9979872499998517---------999--------------999--------
Q ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999982788888989999997789999999999999999999997
Q gi|254780611|r 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286 (302)
Q Consensus 238 rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~ 286 (302)
+=..|..++- -+++++||.+.+..+.+-+.++-..-+..+.+.+++
T Consensus 46 ~l~~I~~lr~---~G~~L~eIk~~l~~~~~~~~~~l~~~~~~i~~~I~~ 91 (96)
T cd04768 46 QLQFILFLRE---LGFSLAEIKELLDTEMEELTAMLLEKKQAIQQKIDR 91 (96)
T ss_pred HHHHHHHHHH---CCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999999999---799999999999399699999999999999999999
No 396
>KOG0923 consensus
Probab=32.63 E-value=26 Score=14.92 Aligned_cols=24 Identities=21% Similarity=0.281 Sum_probs=11.5
Q ss_pred HHHHHHHHHHHHHCCHHHHHHHHHH
Q ss_conf 9999999999982859999999994
Q gi|254780611|r 32 QEEYVLAKRYREHGDLSAAHRLVTS 56 (302)
Q Consensus 32 eee~~l~~~~~~~gd~~Ar~~Li~~ 56 (302)
.|..++..+.++ .|+++...+++.
T Consensus 47 ~eR~e~e~~l~~-kdk~rtr~~~e~ 70 (902)
T KOG0923 47 KERDELEERLEK-KDKDRTRNVVER 70 (902)
T ss_pred HHHHHHHHHHHH-HHHHHHHHCCCC
T ss_conf 889999999877-667765301200
No 397
>PHA00542 putative Cro-like protein
Probab=32.36 E-value=33 Score=14.23 Aligned_cols=24 Identities=17% Similarity=0.221 Sum_probs=19.3
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 888989999997789999999999
Q gi|254780611|r 251 NPVTLENLSSEFEVSRERVRQIEA 274 (302)
Q Consensus 251 ~~~Tl~EIa~~lgiS~eRVrQI~~ 274 (302)
.+.|+.||++.-||++.-+++|-.
T Consensus 30 ~G~tQ~qI~~~tgv~QpsisRils 53 (82)
T PHA00542 30 AGWSQEQIADATDVSQPTICRIYS 53 (82)
T ss_pred CCCCHHHHHHHHCCCCHHHHHHHC
T ss_conf 225699999860877036899980
No 398
>pfam00440 TetR_N Bacterial regulatory proteins, tetR family.
Probab=32.13 E-value=33 Score=14.21 Aligned_cols=20 Identities=20% Similarity=0.326 Sum_probs=16.0
Q ss_pred CCCCHHHHHHHHCCCHHHHH
Q ss_conf 88898999999778999999
Q gi|254780611|r 251 NPVTLENLSSEFEVSRERVR 270 (302)
Q Consensus 251 ~~~Tl~EIa~~lgiS~eRVr 270 (302)
+..|.++||+..|||+..+-
T Consensus 15 ~~~s~~~Ia~~agvs~~~iy 34 (47)
T pfam00440 15 DATTVREIAKEAGVSKGALY 34 (47)
T ss_pred CCCCHHHHHHHHCCCHHHHH
T ss_conf 50779999999796988999
No 399
>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=32.13 E-value=33 Score=14.21 Aligned_cols=18 Identities=28% Similarity=0.322 Sum_probs=9.1
Q ss_pred HHHHHHHCCCCCCCCCCC
Q ss_conf 677888618983211000
Q gi|254780611|r 159 VVAIAKKLNVSESEVISM 176 (302)
Q Consensus 159 ~~eiA~~Lgis~~~v~~l 176 (302)
+.+||+.||++...|.+-
T Consensus 16 ~~eIA~~Lg~~~~tVysW 33 (58)
T pfam06056 16 PAEIAQELGLKARTVYSW 33 (58)
T ss_pred HHHHHHHHCCCCCHHHHH
T ss_conf 999999978993145658
No 400
>cd06898 PX_SNX10 The phosphoinositide binding Phox Homology domain of Sorting Nexin 10. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Some SNXs are localized in early endosome structures such as clathrin-coated pits, while others are located in late structures of the endocytic pathway. SNX10 may be involved in the regulation of endosome homeostasis. Its expression induces the formation of giant vacuoles in mammalian cells.
Probab=31.90 E-value=33 Score=14.18 Aligned_cols=11 Identities=18% Similarity=0.404 Sum_probs=4.2
Q ss_pred HHHHHHHHHHH
Q ss_conf 99999997887
Q gi|254780611|r 136 FFNLRRLKGHL 146 (302)
Q Consensus 136 ~~~~rk~~~~~ 146 (302)
+.....+...+
T Consensus 43 YsDF~~L~~~L 53 (113)
T cd06898 43 YSEFVWLRNRL 53 (113)
T ss_pred HHHHHHHHHHH
T ss_conf 68899999999
No 401
>TIGR00538 hemN oxygen-independent coproporphyrinogen III oxidase; InterPro: IPR004558 This family represents HemN, the oxygen-independent coproporphyrinogen III oxidase that replaces HemF function under anaerobic conditions. HemN catalyses the anaerobic transformation of coproporhyrinogen-III into protoporphyrinogen-IX during porphyrin biosynthesis. Several species, including Escherichia coli, Helicobacter pylori, and Aquifex aeolicus, have both a member of this family and a member of another, closely related family for which there is no evidence of coproporphyrinogen III oxidase activity, IPR004559 from INTERPRO. Members of this family have a perfectly conserved motif PYRT[SC]YP in a region N-terminal to the region of homology with the related uncharacterised protein.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin biosynthetic process, 0005737 cytoplasm.
Probab=31.86 E-value=26 Score=14.88 Aligned_cols=101 Identities=20% Similarity=0.354 Sum_probs=54.2
Q ss_pred HHHHHHHHHHHHHHHHCC----CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHH-HHHHHHHHHHHHHCCCCCHHHC
Q ss_conf 999430778756555579----99988899999988899898621853456899975-7789999998532024600110
Q gi|254780611|r 53 LVTSHLRLVVKIAMGYRG----YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS-MWWIKAAMQEYILRSWSLVKIG 127 (302)
Q Consensus 53 Li~~nlrlV~~iA~~y~~----~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA-~~wIr~~I~~~i~~~~~~IRiP 127 (302)
||..-|.+++-+--.=.| +|+|..-. ||..-=++=+=+-||+|=+-| .|| +|||+...+. |-+. -+|
T Consensus 191 ~i~~~~~~~R~~Gf~SiN~DLIYGLP~Qt~--esF~~Tl~~v~~LnPDRlAvF-nyAyvP~vk~~q~k-~~~~----~LP 262 (462)
T TIGR00538 191 MIFELMEKAREAGFESINLDLIYGLPKQTK--ESFEKTLEKVAELNPDRLAVF-NYAYVPWVKPAQRK-IPEE----ALP 262 (462)
T ss_pred HHHHHHHHHHHCCCCEEEEEEECCCCCCCH--HHHHHHHHHHHHCCCCEEHHH-HHHHHCCHHHHHCC-CCHH----CCC
T ss_conf 999999999866982787420138888786--789999999853187700121-02221015778502-7620----058
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHC---------CCCCCHHHHHHHHHCC
Q ss_conf 230035899999999788786624---------4788824677888618
Q gi|254780611|r 128 TTANQKRLFFNLRRLKGHLQAITD---------NNLKPEQVVAIAKKLN 167 (302)
Q Consensus 128 ~~~~~r~l~~~~rk~~~~~~~~~~---------~~~~~~~~~eiA~~Lg 167 (302)
+.. .+++=++..+..+.. +..+|..--.||..=|
T Consensus 263 S~~------~KL~Il~~~I~~L~~~gY~fIGMDHFAkpddELavAqr~g 305 (462)
T TIGR00538 263 SAE------EKLEILEETIAFLTEAGYVFIGMDHFAKPDDELAVAQRKG 305 (462)
T ss_pred CHH------HHHHHHHHHHHHHHHCCCEEECCCCCCCCCHHHHHHHHCC
T ss_conf 878------9999999999999757975851445779713899998505
No 402
>PRK06424 transcription factor; Provisional
Probab=31.56 E-value=34 Score=14.15 Aligned_cols=40 Identities=13% Similarity=0.223 Sum_probs=29.6
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHH---HHHHHHHHHHHCC
Q ss_conf 888989999997789999999999999---9999999974012
Q gi|254780611|r 251 NPVTLENLSSEFEVSRERVRQIEARAF---KKVQESIQKQVEL 290 (302)
Q Consensus 251 ~~~Tl~EIa~~lgiS~eRVrQI~~~AL---~kLR~~l~~~~~~ 290 (302)
.++|+.|+|..++.+..-|+.|+.--+ .++.+.|++-+.+
T Consensus 96 ~GlsqeeLA~ki~ek~svI~kiE~G~l~P~~~~~kKLEk~L~I 138 (144)
T PRK06424 96 LSMSQADLAAKIFERKNVIASIERGDLLPDIKTARKLEKILGI 138 (144)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCC
T ss_conf 4999999999965449999999838989998999999998496
No 403
>pfam02954 HTH_8 Bacterial regulatory protein, Fis family.
Probab=31.54 E-value=34 Score=14.14 Aligned_cols=17 Identities=12% Similarity=0.153 Sum_probs=14.0
Q ss_pred CHHHHHHHHCCCHHHHH
Q ss_conf 98999999778999999
Q gi|254780611|r 254 TLENLSSEFEVSRERVR 270 (302)
Q Consensus 254 Tl~EIa~~lgiS~eRVr 270 (302)
...+.|+.||||+....
T Consensus 20 n~~~aA~~LGisr~tL~ 36 (42)
T pfam02954 20 NKSKAARLLGISRRTLY 36 (42)
T ss_pred CHHHHHHHHCCCHHHHH
T ss_conf 79999999796999999
No 404
>PRK09775 hypothetical protein; Provisional
Probab=31.31 E-value=34 Score=14.12 Aligned_cols=16 Identities=19% Similarity=0.239 Sum_probs=7.2
Q ss_pred CCHHHHHHHHHHHCCC
Q ss_conf 7405999999840799
Q gi|254780611|r 12 GEIGLSRYIHEIRKIP 27 (302)
Q Consensus 12 ~~~~~~~yl~~i~~~~ 27 (302)
|+.+..++|..-...|
T Consensus 162 Ge~a~~~~l~~~~~~~ 177 (443)
T PRK09775 162 GEGAYQRWLAAPDPPA 177 (443)
T ss_pred CHHHHHHHHCCCCCCC
T ss_conf 7889999970888877
No 405
>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=31.21 E-value=34 Score=14.11 Aligned_cols=21 Identities=19% Similarity=0.181 Sum_probs=16.2
Q ss_pred HHHHHHHHCCCCCCCCCCCCC
Q ss_conf 467788861898321100000
Q gi|254780611|r 158 QVVAIAKKLNVSESEVISMNC 178 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v~~l~~ 178 (302)
++-++|+..|+++..++-+..
T Consensus 2 ~Ige~A~~~gvs~~tlR~Ye~ 22 (123)
T cd04770 2 KIGELAKAAGVSPDTIRYYER 22 (123)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
T ss_conf 689999998959999999998
No 406
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.20 E-value=34 Score=14.11 Aligned_cols=46 Identities=15% Similarity=0.143 Sum_probs=28.0
Q ss_pred HCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 219999999999982788888989999997789999999999999999
Q gi|254780611|r 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280 (302)
Q Consensus 233 ~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kL 280 (302)
+.|++.+-..+.+++--- -+++||-..+|+|.-.||---.+.|++|
T Consensus 40 ~~Lt~d~LeFv~lf~r~R--GnlKEvEr~lg~sYptvR~kld~vlram 85 (122)
T COG3877 40 EYLTSDQLEFVELFLRCR--GNLKEVERELGISYPTVRTKLDEVLRAM 85 (122)
T ss_pred CCCCHHHHHHHHHHHHHC--CCHHHHHHHHCCCCHHHHHHHHHHHHHC
T ss_conf 235875768999999972--5799999997776178998999999980
No 407
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=31.16 E-value=34 Score=14.10 Aligned_cols=21 Identities=19% Similarity=0.154 Sum_probs=16.5
Q ss_pred HHHHHHHHCCCCCCCCCCCCC
Q ss_conf 467788861898321100000
Q gi|254780611|r 158 QVVAIAKKLNVSESEVISMNC 178 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v~~l~~ 178 (302)
++-|+|+.+|+++..++-+..
T Consensus 2 tIgelAk~~gvs~~tlRyYE~ 22 (108)
T cd04773 2 TIGELAHLLGVPPSTLRHWEK 22 (108)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
T ss_conf 689999998979999999997
No 408
>KOG3973 consensus
Probab=31.06 E-value=32 Score=14.30 Aligned_cols=12 Identities=0% Similarity=0.011 Sum_probs=5.5
Q ss_pred CCHHHHHHHHCC
Q ss_conf 898999999778
Q gi|254780611|r 253 VTLENLSSEFEV 264 (302)
Q Consensus 253 ~Tl~EIa~~lgi 264 (302)
++..++|..|--
T Consensus 260 K~~~dvahLLaA 271 (465)
T KOG3973 260 KANSDVAHLLAA 271 (465)
T ss_pred CCHHHHHHHHHH
T ss_conf 200179999985
No 409
>pfam00126 HTH_1 Bacterial regulatory helix-turn-helix protein, lysR family.
Probab=31.05 E-value=35 Score=14.09 Aligned_cols=34 Identities=15% Similarity=0.225 Sum_probs=26.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 89899999977899999999999999999999974012
Q gi|254780611|r 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290 (302)
Q Consensus 253 ~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~~~~ 290 (302)
.++...|+.||||+..|+ ++|++|.+.+.-++-.
T Consensus 14 gs~~~AA~~l~isqs~vs----~~i~~LE~~lg~~Lf~ 47 (60)
T pfam00126 14 GSFTAAAERLGLSQPAVS----RQIKRLEEELGVPLFE 47 (60)
T ss_pred CCHHHHHHHHCCCHHHHH----HHHHHHHHHHCCEEEE
T ss_conf 999999999798988999----9999999995997078
No 410
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=30.99 E-value=33 Score=14.24 Aligned_cols=22 Identities=14% Similarity=0.021 Sum_probs=17.4
Q ss_pred HHHHHHHHHCCCCCCCCCCCCC
Q ss_conf 2467788861898321100000
Q gi|254780611|r 157 EQVVAIAKKLNVSESEVISMNC 178 (302)
Q Consensus 157 ~~~~eiA~~Lgis~~~v~~l~~ 178 (302)
-++-++|+..|++.+.++-+..
T Consensus 8 m~IgelAk~~gvs~~tIRyYE~ 29 (144)
T PRK13752 8 LTIGVFAKAAGVNVETIRFYQR 29 (144)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
T ss_conf 8299999997898456679872
No 411
>COG0853 PanD Aspartate 1-decarboxylase [Coenzyme metabolism]
Probab=30.45 E-value=2.3 Score=22.02 Aligned_cols=46 Identities=20% Similarity=0.293 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHH
Q ss_conf 994307787565555799998889999998889989862185345689997577
Q gi|254780611|r 54 VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107 (302)
Q Consensus 54 i~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~ 107 (302)
.++||-+|-||+ ++ +||+...-|==.+.++=++-+-|.||+||+..
T Consensus 15 T~A~L~Y~GSit-------ID-~dlldaagile~EkV~I~N~nNGaRf~TYvI~ 60 (126)
T COG0853 15 TEADLNYVGSIT-------ID-EDLLDAAGILENEKVDIVNVNNGARFSTYVIA 60 (126)
T ss_pred EECCCCEEEEEE-------EC-HHHHHHCCCCCCCEEEEEECCCCCEEEEEEEE
T ss_conf 502330477688-------89-99996538987766899988888378999987
No 412
>pfam05066 RNA_pol_delta DNA-directed RNA polymerase delta subunit. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich carboxyl-terminal region.
Probab=30.22 E-value=16 Score=16.27 Aligned_cols=51 Identities=22% Similarity=0.256 Sum_probs=34.0
Q ss_pred HHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCC
Q ss_conf 677888618983211000000122343355202323453200000123568
Q gi|254780611|r 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209 (302)
Q Consensus 159 ~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~ 209 (302)
+.+|++.+|++.+++......+..+..+|.-+-+..++...+.++.+-+..
T Consensus 37 ~~ev~~~~g~s~ee~~~~iaqfYTdln~DgRFi~lGen~WgLR~wyp~d~i 87 (94)
T pfam05066 37 VNEIQKLLGISDEEIRERLAQFYTDLNIDGRFISLGENRWGLRSWYPVDQI 87 (94)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCEEECCCCCCCCCCCCCCCCC
T ss_conf 999999959898899999999999985145204636884145323543110
No 413
>PRK02234 recU Holliday junction-specific endonuclease; Reviewed
Probab=29.88 E-value=32 Score=14.34 Aligned_cols=18 Identities=22% Similarity=0.514 Sum_probs=14.6
Q ss_pred HHHCCCCCCHHHHHHHHH
Q ss_conf 555799998889999998
Q gi|254780611|r 66 MGYRGYGLPISEVVSEGN 83 (302)
Q Consensus 66 ~~y~~~g~~~~DLiQeG~ 83 (302)
..|.|||+.+|++|..-|
T Consensus 23 ~~y~nRGM~LE~~IN~tN 40 (199)
T PRK02234 23 VTYANRGMSLEKDINETN 40 (199)
T ss_pred CCCCCCCCHHHHHHHHHH
T ss_conf 752446605999999999
No 414
>pfam11198 DUF2857 Protein of unknown function (DUF2857). This is a bacterial family of uncharacterized proteins.
Probab=29.63 E-value=36 Score=13.93 Aligned_cols=19 Identities=16% Similarity=0.226 Sum_probs=12.6
Q ss_pred HHHHHHHHCCCCCCCCCCC
Q ss_conf 4677888618983211000
Q gi|254780611|r 158 QVVAIAKKLNVSESEVISM 176 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v~~l 176 (302)
+.+-+....|++..+|...
T Consensus 89 S~emm~~~FGLs~~EVa~r 107 (181)
T pfam11198 89 SIEMMQRLFGLSSQEVALR 107 (181)
T ss_pred CHHHHHHHHCCCHHHHHHH
T ss_conf 7999999959998999999
No 415
>cd07282 PX_SNX2 The phosphoinositide binding Phox Homology domain of Sorting Nexin 2. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX2 is a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi. The retromer consists of a cargo-recognition subcomplex and a subcomplex formed by a dimer of sorting nexins (SNX1 and/or SNX2), which ensures efficient cargo sort
Probab=29.09 E-value=31 Score=14.40 Aligned_cols=16 Identities=31% Similarity=0.711 Sum_probs=7.5
Q ss_pred CCCC-CCCHHHHHHHHH
Q ss_conf 8534-568999757789
Q gi|254780611|r 94 DPER-GFRLATYSMWWI 109 (302)
Q Consensus 94 Dp~k-G~~FsTYA~~wI 109 (302)
||.+ |--.++|.+|.|
T Consensus 7 dP~k~gdg~~~Y~~Y~V 23 (124)
T cd07282 7 DPEKVGDGMNAYMAYRV 23 (124)
T ss_pred CCCEECCCCCCEEEEEE
T ss_conf 96284378317799999
No 416
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=29.08 E-value=37 Score=13.87 Aligned_cols=21 Identities=24% Similarity=0.151 Sum_probs=16.3
Q ss_pred HHHHHHHHCCCCCCCCCCCCC
Q ss_conf 467788861898321100000
Q gi|254780611|r 158 QVVAIAKKLNVSESEVISMNC 178 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v~~l~~ 178 (302)
++.++|+.+|+++..++-+..
T Consensus 2 sI~eva~~~gvs~~tlR~Ye~ 22 (100)
T cd00592 2 TIGEVAKLLGVSVRTLRYYEE 22 (100)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
T ss_conf 788999998959999999987
No 417
>TIGR03453 partition_RepA plasmid partitioning protein RepA. Members of this family are the RepA (or ParA) protein involved in replicon partitioning. All known examples occur in bacterial species with two or more replicons, on a plasmid or the smaller chromosome. Note that an apparent exception may be seen as a pseudomolecule from assembly of an incompletely sequenced genome. Members of this family belong to a larger family that also includes the enzyme cobyrinic acid a,c-diamide synthase, but assignment of that name to members of this family would be in error.
Probab=29.01 E-value=37 Score=13.87 Aligned_cols=11 Identities=0% Similarity=0.175 Sum_probs=5.1
Q ss_pred HHHHHHHHHHH
Q ss_conf 88999999888
Q gi|254780611|r 75 ISEVVSEGNIG 85 (302)
Q Consensus 75 ~~DLiQeG~iG 85 (302)
+-||=-.|++-
T Consensus 138 vIDLDPQanlT 148 (387)
T TIGR03453 138 AIDLDPQASLS 148 (387)
T ss_pred EEECCCHHHHH
T ss_conf 99537016788
No 418
>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=28.43 E-value=38 Score=13.80 Aligned_cols=117 Identities=15% Similarity=0.189 Sum_probs=55.6
Q ss_pred CCCCCCH-HHHHHHHHCC--CCCCCCCCCCCCCCCCCCHHHHCCCCC-CCCCCHHCCCCC-CCCCCHHHHHHHHHHHHHH
Q ss_conf 4478882-4677888618--983211000000122343355202323-453200000123-5687056556666666777
Q gi|254780611|r 151 DNNLKPE-QVVAIAKKLN--VSESEVISMNCRLAGDESLNALINSSD-KNSSQWQDWLVY-DHDGQEQVLIEKEERKNRR 225 (302)
Q Consensus 151 ~~~~~~~-~~~eiA~~Lg--is~~~v~~l~~~~~~~~SLd~~i~~~d-~~~~~~~d~l~~-~~~~~~~~~~e~~e~~~~~ 225 (302)
...+-.+ ..++||..+. ||.++|.+...-+.. ..| +.-++ ++.....+.++. .....-+.......+ +..
T Consensus 137 ~~~~~~~~~~~~la~~~~P~IS~~qvk~sl~LL~~-l~l---i~K~~q~G~y~~~~~~vs~~g~e~~~~av~~y~~-Q~~ 211 (281)
T TIGR02147 137 AVMPFADDDPEELAKRLKPKISAEQVKESLDLLER-LGL---IKKNEQDGFYKQTDKAVSMTGSEVIPLAVRQYQK-QMI 211 (281)
T ss_pred HHCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHH-CCC---CEEECCCCCEEEECCCEEECCHHHHHHHHHHHHH-HHH
T ss_conf 75489999868999870798578999999999862-332---0110305876760760660746568999999879-999
Q ss_pred HHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999621999999999998278888898999999778999999999999999999999740
Q gi|254780611|r 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288 (302)
Q Consensus 226 ~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~~ 288 (302)
++=.++|+.+|+.+|.|=.+ .||||.+....| .+-|+.+|+.+-.-+
T Consensus 212 ~La~~al~~~~~~~R~~S~~---------------T~g~~~~~y~~i-~~~i~~fR~~~~~~~ 258 (281)
T TIGR02147 212 DLAKEALDALPPEERDVSTV---------------TLGISEEAYKEI-VKKIQEFRKEVLAIA 258 (281)
T ss_pred HHHHHHHHHCCCCCCCEEEE---------------EECCCHHHHHHH-HHHHHHHHHHHHHHH
T ss_conf 99999997178987631300---------------323359999999-999999999999998
No 419
>KOG3099 consensus
Probab=28.03 E-value=39 Score=13.75 Aligned_cols=56 Identities=16% Similarity=0.181 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf 07787565555799998889999998889989862185345689997577899999985320
Q gi|254780611|r 58 LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119 (302)
Q Consensus 58 lrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~ 119 (302)
.|.|.++|+--...|--|.+|+|||..|...- +| ++-|-|-|---|...|..++-+
T Consensus 9 a~~vAss~r~c~q~~~L~qlllqek~~~~~nk--sf----~~D~kTlAD~l~Qe~Ikq~l~~ 64 (340)
T KOG3099 9 ARKVASSARICQQAGGLFQLLLQEKDLGIVNK--SF----AKDLKTLADRLAQECIKQSLGK 64 (340)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC--CC----CCCHHHHHHHHHHHHHHHHHHH
T ss_conf 99875789999872289999986065550031--01----5672778889999999999985
No 420
>cd01520 RHOD_YbbB Member of the Rhodanese Homology Domain superfamily. This CD includes several putative ATP /GTP binding proteins including E. coli YbbB.
Probab=27.96 E-value=39 Score=13.75 Aligned_cols=35 Identities=26% Similarity=0.582 Sum_probs=22.4
Q ss_pred CCCCCCHHHHHHHHHHHHHHCCHHHHHH---HHHHHHH
Q ss_conf 7999998999999999998285999999---9994307
Q gi|254780611|r 25 KIPMLEKQEEYVLAKRYREHGDLSAAHR---LVTSHLR 59 (302)
Q Consensus 25 ~~~~Lt~eee~~l~~~~~~~gd~~Ar~~---Li~~nlr 59 (302)
.+|+|+.+|=.+.-..|++.|-.+|... ||..|+.
T Consensus 35 NiPll~d~ER~~VGt~YK~~g~~~A~~lG~~lv~~~l~ 72 (128)
T cd01520 35 NLPLLDDEERALVGTLYKQQGREAAIELGLELVSGKLK 72 (128)
T ss_pred CCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH
T ss_conf 36021818899985888854989999999999988999
No 421
>PRK13026 acyl-CoA dehydrogenase; Reviewed
Probab=27.90 E-value=39 Score=13.74 Aligned_cols=35 Identities=26% Similarity=0.287 Sum_probs=18.5
Q ss_pred HCCHHHHHHH------HHHHHHHHHHHHHHHCCCCCCHHHH
Q ss_conf 2859999999------9943077875655557999988899
Q gi|254780611|r 44 HGDLSAAHRL------VTSHLRLVVKIAMGYRGYGLPISEV 78 (302)
Q Consensus 44 ~gd~~Ar~~L------i~~nlrlV~~iA~~y~~~g~~~~DL 78 (302)
.|+...|++| |.++|.|.-.+-|+|...|-+-+||
T Consensus 560 GG~LKrkE~lSaRlgDvLS~LYlasA~LKryed~Gr~~~Dl 600 (771)
T PRK13026 560 GGDLKRKEMLSARLGDVLSQLYLASATLKLFEDNGRQQDDL 600 (771)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 21110888876588999999999999999998649966668
No 422
>pfam06322 Phage_NinH Phage NinH protein. This family consists of several phage NinH proteins. The function of this family is unknown.
Probab=27.89 E-value=39 Score=13.74 Aligned_cols=19 Identities=21% Similarity=0.391 Sum_probs=13.9
Q ss_pred CHHHHHHHHCCCHHHHHHH
Q ss_conf 9899999977899999999
Q gi|254780611|r 254 TLENLSSEFEVSRERVRQI 272 (302)
Q Consensus 254 Tl~EIa~~lgiS~eRVrQI 272 (302)
++.|+|..|++++..||.-
T Consensus 18 N~teVaR~L~c~R~TVrkY 36 (64)
T pfam06322 18 NQTEVARRLNCSRNTVRKY 36 (64)
T ss_pred CHHHHHHHHCCHHHHHHHH
T ss_conf 7999978851108889987
No 423
>pfam00183 HSP90 Hsp90 protein.
Probab=27.85 E-value=39 Score=13.73 Aligned_cols=22 Identities=14% Similarity=0.247 Sum_probs=9.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHCC
Q ss_conf 5574558740599999984079
Q gi|254780611|r 5 NMSIIVNGEIGLSRYIHEIRKI 26 (302)
Q Consensus 5 ~~~~~~~~~~~~~~yl~~i~~~ 26 (302)
+++|.-..++-|-.||+=|..+
T Consensus 164 rVfI~d~~~~llP~yLrFvkGV 185 (529)
T pfam00183 164 RVFIMDDCEDLIPEYLSFVKGV 185 (529)
T ss_pred EEEECCCHHHHCHHHHHHHEEE
T ss_conf 5674165354565877675223
No 424
>pfam06413 Neugrin Neugrin. This family consists of several mouse and human neugrin proteins. Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation.
Probab=27.73 E-value=39 Score=13.72 Aligned_cols=29 Identities=24% Similarity=0.360 Sum_probs=16.6
Q ss_pred CCHHHHHHHHHHHHHHHHHHCCCCC--------CCCHHHHHHH
Q ss_conf 9888999999888998986218534--------5689997577
Q gi|254780611|r 73 LPISEVVSEGNIGLMQAVKKFDPER--------GFRLATYSMW 107 (302)
Q Consensus 73 ~~~~DLiQeG~iGLi~Ai~kFDp~k--------G~~FsTYA~~ 107 (302)
++.+.+-| |++...++|+. ||.-|++|+-
T Consensus 11 Ls~da~e~------IR~Lh~~~Pe~~t~~~LAe~F~VSpeaIr 47 (225)
T pfam06413 11 LTWEAIEQ------IRYLKQEFPEEWTVPRLAEGFDVSTDVIR 47 (225)
T ss_pred CCHHHHHH------HHHHHHHCCHHCCHHHHHHHCCCCHHHHH
T ss_conf 89999999------99998738401158999860788999999
No 425
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR; InterPro: IPR014178 Members of this entry are transcriptional regulators of fatty acid metabolism (FadR), including both biosynthesis and beta-oxidation reactions, which are found exclusively in a subset of Gammaproteobacteria with strictly one copy per genome. Proteins have an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR when expressed in Escherichia coli shows differences in regulatory response and fatty acid binding profiles. All members of this entry are expected to have the same function.; GO: 0000062 acyl-CoA binding, 0003677 DNA binding, 0003700 transcription factor activity, 0019217 regulation of fatty acid metabolic process.
Probab=27.72 E-value=39 Score=13.72 Aligned_cols=14 Identities=0% Similarity=0.095 Sum_probs=8.9
Q ss_pred HHHHHHHHHHCCCC
Q ss_conf 88899898621853
Q gi|254780611|r 83 NIGLMQAVKKFDPE 96 (302)
Q Consensus 83 ~iGLi~Ai~kFDp~ 96 (302)
++-.|+|++-|+.-
T Consensus 127 ~~~VI~s~e~L~~~ 140 (275)
T TIGR02812 127 IENVIKSLEVLANA 140 (275)
T ss_pred HHHHHHHHHHHHCC
T ss_conf 99999999998304
No 426
>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=27.63 E-value=17 Score=16.12 Aligned_cols=21 Identities=38% Similarity=0.415 Sum_probs=17.0
Q ss_pred HHHHHHHHHCCCCCCCCCCCC
Q ss_conf 246778886189832110000
Q gi|254780611|r 157 EQVVAIAKKLNVSESEVISMN 177 (302)
Q Consensus 157 ~~~~eiA~~Lgis~~~v~~l~ 177 (302)
-++.++|+.+|++..++...+
T Consensus 4 itV~elA~~l~~~~~~vi~~L 24 (52)
T pfam04760 4 IRVYELAKELGVSSKELIKKL 24 (52)
T ss_pred EEHHHHHHHHCCCHHHHHHHH
T ss_conf 739999999888899999999
No 427
>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=27.27 E-value=29 Score=14.59 Aligned_cols=40 Identities=20% Similarity=0.388 Sum_probs=29.1
Q ss_pred HHHHCCCHHHHHHHHHHHHHHHHHHHH-HHHCCCCCCCCCC
Q ss_conf 999778999999999999999999999-7401224677645
Q gi|254780611|r 259 SSEFEVSRERVRQIEARAFKKVQESIQ-KQVELSSSPPLLQ 298 (302)
Q Consensus 259 a~~lgiS~eRVrQI~~~AL~kLR~~l~-~~~~~~~~~~~~~ 298 (302)
+..|.||++||+|.-..--.++|+-|- ..+....+-.++|
T Consensus 158 CaQFaVsre~Ir~rP~~~Y~~~r~Wll~t~l~D~~sGrv~E 198 (222)
T pfam11913 158 CAQFAVSRERIRKRPREDYVRYRQWLLETDLDDDLSGRVME 198 (222)
T ss_pred EEEEEEEHHHHHHCCHHHHHHHHHHHHCCCCCCCCEEEEEH
T ss_conf 34232639999868999999999999648899872686501
No 428
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=27.07 E-value=40 Score=13.64 Aligned_cols=11 Identities=27% Similarity=0.670 Sum_probs=5.5
Q ss_pred CCCCCHHHHHH
Q ss_conf 99998889999
Q gi|254780611|r 70 GYGLPISEVVS 80 (302)
Q Consensus 70 ~~g~~~~DLiQ 80 (302)
|.|-+.++|++
T Consensus 63 G~GY~V~~L~~ 73 (211)
T PRK05472 63 GVGYNVKELLD 73 (211)
T ss_pred CCCCCHHHHHH
T ss_conf 98812999999
No 429
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=26.91 E-value=41 Score=13.62 Aligned_cols=21 Identities=5% Similarity=-0.053 Sum_probs=16.7
Q ss_pred HHHHHHHHCCCCCCCCCCCCC
Q ss_conf 467788861898321100000
Q gi|254780611|r 158 QVVAIAKKLNVSESEVISMNC 178 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v~~l~~ 178 (302)
++.++|+.+|+++..++-+..
T Consensus 3 tIgevA~~~Gvs~~tLR~yE~ 23 (91)
T cd04766 3 VISVAAELSGMHPQTLRLYER 23 (91)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
T ss_conf 589999998929999999998
No 430
>COG3824 Predicted Zn-dependent protease [General function prediction only]
Probab=26.49 E-value=37 Score=13.87 Aligned_cols=22 Identities=23% Similarity=0.445 Sum_probs=19.3
Q ss_pred HHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 8999999778999999999999
Q gi|254780611|r 255 LENLSSEFEVSRERVRQIEARA 276 (302)
Q Consensus 255 l~EIa~~lgiS~eRVrQI~~~A 276 (302)
..|||-.||+|-++.-||+.+|
T Consensus 114 iHEIgHhFGLsDdd~~rie~~a 135 (136)
T COG3824 114 IHEIGHHFGLSDDDLERIEWAA 135 (136)
T ss_pred HHHHHHHCCCCHHHHHHHHHCC
T ss_conf 3532212387776898754303
No 431
>COG1426 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]
Probab=26.40 E-value=41 Score=13.56 Aligned_cols=65 Identities=14% Similarity=0.125 Sum_probs=35.5
Q ss_pred HHHHHHHHHHCCCCCCHHHHHHH-------HHHHHHHCCHHHHH--HHHHHHHHHHHHHHHHHCC-CCCCHHHHHHHHHH
Q ss_conf 59999998407999998999999-------99999828599999--9999430778756555579-99988899999988
Q gi|254780611|r 15 GLSRYIHEIRKIPMLEKQEEYVL-------AKRYREHGDLSAAH--RLVTSHLRLVVKIAMGYRG-YGLPISEVVSEGNI 84 (302)
Q Consensus 15 ~~~~yl~~i~~~~~Lt~eee~~l-------~~~~~~~gd~~Ar~--~Li~~nlrlV~~iA~~y~~-~g~~~~DLiQeG~i 84 (302)
.+..+|+.++--.-||-++-..- ++.+ ++||-...- ..++++ -|+|.. -|++.+.|+++=.-
T Consensus 3 ~~Ge~Lr~~Re~~gLsL~dva~~t~I~~~~L~ai-Eeg~~~~lp~~~y~rG~-------ir~YA~~l~ld~~~l~~~~~~ 74 (284)
T COG1426 3 TLGERLRQAREEKGLSLEDVAARTKIRKSYLRAL-EEGNFDKLPGPVYIRGY-------IRSYAKFLGLDEDELLQAFED 74 (284)
T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH-HCCCCCCCCHHHHHHHH-------HHHHHHHHCCCHHHHHHHHHH
T ss_conf 7789999999984999999998857759999998-66770106415767899-------999999968998999998641
Q ss_pred HHH
Q ss_conf 899
Q gi|254780611|r 85 GLM 87 (302)
Q Consensus 85 GLi 87 (302)
+..
T Consensus 75 ~~~ 77 (284)
T COG1426 75 EKP 77 (284)
T ss_pred CCC
T ss_conf 045
No 432
>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=26.25 E-value=2.4 Score=21.81 Aligned_cols=32 Identities=19% Similarity=0.263 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHH
Q ss_conf 89999998889989862185345689997577
Q gi|254780611|r 76 SEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107 (302)
Q Consensus 76 ~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~ 107 (302)
.||+....|--.+-++=|+-+-|.||+|||.+
T Consensus 29 ~~Lm~aa~i~~~E~V~V~N~~NG~Rf~TYvI~ 60 (111)
T cd06919 29 EDLLEAAGILPYEKVLVVNVNNGARFETYVIP 60 (111)
T ss_pred HHHHHHCCCCCCCEEEEEECCCCCEEEEEEEE
T ss_conf 99998759998988999989899478999986
No 433
>cd01980 Chlide_reductase_Y Chlide_reductase_Y : Y subunit of chlorophyllide (chlide) reductase (BchY). Chlide reductase participates in photosynthetic pigment synthesis playing a role in the conversion of chlorophylls(Chl) into bacteriochlorophylls (BChl). Chlide reductase catalyzes the reduction of the B-ring of the tetrapyrolle. Chlide reductase is a three subunit enzyme (subunits are designated BchX, BchY and BchZ). The similarity between these three subunits and the subunits for nitrogenase suggests that BchX serves as an electron donor for the BchY-BchY catalytic subunits.
Probab=26.22 E-value=42 Score=13.54 Aligned_cols=32 Identities=16% Similarity=0.329 Sum_probs=27.5
Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 89999997789999999999999999999997
Q gi|254780611|r 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286 (302)
Q Consensus 255 l~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~ 286 (302)
++.||+.+||+.+++......-..+.|..++.
T Consensus 244 L~ai~~~fgv~~~~~~~v~~~~~~~~~~al~~ 275 (416)
T cd01980 244 LEAVGEALGLDMDQVRKVANEEKAAAKGAIRA 275 (416)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999994989889999987899999999876
No 434
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=26.18 E-value=42 Score=13.54 Aligned_cols=92 Identities=18% Similarity=0.286 Sum_probs=52.2
Q ss_pred HHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCH
Q ss_conf 46778886189832110000001223433552023234532000001235687056556666666777999999621999
Q gi|254780611|r 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~ 237 (302)
++.++|+.+|+++..++-+... -|-.|... +++.-.+ +.. .+.
T Consensus 2 tIgevA~~~Gvs~~tlRyYE~~-----GLl~P~R~-~~gyR~Y---------~~~--------------dl~-------- 44 (96)
T cd04774 2 KVDEVAKRLGLTKRTLKYYEEI-----GLVSPERS-EGRYRLY---------SEE--------------DLK-------- 44 (96)
T ss_pred CHHHHHHHHCCCHHHHHHHHHC-----CCCCCCCC-CCCCCCC---------CHH--------------HHH--------
T ss_conf 4889999989799999999987-----99899869-9998235---------999--------------999--------
Q ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCCC---HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999982788888989999997789---99999999999999999999740
Q gi|254780611|r 238 RERRIFEARRLQENPVTLENLSSEFEVS---RERVRQIEARAFKKVQESIQKQV 288 (302)
Q Consensus 238 rEr~II~~ry~~~~~~Tl~EIa~~lgiS---~eRVrQI~~~AL~kLR~~l~~~~ 288 (302)
+=..|+.++-.. ++||+||.+.|..- ...+.|+....|...+..|..|+
T Consensus 45 rL~~I~~l~~~l--GfsL~eIk~lL~~~~~p~~~~~~~~~e~L~~~~d~l~~~i 96 (96)
T cd04774 45 RLERILRLREVL--GFSLQEVTHFLERPLEPVDGGHRYSAESLREIHDALAQQV 96 (96)
T ss_pred HHHHHHHHHHHC--CCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 999999999957--9989999999819888304599999999999999998309
No 435
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=26.07 E-value=42 Score=13.53 Aligned_cols=17 Identities=24% Similarity=0.430 Sum_probs=7.6
Q ss_pred HCCCCCCCCHHHHHHHH
Q ss_conf 21853456899975778
Q gi|254780611|r 92 KFDPERGFRLATYSMWW 108 (302)
Q Consensus 92 kFDp~kG~~FsTYA~~w 108 (302)
+||++.|------|.+|
T Consensus 156 ~~d~~~g~~~p~LAhhW 172 (551)
T PRK13626 156 RINEENGELEADIAHHW 172 (551)
T ss_pred EEECCCCCCCHHHHHHH
T ss_conf 88578895883366240
No 436
>pfam11662 DUF3263 Protein of unknown function (DUF3263). This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=25.65 E-value=43 Score=13.47 Aligned_cols=44 Identities=18% Similarity=0.239 Sum_probs=28.6
Q ss_pred CCCHHHHHHHHH--HHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 199999999999--82788888989999997789999999999999
Q gi|254780611|r 234 VLNPRERRIFEA--RRLQENPVTLENLSSEFEVSRERVRQIEARAF 277 (302)
Q Consensus 234 ~L~~rEr~II~~--ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL 277 (302)
.|+++|+.|+.+ .+.-..+---.-|-+.||+|.-|--|+-..-|
T Consensus 2 ~Ls~rd~~IL~fEr~ww~~~GaKe~AIRe~fglS~~rYYQ~LN~Li 47 (77)
T pfam11662 2 ELTERDRAILDFERQWWKHAGAKEQAIRELFGLSSTRYYQLLNALI 47 (77)
T ss_pred CCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 8889999999999873368781899999997888899999999986
No 437
>pfam07037 DUF1323 Putative transcription regulator (DUF1323). This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. This family appears to have an HTH domain and is therefore likely to act as a transcriptional regulator.
Probab=25.64 E-value=43 Score=13.47 Aligned_cols=37 Identities=11% Similarity=0.251 Sum_probs=19.5
Q ss_pred HHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCC
Q ss_conf 9999996219999999999982788888989999997789
Q gi|254780611|r 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265 (302)
Q Consensus 226 ~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS 265 (302)
..+..++..|++-||.=+..+.+ -++ ...+=..|||.
T Consensus 84 ~~~i~~~~~mT~~Eqekl~~lLl-REG--I~glL~RLgI~ 120 (122)
T pfam07037 84 RQLITTLEEMTPSEQKQLTSLLS-REG--IAGLLQRLGIR 120 (122)
T ss_pred HHHHHHHHHCCHHHHHHHHHHHH-HHH--HHHHHHHCCCC
T ss_conf 99999999839999999999999-982--99999980876
No 438
>TIGR01326 OAH_OAS_sulfhy O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase; InterPro: IPR006235 This family of sequences is a distinct clade of the Cys/Met metabolism pyridoxal phosphate-dependent enzyme superfamily. Members include examples of OAH/OAS sulfhydrylase, an enzyme with activity both as O-acetylhomoserine sulfhydrylase (OAH, 2.5.1.49 from EC) and O-acetylserine sulfhydrylase (OAS, 2.5.1.47 from EC). An alternate name for OAH sulfhydrylase is homocysteine synthase.; GO: 0016765 transferase activity transferring alkyl or aryl (other than methyl) groups, 0006520 amino acid metabolic process.
Probab=25.51 E-value=43 Score=13.46 Aligned_cols=19 Identities=11% Similarity=0.406 Sum_probs=10.1
Q ss_pred CCCCCHHHHHHHHHHHHHH
Q ss_conf 3456899975778999999
Q gi|254780611|r 96 ERGFRLATYSMWWIKAAMQ 114 (302)
Q Consensus 96 ~kG~~FsTYA~~wIr~~I~ 114 (302)
+-|...|=|..|-+-|.+-
T Consensus 279 D~Gaa~sPFnAFLllQGLE 297 (434)
T TIGR01326 279 DLGAALSPFNAFLLLQGLE 297 (434)
T ss_pred HCCCCCCHHHHHHHHHHHH
T ss_conf 0033401789999998666
No 439
>cd00383 trans_reg_C Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and a response regulator. The former autophosphorylates in a histidine residue on detecting an external stimulus. The phosphate is then transferred to an invariant aspartate residue in a highly conserved receiver domain of the response regulator. Phosphorylation activates a variable effector domain of the response regulator, which triggers the cellular response. The C-terminal effector domain contains DNA and RNA polymerase binding sites. Several dimers or monomers bind head to tail to small tandem repeats upstream of the genes. The RNA polymerase binding sites interact with the alpha or sigma subunite of RNA polymerase.
Probab=25.43 E-value=43 Score=13.45 Aligned_cols=54 Identities=11% Similarity=0.148 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHHHHC-CCCCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 199999999999827-88888989999997-7899999999999999999999974
Q gi|254780611|r 234 VLNPRERRIFEARRL-QENPVTLENLSSEF-EVSRERVRQIEARAFKKVQESIQKQ 287 (302)
Q Consensus 234 ~L~~rEr~II~~ry~-~~~~~Tl~EIa~~l-giS~eRVrQI~~~AL~kLR~~l~~~ 287 (302)
.|+++|..|+.+.+- -+...|-.+|.+.+ |-...--...-...+.+||+.|...
T Consensus 23 ~Lt~~E~~lL~~L~~~~~~vvsr~~l~~~vw~~~~~~~~~~l~~~I~rLRkkl~~~ 78 (95)
T cd00383 23 ELTPKEFELLELLARNPGRVLSREQLLEAVWGDDYDVDDRTVDVHISRLRKKLEDD 78 (95)
T ss_pred ECCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHC
T ss_conf 77999999999998779974569999998539764557454999999999997526
No 440
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=25.39 E-value=43 Score=13.44 Aligned_cols=21 Identities=14% Similarity=0.107 Sum_probs=16.3
Q ss_pred HHHHHHHHCCCCCCCCCCCCC
Q ss_conf 467788861898321100000
Q gi|254780611|r 158 QVVAIAKKLNVSESEVISMNC 178 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v~~l~~ 178 (302)
++-++|+..|+++..++-+..
T Consensus 2 ~IgevA~~~gvs~~TlRyYE~ 22 (126)
T cd04783 2 TIGELAKAAGVNVETIRYYQR 22 (126)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
T ss_conf 789999998939899999998
No 441
>KOG2165 consensus
Probab=25.25 E-value=43 Score=13.43 Aligned_cols=67 Identities=15% Similarity=0.282 Sum_probs=40.5
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHH
Q ss_conf 99999943077875655557999988899999988899898621853456899975778999999853202460011
Q gi|254780611|r 50 AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126 (302)
Q Consensus 50 r~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRi 126 (302)
|..|+++ |+-.+-.+--.-|++--|.+ -+++.=|+|..--||+ |+-... +-+-|.+|++...-+||.
T Consensus 303 r~~ltes---fi~~l~~riL~asv~T~DIL-~~YVstIkalr~lDpt-gV~Le~-----v~~pIR~YLr~R~DtVk~ 369 (765)
T KOG2165 303 RVYLTES---FISDLKTRILTASVDTVDIL-LRYVSTIKALRVLDPT-GVILEK-----VTEPIRDYLRERKDTVKQ 369 (765)
T ss_pred HHHHHHH---HHHHHHHHHCCCCCCHHHHH-HHHHHHHHHHHHHCCC-CEEHHH-----HHHHHHHHHHHCCCHHHH
T ss_conf 6799999---99998766417887589999-9999999999961875-211697-----567689998607409999
No 442
>PRK09480 slmA nucleoid occlusion protein; Provisional
Probab=25.24 E-value=43 Score=13.43 Aligned_cols=30 Identities=17% Similarity=0.161 Sum_probs=20.2
Q ss_pred HHHHHHCCCCCCHHHHHHHHHCCCCCCCCC
Q ss_conf 878662447888246778886189832110
Q gi|254780611|r 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVI 174 (302)
Q Consensus 145 ~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~ 174 (302)
....+...++..-+..+||+.+|+|..-+.
T Consensus 19 ~~~ll~~~~~~~iTt~~iA~~~gvs~aalY 48 (194)
T PRK09480 19 LAQMLESPPGERITTAKLAARVGVSEAALY 48 (194)
T ss_pred HHHHHHHCCCCCCCHHHHHHHHCCCHHHHH
T ss_conf 999986279764229999989099789999
No 443
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=25.23 E-value=44 Score=13.42 Aligned_cols=21 Identities=19% Similarity=0.066 Sum_probs=14.7
Q ss_pred HHHHHHHHCCCCCCCCCCCCC
Q ss_conf 467788861898321100000
Q gi|254780611|r 158 QVVAIAKKLNVSESEVISMNC 178 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v~~l~~ 178 (302)
++.++|+.+|++...++-+..
T Consensus 2 ~I~eva~~~gvs~~tLRyYe~ 22 (124)
T COG0789 2 TIGEVAKLTGVSVRTLRFYER 22 (124)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
T ss_conf 599999997969999999999
No 444
>cd04397 RhoGAP_fLRG1 RhoGAP_fLRG1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of fungal LRG1-like proteins. Yeast Lrg1p is required for efficient cell fusion, and mother-daughter cell separation, possibly through acting as a RhoGAP specifically regulating 1,3-beta-glucan synthesis. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=25.05 E-value=44 Score=13.40 Aligned_cols=182 Identities=15% Similarity=0.186 Sum_probs=84.6
Q ss_pred CCCHHHHHH-HHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCC----CCCHHHCCCCHHHHHHHHHHHHHHHH
Q ss_conf 998889999-9988899898621853456899975778999999853202----46001102300358999999997887
Q gi|254780611|r 72 GLPISEVVS-EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS----WSLVKIGTTANQKRLFFNLRRLKGHL 146 (302)
Q Consensus 72 g~~~~DLiQ-eG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~----~~~IRiP~~~~~r~l~~~~rk~~~~~ 146 (302)
|+|+++|+| +|. |-.-|..+...-++.|-..+.+||..+ -++.|+|-... .+++++..+
T Consensus 2 GvpL~~l~~r~~~----------~~~~~~~~~~~~VP~iv~~~i~~l~~~gl~~EGIFR~sG~~~------~i~~L~~~~ 65 (213)
T cd04397 2 GVPLEILVEKFGA----------DSTLGVGPGKLRIPALIDDIISAMRQMDMSVEGVFRKNGNIR------RLKELTEEI 65 (213)
T ss_pred CCCHHHHHHHHCC----------CCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEECCCCHH------HHHHHHHHH
T ss_conf 9988999987686----------644456877787797999999999981999999544888799------999999998
Q ss_pred HHHHCCCC--CCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf 86624478--8824677888618983211000000122343355202323453200000123568705655666666677
Q gi|254780611|r 147 QAITDNNL--KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224 (302)
Q Consensus 147 ~~~~~~~~--~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~ 224 (302)
+.-..... ....+..+| .+++.+-+ .|-.|+-..+ .+..++...... .....
T Consensus 66 d~~~~~~~~~~~~~~~~vA-----------~lLK~flR--eLPePLi~~~----ly~~~i~~~~~~---------d~~~~ 119 (213)
T cd04397 66 DKNPTEVPDLSKENPVQLA-----------ALLKKFLR--ELPDPLLTFK----LYRLWISSQKIE---------DEEER 119 (213)
T ss_pred HCCCCCCCCCCCCCHHHHH-----------HHHHHHHH--HCCCCCCCHH----HHHHHHHHHCCC---------CHHHH
T ss_conf 2699766676657779999-----------99999998--2898657599----999999997279---------99999
Q ss_pred HHHHHHHHHCCCHHHHHHHHHH--HC---------CC---CCCCHHHHHHHHCCCHH--------HHHHHHHHHHHHHHH
Q ss_conf 7999999621999999999998--27---------88---88898999999778999--------999999999999999
Q gi|254780611|r 225 RNMLTRSMSVLNPRERRIFEAR--RL---------QE---NPVTLENLSSEFEVSRE--------RVRQIEARAFKKVQE 282 (302)
Q Consensus 225 ~~~L~~~l~~L~~rEr~II~~r--y~---------~~---~~~Tl~EIa~~lgiS~e--------RVrQI~~~AL~kLR~ 282 (302)
...+...+..||+--+.++..- |+ .+ ..||..-+|-.+|=|=- -+-+. ..+..-+.-
T Consensus 120 ~~~~~~l~~~LP~~n~~~L~~L~~~L~~V~~~s~v~~~~~NkMt~~NLAvvfaP~ll~~~~~~~~~~~~~-~~~~~~v~~ 198 (213)
T cd04397 120 KRVLHLVYCLLPKYHRDTMEVLFSFLKWVSSFSHIDEETGSKMDIHNLATVITPNILYSKTDNPNTGDEY-FLAIEAVNY 198 (213)
T ss_pred HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHEEECCCCCCCCCCCCCHHHHH-HHHHHHHHH
T ss_conf 9999999997897699999999999999998765311113658742402124240045687784178899-999999999
Q ss_pred HHHHHHCCCCCCCC
Q ss_conf 99974012246776
Q gi|254780611|r 283 SIQKQVELSSSPPL 296 (302)
Q Consensus 283 ~l~~~~~~~~~~~~ 296 (302)
.++..-++...|+-
T Consensus 199 LI~~~~~if~vp~~ 212 (213)
T cd04397 199 LIENNEEFCEVPDE 212 (213)
T ss_pred HHHHHHHHCCCCCC
T ss_conf 99858998049887
No 445
>pfam07900 DUF1670 Protein of unknown function (DUF1670). The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=25.00 E-value=44 Score=13.40 Aligned_cols=23 Identities=22% Similarity=0.096 Sum_probs=15.6
Q ss_pred HHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf 46778886189832110000001
Q gi|254780611|r 158 QVVAIAKKLNVSESEVISMNCRL 180 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v~~l~~~~ 180 (302)
+-+++|.-|++|...|......+
T Consensus 107 T~~Dla~LL~~S~~TI~~~ik~y 129 (220)
T pfam07900 107 THADIAILLGVSTTTISRHVKEY 129 (220)
T ss_pred EHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 17669999889888999999999
No 446
>TIGR01368 CPSaseIIsmall carbamoyl-phosphate synthase, small subunit; InterPro: IPR006274 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates , . CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate . The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain . CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites . The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein . The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP . There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia . CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains . This entry represents the small subunit of the glutamine-dependent form (6.3.5.5 from EC) of carbamoyl phosphate synthase, CPSase II. The small subunit catalyses the hydrolysis of glutamine to ammonia, which in turn used by the large chain to synthesize carbamoyl phosphate. The C-terminal domain of the small subunit of CPSase has glutamine amidotransferase activity. Note that the sequence from the mammalian urea cycle form has lost the active site Cys, resulting in an ammonia-dependent form, CPSase I (6.3.4.16 from EC). CPSases of pyrimidine biosynthesis, arginine biosynthesis, and the urea cycle may be encoded by one or by several genes, depending on the species. ; GO: 0004086 carbamoyl-phosphate synthase activity, 0006807 nitrogen compound metabolic process.
Probab=24.81 E-value=25 Score=15.00 Aligned_cols=39 Identities=23% Similarity=0.435 Sum_probs=28.9
Q ss_pred CCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHHH
Q ss_conf 8740599999984079999989999999999982859999
Q gi|254780611|r 11 NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAA 50 (302)
Q Consensus 11 ~~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~gd~~Ar 50 (302)
-...||.+||++ ..+|.+.-=+-++|-+++|+.|.+.|.
T Consensus 99 ra~~SL~~~L~~-~~ipgI~GvDTRaLv~~iR~~G~m~g~ 137 (383)
T TIGR01368 99 RATESLDQFLKE-HGIPGIYGVDTRALVKKIREKGTMKGV 137 (383)
T ss_pred HHHCCHHHHHHH-CCCEEEECCCHHHHHHHHHHCCCEEEE
T ss_conf 565048999985-698473045779999998635854789
No 447
>pfam07180 DUF1401 Protein of unknown function (DUF1401). This family consists of several hypothetical bacterial proteins of around 135 residues in length. Members of this family appear to be found exclusively in the Enterobacteria Escherichia coli, Citrobacter rodentium and Salmonella typhi. The function of this family is unknown.
Probab=24.74 E-value=44 Score=13.36 Aligned_cols=14 Identities=0% Similarity=-0.007 Sum_probs=6.3
Q ss_pred HHHCCCCCCHHHHH
Q ss_conf 55579999888999
Q gi|254780611|r 66 MGYRGYGLPISEVV 79 (302)
Q Consensus 66 ~~y~~~g~~~~DLi 79 (302)
-.+.++++.-+|+-
T Consensus 32 glLq~~~ftRndIs 45 (150)
T pfam07180 32 CKLQEKWIQRNDIA 45 (150)
T ss_pred HHHHCCCCCHHHHH
T ss_conf 99844774378899
No 448
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=24.65 E-value=45 Score=13.35 Aligned_cols=61 Identities=20% Similarity=0.213 Sum_probs=36.8
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf 999757789999998532024600110230035899999999788786624478882467788861898321100000
Q gi|254780611|r 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178 (302)
Q Consensus 101 FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~ 178 (302)
|+.+-.-|+...|.+|-..++-+ ..-+..+++ ..+ ...++.+.+||+.||++..+|.....
T Consensus 5 ~~~~~~~~~~~~i~~yp~~rsAl------------ip~L~~aQ~----~~G-~l~~~ai~~iA~~L~i~~~~v~~VaT 65 (160)
T COG1905 5 FSAENLELIEAIIAKYPDKRSAL------------IPLLHIAQE----QFG-WLPPEAIEEIADMLGIPRARVYGVAT 65 (160)
T ss_pred CCHHHHHHHHHHHHHCCCCHHHH------------HHHHHHHHH----HHC-CCCHHHHHHHHHHHCCCHHHHEEEEE
T ss_conf 22567999999999777524378------------899999999----858-88878999999985999788310144
No 449
>PRK12435 ferrochelatase; Provisional
Probab=24.54 E-value=45 Score=13.34 Aligned_cols=60 Identities=13% Similarity=0.110 Sum_probs=37.3
Q ss_pred CHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCH-------HHHHHHHHHHH-------HHHHHHHHHHCCCC
Q ss_conf 40599999984079999989999999999982859-------99999999430-------77875655557999
Q gi|254780611|r 13 EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL-------SAAHRLVTSHL-------RLVVKIAMGYRGYG 72 (302)
Q Consensus 13 ~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~gd~-------~Ar~~Li~~nl-------rlV~~iA~~y~~~g 72 (302)
.+.+.-||.++..-+..+.+.-..+..+|+.-|+. ++.-..++..| .+.+.+|.||.+..
T Consensus 19 ~~dV~pyL~~i~~gr~p~~~~l~~~~~~Y~~igg~SPl~~~t~~qa~~L~~~L~~~~~~~~~~v~~gmRy~~P~ 92 (316)
T PRK12435 19 LDDVEAYYTHIRHGRKPSEEALEDLIGRYKAIGGISPLAKITKEQAHKLTDSMNNMFTEYEFNCYLGLKHTAPF 92 (316)
T ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCC
T ss_conf 76899999997068999899999999999982898854999999999999997152589875167742899998
No 450
>TIGR01968 minD_bact septum site-determining protein MinD; InterPro: IPR010223 This entry describes the bacterial and chloroplast form of MinD, a multifunctional cell division protein that guides correct placement of the septum. In Escherichia coli, the cell division site is determined by the cooperative activity of min operon products MinC, MinD, and MinE . MinD is a membrane-associated ATPase and is a septum site-determining factor through the activation and regulation of MinC and MinE. MinD is also known to undergo a rapid pole-to-pole oscillation movement in vivo as observed by fluorescent microscopy. In plants, chloroplast division requires the dimerisation of stromal MinD . The homologous archaeal MinD proteins, with many archaeal genomes having two or more forms, are described by a separate model.; GO: 0016887 ATPase activity, 0000918 selection of site for barrier septum formation.
Probab=24.50 E-value=45 Score=13.34 Aligned_cols=27 Identities=37% Similarity=0.513 Sum_probs=19.4
Q ss_pred CHHHHHHHHHHHHHHHHHH---CCC---------CCCCC
Q ss_conf 8889999998889989862---185---------34568
Q gi|254780611|r 74 PISEVVSEGNIGLMQAVKK---FDP---------ERGFR 100 (302)
Q Consensus 74 ~~~DLiQeG~iGLi~Ai~k---FDp---------~kG~~ 100 (302)
+=+.+-+|.+--|++.... ||. ++||+
T Consensus 92 dK~~~~~E~~~~lv~~Lk~~~~FDYviIDcPAGIE~GF~ 130 (272)
T TIGR01968 92 DKDAVTPEQMKKLVNELKEEEHFDYVIIDCPAGIESGFR 130 (272)
T ss_pred CCCCCCHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHHH
T ss_conf 613469778999999985437930799737877435689
No 451
>TIGR00014 arsC arsenate reductase; InterPro: IPR006659 This entry describes a distinct clade, including ArsC itself, of the broader family of ArsC and related proteins. This clade is almost completely restricted to the proteobacteria. An anion-translocating ATPase has been identified as the product of the arsenical resistance operon of resistance plasmid R773 . When expressed in Escherichia coli this ATP-driven oxyanion pump catalyses extrusion of the oxyanions arsenite, antimonite and arsenate. The pump is composed of two polypeptides, the products of the arsA and arsB genes. The pump alone produces resistance to arsenite and antimonite. This protein, ArsC, catalyzes the reduction of arsenate to arsenite, and thus extends resistance to include arsenate. ; GO: 0008794 arsenate reductase (glutaredoxin) activity, 0006118 electron transport.
Probab=24.42 E-value=39 Score=13.78 Aligned_cols=42 Identities=21% Similarity=0.230 Sum_probs=24.0
Q ss_pred HHHHCCCCCCHHHHHHHHHCCCCC-CCCCCCCCCCCCCCCHHH
Q ss_conf 866244788824677888618983-211000000122343355
Q gi|254780611|r 147 QAITDNNLKPEQVVAIAKKLNVSE-SEVISMNCRLAGDESLNA 188 (302)
Q Consensus 147 ~~~~~~~~~~~~~~eiA~~Lgis~-~~v~~l~~~~~~~~SLd~ 188 (302)
.......++..+++++.++||+++ .+...--........|+.
T Consensus 29 V~YL~~pp~~seL~~~~~~LG~~~ar~~~R~ke~~y~eLgL~~ 71 (114)
T TIGR00014 29 VKYLKNPPTKSELKALLAKLGISSAREMIRTKEELYKELGLDD 71 (114)
T ss_pred EECCCCCCCHHHHHHHHHHCCCCHHHHHCCCCCCCCCCCCCCC
T ss_conf 4145897486889999987089703630117652100047898
No 452
>PRK04570 cell division protein ZipA; Provisional
Probab=24.26 E-value=45 Score=13.31 Aligned_cols=41 Identities=24% Similarity=0.595 Sum_probs=23.1
Q ss_pred CHHHHHHHHC----------CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf 9899999977----------899999999999999999999974012246776458999
Q gi|254780611|r 254 TLENLSSEFE----------VSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKPRY 302 (302)
Q Consensus 254 Tl~EIa~~lg----------iS~eRVrQI~~~AL~kLR~~l~~~~~~~~~~~~~~~~~~ 302 (302)
|-+.||+.|| +|+++|.+. |+.++.--.-.++||+.+-||+
T Consensus 194 tAq~lA~~LgG~vlDe~Rs~lT~Qtiehy--------RqrIr~feR~q~~p~~~~~~~~ 244 (244)
T PRK04570 194 TVQRMAELLDGVVLDDSRNALGRQRVAHI--------RDELRAYDRQHQAPPLTKSPRW 244 (244)
T ss_pred HHHHHHHHCCCEEECCCCCCCCHHHHHHH--------HHHHHHHHHHHCCCCCCCCCCC
T ss_conf 99999997699886788777778999999--------9999999875118984458899
No 453
>pfam04079 DUF387 Putative transcriptional regulators (Ypuh-like). This family of conserved bacterial proteins are thought to possibly be helix-turn-helix type transcriptional regulators.
Probab=24.21 E-value=45 Score=13.30 Aligned_cols=48 Identities=13% Similarity=0.151 Sum_probs=27.2
Q ss_pred CCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHH-HHHHHHHHHHHHHHH
Q ss_conf 1999999999998278888898999999778999-999999999999999
Q gi|254780611|r 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRE-RVRQIEARAFKKVQE 282 (302)
Q Consensus 234 ~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~e-RVrQI~~~AL~kLR~ 282 (302)
.|+.-.-.++-.-.. ..|.|..+|-+.-|++.. -++++..+.|=+...
T Consensus 79 ~LS~a~lEtLAiIAY-~QPitr~~I~~iRGv~s~~~l~~L~~~glI~~~g 127 (159)
T pfam04079 79 RLSQAALETLAIIAY-RQPITRAEIEEIRGVSSDGVIKTLLERGLIEEVG 127 (159)
T ss_pred CCCHHHHHHHHHHHH-CCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHC
T ss_conf 138999999999996-1985799999980978799999999842165307
No 454
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=24.14 E-value=46 Score=13.29 Aligned_cols=29 Identities=10% Similarity=0.023 Sum_probs=20.0
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 989999997789999999999999999999
Q gi|254780611|r 254 TLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302)
Q Consensus 254 Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302)
|...+|..+|||..-|+|- ..-+-.+|..
T Consensus 12 sk~klA~aLgIs~~aVsqW-ge~IPE~rAy 40 (75)
T PRK09744 12 SKTKLANAAGVRLASVAAW-GELVPEGRAM 40 (75)
T ss_pred CHHHHHHHHCCCHHHHHHH-HHHCCHHHHH
T ss_conf 2999999949987999887-4016068899
No 455
>PRK08025 lipid A biosynthesis palmitoleoyl acyltransferase; Reviewed
Probab=23.99 E-value=46 Score=13.27 Aligned_cols=16 Identities=13% Similarity=0.156 Sum_probs=9.7
Q ss_pred CCCCCHHHHHHHHHHH
Q ss_conf 9999989999999999
Q gi|254780611|r 26 IPMLEKQEEYVLAKRY 41 (302)
Q Consensus 26 ~~~Lt~eee~~l~~~~ 41 (302)
+|=+|.+|-..++++.
T Consensus 67 FPe~s~~e~~~i~k~~ 82 (305)
T PRK08025 67 FPQHSAEEREKMIAEN 82 (305)
T ss_pred CCCCCHHHHHHHHHHH
T ss_conf 8899999999999999
No 456
>COG4753 Response regulator containing CheY-like receiver domain and AraC-type DNA-binding domain [Signal transduction mechanisms]
Probab=23.98 E-value=46 Score=13.27 Aligned_cols=45 Identities=22% Similarity=0.310 Sum_probs=34.7
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH--------HHHHHHHHHHHHHCCCCCCC
Q ss_conf 8889899999977899999999999--------99999999997401224677
Q gi|254780611|r 251 NPVTLENLSSEFEVSRERVRQIEAR--------AFKKVQESIQKQVELSSSPP 295 (302)
Q Consensus 251 ~~~Tl~EIa~~lgiS~eRVrQI~~~--------AL~kLR~~l~~~~~~~~~~~ 295 (302)
+++||+.||..|++++-.+.|+-++ -|.|+|-.-.+++-..+..+
T Consensus 387 e~LtL~~la~~f~in~~Ylgqlfk~~~~e~F~~ylnkvRi~~ak~~Ll~t~~~ 439 (475)
T COG4753 387 ENLTLKDLAKVFHINPVYLGQLFKKETGESFTEYLNKVRIEKAKQLLLQTNDS 439 (475)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 78879999877370899999999998614198999999999999999963772
No 457
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=23.97 E-value=46 Score=13.27 Aligned_cols=20 Identities=15% Similarity=0.091 Sum_probs=15.6
Q ss_pred HHHHHHHCCCCCCCCCCCCC
Q ss_conf 67788861898321100000
Q gi|254780611|r 159 VVAIAKKLNVSESEVISMNC 178 (302)
Q Consensus 159 ~~eiA~~Lgis~~~v~~l~~ 178 (302)
+-++|+.+|++...++-+..
T Consensus 3 Ige~a~~~gvs~~tlRyYe~ 22 (112)
T cd01282 3 IGELAARTGVSVRSLRYYEE 22 (112)
T ss_pred HHHHHHHHCCCHHHHHHHHH
T ss_conf 89999998979999999998
No 458
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=23.92 E-value=46 Score=13.26 Aligned_cols=21 Identities=14% Similarity=0.139 Sum_probs=16.1
Q ss_pred HHHHHHHHCCCCCCCCCCCCC
Q ss_conf 467788861898321100000
Q gi|254780611|r 158 QVVAIAKKLNVSESEVISMNC 178 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v~~l~~ 178 (302)
.+.|+|+..|++.+.++-+..
T Consensus 2 ~IgelA~~tGvs~~TIRyYe~ 22 (95)
T cd04780 2 RMSELSKRSGVSVATIKYYLR 22 (95)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
T ss_conf 789999998978999999999
No 459
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=23.91 E-value=46 Score=13.26 Aligned_cols=21 Identities=14% Similarity=0.102 Sum_probs=16.2
Q ss_pred HHHHHHHHCCCCCCCCCCCCC
Q ss_conf 467788861898321100000
Q gi|254780611|r 158 QVVAIAKKLNVSESEVISMNC 178 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v~~l~~ 178 (302)
++-++|+..|++.+.++-+..
T Consensus 3 ~Ige~A~~~gvs~~tiRyYE~ 23 (140)
T PRK09514 3 RIGELAKLCEVTPDTLRFYEK 23 (140)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
T ss_conf 699999998968999999998
No 460
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=23.58 E-value=47 Score=13.22 Aligned_cols=21 Identities=10% Similarity=0.189 Sum_probs=16.3
Q ss_pred HHHHHHHHCCCCCCCCCCCCC
Q ss_conf 467788861898321100000
Q gi|254780611|r 158 QVVAIAKKLNVSESEVISMNC 178 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v~~l~~ 178 (302)
++-++|+..|++...++-+..
T Consensus 2 ~IgelA~~~gvs~~tlRyYE~ 22 (126)
T cd04785 2 SIGELARRTGVNVETIRYYES 22 (126)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
T ss_conf 689999998949999999998
No 461
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=23.49 E-value=47 Score=13.21 Aligned_cols=21 Identities=19% Similarity=0.368 Sum_probs=16.0
Q ss_pred HHHHHHHHCCCCCCCCCCCCC
Q ss_conf 467788861898321100000
Q gi|254780611|r 158 QVVAIAKKLNVSESEVISMNC 178 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v~~l~~ 178 (302)
++-++|+.+|++...++-+..
T Consensus 3 ~Ige~a~~~gis~~tlRyYe~ 23 (102)
T cd04775 3 TIGQMSRKFGVSRSTLLYYES 23 (102)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
T ss_conf 789999998949999999998
No 462
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=23.32 E-value=47 Score=13.19 Aligned_cols=110 Identities=16% Similarity=0.100 Sum_probs=59.4
Q ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHH--HHHHHHH-----HC----C-----CCCCHHH
Q ss_conf 05999999840799999899999999999828599999999943077--8756555-----57----9-----9998889
Q gi|254780611|r 14 IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL--VVKIAMG-----YR----G-----YGLPISE 77 (302)
Q Consensus 14 ~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrl--V~~iA~~-----y~----~-----~g~~~~D 77 (302)
..+...|++.| ||+-|-..++.... .|-..|++..-.++.+. |..|-++ |. | +.++.++
T Consensus 3 ~~~~~~L~~lG----lt~yEa~vY~aLl~-~g~~tA~eis~~sgvP~~kvY~vl~sLe~kG~v~~~~g~P~~y~av~p~~ 77 (247)
T COG1378 3 EELEENLQKLG----LTEYEAKVYLALLC-LGEATAKEISEASGVPRPKVYDVLRSLEKKGLVEVIEGRPKKYRAVPPEE 77 (247)
T ss_pred HHHHHHHHHCC----CCHHHHHHHHHHHH-HCCCCHHHHHHHCCCCCHHHHHHHHHHHHCCCEEECCCCCCEEEECCHHH
T ss_conf 57999999819----97889999999998-18877999998659993229999999987887784079984488579999
Q ss_pred HHHHH-------HHHHHHHHHHCCCCCCCCHHHH------HHHHHHHHHHHHHHCCCCCHHHCCC
Q ss_conf 99999-------8889989862185345689997------5778999999853202460011023
Q gi|254780611|r 78 VVSEG-------NIGLMQAVKKFDPERGFRLATY------SMWWIKAAMQEYILRSWSLVKIGTT 129 (302)
Q Consensus 78 LiQeG-------~iGLi~Ai~kFDp~kG~~FsTY------A~~wIr~~I~~~i~~~~~~IRiP~~ 129 (302)
++..= .--+...+++.-++.. +.++. -.+-|...+.+.+.+....+.+..+
T Consensus 78 ~i~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~i~g~~~i~~~~~e~i~~a~~ei~~~~~ 141 (247)
T COG1378 78 LIERIKEELQELLRELESELEELERELA-RRESPYLWLIKGSEEIIEKIKEVINEAEKEIIIVLP 141 (247)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCCCCCCCCCCCHHHHHHHHHHHHHHCCCEEEEEEC
T ss_conf 9999999999999999999997532121-345761001478899999999999824067999627
No 463
>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=23.26 E-value=47 Score=13.18 Aligned_cols=21 Identities=14% Similarity=0.164 Sum_probs=16.2
Q ss_pred HHHHHHHHCCCCCCCCCCCCC
Q ss_conf 467788861898321100000
Q gi|254780611|r 158 QVVAIAKKLNVSESEVISMNC 178 (302)
Q Consensus 158 ~~~eiA~~Lgis~~~v~~l~~ 178 (302)
++-|+|+..|++...++-+..
T Consensus 2 tIgelA~~~gvs~~tlRyYe~ 22 (113)
T cd01109 2 TIKEVAEKTGLSADTLRYYEK 22 (113)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
T ss_conf 788999998959999999998
No 464
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=22.90 E-value=48 Score=13.13 Aligned_cols=16 Identities=6% Similarity=0.073 Sum_probs=6.5
Q ss_pred HHHHHHHCCCCCCCCC
Q ss_conf 6778886189832110
Q gi|254780611|r 159 VVAIAKKLNVSESEVI 174 (302)
Q Consensus 159 ~~eiA~~Lgis~~~v~ 174 (302)
+++....-|+++.-+.
T Consensus 207 id~~f~~~g~~P~iv~ 222 (324)
T PRK12681 207 LDTAFNRAGLTPRIVF 222 (324)
T ss_pred HHHHHHHCCCCCEEEE
T ss_conf 9999998899760799
No 465
>TIGR01193 bacteriocin_ABC ABC-type bacteriocin transporter; InterPro: IPR005897 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This family contains ABC-type bacteriocin transporter. In general, bacteriocins are agents which are responsible for killing or inhibiting the closely related species or even different strains of the same species. Bacteriocins are encoded by bacterial plasmids. Bacteriocins are named after the species and hence in literature one encounters various names e.g., leucocin from Leuconostic geldium; pedicocin from Pedicoccus acidilactici; sakacin from Lactobacillus sake etc. Peptide bacteriocins are exported across the cytoplasmic membrane by a dedicated ATP-binding cassette (ABC) transporter. These ABC-transporters have an N-terminal peptidase domain that belong to MEROPS peptidase family C39 (clan CA); a central multi-pass transmembrane region and a C-terminal ABC transporter domain. These transporters have dual function: (i) they remove the N-terminal leader peptide from its bacteriocin precursor by cleavage at a Gly-Gly bond and (ii) transport the mature bacteriocin across the cytoplasmic membrane. This represents a novel strategy for secretion of bacterial proteins . Many bacteria are known to regulate diverse physiological processes through this system, such as bioluminescence, regulation of sporulation, virulence factor expression, antibiotics production, competence for genetic transformation, and activation of biofilm formation .; GO: 0008234 cysteine-type peptidase activity, 0019534 toxin transporter activity, 0006810 transport, 0016020 membrane.
Probab=22.76 E-value=41 Score=13.62 Aligned_cols=68 Identities=13% Similarity=0.216 Sum_probs=29.3
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHCCCCCCHHHHHH-----HHH-----HHHHHCCHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 86655745587405999999840799999899999-----999-----9998285999999999430778756555579
Q gi|254780611|r 2 NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYV-----LAK-----RYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70 (302)
Q Consensus 2 ~~~~~~~~~~~~~~~~~yl~~i~~~~~Lt~eee~~-----l~~-----~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~ 70 (302)
|+..|..+.-=.+|+=.=++-|.-++=|+-|++.- .|. ..+ .--.++-|..+.+-+.|..+|.==|.|
T Consensus 323 N~d~Mq~na~LnSsIIEd~nGIETIKsL~sE~~~y~KId~~F~~yL~K~f~-y~k~~~~Q~AiK~~~~LiL~VvILW~G 400 (710)
T TIGR01193 323 NHDAMQANAVLNSSIIEDLNGIETIKSLTSEAERYKKIDSEFEDYLNKSFK-YQKADQVQQAIKAVLKLILNVVILWVG 400 (710)
T ss_pred CHHHHHHHHHHHHHHHHCCCCCCEEECCCHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 857777654544476625875100100523667776667888888888877-788899989999998788766653442
No 466
>cd07281 PX_SNX1 The phosphoinositide binding Phox Homology domain of Sorting Nexin 1. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX1 is both membrane associated and a cytosolic protein that exists as a tetramer in protein complexes. It can associate reversibly with membranes of the endosomal compartment, thereby coating these vesicles. SNX1 is a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval
Probab=22.50 E-value=49 Score=13.08 Aligned_cols=10 Identities=10% Similarity=0.474 Sum_probs=5.1
Q ss_pred CHHHHHHHHH
Q ss_conf 8999757789
Q gi|254780611|r 100 RLATYSMWWI 109 (302)
Q Consensus 100 ~FsTYA~~wI 109 (302)
-.++|.+|-|
T Consensus 14 g~~~y~~Y~V 23 (124)
T cd07281 14 GMNAYVVYKV 23 (124)
T ss_pred CCCCEEEEEE
T ss_conf 8427799999
No 467
>pfam09068 efhand_1 EF hand. Members of this family adopt a helix-loop-helix motif, as per other EF hand domains. However, since they do not contain the canonical pattern of calcium binding residues found in many EF hand domains, they do not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (pfam00397), enhancing dystroglycan binding.
Probab=22.39 E-value=49 Score=13.07 Aligned_cols=20 Identities=25% Similarity=0.516 Sum_probs=14.7
Q ss_pred HHHHHHHHHHCCCCCCCCHHHHH
Q ss_conf 88899898621853456899975
Q gi|254780611|r 83 NIGLMQAVKKFDPERGFRLATYS 105 (302)
Q Consensus 83 ~iGLi~Ai~kFDp~kG~~FsTYA 105 (302)
+.-|++....|| .+|||+|=
T Consensus 2 m~el~~~L~dln---~IrfsaYR 21 (125)
T pfam09068 2 MTELMQELADLN---NIRFSAYR 21 (125)
T ss_pred HHHHHHHHHHHC---CHHHHHHH
T ss_conf 789999998705---05699999
No 468
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=22.38 E-value=49 Score=13.07 Aligned_cols=25 Identities=16% Similarity=0.321 Sum_probs=0.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 8989999997789999999999999
Q gi|254780611|r 253 VTLENLSSEFEVSRERVRQIEARAF 277 (302)
Q Consensus 253 ~Tl~EIa~~lgiS~eRVrQI~~~AL 277 (302)
|+-.|+|+.+|||...+|-=++..|
T Consensus 1 M~IgevAk~~gvs~~TlRyYE~~GL 25 (116)
T cd04769 1 MYIGELAQQTGVTIKAIRLYEEKGL 25 (116)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCC
T ss_conf 9689999998969999999998699
No 469
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=22.27 E-value=49 Score=13.05 Aligned_cols=25 Identities=8% Similarity=0.290 Sum_probs=0.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 8989999997789999999999999
Q gi|254780611|r 253 VTLENLSSEFEVSRERVRQIEARAF 277 (302)
Q Consensus 253 ~Tl~EIa~~lgiS~eRVrQI~~~AL 277 (302)
|+..|+|+..|||.+.||-=|+..|
T Consensus 1 M~IgelAk~tGv~~~TIRyYE~~GL 25 (135)
T PRK10227 1 MNISDVAKITGLTSKAIRFYEEKGL 25 (135)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCC
T ss_conf 9689999998969999999998389
No 470
>PRK12422 chromosomal replication initiation protein; Provisional
Probab=22.20 E-value=50 Score=13.04 Aligned_cols=44 Identities=11% Similarity=0.360 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999982788888989999997789999999999999999999997
Q gi|254780611|r 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286 (302)
Q Consensus 237 ~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~ 286 (302)
+|+-.+...|-+.+ +|+.+||+.+|=...+| -.|++|..+.|++
T Consensus 384 aRqiAMYL~R~lt~--~Sl~~IG~~FgRdHSTV----ihaikkIe~~l~~ 427 (455)
T PRK12422 384 PRQVAMYLCRQKLS--LSYVKIGDVFSRDHSTV----ISSIRAISQKLEE 427 (455)
T ss_pred HHHHHHHHHHHHHC--CCHHHHHHHHCCCCCHH----HHHHHHHHHHHHH
T ss_conf 99999999998836--88999988759985099----9999999999973
No 471
>PHA01083 hypothetical protein
Probab=21.98 E-value=50 Score=13.01 Aligned_cols=19 Identities=11% Similarity=0.466 Sum_probs=0.0
Q ss_pred HHHHHHHCCCHHHHHHHHH
Q ss_conf 9999997789999999999
Q gi|254780611|r 256 ENLSSEFEVSRERVRQIEA 274 (302)
Q Consensus 256 ~EIa~~lgiS~eRVrQI~~ 274 (302)
++||..||+|+.+++.+.+
T Consensus 18 KQIAhDlg~~pq~iS~~Rk 36 (153)
T PHA01083 18 KQIAHDLGVSPQKISKMRT 36 (153)
T ss_pred HHHHHHHCCCHHHHHHHHH
T ss_conf 9999980999899999981
No 472
>PRK07248 hypothetical protein; Provisional
Probab=21.91 E-value=50 Score=13.01 Aligned_cols=55 Identities=15% Similarity=0.242 Sum_probs=0.0
Q ss_pred HHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 9984079999989999999999982859999999994307787565555799998
Q gi|254780611|r 20 IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74 (302)
Q Consensus 20 l~~i~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~ 74 (302)
++.-...|.+.++.|.+.+.++.........+..|..-.+.+.+..++|..+.++
T Consensus 34 ~K~~~~~~v~dp~RE~~il~~~~~~~~~~~~~~~i~~if~~Im~~Sr~~Q~~~l~ 88 (88)
T PRK07248 34 YKKATGKPVLDQKRENAILDRVSYLVENKAYEETIVATFKDIMKLSRQYQTQNLE 88 (88)
T ss_pred HHHHCCCCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 9988599988959999999999976779997799999999999999999998748
No 473
>cd06866 PX_SNX8_Mvp1p_like The phosphoinositide binding Phox Homology domain of Sorting Nexin 8 and yeast Mvp1p. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Some SNXs are localized in early endosome structures such as clathrin-coated pits, while others are located in late structures of the endocytic pathway. SNX8 and the yeast counterpart Mvp1p are involved in sorting and delivery of late-Golgi proteins, such as carboxypeptidase Y, to vacuoles.
Probab=21.80 E-value=51 Score=12.99 Aligned_cols=24 Identities=29% Similarity=0.506 Sum_probs=0.0
Q ss_pred HHHHHHHHHHCCCCCCHHHHHHHH
Q ss_conf 599999984079999989999999
Q gi|254780611|r 15 GLSRYIHEIRKIPMLEKQEEYVLA 38 (302)
Q Consensus 15 ~~~~yl~~i~~~~~Lt~eee~~l~ 38 (302)
+|+.||+.|.++|.|..++....|
T Consensus 78 ~Le~FL~~l~~hP~l~~s~~l~~F 101 (105)
T cd06866 78 GLSRFLNLVARHPVLSEDELVRTF 101 (105)
T ss_pred HHHHHHHHHHCCCCCCCCCHHHHH
T ss_conf 999999999769311059499855
No 474
>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=21.80 E-value=3.1 Score=21.05 Aligned_cols=30 Identities=20% Similarity=0.324 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCHHHHH
Q ss_conf 899999988899898621853456899975
Q gi|254780611|r 76 SEVVSEGNIGLMQAVKKFDPERGFRLATYS 105 (302)
Q Consensus 76 ~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA 105 (302)
.||+....|--.+-++=++-+-|.||+|||
T Consensus 30 ~~Lm~aagi~~~E~V~V~Nv~NG~R~~TYv 59 (116)
T pfam02261 30 EDLLDAAGILEYEKVQIVNVNNGERFETYV 59 (116)
T ss_pred HHHHHHCCCCCCCEEEEEECCCCCEEEEEE
T ss_conf 999987599989889999898996899998
No 475
>pfam08784 RPA_C Replication protein A C terminal. This domain corresponds to the C terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints.
Probab=21.34 E-value=52 Score=12.93 Aligned_cols=42 Identities=14% Similarity=0.330 Sum_probs=0.0
Q ss_pred CCHHHHHHHHHHH---CCCCCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Q ss_conf 9999999999982---788888989999997-789999999999999999
Q gi|254780611|r 235 LNPRERRIFEARR---LQENPVTLENLSSEF-EVSRERVRQIEARAFKKV 280 (302)
Q Consensus 235 L~~rEr~II~~ry---~~~~~~Tl~EIa~~l-giS~eRVrQI~~~AL~kL 280 (302)
|++-.+.|+.+.- ..++++...||+..| |++...| ++|++-|
T Consensus 45 ls~~~~~V~~~i~~~~~~~eG~h~~~l~~~l~~~~~~~i----~~a~d~L 90 (103)
T pfam08784 45 LTPLQDQVLNLIKQSCPGEEGVHVDELAAQLNGLPVNDI----RQAVDFL 90 (103)
T ss_pred CCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCHHHH----HHHHHHH
T ss_conf 789999999999954889887279999999829999999----9999999
No 476
>pfam00486 Trans_reg_C Transcriptional regulatory protein, C terminal.
Probab=21.31 E-value=52 Score=12.93 Aligned_cols=53 Identities=15% Similarity=0.167 Sum_probs=0.0
Q ss_pred CCCHHHHHHHHHHHC-CCCCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 199999999999827-88888989999997-789999999999999999999997
Q gi|254780611|r 234 VLNPRERRIFEARRL-QENPVTLENLSSEF-EVSRERVRQIEARAFKKVQESIQK 286 (302)
Q Consensus 234 ~L~~rEr~II~~ry~-~~~~~Tl~EIa~~l-giS~eRVrQI~~~AL~kLR~~l~~ 286 (302)
.|+++|..|+...+- .+...|-.+|.+.+ |-...--..--...+.+||+.|+.
T Consensus 5 ~Lt~~E~~lL~~L~~~~~~~vsr~~l~~~iw~~~~~~~~~sl~~~I~rLR~kl~~ 59 (77)
T pfam00486 5 ELTPKEFDLLELLARNPGRVVSREELLEEVWGEDFDVDDNTVDVHISRLRKKLED 59 (77)
T ss_pred ECCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHH
T ss_conf 3389999999999967997197999999963876665533099999999998754
No 477
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=21.24 E-value=52 Score=12.92 Aligned_cols=39 Identities=15% Similarity=0.261 Sum_probs=0.0
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf 9899999977899999999999999999999974012246776
Q gi|254780611|r 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPL 296 (302)
Q Consensus 254 Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~~~~~~~~~~ 296 (302)
|+...|+.||||+..| +++|++|.+.+.-++-..+...+
T Consensus 17 s~t~AA~~L~isQ~av----S~~i~~LE~~lg~~Lf~R~~r~~ 55 (292)
T PRK11242 17 NFTRAAEALHVSQPTL----SQQIRQLEESLGVQLFDRSGRTV 55 (292)
T ss_pred CHHHHHHHHCCCHHHH----HHHHHHHHHHHCCEEEEECCCCC
T ss_conf 9999999988798999----99999999996987389889985
No 478
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit; InterPro: IPR002023 Respiratory-chain NADH dehydrogenase (ubiquinone) (1.6.5.3 from EC) , (also known as complex I or NADH-ubiquinone oxidoreductase) is an oligomeric enzymatic complex located in the inner mitochondrial membrane which also seems to exist in the chloroplast and in cyanobacteria (as a NADH-plastoquinone oxidoreductase). Among the 25 to 30 polypeptide subunits of this bioenergetic enzyme complex there is one with a molecular weight of 24 kDa (in mammals), which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulphur cluster. The 24 kDa subunit is nuclear encoded, as a precursor form with a transit peptide in mammals and in Neurospora crassa. There is a highly conserved region located in the central section of this subunit that contains two conserved cysteines, that are probably involved in the binding of the 2Fe-2S centre. The 24 kDa subunit is highly similar to , : Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase ; GO: 0016491 oxidoreductase activity, 0051287 NAD binding, 0006118 electron transport.
Probab=21.20 E-value=52 Score=12.91 Aligned_cols=60 Identities=18% Similarity=0.216 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHCCCCCHHHCC--CCHHHHHHHHHHHHHHH-HHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCC
Q ss_conf 899999985320246001102--30035899999999788-7866244788824677888618983211000000122
Q gi|254780611|r 108 WIKAAMQEYILRSWSLVKIGT--TANQKRLFFNLRRLKGH-LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182 (302)
Q Consensus 108 wIr~~I~~~i~~~~~~IRiP~--~~~~r~l~~~~rk~~~~-~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~ 182 (302)
||-..|.+| |. .....-+..-++.+++. ..++ .++.+++||+.||++..+|.+.....+.
T Consensus 1 ~i~~~~~kY----------P~tP~~~RSA~~~~L~~aQ~~n~Gwv-----~~~~i~~vA~~L~~~~~~V~eVATFY~~ 63 (153)
T TIGR01958 1 EIEEAIAKY----------PDTPDQKRSAILPALRIAQKQNKGWV-----SPEAIEAVAEMLGIPPVWVYEVATFYSM 63 (153)
T ss_pred CHHHHHHCC----------CCCCCHHHHHHHHHHHHHHHHHCCCC-----CHHHHHHHHHHHCCCHHHEEEEEEEHHH
T ss_conf 923365427----------89972368999999999987407864-----8899999999868870130213100100
No 479
>COG4537 ComGC Competence protein ComGC [Intracellular trafficking and secretion]
Probab=20.91 E-value=53 Score=12.87 Aligned_cols=46 Identities=30% Similarity=0.422 Sum_probs=0.0
Q ss_pred CCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHC---CC-CCCHHHHHHHHHH
Q ss_conf 99999899999999999828599999999943077875655557---99-9988899999988
Q gi|254780611|r 26 IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GY-GLPISEVVSEGNI 84 (302)
Q Consensus 26 ~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~---~~-g~~~~DLiQeG~i 84 (302)
+|-+|++-+. +++.|+.+.-. +|.+-|.-|. ++ .-+++||..+|+|
T Consensus 34 iPNltKq~~~-----i~~kGc~A~vk--------mV~sQ~~~YeLdh~~~~pSl~~L~s~G~i 83 (107)
T COG4537 34 IPNLTKQKEV-----IQDKGCEAVVK--------MVESQAEAYELDHNRLPPSLSDLKSDGYI 83 (107)
T ss_pred CCCHHHHHHH-----HHCCHHHHHHH--------HHHHHHHHHHHCCCCCCCCHHHHHHCCCE
T ss_conf 4625443798-----86300899999--------99999999984258899889999768833
No 480
>pfam00988 CPSase_sm_chain Carbamoyl-phosphate synthase small chain, CPSase domain. The carbamoyl-phosphate synthase domain is in the amino terminus of protein. Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. The small chain promotes the hydrolysis of glutamine to ammonia, which is used by the large chain to synthesize carbamoyl phosphate. See pfam00289. The small chain has a GATase domain in the carboxyl terminus. See pfam00117.
Probab=20.64 E-value=53 Score=12.83 Aligned_cols=45 Identities=24% Similarity=0.476 Sum_probs=0.0
Q ss_pred CCCCCCCCC---CHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHH
Q ss_conf 655745587---4059999998407999998999999999998285999
Q gi|254780611|r 4 KNMSIIVNG---EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSA 49 (302)
Q Consensus 4 ~~~~~~~~~---~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~gd~~A 49 (302)
+++....++ ..+|+.||.+ .++|-++-=+-+.|.+++|++|.+.|
T Consensus 81 ~~~~~~~S~~~s~~sL~~~L~~-~~IpgI~gIDTRaLt~~iR~~G~~~~ 128 (131)
T pfam00988 81 RELSDIPSNWRSEESLDEFLKE-HGIPGISGVDTRALTRKLREKGAMKG 128 (131)
T ss_pred CCCCCCCCCHHHHCCHHHHHHH-CCCCEEECCCHHHHHHHHHHCCCCCE
T ss_conf 3566576653233599999997-79722706618999999986698516
No 481
>PRK02842 light-independent protochlorophyllide reductase subunit N; Provisional
Probab=20.55 E-value=54 Score=12.82 Aligned_cols=46 Identities=20% Similarity=0.303 Sum_probs=0.0
Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHH-----HHHHHHHHHHCCCCCCCCCCCC
Q ss_conf 899999977899999999999999-----9999999740122467764589
Q gi|254780611|r 255 LENLSSEFEVSRERVRQIEARAFK-----KVQESIQKQVELSSSPPLLQKP 300 (302)
Q Consensus 255 l~EIa~~lgiS~eRVrQI~~~AL~-----kLR~~l~~~~~~~~~~~~~~~~ 300 (302)
++.||..+||+.++++.....+.. +.|..|+.|==+..+.-.||-|
T Consensus 253 l~aiA~~fgv~~~~~~~~~~~~~aR~al~~~r~~L~GK~VFf~pDsqLEip 303 (425)
T PRK02842 253 LEAAAAAFGIDPDGLEEREAPAWERKALEPYRELLRGKRVFFLPDSQLEIP 303 (425)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCCCH
T ss_conf 999999849988889988887888888986567636974898068655214
No 482
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su
Probab=20.55 E-value=54 Score=12.82 Aligned_cols=25 Identities=20% Similarity=0.361 Sum_probs=0.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 8989999997789999999999999
Q gi|254780611|r 253 VTLENLSSEFEVSRERVRQIEARAF 277 (302)
Q Consensus 253 ~Tl~EIa~~lgiS~eRVrQI~~~AL 277 (302)
|+..|+|+..|||...+|-=++..|
T Consensus 1 M~IgelA~~~gvs~~tlR~YE~~GL 25 (131)
T cd04786 1 MKIGELAKRSGMAASRIRFYEAEGL 25 (131)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCC
T ss_conf 9789999998878899999997799
No 483
>cd06862 PX_SNX9_18_like The phosphoinositide binding Phox Homology domain of Sorting Nexins 9 and 18. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. This subfamily consists of SNX9, SNX18, and similar proteins. They contain an N-terminal Src Homology 3 (SH3) domain, a PX domain, and a C-terminal Bin/Amphiphysin/Rvs (BAR) domain. SNX9 is localized to plasma membrane endocytic sites and acts primarily in clathrin-mediated endocytosis, while SNX18 is loca
Probab=20.47 E-value=43 Score=13.44 Aligned_cols=38 Identities=16% Similarity=0.331 Sum_probs=0.0
Q ss_pred HHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHH
Q ss_conf 59999998407999998999999999998285999999
Q gi|254780611|r 15 GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHR 52 (302)
Q Consensus 15 ~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~ 52 (302)
+|+.||+.|..+|.|...+....+-...+.++-.+..+
T Consensus 80 ~Le~FL~~i~~hp~L~~s~~~~~FL~~~de~~w~~~~~ 117 (125)
T cd06862 80 RLELWMNRLARHPVLSQSEVFRHFLTCTDEKDWKSGKR 117 (125)
T ss_pred HHHHHHHHHHCCCCCCCCCHHHHHCCCCCHHHHHHHHH
T ss_conf 99999999965947266908862234888789998708
No 484
>pfam05930 Phage_AlpA Prophage CP4-57 regulatory protein (AlpA). This family consists of several short bacterial and phage proteins which are related to the E. coli protein AlpA. AlpA suppress two phenotypes of a delta lon protease mutant, overproduction of capsular polysaccharide and sensitivity to UV light. Several of the sequences in this family are thought to be DNA-binding proteins.
Probab=20.45 E-value=54 Score=12.81 Aligned_cols=23 Identities=13% Similarity=0.219 Sum_probs=0.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 89899999977899999999999
Q gi|254780611|r 253 VTLENLSSEFEVSRERVRQIEAR 275 (302)
Q Consensus 253 ~Tl~EIa~~lgiS~eRVrQI~~~ 275 (302)
+.++|+.+.+|+|+..|-+..+.
T Consensus 4 lr~~eV~~~~glsrstiyr~i~~ 26 (51)
T pfam05930 4 LRLKEVEQLTGLSRSTIYRLIKD 26 (51)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHC
T ss_conf 37999999989899999999987
No 485
>COG4533 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=20.20 E-value=54 Score=12.77 Aligned_cols=43 Identities=21% Similarity=0.221 Sum_probs=0.0
Q ss_pred HHHHHHHHHH--H-CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999998--2-788888989999997789999999999999999999
Q gi|254780611|r 237 PRERRIFEAR--R-LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302)
Q Consensus 237 ~rEr~II~~r--y-~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302)
......++++ | |.....|+.|+|+.+.+|+-.||-+ |.||.+.
T Consensus 5 ~~~~~~~rL~q~~~g~~~~~tl~eLA~~lfCS~Rh~R~l----L~q~q~~ 50 (564)
T COG4533 5 RLLQQYIRLWQPYAGQPVETTLNELADILFCSRRHARTL----LRQMQEA 50 (564)
T ss_pred HHHHHHHHHHCCCCCCCCEEEHHHHHHHHCCCHHHHHHH----HHHHHHC
T ss_conf 899999998520179874336999988862677899999----9999875
No 486
>PRK08024 consensus
Probab=20.02 E-value=55 Score=12.75 Aligned_cols=67 Identities=12% Similarity=0.208 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHH-HHHHHHHHHHHHHHHH
Q ss_conf 667779999996219999999999982788888989999997789999999-9999999999999974
Q gi|254780611|r 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ-IEARAFKKVQESIQKQ 287 (302)
Q Consensus 221 ~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQ-I~~~AL~kLR~~l~~~ 287 (302)
++....-|..++-.+++.|+.-|...++..-+.++-|++.....|.+.+.+ ++-..+..|.+.+++.
T Consensus 56 r~ia~~NL~~aFPe~s~~e~~~i~~~~~~~~g~~~~E~~~~~~~~~~~l~~~~~i~g~E~l~~a~~~g 123 (306)
T PRK08024 56 AKIAHRNLELCFPEMSEQERRAMVVKNFESVGMGLMETGMAWFWPDRRIARWTEVSGLEHIRDVQAQK 123 (306)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHCEEEEECHHHHHHHHHCC
T ss_conf 89999999986899999999999999999999999999998517888772468983899999999759
Done!