Query 046578
Match_columns 379
No_of_seqs 312 out of 1558
Neff 7.4
Searched_HMMs 46136
Date Fri Mar 29 13:34:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046578.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046578hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK09210 RNA polymerase sigma 100.0 2.1E-45 4.5E-50 364.0 30.3 250 129-378 117-366 (367)
2 PRK07921 RNA polymerase sigma 100.0 2.9E-45 6.3E-50 356.3 30.3 249 129-378 75-323 (324)
3 PRK05658 RNA polymerase sigma 100.0 2.4E-45 5.3E-50 385.8 30.5 299 80-378 297-617 (619)
4 PRK05901 RNA polymerase sigma 100.0 3E-45 6.5E-50 371.5 29.9 240 140-379 270-509 (509)
5 COG0568 RpoD DNA-directed RNA 100.0 4.4E-45 9.6E-50 351.2 27.4 250 129-378 88-341 (342)
6 PRK07598 RNA polymerase sigma 100.0 1.1E-44 2.3E-49 359.3 30.2 253 124-378 159-411 (415)
7 PRK05949 RNA polymerase sigma 100.0 8.9E-44 1.9E-48 346.7 35.1 250 125-378 76-325 (327)
8 PRK07406 RNA polymerase sigma 100.0 2.2E-44 4.8E-49 354.9 30.9 252 126-379 122-373 (373)
9 TIGR02393 RpoD_Cterm RNA polym 100.0 2.2E-43 4.7E-48 330.6 27.4 237 142-378 1-237 (238)
10 PRK07405 RNA polymerase sigma 100.0 1.1E-42 2.3E-47 338.3 30.5 250 125-378 66-315 (317)
11 TIGR02997 Sig70-cyanoRpoD RNA 100.0 2.1E-42 4.6E-47 334.0 29.3 239 126-366 60-298 (298)
12 PRK07408 RNA polymerase sigma 100.0 1.2E-39 2.6E-44 308.4 29.2 238 128-372 11-254 (256)
13 PRK05657 RNA polymerase sigma 100.0 2.2E-39 4.9E-44 315.9 30.8 247 129-375 74-320 (325)
14 PRK07122 RNA polymerase sigma 100.0 4.7E-39 1E-43 305.5 27.9 224 137-369 33-263 (264)
15 COG1191 FliA DNA-directed RNA 100.0 1.3E-38 2.9E-43 295.9 26.9 234 127-371 10-246 (247)
16 PRK05911 RNA polymerase sigma 100.0 5.6E-38 1.2E-42 297.1 29.7 236 129-371 10-255 (257)
17 PRK07500 rpoH2 RNA polymerase 100.0 8.2E-38 1.8E-42 300.6 30.3 243 128-373 26-281 (289)
18 PRK06596 RNA polymerase factor 100.0 1.2E-37 2.7E-42 298.7 29.6 238 129-371 35-282 (284)
19 TIGR02850 spore_sigG RNA polym 100.0 2.2E-37 4.7E-42 292.7 29.0 231 129-369 22-254 (254)
20 TIGR02394 rpoS_proteo RNA poly 100.0 4.6E-37 1E-41 295.1 30.6 247 128-374 33-279 (285)
21 TIGR02392 rpoH_proteo alternat 100.0 4.8E-37 1E-41 292.8 29.3 238 128-370 21-269 (270)
22 PRK08215 sporulation sigma fac 100.0 1.5E-36 3.1E-41 287.7 28.8 232 128-369 24-257 (258)
23 TIGR02885 spore_sigF RNA polym 100.0 1.7E-36 3.7E-41 282.5 27.8 229 131-369 1-231 (231)
24 TIGR02941 Sigma_B RNA polymera 100.0 4.5E-36 9.7E-41 283.8 29.3 237 127-369 14-253 (255)
25 PRK07670 RNA polymerase sigma 100.0 1.4E-35 3.1E-40 279.9 29.4 236 128-370 8-250 (251)
26 TIGR02980 SigBFG RNA polymeras 100.0 2.9E-35 6.4E-40 273.4 27.5 222 139-369 1-226 (227)
27 PRK06288 RNA polymerase sigma 100.0 7E-35 1.5E-39 277.7 29.2 237 128-371 17-262 (268)
28 PRK05572 sporulation sigma fac 100.0 3.6E-34 7.9E-39 270.4 28.5 232 127-370 18-251 (252)
29 PRK08583 RNA polymerase sigma 100.0 4.2E-34 9.1E-39 270.6 28.6 236 128-372 15-256 (257)
30 TIGR02479 FliA_WhiG RNA polyme 100.0 3.1E-34 6.7E-39 266.2 26.4 217 146-369 1-223 (224)
31 PRK06986 fliA flagellar biosyn 100.0 6E-33 1.3E-37 259.6 28.1 223 140-371 7-234 (236)
32 PRK12427 flagellar biosynthesi 100.0 3.4E-32 7.4E-37 253.7 27.3 209 143-368 17-230 (231)
33 PRK05803 sporulation sigma fac 100.0 2.4E-27 5.1E-32 221.4 23.3 192 128-372 36-230 (233)
34 PRK08301 sporulation sigma fac 100.0 3.2E-27 6.9E-32 220.5 22.8 192 127-371 38-232 (234)
35 TIGR02846 spore_sigmaK RNA pol 100.0 5.4E-27 1.2E-31 218.2 22.9 191 126-369 33-226 (227)
36 PRK08295 RNA polymerase factor 100.0 1.7E-26 3.8E-31 211.1 22.7 197 124-372 7-205 (208)
37 TIGR02835 spore_sigmaE RNA pol 99.9 2.6E-26 5.6E-31 214.6 23.2 192 127-371 38-232 (234)
38 PRK05602 RNA polymerase sigma 99.9 4.9E-26 1.1E-30 204.9 21.6 178 125-374 4-181 (186)
39 PRK09646 RNA polymerase sigma 99.9 4.2E-26 9E-31 207.0 21.2 186 118-371 7-192 (194)
40 TIGR02948 SigW_bacill RNA poly 99.9 1.7E-25 3.8E-30 200.9 21.0 182 128-371 5-186 (187)
41 PRK12513 RNA polymerase sigma 99.9 1.2E-25 2.7E-30 203.6 20.2 182 126-374 11-192 (194)
42 PRK09648 RNA polymerase sigma 99.9 2.8E-25 6E-30 200.5 22.1 177 125-370 8-188 (189)
43 PRK09641 RNA polymerase sigma 99.9 2.2E-25 4.8E-30 200.2 21.2 184 126-371 3-186 (187)
44 TIGR02859 spore_sigH RNA polym 99.9 2E-25 4.4E-30 202.4 21.1 192 126-369 4-197 (198)
45 TIGR02952 Sig70_famx2 RNA poly 99.9 1.7E-25 3.6E-30 197.8 20.0 170 131-369 1-170 (170)
46 PRK12537 RNA polymerase sigma 99.9 1.9E-25 4.1E-30 200.6 19.9 175 125-369 7-181 (182)
47 PRK12524 RNA polymerase sigma 99.9 5E-25 1.1E-29 200.2 21.7 178 126-373 11-188 (196)
48 TIGR02939 RpoE_Sigma70 RNA pol 99.9 9E-25 1.9E-29 196.7 21.7 183 126-370 5-187 (190)
49 PRK12514 RNA polymerase sigma 99.9 6.7E-25 1.5E-29 196.2 20.3 175 126-370 4-178 (179)
50 PRK12538 RNA polymerase sigma 99.9 6.7E-25 1.4E-29 204.9 20.8 176 126-373 48-223 (233)
51 PRK11923 algU RNA polymerase s 99.9 1.3E-24 2.9E-29 196.6 22.1 185 125-371 4-188 (193)
52 PRK12519 RNA polymerase sigma 99.9 7E-25 1.5E-29 198.6 20.3 178 125-370 13-190 (194)
53 PRK09652 RNA polymerase sigma 99.9 9.8E-25 2.1E-29 194.3 20.2 177 132-370 1-177 (182)
54 PRK13919 putative RNA polymera 99.9 1E-24 2.2E-29 196.2 20.3 179 124-370 6-184 (186)
55 PRK06811 RNA polymerase factor 99.9 1.2E-24 2.6E-29 196.6 20.5 180 126-375 3-185 (189)
56 PRK12531 RNA polymerase sigma 99.9 8.1E-25 1.8E-29 198.5 19.4 188 121-374 7-194 (194)
57 PRK12542 RNA polymerase sigma 99.9 4.6E-25 9.9E-30 198.5 16.3 176 135-377 3-178 (185)
58 PRK09643 RNA polymerase sigma 99.9 3.9E-24 8.3E-29 193.9 21.3 174 125-371 11-184 (192)
59 PRK12515 RNA polymerase sigma 99.9 5E-24 1.1E-28 192.4 21.8 180 124-374 5-184 (189)
60 PRK12534 RNA polymerase sigma 99.9 2E-24 4.4E-29 194.4 19.2 177 126-370 10-186 (187)
61 PRK11922 RNA polymerase sigma 99.9 3.8E-24 8.3E-29 199.5 21.1 187 124-371 13-199 (231)
62 PRK06759 RNA polymerase factor 99.9 1.8E-24 4E-29 188.4 17.3 153 138-368 1-153 (154)
63 TIGR02954 Sig70_famx3 RNA poly 99.9 4.2E-24 9.1E-29 189.3 19.6 167 127-370 2-168 (169)
64 TIGR02984 Sig-70_plancto1 RNA 99.9 8.8E-24 1.9E-28 190.0 20.4 181 136-369 2-188 (189)
65 PRK12526 RNA polymerase sigma 99.9 9.2E-24 2E-28 193.6 20.5 179 129-372 26-204 (206)
66 PRK11924 RNA polymerase sigma 99.9 1.6E-23 3.4E-28 186.0 21.2 175 130-372 2-176 (179)
67 TIGR03001 Sig-70_gmx1 RNA poly 99.9 1.5E-23 3.3E-28 197.0 22.2 183 126-377 24-217 (244)
68 PRK09640 RNA polymerase sigma 99.9 3E-24 6.5E-29 193.8 16.7 175 125-371 7-184 (188)
69 PRK09649 RNA polymerase sigma 99.9 5.7E-24 1.2E-28 191.7 18.3 175 126-374 9-183 (185)
70 PRK12543 RNA polymerase sigma 99.9 7.9E-24 1.7E-28 189.6 19.1 168 136-373 2-169 (179)
71 PRK12536 RNA polymerase sigma 99.9 7.5E-24 1.6E-28 190.1 18.5 173 127-372 7-180 (181)
72 PRK12539 RNA polymerase sigma 99.9 1.6E-23 3.5E-28 188.3 20.0 173 126-372 6-182 (184)
73 PRK09638 RNA polymerase sigma 99.9 1.1E-23 2.3E-28 187.7 18.3 172 127-370 4-175 (176)
74 PRK09645 RNA polymerase sigma 99.9 1.4E-23 3.1E-28 186.5 18.5 167 136-373 4-170 (173)
75 TIGR02999 Sig-70_X6 RNA polyme 99.9 2.3E-23 5E-28 186.7 19.0 174 127-369 3-182 (183)
76 PRK12518 RNA polymerase sigma 99.9 1.3E-23 2.9E-28 186.9 17.2 172 131-373 1-172 (175)
77 PRK12529 RNA polymerase sigma 99.9 1.3E-23 2.9E-28 188.1 17.1 168 134-369 6-175 (178)
78 PRK12512 RNA polymerase sigma 99.9 3.8E-23 8.3E-28 185.7 19.7 170 128-372 9-182 (184)
79 PRK12520 RNA polymerase sigma 99.9 3.2E-23 7E-28 187.4 18.6 181 142-373 3-183 (191)
80 PRK12535 RNA polymerase sigma 99.9 5.6E-23 1.2E-27 187.1 19.7 179 122-372 6-184 (196)
81 PRK09415 RNA polymerase factor 99.9 6.1E-23 1.3E-27 183.9 19.1 165 138-371 13-177 (179)
82 COG1595 RpoE DNA-directed RNA 99.9 1.1E-22 2.4E-27 182.7 19.6 175 130-372 4-178 (182)
83 PRK12522 RNA polymerase sigma 99.9 1E-22 2.2E-27 181.3 18.9 167 141-371 3-169 (173)
84 TIGR02947 SigH_actino RNA poly 99.9 4.4E-23 9.5E-28 186.9 16.4 177 135-371 5-181 (193)
85 PRK12523 RNA polymerase sigma 99.9 4.3E-23 9.4E-28 183.5 16.1 167 135-372 4-170 (172)
86 PRK12516 RNA polymerase sigma 99.9 1.6E-22 3.4E-27 182.8 19.0 163 137-373 6-168 (187)
87 TIGR02983 SigE-fam_strep RNA p 99.9 1.1E-22 2.4E-27 178.8 16.8 160 136-371 1-160 (162)
88 PRK12533 RNA polymerase sigma 99.9 2.6E-22 5.7E-27 185.3 19.9 173 137-373 14-186 (216)
89 PRK08241 RNA polymerase factor 99.9 2.9E-22 6.4E-27 196.9 21.3 183 128-368 6-200 (339)
90 PRK09647 RNA polymerase sigma 99.9 4.4E-22 9.5E-27 182.2 20.4 167 136-372 23-189 (203)
91 TIGR02989 Sig-70_gvs1 RNA poly 99.9 1.3E-22 2.8E-27 177.6 16.0 159 141-369 1-159 (159)
92 TIGR02985 Sig70_bacteroi1 RNA 99.9 1.7E-22 3.7E-27 176.2 16.1 161 141-369 1-161 (161)
93 PRK09642 RNA polymerase sigma 99.9 2.1E-22 4.7E-27 176.7 16.4 156 148-372 2-157 (160)
94 TIGR02960 SigX5 RNA polymerase 99.9 5.9E-22 1.3E-26 193.4 20.6 184 137-371 1-192 (324)
95 PRK09644 RNA polymerase sigma 99.9 6.2E-22 1.3E-26 174.8 17.5 158 143-373 3-160 (165)
96 PRK12541 RNA polymerase sigma 99.9 9.2E-22 2E-26 173.0 18.2 158 138-368 2-159 (161)
97 TIGR02943 Sig70_famx1 RNA poly 99.9 1.3E-21 2.9E-26 176.8 18.7 172 145-375 6-185 (188)
98 PRK12545 RNA polymerase sigma 99.9 1.5E-21 3.2E-26 178.3 19.1 182 144-374 11-192 (201)
99 PRK12530 RNA polymerase sigma 99.9 1.9E-21 4.1E-26 175.8 18.8 175 145-372 11-185 (189)
100 PRK12547 RNA polymerase sigma 99.9 2.6E-21 5.7E-26 170.8 19.1 159 140-372 5-163 (164)
101 PRK12532 RNA polymerase sigma 99.9 2.1E-21 4.5E-26 176.2 18.8 178 144-374 8-189 (195)
102 PRK12528 RNA polymerase sigma 99.9 1.8E-21 4E-26 171.0 17.8 158 140-368 3-160 (161)
103 PRK12544 RNA polymerase sigma 99.9 3.1E-21 6.7E-26 177.0 19.7 182 143-374 20-201 (206)
104 PRK09639 RNA polymerase sigma 99.9 2.7E-21 5.9E-26 170.4 18.6 161 140-372 2-162 (166)
105 PRK12517 RNA polymerase sigma 99.9 2.6E-21 5.7E-26 174.9 17.6 164 134-372 16-179 (188)
106 TIGR02937 sigma70-ECF RNA poly 99.9 4E-21 8.6E-26 164.9 17.7 158 141-369 1-158 (158)
107 PRK09651 RNA polymerase sigma 99.9 6.2E-21 1.4E-25 169.8 17.9 165 137-372 6-170 (172)
108 PRK09637 RNA polymerase sigma 99.9 8.1E-21 1.8E-25 170.7 18.6 154 143-371 3-156 (181)
109 PRK12540 RNA polymerase sigma 99.9 8E-21 1.7E-25 170.9 18.4 160 141-374 5-164 (182)
110 PRK12527 RNA polymerase sigma 99.9 9.9E-21 2.1E-25 166.0 17.5 156 147-372 1-156 (159)
111 TIGR02950 SigM_subfam RNA poly 99.9 2.6E-21 5.5E-26 168.4 13.4 153 147-369 1-153 (154)
112 PRK07037 extracytoplasmic-func 99.9 2.6E-20 5.7E-25 163.8 18.7 159 145-372 2-160 (163)
113 PRK12511 RNA polymerase sigma 99.9 1.3E-20 2.7E-25 169.6 16.5 157 143-372 6-162 (182)
114 PRK12546 RNA polymerase sigma 99.9 3.8E-20 8.3E-25 167.4 18.3 158 139-371 6-163 (188)
115 TIGR02959 SigZ RNA polymerase 99.9 3.5E-20 7.6E-25 164.7 17.5 149 148-371 2-150 (170)
116 PRK12525 RNA polymerase sigma 99.8 7.1E-20 1.5E-24 162.3 17.4 160 140-370 8-167 (168)
117 TIGR02895 spore_sigI RNA polym 99.8 2.8E-19 6.1E-24 164.6 20.1 186 133-359 2-198 (218)
118 PRK06704 RNA polymerase factor 99.8 1.3E-19 2.8E-24 168.3 17.8 161 129-371 6-166 (228)
119 PRK09636 RNA polymerase sigma 99.8 1.9E-19 4.2E-24 173.6 18.0 161 140-370 3-164 (293)
120 PRK09047 RNA polymerase factor 99.8 3.2E-19 6.9E-24 156.3 16.3 156 163-374 2-159 (161)
121 PRK09635 sigI RNA polymerase s 99.8 1.3E-18 2.8E-23 167.6 17.9 162 140-369 4-166 (290)
122 TIGR02957 SigX4 RNA polymerase 99.8 2.9E-18 6.2E-23 164.6 17.7 156 145-370 1-157 (281)
123 PF07638 Sigma70_ECF: ECF sigm 99.7 2.1E-16 4.6E-21 142.5 18.3 177 127-370 3-184 (185)
124 TIGR03209 P21_Cbot clostridium 99.7 1.5E-16 3.3E-21 136.9 13.6 136 143-355 1-141 (142)
125 PRK08311 putative RNA polymera 99.7 1.8E-15 3.9E-20 141.4 19.9 92 127-218 4-97 (237)
126 PRK09191 two-component respons 99.7 3.2E-16 7E-21 147.3 13.8 137 142-371 2-138 (261)
127 PF04542 Sigma70_r2: Sigma-70 99.4 5E-13 1.1E-17 100.7 8.0 70 146-215 1-70 (71)
128 PF04545 Sigma70_r4: Sigma-70, 99.3 1.1E-11 2.5E-16 87.6 7.1 50 314-367 1-50 (50)
129 PF08281 Sigma70_r4_2: Sigma-7 99.1 4.4E-10 9.6E-15 80.6 7.4 53 309-365 2-54 (54)
130 PF04539 Sigma70_r3: Sigma-70 99.0 2.2E-09 4.7E-14 83.0 7.8 76 226-301 2-77 (78)
131 PRK06930 positive control sigm 98.9 1.3E-08 2.9E-13 90.5 10.0 70 299-372 96-165 (170)
132 PRK00118 putative DNA-binding 98.7 7.5E-08 1.6E-12 78.3 9.0 62 309-374 9-70 (104)
133 cd06171 Sigma70_r4 Sigma70, re 98.5 2.9E-07 6.3E-12 64.6 7.0 54 309-366 2-55 (55)
134 TIGR00721 tfx DNA-binding prot 98.4 6.5E-07 1.4E-11 76.5 7.0 55 317-376 6-60 (137)
135 PRK03975 tfx putative transcri 98.4 8.9E-07 1.9E-11 76.0 7.1 52 316-372 5-56 (141)
136 PRK04217 hypothetical protein; 98.4 1.1E-06 2.4E-11 72.2 6.8 55 316-374 41-95 (110)
137 PF04297 UPF0122: Putative hel 98.2 7.8E-06 1.7E-10 66.0 8.7 60 311-374 10-70 (101)
138 smart00421 HTH_LUXR helix_turn 98.1 6.7E-06 1.4E-10 58.5 5.9 48 316-368 2-49 (58)
139 COG4941 Predicted RNA polymera 98.1 0.00011 2.5E-09 70.8 15.4 161 142-368 6-167 (415)
140 TIGR01636 phage_rinA phage tra 98.1 1.8E-05 3.9E-10 67.7 8.7 62 306-369 71-132 (134)
141 PF00196 GerE: Bacterial regul 98.1 9.9E-06 2.2E-10 58.8 5.8 48 316-368 2-49 (58)
142 cd06170 LuxR_C_like C-terminal 98.0 2.1E-05 4.6E-10 56.0 6.2 46 318-368 1-46 (57)
143 TIGR03879 near_KaiC_dom probab 98.0 2.2E-05 4.8E-10 59.6 6.1 48 310-360 8-55 (73)
144 PF07374 DUF1492: Protein of u 97.9 5.9E-05 1.3E-09 61.2 8.8 54 308-365 45-99 (100)
145 PF12645 HTH_16: Helix-turn-he 97.9 5E-05 1.1E-09 56.6 6.9 58 130-187 2-65 (65)
146 PF04967 HTH_10: HTH DNA bindi 97.9 6.2E-05 1.4E-09 53.6 6.9 48 318-365 1-51 (53)
147 PRK15201 fimbriae regulatory p 97.8 4.5E-05 9.8E-10 67.3 6.5 47 317-368 133-179 (198)
148 PRK15411 rcsA colanic acid cap 97.8 4E-05 8.6E-10 70.4 6.3 47 317-368 137-183 (207)
149 PRK13719 conjugal transfer tra 97.8 4.5E-05 9.7E-10 69.8 6.2 52 312-368 138-189 (217)
150 COG4566 TtrR Response regulato 97.8 0.00013 2.7E-09 65.3 8.4 63 306-373 131-193 (202)
151 TIGR01321 TrpR trp operon repr 97.7 6E-05 1.3E-09 60.0 5.4 54 309-363 23-80 (94)
152 PRK11475 DNA-binding transcrip 97.7 6.2E-05 1.4E-09 69.1 6.3 47 316-367 133-179 (207)
153 PF02001 DUF134: Protein of un 97.7 0.00012 2.5E-09 59.8 6.5 53 317-373 41-93 (106)
154 PRK10840 transcriptional regul 97.7 8.8E-05 1.9E-09 67.8 6.2 46 316-366 149-194 (216)
155 COG2197 CitB Response regulato 97.6 8.5E-05 1.8E-09 68.4 5.9 48 316-368 147-194 (211)
156 PRK10100 DNA-binding transcrip 97.6 9.7E-05 2.1E-09 68.3 6.1 48 316-368 154-201 (216)
157 TIGR03020 EpsA transcriptional 97.6 0.0001 2.2E-09 69.5 6.2 50 315-369 188-237 (247)
158 PF13936 HTH_38: Helix-turn-he 97.6 9.9E-05 2.2E-09 50.6 4.4 41 316-360 3-43 (44)
159 TIGR03541 reg_near_HchA LuxR f 97.6 0.00013 2.8E-09 68.2 6.4 51 315-370 169-219 (232)
160 PRK10188 DNA-binding transcrip 97.5 0.00021 4.6E-09 67.1 6.4 47 317-368 179-225 (240)
161 PRK13870 transcriptional regul 97.5 0.0002 4.4E-09 67.0 6.2 47 317-368 173-219 (234)
162 TIGR01637 phage_arpU phage tra 97.5 0.0028 6E-08 53.9 12.6 61 308-370 69-130 (132)
163 COG2771 CsgD DNA-binding HTH d 97.4 0.00057 1.2E-08 50.0 6.5 50 316-370 3-52 (65)
164 PRK09483 response regulator; P 97.3 0.0004 8.6E-09 62.6 6.0 46 316-366 147-192 (217)
165 PRK01381 Trp operon repressor; 97.2 0.00048 1E-08 55.3 4.1 55 308-363 22-80 (99)
166 PRK15369 two component system 97.2 0.00092 2E-08 59.0 6.4 47 316-367 148-194 (211)
167 COG2739 Uncharacterized protei 97.1 0.00098 2.1E-08 53.3 5.5 49 317-369 17-65 (105)
168 PRK15320 transcriptional activ 97.1 0.00097 2.1E-08 60.0 5.8 50 313-367 160-209 (251)
169 COG1342 Predicted DNA-binding 97.1 0.0017 3.6E-08 51.4 6.0 52 318-373 34-85 (99)
170 PRK10651 transcriptional regul 97.0 0.0011 2.3E-08 59.2 5.7 48 316-368 154-201 (216)
171 COG1356 tfx Transcriptional re 97.0 0.00058 1.3E-08 56.6 3.2 51 317-372 8-58 (143)
172 PRK09390 fixJ response regulat 96.9 0.0026 5.6E-08 55.8 7.2 55 311-370 135-189 (202)
173 COG3413 Predicted DNA binding 96.9 0.0022 4.7E-08 59.2 6.9 53 317-369 155-210 (215)
174 PF13613 HTH_Tnp_4: Helix-turn 96.7 0.0042 9E-08 44.2 5.5 50 317-369 2-51 (53)
175 PRK10403 transcriptional regul 96.6 0.0038 8.3E-08 55.5 5.9 49 317-370 153-201 (215)
176 PRK10360 DNA-binding transcrip 96.5 0.007 1.5E-07 53.5 6.4 48 316-368 136-183 (196)
177 PRK09935 transcriptional regul 96.4 0.0069 1.5E-07 53.9 6.1 47 317-368 149-195 (210)
178 PRK09958 DNA-binding transcrip 96.4 0.0073 1.6E-07 53.7 6.1 46 316-366 142-187 (204)
179 TIGR02531 yecD_yerC TrpR-relat 96.3 0.0087 1.9E-07 47.3 5.4 39 316-361 35-73 (88)
180 PF13412 HTH_24: Winged helix- 96.3 0.013 2.8E-07 40.5 5.7 41 318-361 1-41 (48)
181 PF13384 HTH_23: Homeodomain-l 96.3 0.0041 8.9E-08 43.3 3.1 33 324-361 9-41 (50)
182 PRK04841 transcriptional regul 96.3 0.007 1.5E-07 66.9 6.4 48 316-368 837-884 (903)
183 PRK13558 bacterio-opsin activa 96.2 0.0098 2.1E-07 63.7 6.9 51 315-369 605-662 (665)
184 PF02796 HTH_7: Helix-turn-hel 96.2 0.0098 2.1E-07 40.8 4.3 33 322-359 11-43 (45)
185 PRK15418 transcriptional regul 96.0 0.0092 2E-07 58.4 5.1 36 324-363 20-55 (318)
186 PF05263 DUF722: Protein of un 95.8 0.039 8.4E-07 46.8 7.3 56 308-365 72-127 (130)
187 PF06056 Terminase_5: Putative 95.7 0.023 5E-07 41.3 4.8 26 336-361 12-37 (58)
188 PF09862 DUF2089: Protein of u 95.5 0.041 8.8E-07 45.5 6.2 50 314-367 30-79 (113)
189 PF00325 Crp: Bacterial regula 95.3 0.023 4.9E-07 36.1 3.1 23 338-360 3-25 (32)
190 PF13404 HTH_AsnC-type: AsnC-t 95.3 0.059 1.3E-06 36.4 5.4 40 318-360 1-40 (42)
191 PF01726 LexA_DNA_bind: LexA D 95.2 0.034 7.4E-07 41.4 4.4 45 315-360 1-49 (65)
192 PF06530 Phage_antitermQ: Phag 95.0 0.16 3.5E-06 42.8 8.5 55 315-373 60-114 (125)
193 PF10668 Phage_terminase: Phag 94.9 0.048 1E-06 39.8 4.4 36 323-360 10-45 (60)
194 cd00569 HTH_Hin_like Helix-tur 94.9 0.068 1.5E-06 33.2 4.7 36 318-357 6-41 (42)
195 COG2390 DeoR Transcriptional r 94.7 0.041 8.9E-07 53.9 4.8 35 325-363 18-52 (321)
196 PF13518 HTH_28: Helix-turn-he 94.6 0.077 1.7E-06 36.9 4.8 27 336-362 11-37 (52)
197 PHA00675 hypothetical protein 94.5 0.085 1.8E-06 40.2 5.0 41 316-359 21-61 (78)
198 PF04218 CENP-B_N: CENP-B N-te 94.5 0.036 7.9E-07 39.4 2.9 46 317-367 6-51 (53)
199 PF12802 MarR_2: MarR family; 94.5 0.1 2.2E-06 37.7 5.3 44 317-361 2-45 (62)
200 PF13730 HTH_36: Helix-turn-he 94.4 0.16 3.5E-06 35.9 6.1 44 317-360 2-48 (55)
201 COG2909 MalT ATP-dependent tra 94.3 0.052 1.1E-06 58.7 4.7 47 317-368 831-877 (894)
202 smart00351 PAX Paired Box doma 94.1 0.13 2.8E-06 43.3 5.9 42 318-363 18-59 (125)
203 PF02650 HTH_WhiA: WhiA C-term 93.7 0.17 3.6E-06 39.8 5.4 44 315-361 35-80 (85)
204 PRK10430 DNA-binding transcrip 93.5 0.16 3.6E-06 47.0 6.1 46 317-363 158-204 (239)
205 PF08279 HTH_11: HTH domain; 93.5 0.21 4.6E-06 35.3 5.2 39 321-361 1-39 (55)
206 PF01371 Trp_repressor: Trp re 93.3 0.25 5.4E-06 39.0 5.8 47 317-364 26-75 (87)
207 PHA02547 55 RNA polymerase sig 93.1 0.44 9.6E-06 41.9 7.4 67 148-214 44-113 (179)
208 PF01047 MarR: MarR family; I 92.8 0.23 5E-06 35.5 4.7 41 318-361 1-41 (59)
209 cd00131 PAX Paired Box domain 92.8 0.28 6.1E-06 41.5 5.9 41 318-362 18-58 (128)
210 PHA02591 hypothetical protein; 92.7 0.14 3.1E-06 39.1 3.4 24 336-359 58-81 (83)
211 PRK14082 hypothetical protein; 92.6 0.46 9.9E-06 34.9 5.7 58 138-197 6-63 (65)
212 smart00550 Zalpha Z-DNA-bindin 92.5 0.35 7.5E-06 36.2 5.4 39 321-360 7-45 (68)
213 PF01022 HTH_5: Bacterial regu 92.5 0.42 9.1E-06 32.8 5.4 37 320-360 2-38 (47)
214 COG3415 Transposase and inacti 92.1 0.28 6.1E-06 42.1 5.0 27 336-362 20-46 (138)
215 PF13022 HTH_Tnp_1_2: Helix-tu 91.8 0.85 1.8E-05 39.0 7.5 50 311-360 4-57 (142)
216 PF01418 HTH_6: Helix-turn-hel 91.7 0.45 9.7E-06 36.4 5.3 53 308-360 4-57 (77)
217 PF13542 HTH_Tnp_ISL3: Helix-t 91.7 0.46 9.9E-06 33.1 4.9 34 323-361 18-51 (52)
218 PF00356 LacI: Bacterial regul 91.6 0.18 3.9E-06 34.8 2.7 22 339-360 1-22 (46)
219 smart00344 HTH_ASNC helix_turn 91.6 0.48 1E-05 38.3 5.7 42 318-362 1-42 (108)
220 PF03444 HrcA_DNA-bdg: Winged 91.6 0.51 1.1E-05 36.3 5.4 42 317-359 1-45 (78)
221 PF12840 HTH_20: Helix-turn-he 91.5 1.1 2.3E-05 32.5 7.0 38 320-360 10-47 (61)
222 PF13011 LZ_Tnp_IS481: leucine 91.5 0.51 1.1E-05 37.0 5.4 43 317-362 8-50 (85)
223 PF01710 HTH_Tnp_IS630: Transp 91.5 2.7 5.8E-05 34.9 10.2 25 336-360 70-94 (119)
224 PF01325 Fe_dep_repress: Iron 91.3 0.43 9.2E-06 34.8 4.6 43 318-360 2-45 (60)
225 PRK11083 DNA-binding response 91.3 0.32 6.9E-06 43.6 4.8 51 317-368 154-209 (228)
226 PF13463 HTH_27: Winged helix 91.2 0.49 1.1E-05 34.6 5.0 43 318-362 1-43 (68)
227 PRK11179 DNA-binding transcrip 90.9 0.66 1.4E-05 40.3 6.2 42 317-361 6-47 (153)
228 PRK10336 DNA-binding transcrip 90.6 0.34 7.5E-06 43.1 4.4 50 317-367 149-203 (219)
229 PRK10046 dpiA two-component re 90.5 0.26 5.6E-06 45.3 3.5 39 318-360 162-200 (225)
230 PF08822 DUF1804: Protein of u 90.5 0.64 1.4E-05 41.0 5.7 42 319-363 4-45 (165)
231 PF01978 TrmB: Sugar-specific 90.3 0.27 5.8E-06 36.4 2.8 41 317-360 5-45 (68)
232 TIGR01610 phage_O_Nterm phage 90.0 1.6 3.5E-05 34.7 7.3 46 315-360 20-70 (95)
233 PF02954 HTH_8: Bacterial regu 90.0 0.52 1.1E-05 31.7 3.7 39 319-360 3-41 (42)
234 PF09339 HTH_IclR: IclR helix- 90.0 0.55 1.2E-05 32.9 4.0 33 328-360 9-41 (52)
235 PRK13413 mpi multiple promoter 90.0 0.58 1.3E-05 42.5 5.3 34 322-360 162-195 (200)
236 PF12728 HTH_17: Helix-turn-he 89.6 0.38 8.3E-06 33.4 3.0 24 338-361 2-25 (51)
237 PRK00423 tfb transcription ini 89.4 17 0.00036 35.5 15.3 180 144-366 119-305 (310)
238 PRK11169 leucine-responsive tr 89.1 0.77 1.7E-05 40.4 5.2 41 317-360 11-51 (164)
239 PF13744 HTH_37: Helix-turn-he 89.1 0.9 1.9E-05 35.0 5.0 39 335-373 29-72 (80)
240 PRK10710 DNA-binding transcrip 89.1 0.61 1.3E-05 42.2 4.8 50 317-367 160-214 (240)
241 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 89.0 0.93 2E-05 31.9 4.5 39 317-359 4-42 (50)
242 PRK12423 LexA repressor; Provi 88.8 0.7 1.5E-05 42.2 4.9 48 316-367 2-52 (202)
243 PRK15479 transcriptional regul 88.7 0.74 1.6E-05 40.9 5.0 50 317-367 148-202 (221)
244 cd04762 HTH_MerR-trunc Helix-T 88.5 0.46 9.9E-06 31.9 2.7 25 338-362 1-25 (49)
245 PF13551 HTH_29: Winged helix- 88.5 0.89 1.9E-05 36.5 4.9 26 336-361 10-36 (112)
246 COG3355 Predicted transcriptio 88.5 2.2 4.9E-05 35.9 7.2 49 310-360 17-65 (126)
247 TIGR01764 excise DNA binding d 88.2 0.49 1.1E-05 32.0 2.7 24 338-361 2-25 (49)
248 TIGR02337 HpaR homoprotocatech 88.1 2.6 5.7E-05 34.6 7.6 41 317-360 25-65 (118)
249 COG2522 Predicted transcriptio 87.9 0.95 2.1E-05 37.8 4.7 24 336-359 21-44 (119)
250 TIGR02154 PhoB phosphate regul 87.8 0.45 9.7E-06 42.5 2.9 50 317-367 154-208 (226)
251 COG1522 Lrp Transcriptional re 87.7 1.4 3E-05 37.8 5.9 42 316-360 4-45 (154)
252 COG2973 TrpR Trp operon repres 87.7 1.8 3.8E-05 34.7 5.7 40 317-356 37-79 (103)
253 PF01381 HTH_3: Helix-turn-hel 87.1 0.66 1.4E-05 32.5 2.9 25 336-360 8-32 (55)
254 PF01726 LexA_DNA_bind: LexA D 86.8 2.8 6.2E-05 31.0 6.3 42 226-267 7-49 (65)
255 PF08220 HTH_DeoR: DeoR-like h 86.8 1.2 2.6E-05 32.0 4.1 25 336-360 13-37 (57)
256 CHL00148 orf27 Ycf27; Reviewed 86.6 0.96 2.1E-05 40.9 4.5 50 317-367 161-217 (240)
257 PF08280 HTH_Mga: M protein tr 86.5 1.5 3.2E-05 31.7 4.5 37 321-360 6-42 (59)
258 TIGR00498 lexA SOS regulatory 86.5 0.91 2E-05 41.0 4.2 45 316-360 2-49 (199)
259 TIGR03787 marine_sort_RR prote 86.5 1.2 2.5E-05 40.1 4.9 50 317-367 156-207 (227)
260 PF00046 Homeobox: Homeobox do 86.4 1.6 3.5E-05 30.8 4.7 51 317-367 6-57 (57)
261 PRK11512 DNA-binding transcrip 86.3 3.8 8.1E-05 35.0 7.7 47 311-360 29-77 (144)
262 PRK07598 RNA polymerase sigma 86.2 8.3 0.00018 39.2 11.2 37 228-264 111-147 (415)
263 cd04761 HTH_MerR-SF Helix-Turn 86.1 0.58 1.3E-05 31.9 2.1 25 338-362 1-25 (49)
264 smart00420 HTH_DEOR helix_turn 86.1 1.9 4.1E-05 29.4 4.8 25 336-360 13-37 (53)
265 PRK00215 LexA repressor; Valid 85.9 1.7 3.7E-05 39.5 5.7 45 318-362 2-49 (205)
266 COG5484 Uncharacterized conser 85.2 0.91 2E-05 42.5 3.5 25 336-360 18-42 (279)
267 COG0856 Orotate phosphoribosyl 84.9 1.3 2.7E-05 39.5 4.0 40 323-367 9-48 (203)
268 PRK10870 transcriptional repre 84.7 5.1 0.00011 35.6 8.1 51 310-361 43-95 (176)
269 smart00345 HTH_GNTR helix_turn 83.9 1.9 4.1E-05 30.2 4.1 25 336-360 18-43 (60)
270 cd06571 Bac_DnaA_C C-terminal 83.9 3.9 8.4E-05 32.2 6.2 31 337-367 44-75 (90)
271 smart00419 HTH_CRP helix_turn_ 83.8 1.7 3.6E-05 29.2 3.6 24 337-360 8-31 (48)
272 PRK09413 IS2 repressor TnpA; R 83.7 3.3 7.2E-05 34.5 6.0 27 336-362 28-54 (121)
273 PRK11337 DNA-binding transcrip 83.3 2.3 5.1E-05 40.7 5.7 60 309-370 17-83 (292)
274 PF01527 HTH_Tnp_1: Transposas 83.3 1.6 3.4E-05 32.7 3.6 27 336-362 22-48 (76)
275 PRK03573 transcriptional regul 83.3 6.2 0.00013 33.5 7.7 42 317-360 28-69 (144)
276 TIGR02844 spore_III_D sporulat 83.2 1.9 4.2E-05 33.4 4.0 36 321-360 7-42 (80)
277 PRK11302 DNA-binding transcrip 83.1 2.3 4.9E-05 40.5 5.5 60 309-370 5-71 (284)
278 PF08535 KorB: KorB domain; I 83.1 1.1 2.4E-05 35.5 2.7 24 336-359 2-25 (93)
279 PF08765 Mor: Mor transcriptio 83.1 2.6 5.7E-05 34.4 5.1 42 321-368 62-103 (108)
280 PF07750 GcrA: GcrA cell cycle 82.9 1.7 3.6E-05 38.4 4.1 25 336-360 17-42 (162)
281 TIGR03830 CxxCG_CxxCG_HTH puta 82.7 5 0.00011 33.2 6.8 45 310-360 57-101 (127)
282 TIGR01884 cas_HTH CRISPR locus 82.7 3.6 7.7E-05 37.4 6.3 45 313-360 136-180 (203)
283 PHA00542 putative Cro-like pro 82.7 2.1 4.6E-05 33.2 4.1 25 336-360 30-54 (82)
284 KOG0484 Transcription factor P 82.7 2.3 4.9E-05 34.5 4.3 52 316-371 27-78 (125)
285 smart00347 HTH_MARR helix_turn 82.7 3.4 7.3E-05 32.1 5.5 41 317-360 7-47 (101)
286 cd00092 HTH_CRP helix_turn_hel 82.3 2.1 4.5E-05 31.0 3.8 25 336-360 24-48 (67)
287 PF05043 Mga: Mga helix-turn-h 82.2 1.2 2.6E-05 34.5 2.7 32 336-367 29-60 (87)
288 PF13560 HTH_31: Helix-turn-he 82.2 1.4 3E-05 32.2 2.8 24 336-359 13-36 (64)
289 PF14493 HTH_40: Helix-turn-he 82.0 3.6 7.8E-05 32.4 5.3 29 336-364 12-40 (91)
290 smart00342 HTH_ARAC helix_turn 82.0 18 0.00039 26.6 9.9 25 337-361 50-75 (84)
291 TIGR00122 birA_repr_reg BirA b 82.0 3.4 7.4E-05 30.5 4.9 25 336-360 12-36 (69)
292 COG1318 Predicted transcriptio 81.9 1.4 3.1E-05 38.9 3.2 25 336-360 60-84 (182)
293 PF13411 MerR_1: MerR HTH fami 81.9 0.79 1.7E-05 33.7 1.4 25 338-362 1-25 (69)
294 TIGR01889 Staph_reg_Sar staphy 81.6 4.3 9.3E-05 33.0 5.8 45 317-361 22-67 (109)
295 TIGR03070 couple_hipB transcri 81.6 1.6 3.5E-05 30.4 2.9 25 336-360 14-38 (58)
296 PRK11564 stationary phase indu 81.4 4 8.8E-05 41.4 6.9 51 317-367 10-60 (426)
297 COG3877 Uncharacterized protei 81.3 4 8.7E-05 33.1 5.2 48 315-366 39-86 (122)
298 PHA01976 helix-turn-helix prot 81.2 1.8 3.9E-05 31.6 3.1 25 336-360 14-38 (67)
299 PRK15482 transcriptional regul 81.0 2.9 6.4E-05 39.9 5.4 59 309-369 5-70 (285)
300 PRK10072 putative transcriptio 81.0 6.9 0.00015 31.4 6.6 24 336-359 45-68 (96)
301 PF13545 HTH_Crp_2: Crp-like h 80.9 2 4.3E-05 32.1 3.4 27 337-367 28-54 (76)
302 TIGR00647 MG103 conserved hypo 80.7 3.9 8.4E-05 39.3 6.0 44 315-361 225-274 (279)
303 PF12116 SpoIIID: Stage III sp 80.5 2.9 6.2E-05 32.3 4.0 46 322-369 6-51 (82)
304 smart00354 HTH_LACI helix_turn 80.5 1.7 3.7E-05 32.5 2.8 23 338-360 1-23 (70)
305 cd00090 HTH_ARSR Arsenical Res 80.4 4.6 0.0001 29.2 5.2 37 320-360 7-43 (78)
306 TIGR02787 codY_Gpos GTP-sensin 79.9 10 0.00022 35.7 8.2 51 308-358 167-219 (251)
307 smart00346 HTH_ICLR helix_turn 79.7 6 0.00013 30.5 5.9 26 336-361 19-44 (91)
308 cd01104 HTH_MlrA-CarA Helix-Tu 79.4 2.4 5.3E-05 31.0 3.3 23 338-360 1-23 (68)
309 PRK01905 DNA-binding protein F 79.3 9.2 0.0002 29.2 6.6 37 321-360 37-73 (77)
310 PF00376 MerR: MerR family reg 79.1 1.3 2.8E-05 29.2 1.5 23 339-361 1-23 (38)
311 COG1476 Predicted transcriptio 78.5 3.5 7.6E-05 30.9 3.9 24 336-359 13-36 (68)
312 smart00418 HTH_ARSR helix_turn 77.9 4 8.6E-05 28.6 4.1 26 336-361 9-34 (66)
313 PF13551 HTH_29: Winged helix- 77.6 3.8 8.1E-05 32.8 4.3 23 246-268 14-36 (112)
314 PRK11557 putative DNA-binding 77.6 3.3 7.2E-05 39.3 4.6 58 311-370 3-67 (278)
315 COG2512 Predicted membrane-ass 77.5 3.8 8.1E-05 39.0 4.8 43 316-360 191-233 (258)
316 PF07037 DUF1323: Putative tra 77.3 2.7 5.9E-05 34.9 3.2 23 338-360 1-23 (122)
317 cd00086 homeodomain Homeodomai 77.1 7.6 0.00017 27.2 5.3 51 317-367 6-57 (59)
318 PRK13777 transcriptional regul 77.1 14 0.00029 33.4 8.0 41 317-360 42-82 (185)
319 cd04764 HTH_MlrA-like_sg1 Heli 75.9 3.6 7.7E-05 30.2 3.4 23 338-360 1-23 (67)
320 PF05225 HTH_psq: helix-turn-h 75.9 9.8 0.00021 25.9 5.3 23 338-360 17-39 (45)
321 COG1405 SUA7 Transcription ini 75.8 33 0.00071 33.2 10.7 121 235-361 148-275 (285)
322 PF00292 PAX: 'Paired box' dom 75.7 6.3 0.00014 33.2 5.1 34 322-360 23-56 (125)
323 PF00440 TetR_N: Bacterial reg 75.5 3.3 7.2E-05 28.2 2.9 24 335-358 14-37 (47)
324 PF12759 HTH_Tnp_IS1: InsA C-t 75.2 3.7 7.9E-05 28.3 2.9 38 318-360 7-44 (46)
325 PF01710 HTH_Tnp_IS630: Transp 75.0 4.5 9.7E-05 33.6 4.1 24 336-359 17-40 (119)
326 COG2944 Predicted transcriptio 74.5 6.9 0.00015 31.9 4.9 42 313-360 39-80 (104)
327 TIGR02698 CopY_TcrY copper tra 74.5 8.6 0.00019 32.5 5.8 44 317-363 1-48 (130)
328 PRK10141 DNA-binding transcrip 74.3 8.6 0.00019 32.0 5.6 44 313-359 8-52 (117)
329 smart00422 HTH_MERR helix_turn 73.9 2.5 5.5E-05 31.0 2.1 25 338-362 1-25 (70)
330 PRK09863 putative frv operon r 73.9 33 0.00072 36.4 11.3 104 243-367 16-122 (584)
331 PF08784 RPA_C: Replication pr 73.7 6.3 0.00014 31.5 4.6 43 317-359 44-87 (102)
332 TIGR00180 parB_part ParB-like 73.5 5.9 0.00013 35.5 4.8 43 316-360 101-143 (187)
333 PF13443 HTH_26: Cro/C1-type H 73.2 3.4 7.4E-05 29.7 2.6 26 336-361 9-34 (63)
334 smart00389 HOX Homeodomain. DN 72.8 9.8 0.00021 26.4 4.9 48 318-365 7-55 (56)
335 PF00165 HTH_AraC: Bacterial r 72.8 5.8 0.00013 26.2 3.5 26 336-361 7-32 (42)
336 PRK10955 DNA-binding transcrip 72.6 2.8 6.1E-05 37.6 2.5 46 317-367 156-210 (232)
337 PRK10161 transcriptional regul 72.4 4.6 0.0001 36.2 3.9 50 317-367 154-208 (229)
338 TIGR02607 antidote_HigA addict 72.2 4.2 9.1E-05 30.5 3.0 24 336-359 17-40 (78)
339 COG1510 Predicted transcriptio 72.0 4.9 0.00011 35.7 3.7 34 325-360 31-64 (177)
340 PRK10411 DNA-binding transcrip 71.9 7.8 0.00017 36.3 5.4 41 320-363 4-44 (240)
341 PHA00738 putative HTH transcri 71.9 10 0.00022 31.1 5.2 37 320-359 12-48 (108)
342 cd07377 WHTH_GntR Winged helix 71.8 5.2 0.00011 28.5 3.4 22 338-359 26-47 (66)
343 PF13556 HTH_30: PucR C-termin 71.7 13 0.00028 26.7 5.4 35 336-370 11-45 (59)
344 COG1654 BirA Biotin operon rep 71.7 14 0.0003 28.6 5.7 29 336-368 18-46 (79)
345 COG1737 RpiR Transcriptional r 71.6 7.2 0.00016 37.4 5.2 52 307-360 5-59 (281)
346 PF00392 GntR: Bacterial regul 71.6 5.5 0.00012 29.0 3.4 25 336-360 22-47 (64)
347 PRK10643 DNA-binding transcrip 71.2 4.8 0.0001 35.6 3.7 47 317-366 149-202 (222)
348 PF06971 Put_DNA-bind_N: Putat 71.0 5.6 0.00012 27.9 3.1 25 334-358 25-49 (50)
349 cd04763 HTH_MlrA-like Helix-Tu 70.6 5.6 0.00012 29.2 3.3 23 338-360 1-23 (68)
350 cd01392 HTH_LacI Helix-turn-he 70.6 3 6.4E-05 28.7 1.7 21 341-361 1-21 (52)
351 smart00352 POU Found in Pit-Oc 70.6 7.6 0.00016 29.7 4.0 24 336-359 23-52 (75)
352 COG1846 MarR Transcriptional r 70.4 9 0.0002 30.7 4.9 41 318-361 20-60 (126)
353 PF02082 Rrf2: Transcriptional 70.4 12 0.00026 28.8 5.3 24 337-360 25-48 (83)
354 PF04539 Sigma70_r3: Sigma-70 70.4 12 0.00027 28.0 5.3 25 336-360 19-43 (78)
355 TIGR03697 NtcA_cyano global ni 70.2 5 0.00011 35.4 3.5 28 337-368 143-170 (193)
356 PRK09726 antitoxin HipB; Provi 70.1 4.7 0.0001 31.5 2.9 25 336-360 24-48 (88)
357 smart00862 Trans_reg_C Transcr 69.4 18 0.0004 26.6 6.1 50 317-367 5-60 (78)
358 COG3093 VapI Plasmid maintenan 69.4 8.3 0.00018 31.4 4.2 35 324-360 12-46 (104)
359 PF12844 HTH_19: Helix-turn-he 69.0 5 0.00011 28.9 2.7 25 336-360 11-35 (64)
360 PRK07406 RNA polymerase sigma 68.7 53 0.0011 33.0 10.7 35 231-265 97-131 (373)
361 TIGR00637 ModE_repress ModE mo 68.3 13 0.00028 29.9 5.2 46 318-368 2-47 (99)
362 cd00383 trans_reg_C Effector d 68.2 14 0.0003 28.5 5.3 50 317-367 23-77 (95)
363 PF11662 DUF3263: Protein of u 68.0 20 0.00044 27.5 5.9 46 317-363 2-48 (77)
364 PF05331 DUF742: Protein of un 67.9 9.2 0.0002 31.7 4.3 40 316-360 39-78 (114)
365 PF00126 HTH_1: Bacterial regu 67.6 13 0.00027 26.7 4.6 31 338-368 14-44 (60)
366 PF02787 CPSase_L_D3: Carbamoy 67.6 73 0.0016 26.7 10.2 43 311-360 53-95 (123)
367 TIGR02612 mob_myst_A mobile my 67.4 13 0.00028 32.4 5.3 38 336-373 37-80 (150)
368 PRK11511 DNA-binding transcrip 67.4 47 0.001 27.6 8.7 41 227-267 8-48 (127)
369 PRK14101 bifunctional glucokin 67.1 14 0.00031 39.7 6.8 62 307-370 343-411 (638)
370 COG4709 Predicted membrane pro 67.1 18 0.00038 32.7 6.2 57 305-361 4-64 (195)
371 PF04552 Sigma54_DBD: Sigma-54 67.0 1.8 4E-05 38.1 0.0 48 310-359 24-71 (160)
372 PF05930 Phage_AlpA: Prophage 66.8 7.3 0.00016 27.1 3.1 24 338-361 4-27 (51)
373 PF10668 Phage_terminase: Phag 66.7 14 0.0003 27.1 4.5 31 235-265 13-43 (60)
374 PF02042 RWP-RK: RWP-RK domain 66.5 14 0.00031 26.2 4.4 21 338-358 16-36 (52)
375 smart00530 HTH_XRE Helix-turn- 66.5 7.2 0.00016 25.6 3.0 25 336-360 9-33 (56)
376 PRK13918 CRP/FNR family transc 66.4 6.3 0.00014 35.1 3.4 23 337-359 149-171 (202)
377 PF04703 FaeA: FaeA-like prote 66.3 6.9 0.00015 28.8 2.9 25 336-360 14-38 (62)
378 TIGR02395 rpoN_sigma RNA polym 66.2 7.6 0.00016 39.7 4.3 24 336-359 317-340 (429)
379 COG1481 Uncharacterized protei 66.0 17 0.00036 35.4 6.2 49 316-368 252-302 (308)
380 PRK13509 transcriptional repre 65.8 11 0.00023 35.6 5.0 39 320-361 5-43 (251)
381 COG2345 Predicted transcriptio 65.7 13 0.00027 34.5 5.2 25 336-360 24-48 (218)
382 PF14394 DUF4423: Domain of un 65.7 14 0.0003 32.8 5.4 87 242-331 37-128 (171)
383 PF04552 Sigma54_DBD: Sigma-54 65.5 4.9 0.00011 35.4 2.4 23 245-267 50-72 (160)
384 TIGR01387 cztR_silR_copR heavy 65.3 9.9 0.00021 33.5 4.5 50 317-367 147-201 (218)
385 PRK11517 transcriptional regul 64.9 13 0.00027 33.0 5.1 49 317-366 147-200 (223)
386 PRK10219 DNA-binding transcrip 64.4 71 0.0015 25.4 9.8 79 228-350 5-83 (107)
387 PRK09706 transcriptional repre 64.4 6.7 0.00015 33.1 3.0 25 336-360 17-41 (135)
388 PF10078 DUF2316: Uncharacteri 64.0 18 0.00038 28.7 5.0 24 336-359 22-45 (89)
389 PF08006 DUF1700: Protein of u 63.8 23 0.0005 31.5 6.5 56 305-360 4-63 (181)
390 PF00486 Trans_reg_C: Transcri 63.3 21 0.00045 26.3 5.3 51 317-368 5-60 (77)
391 PF10654 DUF2481: Protein of u 63.2 19 0.00041 29.7 5.1 43 323-370 71-113 (126)
392 PRK12469 RNA polymerase factor 63.0 11 0.00024 39.1 4.8 24 336-359 368-391 (481)
393 PRK05932 RNA polymerase factor 62.5 9.7 0.00021 39.3 4.3 24 336-359 342-365 (455)
394 cd00093 HTH_XRE Helix-turn-hel 62.3 10 0.00023 25.0 3.2 25 336-360 11-35 (58)
395 cd04768 HTH_BmrR-like Helix-Tu 62.3 5.8 0.00013 31.6 2.1 25 338-362 1-25 (96)
396 cd04775 HTH_Cfa-like Helix-Tur 62.0 5.7 0.00012 32.0 2.1 26 338-363 2-27 (102)
397 PF13309 HTH_22: HTH domain 61.9 5.6 0.00012 29.3 1.8 20 339-358 44-63 (64)
398 PF11994 DUF3489: Protein of u 61.9 26 0.00055 26.6 5.3 41 321-364 11-51 (72)
399 COG2826 Tra8 Transposase and i 61.8 10 0.00022 36.8 3.9 42 317-362 7-48 (318)
400 cd01105 HTH_GlnR-like Helix-Tu 61.6 6.4 0.00014 30.8 2.2 25 338-362 2-26 (88)
401 TIGR02944 suf_reg_Xantho FeS a 61.4 19 0.0004 30.1 5.2 26 335-360 23-48 (130)
402 PRK00430 fis global DNA-bindin 61.3 15 0.00032 29.4 4.2 37 321-360 55-91 (95)
403 TIGR02431 pcaR_pcaU beta-ketoa 61.0 16 0.00034 34.1 5.2 38 323-360 10-47 (248)
404 PF04645 DUF603: Protein of un 60.8 10 0.00023 33.5 3.5 25 336-360 17-42 (181)
405 PRK11753 DNA-binding transcrip 60.6 11 0.00024 33.6 4.0 27 337-367 168-194 (211)
406 PRK11161 fumarate/nitrate redu 60.4 9.5 0.00021 34.9 3.5 27 337-367 184-210 (235)
407 PRK11050 manganese transport r 60.1 17 0.00038 31.4 4.9 26 336-361 50-75 (152)
408 PRK09744 DNA-binding transcrip 59.3 14 0.0003 28.1 3.5 19 339-357 12-30 (75)
409 PRK06266 transcription initiat 59.2 33 0.00072 30.7 6.6 39 319-360 21-59 (178)
410 PHA02535 P terminase ATPase su 59.2 12 0.00025 39.7 4.2 25 336-360 17-41 (581)
411 PF06971 Put_DNA-bind_N: Putat 59.1 28 0.00061 24.4 4.9 46 219-264 3-48 (50)
412 cd01106 HTH_TipAL-Mta Helix-Tu 59.1 7.1 0.00015 31.4 2.1 25 338-362 1-25 (103)
413 COG1321 TroR Mn-dependent tran 59.1 20 0.00043 31.3 5.1 25 336-360 23-47 (154)
414 cd04773 HTH_TioE_rpt2 Second H 59.0 7 0.00015 31.8 2.1 25 338-362 1-25 (108)
415 cd04766 HTH_HspR Helix-Turn-He 58.9 7 0.00015 30.6 2.0 25 338-362 2-26 (91)
416 PRK13698 plasmid-partitioning 58.9 30 0.00064 34.0 6.7 48 311-360 151-199 (323)
417 PF12298 Bot1p: Eukaryotic mit 58.8 23 0.0005 31.6 5.4 39 318-359 17-55 (172)
418 PF06322 Phage_NinH: Phage Nin 58.8 15 0.00033 26.8 3.5 20 339-358 18-37 (64)
419 cd00592 HTH_MerR-like Helix-Tu 58.7 7.4 0.00016 30.9 2.1 25 338-362 1-25 (100)
420 cd01107 HTH_BmrR Helix-Turn-He 58.6 7.5 0.00016 31.6 2.2 26 338-363 1-26 (108)
421 PF14549 P22_Cro: DNA-binding 58.6 15 0.00033 26.8 3.5 19 339-357 11-29 (60)
422 cd04772 HTH_TioE_rpt1 First He 58.4 7.6 0.00017 31.1 2.2 25 338-362 1-25 (99)
423 cd04780 HTH_MerR-like_sg5 Heli 58.4 7.5 0.00016 31.0 2.1 25 338-362 1-25 (95)
424 cd04782 HTH_BltR Helix-Turn-He 58.0 7.7 0.00017 30.9 2.1 25 338-362 1-25 (97)
425 PF04492 Phage_rep_O: Bacterio 57.9 45 0.00098 26.9 6.5 45 316-360 28-77 (100)
426 PRK03902 manganese transport t 57.9 23 0.00051 30.0 5.3 25 336-360 21-45 (142)
427 COG4367 Uncharacterized protei 57.8 30 0.00066 27.2 5.2 41 316-359 1-45 (97)
428 cd04774 HTH_YfmP Helix-Turn-He 57.5 7.7 0.00017 30.9 2.0 25 338-362 1-25 (96)
429 PRK13503 transcriptional activ 57.5 1E+02 0.0022 28.8 10.1 38 230-267 173-210 (278)
430 cd04765 HTH_MlrA-like_sg2 Heli 56.8 13 0.00029 29.7 3.4 23 338-360 1-23 (99)
431 cd04789 HTH_Cfa Helix-Turn-Hel 56.8 8.3 0.00018 31.1 2.1 25 338-362 2-26 (102)
432 PRK10906 DNA-binding transcrip 56.7 19 0.00042 33.9 5.0 38 320-360 5-42 (252)
433 PRK09834 DNA-binding transcrip 56.7 20 0.00043 33.9 5.1 39 322-360 11-49 (263)
434 PRK13890 conjugal transfer pro 56.6 11 0.00024 31.4 2.9 25 336-360 17-41 (120)
435 COG1349 GlpR Transcriptional r 56.5 14 0.0003 34.9 4.0 39 319-360 4-42 (253)
436 TIGR02147 Fsuc_second hypothet 56.3 32 0.00069 33.0 6.4 87 242-331 135-226 (271)
437 cd01109 HTH_YyaN Helix-Turn-He 56.1 8.6 0.00019 31.5 2.2 25 338-362 1-25 (113)
438 PRK10434 srlR DNA-bindng trans 56.0 16 0.00035 34.5 4.3 38 320-360 5-42 (256)
439 PRK10216 DNA-binding transcrip 55.9 26 0.00057 33.6 5.9 46 315-365 5-50 (319)
440 cd04788 HTH_NolA-AlbR Helix-Tu 55.8 8.6 0.00019 30.6 2.1 25 338-362 1-25 (96)
441 TIGR00738 rrf2_super rrf2 fami 55.8 31 0.00066 28.6 5.6 25 336-360 24-48 (132)
442 smart00342 HTH_ARAC helix_turn 55.7 20 0.00044 26.3 4.1 25 338-362 2-26 (84)
443 PF06970 RepA_N: Replication i 55.2 12 0.00026 28.6 2.7 22 338-359 53-74 (76)
444 PRK10163 DNA-binding transcrip 54.9 25 0.00053 33.5 5.4 25 336-360 39-63 (271)
445 cd01282 HTH_MerR-like_sg3 Heli 54.8 9.2 0.0002 31.3 2.1 25 338-362 1-25 (112)
446 PRK15090 DNA-binding transcrip 54.7 23 0.00051 33.2 5.2 25 336-360 27-51 (257)
447 COG3711 BglG Transcriptional a 54.6 21 0.00045 36.8 5.2 114 242-367 17-130 (491)
448 PF04814 HNF-1_N: Hepatocyte n 54.6 9.9 0.00022 34.0 2.4 51 309-362 106-156 (180)
449 PF05269 Phage_CII: Bacterioph 54.5 24 0.00052 28.1 4.3 33 338-370 24-56 (91)
450 COG2963 Transposase and inacti 54.4 28 0.00061 28.3 5.0 44 316-363 6-51 (116)
451 PRK15121 right oriC-binding tr 54.4 1.9E+02 0.0042 27.4 11.6 41 227-267 4-44 (289)
452 PRK06474 hypothetical protein; 54.4 24 0.00053 31.4 5.0 44 316-360 6-50 (178)
453 PRK11014 transcriptional repre 53.9 27 0.00058 29.7 4.9 28 336-367 24-51 (141)
454 PF12085 DUF3562: Protein of u 53.4 28 0.0006 26.0 4.2 31 338-368 8-38 (66)
455 cd01279 HTH_HspR-like Helix-Tu 53.3 9.7 0.00021 30.4 2.0 24 338-361 2-25 (98)
456 PRK06424 transcription factor; 53.3 13 0.00029 32.1 3.0 24 336-359 96-119 (144)
457 PRK00082 hrcA heat-inducible t 52.9 23 0.00049 35.1 4.9 47 316-364 2-53 (339)
458 PRK11569 transcriptional repre 52.9 28 0.0006 33.1 5.4 25 336-360 42-66 (274)
459 cd01111 HTH_MerD Helix-Turn-He 52.7 10 0.00023 30.8 2.1 25 338-362 1-25 (107)
460 COG5625 Predicted transcriptio 52.7 22 0.00047 28.8 3.8 51 310-362 9-61 (113)
461 PRK11886 bifunctional biotin-- 52.7 29 0.00063 33.7 5.6 39 321-362 5-43 (319)
462 COG4190 Predicted transcriptio 52.6 44 0.00096 28.5 5.8 45 313-360 57-101 (144)
463 COG5606 Uncharacterized conser 52.2 12 0.00025 29.5 2.1 27 336-362 40-66 (91)
464 TIGR00373 conserved hypothetic 52.2 48 0.0011 29.0 6.4 39 319-360 13-51 (158)
465 PF04967 HTH_10: HTH DNA bindi 52.1 22 0.00048 25.2 3.4 26 243-268 22-47 (53)
466 PRK14165 winged helix-turn-hel 52.0 29 0.00062 32.2 5.1 30 332-361 16-45 (217)
467 cd04777 HTH_MerR-like_sg1 Heli 52.0 11 0.00024 30.4 2.2 25 338-362 1-25 (107)
468 PRK04424 fatty acid biosynthes 51.8 23 0.0005 31.8 4.4 37 320-359 7-43 (185)
469 PRK08359 transcription factor; 51.8 14 0.0003 33.1 2.9 35 336-370 97-138 (176)
470 PRK09391 fixK transcriptional 51.8 16 0.00036 33.5 3.6 28 337-368 179-206 (230)
471 TIGR02395 rpoN_sigma RNA polym 51.5 79 0.0017 32.4 8.7 23 245-267 319-341 (429)
472 cd04769 HTH_MerR2 Helix-Turn-H 51.4 11 0.00024 31.0 2.1 26 338-363 1-26 (116)
473 PRK06030 hypothetical protein; 51.3 59 0.0013 27.3 6.5 41 320-364 56-96 (124)
474 cd04783 HTH_MerR1 Helix-Turn-H 51.1 11 0.00024 31.5 2.1 25 338-362 1-25 (126)
475 PF04545 Sigma70_r4: Sigma-70, 51.0 49 0.0011 22.5 5.1 30 238-267 14-43 (50)
476 PRK10681 DNA-binding transcrip 51.0 28 0.00062 32.7 5.1 38 320-360 7-44 (252)
477 cd04770 HTH_HMRTR Helix-Turn-H 50.9 12 0.00025 31.1 2.2 26 338-363 1-26 (123)
478 PF07506 RepB: RepB plasmid pa 50.9 37 0.00081 30.3 5.6 41 316-359 3-43 (185)
479 cd04767 HTH_HspR-like_MBC Heli 50.9 11 0.00025 31.4 2.1 26 338-363 2-27 (120)
480 PRK09943 DNA-binding transcrip 50.6 15 0.00033 32.7 3.0 25 336-360 19-43 (185)
481 cd04781 HTH_MerR-like_sg6 Heli 50.1 12 0.00026 31.0 2.1 25 338-362 1-25 (120)
482 PF05344 DUF746: Domain of Unk 49.9 45 0.00098 24.8 4.8 30 336-365 12-41 (65)
483 PRK09836 DNA-binding transcrip 49.4 26 0.00057 31.2 4.5 50 317-367 150-204 (227)
484 PF13542 HTH_Tnp_ISL3: Helix-t 49.4 51 0.0011 22.4 5.0 27 241-267 24-50 (52)
485 cd04776 HTH_GnyR Helix-Turn-He 49.2 13 0.00027 30.9 2.1 25 338-362 1-25 (118)
486 PF03965 Penicillinase_R: Peni 49.0 34 0.00073 27.9 4.7 43 318-363 1-47 (115)
487 PRK09802 DNA-binding transcrip 48.9 31 0.00067 32.8 5.0 38 320-360 17-54 (269)
488 COG1497 Predicted transcriptio 48.9 44 0.00094 31.5 5.7 26 335-360 23-48 (260)
489 PRK09975 DNA-binding transcrip 48.8 16 0.00036 32.7 3.0 25 334-358 28-52 (213)
490 TIGR00270 conserved hypothetic 48.7 17 0.00037 31.7 3.0 24 336-359 81-104 (154)
491 PRK10086 DNA-binding transcrip 48.5 62 0.0013 30.9 7.2 49 312-365 8-56 (311)
492 PF09012 FeoC: FeoC like trans 48.4 19 0.00041 26.6 2.8 25 336-360 13-37 (69)
493 COG0789 SoxR Predicted transcr 48.2 14 0.00031 30.3 2.3 25 338-362 1-25 (124)
494 PRK13832 plasmid partitioning 48.0 39 0.00084 35.3 5.8 53 317-372 101-155 (520)
495 PF06413 Neugrin: Neugrin; In 48.0 36 0.00077 31.7 5.1 42 317-359 10-51 (225)
496 PF07022 Phage_CI_repr: Bacter 47.9 6.6 0.00014 29.0 0.2 23 338-360 13-36 (66)
497 PRK10402 DNA-binding transcrip 47.9 18 0.0004 33.0 3.2 45 319-367 150-195 (226)
498 PRK11511 DNA-binding transcrip 47.9 41 0.0009 28.0 5.1 26 336-361 24-49 (127)
499 COG2411 Uncharacterized conser 47.7 87 0.0019 27.9 7.1 48 315-367 135-184 (188)
500 PRK02277 orotate phosphoribosy 47.7 15 0.00033 33.3 2.6 32 336-367 17-48 (200)
No 1
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=2.1e-45 Score=363.96 Aligned_cols=250 Identities=37% Similarity=0.642 Sum_probs=240.0
Q ss_pred HHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHH
Q 046578 129 NLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIR 208 (379)
Q Consensus 129 ~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~ 208 (379)
.+|+.+++.||..|++.|+..|.++|+++|++|.+++.+++||+|||++|||+++++|||.+|++|+|||+|||++.|.+
T Consensus 117 ~~L~~~~~~Gd~~A~~~Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~ 196 (367)
T PRK09210 117 IELAKRIEEGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITR 196 (367)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHH
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccc
Q 046578 209 AIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQD 288 (379)
Q Consensus 209 ~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d 288 (379)
+++++.+.+|+|+|+...++++.++.+.+...+|++||.+|||+.+|++.+++..++.....++|||.+++++++..+.+
T Consensus 197 ~i~~~~r~irip~~~~~~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d 276 (367)
T PRK09210 197 AIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGD 276 (367)
T ss_pred HHHHcCCceeccHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCCCcchhhh
Confidence 99999999999999999999999999999999999999999999999999999999988888999999998777777889
Q ss_pred cCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 289 IIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 289 ~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
++++....+|++.+....+...|..+|..||++||.||.++||++|++++|++|||+.||||+++|+|+..+|++|||..
T Consensus 277 ~i~d~~~~~p~~~~~~~~~~~~l~~~l~~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~~ 356 (367)
T PRK09210 277 FIEDQDATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHP 356 (367)
T ss_pred hccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhCh
Confidence 98888778899999888888999999999999999999999999877999999999999999999999999999999999
Q ss_pred Hhhchhhhhc
Q 046578 369 NILNNLKVYM 378 (379)
Q Consensus 369 l~~~~L~~y~ 378 (379)
.....|++|+
T Consensus 357 ~~~~~l~~~~ 366 (367)
T PRK09210 357 SRSKQLKDFL 366 (367)
T ss_pred HHHhHHHHhh
Confidence 9999999986
No 2
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=100.00 E-value=2.9e-45 Score=356.27 Aligned_cols=249 Identities=37% Similarity=0.626 Sum_probs=233.1
Q ss_pred HHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHH
Q 046578 129 NLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIR 208 (379)
Q Consensus 129 ~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~ 208 (379)
.++...+. .+..|++.||..|.++|+++|++|.+++.+++||+|||++|||+++++|||++|++|+|||+|||++.|.+
T Consensus 75 ~~l~~~~~-~~~~A~~~Lv~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~ 153 (324)
T PRK07921 75 RDLAAVVR-DGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITR 153 (324)
T ss_pred HHHHHHHh-cCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHH
Confidence 34555555 45789999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccc
Q 046578 209 AIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQD 288 (379)
Q Consensus 209 ~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d 288 (379)
+++++.+.+++|.++....+++.++...+.+.+|+.|+.+|||+.+|++.+++..++......+|||.+++++++..+.+
T Consensus 154 ~i~~~~r~vrlP~~~~~~~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d 233 (324)
T PRK07921 154 GMADQSRTIRLPVHLVEQVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGD 233 (324)
T ss_pred HHHHcCCCccCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCchHHH
Confidence 99999999999999999999999999999999999999999999999999999999888889999999987776667888
Q ss_pred cCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 289 IIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 289 ~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
++++....+|++.+...++...|..+|..|+++|+.||.++||++|++++|++|||+.||||+++|+|+..+|++|||..
T Consensus 234 ~l~d~~~~~pe~~~~~~~~~~~l~~~L~~L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~~ 313 (324)
T PRK07921 234 FIEDSEATSAENAVIAGLLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNG 313 (324)
T ss_pred HhcCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Confidence 88887777888888888888899999999999999999999999877899999999999999999999999999999999
Q ss_pred Hhhchhhhhc
Q 046578 369 NILNNLKVYM 378 (379)
Q Consensus 369 l~~~~L~~y~ 378 (379)
.....|+.|+
T Consensus 314 ~~~~~l~~~~ 323 (324)
T PRK07921 314 ERADRLRSYA 323 (324)
T ss_pred HHHHHHHHhh
Confidence 9999999886
No 3
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=2.4e-45 Score=385.81 Aligned_cols=299 Identities=31% Similarity=0.508 Sum_probs=269.5
Q ss_pred hhhhcCCcccccchhHHHHHHHHHHHHHhhhcccccccchhh----------------hcCcC---cHHHHHHHHhcccH
Q 046578 80 VSFANGAEEVCFDDGECESVLKMMRRRSRRKKRTKESDFLDK----------------ENGEL---DYNLVKYKILCKER 140 (379)
Q Consensus 80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------~~~~~---~~~eLi~~~~~Gd~ 140 (379)
++..+|+++-+|...+.+.+.+..|..+..+.++.+...... ....+ +..+++.+++.||.
T Consensus 297 ~~~~~~m~R~~Fi~~f~gnEt~~~w~~~~~~~~~~~a~~l~~~~~~I~~lq~~L~~ie~~~~Ls~eElk~l~~~i~~g~~ 376 (619)
T PRK05658 297 LVERLKMPRKDFLKLFQGNELDITWLEKEIASGKPWSEFLVRVYDEIKKLQQELEAIEEETGLTIEELKEINRQISKGEA 376 (619)
T ss_pred HHHHcCCCHHHHHHHccCCcCCHHHHHHHHhccCchHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHhccch
Confidence 457899999999999988888887766555544433332211 01112 24678888999965
Q ss_pred ---HHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcc
Q 046578 141 ---ESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTI 217 (379)
Q Consensus 141 ---~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~i 217 (379)
.|+++|+..|.++|.++|++|.++|.+++||+|||++||++|+++|||++|++|+|||+|||+++|.++++++.+++
T Consensus 377 ~~~~a~~~Li~~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA~~wIr~aI~~~i~~~~r~i 456 (619)
T PRK05658 377 KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTI 456 (619)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCchHHHhHHHHHHHHHHHHHHcCCce
Confidence 78899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCC
Q 046578 218 RLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETM 297 (379)
Q Consensus 218 rip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~ 297 (379)
|+|+|+....+++.++...+.+.+|++|+++|||+.+|++.+++..++.....++|||.+++++++..+.+++++....+
T Consensus 457 rip~~~~~~~~k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~Sld~~i~~~~~~~l~d~i~d~~~~~ 536 (619)
T PRK05658 457 RIPVHMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAEL 536 (619)
T ss_pred ecCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCcCCCCCCCCCCCchhhhcCCCCCCC
Confidence 99999999999999999999999999999999999999999999999988889999999998887778889999887788
Q ss_pred hHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchhhhh
Q 046578 298 PERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVY 377 (379)
Q Consensus 298 pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L~~y 377 (379)
|++.+....+...+..+|..||++|+.||.+|||+++.+++|++|||+.||||+++|+|+..+|++|||.......|+.|
T Consensus 537 p~~~~~~~~~~~~l~~~l~~L~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~eRVrQie~~al~kLr~~~~~~~l~~~ 616 (619)
T PRK05658 537 PIDAAIQESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLRSF 616 (619)
T ss_pred hHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHhchHHHHHHHHH
Confidence 99988888888999999999999999999999999877899999999999999999999999999999999999999998
Q ss_pred c
Q 046578 378 M 378 (379)
Q Consensus 378 ~ 378 (379)
+
T Consensus 617 ~ 617 (619)
T PRK05658 617 L 617 (619)
T ss_pred h
Confidence 6
No 4
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=100.00 E-value=3e-45 Score=371.51 Aligned_cols=240 Identities=38% Similarity=0.652 Sum_probs=230.2
Q ss_pred HHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccC
Q 046578 140 RESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRL 219 (379)
Q Consensus 140 ~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~iri 219 (379)
..|++.|+..|+++|+++|++|.++|.+++||+|||++||++|+++|||++|++|+|||+||||+.|.++++++.+.+|+
T Consensus 270 ~~Ar~~LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRv 349 (509)
T PRK05901 270 KRAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRI 349 (509)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceec
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChH
Q 046578 220 PGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPE 299 (379)
Q Consensus 220 p~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe 299 (379)
|+++...++++.++...+.+.+|++|+.+|||+.+|++++++..++.....++|||.+++++++..+.+++.+.....|+
T Consensus 350 P~~~~e~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~~p~ 429 (509)
T PRK05901 350 PVHMVETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSPV 429 (509)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCcccHHHhccCCCCCCHH
Confidence 99999999999999999999999999999999999999999999988888999999999877777788889888777899
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchhhhhcC
Q 046578 300 RMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVYMV 379 (379)
Q Consensus 300 ~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L~~y~~ 379 (379)
+.+....+...|..+|..|+++||.||.+||||+|++++|++|||+.||||+++|+|+..+|++|||.......|++|+.
T Consensus 430 ~~~~~~~l~~~L~~aL~~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~~~~~~~l~~~l~ 509 (509)
T PRK05901 430 DAVSFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRDFLD 509 (509)
T ss_pred HHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 98888888899999999999999999999999987799999999999999999999999999999999999999999973
No 5
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=100.00 E-value=4.4e-45 Score=351.19 Aligned_cols=250 Identities=39% Similarity=0.677 Sum_probs=238.7
Q ss_pred HHHHHHHhcc--cHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHH
Q 046578 129 NLVKYKILCK--ERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAI 206 (379)
Q Consensus 129 ~eLi~~~~~G--d~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i 206 (379)
.++..++..| |..|...++..|+++|.++|++|.++|..+.||+|||.+||++|+++|||++|++|+|||+||||..|
T Consensus 88 ~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAVekFdp~rG~kFsTYA~wWIrqaI 167 (342)
T COG0568 88 KALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQAI 167 (342)
T ss_pred HHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHHHHhcCcccCCcchhHHHHHHHHHH
Confidence 5688899999 89999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcc
Q 046578 207 IRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTM 286 (379)
Q Consensus 207 ~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l 286 (379)
.+++.++.|++|+|.|+.+..+++.+..+++.+.+|++|+.+|||+.+|++++++..++.....++|||.+++++++..+
T Consensus 168 ~raI~~q~rtIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd~~ig~ded~~l 247 (342)
T COG0568 168 TRAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDDEDSEL 247 (342)
T ss_pred HHHHHHhcchhhHhHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccCCcCCCCcccHH
Confidence 99999999999999999999999999999999999999999999999999999999999998889999999999888889
Q ss_pred cccCCCCCCCChHHHHHHHHHHHHHHHHHhc-CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578 287 QDIIPGPDETMPERMVQKQLMKQELKELLQT-LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL 365 (379)
Q Consensus 287 ~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~-L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL 365 (379)
.|++++....+|++.+........+...|.. |+|+|+.||.+|||++|.++.|+.|||+.+|||+.+|+|+..+|++||
T Consensus 248 ~d~leD~~~~~p~~~~~~~~~~~~~~~~L~~~Lt~rE~~Vi~~R~gl~~~~~~TLeevg~~~~isrERvRQIE~kAl~KL 327 (342)
T COG0568 248 GDFLEDDKSVSPEDAVERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEAKALRKL 327 (342)
T ss_pred HHHhhcCCcCCHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCcchHHHHHHHhCCcHHHHHHHHHHHHHHH
Confidence 9999998888999999999999999999999 999999999999999977999999999999999999999999999999
Q ss_pred HhHH-hhchhhhhc
Q 046578 366 QQTN-ILNNLKVYM 378 (379)
Q Consensus 366 R~~l-~~~~L~~y~ 378 (379)
|.+. ....+++|+
T Consensus 328 r~~~~~~~~~~~~l 341 (342)
T COG0568 328 RRHPERSALLRSYL 341 (342)
T ss_pred HHhhhhhhHHHHhh
Confidence 9544 455568876
No 6
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=100.00 E-value=1.1e-44 Score=359.31 Aligned_cols=253 Identities=39% Similarity=0.644 Sum_probs=239.6
Q ss_pred CcCcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHH
Q 046578 124 GELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIK 203 (379)
Q Consensus 124 ~~~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir 203 (379)
-.++..+|+..++.| ..|++.||..|.++|+++|++|.+++.+++||+|||++|||+++++|||++|++|+||++||||
T Consensus 159 ~~l~~~eL~~~l~~G-~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~ravekFDp~rG~rFSTYa~wwIR 237 (415)
T PRK07598 159 AKLTVEELEQIQKQG-LRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIR 237 (415)
T ss_pred ccCCHHHHHHHHHCC-HHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHH
Confidence 346778999999999 6899999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCC
Q 046578 204 QAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGC 283 (379)
Q Consensus 204 ~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~ 283 (379)
+.|.+++.++.+++++|.|+...+++++++.+.+.+.+|+.|+.+|||+.+|+++++++.++.....++|||.+++++++
T Consensus 238 qaI~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~l~~~~~~~SLd~~vg~~~d 317 (415)
T PRK07598 238 QGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETKVGKDKD 317 (415)
T ss_pred HHHHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHccCCcccccccCCCcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999988877
Q ss_pred CcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578 284 MTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT 363 (379)
Q Consensus 284 ~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~ 363 (379)
..+.+.+.+ ...+|++.+...+....|..+|..|||+||.||.++|||+|++++|++|||+.||+|+++|++++++|++
T Consensus 318 ~~l~d~l~~-~~~~pee~~~~~~l~~~L~~~L~~L~~reR~VI~LRygl~d~~~~Tl~EIA~~LGvS~erVRqie~rAl~ 396 (415)
T PRK07598 318 TELGDLLET-DDISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQ 396 (415)
T ss_pred ccHHHhccC-CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 777777764 3457888888888889999999999999999999999988778999999999999999999999999999
Q ss_pred HHHhHHhhchhhhhc
Q 046578 364 KLQQTNILNNLKVYM 378 (379)
Q Consensus 364 kLR~~l~~~~L~~y~ 378 (379)
|||+.-....|++|+
T Consensus 397 KLR~~~~~~~l~~y~ 411 (415)
T PRK07598 397 KLRQPKRRNRIRDYL 411 (415)
T ss_pred HHhchhHHHHHHHHH
Confidence 999999999999996
No 7
>PRK05949 RNA polymerase sigma factor; Validated
Probab=100.00 E-value=8.9e-44 Score=346.70 Aligned_cols=250 Identities=38% Similarity=0.660 Sum_probs=234.0
Q ss_pred cCcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHH
Q 046578 125 ELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQ 204 (379)
Q Consensus 125 ~~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~ 204 (379)
.++..+|+.+++.|+ .|++.||..|.++|+++|++|.+++.+++||+||||+|||+++++||+++|++|+||++||||+
T Consensus 76 ~~~~~eL~~~~~~g~-~A~~~Li~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq 154 (327)
T PRK05949 76 NLSETELKQTLKQGK-RAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQ 154 (327)
T ss_pred cCCHHHHHHHHHccH-HHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHH
Confidence 356788999999996 5999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCC
Q 046578 205 AIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCM 284 (379)
Q Consensus 205 ~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~ 284 (379)
.|.+++.++.+++|+|.|+...++++.++...+...+|++|+.+|||+.+|++++++..++.....++|||.+++++++.
T Consensus 155 ~I~r~i~~~~r~iRlP~~~~~~~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~ 234 (327)
T PRK05949 155 AITRAIAQQARTIRLPIHITEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDT 234 (327)
T ss_pred HHHHHHHHcCCceeCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCc
Confidence 99999999999999999999999999999999999999999999999999999999999998888999999999877666
Q ss_pred cccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046578 285 TMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTK 364 (379)
Q Consensus 285 ~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~k 364 (379)
.+.+.+++.. .+|++.+...+....|..+|+.||++||.||.++|||+|++++|++|||+.||+|+++|++++++|+++
T Consensus 235 ~l~~~l~d~~-~~pe~~~~~~~~~~~L~~~L~~L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~k 313 (327)
T PRK05949 235 ELSELLEDEG-PSPDQYITQELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAH 313 (327)
T ss_pred cHHhhcCCCC-CCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 7777777654 678988888888899999999999999999999999988899999999999999999999999999999
Q ss_pred HHhHHhhchhhhhc
Q 046578 365 LQQTNILNNLKVYM 378 (379)
Q Consensus 365 LR~~l~~~~L~~y~ 378 (379)
||+. ...|++|+
T Consensus 314 Lr~~--~~~l~~~~ 325 (327)
T PRK05949 314 LRRR--RANVKEYL 325 (327)
T ss_pred HHHH--HHHHHHHH
Confidence 9994 45677775
No 8
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=2.2e-44 Score=354.89 Aligned_cols=252 Identities=41% Similarity=0.696 Sum_probs=236.6
Q ss_pred CcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHH
Q 046578 126 LDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA 205 (379)
Q Consensus 126 ~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~ 205 (379)
++..+|..++..| ..|++.||..|.++|+++|++|.+++.+++||+|||++|||+++++||+.+|.+|+|||+||||+.
T Consensus 122 ~~~~~l~~~~~~g-~~A~~~Li~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqa 200 (373)
T PRK07406 122 MPLPKFRRRLMLG-RRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQA 200 (373)
T ss_pred ccHHHHHHHHhcC-HHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHH
Confidence 4567788887777 999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCc
Q 046578 206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMT 285 (379)
Q Consensus 206 i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~ 285 (379)
|.++++++.+.+|+|+++....+++.++...+.+.+|+.|+.+|||+.+|++.+++..++.....++|||.+++++++..
T Consensus 201 I~~~I~~~~r~IRlP~~~~~~~~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~~~ 280 (373)
T PRK07406 201 ITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSR 280 (373)
T ss_pred HHHHHHhcCCceeCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCccc
Confidence 99999999999999999999999999999999999999999999999999999999999888889999999988776667
Q ss_pred ccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578 286 MQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL 365 (379)
Q Consensus 286 l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL 365 (379)
+.+++++. ..+|++.+........|..+|..||++||.||.++||++|.+++|++|||+.||||+++|+|+..+|++||
T Consensus 281 l~d~l~d~-~~~pee~~~~~~~~~~L~~aL~~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KL 359 (373)
T PRK07406 281 LGDFIEAD-GETPEDDVAKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKL 359 (373)
T ss_pred HHHhcCCC-CCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 88888765 45788888888888999999999999999999999998877889999999999999999999999999999
Q ss_pred HhHHhhchhhhhcC
Q 046578 366 QQTNILNNLKVYMV 379 (379)
Q Consensus 366 R~~l~~~~L~~y~~ 379 (379)
|+......|++|++
T Consensus 360 R~~~~~~~l~~~~~ 373 (373)
T PRK07406 360 RHPNRNSVLKEYIR 373 (373)
T ss_pred hchhHHHHHHHHhC
Confidence 99999999999974
No 9
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=100.00 E-value=2.2e-43 Score=330.57 Aligned_cols=237 Identities=39% Similarity=0.681 Sum_probs=224.0
Q ss_pred HHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCc
Q 046578 142 SQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPG 221 (379)
Q Consensus 142 A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~ 221 (379)
|+++|+..|.++|+++|++|.+++.+.+||+|||++||++|+++|||++|.+|+|||+|||++.|.++++++.+.+++|+
T Consensus 1 a~~~Li~~~~~lv~~ia~~~~~~~~~~eDLiQeG~igL~~A~~~fd~~~g~~FstYA~~~Ir~~I~~~l~~~~~~vrip~ 80 (238)
T TIGR02393 1 AKKQLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80 (238)
T ss_pred CHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCChHHHhHHHHHHHHHHHHHHcCCcEEeCH
Confidence 56889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHH
Q 046578 222 SMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERM 301 (379)
Q Consensus 222 ~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~ 301 (379)
++...++++.++...+.+.+|++||.+|||+.+|++.+++..++......+|||.++.+++...+.+.++++...+|++.
T Consensus 81 ~~~~~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~p~~~ 160 (238)
T TIGR02393 81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDTSIESPDDY 160 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCCCCCCcccHHHHhcCCCCCChHHH
Confidence 99999999999999999999999999999999999999999998877789999999877666577788888777788888
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchhhhhc
Q 046578 302 VQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVYM 378 (379)
Q Consensus 302 ~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L~~y~ 378 (379)
+...+....|..+|..||++||.||.++||+++.+++|++|||+.||+|+++|++++.+|++|||+.+....|+.|+
T Consensus 161 ~~~~~~~~~l~~~l~~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~~~~~~~~~~ 237 (238)
T TIGR02393 161 AAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKSFL 237 (238)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhHHHhHHHHhh
Confidence 88888889999999999999999999999888779999999999999999999999999999999999998888886
No 10
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=1.1e-42 Score=338.34 Aligned_cols=250 Identities=38% Similarity=0.657 Sum_probs=233.3
Q ss_pred cCcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHH
Q 046578 125 ELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQ 204 (379)
Q Consensus 125 ~~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~ 204 (379)
.++..+|+.++..|+ .|++.||..|.++|+++|++|.+++.+++||+||||+|||+++++|||++|++|+||++||||+
T Consensus 66 ~~~~~~L~~~~~~g~-~A~~~L~~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~ 144 (317)
T PRK07405 66 KLSEEELRSAIAEGE-AAKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQ 144 (317)
T ss_pred cCCHHHHHHHHhccH-HHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHH
Confidence 356788999999996 8999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCC
Q 046578 205 AIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCM 284 (379)
Q Consensus 205 ~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~ 284 (379)
.|.+++.++.+++|+|.++...++++.++...+...+|+.|+.+|||+.+|++.+++..++......+|||.+++++++.
T Consensus 145 ~I~~~i~~~~~~ir~p~~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~ 224 (317)
T PRK07405 145 AITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDT 224 (317)
T ss_pred HHHHHHHhcCCCccCChHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCc
Confidence 99999999999999999999999999999999999999999999999999999999999998888999999998777666
Q ss_pred cccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046578 285 TMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTK 364 (379)
Q Consensus 285 ~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~k 364 (379)
.+.+.+++. ..+|++.+...+....|..+|+.||++||.||.++|||+|.+++|++|||+.||||+++|+++..+|++|
T Consensus 225 ~l~~~~~d~-~~~pe~~~~~~~~~~~l~~al~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~k 303 (317)
T PRK07405 225 ELGELLEDT-GASPEDFATQSSLQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSK 303 (317)
T ss_pred cHHHhhcCC-CCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 777777765 3678988888888899999999999999999999999988899999999999999999999999999999
Q ss_pred HHhHHhhchhhhhc
Q 046578 365 LQQTNILNNLKVYM 378 (379)
Q Consensus 365 LR~~l~~~~L~~y~ 378 (379)
||+. ...|++|+
T Consensus 304 Lr~~--~~~l~~~~ 315 (317)
T PRK07405 304 LRKR--KANIQEYL 315 (317)
T ss_pred HHHH--HHHHHHHH
Confidence 9996 45667765
No 11
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=100.00 E-value=2.1e-42 Score=334.05 Aligned_cols=239 Identities=46% Similarity=0.771 Sum_probs=224.5
Q ss_pred CcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHH
Q 046578 126 LDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA 205 (379)
Q Consensus 126 ~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~ 205 (379)
++..+|+.+++.| ..|++.||..|.++|+++|++|.+++.+++||+|||++|||+|+++|||.+|++|+||++|||++.
T Consensus 60 ~~~~~l~~~~~~g-~~A~~~Lv~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~ 138 (298)
T TIGR02997 60 LSEAELRQRLRQG-QRAKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQG 138 (298)
T ss_pred CCHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHH
Confidence 5667899999989 689999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCc
Q 046578 206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMT 285 (379)
Q Consensus 206 i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~ 285 (379)
|.+++..+.+.+|+|.++....+++.++...+...+|+.|+.+|+|+.+|++.+++..++......+|||.+++++++..
T Consensus 139 I~r~i~~~~r~vr~p~~~~~~~~~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~ 218 (298)
T TIGR02997 139 ITRAIANQSRTIRLPIHITEKLNKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTE 218 (298)
T ss_pred HHHHHHhcCCCeeCcHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCcch
Confidence 99999999999999999999999999999999999999999999999999999999999988889999999987665556
Q ss_pred ccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578 286 MQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL 365 (379)
Q Consensus 286 l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL 365 (379)
+.+.+++ ...+|++.+...+....|..+|+.||++||.||.++|||+|.+++|++|||+.||||+++|++++++|++||
T Consensus 219 ~~~~~~~-~~~~pe~~~~~~~~~~~L~~~L~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~kL 297 (298)
T TIGR02997 219 LGDLLED-DGESPEEQVERESLRQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKL 297 (298)
T ss_pred HHHhccC-CCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHc
Confidence 6666666 356788888888888899999999999999999999999888999999999999999999999999999999
Q ss_pred H
Q 046578 366 Q 366 (379)
Q Consensus 366 R 366 (379)
|
T Consensus 298 r 298 (298)
T TIGR02997 298 R 298 (298)
T ss_pred C
Confidence 7
No 12
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00 E-value=1.2e-39 Score=308.39 Aligned_cols=238 Identities=24% Similarity=0.348 Sum_probs=207.6
Q ss_pred HHHHHHHH-hcccHHHHHHHHHHhHHHHHHHHHhccCC-CCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHH
Q 046578 128 YNLVKYKI-LCKERESQERIIRSYRSLVVSIATGYQGK-GLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA 205 (379)
Q Consensus 128 ~~eLi~~~-~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~-~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~ 205 (379)
..+++.+. .+||..|+++||..|.|+|+++|++|.+. +.+++||+|||++|||+|+++|||++|++|+||+++||+|.
T Consensus 11 ~~~~~~~~~~~gd~~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~ 90 (256)
T PRK07408 11 TMELLRAYQQNPSIALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGE 90 (256)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHH
Confidence 34555555 47899999999999999999999999875 66799999999999999999999999999999999999999
Q ss_pred HHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH--hcCCccccCCccccCCC
Q 046578 206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIE--RTRHPISLDGAVTDRGC 283 (379)
Q Consensus 206 i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~--~~~~~iSLd~~~~~~~~ 283 (379)
|.+++|++.+.+|+|+++....+++.++...+.+.+|++|+.+|||+.+|++++++..++. .....+|||.++.++++
T Consensus 91 i~~~lr~~~~~vr~pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~~~~ 170 (256)
T PRK07408 91 IQHYLRDKSPTVRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQDED 170 (256)
T ss_pred HHHHHHHcCCeeeeCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCCCCC
Confidence 9999999999999999999999999999999999999999999999999999999998864 35678999998754433
Q ss_pred --CcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578 284 --MTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 284 --~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
..+.+.++++... +.. ...+....|..++..||+++|.||.++|+ +++|++|||+.||+|+++|+++++||
T Consensus 171 ~~~~l~d~~~d~~~~-~~~--~~~~~~~~l~~~l~~L~~~~r~vl~l~y~----~~~s~~eIA~~lgvs~~~V~~~~~ra 243 (256)
T PRK07408 171 GSTSLGDLLPDPRYR-SFQ--LAQEDRIRLQQALAQLEERTREVLEFVFL----HDLTQKEAAERLGISPVTVSRRVKKG 243 (256)
T ss_pred CccccccccCCcccc-hhh--hhHHHHHHHHHHHHcCCHHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 2455666654432 111 23344567999999999999999999995 77999999999999999999999999
Q ss_pred HHHHHhHHhhc
Q 046578 362 LTKLQQTNILN 372 (379)
Q Consensus 362 l~kLR~~l~~~ 372 (379)
+++||+.+..+
T Consensus 244 ~~kLr~~l~~~ 254 (256)
T PRK07408 244 LDQLKKLLQPE 254 (256)
T ss_pred HHHHHHHhhcc
Confidence 99999998754
No 13
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=100.00 E-value=2.2e-39 Score=315.89 Aligned_cols=247 Identities=35% Similarity=0.556 Sum_probs=231.6
Q ss_pred HHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHH
Q 046578 129 NLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIR 208 (379)
Q Consensus 129 ~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~ 208 (379)
.+++.++++||..|++.||..|.++|+++|++|.+++.+++||+||||+++|+++++||+.+|.+|+||++|||+..+.+
T Consensus 74 ~~li~~~~~Gd~~A~~~Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~ 153 (325)
T PRK05657 74 VYFARRALRGDFAARQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIER 153 (325)
T ss_pred HHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHH
Confidence 67899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccc
Q 046578 209 AIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQD 288 (379)
Q Consensus 209 ~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d 288 (379)
+++++.+.+++|+++...++.+.++...+...+|+.|+.++||+.+|++++++..++.......|+|.+..++...++.+
T Consensus 154 ~i~~~~r~ir~p~~~~~~l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~~~~~~~~l~d 233 (325)
T PRK05657 154 AIMNQTRTIRLPVHVVKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLD 233 (325)
T ss_pred HHHHcCCccccCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCCCCCCCcchhh
Confidence 99999999999999998888899999999999999999999999999999999999988778899999887776667777
Q ss_pred cCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 289 IIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 289 ~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
.+.+....+|++.+...+....|..+|..||+++|.||.++|||.+.+++|++|||+.||+|+++|+++++||+++||+.
T Consensus 234 ~l~d~~~~~pe~~~~~~e~~~~L~~aL~~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~ 313 (325)
T PRK05657 234 ILADEQENGPEDTTQDDDMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREI 313 (325)
T ss_pred hccCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 78776667888888888888899999999999999999999988877999999999999999999999999999999999
Q ss_pred Hhhchhh
Q 046578 369 NILNNLK 375 (379)
Q Consensus 369 l~~~~L~ 375 (379)
+...++.
T Consensus 314 l~~~~~~ 320 (325)
T PRK05657 314 LQTQGLS 320 (325)
T ss_pred HHhCccc
Confidence 9887764
No 14
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00 E-value=4.7e-39 Score=305.52 Aligned_cols=224 Identities=23% Similarity=0.362 Sum_probs=200.9
Q ss_pred cccHH---HHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhh
Q 046578 137 CKERE---SQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANK 213 (379)
Q Consensus 137 ~Gd~~---A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~ 213 (379)
.|+.. ++++|+..|.|+|.++|++|.+++.+.+||+|+|++||++|+++|||++|++|+|||++||++.|.++++++
T Consensus 33 ~~~~~~~~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~iGLi~AierFDp~~G~~FsTYA~~~Irg~I~~~lr~~ 112 (264)
T PRK07122 33 AGSPEFQRQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDN 112 (264)
T ss_pred CCCHHHHHHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHc
Confidence 34554 889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCccccCCccccCCC--Cccccc
Q 046578 214 SRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIER--TRHPISLDGAVTDRGC--MTMQDI 289 (379)
Q Consensus 214 ~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~--~~~~iSLd~~~~~~~~--~~l~d~ 289 (379)
.+.+++|+++....+++.++...+.+.+|+.|+.+|||+.||++.+++..++.. ...++|||.++.++++ ..+.+.
T Consensus 113 ~~~ir~Pr~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~~~d~ 192 (264)
T PRK07122 113 SWSVKVPRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSGDDDARAIADT 192 (264)
T ss_pred CCccccCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccccccCCCCCcccchhc
Confidence 999999999999999999999999999999999999999999999999998764 4578999998764332 123333
Q ss_pred CCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578 290 IPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN 369 (379)
Q Consensus 290 i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l 369 (379)
++ +++..++..+....+..++..||+++|.||.++|+ +++|++|||+.||+|.++|++++++|+++||+.+
T Consensus 193 ~~-----~~~~~~e~~~~~~~l~~~l~~L~~rer~vl~l~y~----~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l 263 (264)
T PRK07122 193 LG-----DVDAGLDQIENREALRPLLAALPERERTVLVLRFF----ESMTQTQIAERVGISQMHVSRLLAKTLARLRDQL 263 (264)
T ss_pred cC-----CcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHc
Confidence 32 34555666677788999999999999999999995 7799999999999999999999999999999975
No 15
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=100.00 E-value=1.3e-38 Score=295.93 Aligned_cols=234 Identities=30% Similarity=0.429 Sum_probs=211.3
Q ss_pred cHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCC-CHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHH
Q 046578 127 DYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGL-SLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA 205 (379)
Q Consensus 127 ~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~-d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~ 205 (379)
+...++...++||+.+. .|++.|.|+|.++|++|.+++. +.|||+|-|++||++|+++|||++|.+|+|||..+|+++
T Consensus 10 e~~~~~~~~~~g~~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Ge 88 (247)
T COG1191 10 EEEKLLEYYAEGDEEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGE 88 (247)
T ss_pred HHHHHHHHHHhcCHHHH-HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHH
Confidence 34678889999999999 9999999999999999998766 999999999999999999999999999999999999999
Q ss_pred HHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCccccCCccccCCC
Q 046578 206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERT--RHPISLDGAVTDRGC 283 (379)
Q Consensus 206 i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~--~~~iSLd~~~~~~~~ 283 (379)
|++++|++. .+++|+..++..+++..+.+++..++||+||+.|||+.||++.+++...+... ...+|+|.....+++
T Consensus 89 i~d~LR~~~-~v~vpR~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~d 167 (247)
T COG1191 89 ILDYLRKND-SVKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDD 167 (247)
T ss_pred HHHHHHhCC-CccCcHHHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhccccc
Confidence 999999999 99999999999999999999999999999999999999999999999998775 478888876654433
Q ss_pred CcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578 284 MTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT 363 (379)
Q Consensus 284 ~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~ 363 (379)
.. ..+...+|.+.++..+....+.+++..|+++||.|+.++|+ +++|++|||+.||||+++|+|++++|++
T Consensus 168 ~~-----~~~~~~~~~~~~~~~~~~~~l~~ai~~L~EREk~Vl~l~y~----eelt~kEI~~~LgISes~VSql~kkai~ 238 (247)
T COG1191 168 DD-----VDDQIENPDDGVEKEELLEILKEAIEPLPEREKLVLVLRYK----EELTQKEIAEVLGISESRVSRLHKKAIK 238 (247)
T ss_pred cc-----hhhccccchhHHHHHHHHHHHHHHHHccCHHHHHHHHHHHH----hccCHHHHHHHhCccHHHHHHHHHHHHH
Confidence 22 22233456777888888888999999999999999999995 8899999999999999999999999999
Q ss_pred HHHhHHhh
Q 046578 364 KLQQTNIL 371 (379)
Q Consensus 364 kLR~~l~~ 371 (379)
+||+.+..
T Consensus 239 kLr~~l~~ 246 (247)
T COG1191 239 KLRKELNK 246 (247)
T ss_pred HHHHHhcc
Confidence 99998753
No 16
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=100.00 E-value=5.6e-38 Score=297.14 Aligned_cols=236 Identities=27% Similarity=0.370 Sum_probs=208.9
Q ss_pred HHHHHHH-hcccHHHHHHHHHHhHHHHHHHHHhcc---CCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHH
Q 046578 129 NLVKYKI-LCKERESQERIIRSYRSLVVSIATGYQ---GKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQ 204 (379)
Q Consensus 129 ~eLi~~~-~~Gd~~A~e~Li~~y~~lV~~ia~r~~---~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~ 204 (379)
++++... ..||..|+++|+..|.|+|+++|++|. ..+.+.+||+|+|++|||+|+++|||++|++|+||+.+||++
T Consensus 10 ~~~~~~~~~~~~~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~ 89 (257)
T PRK05911 10 AETWQLYWSTQEIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKA 89 (257)
T ss_pred HHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHH
Confidence 4555555 469999999999999999999999985 235689999999999999999999999999999999999999
Q ss_pred HHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCccccCCcccc--
Q 046578 205 AIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERT--RHPISLDGAVTD-- 280 (379)
Q Consensus 205 ~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~--~~~iSLd~~~~~-- 280 (379)
+|.+++|+.. ++|+++....+++..+...+.+.+|++|+.+|||+.+|++.+++...+... ...+|+|.++.+
T Consensus 90 ~i~~~lr~~~---~~pr~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~Sld~~~~~~~ 166 (257)
T PRK05911 90 AIIDDLRKQD---WVPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPCQS 166 (257)
T ss_pred HHHHHHHhcC---CCCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHHhhccceeeccccCCCCC
Confidence 9999999876 489999999999999999999999999999999999999999999887653 356899987643
Q ss_pred C--CCCcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHH
Q 046578 281 R--GCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIR 358 (379)
Q Consensus 281 ~--~~~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~ 358 (379)
+ +...+.+.+++.....|++.+...+....|..+|..||+++|.||.++|+ +++|++|||+.||+|.++|++++
T Consensus 167 ~~~~~~~l~~~l~d~~~~~~~~~~~~~~~~~~l~~al~~L~~~er~vi~l~y~----e~~t~~EIA~~lgis~~~V~~~~ 242 (257)
T PRK05911 167 DDEAGLALEERIADERAETGYDVVDKKEFSSILAEAILALEEKERKVMALYYY----EELVLKEIGKILGVSESRVSQIH 242 (257)
T ss_pred CCccccchhhhccCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHH
Confidence 1 22346677777766678888888888889999999999999999999995 78999999999999999999999
Q ss_pred HHHHHHHHhHHhh
Q 046578 359 GIALTKLQQTNIL 371 (379)
Q Consensus 359 ~rAl~kLR~~l~~ 371 (379)
++|+++||+.+..
T Consensus 243 ~ral~kLr~~l~~ 255 (257)
T PRK05911 243 SKALLKLRATLSA 255 (257)
T ss_pred HHHHHHHHHHHHh
Confidence 9999999999754
No 17
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=100.00 E-value=8.2e-38 Score=300.58 Aligned_cols=243 Identities=29% Similarity=0.450 Sum_probs=206.0
Q ss_pred HHHHHHHH-hcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHH
Q 046578 128 YNLVKYKI-LCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAI 206 (379)
Q Consensus 128 ~~eLi~~~-~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i 206 (379)
..+|+.+. ..||..|+++||..|.|+|+++|++|.+++.+++||+||||+|||+++++||+.+|.+|+||+++||++.|
T Consensus 26 e~~L~~~~~~~gd~~A~~~Lv~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I 105 (289)
T PRK07500 26 EHALAYRWKDHRDEDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASI 105 (289)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHH
Confidence 46788886 48999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhcCcccCCcchHH--HHHHHHHHHHHHHH---HhCCCCCHHHHHHHhCCCHHHHHHHHHh-cCCccccCCcccc
Q 046578 207 IRAIANKSRTIRLPGSMAG--MVAKIAEANNVLSR---RLRRMPTDSEIAEMLNIHVSTVRLAIER-TRHPISLDGAVTD 280 (379)
Q Consensus 207 ~~~lr~~~r~irip~~~~~--~~~ki~~a~~~l~~---~lgr~pt~~eia~~Lgis~~~~~~~l~~-~~~~iSLd~~~~~ 280 (379)
.+++++..+.+|+|.+... ...++.+....+.. .+|+.|+.+|||+.||++.+++...... ....+|||.++++
T Consensus 106 ~~~lr~~~~~iR~p~~~~~~~~~~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~ 185 (289)
T PRK07500 106 QDYILRNWSIVRGGTSSAQKALFFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSE 185 (289)
T ss_pred HHHHHHCCCceecCccHHHHHHHHHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCC
Confidence 9999999999999988654 33444444444444 6899999999999999999999877543 5579999999875
Q ss_pred CCCC--cccccCCCCCCCChHHHHHH----HHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHH
Q 046578 281 RGCM--TMQDIIPGPDETMPERMVQK----QLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERI 354 (379)
Q Consensus 281 ~~~~--~l~d~i~~~~~~~pe~~~~~----~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~V 354 (379)
+++. .+.+.+.+.. .+|++.+.. .+....|..+|+.||++||.||.++|+ . .+++|++|||+.||+|+++|
T Consensus 186 ~~~~~~~l~d~i~d~~-~~pe~~~~~~~~~~~~~~~l~~al~~L~~rer~vl~lr~~-~-~~~~t~~EIa~~lgvs~~~V 262 (289)
T PRK07500 186 EDEGRSERMDFLVDDS-PLPDEQVESSIDGERRRRWLTQALQTLNERELRIIRERRL-R-EDGATLEALGEELGISKERV 262 (289)
T ss_pred CCCCcccHHHhccCCC-CCchHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhc-C-CCCCCHHHHHHHHCCCHHHH
Confidence 5432 4667777653 356655432 345677999999999999999999984 2 27799999999999999999
Q ss_pred HHHHHHHHHHHHhHHhhch
Q 046578 355 RQIRGIALTKLQQTNILNN 373 (379)
Q Consensus 355 r~~~~rAl~kLR~~l~~~~ 373 (379)
++++++|+++||..+....
T Consensus 263 ~q~~~~Al~kLr~~l~~~~ 281 (289)
T PRK07500 263 RQIEARALEKLRRALLSQS 281 (289)
T ss_pred HHHHHHHHHHHHHHHHhcC
Confidence 9999999999999987543
No 18
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=100.00 E-value=1.2e-37 Score=298.73 Aligned_cols=238 Identities=29% Similarity=0.409 Sum_probs=200.9
Q ss_pred HHHHHH-HhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHH
Q 046578 129 NLVKYK-ILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAII 207 (379)
Q Consensus 129 ~eLi~~-~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~ 207 (379)
.+|+.+ ...||..|++.||..|.|+|+++|++|.+.+.+.+||+|||++||++|+++|||++|.+|+|||++||++.|.
T Consensus 35 ~~l~~~~~~~Gd~~a~~~Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~ 114 (284)
T PRK06596 35 YMLAKRLREHGDLEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIH 114 (284)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHH
Confidence 567888 4689999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHh--CCCCCHHHHHHHhCCCHHHHHHHHHh-cCCccccCCccccCC--
Q 046578 208 RAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRL--RRMPTDSEIAEMLNIHVSTVRLAIER-TRHPISLDGAVTDRG-- 282 (379)
Q Consensus 208 ~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~l--gr~pt~~eia~~Lgis~~~~~~~l~~-~~~~iSLd~~~~~~~-- 282 (379)
+++++..+.+++|.+... +++......+...+ +++|+.+|||+.||++.+++..++.. ....+|||.++++++
T Consensus 115 ~~l~~~~~~vr~p~~~~~--~~~~~~~~~~~~~l~~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~ 192 (284)
T PRK06596 115 EYILRNWRIVKVATTKAQ--RKLFFNLRKAKKRLGWLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEE 192 (284)
T ss_pred HHHHHcCCeeeccchHHH--HHHHHHHHHHHHHhccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCCCCC
Confidence 999998778899987532 23333333444444 48999999999999999999998753 458999999886442
Q ss_pred CCcccccCCCCCCCChHHHHHHH----HHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHH
Q 046578 283 CMTMQDIIPGPDETMPERMVQKQ----LMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIR 358 (379)
Q Consensus 283 ~~~l~d~i~~~~~~~pe~~~~~~----e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~ 358 (379)
...+.+.+++. ..+|++.+... +....|..+++.||++||.||.++|| .+ +++|++|||+.||||+++|+|++
T Consensus 193 ~~~l~~~l~d~-~~~p~~~~~~~~~~~~~~~~L~~al~~L~~rEr~VL~lry~-~~-~~~Tl~EIA~~lgvS~~rVrqi~ 269 (284)
T PRK06596 193 SGAPQDYLEDK-SSDPADVLEEDNWEDQRRALLADALEGLDERSRDIIEARWL-DD-DKSTLQELAAEYGVSAERVRQIE 269 (284)
T ss_pred cchHHHHcCCC-CCCchHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhc-CC-CCcCHHHHHHHHCCCHHHHHHHH
Confidence 23466777765 34677666543 35678999999999999999999995 32 68999999999999999999999
Q ss_pred HHHHHHHHhHHhh
Q 046578 359 GIALTKLQQTNIL 371 (379)
Q Consensus 359 ~rAl~kLR~~l~~ 371 (379)
++|++|||+.+..
T Consensus 270 ~~Al~kLR~~l~~ 282 (284)
T PRK06596 270 KNAMKKLKAAIEA 282 (284)
T ss_pred HHHHHHHHHHHHh
Confidence 9999999998764
No 19
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=100.00 E-value=2.2e-37 Score=292.71 Aligned_cols=231 Identities=24% Similarity=0.363 Sum_probs=205.4
Q ss_pred HHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHH
Q 046578 129 NLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIR 208 (379)
Q Consensus 129 ~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~ 208 (379)
.+++.+++.||..|++.||..|.|+|+++|++|.+++.+++||+||||++||+++++||+.+|.+|+||+++||+|.+.+
T Consensus 22 ~~li~~~~~gd~~a~~~L~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~ 101 (254)
T TIGR02850 22 RELFIRMQSGDTTAREKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRR 101 (254)
T ss_pred HHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHH
Confidence 67888999999999999999999999999999999999999999999999999999999999899999999999999999
Q ss_pred HHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCC--Ccc
Q 046578 209 AIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGC--MTM 286 (379)
Q Consensus 209 ~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~--~~l 286 (379)
++|+.. .+++|+++.....++.++..++...+|++|+.+|||+.+|++++++..++.....++|||.++.++++ ..+
T Consensus 102 ~lr~~~-~ir~p~~~~~~~~~~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~~~~~~~~ 180 (254)
T TIGR02850 102 YLRDNN-PIRVSRSLRDIAYKALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDGGDPIYV 180 (254)
T ss_pred HHHhCC-CccCchHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCCCCCcchh
Confidence 999975 78999999999999999999999999999999999999999999999999888888999988754433 234
Q ss_pred cccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 046578 287 QDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQ 366 (379)
Q Consensus 287 ~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR 366 (379)
.+.+.+... .++ .......+..++..|++++|.||.++|+ +++|++|||+.||+|+++|++++++|+++||
T Consensus 181 ~~~~~d~~~-~~~----~~~~~~~l~~~l~~L~~rer~vi~~~~~----~~~t~~eIA~~lgis~~~V~~~~~ral~kLr 251 (254)
T TIGR02850 181 MDQISDEKN-KDS----QWLEGIALKEAMKRLNEREKMILNMRFF----EGKTQMEVAEEIGISQAQVSRLEKAALKHMR 251 (254)
T ss_pred hhhcCCccc-cHH----HHHhHHHHHHHHHcCCHHHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 555555422 122 1223456889999999999999999994 6799999999999999999999999999999
Q ss_pred hHH
Q 046578 367 QTN 369 (379)
Q Consensus 367 ~~l 369 (379)
+.+
T Consensus 252 ~~~ 254 (254)
T TIGR02850 252 KYV 254 (254)
T ss_pred hhC
Confidence 863
No 20
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model 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 prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=100.00 E-value=4.6e-37 Score=295.14 Aligned_cols=247 Identities=36% Similarity=0.566 Sum_probs=227.2
Q ss_pred HHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHH
Q 046578 128 YNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAII 207 (379)
Q Consensus 128 ~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~ 207 (379)
..+|+.++++||..|++.||..|.++|+++|++|.+++.+++||+||||+|+|+++++||+..|.+|+||+.|+++..+.
T Consensus 33 ~~~li~~~~~gd~~a~~~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ain 112 (285)
T TIGR02394 33 EIAYARRALAGDFEARKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIE 112 (285)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHHH
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCccc
Q 046578 208 RAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQ 287 (379)
Q Consensus 208 ~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~ 287 (379)
++++++.+.+++|+++...++.+.+..+.+...+|+.|+..++|+.+|++.+.+..++....+..|+|.+..+++...+.
T Consensus 113 ~~i~~~~~~~~~p~~~~~~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~ 192 (285)
T TIGR02394 113 RAIMNQARTIRLPVHVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLL 192 (285)
T ss_pred HHHHHcCCceeCcHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCCCCCCCcchh
Confidence 99999999999999999999999888888889999999999999999999999999998888899999877665544555
Q ss_pred ccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578 288 DIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 288 d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~ 367 (379)
+.+.++...+|++.+...+....|..+|.+||+++|.||.++|||.+.+++|++|||+.||+|.++|++++++|+++||+
T Consensus 193 ~~~~~~~~~~pe~~~~~~e~~~~L~~al~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~ 272 (285)
T TIGR02394 193 DTIADEQSIDPESLVQNDDLKQLIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRR 272 (285)
T ss_pred hhhcCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 56665555678888888888899999999999999999999997766788999999999999999999999999999999
Q ss_pred HHhhchh
Q 046578 368 TNILNNL 374 (379)
Q Consensus 368 ~l~~~~L 374 (379)
.+...++
T Consensus 273 ~l~~~~~ 279 (285)
T TIGR02394 273 ILERDGV 279 (285)
T ss_pred HHHHhhh
Confidence 9987655
No 21
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. 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.
Probab=100.00 E-value=4.8e-37 Score=292.82 Aligned_cols=238 Identities=28% Similarity=0.415 Sum_probs=196.5
Q ss_pred HHHHHHH-HhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHH
Q 046578 128 YNLVKYK-ILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAI 206 (379)
Q Consensus 128 ~~eLi~~-~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i 206 (379)
..+|+.+ .+.||..|++.|+..|.|+|+++|++|.+++.+++||+|||++||++++++|||++|.+|+|||.+||+++|
T Consensus 21 e~~l~~~~~~~gd~~a~~~Lv~~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA~~~Ir~~i 100 (270)
T TIGR02392 21 EYQLAKRLREHGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEI 100 (270)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhhHHHHHHHH
Confidence 3567887 578999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhcCcccCCcchH--HHHHHHHHHHHHHHHHhCCCC-CHHHHHHHhCCCHHHHHHHHHh-cCCccccCCccccCC
Q 046578 207 IRAIANKSRTIRLPGSMA--GMVAKIAEANNVLSRRLRRMP-TDSEIAEMLNIHVSTVRLAIER-TRHPISLDGAVTDRG 282 (379)
Q Consensus 207 ~~~lr~~~r~irip~~~~--~~~~ki~~a~~~l~~~lgr~p-t~~eia~~Lgis~~~~~~~l~~-~~~~iSLd~~~~~~~ 282 (379)
.+++++..+.+|+|.+.. ....++.+....+. .++.| +.+|||+.||++.+++.+++.. ....+|||.++++++
T Consensus 101 ~~~l~~~~~~ir~p~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~~~ 178 (270)
T TIGR02392 101 HEYILRNWRLVKVATTKAQRKLFFNLRKMKKRLQ--GWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDDE 178 (270)
T ss_pred HHHHHHcCCceecCchHHHHHHHHHHHHHHHHHh--cCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCCCC
Confidence 999999877789897654 23334443333332 12555 5899999999999999998654 335899999886644
Q ss_pred C--CcccccCCCCCCCChHHHHHHH----HHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHH
Q 046578 283 C--MTMQDIIPGPDETMPERMVQKQ----LMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQ 356 (379)
Q Consensus 283 ~--~~l~d~i~~~~~~~pe~~~~~~----e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~ 356 (379)
+ ..+.+.+.+.. .+|++.+... +....|..+|..||++||.||.++|+ . .+++|++|||+.||||+++|++
T Consensus 179 ~~~~~~~~~l~d~~-~~pe~~~~~~~~~~~~~~~L~~al~~L~~rer~vl~l~y~-~-~~~~t~~eIA~~lgvS~~~V~q 255 (270)
T TIGR02392 179 DDGGAPIAYLVDKT-SDPEDTLEEEQWEELQRQALANALGSLDARSRRIIEARWL-D-DDKLTLQELAAEYGVSAERIRQ 255 (270)
T ss_pred CccccHHHHhcCCC-CChHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhc-C-CCCcCHHHHHHHHCCCHHHHHH
Confidence 3 24556666654 4567666543 35577999999999999999999995 2 2579999999999999999999
Q ss_pred HHHHHHHHHHhHHh
Q 046578 357 IRGIALTKLQQTNI 370 (379)
Q Consensus 357 ~~~rAl~kLR~~l~ 370 (379)
++.+|++|||+.+.
T Consensus 256 ~~~~Al~kLr~~l~ 269 (270)
T TIGR02392 256 IEKNAMKKLKAALA 269 (270)
T ss_pred HHHHHHHHHHHHhc
Confidence 99999999999864
No 22
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=100.00 E-value=1.5e-36 Score=287.70 Aligned_cols=232 Identities=25% Similarity=0.360 Sum_probs=205.9
Q ss_pred HHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHH
Q 046578 128 YNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAII 207 (379)
Q Consensus 128 ~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~ 207 (379)
..+|+.+++.||..+++.||..|.|+|+++|++|.+++.+++||+|||++++|+++++||+.+|.+|.||+++||+|.|.
T Consensus 24 ~~~l~~~~~~gd~~a~~~l~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~ 103 (258)
T PRK08215 24 MRELFERMQNGDKEAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIR 103 (258)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHH
Confidence 36688899999999999999999999999999999999999999999999999999999999998999999999999999
Q ss_pred HHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCC--c
Q 046578 208 RAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCM--T 285 (379)
Q Consensus 208 ~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~--~ 285 (379)
+++|+.. .+++|++......++.++..++...+|+.|+..|+|+.+|++++++...+.....+.|++.++.++++. .
T Consensus 104 ~~lr~~~-~vrip~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~ 182 (258)
T PRK08215 104 RYLRDNN-PIRVSRSLRDIAYKALQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIY 182 (258)
T ss_pred HHHHhCC-ceEecHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCCCCcchh
Confidence 9999985 789999999999999999999999999999999999999999999999888777888999887654432 2
Q ss_pred ccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578 286 MQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL 365 (379)
Q Consensus 286 l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL 365 (379)
+.+.++++.. .++. ......+..++..||++++.||.++|+ +++|++|||+.||+|+++|++++++|+++|
T Consensus 183 ~~~~~~~~~~-~~~~----~~~~~~l~~~l~~L~~~er~vi~~~~~----~~~t~~eIA~~lgis~~~V~~~~~~al~kL 253 (258)
T PRK08215 183 VMDQISDEKN-KDEN----WLEEIALKEAMKKLNDREKLILNLRFF----QGKTQMEVAEEIGISQAQVSRLEKAALKHM 253 (258)
T ss_pred hhhhccCccc-cHHH----HHhHHHHHHHHHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 3455554322 2222 223356889999999999999999994 679999999999999999999999999999
Q ss_pred HhHH
Q 046578 366 QQTN 369 (379)
Q Consensus 366 R~~l 369 (379)
|+.+
T Consensus 254 r~~l 257 (258)
T PRK08215 254 RKYI 257 (258)
T ss_pred HHHh
Confidence 9876
No 23
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=100.00 E-value=1.7e-36 Score=282.51 Aligned_cols=229 Identities=27% Similarity=0.373 Sum_probs=202.2
Q ss_pred HHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHH
Q 046578 131 VKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAI 210 (379)
Q Consensus 131 Li~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~l 210 (379)
|+.+++.||..|++.||..|.|+|+++|++|.+++.+++||+||||+++|+++++||+..|.+|.||+++||+|.|.+++
T Consensus 1 li~~~~~gd~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~l 80 (231)
T TIGR02885 1 LIKLAQNGDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFL 80 (231)
T ss_pred ChHHHHcCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHH
Confidence 35677899999999999999999999999999999999999999999999999999998888999999999999999999
Q ss_pred HhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCC--cccc
Q 046578 211 ANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCM--TMQD 288 (379)
Q Consensus 211 r~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~--~l~d 288 (379)
|++. .+++|+++.....++.++...+...+|+.|+.+|||+.+|++.+++..++.......|||.++.++++. .+.+
T Consensus 81 r~~~-~i~~p~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d 159 (231)
T TIGR02885 81 RDDG-IIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPIYLLD 159 (231)
T ss_pred HhCC-CeECCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCCCCCcchhhh
Confidence 9986 789999999999999999999999999999999999999999999999988877889999887654332 3345
Q ss_pred cCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 289 IIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 289 ~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
.+.++.. .++. ......+..+++.||++++.||.++|+ +++|++|||+.||+|+++|++++++|+++||+.
T Consensus 160 ~~~~~~~-~~~~----~~~~~~l~~~l~~L~~~e~~i~~~~~~----~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr~~ 230 (231)
T TIGR02885 160 QIADKGS-EDSD----WLEKIALKEAISKLDERERQIIMLRYF----KDKTQTEVANMLGISQVQVSRLEKKVLKKMKEK 230 (231)
T ss_pred hcCCCCc-cHHh----HHHHHHHHHHHHcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHh
Confidence 5554422 1222 123457889999999999999999995 679999999999999999999999999999986
Q ss_pred H
Q 046578 369 N 369 (379)
Q Consensus 369 l 369 (379)
|
T Consensus 231 l 231 (231)
T TIGR02885 231 L 231 (231)
T ss_pred C
Confidence 4
No 24
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=100.00 E-value=4.5e-36 Score=283.83 Aligned_cols=237 Identities=25% Similarity=0.342 Sum_probs=210.3
Q ss_pred cHHHHHHHHhc-ccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHH
Q 046578 127 DYNLVKYKILC-KERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA 205 (379)
Q Consensus 127 ~~~eLi~~~~~-Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~ 205 (379)
+..+|+.+++. ||..|+++||..|.|+|+++|++|.+++.++|||+||||+++|+++++|+++.|.+|.||+++|++|.
T Consensus 14 ~~~~li~~~~~~gd~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~ 93 (255)
T TIGR02941 14 DVIQWIAEFQQNQNGEAQEKLVDHYQNLVYSIAYKYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGE 93 (255)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHH
Confidence 34678999988 79999999999999999999999999999999999999999999999999998889999999999999
Q ss_pred HHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCccccCCccccCCC
Q 046578 206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIER--TRHPISLDGAVTDRGC 283 (379)
Q Consensus 206 i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~--~~~~iSLd~~~~~~~~ 283 (379)
|.+++|+..+.+++|++.....+++.++.+.+...+|+.|+.+|+|+.+|++.+++..++.. .....|||.++.++++
T Consensus 94 ~~~~lr~~~~~iri~~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~~~ 173 (255)
T TIGR02941 94 IKRYLRDKTWSVHVPRRIKELGPKIKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSD 173 (255)
T ss_pred HHHHHHHcCCCcCCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCCCC
Confidence 99999999889999999999999999999999999999999999999999999999887765 4577899988765544
Q ss_pred CcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578 284 MTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT 363 (379)
Q Consensus 284 ~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~ 363 (379)
......+. ...+|++.+...+....+..+++.||+++|.||.++|+ +|+|++|||+.||+|.++|++++++|++
T Consensus 174 ~~~~~~~~--~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~ii~l~~~----~g~s~~eIA~~lgis~~~V~~~~~ra~~ 247 (255)
T TIGR02941 174 GSTVARLD--SVGEVEDGYDQTERRMVLEKILPILSEREKSIIHCTFE----ENLSQKETGERLGISQMHVSRLQRQAIS 247 (255)
T ss_pred Cccccccc--ccCCcchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 32222111 11235666667777788999999999999999999994 7799999999999999999999999999
Q ss_pred HHHhHH
Q 046578 364 KLQQTN 369 (379)
Q Consensus 364 kLR~~l 369 (379)
+||+.+
T Consensus 248 ~Lr~~~ 253 (255)
T TIGR02941 248 KLKEAA 253 (255)
T ss_pred HHHHHh
Confidence 999875
No 25
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=1.4e-35 Score=279.86 Aligned_cols=236 Identities=28% Similarity=0.372 Sum_probs=208.2
Q ss_pred HHHHHHH-HhcccHHHHHHHHHHhHHHHHHHHHhccC---CCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHH
Q 046578 128 YNLVKYK-ILCKERESQERIIRSYRSLVVSIATGYQG---KGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIK 203 (379)
Q Consensus 128 ~~eLi~~-~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~---~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir 203 (379)
..+|+.+ ...||..|++.||..|.|+|+++|++|.+ ++.+++|++||||++||+++++||+.+|.+|.||+++|++
T Consensus 8 e~~l~~~~~~~~d~~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~~~ir 87 (251)
T PRK07670 8 EQKLWDRWKEERDPDAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIR 87 (251)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHH
Confidence 3678888 45579999999999999999999999965 6789999999999999999999999998999999999999
Q ss_pred HHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCccccCCccccC
Q 046578 204 QAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIER--TRHPISLDGAVTDR 281 (379)
Q Consensus 204 ~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~--~~~~iSLd~~~~~~ 281 (379)
|.+.+++|++. ++|+++...++++.++.+.+.+.+|+.|+.+|+|+.+|++.+++..++.. .....|+|.++.++
T Consensus 88 n~~~d~lR~~~---~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~ 164 (251)
T PRK07670 88 GAIIDGLRKED---WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQ 164 (251)
T ss_pred HHHHHHHHhcC---CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCccccCC
Confidence 99999999865 68999999999999999999999999999999999999999999998764 56889999987654
Q ss_pred CCC-cccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 282 GCM-TMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 282 ~~~-~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
++. .+.+.+.+....++++.+...+....|..+|..||+++|.||.++|+ +|+|++|||+.||+|.++|+++++|
T Consensus 165 ~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~EIA~~lgis~~tV~~~~~r 240 (251)
T PRK07670 165 DDGENVSVTIRDDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLVISLFYK----EELTLTEIGQVLNLSTSRISQIHSK 240 (251)
T ss_pred CCcchhhhhhcCcCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 332 22233344455677877777788888999999999999999999994 7799999999999999999999999
Q ss_pred HHHHHHhHHh
Q 046578 361 ALTKLQQTNI 370 (379)
Q Consensus 361 Al~kLR~~l~ 370 (379)
|+++||+++.
T Consensus 241 a~~~Lr~~l~ 250 (251)
T PRK07670 241 ALFKLKKLLE 250 (251)
T ss_pred HHHHHHHHhh
Confidence 9999999864
No 26
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=100.00 E-value=2.9e-35 Score=273.42 Aligned_cols=222 Identities=31% Similarity=0.445 Sum_probs=197.1
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCccc
Q 046578 139 ERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIR 218 (379)
Q Consensus 139 d~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~ir 218 (379)
|..|+++|+..|.|+|+++|++|.+++.++|||+|||++++|+++++||+.+|.+|+||+++||+|.|.++++++.+.++
T Consensus 1 ~~~a~~~lv~~y~~~v~~~a~~~~~~~~~~eDl~Qe~~i~l~~a~~~f~~~~~~~F~ty~~~~i~~~~~~~~r~~~~~~r 80 (227)
T TIGR02980 1 DKEAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTWAVR 80 (227)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCcHHHHHHHHHHHHHHHHHHcCCcee
Confidence 56799999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcC--CccccCCccccCCC--CcccccCCCCC
Q 046578 219 LPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTR--HPISLDGAVTDRGC--MTMQDIIPGPD 294 (379)
Q Consensus 219 ip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~--~~iSLd~~~~~~~~--~~l~d~i~~~~ 294 (379)
+|+++....+++.++...+...+|+.|+.+|+|+.+|++.+++..++.... ...|+|.++.++++ ..+.+.+.
T Consensus 81 i~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~d~~~--- 157 (227)
T TIGR02980 81 VPRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIEDDDGDPIALLDTLG--- 157 (227)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCCCCCCCcccccccC---
Confidence 999999999999999999999999999999999999999999998877644 48999988763222 12233332
Q ss_pred CCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578 295 ETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN 369 (379)
Q Consensus 295 ~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l 369 (379)
++++.+...+....+..++..||++++.||.++|+ +|+|++|||+.||+|+++|++++++|+++||+.+
T Consensus 158 --~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~y~----~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~l 226 (227)
T TIGR02980 158 --DEDDALETVEDRLALKPLLAALPERERRILLLRFF----EDKTQSEIAERLGISQMHVSRLLRRALKKLREQL 226 (227)
T ss_pred --CcchHHHhHHHHHHHHHHHHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 23444555566678999999999999999999995 6799999999999999999999999999999875
No 27
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=100.00 E-value=7e-35 Score=277.66 Aligned_cols=237 Identities=26% Similarity=0.401 Sum_probs=210.2
Q ss_pred HHHHHHHHh-cccHHHHHHHHHHhHHHHHHHHHhcc-C--CCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHH
Q 046578 128 YNLVKYKIL-CKERESQERIIRSYRSLVVSIATGYQ-G--KGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIK 203 (379)
Q Consensus 128 ~~eLi~~~~-~Gd~~A~e~Li~~y~~lV~~ia~r~~-~--~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir 203 (379)
..+|+.+++ .||.++++.++..|.|+|+.+|+++. + .+.+++||+||||+|||+++++||+.+|.+|+||+++||+
T Consensus 17 e~~l~~~~~~~~d~~a~~~l~~~y~~lv~~~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir 96 (268)
T PRK06288 17 ETELWREYKKTGDPKIREYLILKYSPLVKYVAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIR 96 (268)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHH
Confidence 467888855 58999999999999999999999986 2 4678999999999999999999999888899999999999
Q ss_pred HHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCccccCCcccc-
Q 046578 204 QAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIER--TRHPISLDGAVTD- 280 (379)
Q Consensus 204 ~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~--~~~~iSLd~~~~~- 280 (379)
|.+.+++|+. .++|+++....+++.++...+.+.+|++|+.+|||+.+|++.+.+..++.. ....+|+|..+..
T Consensus 97 ~~i~d~~R~~---~~~p~~~~~~~~~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~~~ 173 (268)
T PRK06288 97 GAIFDELRSI---DWIPRSVRQKARQIERAIAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGG 173 (268)
T ss_pred HHHHHHHHhc---CccCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhccC
Confidence 9999999965 468999999999999999999999999999999999999999999988765 3567899887632
Q ss_pred C--CCCcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHH
Q 046578 281 R--GCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIR 358 (379)
Q Consensus 281 ~--~~~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~ 358 (379)
+ +...+.+.++++...+|++.+...+....|..+|..||+++|.||.++|+ +++|++|||+.||+|.++|++++
T Consensus 174 ~~~~~~~l~~~~~~~~~~~pe~~~~~~e~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~tV~~~~ 249 (268)
T PRK06288 174 DEGDEVSLMDTLESPAALNPDEIAEREEIKRVIVEAIKTLPEREKKVLILYYY----EDLTLKEIGKVLGVTESRISQLH 249 (268)
T ss_pred CCcccchhhhhccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHH
Confidence 2 12345566777667788988888888899999999999999999999995 77999999999999999999999
Q ss_pred HHHHHHHHhHHhh
Q 046578 359 GIALTKLQQTNIL 371 (379)
Q Consensus 359 ~rAl~kLR~~l~~ 371 (379)
+||+++||+++..
T Consensus 250 ~ra~~~Lr~~l~~ 262 (268)
T PRK06288 250 TKAVLQLRAKLAE 262 (268)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999999864
No 28
>PRK05572 sporulation sigma factor SigF; Validated
Probab=100.00 E-value=3.6e-34 Score=270.39 Aligned_cols=232 Identities=27% Similarity=0.370 Sum_probs=203.6
Q ss_pred cHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHH
Q 046578 127 DYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAI 206 (379)
Q Consensus 127 ~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i 206 (379)
+..+++.+++.||..|++.||..|.++|+++|++|.+++.+++|++||||+++|+++++|++..+.+|.||+++||+|.|
T Consensus 18 ~~~~li~~~~~gd~~a~~~L~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i 97 (252)
T PRK05572 18 ENKELIKKSQDGDQEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEI 97 (252)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHH
Confidence 34678899999999999999999999999999999999999999999999999999999999888899999999999999
Q ss_pred HHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCC--
Q 046578 207 IRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCM-- 284 (379)
Q Consensus 207 ~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~-- 284 (379)
.+++|+.. .+++|+++....+++.++...+...+|+.|+..|+|+.+|++.+.+..+........|++.++.+++..
T Consensus 98 ~~~lr~~~-~~r~~~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~ 176 (252)
T PRK05572 98 QRFLRDDG-TVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGDPI 176 (252)
T ss_pred HHHHHhCC-CCCCCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCcccCCCCcc
Confidence 99999885 789999999999999999999999999999999999999999999998887777888998877554322
Q ss_pred cccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046578 285 TMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTK 364 (379)
Q Consensus 285 ~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~k 364 (379)
.+.+.+.++.. +. ......+..++..||++++.||.++|+ +++|++|||+.+|+|.++|++++++|+++
T Consensus 177 ~~~d~~~~~~~---~~----~~~~~~l~~~l~~L~~~~~~v~~l~~~----~~~s~~eIA~~lgis~~~V~~~~~ral~k 245 (252)
T PRK05572 177 TLLDQIADQSE---ED----WFDKIALKEAIRELDERERLIVYLRYF----KDKTQSEVAKRLGISQVQVSRLEKKILKQ 245 (252)
T ss_pred hhhhhcCCCch---hh----HHHHHHHHHHHHcCCHHHHHHHHHHHh----CCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 22333333211 11 223456889999999999999999994 67999999999999999999999999999
Q ss_pred HHhHHh
Q 046578 365 LQQTNI 370 (379)
Q Consensus 365 LR~~l~ 370 (379)
||+.+.
T Consensus 246 Lr~~l~ 251 (252)
T PRK05572 246 MKEKLD 251 (252)
T ss_pred HHHHhc
Confidence 998864
No 29
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=100.00 E-value=4.2e-34 Score=270.65 Aligned_cols=236 Identities=27% Similarity=0.394 Sum_probs=208.1
Q ss_pred HHHHHHHHhc-ccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHH
Q 046578 128 YNLVKYKILC-KERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAI 206 (379)
Q Consensus 128 ~~eLi~~~~~-Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i 206 (379)
..+|+.+++. ||..|++.||..|.|+|+++|++|.++..+++|++||||+++|+++++||+..|.+|.||+++||+|.|
T Consensus 15 ~~~li~~~~~~gd~~a~~~l~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~tyl~~~i~n~~ 94 (257)
T PRK08583 15 VNKWIAEYQENQDEEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEI 94 (257)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHH
Confidence 4678898875 899999999999999999999999999999999999999999999999999888899999999999999
Q ss_pred HHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCccccCCccccCCCC
Q 046578 207 IRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIER--TRHPISLDGAVTDRGCM 284 (379)
Q Consensus 207 ~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~--~~~~iSLd~~~~~~~~~ 284 (379)
.+++|++.+.+++|++.....+++.++...+...+++.|+.+++++.+|++.+.+..+... .....|+|.+++++++.
T Consensus 95 ~~~lr~~~~~~~i~r~~~~~~~~~~~~~~~~~~~~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~~~~ 174 (257)
T PRK08583 95 KRYLRDKTWSVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSDG 174 (257)
T ss_pred HHHHHhcCCCcCCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCCCCC
Confidence 9999999999999999999999999999999999999999999999999999999887654 34677888877544322
Q ss_pred c---ccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578 285 T---MQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 285 ~---l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
. +.+.. .+|++.+...+....+..++..||+++|+||.++|+ +|+|++|||+.||||+++|++++++|
T Consensus 175 ~~~~~~~~~-----~~~e~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~eIA~~l~is~~tV~~~~~ra 245 (257)
T PRK08583 175 STVTLLDIV-----GQQEDGYELTEQRMILEKILPVLSDREKSIIQCTFI----ENLSQKETGERLGISQMHVSRLQRQA 245 (257)
T ss_pred ccchHhhhc-----CCcchhHHHHHHHHHHHHHHHhCCHHHHHHHHHHHh----CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 1 11222 245555666677778999999999999999999995 77999999999999999999999999
Q ss_pred HHHHHhHHhhc
Q 046578 362 LTKLQQTNILN 372 (379)
Q Consensus 362 l~kLR~~l~~~ 372 (379)
+++||+.+...
T Consensus 246 ~~kLr~~l~~~ 256 (257)
T PRK08583 246 IKKLREAAFLD 256 (257)
T ss_pred HHHHHHHhccC
Confidence 99999998653
No 30
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. 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.
Probab=100.00 E-value=3.1e-34 Score=266.19 Aligned_cols=217 Identities=33% Similarity=0.481 Sum_probs=194.2
Q ss_pred HHHHhHHHHHHHHHhccC---CCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcc
Q 046578 146 IIRSYRSLVVSIATGYQG---KGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGS 222 (379)
Q Consensus 146 Li~~y~~lV~~ia~r~~~---~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~ 222 (379)
|+..|.|+|+++|++|.+ ++.+++||+|||++|+|+++++||+++|.+|+||+++||+|.+.+++|+.. ++|++
T Consensus 1 L~~~~~~lv~~~a~~~~~~~~~~~~~eDl~Qe~~~~l~~a~~~fd~~~~~~f~t~~~~~i~~~~~~~lr~~~---~~p~~ 77 (224)
T TIGR02479 1 LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLD---WVPRS 77 (224)
T ss_pred CHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHHcC---ccCHH
Confidence 578999999999999985 689999999999999999999999999999999999999999999999764 68999
Q ss_pred hHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCccccCCccccC-CCCcccccCCCCCCCChH
Q 046578 223 MAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIER--TRHPISLDGAVTDR-GCMTMQDIIPGPDETMPE 299 (379)
Q Consensus 223 ~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~--~~~~iSLd~~~~~~-~~~~l~d~i~~~~~~~pe 299 (379)
....++++.++..++.+.+|++|+.+|+|+.+|++.+++..++.. ....+|+|....++ +...+.+.++++...+|+
T Consensus 78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (224)
T TIGR02479 78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLIDRIEDDKSEDPE 157 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcccCCCccchhhhhccccccCCHH
Confidence 999999999999999999999999999999999999999999864 45677888765432 233455556655666888
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578 300 RMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN 369 (379)
Q Consensus 300 ~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l 369 (379)
+.+...+....+..+|+.||+++|+||.++|+ +++|++|||+.||+|.++|++++++|+++||+.+
T Consensus 158 ~~~~~~~~~~~l~~~l~~L~~~~r~il~l~y~----~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 223 (224)
T TIGR02479 158 EELEREELREALAEAIESLSEREQLVLSLYYY----EELNLKEIGEVLGLTESRVSQIHSQALKKLRAKL 223 (224)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHh----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHc
Confidence 88888888899999999999999999999994 7799999999999999999999999999999875
No 31
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=100.00 E-value=6e-33 Score=259.60 Aligned_cols=223 Identities=28% Similarity=0.425 Sum_probs=194.3
Q ss_pred HHHHHHHHHHhHHHHHHHHHhcc---CCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCc
Q 046578 140 RESQERIIRSYRSLVVSIATGYQ---GKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRT 216 (379)
Q Consensus 140 ~~A~e~Li~~y~~lV~~ia~r~~---~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~ 216 (379)
.-+.++||..|.|+|+++|++|. +++.+++||+||||++||+++++|+++.|.+|+||+++|++|.+.+++|++.
T Consensus 7 ~~~~~~L~~~~~~~v~~~a~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~~~lR~~~-- 84 (236)
T PRK06986 7 KMDQDELVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLD-- 84 (236)
T ss_pred cccHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHcC--
Confidence 45789999999999999999997 6789999999999999999999999988889999999999999999999875
Q ss_pred ccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCccccCCccccCCCCcccccCCCCC
Q 046578 217 IRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIER--TRHPISLDGAVTDRGCMTMQDIIPGPD 294 (379)
Q Consensus 217 irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~--~~~~iSLd~~~~~~~~~~l~d~i~~~~ 294 (379)
++|.+......++.++...+.+.+|++|+.+|||+.+|++.+++..++.. ....+|++..++++++. +.. .....
T Consensus 85 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~-~~~-~~~~~ 161 (236)
T PRK06986 85 -WVPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGDS-ILV-TEDHQ 161 (236)
T ss_pred -CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccccCCCcc-ccc-ccCCC
Confidence 36777777778888899999999999999999999999999999988875 44667888876554432 222 22233
Q ss_pred CCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhh
Q 046578 295 ETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNIL 371 (379)
Q Consensus 295 ~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~ 371 (379)
..+|++.+...+....|..+|+.||+++|.||.++|+ +|+|++|||+.||+|.++|+++++||+++||+.+..
T Consensus 162 ~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~~ 234 (236)
T PRK06986 162 DEDPLQQLEDEELREALVEAIESLPEREQLVLSLYYQ----EELNLKEIGAVLGVSESRVSQIHSQAIKRLRARLGE 234 (236)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHhc----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 4567888888888889999999999999999999994 779999999999999999999999999999998754
No 32
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=100.00 E-value=3.4e-32 Score=253.69 Aligned_cols=209 Identities=23% Similarity=0.304 Sum_probs=179.4
Q ss_pred HHHHHHHhHHHHHHHHHhccC---CCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccC
Q 046578 143 QERIIRSYRSLVVSIATGYQG---KGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRL 219 (379)
Q Consensus 143 ~e~Li~~y~~lV~~ia~r~~~---~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~iri 219 (379)
..+++..|.|+|..++++|.. .+.+.+||+|||++|||+++++||+..+ +|+||+++||+|.|.+++|+.. +.
T Consensus 17 ~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~il~~lr~~~---~~ 92 (231)
T PRK12427 17 EGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELRELD---WR 92 (231)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHHHHhcC---CC
Confidence 357899999999999999874 4679999999999999999999997655 8999999999999999999854 47
Q ss_pred CcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCccccCCccccCCCCcccccCCCCCCCC
Q 046578 220 PGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIER--TRHPISLDGAVTDRGCMTMQDIIPGPDETM 297 (379)
Q Consensus 220 p~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~--~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~ 297 (379)
|+++....+++.++...+.+.+|++|+.+|||+.||++.+++.+++.. .....|||.++.+++... .+++ ..
T Consensus 93 ~r~vr~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~---~~~~---~~ 166 (231)
T PRK12427 93 PRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALEAHND---ILQS---RD 166 (231)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccCCCccc---ccCC---CC
Confidence 899999999999999999999999999999999999999999988753 467899999876654321 2211 22
Q ss_pred hHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 298 PERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 298 pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
+++.. .....+..++..||+++|.||.++|+ +++|++|||+.||+|+++|+++..+++++||..
T Consensus 167 ~~~~~---~~~~~l~~~l~~L~~~er~vi~l~~~----~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr~~ 230 (231)
T PRK12427 167 LEENI---IIEDNLKQALSQLDEREQLILHLYYQ----HEMSLKEIALVLDLTEARICQLNKKIAQKIKSF 230 (231)
T ss_pred HHHHH---HHHHHHHHHHHcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence 33322 23456889999999999999999995 779999999999999999999999999999964
No 33
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=99.96 E-value=2.4e-27 Score=221.39 Aligned_cols=192 Identities=24% Similarity=0.385 Sum_probs=155.9
Q ss_pred HHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHH
Q 046578 128 YNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAII 207 (379)
Q Consensus 128 ~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~ 207 (379)
...++..+..||..|++.++..|.|+|+++|.++.+++.++||++||+|+++|+++.+|+++++.+|.+|++++++|.++
T Consensus 36 e~~l~~~~~~gd~~a~~~l~~~y~~~l~~~a~~~~~~~~daeDlvQE~fi~l~~~~~~f~~~~~~~f~~wl~~i~rn~~i 115 (233)
T PRK05803 36 ERKYLELMKEGDEEARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEIL 115 (233)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHH
Confidence 35789999999999999999999999999999999999999999999999999999999998888999999999999999
Q ss_pred HHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccc-cC--CCC
Q 046578 208 RAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVT-DR--GCM 284 (379)
Q Consensus 208 ~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~-~~--~~~ 284 (379)
+++|+..+.. ...+++.... ++ ...
T Consensus 116 d~~Rk~~~~~----------------------------------------------------~~~~~~~~~~~~~~~~~~ 143 (233)
T PRK05803 116 MHLRNLKKTK----------------------------------------------------KEVSLQDPIGVDKEGNEI 143 (233)
T ss_pred HHHHHHhccc----------------------------------------------------cCCCccccccCCCCcCcc
Confidence 9999765310 1112221111 10 111
Q ss_pred cccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046578 285 TMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTK 364 (379)
Q Consensus 285 ~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~k 364 (379)
.+.+..++. ...+++.+...+....+..++..||+++|+||.++|++.+.+|+|++|||+.||+|.++|+++++||+++
T Consensus 144 ~~~~~~~~~-~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~k 222 (233)
T PRK05803 144 SLIDILGSE-EDDVIEQVELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKK 222 (233)
T ss_pred cHHHHccCC-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 222222222 2346676777777778999999999999999999996554588999999999999999999999999999
Q ss_pred HHhHHhhc
Q 046578 365 LQQTNILN 372 (379)
Q Consensus 365 LR~~l~~~ 372 (379)
||+.+...
T Consensus 223 Lr~~l~~~ 230 (233)
T PRK05803 223 LFKELYRA 230 (233)
T ss_pred HHHHHHHh
Confidence 99998653
No 34
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=99.96 E-value=3.2e-27 Score=220.51 Aligned_cols=192 Identities=26% Similarity=0.452 Sum_probs=150.2
Q ss_pred cHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHH
Q 046578 127 DYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAI 206 (379)
Q Consensus 127 ~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i 206 (379)
...+++.++++||..|++.++..|.++|+.+|+++.+++.++||++||+|+++|+++++|++..+.+|.||++++++|.+
T Consensus 38 ~~~~L~~~~~~gd~~af~~l~~~y~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~ 117 (234)
T PRK08301 38 EEEYLLNKLPKGDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEI 117 (234)
T ss_pred HHHHHHHHHHccCHHHHHHHHHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHH
Confidence 45789999999999999999999999999999999999999999999999999999999998777789999999999999
Q ss_pred HHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccC--C-C
Q 046578 207 IRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDR--G-C 283 (379)
Q Consensus 207 ~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~--~-~ 283 (379)
++++|++.+.. ...+++.+..++ + .
T Consensus 118 ~d~lRk~~~~~----------------------------------------------------~~~~~~~~~~~~~~~~~ 145 (234)
T PRK08301 118 LMYLRRNNKVK----------------------------------------------------AEVSFDEPLNIDWDGNE 145 (234)
T ss_pred HHHHHHHhccc----------------------------------------------------cccccccccccccCCCc
Confidence 99999865310 111222211100 0 0
Q ss_pred CcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578 284 MTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT 363 (379)
Q Consensus 284 ~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~ 363 (379)
....+.... ....+...+........+..++++||+++|.||.++|++...+|+|++|||+.||+|.+||+++++||++
T Consensus 146 ~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~ 224 (234)
T PRK08301 146 LLLSDVLGT-DNDIIYKDIEDEVDRKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIK 224 (234)
T ss_pred ccHHHhccC-cccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 011111111 1123334444445556799999999999999999998543347799999999999999999999999999
Q ss_pred HHHhHHhh
Q 046578 364 KLQQTNIL 371 (379)
Q Consensus 364 kLR~~l~~ 371 (379)
+||+.+..
T Consensus 225 ~Lr~~l~~ 232 (234)
T PRK08301 225 RLKKEINK 232 (234)
T ss_pred HHHHHHHh
Confidence 99998753
No 35
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. 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 homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also 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.
Probab=99.95 E-value=5.4e-27 Score=218.18 Aligned_cols=191 Identities=24% Similarity=0.392 Sum_probs=151.6
Q ss_pred CcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHH
Q 046578 126 LDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA 205 (379)
Q Consensus 126 ~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~ 205 (379)
.+..+++.++++||..|++.+|+.|.|.|+++|.++.++..++||++||+|+++|+++++|+++.+.+|.||++++++|.
T Consensus 33 ~~~~~li~~~~~gd~~af~~l~~~y~~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~ 112 (227)
T TIGR02846 33 EEEKKYLDRLKEGDEEARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENE 112 (227)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHH
Confidence 34578999999999999999999999999999999999999999999999999999999999887778999999999999
Q ss_pred HHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCcccc--C-C
Q 046578 206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTD--R-G 282 (379)
Q Consensus 206 i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~--~-~ 282 (379)
+.+++|+..+.. ...+++..... + .
T Consensus 113 ~~d~~Rk~~r~~----------------------------------------------------~~~~~~~~~~~~~~~~ 140 (227)
T TIGR02846 113 ILMHLRALKKTK----------------------------------------------------GEVSLQDPIGVDKEGN 140 (227)
T ss_pred HHHHHHHHhccc----------------------------------------------------cceeccccccCCcccC
Confidence 999999865310 01111111100 0 0
Q ss_pred CCcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 283 CMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 283 ~~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
...+.+...+ ....+++.....+....|..+++.||+++|+||.++|+++..+++|++|||+.||+|+++|+++++||+
T Consensus 141 ~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl 219 (227)
T TIGR02846 141 EISLIDILGS-DGDSVIEQVELNLEIKKLYKKLSVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRAL 219 (227)
T ss_pred cccHHHHhcC-CCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 0011121111 223456666666666789999999999999999999853323679999999999999999999999999
Q ss_pred HHHHhHH
Q 046578 363 TKLQQTN 369 (379)
Q Consensus 363 ~kLR~~l 369 (379)
++||+.+
T Consensus 220 ~~Lr~~~ 226 (227)
T TIGR02846 220 MKLYKEL 226 (227)
T ss_pred HHHHHHh
Confidence 9999875
No 36
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=99.95 E-value=1.7e-26 Score=211.09 Aligned_cols=197 Identities=24% Similarity=0.323 Sum_probs=153.2
Q ss_pred CcCcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHH
Q 046578 124 GELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIK 203 (379)
Q Consensus 124 ~~~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir 203 (379)
..+....++.++++||..|++.||+.|.|.|+++|.++.++..++||++||+|+++|+++.+|++.++.+|.||++.+++
T Consensus 7 ~~~~~~~l~~~~~~~d~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~~ 86 (208)
T PRK08295 7 DELEDEELVELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCIT 86 (208)
T ss_pred cCCChHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHH
Confidence 34566789999999999999999999999999999999999999999999999999999999998876799999999999
Q ss_pred HHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCcccc-CC
Q 046578 204 QAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTD-RG 282 (379)
Q Consensus 204 ~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~-~~ 282 (379)
|.+.+++++..+..+.+. ....+.+....+ +.
T Consensus 87 n~~~d~~r~~~r~~~~~~-----------------------------------------------~~~~s~~~~~~~~~~ 119 (208)
T PRK08295 87 RQIITAIKTANRQKHIPL-----------------------------------------------NSYVSLDKPIYDEES 119 (208)
T ss_pred HHHHHHHHHhhhhccccc-----------------------------------------------cceeecCCcccCCcc
Confidence 999999997553111110 011223322211 11
Q ss_pred CCcccccCCCCCCCChHHHHHHHHHHHHH-HHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578 283 CMTMQDIIPGPDETMPERMVQKQLMKQEL-KELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 283 ~~~l~d~i~~~~~~~pe~~~~~~e~~~~L-~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
...+.+.+.++...+|++.+...+....+ ..++..||+.+|.||.+ |+ +|+|++|||+.||+|.++|++.++||
T Consensus 120 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~~r~vl~l-~~----e~~s~~EIA~~lgis~~tV~~~l~ra 194 (208)
T PRK08295 120 DRTLLDVISEAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLEL-YL----DGKSYQEIAEELNRHVKSIDNALQRV 194 (208)
T ss_pred chhHHHHhcCcccCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHH-HH----ccCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 11223333333334667666555555555 45678999999999999 74 77999999999999999999999999
Q ss_pred HHHHHhHHhhc
Q 046578 362 LTKLQQTNILN 372 (379)
Q Consensus 362 l~kLR~~l~~~ 372 (379)
+++||+++...
T Consensus 195 r~~Lr~~l~~~ 205 (208)
T PRK08295 195 KRKLEKYLENR 205 (208)
T ss_pred HHHHHHHHHhh
Confidence 99999998654
No 37
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=99.95 E-value=2.6e-26 Score=214.58 Aligned_cols=192 Identities=26% Similarity=0.462 Sum_probs=150.5
Q ss_pred cHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHH
Q 046578 127 DYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAI 206 (379)
Q Consensus 127 ~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i 206 (379)
...+++.++..||..|++.++..|.+.|+++|+++.+++.++||++||+|+++|+++++|++..+.+|.||++++++|.+
T Consensus 38 ~~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~ 117 (234)
T TIGR02835 38 EEEALLQKLTQGDESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEI 117 (234)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHH
Confidence 34778999999999999999999999999999999999999999999999999999999998777789999999999999
Q ss_pred HHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccC--CC-
Q 046578 207 IRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDR--GC- 283 (379)
Q Consensus 207 ~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~--~~- 283 (379)
.+++|++.+.. ...+++.....+ +.
T Consensus 118 ~d~~Rk~~r~~----------------------------------------------------~~~~~~~~~~~~~~~~~ 145 (234)
T TIGR02835 118 LMYLRRNNKTR----------------------------------------------------SEVSFDEPLNVDWDGNE 145 (234)
T ss_pred HHHHHHhcccc----------------------------------------------------CcccccccccCCCCCCc
Confidence 99999865310 011112111100 00
Q ss_pred CcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578 284 MTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT 363 (379)
Q Consensus 284 ~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~ 363 (379)
....+. .++....+++.+........+..+|+.||+++|.|+.++|++.+.+|+|++|||+.||+|.+||+++++||++
T Consensus 146 ~~~~~~-~~~~~~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~ 224 (234)
T TIGR02835 146 LLLSDV-LGTDSDIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILK 224 (234)
T ss_pred chHHHh-cCCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 001111 1112222334445555567799999999999999999998544337799999999999999999999999999
Q ss_pred HHHhHHhh
Q 046578 364 KLQQTNIL 371 (379)
Q Consensus 364 kLR~~l~~ 371 (379)
+||+.+..
T Consensus 225 ~LR~~l~~ 232 (234)
T TIGR02835 225 RLKKEINR 232 (234)
T ss_pred HHHHHhhc
Confidence 99998764
No 38
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=99.95 E-value=4.9e-26 Score=204.93 Aligned_cols=178 Identities=12% Similarity=0.176 Sum_probs=149.9
Q ss_pred cCcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHH
Q 046578 125 ELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQ 204 (379)
Q Consensus 125 ~~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~ 204 (379)
..+..+++.+++.||..|++.||..|.++|+.+|++++++..+++|++||+|+++|+++.+|+++ +.+|.+|++.+++|
T Consensus 4 ~~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n 82 (186)
T PRK05602 4 ADPDEELLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLN 82 (186)
T ss_pred cccHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHH
Confidence 35668899999999999999999999999999999999999999999999999999999999975 34899999999999
Q ss_pred HHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCC
Q 046578 205 AIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCM 284 (379)
Q Consensus 205 ~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~ 284 (379)
.+.+++|++... ..+.
T Consensus 83 ~~~d~~R~~~~~--------------------------------------------------------~~~~-------- 98 (186)
T PRK05602 83 LCYDRLRRRREV--------------------------------------------------------PVED-------- 98 (186)
T ss_pred HHHHHHHhcCCC--------------------------------------------------------Cccc--------
Confidence 999999975420 0000
Q ss_pred cccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046578 285 TMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTK 364 (379)
Q Consensus 285 ~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~k 364 (379)
..+ ..+ ....++..+...+....+..+|..||+++|+||.++|+ +|+|++|||+.||+|.++|+++++||+++
T Consensus 99 -~~~-~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~ 171 (186)
T PRK05602 99 -APD-VPD-PAPGPDAGLEARQRARRVEQALAALPERQREAIVLQYY----QGLSNIEAAAVMDISVDALESLLARGRRA 171 (186)
T ss_pred -ccc-cCC-CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHh----cCCCHHHHHHHhCcCHHHHHHHHHHHHHH
Confidence 000 001 12235555666666778999999999999999999985 77999999999999999999999999999
Q ss_pred HHhHHhhchh
Q 046578 365 LQQTNILNNL 374 (379)
Q Consensus 365 LR~~l~~~~L 374 (379)
||+.+...+.
T Consensus 172 Lr~~l~~~~~ 181 (186)
T PRK05602 172 LRAQLADLPG 181 (186)
T ss_pred HHHHHHhccc
Confidence 9999987654
No 39
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=99.95 E-value=4.2e-26 Score=207.01 Aligned_cols=186 Identities=12% Similarity=0.197 Sum_probs=150.2
Q ss_pred chhhhcCcCcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhH
Q 046578 118 FLDKENGELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTY 197 (379)
Q Consensus 118 ~~~~~~~~~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTY 197 (379)
+...+.+.-+..+|+..+.+||..+++.||+.|.+.|+++|.+++++..++||++||+|+++|+++++|++.+| .|.+|
T Consensus 7 ~~~~~~~~~~~~~li~~~~~g~~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi~l~~~~~~~~~~~~-~~~~w 85 (194)
T PRK09646 7 MTGPPAESPDLDALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SALAW 85 (194)
T ss_pred ccCCCCCcccHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCcccc-cHHHH
Confidence 33344556778999999999999999999999999999999999999999999999999999999999997655 79999
Q ss_pred HHHHHHHHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCc
Q 046578 198 VYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGA 277 (379)
Q Consensus 198 a~~~Ir~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~ 277 (379)
++.+++|.+++++|++.+..+. ....
T Consensus 86 l~~ia~n~~~d~~r~~~~~~~~---------------------------------------------------~~~~--- 111 (194)
T PRK09646 86 LLTLAHRRAVDRVRSEQAASQR---------------------------------------------------EVRY--- 111 (194)
T ss_pred HHHHHHHHHHHHHHhhcccccc---------------------------------------------------cccc---
Confidence 9999999999999986531000 0000
Q ss_pred cccCCCCcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHH
Q 046578 278 VTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQI 357 (379)
Q Consensus 278 ~~~~~~~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~ 357 (379)
.. .+. ......+.+.+...+....+..+|..||+++|.||.++|+ +|+|++|||+.||+|.++|+++
T Consensus 112 -~~------~~~--~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~EIA~~Lgis~~tVk~~ 178 (194)
T PRK09646 112 -GA------RNV--DPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAYY----GGLTYREVAERLAVPLGTVKTR 178 (194)
T ss_pred -cc------ccc--cccccchHHHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCChHhHHHH
Confidence 00 000 0011123444444555678999999999999999999984 6799999999999999999999
Q ss_pred HHHHHHHHHhHHhh
Q 046578 358 RGIALTKLQQTNIL 371 (379)
Q Consensus 358 ~~rAl~kLR~~l~~ 371 (379)
++||+++||+.+..
T Consensus 179 l~ra~~~Lr~~l~~ 192 (194)
T PRK09646 179 MRDGLIRLRDCLGV 192 (194)
T ss_pred HHHHHHHHHHHhcc
Confidence 99999999999854
No 40
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=99.94 E-value=1.7e-25 Score=200.88 Aligned_cols=182 Identities=18% Similarity=0.250 Sum_probs=146.5
Q ss_pred HHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHH
Q 046578 128 YNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAII 207 (379)
Q Consensus 128 ~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~ 207 (379)
.++++..+.+||..++++||..|.|.|+.+|.++.++..+++|++||+|+++|+++.+|++.. +|.+|++++++|.+.
T Consensus 5 ~~~li~~~~~gd~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~ 82 (187)
T TIGR02948 5 IKKRIKEVRKGDENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQR--KFSTWLYRIATNLTI 82 (187)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHHH
Confidence 356899999999999999999999999999999999999999999999999999999999764 699999999999999
Q ss_pred HHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCccc
Q 046578 208 RAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQ 287 (379)
Q Consensus 208 ~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~ 287 (379)
+++|+..+.. .++......+...+.
T Consensus 83 ~~~rk~~~~~-------------------------------------------------------~~~~~~~~~~~~~~~ 107 (187)
T TIGR02948 83 DRLRKRKPDF-------------------------------------------------------YLDDEVQGTDGLTME 107 (187)
T ss_pred HHHHhhcccc-------------------------------------------------------cccccccCccccccc
Confidence 9999754210 000000000000111
Q ss_pred ccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578 288 DIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 288 d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~ 367 (379)
+...+ ..+.|++.+...+....+..++.+|||++|.||.++|+ +|+|++|||+.||+|.++|++.++||+++||+
T Consensus 108 ~~~~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 108 SQLAA-DEAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKYM----EDLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred ccccc-CcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 11111 12356666666666778999999999999999999884 67999999999999999999999999999999
Q ss_pred HHhh
Q 046578 368 TNIL 371 (379)
Q Consensus 368 ~l~~ 371 (379)
.+..
T Consensus 183 ~l~~ 186 (187)
T TIGR02948 183 QLRH 186 (187)
T ss_pred Hhhc
Confidence 8754
No 41
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=99.94 E-value=1.2e-25 Score=203.62 Aligned_cols=182 Identities=15% Similarity=0.220 Sum_probs=151.0
Q ss_pred CcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHH
Q 046578 126 LDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA 205 (379)
Q Consensus 126 ~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~ 205 (379)
.+..+++.+++.||..|++.|+..|.+.|+++|.++.++..++||++||+|+++|+++.+|++. .+|.+|++++++|.
T Consensus 11 ~~~~~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~~~~~~~~--~~f~~wl~~i~~n~ 88 (194)
T PRK12513 11 ASDEALMLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPR--ARFRTWLYQIARNL 88 (194)
T ss_pred CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CchHHHHHHHHHHH
Confidence 4568899999999999999999999999999999999999999999999999999999999864 37999999999999
Q ss_pred HHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCc
Q 046578 206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMT 285 (379)
Q Consensus 206 i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~ 285 (379)
+++++|+..+....+ .+. +. .
T Consensus 89 ~~~~~R~~~~~~~~~-----------------------------------------------------~~~----~~--~ 109 (194)
T PRK12513 89 LIDHWRRHGARQAPS-----------------------------------------------------LDA----DE--Q 109 (194)
T ss_pred HHHHHHHhccccccc-----------------------------------------------------ccc----ch--h
Confidence 999999876421110 000 00 0
Q ss_pred ccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578 286 MQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL 365 (379)
Q Consensus 286 l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL 365 (379)
. ... ......|+..+...+....+..+|+.||+++|.||.++|+ +|+|++|||+.||+|+++|+++++||+++|
T Consensus 110 ~-~~~-~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~L 183 (194)
T PRK12513 110 L-HAL-ADDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREH----GDLELEEIAELTGVPEETVKSRLRYALQKL 183 (194)
T ss_pred h-hhc-CCCCCCHHHHHHHHHHHHHHHHHHHhCCHhHhhheeeehc----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 0 000 1122356666677777788999999999999999999984 779999999999999999999999999999
Q ss_pred HhHHhhchh
Q 046578 366 QQTNILNNL 374 (379)
Q Consensus 366 R~~l~~~~L 374 (379)
|+.+...++
T Consensus 184 r~~l~~~~~ 192 (194)
T PRK12513 184 RELLAEEVA 192 (194)
T ss_pred HHHHHHhhc
Confidence 999887654
No 42
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=99.94 E-value=2.8e-25 Score=200.53 Aligned_cols=177 Identities=21% Similarity=0.320 Sum_probs=146.3
Q ss_pred cCcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCC----CCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHH
Q 046578 125 ELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGK----GLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYW 200 (379)
Q Consensus 125 ~~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~----~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~ 200 (379)
..+..+++..+.+||..|++.||..|.+.|+++|.++.++ ..++||++||+|+++|+++.+|++. +.+|.+|++.
T Consensus 8 ~~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~~~~wl~~ 86 (189)
T PRK09648 8 GEELDALVAEAVAGDRRALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITALPRYRDQ-GRPFLAFVYG 86 (189)
T ss_pred chHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHHHHHHhcc-CCcHHHHHHH
Confidence 3456889999999999999999999999999999998765 3689999999999999999999864 4589999999
Q ss_pred HHHHHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCcccc
Q 046578 201 WIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTD 280 (379)
Q Consensus 201 ~Ir~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~ 280 (379)
+++|.+.+++|++.+....+ .+.
T Consensus 87 i~~n~~~d~~r~~~r~~~~~-----------------------------------------------------~~~---- 109 (189)
T PRK09648 87 IAAHKVADAHRAAGRDKAVP-----------------------------------------------------TEE---- 109 (189)
T ss_pred HHHHHHHHHHHHhCCCcccc-----------------------------------------------------ccc----
Confidence 99999999999866311000 000
Q ss_pred CCCCcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 281 RGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 281 ~~~~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
..+... ...+|++.+...+....+..+|..||+++|+||.++|+ +|+|++|||+.||+|.++|+++++|
T Consensus 110 -----~~~~~~--~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~R 178 (189)
T PRK09648 110 -----VPERPS--DDAGPEERALRSESSNRMRELLDTLPEKQREILILRVV----VGLSAEETAEAVGSTPGAVRVAQHR 178 (189)
T ss_pred -----cccccc--cCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 000011 12356776667777788999999999999999999995 6799999999999999999999999
Q ss_pred HHHHHHhHHh
Q 046578 361 ALTKLQQTNI 370 (379)
Q Consensus 361 Al~kLR~~l~ 370 (379)
|+++||+.+.
T Consensus 179 a~~~Lr~~l~ 188 (189)
T PRK09648 179 ALARLRAEIE 188 (189)
T ss_pred HHHHHHHHhc
Confidence 9999999864
No 43
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=99.94 E-value=2.2e-25 Score=200.19 Aligned_cols=184 Identities=18% Similarity=0.261 Sum_probs=148.8
Q ss_pred CcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHH
Q 046578 126 LDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA 205 (379)
Q Consensus 126 ~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~ 205 (379)
++...++.++.+||..+++.+|..|.|.|+++|+++.++..+++|++||+|+++|+++++|++.. +|.+|++++++|.
T Consensus 3 ~~~~~li~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn~ 80 (187)
T PRK09641 3 LLIKRLIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATNL 80 (187)
T ss_pred hHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHHH
Confidence 34578999999999999999999999999999999999999999999999999999999998753 7999999999999
Q ss_pred HHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCc
Q 046578 206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMT 285 (379)
Q Consensus 206 i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~ 285 (379)
+.+++|+..+.. +++....+++...
T Consensus 81 ~~d~~R~~~~~~-------------------------------------------------------~~~~~~~~~~~~~ 105 (187)
T PRK09641 81 TIDRLRKRKPDY-------------------------------------------------------YLDAEVAGTEGLT 105 (187)
T ss_pred HHHHHHhcCccc-------------------------------------------------------cccccccCCcchh
Confidence 999999865210 0111111111111
Q ss_pred ccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578 286 MQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL 365 (379)
Q Consensus 286 l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL 365 (379)
..+.+.+ ...+|++.+...+....+..++..||+++++||.++|+ +|+|++|||+.||+|.++|++.++||+++|
T Consensus 106 ~~~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~~----~~~s~~eIA~~lgis~~~v~~~l~Rar~~L 180 (187)
T PRK09641 106 MYSQLAA-DDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYI----EDLSLKEISEILDLPVGTVKTRIHRGREAL 180 (187)
T ss_pred hhccccc-CcCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHh----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 1111111 22356666667777778999999999999999999984 679999999999999999999999999999
Q ss_pred HhHHhh
Q 046578 366 QQTNIL 371 (379)
Q Consensus 366 R~~l~~ 371 (379)
|+.+..
T Consensus 181 r~~l~~ 186 (187)
T PRK09641 181 RKQLRH 186 (187)
T ss_pred HHHHhc
Confidence 998753
No 44
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=99.94 E-value=2e-25 Score=202.38 Aligned_cols=192 Identities=24% Similarity=0.321 Sum_probs=147.6
Q ss_pred CcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHH
Q 046578 126 LDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA 205 (379)
Q Consensus 126 ~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~ 205 (379)
++..+++..+++||..|++.||+.|.|.|+++|+++.++..+++|++||+|+++|+++.+|++..+.+|.||++.++++.
T Consensus 4 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~a~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~~~f~~wl~~~~~~~ 83 (198)
T TIGR02859 4 LEDEEIVELARQGNTHALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELCVTRQ 83 (198)
T ss_pred cchHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHccccCcHHHHHHHHHHHHHHHHHHhCcccCCChHHHHHHHHHHH
Confidence 45678999999999999999999999999999999999999999999999999999999999877679999999999999
Q ss_pred HHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCcccc-CCCC
Q 046578 206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTD-RGCM 284 (379)
Q Consensus 206 i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~-~~~~ 284 (379)
+.+++|+..+..+.+ .....|++.+..+ +++.
T Consensus 84 ~~~~~r~~~~~~~~~-----------------------------------------------~~~~~~~~~~~~~~~~~~ 116 (198)
T TIGR02859 84 IITAIKTATRQKHIP-----------------------------------------------LNSYVSLNKPIYDEESDR 116 (198)
T ss_pred HHHHHHHHHHhcccc-----------------------------------------------hhhhcCcccccccccccc
Confidence 999988653211100 0011222322111 1111
Q ss_pred cccccCCCCCCCChHHHHHHHHHHHHHHHHHhcC-CHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578 285 TMQDIIPGPDETMPERMVQKQLMKQELKELLQTL-SEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT 363 (379)
Q Consensus 285 ~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L-~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~ 363 (379)
.+.+.+.+....+|++.+...+....+.++|..| ++.++.|+. .|+ +|+|++|||+.||+|.++|++.++||++
T Consensus 117 ~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~~-~~~----~~~s~~eIA~~l~~s~~tV~~~l~r~r~ 191 (198)
T TIGR02859 117 TLLDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVLQ-SYL----DGKSYQEIACDLNRHVKSIDNALQRVKR 191 (198)
T ss_pred hHHHHhhccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHH-HHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 2222222222346777777777778899999985 566666665 463 6799999999999999999999999999
Q ss_pred HHHhHH
Q 046578 364 KLQQTN 369 (379)
Q Consensus 364 kLR~~l 369 (379)
+||+.+
T Consensus 192 ~L~~~l 197 (198)
T TIGR02859 192 KLEKYL 197 (198)
T ss_pred HHHHhc
Confidence 999875
No 45
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and 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.
Probab=99.94 E-value=1.7e-25 Score=197.81 Aligned_cols=170 Identities=19% Similarity=0.310 Sum_probs=141.9
Q ss_pred HHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHH
Q 046578 131 VKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAI 210 (379)
Q Consensus 131 Li~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~l 210 (379)
|+.++++||..|++.||..|.+.+++++.++.++..++||++||+|+.+|+++++|+...+ +|.+|++.+++|.+++++
T Consensus 1 li~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~~ 79 (170)
T TIGR02952 1 LLERAQDREEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVNDYF 79 (170)
T ss_pred ChHHHHccCHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHHHH
Confidence 4778999999999999999999999999999988899999999999999999999986544 899999999999999999
Q ss_pred HhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccC
Q 046578 211 ANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDII 290 (379)
Q Consensus 211 r~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i 290 (379)
|++.+... .+.+. ..+..
T Consensus 80 R~~~~~~~-----------------------------------------------------~~~~~---------~~~~~ 97 (170)
T TIGR02952 80 RGSKRHPL-----------------------------------------------------FSLDV---------FKELL 97 (170)
T ss_pred HhcCCCCC-----------------------------------------------------CcHHH---------HhhcC
Confidence 98653110 00000 00000
Q ss_pred CCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578 291 PGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN 369 (379)
Q Consensus 291 ~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l 369 (379)
. ...+|++.+...+....+..++..|||++|+||.++|+ +|+|++|||+.||+|.++|++.++||+++||+.+
T Consensus 98 ~--~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~~l 170 (170)
T TIGR02952 98 S--NEPNPEEAILKEEANEKLLKALKILTPKQQHVIALRFG----QNLPIAEVARILGKTEGAVKILQFRAIKKLARQM 170 (170)
T ss_pred C--CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence 1 12246666666677788999999999999999999984 7799999999999999999999999999999864
No 46
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=99.94 E-value=1.9e-25 Score=200.59 Aligned_cols=175 Identities=13% Similarity=0.183 Sum_probs=144.3
Q ss_pred cCcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHH
Q 046578 125 ELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQ 204 (379)
Q Consensus 125 ~~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~ 204 (379)
.+++.+|+..+..||..+++.||..|.+.++.++.++.++..+++|++||+|+.+|+.+++|++.. ..|.+|++++++|
T Consensus 7 ~~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~-~~~~~wL~~iarn 85 (182)
T PRK12537 7 PFDYEACLLACARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPAR-GSARGWIYSVTRH 85 (182)
T ss_pred hhhHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCccc-ccHHHHHHHHHHH
Confidence 477889999999999999999999999999999999999999999999999999999999998643 3799999999999
Q ss_pred HHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCC
Q 046578 205 AIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCM 284 (379)
Q Consensus 205 ~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~ 284 (379)
.+++++|+..+... .+. .
T Consensus 86 ~~~d~~r~~~~~~~-------------------------------------------------------~~~----~--- 103 (182)
T PRK12537 86 LALNVLRDTRREVV-------------------------------------------------------LDD----D--- 103 (182)
T ss_pred HHHHHHHhccccCc-------------------------------------------------------ccc----c---
Confidence 99999998653100 000 0
Q ss_pred cccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046578 285 TMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTK 364 (379)
Q Consensus 285 ~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~k 364 (379)
..+... ....+++.....+....+..+|+.||+++|+||.++|+ +|+|++|||+.||+|.++|+++++||+++
T Consensus 104 -~~~~~~--~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~~~s~~eIA~~lgis~~tV~~~l~ra~~~ 176 (182)
T PRK12537 104 -AEETAQ--TLHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAYV----DGCSHAEIAQRLGAPLGTVKAWIKRSLKA 176 (182)
T ss_pred -hhhhcc--cccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCChhhHHHHHHHHHHH
Confidence 000000 01123334444455667999999999999999999985 77999999999999999999999999999
Q ss_pred HHhHH
Q 046578 365 LQQTN 369 (379)
Q Consensus 365 LR~~l 369 (379)
||+++
T Consensus 177 Lr~~l 181 (182)
T PRK12537 177 LRECM 181 (182)
T ss_pred HHHHh
Confidence 99986
No 47
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=99.94 E-value=5e-25 Score=200.22 Aligned_cols=178 Identities=16% Similarity=0.174 Sum_probs=148.5
Q ss_pred CcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHH
Q 046578 126 LDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA 205 (379)
Q Consensus 126 ~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~ 205 (379)
++...|+.++..||..|++.||..|.|.|+.+|.++.++..+++|++||+|+++|+.+.+|++.. .+|.+|++.+++|.
T Consensus 11 ~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~-~~~~~wl~~ia~n~ 89 (196)
T PRK12524 11 VSDEALLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGE-ARVSTWLYRVVCNL 89 (196)
T ss_pred cCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhcccccc-chHHHHHHHHHHHH
Confidence 45689999999999999999999999999999999999999999999999999999999997533 47999999999999
Q ss_pred HHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCc
Q 046578 206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMT 285 (379)
Q Consensus 206 i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~ 285 (379)
+++++|++.+. ...++.. .
T Consensus 90 ~~d~~Rk~~~~------------------------------------------------------~~~~~~~-----~-- 108 (196)
T PRK12524 90 CTDRLRRRRRA------------------------------------------------------SVDLDDA-----P-- 108 (196)
T ss_pred HHHHHHhhcCC------------------------------------------------------CCCcccc-----c--
Confidence 99999976520 0001100 0
Q ss_pred ccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578 286 MQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL 365 (379)
Q Consensus 286 l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL 365 (379)
+. .+ ....+++.+...+....+..+++.||+++|.||.|+|+ +|++++|||+.||+|.+||+++++||+++|
T Consensus 109 --~~-~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~L~~~----~g~s~~eIA~~lgis~~tV~~~l~Ra~~~L 180 (196)
T PRK12524 109 --EP-AD-AAPGAEEALIEGDRMRALDAALAALPERQRQAVVLRHI----EGLSNPEIAEVMEIGVEAVESLTARGKRAL 180 (196)
T ss_pred --cc-cc-cCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 00 01 11245566666677788999999999999999999985 779999999999999999999999999999
Q ss_pred HhHHhhch
Q 046578 366 QQTNILNN 373 (379)
Q Consensus 366 R~~l~~~~ 373 (379)
|+++...+
T Consensus 181 r~~l~~~~ 188 (196)
T PRK12524 181 AALLAGQR 188 (196)
T ss_pred HHHHHhcc
Confidence 99987644
No 48
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=99.93 E-value=9e-25 Score=196.74 Aligned_cols=183 Identities=15% Similarity=0.192 Sum_probs=146.6
Q ss_pred CcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHH
Q 046578 126 LDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA 205 (379)
Q Consensus 126 ~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~ 205 (379)
.+...++..+.+||+.+++.||..|.+.|+.+|+++.++..+++|++||+|+++|+++++|++. .+|.+|++.+++|.
T Consensus 5 ~~d~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~--~~~~~wl~~iarn~ 82 (190)
T TIGR02939 5 ELDLELVERVQRGEKQAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGD--SAFYTWLYRIAVNT 82 (190)
T ss_pred ccHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCC--CccHhHHHHHHHHH
Confidence 3457899999999999999999999999999999999999999999999999999999999864 37999999999999
Q ss_pred HHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCc
Q 046578 206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMT 285 (379)
Q Consensus 206 i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~ 285 (379)
+.+++++..+..... ..+.+.. +...
T Consensus 83 ~~~~~r~~~r~~~~~--------------------------------------------------~~~~~~~----~~~~ 108 (190)
T TIGR02939 83 AKNHLVAQGRRPPTS--------------------------------------------------DVEIEDA----EHFE 108 (190)
T ss_pred HHHHHHHhccCCCcc--------------------------------------------------cccccch----hhhc
Confidence 999998755311000 0000000 0000
Q ss_pred ccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578 286 MQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL 365 (379)
Q Consensus 286 l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL 365 (379)
..+.+ ....+|++.+...+....+..++..||+++|.||.++|+ +|+|++|||+.||+|.++|++.++||+++|
T Consensus 109 ~~~~~--~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~EIA~~lgis~~tv~~~l~rar~~L 182 (190)
T TIGR02939 109 GADRL--REIDTPERLLLSRELEQTVMRAVEALPEDLRTAITLREL----EGLSYEDIARIMDCPVGTVRSRIFRAREAI 182 (190)
T ss_pred ccccc--cccCChHHHHHHHHHHHHHHHHHHcCCHHHhhhhhhhhh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 00000 012346666666777788999999999999999999984 779999999999999999999999999999
Q ss_pred HhHHh
Q 046578 366 QQTNI 370 (379)
Q Consensus 366 R~~l~ 370 (379)
|+++.
T Consensus 183 r~~l~ 187 (190)
T TIGR02939 183 AIRLR 187 (190)
T ss_pred HHHhh
Confidence 99975
No 49
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=99.93 E-value=6.7e-25 Score=196.21 Aligned_cols=175 Identities=15% Similarity=0.167 Sum_probs=143.9
Q ss_pred CcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHH
Q 046578 126 LDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA 205 (379)
Q Consensus 126 ~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~ 205 (379)
.+..+|+..+..||..+++.|+..|.+.++.+|.++.++..++||++||+|+++|+++++|++.. ..|.||++.+++|.
T Consensus 4 ~~~~~li~~~~~g~~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~~-~~~~~wl~~ia~n~ 82 (179)
T PRK12514 4 DDIEKLIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSG-LSPMTWLITIARNH 82 (179)
T ss_pred hHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHH
Confidence 34678999999999999999999999999999999999999999999999999999999998643 37999999999999
Q ss_pred HHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCc
Q 046578 206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMT 285 (379)
Q Consensus 206 i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~ 285 (379)
+++++|++.+. . ...+.
T Consensus 83 ~~d~~R~~~~~-~-----------------------------------------------------~~~~~--------- 99 (179)
T PRK12514 83 AIDRLRARKAV-A-----------------------------------------------------VDIDE--------- 99 (179)
T ss_pred HHHHHHhcCCc-c-----------------------------------------------------ccccc---------
Confidence 99999975420 0 00000
Q ss_pred ccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578 286 MQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL 365 (379)
Q Consensus 286 l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL 365 (379)
..+ ..+ ....|++.+...+....+..+|..||+++++||.++|+ +|+|++|||+.||+|.++|++.++||+++|
T Consensus 100 ~~~-~~~-~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~Rar~~L 173 (179)
T PRK12514 100 AHD-LAD-PSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYL----EGLSYKELAERHDVPLNTMRTWLRRSLLKL 173 (179)
T ss_pred chh-ccc-cCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCChHHHHHHHHHHHHHH
Confidence 000 001 11245555555555567899999999999999999995 679999999999999999999999999999
Q ss_pred HhHHh
Q 046578 366 QQTNI 370 (379)
Q Consensus 366 R~~l~ 370 (379)
|+++.
T Consensus 174 r~~l~ 178 (179)
T PRK12514 174 RECLS 178 (179)
T ss_pred HHHhc
Confidence 99874
No 50
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=99.93 E-value=6.7e-25 Score=204.90 Aligned_cols=176 Identities=13% Similarity=0.195 Sum_probs=145.9
Q ss_pred CcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHH
Q 046578 126 LDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA 205 (379)
Q Consensus 126 ~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~ 205 (379)
.+..+|+.++++||..+++.||..|.+.|++++.++.++..++||++||+|+.+|+++++|++..+ +|.+|++.+++|.
T Consensus 48 ~~d~~Li~~~~~gd~~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN~ 126 (233)
T PRK12538 48 DEDEELLDRLATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSNR 126 (233)
T ss_pred ccHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHHH
Confidence 355789999999999999999999999999999999999999999999999999999999986444 7999999999999
Q ss_pred HHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCc
Q 046578 206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMT 285 (379)
Q Consensus 206 i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~ 285 (379)
+++++|++.+. . ++. .
T Consensus 127 ~id~~Rk~~~~-----------------------------------------------------~---~~~-~------- 142 (233)
T PRK12538 127 CIDLRRKPRTE-----------------------------------------------------N---VDA-V------- 142 (233)
T ss_pred HHHHHHhhccc-----------------------------------------------------c---ccc-c-------
Confidence 99999874310 0 000 0
Q ss_pred ccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578 286 MQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL 365 (379)
Q Consensus 286 l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL 365 (379)
.+.. + ....+++.+...+....+..+|..||+++|+||.|+|+ +|+|++|||+.||+|.++|+++++||+++|
T Consensus 143 -~~~~-~-~~~~~~~~~~~~e~~~~l~~~L~~Lp~~~R~v~~L~~~----eg~s~~EIA~~Lgis~~tVk~~l~RAr~kL 215 (233)
T PRK12538 143 -PEVA-D-GKPDAVSVIERNELSDLLEAAMQRLPEQQRIAVILSYH----ENMSNGEIAEVMDTTVAAVESLLKRGRQQL 215 (233)
T ss_pred -cccc-c-CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 0000 0 11234455555666678999999999999999999994 779999999999999999999999999999
Q ss_pred HhHHhhch
Q 046578 366 QQTNILNN 373 (379)
Q Consensus 366 R~~l~~~~ 373 (379)
|+.+....
T Consensus 216 r~~l~~~~ 223 (233)
T PRK12538 216 RDLLRRHE 223 (233)
T ss_pred HHHHHHhh
Confidence 99987544
No 51
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=99.93 E-value=1.3e-24 Score=196.57 Aligned_cols=185 Identities=14% Similarity=0.176 Sum_probs=147.8
Q ss_pred cCcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHH
Q 046578 125 ELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQ 204 (379)
Q Consensus 125 ~~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~ 204 (379)
..+...++..++.||..+++.||..|.|.|+++++++.++..++||++||+|+++|+++.+|++.. .|.+|++++++|
T Consensus 4 ~~~~~~ll~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~l~~~~~~~~~~~--~~~~wl~~ia~n 81 (193)
T PRK11923 4 QEEDQQLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDS--AFYTWLYRIAIN 81 (193)
T ss_pred cccHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHhCcCCCC--ccHhHHHHHHHH
Confidence 345578999999999999999999999999999999999999999999999999999999998764 699999999999
Q ss_pred HHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCC
Q 046578 205 AIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCM 284 (379)
Q Consensus 205 ~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~ 284 (379)
.+.+++|++.+.... ....++......+
T Consensus 82 ~~~d~~rk~~~~~~~--------------------------------------------------~~~~~~~~~~~~~-- 109 (193)
T PRK11923 82 TAKNHLVSRGRRPPD--------------------------------------------------SDVSSEDAEFYDG-- 109 (193)
T ss_pred HHHHHHHHhcCCCcc--------------------------------------------------ccccccchhhhcc--
Confidence 999999976531000 0000110000000
Q ss_pred cccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046578 285 TMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTK 364 (379)
Q Consensus 285 ~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~k 364 (379)
...+. ....|++.+...+....+..++..||+++|.||.++|+ +|+|++|||+.||+|.++|+++++||+++
T Consensus 110 --~~~~~--~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tv~~~l~Rar~~ 181 (193)
T PRK11923 110 --DHALK--DIESPERALLRDEIEGTVHRTIQQLPEDLRTALTLREF----DGLSYEDIASVMQCPVGTVRSRIFRAREA 181 (193)
T ss_pred --ccccc--CcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHHhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 00011 12356666666777788999999999999999999984 67999999999999999999999999999
Q ss_pred HHhHHhh
Q 046578 365 LQQTNIL 371 (379)
Q Consensus 365 LR~~l~~ 371 (379)
||++++.
T Consensus 182 Lr~~l~~ 188 (193)
T PRK11923 182 IDKALQP 188 (193)
T ss_pred HHHHHHH
Confidence 9999763
No 52
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=99.93 E-value=7e-25 Score=198.60 Aligned_cols=178 Identities=19% Similarity=0.238 Sum_probs=143.9
Q ss_pred cCcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHH
Q 046578 125 ELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQ 204 (379)
Q Consensus 125 ~~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~ 204 (379)
..+..+++.+++.||..+++.|+..|.+.|+++++++.++..++||++||+|+++|+. ..|++..+ +|.||++++++|
T Consensus 13 ~~~~~~l~~~~~~gd~~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn 90 (194)
T PRK12519 13 SRSDAELFSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRS 90 (194)
T ss_pred cccHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHH
Confidence 4556889999999999999999999999999999999999899999999999999976 67876544 799999999999
Q ss_pred HHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCC
Q 046578 205 AIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCM 284 (379)
Q Consensus 205 ~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~ 284 (379)
.+++++|++.+..... . ..+.
T Consensus 91 ~~~d~~Rk~~~~~~~~-------------------------------------------------~--~~~~-------- 111 (194)
T PRK12519 91 RAIDRLRSRRSRQRLL-------------------------------------------------E--RWQQ-------- 111 (194)
T ss_pred HHHHHHHhcccccchh-------------------------------------------------h--hhhh--------
Confidence 9999999865310000 0 0000
Q ss_pred cccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046578 285 TMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTK 364 (379)
Q Consensus 285 ~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~k 364 (379)
.. ..+.....+++.+...+....+..++..||+++++||.++|+ +|+|++|||+.||+|.++|+++++||+++
T Consensus 112 ~~---~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~ 184 (194)
T PRK12519 112 EL---LGEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYY----EGLSQSEIAKRLGIPLGTVKARARQGLLK 184 (194)
T ss_pred hh---cccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhhh----cCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 00 000112245555666666677999999999999999999984 67999999999999999999999999999
Q ss_pred HHhHHh
Q 046578 365 LQQTNI 370 (379)
Q Consensus 365 LR~~l~ 370 (379)
||+.+.
T Consensus 185 Lr~~l~ 190 (194)
T PRK12519 185 LRELLQ 190 (194)
T ss_pred HHHHHH
Confidence 999865
No 53
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=99.93 E-value=9.8e-25 Score=194.32 Aligned_cols=177 Identities=18% Similarity=0.237 Sum_probs=142.5
Q ss_pred HHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHH
Q 046578 132 KYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIA 211 (379)
Q Consensus 132 i~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr 211 (379)
|.++++||..|++.|+..|.+.|+++++++.+++.+++|++||+|+++|+++++|+ .+.+|.+|++.+++|.+.+++|
T Consensus 1 v~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~r 78 (182)
T PRK09652 1 VERVQRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR--GGAAFYTWLYRIARNTAINYLR 78 (182)
T ss_pred CchhhcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHHHHHHHH
Confidence 35788999999999999999999999999999989999999999999999999998 3458999999999999999999
Q ss_pred hhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCC
Q 046578 212 NKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIP 291 (379)
Q Consensus 212 ~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~ 291 (379)
+..+....+ +++ ..+.+.....+...
T Consensus 79 ~~~~~~~~~----------------------------------------------------~~~--~~~~~~~~~~~~~~ 104 (182)
T PRK09652 79 KQGRRPPAS----------------------------------------------------DVD--AEEAEDFDLADALR 104 (182)
T ss_pred cccCCCCcc----------------------------------------------------ccc--cccccccccccccc
Confidence 865311100 000 00000001111111
Q ss_pred CCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHh
Q 046578 292 GPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNI 370 (379)
Q Consensus 292 ~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~ 370 (379)
...+|++.+...+....+..++..|||+++.||.++|+ +|+|++|||+.||+|+++|++.++||+++||+.+.
T Consensus 105 --~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 177 (182)
T PRK09652 105 --DISTPENELLSAELEQRVRAAIESLPEELRTAITLREI----EGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKLQ 177 (182)
T ss_pred --cccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 12356777777777788999999999999999999984 67999999999999999999999999999999875
No 54
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=99.93 E-value=1e-24 Score=196.15 Aligned_cols=179 Identities=21% Similarity=0.300 Sum_probs=141.0
Q ss_pred CcCcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHH
Q 046578 124 GELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIK 203 (379)
Q Consensus 124 ~~~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir 203 (379)
..++..+++.++++||..+++.+|..|.|.|+.+++++.+++.+++|++||+|+++|+++.+|++.. ..|.+|++++++
T Consensus 6 ~~~~~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~-~~~~~wl~~ia~ 84 (186)
T PRK13919 6 ESLSDEALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRR-GSARAWLLALAH 84 (186)
T ss_pred cccCHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCccc-cchHHHHHHHHH
Confidence 3456789999999999999999999999999999999998889999999999999999999998654 369999999999
Q ss_pred HHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCC
Q 046578 204 QAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGC 283 (379)
Q Consensus 204 ~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~ 283 (379)
|.+.+++|+..+... . ++. +...
T Consensus 85 n~~~d~~rk~~~~~~----------------------------------------------------~--~~~---~~~~ 107 (186)
T PRK13919 85 HAAVDHVRRRAARPQ----------------------------------------------------P--LEP---DERE 107 (186)
T ss_pred HHHHHHHHhhhcccc----------------------------------------------------c--ccc---cccc
Confidence 999999998652100 0 000 0000
Q ss_pred CcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578 284 MTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT 363 (379)
Q Consensus 284 ~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~ 363 (379)
....+ .+++ .......+....+..++..||+++++||.++|+ +|+|++|||+.||+|.++|+++++||++
T Consensus 108 ~~~~~-~~~~-----~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~~V~~~l~ra~~ 177 (186)
T PRK13919 108 PEAFD-LPGP-----GLDEEGHLDRTRLGRALKALSPEERRVIEVLYY----QGYTHREAAQLLGLPLGTLKTRARRALS 177 (186)
T ss_pred ccccc-CCCc-----cccHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 00000 0111 111112223456889999999999999999984 7799999999999999999999999999
Q ss_pred HHHhHHh
Q 046578 364 KLQQTNI 370 (379)
Q Consensus 364 kLR~~l~ 370 (379)
+||+.+.
T Consensus 178 ~Lr~~l~ 184 (186)
T PRK13919 178 RLKEVLR 184 (186)
T ss_pred HHHHHhc
Confidence 9999875
No 55
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=99.93 E-value=1.2e-24 Score=196.63 Aligned_cols=180 Identities=18% Similarity=0.231 Sum_probs=147.5
Q ss_pred CcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCC---CCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHH
Q 046578 126 LDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGK---GLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWI 202 (379)
Q Consensus 126 ~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~---~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~I 202 (379)
++..+|+.++++||..|++++++.|.|.|++++.++.++ ..++||++||+|+++|+++++|+++.+ +|.+|++.++
T Consensus 3 ~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~-~~~~wl~~ia 81 (189)
T PRK06811 3 INEDNFIKELKKKNEKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKG-SFKKWIAAIS 81 (189)
T ss_pred CcHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccc-cHHHHHHHHH
Confidence 455789999999999999999999999999999999875 357999999999999999999986544 7999999999
Q ss_pred HHHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCC
Q 046578 203 KQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRG 282 (379)
Q Consensus 203 r~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~ 282 (379)
+|.+.+++|++.+.... .+.+.
T Consensus 82 rn~~~d~~rk~~~~~~~----------------------------------------------------~~~~~------ 103 (189)
T PRK06811 82 KYKAIDYKRKLTKNNEI----------------------------------------------------DSIDE------ 103 (189)
T ss_pred HHHHHHHHHHhcccccc----------------------------------------------------ccchh------
Confidence 99999999986631000 00000
Q ss_pred CCcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 283 CMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 283 ~~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
... ....+|++.+...+....+..++..|||++|.||.++|+ +|+|++|||+.||+|.++|+++++||+
T Consensus 104 -----~~~--~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIAe~lgis~~~V~~~l~Ra~ 172 (189)
T PRK06811 104 -----FIL--ISEESIENEIILKENKEEILKLINDLEKLDREIFIRRYL----LGEKIEEIAKKLGLTRSAIDNRLSRGR 172 (189)
T ss_pred -----hhh--cccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----ccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 000 012345666666777788999999999999999999984 679999999999999999999999999
Q ss_pred HHHHhHHhhchhh
Q 046578 363 TKLQQTNILNNLK 375 (379)
Q Consensus 363 ~kLR~~l~~~~L~ 375 (379)
++||+..-...++
T Consensus 173 ~~Lr~~~~~~~~~ 185 (189)
T PRK06811 173 KKLQKNKLNISLG 185 (189)
T ss_pred HHHHHcccCcccC
Confidence 9999986655443
No 56
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=99.93 E-value=8.1e-25 Score=198.54 Aligned_cols=188 Identities=15% Similarity=0.245 Sum_probs=146.7
Q ss_pred hhcCcCcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHH
Q 046578 121 KENGELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYW 200 (379)
Q Consensus 121 ~~~~~~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~ 200 (379)
...+..++.+++.++..||..+++.||+.|.|.|+.+|.++.++..+++|++||+|+.+|+.+++|++..+ +|.+|+++
T Consensus 7 ~~~~~~~~~~li~~~~~~d~~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l~l~~~~~~~~~~~~-~~~~wL~~ 85 (194)
T PRK12531 7 HTFGRQEWLECMEKVKSRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYT 85 (194)
T ss_pred cccccHhHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-hHHHHHHH
Confidence 34556788999999999999999999999999999999999999889999999999999999999986444 79999999
Q ss_pred HHHHHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCcccc
Q 046578 201 WIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTD 280 (379)
Q Consensus 201 ~Ir~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~ 280 (379)
+++|.+++++|+..+.... ...+....+
T Consensus 86 iarn~~ld~~Rk~~~~~~~----------------------------------------------------~~~~~~~~~ 113 (194)
T PRK12531 86 IIRNLCFDLLRKQKGKDLH----------------------------------------------------IHADDIWPS 113 (194)
T ss_pred HHHHHHHHHHHHhcccccc----------------------------------------------------cchhhcccc
Confidence 9999999999986521000 000000000
Q ss_pred CCCCcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 281 RGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 281 ~~~~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
+ .....+. ....++.. .....+..++.+||+++|+||.++|+ +|+|++|||+.||+|.++|+.+++|
T Consensus 114 ~---~~~~~~~--~~~~~e~~----~~~~~l~~~l~~Lp~~~r~v~~l~~~----eg~s~~EIA~~lgis~~tVk~rl~r 180 (194)
T PRK12531 114 D---YYPPDLV--DHYSPEQD----MLKEQVMKFLDRLPKAQRDVLQAVYL----EELPHQQVAEMFDIPLGTVKSRLRL 180 (194)
T ss_pred c---ccccccc--cccCHHHH----HHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCcCHHHHHHHHHH
Confidence 0 0000000 01122222 22356889999999999999999985 7799999999999999999999999
Q ss_pred HHHHHHhHHhhchh
Q 046578 361 ALTKLQQTNILNNL 374 (379)
Q Consensus 361 Al~kLR~~l~~~~L 374 (379)
|+++||+.+..+.|
T Consensus 181 a~~~Lr~~l~~~~~ 194 (194)
T PRK12531 181 AVEKLRHSMDAESL 194 (194)
T ss_pred HHHHHHHHhhhccC
Confidence 99999999887653
No 57
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=99.93 E-value=4.6e-25 Score=198.54 Aligned_cols=176 Identities=15% Similarity=0.210 Sum_probs=140.0
Q ss_pred HhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhc
Q 046578 135 ILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKS 214 (379)
Q Consensus 135 ~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~ 214 (379)
+.+||..+++.||..|.+.|+.+|.+++++..++||++||+|+.+|+++.+|+...+..|.||++++++|.+++++|++.
T Consensus 3 ~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn~~~d~~Rk~~ 82 (185)
T PRK12542 3 VTNNDYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRKNK 82 (185)
T ss_pred ccccCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 56799999999999999999999999999999999999999999999999998644457999999999999999999865
Q ss_pred CcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCC
Q 046578 215 RTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPD 294 (379)
Q Consensus 215 r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~ 294 (379)
+.... .+. ... +.... .
T Consensus 83 ~~~~~------------------------------------------------------~~~-~~~-------~~~~~-~ 99 (185)
T PRK12542 83 RHETF------------------------------------------------------LEE-YER-------ESIEA-V 99 (185)
T ss_pred hhhhh------------------------------------------------------hhh-ccc-------cchhh-h
Confidence 20000 000 000 00000 0
Q ss_pred CCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchh
Q 046578 295 ETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNL 374 (379)
Q Consensus 295 ~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L 374 (379)
...+++.....+....|..+|..|||++|+||.|+|+ +|+|++|||+.||+|.++|+++++||+++||+.+.....
T Consensus 100 ~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~ 175 (185)
T PRK12542 100 DENIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVF----YNLTYQEISSVMGITEANVRKQFERARKRVQNMIGGIQH 175 (185)
T ss_pred hccHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcccch
Confidence 1123333333444567999999999999999999985 779999999999999999999999999999999877665
Q ss_pred hhh
Q 046578 375 KVY 377 (379)
Q Consensus 375 ~~y 377 (379)
..|
T Consensus 176 ~~~ 178 (185)
T PRK12542 176 DEF 178 (185)
T ss_pred HHH
Confidence 554
No 58
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=99.93 E-value=3.9e-24 Score=193.93 Aligned_cols=174 Identities=12% Similarity=0.115 Sum_probs=143.8
Q ss_pred cCcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHH
Q 046578 125 ELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQ 204 (379)
Q Consensus 125 ~~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~ 204 (379)
..+..+++..+.+||..+++.+|+.|.+.|++++.++.++..++||++||+|+.+|+++++|++.. +|.+|++++++|
T Consensus 11 ~~~~~~l~~~~~~gd~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~~--~f~~wL~~i~rn 88 (192)
T PRK09643 11 ERSDAELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDA--AVSSWLHRIVVN 88 (192)
T ss_pred CcCHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCCC--ccHHHHHHHHHH
Confidence 355688999999999999999999999999999999999999999999999999999999998643 699999999999
Q ss_pred HHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCC
Q 046578 205 AIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCM 284 (379)
Q Consensus 205 ~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~ 284 (379)
.+++++|+..+... .+++. . .
T Consensus 89 ~~~d~~Rk~~~~~~-----------------------------------------------------~~~~~----~-~- 109 (192)
T PRK09643 89 ACLDRLRRAKARPT-----------------------------------------------------VPLDD----V-Y- 109 (192)
T ss_pred HHHHHHHccccCCC-----------------------------------------------------CCccc----c-c-
Confidence 99999997653100 00100 0 0
Q ss_pred cccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046578 285 TMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTK 364 (379)
Q Consensus 285 ~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~k 364 (379)
+ .. ..+++.+...+....+..+|+.||+++|+||.|+|+ +|+|++|||+.||+|.++|+++++||+++
T Consensus 110 ---~-~~----~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~i~~l~~~----~g~s~~EIA~~lg~s~~tV~~rl~rar~~ 177 (192)
T PRK09643 110 ---P-VA----QLERDPTARVETALAVQRALMRLPVEQRAALVAVDM----QGYSVADAARMLGVAEGTVKSRCARGRAR 177 (192)
T ss_pred ---c-cc----CCcccHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 0 00 012233444455667999999999999999999984 77999999999999999999999999999
Q ss_pred HHhHHhh
Q 046578 365 LQQTNIL 371 (379)
Q Consensus 365 LR~~l~~ 371 (379)
||+.+..
T Consensus 178 Lr~~l~~ 184 (192)
T PRK09643 178 LAELLGY 184 (192)
T ss_pred HHHHHHH
Confidence 9999864
No 59
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=99.93 E-value=5e-24 Score=192.44 Aligned_cols=180 Identities=17% Similarity=0.221 Sum_probs=149.6
Q ss_pred CcCcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHH
Q 046578 124 GELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIK 203 (379)
Q Consensus 124 ~~~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir 203 (379)
+..+..+++..+++||..|++.||..|.+.++.++.++.++..++||++||+|+.+|++.++|++. ..|.+|++.+++
T Consensus 5 ~~~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~~~~~~~--~~~~~wl~~i~~ 82 (189)
T PRK12515 5 QATTDEMLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIAR 82 (189)
T ss_pred cccCHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CChHHHHHHHHH
Confidence 345668899999999999999999999999999999999999999999999999999999999864 379999999999
Q ss_pred HHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCC
Q 046578 204 QAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGC 283 (379)
Q Consensus 204 ~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~ 283 (379)
|.+.+++|+..+. . +. ++
T Consensus 83 n~~~d~~r~~~~~------------------------------------------------------~--~~----~~-- 100 (189)
T PRK12515 83 FKALSALRRRKHE------------------------------------------------------E--ID----DE-- 100 (189)
T ss_pred HHHHHHHHccCCC------------------------------------------------------C--Cc----cc--
Confidence 9999999975420 0 00 00
Q ss_pred CcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578 284 MTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT 363 (379)
Q Consensus 284 ~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~ 363 (379)
.. ....+ ...+|+......+....+..++..||+++|+||.++|+ +|+|++|||+.||+|.++|+++++||++
T Consensus 101 -~~-~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~tV~~~l~Rar~ 173 (189)
T PRK12515 101 -AA-AAIED-GADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVYY----HEKSVEEVGEIVGIPESTVKTRMFYARK 173 (189)
T ss_pred -cc-cccCC-CCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 00 00111 12345665666666778999999999999999999995 7799999999999999999999999999
Q ss_pred HHHhHHhhchh
Q 046578 364 KLQQTNILNNL 374 (379)
Q Consensus 364 kLR~~l~~~~L 374 (379)
+||+.+...++
T Consensus 174 ~Lr~~l~~~~~ 184 (189)
T PRK12515 174 KLAELLKAAGV 184 (189)
T ss_pred HHHHHHHHhcc
Confidence 99999887654
No 60
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=99.93 E-value=2e-24 Score=194.45 Aligned_cols=177 Identities=12% Similarity=0.169 Sum_probs=144.3
Q ss_pred CcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHH
Q 046578 126 LDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA 205 (379)
Q Consensus 126 ~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~ 205 (379)
.+..+++.+...||..+++++|..|.+.|+++|.++.++..++||++||+|+++|+++++|++..+ +|.+|++.+++|.
T Consensus 10 ~~~~~l~~~~~~~~~~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~~n~ 88 (187)
T PRK12534 10 DETGRLLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIARNK 88 (187)
T ss_pred chHHHHHHHHHcCCHHHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHH
Confidence 345788999999999999999999999999999999999999999999999999999999987544 6899999999999
Q ss_pred HHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCc
Q 046578 206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMT 285 (379)
Q Consensus 206 i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~ 285 (379)
+++++|+..+.. ...+.+.
T Consensus 89 ~~d~~R~~~~~~----------------------------------------------------~~~~~~~--------- 107 (187)
T PRK12534 89 AIDHLRANAPQR----------------------------------------------------RNVALDD--------- 107 (187)
T ss_pred HHHHHHhccccc----------------------------------------------------ccccccc---------
Confidence 999999754200 0000110
Q ss_pred ccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578 286 MQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL 365 (379)
Q Consensus 286 l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL 365 (379)
...... ...++++.....+....+..+|..||++++.|+.++|+ +|+|++|||+.||+|.++|+++++||+++|
T Consensus 108 ~~~~~~--~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~~v~~~l~Rar~~L 181 (187)
T PRK12534 108 AGELRA--ADASPLERTERASTRRRIDHCLAELEPPRSELIRTAFF----EGITYEELAARTDTPIGTVKSWIRRGLAKL 181 (187)
T ss_pred hhhhcc--ccCChhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCChhHHHHHHHHHHHHH
Confidence 000000 01133444455566778999999999999999999984 779999999999999999999999999999
Q ss_pred HhHHh
Q 046578 366 QQTNI 370 (379)
Q Consensus 366 R~~l~ 370 (379)
|+.+.
T Consensus 182 r~~l~ 186 (187)
T PRK12534 182 KACLE 186 (187)
T ss_pred HHHHc
Confidence 99874
No 61
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=99.93 E-value=3.8e-24 Score=199.50 Aligned_cols=187 Identities=14% Similarity=0.191 Sum_probs=151.0
Q ss_pred CcCcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHH
Q 046578 124 GELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIK 203 (379)
Q Consensus 124 ~~~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir 203 (379)
+..+..+|+.++.+||..+++.+|..|.+.|++++.++.++..++||++||+|+++|+++++|++. ..|.+|++++++
T Consensus 13 ~~~~~~~l~~~~~~gd~~a~~~l~~~y~~~l~~~a~~~~~~~~~AEDlvQE~fi~l~~~~~~~~~~--~~~~~wL~~iar 90 (231)
T PRK11922 13 SAASDRELVARVLAGDEAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGD--ASLSTWLSRIVL 90 (231)
T ss_pred CcccHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHhcCCC--chhHHHHHHHHH
Confidence 345568899999999999999999999999999999999999999999999999999999999875 379999999999
Q ss_pred HHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCC
Q 046578 204 QAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGC 283 (379)
Q Consensus 204 ~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~ 283 (379)
|.+++++|+..+....+. . .+.....+ +
T Consensus 91 n~~~d~~Rk~~r~~~~~~--------------------------------------------------~-~~~~~~~~-~ 118 (231)
T PRK11922 91 NEALGRLRRRRRLVNLAE--------------------------------------------------M-VMASTIAG-G 118 (231)
T ss_pred HHHHHHHHhhcccccchh--------------------------------------------------c-cccccccc-c
Confidence 999999998664211100 0 00000000 0
Q ss_pred CcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578 284 MTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT 363 (379)
Q Consensus 284 ~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~ 363 (379)
... .......+|++.+...+..+.+..+|..||+++|+||.++|+ +|+|++|||+.||+|.++|+++++||++
T Consensus 119 --~~~-~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIAe~lgis~~tVk~~l~Rar~ 191 (231)
T PRK11922 119 --ERT-PLADPAEDPERAAARREIRALLERAIDALPDAFRAVFVLRVV----EELSVEETAQALGLPEETVKTRLHRARR 191 (231)
T ss_pred --ccc-ccCcccCChHHHHHHHHHHHHHHHHHHhCCHHHhhhheeehh----cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 000 001123356777777788888999999999999999999884 6799999999999999999999999999
Q ss_pred HHHhHHhh
Q 046578 364 KLQQTNIL 371 (379)
Q Consensus 364 kLR~~l~~ 371 (379)
+||+.+..
T Consensus 192 kLr~~l~~ 199 (231)
T PRK11922 192 LLRESLAR 199 (231)
T ss_pred HHHHHHHH
Confidence 99999875
No 62
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=99.92 E-value=1.8e-24 Score=188.37 Aligned_cols=153 Identities=18% Similarity=0.257 Sum_probs=124.9
Q ss_pred ccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcc
Q 046578 138 KERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTI 217 (379)
Q Consensus 138 Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~i 217 (379)
+|..||++|++.|.|+|+++++++ ++..++||++||+|+++|+++++|++..+ +|.+|++.+++|.+++++|++.+..
T Consensus 1 ~~~~af~~l~~~y~~~l~~~~~~~-~~~~~aeDi~Qe~~l~l~~~~~~~~~~~~-~f~~wl~~i~~n~~ld~~rk~~~~~ 78 (154)
T PRK06759 1 MKPATFTEAVVLYEGLIVNQIKKL-GIYQDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYILERLKKEFAVQ 78 (154)
T ss_pred CCcccHHHHHHHHHHHHHHHHHHh-CCcccHHHHHHHHHHHHHHHHHHhCccCC-chHHHHHHHHHHHHHHHHHHHHhhc
Confidence 366899999999999999999986 56689999999999999999999997665 7999999999999999999864200
Q ss_pred cCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCC
Q 046578 218 RLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETM 297 (379)
Q Consensus 218 rip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~ 297 (379)
+.... . +.
T Consensus 79 ---------------------------------------------------------~~~~~----------~-----~~ 86 (154)
T PRK06759 79 ---------------------------------------------------------EKCVC----------V-----GE 86 (154)
T ss_pred ---------------------------------------------------------ccccc----------c-----CC
Confidence 00000 0 01
Q ss_pred hHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 298 PERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 298 pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
|++.....+....+..++.+||+++|.||.++|+ +|+|++|||+.||+|.++|+++++||+++||+.
T Consensus 87 ~~~~~~~~~~~~~l~~~l~~L~~~~r~ii~l~~~----~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~ 153 (154)
T PRK06759 87 YEDHFHFEDVEMKVKDFMSVLDEKEKYIIFERFF----VGKTMGEIALETEMTYYQVRWIYRQALEKMRNS 153 (154)
T ss_pred CcccccHHHHHHHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence 1112223334567899999999999999999994 779999999999999999999999999999974
No 63
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=99.92 E-value=4.2e-24 Score=189.33 Aligned_cols=167 Identities=16% Similarity=0.179 Sum_probs=136.4
Q ss_pred cHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHH
Q 046578 127 DYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAI 206 (379)
Q Consensus 127 ~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i 206 (379)
+..+++..+.+||..|++.+|..|.+.|++++.++.++..++||++||+|+.+|+++.+|++. .+|.+|++.+++|.+
T Consensus 2 ~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~--~~~~~wl~~i~~n~~ 79 (169)
T TIGR02954 2 NDEELVKKAKRGNKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHP--KYFNTWLTRILINEC 79 (169)
T ss_pred CHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCc--cccHHHHHHHHHHHH
Confidence 356889999999999999999999999999999999999999999999999999999999864 379999999999999
Q ss_pred HHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcc
Q 046578 207 IRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTM 286 (379)
Q Consensus 207 ~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l 286 (379)
++++|+..+. . .++....
T Consensus 80 ~d~~R~~~~~--~-----------------------------------------------------~~~~~~~------- 97 (169)
T TIGR02954 80 IDLLKKKKKV--I-----------------------------------------------------PFDPNTS------- 97 (169)
T ss_pred HHHHHhcCCc--C-----------------------------------------------------ccccccc-------
Confidence 9999976521 0 0000000
Q ss_pred cccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 046578 287 QDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQ 366 (379)
Q Consensus 287 ~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR 366 (379)
..+ ..++ ....+ ...+..+|+.||+++|+||.++|+ +|+|++|||+.||+|.++|+++++||+++||
T Consensus 98 ---~~~---~~~~--~~~~~-~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr 164 (169)
T TIGR02954 98 ---IEK---GECE--THADS-RLDLYKAIDTLNDKYQTAIILRYY----HDLTIKEIAEVMNKPEGTVKTYLHRALKKLK 164 (169)
T ss_pred ---ccc---chhh--hchHH-HHHHHHHHHhCCHHHhHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 000 0011 11111 226889999999999999999995 7799999999999999999999999999999
Q ss_pred hHHh
Q 046578 367 QTNI 370 (379)
Q Consensus 367 ~~l~ 370 (379)
+.+.
T Consensus 165 ~~l~ 168 (169)
T TIGR02954 165 KRLE 168 (169)
T ss_pred HHhc
Confidence 9864
No 64
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=99.92 E-value=8.8e-24 Score=189.98 Aligned_cols=181 Identities=17% Similarity=0.209 Sum_probs=140.1
Q ss_pred hcccHHHHHHHHHHhHHHHHHHHHhcc----CCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHH
Q 046578 136 LCKERESQERIIRSYRSLVVSIATGYQ----GKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIA 211 (379)
Q Consensus 136 ~~Gd~~A~e~Li~~y~~lV~~ia~r~~----~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr 211 (379)
+.||..|+++|+..|.+.|+.+|+++. ++..++||++||+|+.+|+++.+|+...+.+|.+|++++++|.+.+++|
T Consensus 2 ~~~~~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r 81 (189)
T TIGR02984 2 RGGDQEALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNVLADALR 81 (189)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHHHHHH
Confidence 579999999999999999999999874 3567999999999999999999998765568999999999999999999
Q ss_pred hhcC-cccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCcc-ccCCCCccccc
Q 046578 212 NKSR-TIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAV-TDRGCMTMQDI 289 (379)
Q Consensus 212 ~~~r-~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~-~~~~~~~l~d~ 289 (379)
+..+ ..+.+ ....+++... .++....+.+.
T Consensus 82 ~~~~~~~r~~------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~ 113 (189)
T TIGR02984 82 RHLGAQKRDI------------------------------------------------RREQSLDAGGRLDESSVRLAAQ 113 (189)
T ss_pred HHHHHHhhhc------------------------------------------------ccccCCCcccccCCcchhHHHH
Confidence 7521 00000 0111222211 01111122222
Q ss_pred CCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578 290 IPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN 369 (379)
Q Consensus 290 i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l 369 (379)
+.+ ...+|++.+...+....|..+|..|||++|.||.++|+ +|+|++|||+.||+|+++|++.++||+++||+.+
T Consensus 114 ~~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vi~l~~~----~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~l 188 (189)
T TIGR02984 114 LAA-DGPSPSQVAARREAAVRLAQALAKLPEDYREVILLRHL----EGLSFAEVAERMDRSEGAVSMLWVRGLARLRQIL 188 (189)
T ss_pred ccC-CCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 222 23456777777777788999999999999999999985 6799999999999999999999999999999876
No 65
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=99.92 E-value=9.2e-24 Score=193.58 Aligned_cols=179 Identities=13% Similarity=0.245 Sum_probs=139.7
Q ss_pred HHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHH
Q 046578 129 NLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIR 208 (379)
Q Consensus 129 ~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~ 208 (379)
..++..+.+||..++++||..|.+.|++++.++.++..+++|++||+|+.+|++++.|++.++ .|.+|++.+++|.+++
T Consensus 26 ~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wl~~I~rn~~~d 104 (206)
T PRK12526 26 QWLILVAISRDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYTVMRNAAFD 104 (206)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCccc-chhHHHHHHHHHHHHH
Confidence 445667889999999999999999999999999999899999999999999999999987654 6999999999999999
Q ss_pred HHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccc
Q 046578 209 AIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQD 288 (379)
Q Consensus 209 ~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d 288 (379)
++|+..+..... ... + .....+
T Consensus 105 ~~Rk~~~~~~~~-----------------------------------------------------~~~----~-~~~~~~ 126 (206)
T PRK12526 105 MLRKIKAKKEQN-----------------------------------------------------LGD----D-IWPIEQ 126 (206)
T ss_pred HHHHhccccccc-----------------------------------------------------ccc----c-cchhhh
Confidence 999865311000 000 0 000001
Q ss_pred cCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 289 IIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 289 ~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
.+.+. ...+. ..........|..+|..||+++|.||.++|+ +|+|++|||+.||+|.++|+.+++||+++||+.
T Consensus 127 ~~~~~-~~~~~-~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 200 (206)
T PRK12526 127 ALAES-QSESE-EFSDHLMDKQILSYIEKLPEAQQTVVKGVYF----QELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQ 200 (206)
T ss_pred hcccc-cCchH-HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 11111 11122 2223333457899999999999999999995 779999999999999999999999999999999
Q ss_pred Hhhc
Q 046578 369 NILN 372 (379)
Q Consensus 369 l~~~ 372 (379)
+...
T Consensus 201 l~~~ 204 (206)
T PRK12526 201 MGEQ 204 (206)
T ss_pred Hhhc
Confidence 8653
No 66
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=99.92 E-value=1.6e-23 Score=186.04 Aligned_cols=175 Identities=14% Similarity=0.128 Sum_probs=146.2
Q ss_pred HHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHH
Q 046578 130 LVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRA 209 (379)
Q Consensus 130 eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~ 209 (379)
.|+..+..||..|++.||+.|.+.|+++++++.++..+++|++||+|+++|+++++|+ .+.+|.+|++.++++.+.++
T Consensus 2 ~~~~~~~~~~~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~~~d~ 79 (179)
T PRK11924 2 QLMPVDATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNVCYDL 79 (179)
T ss_pred hHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHHHHHH
Confidence 4678899999999999999999999999999999999999999999999999999998 34489999999999999999
Q ss_pred HHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCccccc
Q 046578 210 IANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDI 289 (379)
Q Consensus 210 lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~ 289 (379)
+++..+.... ..+. ..+.
T Consensus 80 ~r~~~~~~~~-----------------------------------------------------~~~~---------~~~~ 97 (179)
T PRK11924 80 LRRRRREKAV-----------------------------------------------------LSDD---------ALEP 97 (179)
T ss_pred HHhccccccc-----------------------------------------------------Cccc---------cccc
Confidence 9976531100 0000 0000
Q ss_pred CCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578 290 IPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN 369 (379)
Q Consensus 290 i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l 369 (379)
..+....+|++.+...+....+..++..||++++.||.++|+ +|+|++|||+.||+|+++|++.++||+++||+.+
T Consensus 98 ~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l 173 (179)
T PRK11924 98 EFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYV----EGLSYREIAEILGVPVGTVKSRLRRARQLLRECL 173 (179)
T ss_pred ccCCccCCHHHHHhhHHHHHHHHHHHHhCCHHHHHHhhHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 000023467788888888889999999999999999999984 6799999999999999999999999999999998
Q ss_pred hhc
Q 046578 370 ILN 372 (379)
Q Consensus 370 ~~~ 372 (379)
...
T Consensus 174 ~~~ 176 (179)
T PRK11924 174 EAQ 176 (179)
T ss_pred HHH
Confidence 754
No 67
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=99.92 E-value=1.5e-23 Score=196.98 Aligned_cols=183 Identities=20% Similarity=0.206 Sum_probs=145.9
Q ss_pred CcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHH-------HHhccCCCCCCCchhHH
Q 046578 126 LDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLR-------GAKRFNPERGYKLSTYV 198 (379)
Q Consensus 126 ~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~-------ai~~fD~~~g~~FsTYa 198 (379)
.+...|+.++++||..||+.|++.|.+.++.++.++.++..++||++||+|+.+|. .+++|++. ..|.||+
T Consensus 24 ~~d~~Li~~~~~gd~~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~--~~~~tWL 101 (244)
T TIGR03001 24 AADLYLACACAQGEPAALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGR--GPLLSWV 101 (244)
T ss_pred ccHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccchhhhhhccCCC--CchHhHH
Confidence 34577999999999999999999999999999999999999999999999999994 78889863 3799999
Q ss_pred HHHHHHHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCcc
Q 046578 199 YWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAV 278 (379)
Q Consensus 199 ~~~Ir~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~ 278 (379)
+++++|.+++++|++.+... ++.
T Consensus 102 ~~Ia~N~~id~lRk~~r~~~-------------------------------------------------------~~~-- 124 (244)
T TIGR03001 102 RIVATRIALELQAQERRHSP-------------------------------------------------------VEE-- 124 (244)
T ss_pred HHHHHHHHHHHHHHhcccCc-------------------------------------------------------ccc--
Confidence 99999999999997653100 000
Q ss_pred ccCCCCcccccCCCCCCCChHHHHHH----HHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHH
Q 046578 279 TDRGCMTMQDIIPGPDETMPERMVQK----QLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERI 354 (379)
Q Consensus 279 ~~~~~~~l~d~i~~~~~~~pe~~~~~----~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~V 354 (379)
+. ...+ ..+ ...+|++.... .+....|..+|++||+++|+||.|+|+ +|+|++|||+.||||.+||
T Consensus 125 --~~--~~~~-~~~-~~~~~e~~~~~~e~~~e~~~~l~~aL~~Lp~~~R~v~~L~~~----eg~S~~EIA~~Lgis~~TV 194 (244)
T TIGR03001 125 --PT--ELAA-LPA-PGSDPELDLLRERYRQDFRQALREALAALSERERHLLRLHFV----DGLSMDRIGAMYQVHRSTV 194 (244)
T ss_pred --cc--cccc-ccC-CCCCHHHHHHHHhhHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHH
Confidence 00 0000 001 11234444332 235567999999999999999999995 7799999999999999999
Q ss_pred HHHHHHHHHHHHhHHhhchhhhh
Q 046578 355 RQIRGIALTKLQQTNILNNLKVY 377 (379)
Q Consensus 355 r~~~~rAl~kLR~~l~~~~L~~y 377 (379)
+.+++||+++||+.+.......|
T Consensus 195 k~rl~RAr~~Lr~~l~~~~~~~~ 217 (244)
T TIGR03001 195 SRWVAQARERLLERTRRRLAERL 217 (244)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhc
Confidence 99999999999999987765443
No 68
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=99.92 E-value=3e-24 Score=193.78 Aligned_cols=175 Identities=20% Similarity=0.273 Sum_probs=138.8
Q ss_pred cCcHHHHHHHHhc---ccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHH
Q 046578 125 ELDYNLVKYKILC---KERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWW 201 (379)
Q Consensus 125 ~~~~~eLi~~~~~---Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~ 201 (379)
.++..+++..+++ ||..|++.||..|.|.|+++|.++.++..+++|++||+|+.+|+++++|++. .+|.+|++++
T Consensus 7 ~~~~~~li~~~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~~~~~~~~~--~~~~~wl~~i 84 (188)
T PRK09640 7 ELNDEELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGK--SKFKTWLYSI 84 (188)
T ss_pred CCCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHHHhcCC--CcchHHHHHH
Confidence 4566788888885 6999999999999999999999999999999999999999999999999853 4799999999
Q ss_pred HHHHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccC
Q 046578 202 IKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDR 281 (379)
Q Consensus 202 Ir~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~ 281 (379)
++|.+++++|+..+... ...+..
T Consensus 85 a~n~~~d~~R~~~~~~~-----------------------------------------------------~~~~~~---- 107 (188)
T PRK09640 85 TYNECITQYRKERRKRR-----------------------------------------------------LMDALS---- 107 (188)
T ss_pred HHHHHHHHHHHhccccc-----------------------------------------------------Ccchhh----
Confidence 99999999997542100 000000
Q ss_pred CCCcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578 282 GCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 282 ~~~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
. +...++. ++.....+....|..+++.||+++|+||.++|+ +|+|++|||+.||+|.++|+.+++||
T Consensus 108 ----~-~~~~~~~----~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra 174 (188)
T PRK09640 108 ----L-DPLEEAS----EEKAPKPEERGGLDRWLVHVNPIDREILVLRFV----AELEFQEIADIMHMGLSATKMRYKRA 174 (188)
T ss_pred ----h-ccccccc----ccccccHHHHHHHHHHHHhcChhheeeeeeHHh----cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 0 0000000 000112233456899999999999999999984 77999999999999999999999999
Q ss_pred HHHHHhHHhh
Q 046578 362 LTKLQQTNIL 371 (379)
Q Consensus 362 l~kLR~~l~~ 371 (379)
+++||+.+..
T Consensus 175 ~~~Lr~~l~~ 184 (188)
T PRK09640 175 LDKLREKFAG 184 (188)
T ss_pred HHHHHHHHHH
Confidence 9999998753
No 69
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=99.92 E-value=5.7e-24 Score=191.72 Aligned_cols=175 Identities=15% Similarity=0.108 Sum_probs=137.7
Q ss_pred CcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHH
Q 046578 126 LDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA 205 (379)
Q Consensus 126 ~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~ 205 (379)
.....|+.++.+||..|+++||..|.+.++.++. +.++..++||++||+|+.+|+.+++|++. .+|.+|++.+++|.
T Consensus 9 ~~~~~l~~~~~~gd~~af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~flkl~~~~~~~~~~--~~~~~Wl~~Iarn~ 85 (185)
T PRK09649 9 EAVTALALSAAKGNGRALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHV 85 (185)
T ss_pred HHHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHhccccCcc--chHHHHHHHHHHHH
Confidence 3457899999999999999999999999999995 57788899999999999999999999864 37999999999999
Q ss_pred HHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCc
Q 046578 206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMT 285 (379)
Q Consensus 206 i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~ 285 (379)
+++++|+..+.... +.+. .
T Consensus 86 ~~d~~Rk~~~~~~~-----------------------------------------------------~~~~----~---- 104 (185)
T PRK09649 86 VADHIRHVRSRPRT-----------------------------------------------------TRGA----R---- 104 (185)
T ss_pred HHHHHHHhcccccc-----------------------------------------------------cccc----c----
Confidence 99999985421000 0000 0
Q ss_pred ccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578 286 MQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL 365 (379)
Q Consensus 286 l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL 365 (379)
.+...+. +......+....+..+|.+||+++|+||.|+|+ +|+|++|||+.||+|.++|+++++||+++|
T Consensus 105 -~~~~~~~-----~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar~~L 174 (185)
T PRK09649 105 -PEHLIDG-----DRHARGFEDLVEVTTMIADLTTDQREALLLTQL----LGLSYADAAAVCGCPVGTIRSRVARARDAL 174 (185)
T ss_pred -hhhccCh-----hhhhhhHHHHHHHHHHHHhCCHHHhHHhhhHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 0000000 000111122245888999999999999999995 779999999999999999999999999999
Q ss_pred HhHHhhchh
Q 046578 366 QQTNILNNL 374 (379)
Q Consensus 366 R~~l~~~~L 374 (379)
|+.+....|
T Consensus 175 r~~~~~~~~ 183 (185)
T PRK09649 175 LADAEPDDL 183 (185)
T ss_pred HhhCCcccc
Confidence 998766554
No 70
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=99.92 E-value=7.9e-24 Score=189.57 Aligned_cols=168 Identities=18% Similarity=0.222 Sum_probs=137.1
Q ss_pred hcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcC
Q 046578 136 LCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSR 215 (379)
Q Consensus 136 ~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r 215 (379)
++||..|++.+|..|.|.|+.++.++.++..++||++||+|+.+|+++.+|++.. +|.+|++.+++|.+.+++|+..+
T Consensus 2 ~~~d~~af~~l~~~~~~~l~~~~~~~~~~~~daeDl~Qevfl~l~~~~~~~~~~~--~f~~wl~~iarn~~~~~~r~~~~ 79 (179)
T PRK12543 2 LSGDQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNR--PFRFWLIGLVIKQIHSWRRKRWR 79 (179)
T ss_pred cCchHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--ChHHHHHHHHHHHHHHHHHhhcc
Confidence 5799999999999999999999999999999999999999999999999998764 79999999999999999876542
Q ss_pred cccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCC
Q 046578 216 TIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDE 295 (379)
Q Consensus 216 ~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~ 295 (379)
..+ .++. ..+ ..+. ...
T Consensus 80 ~~~------------------------------------------------------~~~~-~~~-----~~~~---~~~ 96 (179)
T PRK12543 80 RFR------------------------------------------------------IFEK-AEE-----QRKP---VSI 96 (179)
T ss_pred ccc------------------------------------------------------cccc-ccc-----cccc---ccc
Confidence 100 0000 000 0000 011
Q ss_pred CChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhch
Q 046578 296 TMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN 373 (379)
Q Consensus 296 ~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~ 373 (379)
..|+. +...+....+..++..|||++|+||.++|+ +|+|++|||+.||+|.++|+..++||+++||+.+....
T Consensus 97 ~~~~~-~~~~~~~~~l~~~l~~Lp~~~r~i~~l~~~----e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~ 169 (179)
T PRK12543 97 DFSED-VLSKESNQELIELIHKLPYKLRQVIILRYL----HDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIEE 169 (179)
T ss_pred cChHH-HHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 13444 555666678999999999999999999985 77999999999999999999999999999999997654
No 71
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=99.92 E-value=7.5e-24 Score=190.05 Aligned_cols=173 Identities=13% Similarity=0.144 Sum_probs=137.5
Q ss_pred cHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccC-CCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHH
Q 046578 127 DYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQG-KGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA 205 (379)
Q Consensus 127 ~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~-~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~ 205 (379)
....++.++.+||..|++.+|..|.+.|+.++.++.+ +..++||++||+|+.+|+.++.|++. .+|.+|++.+++|.
T Consensus 7 ~~~~~~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~--~~~~~wl~~iarN~ 84 (181)
T PRK12536 7 RLRALLLRGLAGDAAAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRAD--QPLTAWVHAIARYK 84 (181)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCC--CchHHHHHHHHHHH
Confidence 4577999999999999999999999999999988764 57899999999999999999999974 37999999999999
Q ss_pred HHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCc
Q 046578 206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMT 285 (379)
Q Consensus 206 i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~ 285 (379)
++|++|+..+... .+....+.
T Consensus 85 ~~d~~Rk~~~~~~-------------------------------------------------------~~~~~~~~---- 105 (181)
T PRK12536 85 LMDFLRSRARREA-------------------------------------------------------LHDPLDDE---- 105 (181)
T ss_pred HHHHHHHHhcccc-------------------------------------------------------ccCCccch----
Confidence 9999998653100 00000000
Q ss_pred ccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578 286 MQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL 365 (379)
Q Consensus 286 l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL 365 (379)
.+...+. ...+ .+....+..++..||++++.||.++|. +|+|++|||+.||+|+++|+++++||+++|
T Consensus 106 -~~~~~~~-~~~~------~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~l~is~~tV~~~l~rar~~L 173 (181)
T PRK12536 106 -SELFATS-DDEA------AEARRDLGKLLEQLPDRQRLPIVHVKL----EGLSVAETAQLTGLSESAVKVGIHRGLKAL 173 (181)
T ss_pred -hhhcCCC-Ccch------HHHHHHHHHHHHHCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 0000011 0111 123346889999999999999999984 779999999999999999999999999999
Q ss_pred HhHHhhc
Q 046578 366 QQTNILN 372 (379)
Q Consensus 366 R~~l~~~ 372 (379)
|+.+..+
T Consensus 174 r~~l~~~ 180 (181)
T PRK12536 174 AAKIRGE 180 (181)
T ss_pred HHHhcCC
Confidence 9998754
No 72
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=99.92 E-value=1.6e-23 Score=188.35 Aligned_cols=173 Identities=13% Similarity=0.145 Sum_probs=138.3
Q ss_pred CcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHH----hccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHH
Q 046578 126 LDYNLVKYKILCKERESQERIIRSYRSLVVSIAT----GYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWW 201 (379)
Q Consensus 126 ~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~----r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~ 201 (379)
.+..+++.+++.||..|++++|..|.+.++.+++ ++.++..+++|++||+|+.+|++++.|++.. .|.+|++.+
T Consensus 6 ~~~~~l~~~~~~gd~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~--~f~~wl~~i 83 (184)
T PRK12539 6 NELKALMLASLDGDAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTPWVYAI 83 (184)
T ss_pred hHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCCC--ChHHHHHHH
Confidence 3468899999999999999999999999999976 4557889999999999999999999998743 699999999
Q ss_pred HHHHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccC
Q 046578 202 IKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDR 281 (379)
Q Consensus 202 Ir~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~ 281 (379)
++|.++|++|+..+. . .....+. .
T Consensus 84 ~~n~~~d~~R~~~~~-~---------------------------------------------------~~~~~~~----~ 107 (184)
T PRK12539 84 ARYKLIDHLRRTRAS-L---------------------------------------------------ADVPIDD----A 107 (184)
T ss_pred HHHHHHHHHHHHhcc-c---------------------------------------------------cccChhh----h
Confidence 999999999985420 0 0000000 0
Q ss_pred CCCcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578 282 GCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 282 ~~~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
..... .+.....+....+..++..||+++|+|+.++|+ +|+|++|||+.||+|.++|+++++||
T Consensus 108 -----~~~~~-------~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~ra 171 (184)
T PRK12539 108 -----DELVA-------HDDHAAVESTLDLGRLLARLPEKMRLAIQAVKL----EGLSVAEAATRSGMSESAVKVSVHRG 171 (184)
T ss_pred -----ccccC-------CcHHhhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCcHHHHHHHHCcCHHHHHHHHHHH
Confidence 00000 001122233456899999999999999999984 67999999999999999999999999
Q ss_pred HHHHHhHHhhc
Q 046578 362 LTKLQQTNILN 372 (379)
Q Consensus 362 l~kLR~~l~~~ 372 (379)
+++||+.+...
T Consensus 172 ~~~Lr~~l~~~ 182 (184)
T PRK12539 172 LKALAALIGRE 182 (184)
T ss_pred HHHHHHHHhhc
Confidence 99999998654
No 73
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=99.92 E-value=1.1e-23 Score=187.71 Aligned_cols=172 Identities=12% Similarity=0.068 Sum_probs=138.4
Q ss_pred cHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHH
Q 046578 127 DYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAI 206 (379)
Q Consensus 127 ~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i 206 (379)
+..+++..+.+||..+++.||..|.|.|+++|+++.++..+++|++||+|+++|+++++|++. .+|.+|++.+++|.+
T Consensus 4 ~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~--~~~~~wl~~i~~n~~ 81 (176)
T PRK09638 4 DEKELIQKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGR--SKFSTWLISIASRLY 81 (176)
T ss_pred cHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHH
Confidence 456789999999999999999999999999999999999999999999999999999999864 489999999999999
Q ss_pred HHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcc
Q 046578 207 IRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTM 286 (379)
Q Consensus 207 ~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l 286 (379)
++++|+..+..... +. ..+
T Consensus 82 ~d~~r~~~~~~~~~------------------------------------------------------~~-~~~------ 100 (176)
T PRK09638 82 KDHLRKQKREKLRL------------------------------------------------------QR-AKE------ 100 (176)
T ss_pred HHHHHHhccccchh------------------------------------------------------hh-ccc------
Confidence 99999865310000 00 000
Q ss_pred cccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 046578 287 QDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQ 366 (379)
Q Consensus 287 ~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR 366 (379)
+ ..+.. .. +.....+....+..+|..||+++|+||.++|+ +|+|++|||+.||+|.++|++.++||+++||
T Consensus 101 -~-~~~~~--~~-~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~ 171 (176)
T PRK09638 101 -E-TLRKE--KW-EAAIKGAEWSEMLDALSKLDPEFRAPVILKHY----YGYTYEEIAKMLNIPEGTVKSRVHHGIKQLR 171 (176)
T ss_pred -c-cCCcc--ch-HHHHHhhhHHHHHHHHHcCCHHHhheeeehhh----cCCCHHHHHHHHCCChhHHHHHHHHHHHHHH
Confidence 0 00000 00 11222334456889999999999999999884 6799999999999999999999999999999
Q ss_pred hHHh
Q 046578 367 QTNI 370 (379)
Q Consensus 367 ~~l~ 370 (379)
+.+.
T Consensus 172 ~~l~ 175 (176)
T PRK09638 172 KEWG 175 (176)
T ss_pred HHhc
Confidence 9863
No 74
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=99.92 E-value=1.4e-23 Score=186.47 Aligned_cols=167 Identities=13% Similarity=0.094 Sum_probs=133.1
Q ss_pred hcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcC
Q 046578 136 LCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSR 215 (379)
Q Consensus 136 ~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r 215 (379)
..+|+.+++.||..|.+.++++|.++.++..++||++||+|+.+|+..++|++.. ..|.+|++++++|.+++++|++.+
T Consensus 4 ~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~~~~~~~~~~-~~~~~wL~~iarn~~~d~~Rk~~~ 82 (173)
T PRK09645 4 ATAEAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTG-RSARAWLFTVARNLVIDERRSARA 82 (173)
T ss_pred CcchHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHHHHHHHhhcc
Confidence 4579999999999999999999999999989999999999999999999997432 479999999999999999997652
Q ss_pred cccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCC
Q 046578 216 TIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDE 295 (379)
Q Consensus 216 ~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~ 295 (379)
... ...+. . .+ .++
T Consensus 83 ~~~-----------------------------------------------------~~~~~------~---~~-~~~--- 96 (173)
T PRK09645 83 RPV-----------------------------------------------------EGGDD------V---LG-VPE--- 96 (173)
T ss_pred ccc-----------------------------------------------------ccccc------c---cc-CCC---
Confidence 100 00000 0 00 000
Q ss_pred CChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhch
Q 046578 296 TMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN 373 (379)
Q Consensus 296 ~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~ 373 (379)
..+.+.+...+....|..+|+.||+++|+||.|+|+ +|+|++|||+.||+|.++|+++++||+++||+.+...+
T Consensus 97 ~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~L~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~ 170 (173)
T PRK09645 97 QSAPDEVDRALDRLLVADALAQLSPEHRAVLVRSYY----RGWSTAQIAADLGIPEGTVKSRLHYALRALRLALQERG 170 (173)
T ss_pred CCCchHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhccc
Confidence 111222333334457889999999999999999995 77999999999999999999999999999999987543
No 75
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=99.91 E-value=2.3e-23 Score=186.70 Aligned_cols=174 Identities=11% Similarity=0.153 Sum_probs=132.1
Q ss_pred cHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCC-----CHHHHHHHHHHHHHH-HHhccCCCCCCCchhHHHH
Q 046578 127 DYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGL-----SLKDLIQEGSIGLLR-GAKRFNPERGYKLSTYVYW 200 (379)
Q Consensus 127 ~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~-----d~eDLvQEg~i~L~~-ai~~fD~~~g~~FsTYa~~ 200 (379)
...+++..++.||..|++.||..|.+.++.+|.++.++.. +++|++||+|+.+|+ ..++|++. ..|.+|++.
T Consensus 3 ~~~~li~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~--~~~~~wl~~ 80 (183)
T TIGR02999 3 PVTELLQQWQNGDAAARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR--AHFFAAAAK 80 (183)
T ss_pred cHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCCch--HHHHHHHHH
Confidence 3578899999999999999999999999999999998877 899999999999998 77888754 379999999
Q ss_pred HHHHHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCcccc
Q 046578 201 WIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTD 280 (379)
Q Consensus 201 ~Ir~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~ 280 (379)
+++|.+++++|+..+..+.. . ..+.
T Consensus 81 i~~n~~~d~~R~~~~~~~~~-------------------------------------------------~--~~~~---- 105 (183)
T TIGR02999 81 AMRRILVDHARRRRAQKRGG-------------------------------------------------G--AVRV---- 105 (183)
T ss_pred HHHHHHHHHHHHHHHHhccC-------------------------------------------------C--cccc----
Confidence 99999999999754210000 0 0000
Q ss_pred CCCCcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 281 RGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 281 ~~~~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.+.+..+. . .++.. ........+...|++||+++|+||.|+|+ +|+|++|||+.||+|.+||+.+++|
T Consensus 106 ----~~~~~~~~-~--~~~~~-~~~~~l~~~~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tVk~~l~R 173 (183)
T TIGR02999 106 ----PLDEVLPD-A--EADLD-EELLDLDDALDKLAQVDPRQAEVVELRFF----AGLTVEEIAELLGVSVRTVERDWRF 173 (183)
T ss_pred ----ccccccCC-C--CccHH-HHHHHHHHHHHHhhcCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 00000000 0 11111 11111223445567799999999999995 7799999999999999999999999
Q ss_pred HHHHHHhHH
Q 046578 361 ALTKLQQTN 369 (379)
Q Consensus 361 Al~kLR~~l 369 (379)
|+++||+.+
T Consensus 174 ar~~Lr~~l 182 (183)
T TIGR02999 174 ARAWLADEL 182 (183)
T ss_pred HHHHHHHHh
Confidence 999999986
No 76
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=99.91 E-value=1.3e-23 Score=186.91 Aligned_cols=172 Identities=19% Similarity=0.194 Sum_probs=134.8
Q ss_pred HHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHH
Q 046578 131 VKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAI 210 (379)
Q Consensus 131 Li~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~l 210 (379)
++.+++.||..+++.+|..|.|.|+.+++++.+ ..++||++||+|+.+|+.++.|++. .+|.+|++++++|.++|++
T Consensus 1 l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~ 77 (175)
T PRK12518 1 LILRCQRGDRQSFRQLYRRYQQKVRSTLYQLCG-RELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATDAR 77 (175)
T ss_pred ChhHHHcCCHHHHHHHHHHHHHHHHHHHHHHcC-HhHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHHHH
Confidence 467889999999999999999999999999874 4789999999999999999999864 3799999999999999999
Q ss_pred HhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccC
Q 046578 211 ANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDII 290 (379)
Q Consensus 211 r~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i 290 (379)
|+..+... . .+... . . ..
T Consensus 78 R~~~~~~~----------------------------------------------------~--~~~~~-~--~---~~-- 95 (175)
T PRK12518 78 RQFAQRPS----------------------------------------------------R--IQDDS-L--N---DQ-- 95 (175)
T ss_pred HHhhcccc----------------------------------------------------c--hhccc-c--c---cc--
Confidence 97542000 0 00000 0 0 00
Q ss_pred CCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHh
Q 046578 291 PGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNI 370 (379)
Q Consensus 291 ~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~ 370 (379)
+......++ ....+....+..+++.||+++|.||.++|+ +|+|++|||+.||+|.++|++.++||+++||+.+.
T Consensus 96 ~~~~~~~~~--~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~ 169 (175)
T PRK12518 96 PSRPSDTPD--LMQLHYQDLVQQGLQTLSLEHRAVLVLHDL----EDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQ 169 (175)
T ss_pred ccCCCCcHH--HHHHHHHHHHHHHHHhCCHHHeeeeeehHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 000111222 222233456889999999999999999984 77999999999999999999999999999999987
Q ss_pred hch
Q 046578 371 LNN 373 (379)
Q Consensus 371 ~~~ 373 (379)
..+
T Consensus 170 ~~~ 172 (175)
T PRK12518 170 QQG 172 (175)
T ss_pred hcc
Confidence 644
No 77
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=99.91 E-value=1.3e-23 Score=188.07 Aligned_cols=168 Identities=14% Similarity=0.105 Sum_probs=133.9
Q ss_pred HHhcccHHHHHHHHHHhHHHHHHHHHhccC--CCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHH
Q 046578 134 KILCKERESQERIIRSYRSLVVSIATGYQG--KGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIA 211 (379)
Q Consensus 134 ~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~--~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr 211 (379)
.+..||..+++.||..|.+.|+.++.+.++ +..++||++||+|+.+|+..+.|+......|.||++++++|.+++++|
T Consensus 6 ~~~~~d~~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~~R 85 (178)
T PRK12529 6 SCLSADRDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSWRR 85 (178)
T ss_pred cCCCCCHHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999999998666555 467899999999999999999997544457999999999999999998
Q ss_pred hhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCC
Q 046578 212 NKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIP 291 (379)
Q Consensus 212 ~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~ 291 (379)
+..+. . . ..+. ..+ ..
T Consensus 86 k~~~~---~-------------------------------------------------~--~~~~---------~~~-~~ 101 (178)
T PRK12529 86 RQSLE---L-------------------------------------------------A--WLEA---------LAT-LP 101 (178)
T ss_pred HHHHH---h-------------------------------------------------h--hhhH---------hhh-cc
Confidence 75310 0 0 0000 000 00
Q ss_pred CCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578 292 GPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN 369 (379)
Q Consensus 292 ~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l 369 (379)
....++|++.+...+....|..+|.+||+++|.||.|+|+ +|+|++|||+.||+|.+||+.+++||+.+|++.+
T Consensus 102 ~~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~~ 175 (178)
T PRK12529 102 EPLHPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMATL----DGMKQKDIAQALDIALPTVKKYIHQAYVTCLSLM 175 (178)
T ss_pred CcCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence 1112355666666666678999999999999999999985 7799999999999999999999999999999875
No 78
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=99.91 E-value=3.8e-23 Score=185.68 Aligned_cols=170 Identities=15% Similarity=0.226 Sum_probs=136.2
Q ss_pred HHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccC----CCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHH
Q 046578 128 YNLVKYKILCKERESQERIIRSYRSLVVSIATGYQG----KGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIK 203 (379)
Q Consensus 128 ~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~----~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir 203 (379)
+..++..+..||..|+++||..|.+.|+.+|.++++ +..+++|++||+|+.+|...++|+.. .+|.+|++.+++
T Consensus 9 ~~~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~--~~~~~wl~~i~r 86 (184)
T PRK12512 9 WTDLMRSANAGDAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWLFAIAR 86 (184)
T ss_pred HHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCcc--ccHHHHHHHHHH
Confidence 567899999999999999999999999999998875 35699999999999999999999863 379999999999
Q ss_pred HHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCC
Q 046578 204 QAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGC 283 (379)
Q Consensus 204 ~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~ 283 (379)
|.+.+++|++.+... ..++.
T Consensus 87 n~~~d~~Rr~~~~~~-----------------------------------------------------~~~~~------- 106 (184)
T PRK12512 87 NKLIDALRRRGRRVF-----------------------------------------------------VDIDD------- 106 (184)
T ss_pred HHHHHHHHhhccccc-----------------------------------------------------CCchh-------
Confidence 999999997653100 00110
Q ss_pred CcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578 284 MTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT 363 (379)
Q Consensus 284 ~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~ 363 (379)
..+.+++.. +.+ ......+..+|+.||+++++||.++|+ +|+|++|||+.||+|.++|+..++||++
T Consensus 107 --~~~~~~~~~---~~~----~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~l~is~~tV~~~l~ra~~ 173 (184)
T PRK12512 107 --FAETLPAEP---ATE----TLPAGDVGRHLETLPPRQRDVVQSISV----EGASIKETAAKLSMSEGAVRVALHRGLA 173 (184)
T ss_pred --ccccccccc---hhh----HHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 001111110 011 122345788999999999999999984 6799999999999999999999999999
Q ss_pred HHHhHHhhc
Q 046578 364 KLQQTNILN 372 (379)
Q Consensus 364 kLR~~l~~~ 372 (379)
+||+.+..+
T Consensus 174 ~Lr~~l~~~ 182 (184)
T PRK12512 174 ALAAKFRSE 182 (184)
T ss_pred HHHHHhhcC
Confidence 999998764
No 79
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=99.91 E-value=3.2e-23 Score=187.42 Aligned_cols=181 Identities=18% Similarity=0.193 Sum_probs=136.4
Q ss_pred HHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCc
Q 046578 142 SQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPG 221 (379)
Q Consensus 142 A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~ 221 (379)
++++||..|.+.|+.+|.+++++..++||++||+|+.+|+.+++|+.. .+|.+|++++++|.+++++|++.+......
T Consensus 3 ~~~~l~~~~~~~l~~~a~~~~~~~~~AeDivQevfl~~~~~~~~~~~~--~~~~~WL~~ia~n~~~d~~Rk~~r~~~~~~ 80 (191)
T PRK12520 3 IAPAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQ--SSLKTYLVGILKHKIIDAIRSGRREVRLSL 80 (191)
T ss_pred chHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--ccHHHHHHHHHHHHHHHHHHhhcCcCcccc
Confidence 689999999999999999999999999999999999999999999854 379999999999999999998764211110
Q ss_pred chHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHH
Q 046578 222 SMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERM 301 (379)
Q Consensus 222 ~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~ 301 (379)
... ......++ ++..... . ......++ ...+|++.
T Consensus 81 ~~~------------------~~~~~~~~-----------------------~~~~~~~--~-~~~~~~~~-~~~~~~~~ 115 (191)
T PRK12520 81 DDA------------------DEQSDDDL-----------------------FDALFAA--D-GHYREPPS-DWGDPDAA 115 (191)
T ss_pred ccc------------------ccchhhhh-----------------------hhhhccc--c-cccccCcc-ccCCHHHH
Confidence 000 00000000 0000000 0 00000111 12356777
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhch
Q 046578 302 VQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN 373 (379)
Q Consensus 302 ~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~ 373 (379)
+...+....|..+|.+||+++|.||.|+|+ +|+|++|||+.||+|.++|+++++||+++||+++...+
T Consensus 116 ~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 183 (191)
T PRK12520 116 LSRREFFEVLQACVDRLPPRTGRVFMMREW----LELETEEICQELQITATNAWVLLYRARMRLRECLDLHW 183 (191)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 777777788999999999999999999995 77999999999999999999999999999999998765
No 80
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=99.91 E-value=5.6e-23 Score=187.07 Aligned_cols=179 Identities=15% Similarity=0.101 Sum_probs=140.4
Q ss_pred hcCcCcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHH
Q 046578 122 ENGELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWW 201 (379)
Q Consensus 122 ~~~~~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~ 201 (379)
..++..+.+|+.++..||..+++.+|..|.+.++.+++ +.++..++||++||+|+.+|+...+|++. .+|.+|++.+
T Consensus 6 ~~~~~~~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~-~~~~~~~AEDivQevflkl~~~~~~~~~~--~~~~~WL~~I 82 (196)
T PRK12535 6 ERDDAHVTDLALAAGRGDRAALTEFIRETQDDVWRLLA-HLGGHDIADDLTQETYLRVMSALPRFAAR--SSARTWLLSL 82 (196)
T ss_pred ccccHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHHhhhcCCc--ccHHHHHHHH
Confidence 34566778999999999999999999999999999975 56788899999999999999999999863 3799999999
Q ss_pred HHHHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccC
Q 046578 202 IKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDR 281 (379)
Q Consensus 202 Ir~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~ 281 (379)
++|.+++++|+..+..+ ...+. ..
T Consensus 83 arn~~id~~Rk~~~~~~-----------------------------------------------------~~~~~-~~-- 106 (196)
T PRK12535 83 ARRVWVDNIRHDMARPR-----------------------------------------------------KSATE-YE-- 106 (196)
T ss_pred HHHHHHHHHHhhccCCC-----------------------------------------------------ccccc-cc--
Confidence 99999999998653100 00000 00
Q ss_pred CCCcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578 282 GCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 282 ~~~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
...+ . ...++..... +....+..+|+.||+++|+||.|+|+ +|+|++|||+.||+|.++|+++++||
T Consensus 107 ---~~~~---~--~~~~~~~~~~-~~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIAe~lgis~~tV~~~l~Ra 173 (196)
T PRK12535 107 ---DAAA---T--TASNETTGSW-SEWIDVRTLIDALPPERREALILTQV----LGYTYEEAAKIADVRVGTIRSRVARA 173 (196)
T ss_pred ---cccc---c--cCCcchhHHH-HHHHHHHHHHHcCCHHHHHHhhhHHH----hCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 0000 0 0111111111 12346889999999999999999995 77999999999999999999999999
Q ss_pred HHHHHhHHhhc
Q 046578 362 LTKLQQTNILN 372 (379)
Q Consensus 362 l~kLR~~l~~~ 372 (379)
+++||+.+...
T Consensus 174 r~~Lr~~l~~~ 184 (196)
T PRK12535 174 RADLIAATATG 184 (196)
T ss_pred HHHHHHHhccc
Confidence 99999997643
No 81
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=99.91 E-value=6.1e-23 Score=183.89 Aligned_cols=165 Identities=14% Similarity=0.159 Sum_probs=135.5
Q ss_pred ccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcc
Q 046578 138 KERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTI 217 (379)
Q Consensus 138 Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~i 217 (379)
.|+.|++++|..|.|.|+++|.++.++..+++|++||+|+.+|+++++|++. .+|.+|++.+++|.+.+++|+..+..
T Consensus 13 ~~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~--~~~~awl~~ia~n~~~d~~Rk~~~~~ 90 (179)
T PRK09415 13 DKEDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGK--SSLKTWLYRIAINHCKDYLKSWHNKK 90 (179)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--cccHHHHHHHHHHHHHHHHHhhcccc
Confidence 5788999999999999999999999999999999999999999999999864 37999999999999999999854210
Q ss_pred cCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCC
Q 046578 218 RLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETM 297 (379)
Q Consensus 218 rip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~ 297 (379)
. ...+. ...... ....+
T Consensus 91 ~-----------------------------------------------------~~~~~--------~~~~~~--~~~~~ 107 (179)
T PRK09415 91 V-----------------------------------------------------IVTED--------IFTYME--SQKES 107 (179)
T ss_pred c-----------------------------------------------------ccccc--------cccccc--ccccC
Confidence 0 00000 000000 11234
Q ss_pred hHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhh
Q 046578 298 PERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNIL 371 (379)
Q Consensus 298 pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~ 371 (379)
|++.+...+....+..+|.+||+++|+||.++|+ +|+|++|||+.||+|.++|+++++||+++||+.+..
T Consensus 108 ~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l~~ 177 (179)
T PRK09415 108 VEEEVIQNAEDERLASAVMSLPIKYREVIYLFYY----EELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLEE 177 (179)
T ss_pred cHHHHHHHHHHHHHHHHHHhCCHHHhhHhHhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 5666666677778999999999999999999984 779999999999999999999999999999998754
No 82
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=99.90 E-value=1.1e-22 Score=182.71 Aligned_cols=175 Identities=17% Similarity=0.235 Sum_probs=140.6
Q ss_pred HHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHH
Q 046578 130 LVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRA 209 (379)
Q Consensus 130 eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~ 209 (379)
.+......|+..++.+++..|.+.++.+++++.++..++|||+||+|+.+|+++..| .. +.+|.||++++++|.++|+
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~-~~~~~~wl~~Ia~n~~iD~ 81 (182)
T COG1595 4 LLLAEALRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RG-RSSFKAWLYRIARNLAIDR 81 (182)
T ss_pred HHHHHHHhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CC-CCchHHHHHHHHHHHHHHH
Confidence 456778899999999999999999999999999998899999999999999999999 33 3489999999999999999
Q ss_pred HHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCccccc
Q 046578 210 IANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDI 289 (379)
Q Consensus 210 lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~ 289 (379)
+|+.++.... .+. .+. .+.
T Consensus 82 ~R~~~r~~~~------------------------------------------------------~~~----~~~---~~~ 100 (182)
T COG1595 82 LRKRKRRRAR------------------------------------------------------VEE----ADL---LPE 100 (182)
T ss_pred HHHhcccccc------------------------------------------------------ccc----ccc---ccc
Confidence 9987642110 000 000 000
Q ss_pred CCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578 290 IPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN 369 (379)
Q Consensus 290 i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l 369 (379)
......... +.+...+....+..+|..||+++|++|.|+|+ +|+|++|||+.||||.+||+++++||+++||+.+
T Consensus 101 ~~~~~~~~~-~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~~----~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l 175 (182)
T COG1595 101 EADPAPDLA-ELLLAEEELERLRRALARLPPRQREAFLLRYL----EGLSYEEIAEILGISVGTVKSRLHRARKKLREQL 175 (182)
T ss_pred ccCcccccc-hHHHHHHHHHHHHHHHHhCCHHHhHHhhhHhh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 000000000 24555666788999999999999999999994 7799999999999999999999999999999998
Q ss_pred hhc
Q 046578 370 ILN 372 (379)
Q Consensus 370 ~~~ 372 (379)
...
T Consensus 176 ~~~ 178 (182)
T COG1595 176 EEA 178 (182)
T ss_pred hhc
Confidence 754
No 83
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=99.90 E-value=1e-22 Score=181.28 Aligned_cols=167 Identities=15% Similarity=0.160 Sum_probs=130.8
Q ss_pred HHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCC
Q 046578 141 ESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLP 220 (379)
Q Consensus 141 ~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip 220 (379)
..+++++..|.++|+.+|+++.++..++||++||+|+.+|+++++|++.. +|.+|++.+++|.+.+++|++.+....+
T Consensus 3 ~~~~~l~~~y~~~i~~~~~~~~~~~~daeDvvQe~~i~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~Rk~~~~~~~~ 80 (173)
T PRK12522 3 EKVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVE--NYKKWITTICVRTFYDFYRKKKRWKDRI 80 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcCCcc--chHHHHHHHHHHHHHHHHHHhccccccc
Confidence 46899999999999999999999999999999999999999999998753 7999999999999999999866310000
Q ss_pred cchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHH
Q 046578 221 GSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPER 300 (379)
Q Consensus 221 ~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~ 300 (379)
.. ..+. +. ..+.........++.
T Consensus 81 ~~--------------------------------------------------~~~~----~~---~~~~~~~~~~~~~~~ 103 (173)
T PRK12522 81 LD--------------------------------------------------LFHK----ED---GGEIEFADDVNISEE 103 (173)
T ss_pred cc--------------------------------------------------ccch----hh---hhhhccccCCCChHH
Confidence 00 0000 00 000000011112333
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhh
Q 046578 301 MVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNIL 371 (379)
Q Consensus 301 ~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~ 371 (379)
....+..+.+..++..||+++++||.++|. +|+|++|||+.||+|.++|+.+++||+++||+.+..
T Consensus 104 -~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~ 169 (173)
T PRK12522 104 -FIQKVEAEMIREVIQLLNEKYKTVLVLYYY----EQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHLEG 169 (173)
T ss_pred -HHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 444556678999999999999999999984 779999999999999999999999999999999754
No 84
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) 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 in an apparent operon.
Probab=99.90 E-value=4.4e-23 Score=186.86 Aligned_cols=177 Identities=16% Similarity=0.149 Sum_probs=134.0
Q ss_pred HhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhc
Q 046578 135 ILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKS 214 (379)
Q Consensus 135 ~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~ 214 (379)
...++..+|+.|+..|.+.|+.+|.+++++..++||++||+|+.+|+.+.+|++. .+|.+|++++++|.+++++|++.
T Consensus 5 ~~~~~~~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~~~~~~~~~--~~~~~wL~~iarN~~~d~~Rk~~ 82 (193)
T TIGR02947 5 TKTQRAQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPG--TNLKAWLYRILTNTYINSYRKAQ 82 (193)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcccCCC--CcchHHHHHHHHHHHHHHHHHhc
Confidence 4457789999999999999999999999999999999999999999999999864 37999999999999999999865
Q ss_pred CcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCC
Q 046578 215 RTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPD 294 (379)
Q Consensus 215 r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~ 294 (379)
+..... ......+.......+ .....
T Consensus 83 ~~~~~~-----------------------------------------------------~~~~~~~~~~~~~~~-~~~~~ 108 (193)
T TIGR02947 83 RRPQQS-----------------------------------------------------DDDDIEDWQLAKAAS-HTSNG 108 (193)
T ss_pred CCcccc-----------------------------------------------------cchhhhhhhhccccc-ccccc
Confidence 311000 000000000000000 00001
Q ss_pred CCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhh
Q 046578 295 ETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNIL 371 (379)
Q Consensus 295 ~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~ 371 (379)
...++......+....|..+|.+||+++|+||.|+|+ +|+|++|||+.||+|.++|+++++||+++||+.+..
T Consensus 109 ~~~~e~~~~~~~~~~~l~~~l~~Lp~~~r~i~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~ 181 (193)
T TIGR02947 109 LRSAELEALDGLPDQDIKDALQGLPEEFRQAVYLADV----EGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLVD 181 (193)
T ss_pred ccchhHHHHhhhhHHHHHHHHHhCCHHHhhheeehhh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 1123333333344567899999999999999999984 779999999999999999999999999999999864
No 85
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=99.90 E-value=4.3e-23 Score=183.53 Aligned_cols=167 Identities=15% Similarity=0.093 Sum_probs=132.4
Q ss_pred HhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhc
Q 046578 135 ILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKS 214 (379)
Q Consensus 135 ~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~ 214 (379)
.++||..++..+|..|.+.|+.+|.+++++..++||++||+|+.+|+. ..|... ..|.+|++++++|.+++++|++.
T Consensus 4 ~~~~~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~~~d~~Rk~~ 80 (172)
T PRK12523 4 AQSPHSELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRRAA 80 (172)
T ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHHHHHHHHHHH
Confidence 478999999999999999999999999999999999999999999986 456543 37999999999999999999854
Q ss_pred CcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCC
Q 046578 215 RTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPD 294 (379)
Q Consensus 215 r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~ 294 (379)
+.. . .... +.. .....
T Consensus 81 ~~~-----------~-------~~~~---------------------------------~~~-------------~~~~~ 96 (172)
T PRK12523 81 LEQ-----------A-------YLAE---------------------------------LAL-------------VPEAE 96 (172)
T ss_pred HHH-----------H-------HHHH---------------------------------Hhh-------------ccccc
Confidence 200 0 0000 000 00001
Q ss_pred CCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhc
Q 046578 295 ETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILN 372 (379)
Q Consensus 295 ~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~ 372 (379)
...|+......+....+..+|..||+++|.||.|+|+ +|+|++|||+.||+|.++|+++++||+++||..+..+
T Consensus 97 ~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~L~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l~~~ 170 (172)
T PRK12523 97 QPSPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRL----DGMGHAEIAERLGVSVSRVRQYLAQGLRQCYIALYGE 170 (172)
T ss_pred CCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcCC
Confidence 1234444444444567999999999999999999995 7799999999999999999999999999999988654
No 86
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=99.90 E-value=1.6e-22 Score=182.76 Aligned_cols=163 Identities=12% Similarity=0.181 Sum_probs=130.3
Q ss_pred cccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCc
Q 046578 137 CKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRT 216 (379)
Q Consensus 137 ~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~ 216 (379)
-||..+++++|..|.+.++.+|.+++++..++||++||+|+.+|+..++|+.. ..|.+|++++++|.+++++|++.+.
T Consensus 6 ~~~~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~awL~~Ia~n~~~d~~R~~~~~ 83 (187)
T PRK12516 6 VEGTPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVG--TNMKAWLFTILRNEFYSQMRKRGRE 83 (187)
T ss_pred cccHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCc--ccHHHHHHHHHHHHHHHHHHhhcCC
Confidence 36889999999999999999999999999999999999999999999999854 3699999999999999999986531
Q ss_pred ccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCC
Q 046578 217 IRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDET 296 (379)
Q Consensus 217 irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~ 296 (379)
. ...+.. ..+.... .+
T Consensus 84 ~------------------------------------------------------~~~~~~--------~~~~~~~--~~ 99 (187)
T PRK12516 84 V------------------------------------------------------QDTDGM--------FTEQLAV--HP 99 (187)
T ss_pred c------------------------------------------------------cccccc--------cccccCC--Cc
Confidence 0 000000 0000000 00
Q ss_pred ChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhch
Q 046578 297 MPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN 373 (379)
Q Consensus 297 ~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~ 373 (379)
... .......+..+|..||+++|+||.|+|+ +|+|++|||+.||+|.++|+++++||+++||+.+...+
T Consensus 100 ~~~----~~~~~~~l~~~L~~Lp~~~r~i~~L~~~----~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~~~ 168 (187)
T PRK12516 100 SQY----GTLDLQDFRAALDQLPDDQREAIILVGA----SGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQIEG 168 (187)
T ss_pred chh----hHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhc
Confidence 111 1112346889999999999999999984 77999999999999999999999999999999997654
No 87
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=99.90 E-value=1.1e-22 Score=178.77 Aligned_cols=160 Identities=14% Similarity=0.131 Sum_probs=130.1
Q ss_pred hcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcC
Q 046578 136 LCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSR 215 (379)
Q Consensus 136 ~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r 215 (379)
++||..+++.+|..|.+.|+.++.++.++..+++|++||+|+.+|+.+++|+. ...|.+|++.+++|.+++++|+..+
T Consensus 1 ~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~--~~~~~~wl~~i~~n~~~d~~rk~~~ 78 (162)
T TIGR02983 1 RSATEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRD--PDAPDAYVRRVLVNLARSRWRRRRL 78 (162)
T ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCC--cccHHHHHHHHHHHHHHHHHHhhcc
Confidence 37999999999999999999999999999999999999999999999999964 3489999999999999999997652
Q ss_pred cccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCC
Q 046578 216 TIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDE 295 (379)
Q Consensus 216 ~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~ 295 (379)
. . ...+. ..+ . ..
T Consensus 79 ~-~-----------------------------------------------------~~~~~---------~~~---~-~~ 91 (162)
T TIGR02983 79 L-E-----------------------------------------------------LPTRE---------LPD---A-AA 91 (162)
T ss_pred c-c-----------------------------------------------------ccccc---------cCc---c-cC
Confidence 0 0 00000 000 0 00
Q ss_pred CChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhh
Q 046578 296 TMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNIL 371 (379)
Q Consensus 296 ~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~ 371 (379)
.+.....+....|..++..||+++|+||.++|+ +|+|++|||+.||+|.++|+++++||+++||+.+..
T Consensus 92 ---~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~~ 160 (162)
T TIGR02983 92 ---PDPAPDVALRAALARALRRLPARQRAVVVLRYY----EDLSEAQVAEALGISVGTVKSRLSRALARLRELLEE 160 (162)
T ss_pred ---CccchhHHHHHHHHHHHHhCCHHHHHHhhhHHH----hcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 001122334466889999999999999999984 679999999999999999999999999999998754
No 88
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=99.90 E-value=2.6e-22 Score=185.33 Aligned_cols=173 Identities=13% Similarity=0.133 Sum_probs=137.9
Q ss_pred cccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCc
Q 046578 137 CKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRT 216 (379)
Q Consensus 137 ~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~ 216 (379)
.....+++.||..|.+.+++++.++.++..++||++||+|+.+|+.+++|++ + .|.+|++++++|.+++++|++.+.
T Consensus 14 ~~~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~--~-~~~aWL~~IarN~~~d~~Rk~~~~ 90 (216)
T PRK12533 14 AARGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRG--D-NARPWLLAIVRHTWYSEWRRRANA 90 (216)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCc--c-chHhHHHHHHHHHHHHHHHhhccc
Confidence 3567899999999999999999999999999999999999999999999975 2 599999999999999999986531
Q ss_pred ccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCC
Q 046578 217 IRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDET 296 (379)
Q Consensus 217 irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~ 296 (379)
... ...+. ..+.. .... . .+...
T Consensus 91 ~~~----------------------------------------------------~~~~~-~~~~~--~~~~-~-~~~~~ 113 (216)
T PRK12533 91 HEV----------------------------------------------------AAPDT-LDDAD--SLDD-W-QPAGE 113 (216)
T ss_pred ccc----------------------------------------------------ccccc-ccccc--cccc-c-ccCCC
Confidence 000 00000 00000 0000 0 11123
Q ss_pred ChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhch
Q 046578 297 MPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN 373 (379)
Q Consensus 297 ~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~ 373 (379)
+|++.+...+....|..+|..||+++|+||.|+|+ +++|++|||+.||||.++|+++++||+++||+.+....
T Consensus 114 ~~e~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y~----eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~~~ 186 (216)
T PRK12533 114 DPLALLLRAEDVRLVNAALAKLPVEYREVLVLREL----EDMSYREIAAIADVPVGTVMSRLARARRRLAALLGGAS 186 (216)
T ss_pred CHHHHHHHHHHHHHHHHHHHcCCHHHHhHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcccc
Confidence 56777777777888999999999999999999984 77999999999999999999999999999999986543
No 89
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=99.90 E-value=2.9e-22 Score=196.88 Aligned_cols=183 Identities=19% Similarity=0.236 Sum_probs=142.2
Q ss_pred HHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHH
Q 046578 128 YNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAII 207 (379)
Q Consensus 128 ~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~ 207 (379)
..+|+.++++||..++++||+.|.+.|+++|.+++++..++||++||+|+.+|+.+++|++. .+|.+|++++++|.++
T Consensus 6 ~~~l~~~~~~gd~~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~ 83 (339)
T PRK08241 6 AAALLARAAAGDRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGR--SSLRTWLYRIATNVCL 83 (339)
T ss_pred HHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhhhccccc--cchHHHHHHHHHHHHH
Confidence 36899999999999999999999999999999999999999999999999999999999853 3799999999999999
Q ss_pred HHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccC-C----
Q 046578 208 RAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDR-G---- 282 (379)
Q Consensus 208 ~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~-~---- 282 (379)
+++|++.+... + ...+.+..+. +
T Consensus 84 d~~Rk~~~~~~-~---------------------------------------------------~~~~~~~~~~~~~~~~ 111 (339)
T PRK08241 84 DALEGRARRPL-P---------------------------------------------------TDLGAPAADPVDELVE 111 (339)
T ss_pred HHHHhhccccC-c---------------------------------------------------cccCCCcCcccccccc
Confidence 99998653100 0 0000000000 0
Q ss_pred --CCcccccCCC----CCCCChHHHHHHHH-HHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHH
Q 046578 283 --CMTMQDIIPG----PDETMPERMVQKQL-MKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIR 355 (379)
Q Consensus 283 --~~~l~d~i~~----~~~~~pe~~~~~~e-~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr 355 (379)
...+.+.+.+ ....+|++.+...+ ....+..+|.+||+++|+||.|+|+ +|+|++|||+.||+|.++|+
T Consensus 112 ~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tVk 187 (339)
T PRK08241 112 RPEVPWLEPYPDALLDPAAADPAARVVARESVRLAFVAALQHLPPRQRAVLILRDV----LGWSAAEVAELLDTSVAAVN 187 (339)
T ss_pred cccccccCCCCcccccccCCChHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhHHh----hCCCHHHHHHHhCCCHHHHH
Confidence 0001111111 01235666555444 3456889999999999999999994 77999999999999999999
Q ss_pred HHHHHHHHHHHhH
Q 046578 356 QIRGIALTKLQQT 368 (379)
Q Consensus 356 ~~~~rAl~kLR~~ 368 (379)
++++||+++||+.
T Consensus 188 ~~l~RAr~~Lr~~ 200 (339)
T PRK08241 188 SALQRARATLAER 200 (339)
T ss_pred HHHHHHHHHHhhc
Confidence 9999999999993
No 90
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=99.90 E-value=4.4e-22 Score=182.17 Aligned_cols=167 Identities=20% Similarity=0.267 Sum_probs=137.8
Q ss_pred hcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcC
Q 046578 136 LCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSR 215 (379)
Q Consensus 136 ~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r 215 (379)
..||..+++++|..|.+.|+.++.++.++..++||++||+|+.+|+...+|++ + +|.+|++++++|.+++++|+..+
T Consensus 23 ~~~d~~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~~~d~~Rk~~~ 99 (203)
T PRK09647 23 DKATMPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNLFLDMVRRRAR 99 (203)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHHHHHHHHhccc
Confidence 45899999999999999999999999999999999999999999999999974 3 69999999999999999998642
Q ss_pred cccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCC
Q 046578 216 TIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDE 295 (379)
Q Consensus 216 ~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~ 295 (379)
.+. ..++. + . +... ...
T Consensus 100 -~~~----------------------------------------------------~~~~~-----~---~-~~~~-~~~ 116 (203)
T PRK09647 100 -IRM----------------------------------------------------EALPE-----D---Y-DRVP-GDE 116 (203)
T ss_pred -Ccc----------------------------------------------------ccccc-----c---c-cccC-CCC
Confidence 000 00000 0 0 0011 122
Q ss_pred CChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhc
Q 046578 296 TMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILN 372 (379)
Q Consensus 296 ~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~ 372 (379)
.+|+..+...+....|..+|..||++++.||.|+|+ +|++++|||+.||+|.++|++.++||+++||+.+...
T Consensus 117 ~~~~~~~~~~~~~~~l~~~L~~L~~~~r~v~~L~~~----~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~~~ 189 (203)
T PRK09647 117 PNPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDI----EGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALAAH 189 (203)
T ss_pred CCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 355666667777778999999999999999999985 7799999999999999999999999999999998653
No 91
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=99.90 E-value=1.3e-22 Score=177.56 Aligned_cols=159 Identities=13% Similarity=0.184 Sum_probs=125.6
Q ss_pred HHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCC
Q 046578 141 ESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLP 220 (379)
Q Consensus 141 ~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip 220 (379)
++++.++..|.|.|+++++++.++..++||++||+|+.+|+++++|++.. .|.+|++++++|.+++++|++.+... +
T Consensus 1 ~~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~-~ 77 (159)
T TIGR02989 1 EAFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRDRL-V 77 (159)
T ss_pred CHHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhccccc-c
Confidence 37899999999999999999999999999999999999999999998653 69999999999999999998763110 0
Q ss_pred cchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHH
Q 046578 221 GSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPER 300 (379)
Q Consensus 221 ~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~ 300 (379)
++.. ..+.+.+.. ++.+
T Consensus 78 -----------------------------------------------------~~~~--------~~~~~~~~~--~~~~ 94 (159)
T TIGR02989 78 -----------------------------------------------------FDDE--------LLEALAAEA--EATE 94 (159)
T ss_pred -----------------------------------------------------cCHH--------HHHHHHhhc--ccch
Confidence 0000 000000000 1111
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578 301 MVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN 369 (379)
Q Consensus 301 ~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l 369 (379)
.....+....+..+++.||++++.||.++|+ +|+|++|||+.||+|.++|++.++||+++||+++
T Consensus 95 ~~~~~~~~~~l~~~i~~L~~~~r~v~~l~~~----~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~~~ 159 (159)
T TIGR02989 95 ADRSEDELQALEGCLEKLPERQRELLQLRYQ----RGVSLTALAEQLGRTVNAVYKALSRLRVRLRDCV 159 (159)
T ss_pred HhhHHHHHHHHHHHHHHCCHHHHHHHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcC
Confidence 1223334467889999999999999999884 6799999999999999999999999999999864
No 92
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=99.89 E-value=1.7e-22 Score=176.15 Aligned_cols=161 Identities=17% Similarity=0.214 Sum_probs=129.7
Q ss_pred HHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCC
Q 046578 141 ESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLP 220 (379)
Q Consensus 141 ~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip 220 (379)
.|+++|+..|.|.|+++++++.++..++||++||+|+++|+++++|++. .+|.+|++.++++.+.+++++..+...
T Consensus 1 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~--~~~~~wl~~i~r~~~~d~~r~~~~~~~-- 76 (161)
T TIGR02985 1 KAFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEV--ESFKAYLFTIVKNRSLNYLRHKQVEEK-- 76 (161)
T ss_pred ChHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc--ccHHHHHHHHHHHHHHHHHHHHHhHhH--
Confidence 3789999999999999999999998999999999999999999999864 379999999999999999997652000
Q ss_pred cchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHH
Q 046578 221 GSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPER 300 (379)
Q Consensus 221 ~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~ 300 (379)
.... + .+... ......++++
T Consensus 77 ----------------~~~~---------------------------------~----~~~~~-------~~~~~~~~~~ 96 (161)
T TIGR02985 77 ----------------YQEE---------------------------------I----LEIEV-------DELSENDPEE 96 (161)
T ss_pred ----------------HHHH---------------------------------H----Hhhcc-------cccCCCCcHH
Confidence 0000 0 00000 0001124555
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578 301 MVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN 369 (379)
Q Consensus 301 ~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l 369 (379)
.+...+....+..++..||+++++||.++|. +|+|.+|||+.||+|+++|+++++||+++||+.|
T Consensus 97 ~~~~~e~~~~l~~~l~~L~~~~r~il~l~~~----~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~~l 161 (161)
T TIGR02985 97 ELEAKELQLIIYKAIEKLPEQCRKIFILSRF----EGKSYKEIAEELGISVKTVEYHISKALKELRKEL 161 (161)
T ss_pred HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 6666677778999999999999999999884 6799999999999999999999999999999864
No 93
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=99.89 E-value=2.1e-22 Score=176.68 Aligned_cols=156 Identities=16% Similarity=0.128 Sum_probs=125.8
Q ss_pred HHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcchHHHH
Q 046578 148 RSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMV 227 (379)
Q Consensus 148 ~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~~~~~~ 227 (379)
+.|.+.|+.+|.+++++..++||++||+|+.+|+++++|++. .|.+|++++++|.++|++|+..+...
T Consensus 2 ~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wl~~ia~n~~~d~~Rk~~~~~~--------- 69 (160)
T PRK09642 2 QTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFR---GLKTWMARIATNHAIDYKRKKARENE--------- 69 (160)
T ss_pred chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcccccccc---hhHHHHHHHHHHHHHHHHHHhccccc---------
Confidence 579999999999999999999999999999999999999852 59999999999999999998653100
Q ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHHHHHHHH
Q 046578 228 AKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLM 307 (379)
Q Consensus 228 ~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~~~~~e~ 307 (379)
...... + ..+... ....+++.+...+.
T Consensus 70 -------------------------------------------~~~~~~----~----~~~~~~--~~~~~~~~~~~~e~ 96 (160)
T PRK09642 70 -------------------------------------------ELSLCK----E----TEENIK--SSHNIEDLLLTKEQ 96 (160)
T ss_pred -------------------------------------------ccccch----h----hhhhcc--CCCChHHHHHHHHH
Confidence 000000 0 000000 12245566666677
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhc
Q 046578 308 KQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILN 372 (379)
Q Consensus 308 ~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~ 372 (379)
...+..+|+.||+.+|.||.++|+ +|+|++|||+.||+|.++|+++++||+++||+.+...
T Consensus 97 ~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 157 (160)
T PRK09642 97 KLLIAQKLRELPENYRDVVLAHYL----EEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKEE 157 (160)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhh
Confidence 778999999999999999999994 7799999999999999999999999999999998654
No 94
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=99.89 E-value=5.9e-22 Score=193.37 Aligned_cols=184 Identities=17% Similarity=0.181 Sum_probs=136.3
Q ss_pred cccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCc
Q 046578 137 CKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRT 216 (379)
Q Consensus 137 ~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~ 216 (379)
.||..++++||..|.+.|+++|.+++++..++||++||+|+.+|+.+++|+.. .+|.+|++++++|.++|++|++.+.
T Consensus 1 ~gd~~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~~~ 78 (324)
T TIGR02960 1 SVDGAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGR--SSVRTWLYRIATNACLDALEARQRR 78 (324)
T ss_pred CCcHHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCcc--cchHHHHHHHHHHHHHHHHHhccCC
Confidence 48999999999999999999999999999999999999999999999999864 3799999999999999999986531
Q ss_pred ccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCC-----
Q 046578 217 IRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIP----- 291 (379)
Q Consensus 217 irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~----- 291 (379)
....... ......... ..++......+.++
T Consensus 79 ~~~~~~~--------------------------------------------~~~~~~~~~-~~~~~~~~~~~~~~~~~~~ 113 (324)
T TIGR02960 79 PRPVGLG--------------------------------------------APSADGTAA-ASEAAEVTWLEPLPDLTLD 113 (324)
T ss_pred cCccccC--------------------------------------------CCCCccccc-ccccccccccCCCCccccc
Confidence 1000000 000000000 00000000000000
Q ss_pred --CCCCCChHHHHHHHH-HHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 292 --GPDETMPERMVQKQL-MKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 292 --~~~~~~pe~~~~~~e-~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
.....+|++.+...+ ....+..+|.+||+++|.||.|+|+ +++|++|||+.||+|.++|+++++||+++||++
T Consensus 114 ~~~~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 189 (324)
T TIGR02960 114 LDDPAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRDV----LGWRAAETAELLGTSTASVNSALQRARATLDEV 189 (324)
T ss_pred cccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 111235666555444 4456889999999999999999995 779999999999999999999999999999999
Q ss_pred Hhh
Q 046578 369 NIL 371 (379)
Q Consensus 369 l~~ 371 (379)
+..
T Consensus 190 l~~ 192 (324)
T TIGR02960 190 GPS 192 (324)
T ss_pred ccc
Confidence 874
No 95
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=99.89 E-value=6.2e-22 Score=174.83 Aligned_cols=158 Identities=15% Similarity=0.127 Sum_probs=130.7
Q ss_pred HHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcc
Q 046578 143 QERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGS 222 (379)
Q Consensus 143 ~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~ 222 (379)
++.||+.|.|.|+++|+++.++..++||++||+|+.+|+++++|++. .|.+|++++++|.+.+++|+..+.....
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wL~~i~~n~~~d~~R~~~~~~~~~-- 77 (165)
T PRK09644 3 IEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYHTFIDFVRKEKKVSFVG-- 77 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc---chHHHHHHHHHHHHHHHHHhhhhccccc--
Confidence 68899999999999999999999999999999999999999999852 6999999999999999999865310000
Q ss_pred hHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHHH
Q 046578 223 MAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMV 302 (379)
Q Consensus 223 ~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~~ 302 (379)
.+ .+ +.+. ..+|++.+
T Consensus 78 ---------------------------------------------------------~~---~~-~~~~---~~~~~~~~ 93 (165)
T PRK09644 78 ---------------------------------------------------------TD---EI-EAIQ---AESTEEYV 93 (165)
T ss_pred ---------------------------------------------------------hh---HH-hhhc---ccChHHHH
Confidence 00 00 0000 12355555
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhch
Q 046578 303 QKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN 373 (379)
Q Consensus 303 ~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~ 373 (379)
...+....+..++..||+++|++|.++|+ +|+|++|||+.||+|.++|+++++||+++||+.+....
T Consensus 94 ~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~~~ 160 (165)
T PRK09644 94 VAKNSYEKLIQIIHTLPVIEAQAILLCDV----HELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKEEK 160 (165)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHhHHH----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhh
Confidence 66666778999999999999999999984 77999999999999999999999999999999987554
No 96
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=99.89 E-value=9.2e-22 Score=172.95 Aligned_cols=158 Identities=15% Similarity=0.140 Sum_probs=125.8
Q ss_pred ccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcc
Q 046578 138 KERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTI 217 (379)
Q Consensus 138 Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~i 217 (379)
|+..+++++|..|.+.|+.+|.++.++..++||++||+|+.+|+.+++|++. +|.||++++++|.+++++|+..+..
T Consensus 2 ~~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDv~Qe~f~~~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~~ 78 (161)
T PRK12541 2 KRKQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE---EIRPWLFTIAYNAFIDWYRKEKKYK 78 (161)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhHHHccCC---ChHHHHHHHHHHHHHHHHHhccccc
Confidence 6788999999999999999999999999999999999999999999999853 5999999999999999999865310
Q ss_pred cCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCC
Q 046578 218 RLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETM 297 (379)
Q Consensus 218 rip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~ 297 (379)
. ...+. . . .......
T Consensus 79 ~-----------------------------------------------------~~~~~---------~-~--~~~~~~~ 93 (161)
T PRK12541 79 T-----------------------------------------------------TTIEE---------F-H--LPNVPST 93 (161)
T ss_pred c-----------------------------------------------------cchhh---------h-h--ccCCCCc
Confidence 0 00000 0 0 0000111
Q ss_pred hHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 298 PERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 298 pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
+++.....+. ..+..++..||+++|.||.|+|+ +|+|++|||+.||+|.++|++.++||+++||+.
T Consensus 94 ~~~~~~~~~~-~~~~~~l~~L~~~~r~v~~l~~~----~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 94 EHEYFIKHEI-ASWLDSLSSLPLERRNVLLLRDY----YGFSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred HHHHHHHhHH-HHHHHHHHHCCHHHHHHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 2222333333 34568899999999999999984 679999999999999999999999999999975
No 97
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=99.88 E-value=1.3e-21 Score=176.78 Aligned_cols=172 Identities=19% Similarity=0.201 Sum_probs=134.2
Q ss_pred HHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcchH
Q 046578 145 RIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMA 224 (379)
Q Consensus 145 ~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~~~ 224 (379)
+.+..|.+.|+.+|++++++..++||++||+|+.+|+...+|++. .+|.+|++++++|.+++++|++.+....+
T Consensus 6 ~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R~~~r~~~~~---- 79 (188)
T TIGR02943 6 QELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKNKIIDALRAKGREVKVS---- 79 (188)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHHHHHHHHHhhcccCCcc----
Confidence 578899999999999999999999999999999999999999864 38999999999999999999866311110
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCcccc--------CCCCcccccCCCCCCC
Q 046578 225 GMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTD--------RGCMTMQDIIPGPDET 296 (379)
Q Consensus 225 ~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~--------~~~~~l~d~i~~~~~~ 296 (379)
+++....+ +.+....+..++ ..+
T Consensus 80 ------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~ 110 (188)
T TIGR02943 80 ------------------------------------------------DLDDELDDEAFNALFTQNGHWAQHGQPQ-HWN 110 (188)
T ss_pred ------------------------------------------------ccccccccchhhhhhccccchhcccccc-ccC
Confidence 00000000 000000011111 223
Q ss_pred ChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchhh
Q 046578 297 MPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLK 375 (379)
Q Consensus 297 ~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L~ 375 (379)
.|+..+...+....+..+|.+||+++|+||.++|+ +|+|++|||+.||+|.++|+++++||+++||+++....+.
T Consensus 111 ~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~~~~~ 185 (188)
T TIGR02943 111 TPEKQLENKEFWEVFEACLYHLPEQTARVFMMREV----LGFESDEICQELEISTSNCHVLLYRARLSLRACLSINWFG 185 (188)
T ss_pred CHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 56677777777788999999999999999999985 7799999999999999999999999999999999876553
No 98
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=99.88 E-value=1.5e-21 Score=178.34 Aligned_cols=182 Identities=18% Similarity=0.168 Sum_probs=131.5
Q ss_pred HHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcch
Q 046578 144 ERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSM 223 (379)
Q Consensus 144 e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~~ 223 (379)
+.++..|.+.++.+|.+++++..++||++||+|+.+|+.+++|++.. +|.+|++++++|.+++++|++.+....+...
T Consensus 11 ~~~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~~--~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~~ 88 (201)
T PRK12545 11 PAYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQS--AHKTWVFGILRNKLIDTLRARQRTVNLSALD 88 (201)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhccccc--hHHHHHHHHHHHHHHHHHHhhcccccccccc
Confidence 34589999999999999999999999999999999999999998653 6999999999999999999876311110000
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHHHH
Q 046578 224 AGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQ 303 (379)
Q Consensus 224 ~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~~~ 303 (379)
.+.. ....++............+..++ ....+++...
T Consensus 89 ------------------------~~~~------------------~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~ 125 (201)
T PRK12545 89 ------------------------AELD------------------GEALLDRELFKDNGHWAAHAKPR-PWPKPETILQ 125 (201)
T ss_pred ------------------------cccc------------------hhhhhhhhhhcccccccccccCc-CCCCHHHHHH
Confidence 0000 00000000000000000000111 1224555565
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchh
Q 046578 304 KQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNL 374 (379)
Q Consensus 304 ~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L 374 (379)
..+....+..+|..||+++|.||.|+|+ +|+|++|||+.||+|.++|+++++||+++||+++...++
T Consensus 126 ~~~~~~~l~~~L~~Lp~~~r~v~~L~~~----eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~~ 192 (201)
T PRK12545 126 QQQFWTLFETCLDHLPEQIGRVFMMREF----LDFEIDDICTELTLTANHCSVLLYRARTRLRTCLSEKGL 192 (201)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 6666677999999999999999999995 779999999999999999999999999999999975543
No 99
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=99.88 E-value=1.9e-21 Score=175.83 Aligned_cols=175 Identities=18% Similarity=0.142 Sum_probs=130.1
Q ss_pred HHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcchH
Q 046578 145 RIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMA 224 (379)
Q Consensus 145 ~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~~~ 224 (379)
+-+..|.+.++.+|.+++++..++||++||+|+.+|+.+++|++.. +|.+|++++++|.+++++|++.+..... ...
T Consensus 11 ~~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~~--~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~-~~~ 87 (189)
T PRK12530 11 LEIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQS--ALKTWIFAILKNKIIDLIRYRKRFVNES-ELI 87 (189)
T ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCCc--cHHHHHHHHHHHHHHHHHHhhccCCCcc-ccc
Confidence 4578899999999999999989999999999999999999998643 6999999999999999999865311100 000
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHHHHH
Q 046578 225 GMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQK 304 (379)
Q Consensus 225 ~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~~~~ 304 (379)
....... ..+.......+.........|+..+..
T Consensus 88 ---------------------------------------------~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~ 121 (189)
T PRK12530 88 ---------------------------------------------EEDSPNS-FFDEKGHWKPEYYEPSEWQEVENTVYK 121 (189)
T ss_pred ---------------------------------------------ccccchh-hhcccccccccccCCccccCHHHHHHH
Confidence 0000000 000000000000001112345666666
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhc
Q 046578 305 QLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILN 372 (379)
Q Consensus 305 ~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~ 372 (379)
.+....+..+|++||+++|+||.|+|+ +|+|++|||+.||+|.+||+++++||+++||+++...
T Consensus 122 ~~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~ 185 (189)
T PRK12530 122 EEFWLIFEACLNHLPAQQARVFMMREY----LELSSEQICQECDISTSNLHVLLYRARLQLQACLSKN 185 (189)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHhHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 777788999999999999999999995 6799999999999999999999999999999998654
No 100
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=99.88 E-value=2.6e-21 Score=170.83 Aligned_cols=159 Identities=14% Similarity=0.186 Sum_probs=126.1
Q ss_pred HHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccC
Q 046578 140 RESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRL 219 (379)
Q Consensus 140 ~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~iri 219 (379)
...|.++|..|.+.++.+|+++.++..++||++||+|+.+|+..++|+... .|.+|++++++|.+++++|+..+...
T Consensus 5 ~~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~~~~- 81 (164)
T PRK12547 5 SKNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGT--NLKAWLFTILRNEFYSQMRKRGREVQ- 81 (164)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCcc--cHHHHHHHHHHHHHHHHHHhhccccc-
Confidence 468899999999999999999999999999999999999999999997533 69999999999999999998653100
Q ss_pred CcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChH
Q 046578 220 PGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPE 299 (379)
Q Consensus 220 p~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe 299 (379)
. .+. .... ... ..++
T Consensus 82 ---------------------------------------------------~--~~~--------~~~~-~~~---~~~~ 96 (164)
T PRK12547 82 ---------------------------------------------------D--SDG--------VFTA-RVA---VHPA 96 (164)
T ss_pred ---------------------------------------------------c--ccc--------cccc-cCC---CCch
Confidence 0 000 0000 000 0111
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhc
Q 046578 300 RMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILN 372 (379)
Q Consensus 300 ~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~ 372 (379)
. ........+..+|..||+.+|+||.++|+ +|+|++|||+.||+|.++|+++++||+++||+.+...
T Consensus 97 ~--~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 163 (164)
T PRK12547 97 Q--YGSLDLQDFKKALNLLSADQREAIILIGA----SGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLKVD 163 (164)
T ss_pred h--hhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence 1 11122356889999999999999999984 7799999999999999999999999999999998643
No 101
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=99.88 E-value=2.1e-21 Score=176.18 Aligned_cols=178 Identities=18% Similarity=0.179 Sum_probs=133.1
Q ss_pred HHHHHHhHHHHHHHHHhccCCCCC-HHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcc
Q 046578 144 ERIIRSYRSLVVSIATGYQGKGLS-LKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGS 222 (379)
Q Consensus 144 e~Li~~y~~lV~~ia~r~~~~~~d-~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~ 222 (379)
++.+..|.+.|+++|.++.++..+ +||++||+|+.+|+++++|++. .+|.+|++++++|.+++++|++.+.......
T Consensus 8 ~~~~~~~~~~l~~~a~~~~~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~~~ 85 (195)
T PRK12532 8 DAELIESRKLLLHFARLQLPDHPDLAEDLVQETLLSAYSAGDSFQGR--ALVNSWLFAILKNKIIDALRQIGRQRKVFTL 85 (195)
T ss_pred hhhHHHHHHHHHHHHHHHcCChhhhHHHHHHHHHHHHHHhccccccc--chHHHHHHHHHHHHHHHHHHHhccccccccc
Confidence 467889999999999999998888 9999999999999999999864 3799999999999999999986531110000
Q ss_pred hHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccc---cCCCCcccccCCCCCCCChH
Q 046578 223 MAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVT---DRGCMTMQDIIPGPDETMPE 299 (379)
Q Consensus 223 ~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~---~~~~~~l~d~i~~~~~~~pe 299 (379)
. .....+.... ..+.....+.. .....+|+
T Consensus 86 ~----------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~e 118 (195)
T PRK12532 86 L----------------------------------------------DDELLDEAFESHFSQNGHWTPEGQ-PQHWNTPE 118 (195)
T ss_pred c----------------------------------------------cccccchhhhhhhccccccccccC-ccccCCHH
Confidence 0 0000000000 00000000000 11223677
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchh
Q 046578 300 RMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNL 374 (379)
Q Consensus 300 ~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L 374 (379)
..+...+....+..++..||+++|+||.|+|+ +|+|++|||+.||+|.++|+++++||+++||+++....+
T Consensus 119 ~~~~~~e~~~~l~~~l~~L~~~~r~i~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~ 189 (195)
T PRK12532 119 KSLNNNEFQKILQSCLYNLPENTARVFTLKEI----LGFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQIKWF 189 (195)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 77777777788999999999999999999984 779999999999999999999999999999999976654
No 102
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=99.88 E-value=1.8e-21 Score=171.02 Aligned_cols=158 Identities=14% Similarity=0.059 Sum_probs=124.8
Q ss_pred HHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccC
Q 046578 140 RESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRL 219 (379)
Q Consensus 140 ~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~iri 219 (379)
..++++||+.|.+.+++++.++.++..++||++||+|+.+|+..+.|++ ..|.+|++++++|.+++++|+..+...
T Consensus 3 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~---~~~~~wl~~i~~n~~~d~~R~~~~~~~- 78 (161)
T PRK12528 3 SATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQI---IEPRAFLTTIAKRVLCNHYRRQDLERA- 78 (161)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhccccccc---cCHHHHHHHHHHHHHHHHHHHHHHHHh-
Confidence 3689999999999999999999999999999999999999999887764 269999999999999999997541000
Q ss_pred CcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChH
Q 046578 220 PGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPE 299 (379)
Q Consensus 220 p~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe 299 (379)
....++ + .+......++
T Consensus 79 --------------------------------------------------~~~~~~------------~-~~~~~~~~~~ 95 (161)
T PRK12528 79 --------------------------------------------------YLEALA------------Q-LPERVAPSEE 95 (161)
T ss_pred --------------------------------------------------hHHHhh------------c-cccccCCCHH
Confidence 000000 0 0001112333
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 300 RMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 300 ~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
......+....+..+|.+||+++|+||.|+|+ +|+|++|||+.||+|.+||+++++||+++||..
T Consensus 96 ~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~----~g~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~ 160 (161)
T PRK12528 96 ERAIILETLVELDQLLDGLPPLVKRAFLLAQV----DGLGYGEIATELGISLATVKRYLNKAAMRCYFA 160 (161)
T ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhc
Confidence 33333344567899999999999999999995 779999999999999999999999999999975
No 103
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=99.88 E-value=3.1e-21 Score=176.98 Aligned_cols=182 Identities=18% Similarity=0.185 Sum_probs=134.5
Q ss_pred HHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcc
Q 046578 143 QERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGS 222 (379)
Q Consensus 143 ~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~ 222 (379)
-..+++.|.+.|+.+|++++++..++||++||+|+.+|+.+.+|+.. .+|.+|++++++|.+++++|+..+....+..
T Consensus 20 ~~~~~~~~~~~l~~~~~~~~~d~~~AEDivQEvfikl~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~~~~~~~~~ 97 (206)
T PRK12544 20 DPVFLEDLRKQMIKFATLQLSDLHLAEDAVQEALIGALKNADSFAGR--AAFKTWVFAILKNKIIDLLRQKKRHVSASSL 97 (206)
T ss_pred hHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhhccccccccc
Confidence 36799999999999999999999999999999999999999999854 3799999999999999999986531111000
Q ss_pred hHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHHH
Q 046578 223 MAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMV 302 (379)
Q Consensus 223 ~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~~ 302 (379)
. +....... ++... +. ...............|+..+
T Consensus 98 ~------------------~~~~~~~~------------------------~~~~~-~~-~~~~~~~~~~~~~~~~e~~~ 133 (206)
T PRK12544 98 L------------------RDEEEEED------------------------FEELF-DE-SGHWQKDERPQAWGNPEESL 133 (206)
T ss_pred c------------------cccchhhH------------------------HHHhh-cc-cccccccccccccCCHHHHH
Confidence 0 00000000 00000 00 00000000011223567777
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchh
Q 046578 303 QKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNL 374 (379)
Q Consensus 303 ~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L 374 (379)
...+....+..+|..||+++|+||.|+|+ +|+|++|||+.||+|.++|+++++||+++||+.+....+
T Consensus 134 ~~~e~~~~l~~~L~~L~~~~r~v~~L~~~----~g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~~~ 201 (206)
T PRK12544 134 EQEQFWRIFEACLDGLPAKYARVFMMREF----IELETNEICHAVDLSVSNLNVLLYRARLRLRECLENKWF 201 (206)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 77777778999999999999999999995 779999999999999999999999999999999876443
No 104
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=99.88 E-value=2.7e-21 Score=170.43 Aligned_cols=161 Identities=20% Similarity=0.211 Sum_probs=130.7
Q ss_pred HHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccC
Q 046578 140 RESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRL 219 (379)
Q Consensus 140 ~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~iri 219 (379)
+.+++.+|+.|.+.++.+|.++.++..++||++||+|+.+|++ .|+. +..|.+|++.+++|.+.+++|+..+....
T Consensus 2 ~~~f~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fi~~~~~--~~~~--~~~~~~wl~~i~rn~~~d~~rk~~~~~~~ 77 (166)
T PRK09639 2 DETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKG--IENEKGWLIKSARNVAYNYLRSEKRRRAR 77 (166)
T ss_pred chHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH--hccc--ccchHHHHHHHHHHHHHHHHHHhcccccc
Confidence 4689999999999999999999999999999999999999999 6763 34799999999999999999986531110
Q ss_pred CcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChH
Q 046578 220 PGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPE 299 (379)
Q Consensus 220 p~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe 299 (379)
. +... ...+. .....|+
T Consensus 78 ~------------------------------------------------------~~~~------~~~~~---~~~~~~e 94 (166)
T PRK09639 78 I------------------------------------------------------LGEF------QWQEV---DNEPSPE 94 (166)
T ss_pred c------------------------------------------------------cchh------hhhhc---cCCCChH
Confidence 0 0000 00000 1123566
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhc
Q 046578 300 RMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILN 372 (379)
Q Consensus 300 ~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~ 372 (379)
+.....+....+..+|..||+++|.||.++| +|+|++|||+.||+|.++|++.++||+++||+.+...
T Consensus 95 ~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~-----~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~~~ 162 (166)
T PRK09639 95 EIWIRKEEITKVQEVLAKMTERDRTVLLLRF-----SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIYEQM 162 (166)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 6666667777899999999999999999998 4599999999999999999999999999999998643
No 105
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=99.87 E-value=2.6e-21 Score=174.86 Aligned_cols=164 Identities=15% Similarity=0.137 Sum_probs=130.0
Q ss_pred HHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhh
Q 046578 134 KILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANK 213 (379)
Q Consensus 134 ~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~ 213 (379)
.=..++..+++.+|..|.+.|+.+|.++.++..++||++||+|+.+|+.++.|++. ..|.+|++++++|.+.+..++.
T Consensus 16 ~~~~~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~--~~~~~wL~~Iarn~~~~~~r~~ 93 (188)
T PRK12517 16 SDMLSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDE--KAAKAWLITILRRENARRFERK 93 (188)
T ss_pred HhhhccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCc--cchHHHHHHHHHHHHHHHHHHh
Confidence 33456899999999999999999999999999999999999999999999999864 3799999999999988776653
Q ss_pred cCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCC
Q 046578 214 SRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGP 293 (379)
Q Consensus 214 ~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~ 293 (379)
.+ .....+. +...+.
T Consensus 94 ~~------------------------------------------------------~~~~~~~-----------~~~~~~ 108 (188)
T PRK12517 94 QF------------------------------------------------------DLVDIED-----------DSIEDD 108 (188)
T ss_pred cc------------------------------------------------------CccCccc-----------ccccCc
Confidence 31 0000000 000111
Q ss_pred CCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhc
Q 046578 294 DETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILN 372 (379)
Q Consensus 294 ~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~ 372 (379)
....++... ....|..+|..||+++|.||.++|+ +|++++|||+.||+|.++|+.+++||+++||+.+...
T Consensus 109 ~~~~~e~~~----~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 179 (188)
T PRK12517 109 ASHSSEEEM----EQEWLRRQIAKLDPEYREPLLLQVI----GGFSGEEIAEILDLNKNTVMTRLFRARNQLKEALEKP 179 (188)
T ss_pred cccChhHHH----HHHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 112233222 2246889999999999999999995 7799999999999999999999999999999998754
No 106
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=99.87 E-value=4e-21 Score=164.87 Aligned_cols=158 Identities=27% Similarity=0.412 Sum_probs=131.3
Q ss_pred HHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCC
Q 046578 141 ESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLP 220 (379)
Q Consensus 141 ~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip 220 (379)
+|++.++..|.|+|+++++++..+..+++|++||+++++|++++.|++. .+|.+|+..++++.+.+++++..+ .+
T Consensus 1 ~a~~~l~~~~~~~v~~~~~~~~~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~rk~~~---~~ 75 (158)
T TIGR02937 1 EAFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRR---LR 75 (158)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHHHHHHHHhcc---CC
Confidence 3789999999999999999999998999999999999999999999987 589999999999999999998763 11
Q ss_pred cchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHH
Q 046578 221 GSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPER 300 (379)
Q Consensus 221 ~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~ 300 (379)
... .... . . ......+++
T Consensus 76 ~~~---------------------------------------------------~~~~------~----~-~~~~~~~~~ 93 (158)
T TIGR02937 76 REL---------------------------------------------------DLLE------E----L-LDSDPSPEE 93 (158)
T ss_pred cch---------------------------------------------------hhhh------h----c-ccccCCHHH
Confidence 000 0000 0 0 011224566
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578 301 MVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN 369 (379)
Q Consensus 301 ~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l 369 (379)
.....+....+..++..||+.++.||.++|+ .|+|.+|||+.+|+|+++|++++++++++||+.+
T Consensus 94 ~~~~~~~~~~l~~~l~~L~~~~~~ii~~~~~----~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~~l 158 (158)
T TIGR02937 94 ELEQEEEREALREALEKLPEREREVLVLRYL----EGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158 (158)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 6667777788999999999999999999884 6699999999999999999999999999999864
No 107
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=99.87 E-value=6.2e-21 Score=169.79 Aligned_cols=165 Identities=13% Similarity=0.127 Sum_probs=128.7
Q ss_pred cccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCc
Q 046578 137 CKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRT 216 (379)
Q Consensus 137 ~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~ 216 (379)
.-+..|++.+|+.|.+.|+.++.++.++..++||++||+|+.+|+. ..|++.. +|.+|++++++|.+++++|+..+.
T Consensus 6 ~~~~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~-~~~~~~~--~~~~wL~~iarn~~~d~~R~~~~~ 82 (172)
T PRK09651 6 TTASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRNALE 82 (172)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhh-ccccccc--CHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567899999999999999999999999999999999999999998 3554332 689999999999999999975410
Q ss_pred ccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCC
Q 046578 217 IRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDET 296 (379)
Q Consensus 217 irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~ 296 (379)
. .. .+. .. .+ ......
T Consensus 83 ~----------------------------------------------------~~--~~~-~~-----~~----~~~~~~ 98 (172)
T PRK09651 83 K----------------------------------------------------AY--LEM-LA-----LM----PEGGAP 98 (172)
T ss_pred h----------------------------------------------------hh--hhH-Hh-----hc----cccCCC
Confidence 0 00 000 00 00 001112
Q ss_pred ChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhc
Q 046578 297 MPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILN 372 (379)
Q Consensus 297 ~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~ 372 (379)
+|+......+....+..+|..||+++|+||.++|+ +|+|++|||+.||+|.++|+++++||+++|+......
T Consensus 99 ~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~~~~~ 170 (172)
T PRK09651 99 SPEERESQLETLQLLDSMLDGLNGKTREAFLLSQL----DGLTYSEIAHKLGVSVSSVKKYVAKATEHCLLFRLEY 170 (172)
T ss_pred ChHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhhhc----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHc
Confidence 33444444455567999999999999999999995 7799999999999999999999999999999875543
No 108
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=99.87 E-value=8.1e-21 Score=170.66 Aligned_cols=154 Identities=21% Similarity=0.220 Sum_probs=126.4
Q ss_pred HHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcc
Q 046578 143 QERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGS 222 (379)
Q Consensus 143 ~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~ 222 (379)
++.+|+.|.+.|+.++.++.++..++||++||+|+.+|+.+..|+.. .+|.+|++++++|.++|++|++.+....+
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~aeDi~QEvflkl~~~~~~~~~~--~~~~~wL~~i~~n~~~d~~Rk~~~~~~~~-- 78 (181)
T PRK09637 3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDG--SSIKSWLYQIANNTIIDFYRKKNRSEELP-- 78 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHhHHHhccc--cchHHHHHHHHHHHHHHHHHhccccCCcc--
Confidence 68899999999999999999999999999999999999999999853 37999999999999999999765310000
Q ss_pred hHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHHH
Q 046578 223 MAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMV 302 (379)
Q Consensus 223 ~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~~ 302 (379)
++ +...+ .+++..
T Consensus 79 ---------------------------------------------------------~~------~~~~~----~~~~~~ 91 (181)
T PRK09637 79 ---------------------------------------------------------DD------LLFED----EEREEN 91 (181)
T ss_pred ---------------------------------------------------------hh------hhccC----CChhHH
Confidence 00 00000 112223
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhh
Q 046578 303 QKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNIL 371 (379)
Q Consensus 303 ~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~ 371 (379)
...+....+..++..||+++|.||.++|+ +|++++|||+.||+|.++|++++.||+++||+.+..
T Consensus 92 ~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 156 (181)
T PRK09637 92 AKKELAPCLRPFIDALPEKYAEALRLTEL----EGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG 156 (181)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 34455677999999999999999999984 779999999999999999999999999999999864
No 109
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=99.87 E-value=8e-21 Score=170.90 Aligned_cols=160 Identities=17% Similarity=0.227 Sum_probs=126.6
Q ss_pred HHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCC
Q 046578 141 ESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLP 220 (379)
Q Consensus 141 ~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip 220 (379)
.++..+|..|.+.|+++|.+++++..++||++||+|+.+|+..++|++.. +|.+|++++++|.+++++|++.+...
T Consensus 5 ~~~~~~~~~~~~~l~~~~~~~~~~~~~AEDivQevflkl~~~~~~~~~~~--~~~~WL~~Ia~n~~~d~~Rk~~~~~~-- 80 (182)
T PRK12540 5 DSLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGS--NLPAWLFTILRNLFRSDYRKRRREVE-- 80 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCc--hHHHHHHHHHHHHHHHHHHhcccccc--
Confidence 46788999999999999999999999999999999999999999998653 69999999999999999997653100
Q ss_pred cchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHH
Q 046578 221 GSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPER 300 (379)
Q Consensus 221 ~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~ 300 (379)
. .+. ...+... . ....+.
T Consensus 81 ---------------------------------------------------~-~~~--------~~~~~~~-~-~~~~~~ 98 (182)
T PRK12540 81 ---------------------------------------------------D-ADG--------SYAKTLK-S-QPGQNA 98 (182)
T ss_pred ---------------------------------------------------c-ccc--------ccccccc-C-CCchHH
Confidence 0 000 0000000 0 011111
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchh
Q 046578 301 MVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNL 374 (379)
Q Consensus 301 ~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L 374 (379)
......+..+|++||+++|+||.|+|+ +|+|++|||+.||+|.++|+++++||+++||+.+.....
T Consensus 99 ----~~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~~~ 164 (182)
T PRK12540 99 ----HLEFEEFRAALDKLPQDQREALILVGA----SGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLYVDGA 164 (182)
T ss_pred ----HHHHHHHHHHHHhCCHHHHHHhhHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhccc
Confidence 112245889999999999999999984 779999999999999999999999999999999986553
No 110
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=99.86 E-value=9.9e-21 Score=166.04 Aligned_cols=156 Identities=12% Similarity=0.104 Sum_probs=125.6
Q ss_pred HHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcchHHH
Q 046578 147 IRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGM 226 (379)
Q Consensus 147 i~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~~~~~ 226 (379)
+..|.+.++.++.+++++..++||++||+|+.+|+..+.|++ .+|.+|++.+++|.++|++|++.+.
T Consensus 1 ~~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~---~~~~~wL~~ia~n~~~d~~R~~~~~---------- 67 (159)
T PRK12527 1 MENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQI---EHPRAFLYRTALNLVVDRHRRHRVR---------- 67 (159)
T ss_pred ChhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhccccccc---cchHHHHHHHHHHHHHHHHHHHhcc----------
Confidence 357899999999999999899999999999999999998864 2799999999999999999975420
Q ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHHHHHHH
Q 046578 227 VAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQL 306 (379)
Q Consensus 227 ~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~~~~~e 306 (379)
....++. +.+. .....++|++.+..++
T Consensus 68 -------------------------------------------~~~~~~~---------~~~~-~~~~~~~~~~~~~~~~ 94 (159)
T PRK12527 68 -------------------------------------------QAEPLEV---------LDEE-ERLHSPSPQTRLDLGQ 94 (159)
T ss_pred -------------------------------------------cccchhh---------hhcc-ccccCCCHHHHHHHHH
Confidence 0000000 0000 0011235677776777
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhc
Q 046578 307 MKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILN 372 (379)
Q Consensus 307 ~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~ 372 (379)
....+..+|.+||+++++||.|+|+ +|+|++|||+.||+|.++|++.+.||+++||+.+...
T Consensus 95 ~~~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~~~ 156 (159)
T PRK12527 95 RLALLQRALAELPPACRDSFLLRKL----EGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQW 156 (159)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 7778999999999999999999995 7799999999999999999999999999999998754
No 111
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=99.86 E-value=2.6e-21 Score=168.41 Aligned_cols=153 Identities=20% Similarity=0.206 Sum_probs=123.6
Q ss_pred HHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcchHHH
Q 046578 147 IRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGM 226 (379)
Q Consensus 147 i~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~~~~~ 226 (379)
|+.|.|.|++++.++.++..+++|++||+|+.+|+++++|++ .+|.+|++.+++|.+.+++|++.+.....
T Consensus 1 y~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~~~d~~r~~~~~~~~~------ 71 (154)
T TIGR02950 1 YREYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNAFIDWYRKDKKIQTID------ 71 (154)
T ss_pred CchHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHHHHHHHHHhhhhcccc------
Confidence 467999999999999999899999999999999999999986 37999999999999999999765310000
Q ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHHHHHHH
Q 046578 227 VAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQL 306 (379)
Q Consensus 227 ~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~~~~~e 306 (379)
+. .+.+... .....|++.+...+
T Consensus 72 ------------------------------------------------~~--------~~~~~~~-~~~~~~~~~~~~~~ 94 (154)
T TIGR02950 72 ------------------------------------------------DD--------AIGDLEQ-HPVESPEHHLLIKI 94 (154)
T ss_pred ------------------------------------------------Hh--------hhhhccc-cccCChhHHHHHHH
Confidence 00 0000000 11224555566666
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578 307 MKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN 369 (379)
Q Consensus 307 ~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l 369 (379)
....+..+|..||+.+++||.+.|+ +|+|++|||+.||+|.++|++.++||+++||+.+
T Consensus 95 ~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~l 153 (154)
T TIGR02950 95 EQEEITHHLSRLPENYRTVLILREF----KEFSYKEIAELLNLSLAKVKSNLFRARKELKKLL 153 (154)
T ss_pred HHHHHHHHHHhCCHhheeeeeehhh----ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 6678999999999999999999984 6799999999999999999999999999999875
No 112
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=99.86 E-value=2.6e-20 Score=163.80 Aligned_cols=159 Identities=17% Similarity=0.208 Sum_probs=125.8
Q ss_pred HHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcchH
Q 046578 145 RIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMA 224 (379)
Q Consensus 145 ~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~~~ 224 (379)
.++..|.+.++++|.++.++..++||++||+|+.+|+....|++. +|.+|++.+++|.+++++|+..+...
T Consensus 2 ~~~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~---~~~~wl~~iarn~~~d~~R~~~~~~~------ 72 (163)
T PRK07037 2 DVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVK---QPVAYLFRIVRNLAIDHYRRQALENK------ 72 (163)
T ss_pred hHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhccccCCcc---cHHHHHHHHHHHHHHHHHHhhccccc------
Confidence 367889999999999999999999999999999999988777642 58899999999999999997652100
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHHHHH
Q 046578 225 GMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQK 304 (379)
Q Consensus 225 ~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~~~~ 304 (379)
.... ++.. . + ... ...+|+..+..
T Consensus 73 -----------------------------------------------~~~~----~~~~--~-~-~~~-~~~~~~~~~~~ 96 (163)
T PRK07037 73 -----------------------------------------------YHGD----EEDG--L-D-VPS-PEASPEAALIN 96 (163)
T ss_pred -----------------------------------------------cccc----cccc--c-c-cCC-CCCCHHHHHHH
Confidence 0000 0000 0 0 011 12345666666
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhc
Q 046578 305 QLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILN 372 (379)
Q Consensus 305 ~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~ 372 (379)
.+..+.+..+|+.|||++|.||.++|+ +|+|++|||+.||+|.++|++.++||+++||+.+...
T Consensus 97 ~~~~~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l~~~ 160 (163)
T PRK07037 97 RDTLRHVADALSELPARTRYAFEMYRL----HGETQKDIARELGVSPTLVNFMIRDALVHCRKCLDAC 160 (163)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence 666778999999999999999999985 7799999999999999999999999999999998653
No 113
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=1.3e-20 Score=169.65 Aligned_cols=157 Identities=13% Similarity=0.136 Sum_probs=122.7
Q ss_pred HHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcc
Q 046578 143 QERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGS 222 (379)
Q Consensus 143 ~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~ 222 (379)
.+..+..|++.|+.+|.++.++..++||++||+|+.+|+.+..|+.. .+|.+|++.+++|.+++++|++.+....
T Consensus 6 ~~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~Rk~~~~~~~--- 80 (182)
T PRK12511 6 KRFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSG--GNLRTWLMSILHNAFIDELRRRRVEARR--- 80 (182)
T ss_pred hhhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCc--cchHHHHHHHHHHHHHHHHHhhcccccc---
Confidence 45568899999999999999999999999999999999999999863 3799999999999999999986531000
Q ss_pred hHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHHH
Q 046578 223 MAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMV 302 (379)
Q Consensus 223 ~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~~ 302 (379)
.+. .. +. .+.....+..
T Consensus 81 ---------------------------------------------------~~~-~~--------~~-~~~~~~~~~~-- 97 (182)
T PRK12511 81 ---------------------------------------------------ADE-LA--------VL-ADASLPAAQE-- 97 (182)
T ss_pred ---------------------------------------------------ccc-hh--------hc-cccCCCcchH--
Confidence 000 00 00 0000001111
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhc
Q 046578 303 QKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILN 372 (379)
Q Consensus 303 ~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~ 372 (379)
.......+..+|..||+++|+||.|+|+ +|+|++|||+.||+|.++|+++++||+++||+.+...
T Consensus 98 -~~~~~~~l~~~l~~Lp~~~R~v~~L~~~----eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~~~ 162 (182)
T PRK12511 98 -HAVRLAQIRDAFFDLPEEQRAALHLVAI----EGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFEEGT 162 (182)
T ss_pred -HHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHhc
Confidence 1223356889999999999999999984 7799999999999999999999999999999998754
No 114
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=3.8e-20 Score=167.38 Aligned_cols=158 Identities=11% Similarity=0.191 Sum_probs=122.2
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCccc
Q 046578 139 ERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIR 218 (379)
Q Consensus 139 d~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~ir 218 (379)
+...++.|+. |.+.++++|.++.++..++||++||+|+.+|+.+..|+.. ..|.+|++.+++|.+++++|+..+.
T Consensus 6 ~~~~~~~l~~-~~~~l~~~a~~~l~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n~~~d~~Rk~~r~-- 80 (188)
T PRK12546 6 HRDPRDELVE-HLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSDRRKHKRE-- 80 (188)
T ss_pred hhhHHHHHHH-HHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHHHHHHHHHHhccc--
Confidence 3455566655 7799999999999999999999999999999999999863 3799999999999999999986531
Q ss_pred CCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCCh
Q 046578 219 LPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMP 298 (379)
Q Consensus 219 ip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~p 298 (379)
+ ...+. ...+.... ....
T Consensus 81 -~---------------------------------------------------~~~~~--------~~~~~~~~--~~~~ 98 (188)
T PRK12546 81 -V---------------------------------------------------PDPEG--------VHAASLAV--KPAH 98 (188)
T ss_pred -c---------------------------------------------------cCccc--------cccccccc--CCcc
Confidence 0 00000 00000000 0011
Q ss_pred HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhh
Q 046578 299 ERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNIL 371 (379)
Q Consensus 299 e~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~ 371 (379)
+ .......+..+|..||+++|+||.|+|+ +|+|++|||+.||+|.++|+++++||+++||+.+..
T Consensus 99 ~----~~~~~~~l~~~L~~Lp~~~r~v~~L~~~----~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~ 163 (188)
T PRK12546 99 D----GRLAMSDFRAAFAQLPDEQREALILVGA----SGFSYEEAAEMCGVAVGTVKSRANRARARLAELLQL 163 (188)
T ss_pred h----hHHHHHHHHHHHHhCCHHHhHHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 1 1122245889999999999999999984 779999999999999999999999999999999865
No 115
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=99.85 E-value=3.5e-20 Score=164.72 Aligned_cols=149 Identities=20% Similarity=0.264 Sum_probs=121.3
Q ss_pred HHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcchHHHH
Q 046578 148 RSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMV 227 (379)
Q Consensus 148 ~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~~~~~~ 227 (379)
..|.+.++.++.++.++..++||++||+|+.+|+++++|+.. .+|.+|++.+++|.+++++|+..+...++
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~l~~~~~~~~~~--~~f~~wl~~iarn~~~d~~Rk~~~~~~~~------- 72 (170)
T TIGR02959 2 DEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDG--QKIQSWLYQIARNTIIDFYRSKSRSVELP------- 72 (170)
T ss_pred chHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhccCccccc-------
Confidence 578999999999999999999999999999999999999863 48999999999999999999865311000
Q ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHHHHHHHH
Q 046578 228 AKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLM 307 (379)
Q Consensus 228 ~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~~~~~e~ 307 (379)
+. .... . .+++.....+.
T Consensus 73 -----------------------------------------------~~------------~~~~-~--~~~~~~~~~e~ 90 (170)
T TIGR02959 73 -----------------------------------------------ES------------LLAA-D--SAREETFVKEL 90 (170)
T ss_pred -----------------------------------------------hh------------hccc-C--CccHHHHHHHH
Confidence 00 0000 0 11222334445
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhh
Q 046578 308 KQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNIL 371 (379)
Q Consensus 308 ~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~ 371 (379)
...+..+|..||+++|.||.++|+ +|+|++|||+.||+|.++|++.++||+++||+.+..
T Consensus 91 ~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 150 (170)
T TIGR02959 91 SQCIPPMIKELPDEYREAIRLTEL----EGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLET 150 (170)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 567899999999999999999984 679999999999999999999999999999999863
No 116
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=99.84 E-value=7.1e-20 Score=162.29 Aligned_cols=160 Identities=15% Similarity=0.087 Sum_probs=126.7
Q ss_pred HHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccC
Q 046578 140 RESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRL 219 (379)
Q Consensus 140 ~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~iri 219 (379)
..++.++|..|.+.++.+|.+++++..++||++||+|+.+|+....++. ..|.+|++++++|.+.+++|+.... +
T Consensus 8 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~~---~~~~~wl~~Iarn~~~d~~Rr~~~~-~- 82 (168)
T PRK12525 8 NTLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEGWRRQDLE-R- 82 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCcccc---cCHHHHHHHHHHHHHHHHHHHHHHH-H-
Confidence 4688999999999999999999999899999999999999986554432 3799999999999999999874310 0
Q ss_pred CcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChH
Q 046578 220 PGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPE 299 (379)
Q Consensus 220 p~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe 299 (379)
. . .+. ..+ .+.....+|+
T Consensus 83 ---------~-------~------------------------------------~~~---------~~~-~~~~~~~~~~ 100 (168)
T PRK12525 83 ---------A-------Y------------------------------------LQS---------LAE-APEAVQPSPE 100 (168)
T ss_pred ---------H-------H------------------------------------HHH---------Hhc-ccccccCChH
Confidence 0 0 000 000 0001123455
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHh
Q 046578 300 RMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNI 370 (379)
Q Consensus 300 ~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~ 370 (379)
+.+...+....+..++..||+++|.||.|+|+ +|+|++|||+.||+|.+||++.+.||+++||..+.
T Consensus 101 ~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~----eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~~~ 167 (168)
T PRK12525 101 EQWMVIETLLAIDRLLDGLSGKARAAFLMSQL----EGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQGFQ 167 (168)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhc
Confidence 55556666688999999999999999999984 77999999999999999999999999999998763
No 117
>TIGR02895 spore_sigI RNA polymerase sigma-I factor. Members of this sigma factor protein family are strictly limited to endospore-forming species in the Firmicutes lineage of bacteria, but are not universally present among such species. Sigma-I was shown to be induced by heat shock (PubMed:11157964) in Bacillus subtilis and is suggested by its phylogenetic profile to be connected to the program of sporulation (PubMed:16311624).
Probab=99.84 E-value=2.8e-19 Score=164.62 Aligned_cols=186 Identities=17% Similarity=0.248 Sum_probs=138.6
Q ss_pred HHHhcccHHHHHHHHHHhHHHHHHHHHhccCCC--CCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHH
Q 046578 133 YKILCKERESQERIIRSYRSLVVSIATGYQGKG--LSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAI 210 (379)
Q Consensus 133 ~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~--~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~l 210 (379)
..+++||.. +++|+..|.|+|.++|.+|.++. .+.||++|+|++|+|+|+++||+++|.+|.+|+.++|++.+.+++
T Consensus 2 ~~~~~gd~~-~e~LI~~Y~plI~~~a~~~~~~~~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~sya~~~Ir~~i~dyl 80 (218)
T TIGR02895 2 QPIQPGNEE-REELIRQYKPFIAKIVSSVCGRYIDTKSDDELSIGLIAFNEAIESYDSNKGKSFLSFAKLIIKRRLIDYI 80 (218)
T ss_pred chhhcCChH-HHHHHHHhHHHHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHH
Confidence 568899999 99999999999999999997664 589999999999999999999999999999999999999999999
Q ss_pred Hhhc---CcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHH------hCCCHHHHHHHHHhcCCccccCCccccC
Q 046578 211 ANKS---RTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEM------LNIHVSTVRLAIERTRHPISLDGAVTDR 281 (379)
Q Consensus 211 r~~~---r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~------Lgis~~~~~~~l~~~~~~iSLd~~~~~~ 281 (379)
|+.. ..+++|+........+..+..++...+++.|+.+||+.. .|++.+.+-.
T Consensus 81 Rk~~k~~~~v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~~~~~L~~~gi~~~dLv~------------------ 142 (218)
T TIGR02895 81 RKNQKYQNLLYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILEYKKLLKQFGIEFVELVK------------------ 142 (218)
T ss_pred HhcccccCeeeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcCCcHHHHhh------------------
Confidence 9987 456888766666667777888899999999999998743 2444332221
Q ss_pred CCCcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 046578 282 GCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRG 359 (379)
Q Consensus 282 ~~~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~ 359 (379)
. +|-.. +..+....+...+..=+.--..+.. ...++.+|++..+|||+.|+.+...
T Consensus 143 ----------~----sPkh~-d~r~~~i~ia~~~~~~~~l~~~l~~-------kk~LP~k~l~~~~~v~rktier~rk 198 (218)
T TIGR02895 143 ----------V----SPKHR-DTRKKAIKIAKVIVENEELLEYLIR-------KKKLPIKEIEERVRISRKTIERYRK 198 (218)
T ss_pred ----------c----CCCCH-HHHHHHHHHHHHHhcCHHHHHHHHH-------hCCCCHHHHHHHcCCCHHHHHHhhH
Confidence 1 11111 1112222233333322222222222 2569999999999999999876544
No 118
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=99.84 E-value=1.3e-19 Score=168.33 Aligned_cols=161 Identities=17% Similarity=0.155 Sum_probs=128.6
Q ss_pred HHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHH
Q 046578 129 NLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIR 208 (379)
Q Consensus 129 ~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~ 208 (379)
..++++..+||..+++.+++.| +.++++|.++.++..++||++||+|+.+|+. |+.. ..|.+|++++++|.++|
T Consensus 6 ~~~~~~~~~~~~~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~~---~~~~--~~~~~WL~~IarN~~id 79 (228)
T PRK06704 6 THILKNHIDMNHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQK---YSNK--DICMTLVYKIARNRWLD 79 (228)
T ss_pred HHHHhcccCCCHHHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH---cCcc--ccHHHHHHHHHHHHHHH
Confidence 4568889999999999888888 7899999999999999999999999999986 5432 25999999999999999
Q ss_pred HHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccc
Q 046578 209 AIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQD 288 (379)
Q Consensus 209 ~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d 288 (379)
++|++.+... +. ++
T Consensus 80 ~~Rk~k~~~~-------------------------------------------------------~~----~~------- 93 (228)
T PRK06704 80 QIKSKSVHEK-------------------------------------------------------IR----DQ------- 93 (228)
T ss_pred HHhccccccc-------------------------------------------------------cc----cc-------
Confidence 9997652000 00 00
Q ss_pred cCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 289 IIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 289 ~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
... ..+.... .+..+.+..+++.||+++|.||.|+|+ +++|++|||+.||+|.++|+++++||+++||+.
T Consensus 94 -~~~---~~~~~~~--~~~~~~l~~~L~~Lp~~~R~v~lL~~~----eg~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~ 163 (228)
T PRK06704 94 -ITF---EEPHEKI--ADLHEMVGKVLSSLNVQQSAILLLKDV----FQYSIADIAKVCSVSEGAVKASLFRSRNRLKTV 163 (228)
T ss_pred -ccc---CChHHHH--HHHHHHHHHHHHhCCHHHhhHhhhHHh----hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 000 0111111 223356889999999999999999984 779999999999999999999999999999998
Q ss_pred Hhh
Q 046578 369 NIL 371 (379)
Q Consensus 369 l~~ 371 (379)
+..
T Consensus 164 l~~ 166 (228)
T PRK06704 164 SEE 166 (228)
T ss_pred HHh
Confidence 854
No 119
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=99.83 E-value=1.9e-19 Score=173.60 Aligned_cols=161 Identities=16% Similarity=0.116 Sum_probs=124.3
Q ss_pred HHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccC
Q 046578 140 RESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRL 219 (379)
Q Consensus 140 ~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~iri 219 (379)
...++++|+.|.+.++.+|++++++..++||++||+|+. |.....|+ ...|.+|++++++|.++|++|+..+..
T Consensus 3 ~~~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~-~~~~~~~~---~~~~~~WL~~Ia~n~~~d~lR~~~~~~-- 76 (293)
T PRK09636 3 MADAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQ---IRDPRAWLTRVVTRLCLDRLRSARHRR-- 76 (293)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHhccccc---ccCHHHHHHHHHHHHHHHHHHhhhccc--
Confidence 456789999999999999999999999999999999999 66667775 247999999999999999999764200
Q ss_pred CcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChH
Q 046578 220 PGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPE 299 (379)
Q Consensus 220 p~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe 299 (379)
...... .+.+...+. ..+|+
T Consensus 77 ---------------------------------------------------~~~~~~--------~~~e~~~~~-~~~~~ 96 (293)
T PRK09636 77 ---------------------------------------------------ETYVGP--------WLPEPVVEE-LDDPL 96 (293)
T ss_pred ---------------------------------------------------ccccCC--------cCCcCCCCC-CCChH
Confidence 000000 000001111 11234
Q ss_pred HHH-HHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHh
Q 046578 300 RMV-QKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNI 370 (379)
Q Consensus 300 ~~~-~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~ 370 (379)
+.. ...+....+..+|++|||++|.||.|+|+ +++|++|||+.||+|.++|+++++||+++||+.+.
T Consensus 97 ~~~~~~~~~~~~l~~~l~~L~~~~R~v~~L~~~----~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~ 164 (293)
T PRK09636 97 EAVVAAEDLSLALMLALERLSPLERAAFLLHDV----FGVPFDEIASTLGRSPAACRQLASRARKHVRAARP 164 (293)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 333 34444567899999999999999999994 67999999999999999999999999999999764
No 120
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=99.82 E-value=3.2e-19 Score=156.34 Aligned_cols=156 Identities=13% Similarity=0.121 Sum_probs=113.3
Q ss_pred CCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhC
Q 046578 163 GKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLR 242 (379)
Q Consensus 163 ~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lg 242 (379)
++..++||++||+|+.+|+.++.+ + +..|.+|++++++|.+++++|++.+......
T Consensus 2 ~~~~~AeDivQe~fl~~~~~~~~~-~--~~~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~--------------------- 57 (161)
T PRK09047 2 RDDDAALDIVQDAMIKLAEKYGDR-P--AAEWPPLFQRILQNRIHDWFRRQKVRNTWVS--------------------- 57 (161)
T ss_pred CCHHHHHHHHHHHHHHHHHHHhhc-c--cCchHHHHHHHHHHHHHHHHHhhcccccccc---------------------
Confidence 445689999999999999998863 2 3479999999999999999998653110000
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCC--CCChHHHHHHHHHHHHHHHHHhcCCH
Q 046578 243 RMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPD--ETMPERMVQKQLMKQELKELLQTLSE 320 (379)
Q Consensus 243 r~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~--~~~pe~~~~~~e~~~~L~~~L~~L~~ 320 (379)
...++.....+++. ...+.+.+.. ..+|++.+...+....+..+|..||+
T Consensus 58 ---------------------------~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~ 109 (161)
T PRK09047 58 ---------------------------LFSSFSDDDDDDDF-DPLETLDSADEGAESPADKLERAQVLQLIEEAIQKLPA 109 (161)
T ss_pred ---------------------------cccccccccccccc-cHHHHhccccccCCCHHHHHHHHHHHHHHHHHHHhCCH
Confidence 00000000000000 1111111111 24677777777788889999999999
Q ss_pred HHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchh
Q 046578 321 READILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNL 374 (379)
Q Consensus 321 rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L 374 (379)
++|+||.|+|+ +|+|++|||+.||+|.++|+++++||+++||+.+...++
T Consensus 110 ~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~~ 159 (161)
T PRK09047 110 RQREAFLLRYW----EDMDVAETAAAMGCSEGSVKTHCSRATHALAKALEAKGI 159 (161)
T ss_pred HHHHHHHHHHH----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcCc
Confidence 99999999995 779999999999999999999999999999999876554
No 121
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=99.80 E-value=1.3e-18 Score=167.58 Aligned_cols=162 Identities=17% Similarity=0.152 Sum_probs=124.2
Q ss_pred HHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccC
Q 046578 140 RESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRL 219 (379)
Q Consensus 140 ~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~iri 219 (379)
...+..+|+.|.+.++++|++++++..++||++||+|+.+|++...+ ...|.+|++++++|.++|++|+..+...
T Consensus 4 ~~~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~----~~~~~aWL~~Ia~n~~id~lRk~~~rr~- 78 (290)
T PRK09635 4 HDPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGD----IDDERGWLIVVTSRLCLDHIKSASTRRE- 78 (290)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCccc----cccHHHHHHHHHHHHHHHHHhhhhccCc-
Confidence 35678999999999999999999999999999999999999986542 2369999999999999999997542000
Q ss_pred CcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChH
Q 046578 220 PGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPE 299 (379)
Q Consensus 220 p~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe 299 (379)
.....+... . .+..+ ...+|+
T Consensus 79 --------------------------------------------------~~~~~~~~~-~------~~~~~--~~~~~~ 99 (290)
T PRK09635 79 --------------------------------------------------RPQDIAAWH-D------GDASV--SSVDPA 99 (290)
T ss_pred --------------------------------------------------CcccccccC-c------cccCC--CCCCcH
Confidence 000000000 0 00011 112333
Q ss_pred H-HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578 300 R-MVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN 369 (379)
Q Consensus 300 ~-~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l 369 (379)
+ ....++....+..+|..|||+||.||.|+|+ .++|++|||+.||+|.++|+++++||+++||+..
T Consensus 100 ~~~~~~~e~~~al~~~L~~L~p~~R~vf~L~~~----~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~ 166 (290)
T PRK09635 100 DRVTLDDEVRLALLIMLERLGPAERVVFVLHEI----FGLPYQQIATTIGSQASTCRQLAHRARRKINESR 166 (290)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHH----hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhC
Confidence 3 3445556678999999999999999999995 6799999999999999999999999999999864
No 122
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=99.79 E-value=2.9e-18 Score=164.58 Aligned_cols=156 Identities=17% Similarity=0.143 Sum_probs=119.5
Q ss_pred HHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcchH
Q 046578 145 RIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMA 224 (379)
Q Consensus 145 ~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~~~ 224 (379)
++|+.|.+.++.+|++++++..++||++||+|+.+++. .|+. ...|.+|++++++|.++|++|+..+..
T Consensus 1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~--~~~~~awL~~Ia~n~~ld~lR~~~~~~------- 69 (281)
T TIGR02957 1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQ--IENPKAYLTKVVTRRCIDVLRSARARR------- 69 (281)
T ss_pred ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Cccc--ccCHHHHHHHHHHHHHHHHHHHhhhcc-------
Confidence 37899999999999999999999999999999997764 4543 237999999999999999999764200
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHHHHH
Q 046578 225 GMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQK 304 (379)
Q Consensus 225 ~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~~~~ 304 (379)
.. ...+ .+.+.... ...+|++....
T Consensus 70 ---------------------------------------------~~--~~~~-------~~~e~~~~-~~~~~~~~~~~ 94 (281)
T TIGR02957 70 ---------------------------------------------EV--YVGP-------WLPEPLLT-TSADPAESVEL 94 (281)
T ss_pred ---------------------------------------------cc--cCCC-------CCCcccCC-CCCChHHHHHH
Confidence 00 0000 00000111 11245554443
Q ss_pred -HHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHh
Q 046578 305 -QLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNI 370 (379)
Q Consensus 305 -~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~ 370 (379)
+++...+..+|++|||+||.||.|+|+ +++|++|||+.||+|.++|+++++||+++||+...
T Consensus 95 ~e~~~~~l~~~l~~L~~~~R~v~~L~~~----~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~ 157 (281)
T TIGR02957 95 AESLSMAYLLLLERLSPLERAVFVLREV----FDYPYEEIASIVGKSEANCRQLVSRARRHLDARRP 157 (281)
T ss_pred HHHHHHHHHHHHhhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 344567889999999999999999984 67999999999999999999999999999998754
No 123
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=99.73 E-value=2.1e-16 Score=142.54 Aligned_cols=177 Identities=18% Similarity=0.250 Sum_probs=127.6
Q ss_pred cHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCC---CCCHHH--HHHHHHHHHHHHHhccCCCCCCCchhHHHHH
Q 046578 127 DYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGK---GLSLKD--LIQEGSIGLLRGAKRFNPERGYKLSTYVYWW 201 (379)
Q Consensus 127 ~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~---~~d~eD--LvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~ 201 (379)
++.+||.++++||+.|+++|+..|++.+..+|+++... +.+.+| +++|+|+.++......+.+....|..|+..+
T Consensus 3 ~it~ll~~~~~GD~~A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~~lv~ea~lrl~~~~~~~~~~~~~~f~~~~~~~ 82 (185)
T PF07638_consen 3 EITELLDRWRQGDEAALDQLFERYYPELRRLARRRLRRERRGHDLQDTALVHEAFLRLARRGRFVQFSDRRHFWALLARI 82 (185)
T ss_pred hHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHhccccCCchhHHHHHHHHHHHHhccccccCCCCHHHHHHHHHHH
Confidence 46789999999999999999999999999999987533 334444 4778888777643332333334799999999
Q ss_pred HHHHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccC
Q 046578 202 IKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDR 281 (379)
Q Consensus 202 Ir~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~ 281 (379)
+++.++|+.|++.+..|-... ...+++..
T Consensus 83 ~rr~lid~~R~~~a~KRg~~~-----------------------------------------------~~~~l~~~---- 111 (185)
T PF07638_consen 83 MRRKLIDHARRRQAQKRGGDQ-----------------------------------------------VRVELDER---- 111 (185)
T ss_pred HHHHHHHHHHHHHHHhcCCCC-----------------------------------------------cccchhhh----
Confidence 999999999986642221100 01112211
Q ss_pred CCCcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578 282 GCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 282 ~~~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
..+...+.|+..+. +.+.+..+.. |+|+++++|.++|+ +|+|.+|||+.||||+.||++.+..|
T Consensus 112 --------~~~~~~~~~~~~~~---l~e~l~~L~~-l~~~~~~~v~l~~~----~Gls~~EIA~~lgiS~~tV~r~l~~a 175 (185)
T PF07638_consen 112 --------ADSGDEPSPEELLE---LEEALERLLA-LDPRQRRVVELRFF----EGLSVEEIAERLGISERTVRRRLRRA 175 (185)
T ss_pred --------hccccCCCHHHHHH---HHHHHHHHHc-cCHHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 11111234555443 3344555555 99999999999985 67999999999999999999999999
Q ss_pred HHHHHhHHh
Q 046578 362 LTKLQQTNI 370 (379)
Q Consensus 362 l~kLR~~l~ 370 (379)
+.+|++.+.
T Consensus 176 R~~l~~~l~ 184 (185)
T PF07638_consen 176 RAWLRRELR 184 (185)
T ss_pred HHHHHHHhc
Confidence 999998864
No 124
>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=99.71 E-value=1.5e-16 Score=136.86 Aligned_cols=136 Identities=18% Similarity=0.265 Sum_probs=99.8
Q ss_pred HHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhc-----cCCCCCCCchhHHHHHHHHHHHHHHHhhcCcc
Q 046578 143 QERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKR-----FNPERGYKLSTYVYWWIKQAIIRAIANKSRTI 217 (379)
Q Consensus 143 ~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~-----fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~i 217 (379)
++.+|..|.++++.+|+++.. .+|+ ||+|+.+|....+ |++. .+|.||++++++|.++|++|++.+..
T Consensus 1 f~~~~~~y~~~l~~~~~~~~~----~~~~-qdvf~~~w~~~~~~~~~~~~~~--~~~~~wL~~iarN~~id~~Rk~~~~~ 73 (142)
T TIGR03209 1 FEEIYMNFKNTIDIFTRKYNL----YYDY-NDILYHLWIILKKIDLNKFNTE--NDLEKYISTSLKRYCLDICNKKNRDK 73 (142)
T ss_pred ChHHHHHHHHHHHHHHHHhcc----hhhH-HHHHHHHHHHHHHhhhhhcCch--hHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 467999999999999999964 3344 9999999999865 5532 47999999999999999999765200
Q ss_pred cCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCC
Q 046578 218 RLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETM 297 (379)
Q Consensus 218 rip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~ 297 (379)
.. .. +. ...+ . ...
T Consensus 74 ~~----------------------------------------------------~~-~~--------~~~~----~-~~~ 87 (142)
T TIGR03209 74 KI----------------------------------------------------IY-NS--------EITD----I-KLS 87 (142)
T ss_pred hh----------------------------------------------------hh-hh--------hhhc----c-ccc
Confidence 00 00 00 0000 0 001
Q ss_pred hHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHH
Q 046578 298 PERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIR 355 (379)
Q Consensus 298 pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr 355 (379)
+.+.....+....+..+++.||+.+|+||.|+|+ +|+|++|||+.||+|.+||+
T Consensus 88 ~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~----~~~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 88 LINVYSSNDLEFEFNDLISILPNKQKKIIYMKFF----EDMKEIDIAKKLHISRQSVY 141 (142)
T ss_pred hhHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHhhc
Confidence 1222333444566889999999999999999985 77999999999999999996
No 125
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=99.70 E-value=1.8e-15 Score=141.38 Aligned_cols=92 Identities=17% Similarity=0.300 Sum_probs=84.7
Q ss_pred cHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCC--CHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHH
Q 046578 127 DYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGL--SLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQ 204 (379)
Q Consensus 127 ~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~--d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~ 204 (379)
+..+++.++++||..|++.|++.|.|+|+++|.+++++.. ++||++|+||+++|+++++|++++|.+|.+|+.++++|
T Consensus 4 ~~~~Li~~~~~gD~~AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~awl~~Iirn 83 (237)
T PRK08311 4 SLEDILEKIKNGDEELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELVIKR 83 (237)
T ss_pred cHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHH
Confidence 5788999999999999999999999999999999988765 59999999999999999999998887999999999999
Q ss_pred HHHHHHHhhcCccc
Q 046578 205 AIIRAIANKSRTIR 218 (379)
Q Consensus 205 ~i~~~lr~~~r~ir 218 (379)
.++|++|+..+...
T Consensus 84 ~~iDylRk~~~~~~ 97 (237)
T PRK08311 84 RLIDYFRKESKHNL 97 (237)
T ss_pred HHHHHHHHhhcccc
Confidence 99999998765433
No 126
>PRK09191 two-component response regulator; Provisional
Probab=99.69 E-value=3.2e-16 Score=147.29 Aligned_cols=137 Identities=15% Similarity=0.091 Sum_probs=111.9
Q ss_pred HHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCc
Q 046578 142 SQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPG 221 (379)
Q Consensus 142 A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~ 221 (379)
++.++|..|.+.++++|.++.++..++||++||+|+.+|+...+|++. ..|.+|+++++++...+. ..
T Consensus 2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~--~~~~~wl~~~~~~~~~~~----~~------ 69 (261)
T PRK09191 2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEA--SSPRVGLYRLFHRLWSSA----GA------ 69 (261)
T ss_pred chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCC--cchhhHHHHHHHHHhccc----cc------
Confidence 578999999999999999999999999999999999999999999864 369999999876542110 00
Q ss_pred chHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHH
Q 046578 222 SMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERM 301 (379)
Q Consensus 222 ~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~ 301 (379)
+ . . ... .+..
T Consensus 70 -----------------------------------------------------~----~--~--------~~~--~~~~- 79 (261)
T PRK09191 70 -----------------------------------------------------N----D--P--------EPG--SPFE- 79 (261)
T ss_pred -----------------------------------------------------c----C--C--------CCC--CCch-
Confidence 0 0 0 000 1111
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhh
Q 046578 302 VQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNIL 371 (379)
Q Consensus 302 ~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~ 371 (379)
..+..+|++||+++|+|+.|+|+ +|+|++|||+.||+|.++|+.+++||+++||+.+..
T Consensus 80 -------~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~~ 138 (261)
T PRK09191 80 -------ARAERRLAGLTPLPRQAFLLTAL----EGFSVEEAAEILGVDPAEAEALLDDARAEIARQVAT 138 (261)
T ss_pred -------HHHHHHHHhCCHHHhHHHHHHHH----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHhccCCC
Confidence 15889999999999999999984 779999999999999999999999999999987753
No 127
>PF04542 Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR007627 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 recognised by the major sigma factors [, ]. 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 thought to mediate strand separation, thereby allowing transcription initiation [, ].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1OR7_B 1H3L_B 2Z2S_C 2Q1Z_C 2O7G_B 1SMY_F 1IW7_P 2BE5_F 2A6E_F 2CW0_F ....
Probab=99.43 E-value=5e-13 Score=100.66 Aligned_cols=70 Identities=24% Similarity=0.497 Sum_probs=66.8
Q ss_pred HHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcC
Q 046578 146 IIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSR 215 (379)
Q Consensus 146 Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r 215 (379)
||+.|.|.|++++.++.++..++||++||+++++|+++++|+++.+.+|.+|++.+++|.+.+++|++.+
T Consensus 1 L~~~~~~~l~~~~~~~~~~~~~~eD~~qe~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~r~~~r 70 (71)
T PF04542_consen 1 LYERYYPLLYRYARRYTGDPEDAEDLVQEAFIKLWRAIDSYDPDRGDSFRAWLFRIARNRILDYLRKRRR 70 (71)
T ss_dssp HHHHTHHHHHHHHHTCTTCSSHHHHHHHHHHHHHHHHHHHTSTTSSSHHHHHHHHHHHHHHHHHHHCSSS
T ss_pred CHHHHHHHHHHHHHHHhCCHhhHHHHhhHHHHHHHhhhhcccccccCCHHHHHHHHHHHHHHHHHHHhcC
Confidence 6899999999999999999999999999999999999999999888889999999999999999998764
No 128
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=99.28 E-value=1.1e-11 Score=87.60 Aligned_cols=50 Identities=34% Similarity=0.528 Sum_probs=45.7
Q ss_pred HHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578 314 LLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 314 ~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~ 367 (379)
+|+.||++|++||.++|+ +++|+.|||+.||+|+++|+++..+|+++||+
T Consensus 1 Al~~L~~~er~vi~~~y~----~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 1 ALDQLPPREREVIRLRYF----EGLTLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp HHCTS-HHHHHHHHHHHT----ST-SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred ChhhCCHHHHHHHHHHhc----CCCCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 588999999999999995 78999999999999999999999999999995
No 129
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=99.08 E-value=4.4e-10 Score=80.62 Aligned_cols=53 Identities=28% Similarity=0.413 Sum_probs=45.1
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578 309 QELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL 365 (379)
Q Consensus 309 ~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL 365 (379)
+.|..++..||+++|.||.++|+ +|+|++|||+.+|+|.++|++.++||+++|
T Consensus 2 ~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIa~~l~~s~~~v~~~l~ra~~~L 54 (54)
T PF08281_consen 2 EALQQALAQLPERQREIFLLRYF----QGMSYAEIAEILGISESTVKRRLRRARKKL 54 (54)
T ss_dssp HHHHHHHHCS-HHHHHHHHHHHT----S---HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHHHHHH----HCcCHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence 46889999999999999999994 779999999999999999999999999987
No 130
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=98.97 E-value=2.2e-09 Score=82.96 Aligned_cols=76 Identities=41% Similarity=0.526 Sum_probs=65.1
Q ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHH
Q 046578 226 MVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERM 301 (379)
Q Consensus 226 ~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~ 301 (379)
.++++.++...|.+.+||.||.+|||+.||++.+++..++......+||+.+...+++..+.+++.++...+|++.
T Consensus 2 ~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~~~~l~~~i~d~~~~~P~e~ 77 (78)
T PF04539_consen 2 KLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDEDDSTLGDFIEDDDAPSPEEE 77 (78)
T ss_dssp HHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSSSEEGGGSSB-SSS--HHHH
T ss_pred hHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCCCCchhheecCCCCCChhhc
Confidence 5789999999999999999999999999999999999999999999999999988888899999999888888765
No 131
>PRK06930 positive control sigma-like factor; Validated
Probab=98.87 E-value=1.3e-08 Score=90.52 Aligned_cols=70 Identities=21% Similarity=0.296 Sum_probs=61.0
Q ss_pred HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhc
Q 046578 299 ERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILN 372 (379)
Q Consensus 299 e~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~ 372 (379)
.+.....+....+..++..||+++|.||.++|+ +|+|++|||+.||+|.++|+++++||+++|++.+...
T Consensus 96 ~~~~~~~e~~~~l~~al~~L~~rer~V~~L~~~----eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~~ 165 (170)
T PRK06930 96 PESVISEWDKIRIEDALSVLTEREKEVYLMHRG----YGLSYSEIADYLNIKKSTVQSMIERAEKKIARQINES 165 (170)
T ss_pred hhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence 333444555678999999999999999999884 7799999999999999999999999999999987653
No 132
>PRK00118 putative DNA-binding protein; Validated
Probab=98.72 E-value=7.5e-08 Score=78.33 Aligned_cols=62 Identities=16% Similarity=0.095 Sum_probs=55.5
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchh
Q 046578 309 QELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNL 374 (379)
Q Consensus 309 ~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L 374 (379)
..+.-....||+++++++.++|+ +++|++|||+.+|+|++||++++.||+++||+++...++
T Consensus 9 ~l~d~~~~~L~ekqRevl~L~y~----eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~~ 70 (104)
T PRK00118 9 LLFDFYGSLLTEKQRNYMELYYL----DDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHL 70 (104)
T ss_pred HHHHHHhccCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHCh
Confidence 44555778999999999999985 789999999999999999999999999999999987654
No 133
>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=98.55 E-value=2.9e-07 Score=64.59 Aligned_cols=54 Identities=41% Similarity=0.622 Sum_probs=49.0
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 046578 309 QELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQ 366 (379)
Q Consensus 309 ~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR 366 (379)
..+..++..|++.++.++.++|+ +++|.++||+.+|+|.++|++++++++.+||
T Consensus 2 ~~~~~~~~~l~~~~~~~~~~~~~----~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 2 ERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 35778899999999999999984 6699999999999999999999999998875
No 134
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=98.42 E-value=6.5e-07 Score=76.47 Aligned_cols=55 Identities=24% Similarity=0.316 Sum_probs=48.7
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchhhh
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKV 376 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L~~ 376 (379)
.|+++|++|+.+++ +|+|++|||+.||+|+++|++++++|+++|++......+-.
T Consensus 6 ~Lte~qr~VL~Lr~-----~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~a~~~~~l~~ 60 (137)
T TIGR00721 6 FLTERQIKVLELRE-----KGLSQKEIAKELKTTRANVSAIEKRAMENIEKARNTLDFVK 60 (137)
T ss_pred CCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHhHHHHHHHHhhHHHHHH
Confidence 59999999999975 77999999999999999999999999999998766554433
No 135
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=98.38 E-value=8.9e-07 Score=75.98 Aligned_cols=52 Identities=25% Similarity=0.349 Sum_probs=47.6
Q ss_pred hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhc
Q 046578 316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILN 372 (379)
Q Consensus 316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~ 372 (379)
..|+|+|++||.+++ +|+|++|||+.||+|+++|++++++++++||+.....
T Consensus 5 ~~Lt~rqreVL~lr~-----~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~tl 56 (141)
T PRK03975 5 SFLTERQIEVLRLRE-----RGLTQQEIADILGTSRANVSSIEKRARENIEKARETL 56 (141)
T ss_pred cCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 469999999999965 7899999999999999999999999999999987653
No 136
>PRK04217 hypothetical protein; Provisional
Probab=98.36 E-value=1.1e-06 Score=72.23 Aligned_cols=55 Identities=20% Similarity=0.148 Sum_probs=50.0
Q ss_pred hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchh
Q 046578 316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNL 374 (379)
Q Consensus 316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L 374 (379)
..|++.|++++.++|+ +++|++|||+.||||++||++++++|+++|++++.....
T Consensus 41 ~~Lt~eereai~l~~~----eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~~~ 95 (110)
T PRK04217 41 IFMTYEEFEALRLVDY----EGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGRE 95 (110)
T ss_pred ccCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhccc
Confidence 4699999999999984 779999999999999999999999999999999876544
No 137
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=98.22 E-value=7.8e-06 Score=66.00 Aligned_cols=60 Identities=27% Similarity=0.314 Sum_probs=45.7
Q ss_pred HHHHHh-cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchh
Q 046578 311 LKELLQ-TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNL 374 (379)
Q Consensus 311 L~~~L~-~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L 374 (379)
+..... -|+++|+.++.++|. +++|+.|||+.+|||+.+|+-.++||.++|...-...+|
T Consensus 10 L~d~Yg~LLT~kQ~~~l~lyy~----eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~yE~kL~l 70 (101)
T PF04297_consen 10 LFDFYGELLTEKQREILELYYE----EDLSLSEIAEELGISRQAVYDSIKRAEKKLEEYEEKLGL 70 (101)
T ss_dssp HHHHHGGGS-HHHHHHHHHHCT----S---HHHHHHHCTS-HHHHHHHHHHHHHHHHHHHHHH-H
T ss_pred HHHHHHHHCCHHHHHHHHHHHc----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 444444 599999999999994 779999999999999999999999999999877655444
No 138
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=98.12 E-value=6.7e-06 Score=58.52 Aligned_cols=48 Identities=27% Similarity=0.374 Sum_probs=42.2
Q ss_pred hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
..|++.|+.++.+.+ .|+|.+|||+.+|+|+++|++++.+++++|+-.
T Consensus 2 ~~l~~~e~~i~~~~~-----~g~s~~eia~~l~is~~tv~~~~~~~~~kl~~~ 49 (58)
T smart00421 2 ASLTPREREVLRLLA-----EGLTNKEIAERLGISEKTVKTHLSNIMRKLGVR 49 (58)
T ss_pred CCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence 468999999987743 669999999999999999999999999988744
No 139
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=98.11 E-value=0.00011 Score=70.76 Aligned_cols=161 Identities=14% Similarity=0.109 Sum_probs=108.5
Q ss_pred HHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCc
Q 046578 142 SQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPG 221 (379)
Q Consensus 142 A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~ 221 (379)
..+..+..-.|.+..---+|+++-.-+||.+||+|+..++...+=-+-. .-.+|++..-||..+|.+|++.+.-..|.
T Consensus 6 ~ie~~~r~~~~r~~a~L~r~~rd~dlAEEa~~dA~~~Ale~WPr~G~P~--~PaAWL~~v~R~~aiD~~Rr~~~~~~~~~ 83 (415)
T COG4941 6 WIEAAARIERPRAMAALARYLRDLDLAEEALQDAFAAALERWPRAGPPR--NPAAWLIAVGRNRAIDRVRRRARRDAAPP 83 (415)
T ss_pred HHHHHHHHhhhHHHHHHHHHhcccchHHHHHHHHHHHHHHhCcccCCCC--ChHHHHHHHHhhhHHHHHHHHHHhccCCh
Confidence 4466677777777776667777777899999999987766554333322 46899999999999999998764222221
Q ss_pred chHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHH
Q 046578 222 SMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERM 301 (379)
Q Consensus 222 ~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~ 301 (379)
+. .++. ++.+....+.. ++.
T Consensus 84 el-----------------------------------------------~~~~-----e~~e~~~a~~~--------~d~ 103 (415)
T COG4941 84 EL-----------------------------------------------LLSD-----EDEEMEEAEAL--------DDE 103 (415)
T ss_pred hh-----------------------------------------------cccc-----cchhhhccccc--------ccc
Confidence 10 0000 01110100000 111
Q ss_pred HHHHHHHHHHHHHHh-cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 302 VQKQLMKQELKELLQ-TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 302 ~~~~e~~~~L~~~L~-~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
...++....|.-|.. -|++.+|-.+.|+. + .|+|..|||..|=+++.++-|++-||.++++..
T Consensus 104 ~i~Dd~LRLiFvccHPal~~~~riALtLR~-v---~GLs~~eIArAFLv~e~am~QRivRAK~ri~~a 167 (415)
T COG4941 104 HIRDDRLRLIFVCCHPALPPEQRIALTLRL-V---GGLSTAEIARAFLVPEAAMAQRIVRAKARIREA 167 (415)
T ss_pred ccchhhHHhhhhhcCCCCChhhHHHHHHHH-H---cCCcHHHHHHHHcCCcHHHHHHHHHHHHHHHhc
Confidence 112223344555555 79999999999998 3 559999999999999999999999999999975
No 140
>TIGR01636 phage_rinA phage transcriptional activator, RinA family. This model represents 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=98.08 E-value=1.8e-05 Score=67.71 Aligned_cols=62 Identities=11% Similarity=0.205 Sum_probs=54.7
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578 306 LMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN 369 (379)
Q Consensus 306 e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l 369 (379)
.....|..+++.|++.++.||.++|+ .+ ..+|..+||..||+|+.+|+++..+++.+|++.+
T Consensus 71 ~~~~~I~~~l~~Ld~~er~II~~rY~-~~-~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~l 132 (134)
T TIGR01636 71 RNRDAIENCLNEADEQTRVIIQELYM-KK-RPLTLVGLAQQLFISKSTAYRLRNHIIEAVAEEL 132 (134)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHc-cC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 34567999999999999999999994 33 3469999999999999999999999999999874
No 141
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=98.06 E-value=9.9e-06 Score=58.84 Aligned_cols=48 Identities=33% Similarity=0.445 Sum_probs=41.3
Q ss_pred hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
..|+++|.+|+.+.. .|++.+|||+.+|+|..||+.++.++++||.-.
T Consensus 2 ~~LT~~E~~vl~~l~-----~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~ 49 (58)
T PF00196_consen 2 PSLTERELEVLRLLA-----QGMSNKEIAEELGISEKTVKSHRRRIMKKLGVK 49 (58)
T ss_dssp GSS-HHHHHHHHHHH-----TTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT-S
T ss_pred CccCHHHHHHHHHHH-----hcCCcchhHHhcCcchhhHHHHHHHHHHHhCCC
Confidence 479999999999876 779999999999999999999999999998643
No 142
>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=97.98 E-value=2.1e-05 Score=55.98 Aligned_cols=46 Identities=28% Similarity=0.379 Sum_probs=41.0
Q ss_pred CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
|+++|+.++.+.+ .++|.+|||+.+|+|+++|++++++++++|+..
T Consensus 1 l~~~e~~i~~~~~-----~~~s~~eia~~l~~s~~tv~~~~~~~~~~l~~~ 46 (57)
T cd06170 1 LTPREREVLRLLA-----EGKTNKEIADILGISEKTVKTHLRNIMRKLGVK 46 (57)
T ss_pred CCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence 6889999998754 669999999999999999999999999988764
No 143
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=97.96 E-value=2.2e-05 Score=59.58 Aligned_cols=48 Identities=17% Similarity=0.070 Sum_probs=41.6
Q ss_pred HHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 310 ELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 310 ~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.+.+-++.||++.+.++.|.+.+ +++|++|||+.||+|.++|++++++
T Consensus 8 ~~~~~l~~l~~~~r~af~L~R~~---eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 8 KLAERLTWVDSLAEAAAALAREE---AGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred hHHHHHhcCCHHHHHHHHHHHHH---cCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 46677899999999999996432 6699999999999999999998875
No 144
>PF07374 DUF1492: Protein of unknown function (DUF1492); InterPro: IPR010861 This entry is represented by Streptococcus phage 7201, Orf19. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several hypothetical, highly conserved Streptococcal and related phage proteins. The function of this family is unknown.
Probab=97.94 E-value=5.9e-05 Score=61.22 Aligned_cols=54 Identities=28% Similarity=0.413 Sum_probs=47.9
Q ss_pred HHHHHHHHhcCC-HHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578 308 KQELKELLQTLS-EREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL 365 (379)
Q Consensus 308 ~~~L~~~L~~L~-~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL 365 (379)
...+..++++|+ +.+|.||.++|. .+++..+||+.||+|+.++.+++.+|++.|
T Consensus 45 k~ei~~~I~~l~d~~~r~iL~~~Yi----~~~~~~~I~~~l~~S~~t~yr~~~~Al~~L 99 (100)
T PF07374_consen 45 KLEIRRAINKLEDPDERLILRMRYI----NKLTWEQIAEELNISRRTYYRIHKKALKEL 99 (100)
T ss_pred HHHHHHHHHHccChhHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHhc
Confidence 345788889886 789999999994 559999999999999999999999999876
No 145
>PF12645 HTH_16: Helix-turn-helix domain; InterPro: IPR024760 This domain appears to be a helix-turn-helix domain, suggesting a transcriptional regulatory protein. Some proteins with this domain are annotated as conjugative transposon proteins.
Probab=97.89 E-value=5e-05 Score=56.63 Aligned_cols=58 Identities=22% Similarity=0.256 Sum_probs=50.6
Q ss_pred HHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCC------CCCHHHHHHHHHHHHHHHHhccC
Q 046578 130 LVKYKILCKERESQERIIRSYRSLVVSIATGYQGK------GLSLKDLIQEGSIGLLRGAKRFN 187 (379)
Q Consensus 130 eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~------~~d~eDLvQEg~i~L~~ai~~fD 187 (379)
++|.++++||+.|.++++..|.|+|.+++.+-..+ +.--+|+-|+--..|++++.+|+
T Consensus 2 ~vI~~A~~GD~~A~~~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kLi~~I~~F~ 65 (65)
T PF12645_consen 2 EVIKAAKQGDPEAMEEILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKLIEAILKFE 65 (65)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHHHHHHHccC
Confidence 57899999999999999999999999999884322 34459999999999999999985
No 146
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=97.87 E-value=6.2e-05 Score=53.64 Aligned_cols=48 Identities=23% Similarity=0.373 Sum_probs=41.1
Q ss_pred CCHHHHHHHHHHhhcC---CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578 318 LSEREADILRLHFGLD---GQTPVSCKEIGRLLSLSRERIRQIRGIALTKL 365 (379)
Q Consensus 318 L~~rer~Vl~l~ygL~---g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL 365 (379)
|+++|++++...|-.+ -..+.|..|||+.||||.+++..++++|.+||
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRrae~kl 51 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRRAERKL 51 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 7899999999875322 23578999999999999999999999999987
No 147
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=97.81 E-value=4.5e-05 Score=67.28 Aligned_cols=47 Identities=30% Similarity=0.370 Sum_probs=43.7
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
.|+++|++|+.+.- +|+|.+|||+.|++|.+||+....++++||.-.
T Consensus 133 ~LSpRErEVLrLLA-----qGkTnKEIAe~L~IS~rTVkth~srImkKLgV~ 179 (198)
T PRK15201 133 HFSVTERHLLKLIA-----SGYHLSETAALLSLSEEQTKSLRRSIMRKLHVK 179 (198)
T ss_pred CCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 58999999999886 889999999999999999999999999999754
No 148
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=97.80 E-value=4e-05 Score=70.35 Aligned_cols=47 Identities=17% Similarity=0.327 Sum_probs=43.8
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
.|+|+|++|+.+.- +|+|.+|||+.||+|..||+.+.++.++||.-.
T Consensus 137 ~LT~RE~eVL~lla-----~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~v~ 183 (207)
T PRK15411 137 SLSRTESSMLRMWM-----AGQGTIQISDQMNIKAKTVSSHKGNIKRKIKTH 183 (207)
T ss_pred cCCHHHHHHHHHHH-----cCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCCC
Confidence 49999999999986 889999999999999999999999999999753
No 149
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=97.78 E-value=4.5e-05 Score=69.83 Aligned_cols=52 Identities=15% Similarity=0.110 Sum_probs=47.4
Q ss_pred HHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 312 KELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 312 ~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
.++...|+|+|++|+.+.- +|+|.+|||+.|++|.+||+..+.+.++||.-.
T Consensus 138 ~~~~~~LS~RE~eVL~Lia-----~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLgv~ 189 (217)
T PRK13719 138 LEAKNKVTKYQNDVFILYS-----FGFSHEYIAQLLNITVGSSKNKISEILKFFGIS 189 (217)
T ss_pred hhccCCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 5667899999999999986 789999999999999999999999999998643
No 150
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=97.76 E-value=0.00013 Score=65.27 Aligned_cols=63 Identities=22% Similarity=0.268 Sum_probs=54.7
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhch
Q 046578 306 LMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN 373 (379)
Q Consensus 306 e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~ 373 (379)
+....+...+.+|+|+||+|+...- .|+..++||..||||+.||..+..+..+||+..-....
T Consensus 131 ~~~~~~~~~l~tLT~RERqVl~~vV-----~G~~NKqIA~dLgiS~rTVe~HRanvM~Km~a~SlaeL 193 (202)
T COG4566 131 DRQAAIRARLATLTPRERQVLDLVV-----RGLMNKQIAFDLGISERTVELHRANVMEKMQARSLAEL 193 (202)
T ss_pred HHHHHHHHHHHhcCHHHHHHHHHHH-----cCcccHHHHHHcCCchhhHHHHHHHHHHHHhhccHHHH
Confidence 3456788999999999999999875 77999999999999999999999999999987654433
No 151
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=97.73 E-value=6e-05 Score=59.99 Aligned_cols=54 Identities=22% Similarity=0.238 Sum_probs=44.3
Q ss_pred HHHHHHHh-cCCHHHHHHHHHHhhcCC---CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578 309 QELKELLQ-TLSEREADILRLHFGLDG---QTPVSCKEIGRLLSLSRERIRQIRGIALT 363 (379)
Q Consensus 309 ~~L~~~L~-~L~~rer~Vl~l~ygL~g---~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~ 363 (379)
+.+..++. -|+|+|+.++..||++.+ ..++|++|||+.+|||..+|.+. .++++
T Consensus 23 ~~l~~~l~~lLTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~-sn~lk 80 (94)
T TIGR01321 23 DDMQLLLELILTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRG-SNNLK 80 (94)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHH-Hhhcc
Confidence 34566664 599999999999999986 57899999999999999999764 44444
No 152
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=97.73 E-value=6.2e-05 Score=69.15 Aligned_cols=47 Identities=28% Similarity=0.265 Sum_probs=43.6
Q ss_pred hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578 316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~ 367 (379)
..|+++|++|+.+.. +|+|.+|||+.|++|..||+.++.+.++||.-
T Consensus 133 ~~LT~RE~eVL~ll~-----~G~snkeIA~~L~iS~~TV~~h~~~I~~KLgv 179 (207)
T PRK11475 133 RMLSPTEREILRFMS-----RGYSMPQIAEQLERNIKTIRAHKFNVMSKLGV 179 (207)
T ss_pred CCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 469999999999986 78999999999999999999999999999953
No 153
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=97.68 E-value=0.00012 Score=59.79 Aligned_cols=53 Identities=21% Similarity=0.201 Sum_probs=48.5
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhch
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN 373 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~ 373 (379)
.|+..|-+.|+|.++ +++|++|-|+.||||+.|+.+++..|++|+-++|-...
T Consensus 41 ~L~~dElEAiRL~D~----egl~QeeaA~~MgVSR~T~~ril~~ARkKiA~ALv~Gk 93 (106)
T PF02001_consen 41 VLTVDELEAIRLVDY----EGLSQEEAAERMGVSRPTFQRILESARKKIADALVEGK 93 (106)
T ss_pred EeeHHHHHHHHHHHH----cCCCHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHCCC
Confidence 488899999999984 77999999999999999999999999999999987654
No 154
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=97.65 E-value=8.8e-05 Score=67.78 Aligned_cols=46 Identities=30% Similarity=0.377 Sum_probs=43.0
Q ss_pred hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 046578 316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQ 366 (379)
Q Consensus 316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR 366 (379)
..|+++|++|+.+.- +|+|.+|||+.|++|..||+.++.+.++||-
T Consensus 149 ~~Lt~rE~evl~~~~-----~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~ 194 (216)
T PRK10840 149 KRLSPKESEVLRLFA-----EGFLVTEIAKKLNRSIKTISSQKKSAMMKLG 194 (216)
T ss_pred ccCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 359999999999886 7899999999999999999999999999995
No 155
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=97.64 E-value=8.5e-05 Score=68.43 Aligned_cols=48 Identities=33% Similarity=0.386 Sum_probs=44.0
Q ss_pred hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
..|++||++|+.+.- +|+|.+|||+.|++|.+||+.++++.++||.-.
T Consensus 147 ~~LT~RE~eVL~lla-----~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~v~ 194 (211)
T COG2197 147 ELLTPRELEVLRLLA-----EGLSNKEIAEELNLSEKTVKTHVSNILRKLGVR 194 (211)
T ss_pred CCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHhHHHHHHHHHHHHcCCC
Confidence 469999999999875 789999999999999999999999999998643
No 156
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=97.63 E-value=9.7e-05 Score=68.33 Aligned_cols=48 Identities=25% Similarity=0.232 Sum_probs=44.3
Q ss_pred hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
..|+++|++|+.+.+ +|+|.+|||+.|++|..||+.++.++++||.-.
T Consensus 154 ~~Lt~rE~~Vl~l~~-----~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v~ 201 (216)
T PRK10100 154 ALLTHREKEILNKLR-----IGASNNEIARSLFISENTVKTHLYNLFKKIAVK 201 (216)
T ss_pred CCCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 359999999999987 689999999999999999999999999999754
No 157
>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=97.62 E-value=0.0001 Score=69.53 Aligned_cols=50 Identities=24% Similarity=0.270 Sum_probs=45.2
Q ss_pred HhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578 315 LQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN 369 (379)
Q Consensus 315 L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l 369 (379)
+..|+++|++|+.+.. +|+|.+|||+.||||+.||+.+++++++||.-.-
T Consensus 188 ~~~LT~RE~evl~l~a-----~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v~n 237 (247)
T TIGR03020 188 AGLITAREAEILAWVR-----DGKTNEEIAAILGISSLTVKNHLQHIFKKLDVRN 237 (247)
T ss_pred ccCCCHHHHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCCCC
Confidence 4579999999999875 7899999999999999999999999999997543
No 158
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=97.61 E-value=9.9e-05 Score=50.60 Aligned_cols=41 Identities=20% Similarity=0.255 Sum_probs=24.2
Q ss_pred hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
..|++.||..|...+ .+|+|..+||+.||++++||++.+.|
T Consensus 3 ~~Lt~~eR~~I~~l~----~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 3 KHLTPEERNQIEALL----EQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ---------HHHHHH----CS---HHHHHHHTT--HHHHHHHHHH
T ss_pred cchhhhHHHHHHHHH----HcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 468999999998776 48899999999999999999998876
No 159
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=97.59 E-value=0.00013 Score=68.22 Aligned_cols=51 Identities=24% Similarity=0.230 Sum_probs=45.6
Q ss_pred HhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHh
Q 046578 315 LQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNI 370 (379)
Q Consensus 315 L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~ 370 (379)
...|+++|++|+.+.. +|+|.+|||+.||+|..||+.++.++++||+..-+
T Consensus 169 ~~~Lt~re~evl~~~a-----~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~~~ 219 (232)
T TIGR03541 169 AGVLSEREREVLAWTA-----LGRRQADIAAILGISERTVENHLRSARRKLGVATT 219 (232)
T ss_pred hccCCHHHHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCH
Confidence 3479999999999965 77999999999999999999999999999985543
No 160
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=97.49 E-value=0.00021 Score=67.12 Aligned_cols=47 Identities=23% Similarity=0.306 Sum_probs=43.6
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
.|+++|++||.+.. +|+|.+|||+.||||..||+.++.++++||--.
T Consensus 179 ~LT~rE~evl~~~a-----~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~~~ 225 (240)
T PRK10188 179 NFSKREKEILKWTA-----EGKTSAEIAMILSISENTVNFHQKNMQKKFNAP 225 (240)
T ss_pred CCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 69999999999886 789999999999999999999999999999644
No 161
>PRK13870 transcriptional regulator TraR; Provisional
Probab=97.48 E-value=0.0002 Score=67.02 Aligned_cols=47 Identities=19% Similarity=0.186 Sum_probs=43.2
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
.|++||+++|...- +|.|..|||.+||||+.||..+++.|++||--.
T Consensus 173 ~LT~RE~E~L~W~A-----~GKT~~EIa~ILgISe~TV~~Hl~na~~KLga~ 219 (234)
T PRK13870 173 WLDPKEATYLRWIA-----VGKTMEEIADVEGVKYNSVRVKLREAMKRFDVR 219 (234)
T ss_pred CCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCC
Confidence 59999999999875 889999999999999999999999999999543
No 162
>TIGR01637 phage_arpU phage transcriptional regulator, ArpU family. This model represents 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. We propose that this is a phage transcriptional activator family.
Probab=97.48 E-value=0.0028 Score=53.85 Aligned_cols=61 Identities=18% Similarity=0.149 Sum_probs=53.3
Q ss_pred HHHHHHHH-hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHh
Q 046578 308 KQELKELL-QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNI 370 (379)
Q Consensus 308 ~~~L~~~L-~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~ 370 (379)
...+..++ +.|++.+|.||..+| +.+ ++++..+|+..+|+|+.+.+++..+|+.++-..+.
T Consensus 69 ~~~i~~ai~~~l~~~~r~Il~~~Y-l~~-~~~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~~l~ 130 (132)
T TIGR01637 69 ARAIVNAIVNQLDEISRQILYDKY-LEP-DQKYDYQIMMELGYSHRQYYRIKKRALLRFATLYG 130 (132)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHH-cCc-cccchHHHHHHhCCcHHHHHHHHHHHHHHHHHHhC
Confidence 45677777 899999999999999 442 46899999999999999999999999999988764
No 163
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=97.39 E-value=0.00057 Score=50.00 Aligned_cols=50 Identities=36% Similarity=0.398 Sum_probs=44.1
Q ss_pred hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHh
Q 046578 316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNI 370 (379)
Q Consensus 316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~ 370 (379)
..|+++|.+++.+.- .|.+.+|||..+|+|..||+..+.++.+||.-.-+
T Consensus 3 ~~Lt~rE~~v~~l~~-----~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~~~~r 52 (65)
T COG2771 3 ADLTPREREILRLVA-----QGKSNKEIARILGISEETVKTHLRNIYRKLGVKNR 52 (65)
T ss_pred ccCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCH
Confidence 368999999998875 67999999999999999999999999999875543
No 164
>PRK09483 response regulator; Provisional
Probab=97.33 E-value=0.0004 Score=62.60 Aligned_cols=46 Identities=30% Similarity=0.363 Sum_probs=42.2
Q ss_pred hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 046578 316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQ 366 (379)
Q Consensus 316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR 366 (379)
..|+++|++|+.+.. +|+|.+|||+.|++|..||+.++++.++||-
T Consensus 147 ~~Lt~rE~~vl~~~~-----~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~ 192 (217)
T PRK09483 147 ASLSERELQIMLMIT-----KGQKVNEISEQLNLSPKTVNSYRYRMFSKLN 192 (217)
T ss_pred cccCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 459999999998764 7799999999999999999999999999984
No 165
>PRK01381 Trp operon repressor; Provisional
Probab=97.17 E-value=0.00048 Score=55.25 Aligned_cols=55 Identities=20% Similarity=0.196 Sum_probs=42.5
Q ss_pred HHHHHHHHhc-CCHHHHHHHHHHhhcCC---CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578 308 KQELKELLQT-LSEREADILRLHFGLDG---QTPVSCKEIGRLLSLSRERIRQIRGIALT 363 (379)
Q Consensus 308 ~~~L~~~L~~-L~~rer~Vl~l~ygL~g---~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~ 363 (379)
.+.+..++.. |+|.|+..|..|+++.. ..++|++|||+.+|+|..||.+ -+++|+
T Consensus 22 ~~~~~~~l~~llTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITR-gsn~Lk 80 (99)
T PRK01381 22 EDLHLPLLTLLLTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATITR-GSNSLK 80 (99)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeehh-hHHHhc
Confidence 3456666664 99999999999988763 2469999999999999998865 344444
No 166
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=97.16 E-value=0.00092 Score=58.97 Aligned_cols=47 Identities=28% Similarity=0.321 Sum_probs=42.7
Q ss_pred hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578 316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~ 367 (379)
..|+++|++|+.+.. +|++.+|||+.+++|..||+.++.++++||.-
T Consensus 148 ~~lt~~e~~vl~l~~-----~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~ 194 (211)
T PRK15369 148 PLLTPRERQILKLIT-----EGYTNRDIAEQLSISIKTVETHRLNMMRKLDV 194 (211)
T ss_pred cCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 359999999999853 77999999999999999999999999999964
No 167
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=97.14 E-value=0.00098 Score=53.26 Aligned_cols=49 Identities=20% Similarity=0.232 Sum_probs=43.2
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN 369 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l 369 (379)
-|+.+|+..+.++|. +++|+.|||+.++||+++|...++|+-+.|-+.-
T Consensus 17 LLT~KQ~~Y~~lyy~----dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~~YE 65 (105)
T COG2739 17 LLTKKQKNYLELYYL----DDLSLSEIAEEFNVSRQAIYDNIKRTEKILEDYE 65 (105)
T ss_pred HHhHHHHHHHHHHHH----hhccHHHHHHHhCccHHHHHHHHHHHHHHHHHHH
Confidence 589999999999994 5699999999999999999999999877765543
No 168
>PRK15320 transcriptional activator SprB; Provisional
Probab=97.11 E-value=0.00097 Score=59.96 Aligned_cols=50 Identities=14% Similarity=0.185 Sum_probs=44.1
Q ss_pred HHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578 313 ELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 313 ~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~ 367 (379)
.+--.|+++|.+|+.+-- +|+|.+|||+.|++|.+||+..+++.+.||.-
T Consensus 160 ~~~~~LSdREIEVL~LLA-----kG~SNKEIAekL~LS~KTVSTYKnRLLeKLgA 209 (251)
T PRK15320 160 NLPPGVTQAKYALLILLS-----SGHPAIELAKKFGLGTKTVSIYRKKVMYRLGM 209 (251)
T ss_pred cCCCCCCHHHHHHHHHHH-----cCCCHHHHHHHhccchhhHHHHHHHHHHHcCC
Confidence 344578999999999875 78999999999999999999999999999864
No 169
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=97.06 E-value=0.0017 Score=51.43 Aligned_cols=52 Identities=19% Similarity=0.176 Sum_probs=46.6
Q ss_pred CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhch
Q 046578 318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN 373 (379)
Q Consensus 318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~ 373 (379)
|+..|-+.|+|... ++++++|-|..||||+.|+.+.+..|++|+-.+|-...
T Consensus 34 lt~eElEAlRLvD~----~~l~QeeAA~rMgISr~Tfwr~l~sAR~KvA~aLveGk 85 (99)
T COG1342 34 LTIEELEALRLVDY----EGLTQEEAALRMGISRQTFWRLLTSARKKVADALVEGK 85 (99)
T ss_pred ecHHHHHHHHHHhH----hhccHHHHHHHhcccHHHHHHHHHHHHHHHHHHHhcCC
Confidence 77788899999874 77999999999999999999999999999999986543
No 170
>PRK10651 transcriptional regulator NarL; Provisional
Probab=97.05 E-value=0.0011 Score=59.20 Aligned_cols=48 Identities=27% Similarity=0.353 Sum_probs=43.2
Q ss_pred hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
..|+++|++|+.+.. +|++.++||+.+++|..||+.++++.++||.-.
T Consensus 154 ~~Lt~rE~~vl~~l~-----~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl~~~ 201 (216)
T PRK10651 154 NQLTPRERDILKLIA-----QGLPNKMIARRLDITESTVKVHVKHMLKKMKLK 201 (216)
T ss_pred ccCCHHHHHHHHHHH-----cCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCCC
Confidence 359999999999865 779999999999999999999999999998643
No 171
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=97.00 E-value=0.00058 Score=56.64 Aligned_cols=51 Identities=24% Similarity=0.331 Sum_probs=46.3
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhc
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILN 372 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~ 372 (379)
-|+++|-+|+.||- .|.|++|||++||.|+.+|+-+.++|+..+.++-+-.
T Consensus 8 flte~qikvl~lRe-----kG~tQ~eIA~~L~TTraNvSaIEkrA~enIekarnTL 58 (143)
T COG1356 8 FLTEQQIKVLVLRE-----KGLTQSEIARILKTTRANVSAIEKRALENIEKARNTL 58 (143)
T ss_pred eeehhheeeeehhh-----ccccHHHHHHHHccchhhHHHHHHHHHHHHHHHHHHH
Confidence 48999999999996 8899999999999999999999999999998875543
No 172
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=96.95 E-value=0.0026 Score=55.75 Aligned_cols=55 Identities=27% Similarity=0.376 Sum_probs=47.7
Q ss_pred HHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHh
Q 046578 311 LKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNI 370 (379)
Q Consensus 311 L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~ 370 (379)
+...+..|++++++|+.+.+ .+++.++||+.+|+|..+|+....++++||+..-.
T Consensus 135 ~~~~~~~l~~~e~~vl~~~~-----~~~~~~~ia~~l~~s~~tv~~~~~~~~~kl~~~~~ 189 (202)
T PRK09390 135 IRARIASLSERERQVMDGLV-----AGLSNKVIARDLDISPRTVEVYRANVMTKMQAGSL 189 (202)
T ss_pred HHHHHHhhhhhHHHHHHHHH-----ccCchHHHHHHcCCCHHHHHHHHHHHHHHHccccH
Confidence 45667789999999999754 56999999999999999999999999999976543
No 173
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=96.94 E-value=0.0022 Score=59.20 Aligned_cols=53 Identities=25% Similarity=0.379 Sum_probs=45.1
Q ss_pred cCCHHHHHHHHHHhhcC---CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578 317 TLSEREADILRLHFGLD---GQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN 369 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~---g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l 369 (379)
.|+++|+++|...|-.+ -....+.+|||+.||||.+|+.++++||.+||=..+
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~~~ 210 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLIEAY 210 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 59999999999876322 225679999999999999999999999999997664
No 174
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=96.74 E-value=0.0042 Score=44.24 Aligned_cols=50 Identities=16% Similarity=0.181 Sum_probs=43.7
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN 369 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l 369 (379)
+|+..++-++.+.|. ..+.+++++|..+|||++||+++.+..+.-|...+
T Consensus 2 kLs~~d~lll~L~~L---R~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~l 51 (53)
T PF13613_consen 2 KLSLEDQLLLTLMYL---RLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQVL 51 (53)
T ss_pred CCCHHHHHHHHHHHH---HcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHhc
Confidence 688899999998874 37799999999999999999999999988877653
No 175
>PRK10403 transcriptional regulator NarP; Provisional
Probab=96.63 E-value=0.0038 Score=55.46 Aligned_cols=49 Identities=29% Similarity=0.329 Sum_probs=43.5
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHh
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNI 370 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~ 370 (379)
.|+++|.+|+.+.. +|+|.+|||+.+|+|..||+.++.+.++||.-.-+
T Consensus 153 ~Lt~~e~~vl~~~~-----~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~~~ 201 (215)
T PRK10403 153 VLTERELDVLHELA-----QGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSR 201 (215)
T ss_pred cCCHHHHHHHHHHH-----CCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCCCCH
Confidence 59999999998765 67999999999999999999999999999865433
No 176
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=96.47 E-value=0.007 Score=53.45 Aligned_cols=48 Identities=25% Similarity=0.294 Sum_probs=43.1
Q ss_pred hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
..|+++|.+|+.+.. +|++.++||+.+++|..||+.++++.++||.-.
T Consensus 136 ~~Lt~~E~~il~~l~-----~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~~~ 183 (196)
T PRK10360 136 DPLTKRERQVAEKLA-----QGMAVKEIAAELGLSPKTVHVHRANLMEKLGVS 183 (196)
T ss_pred cCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 369999999999865 679999999999999999999999999998643
No 177
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=96.41 E-value=0.0069 Score=53.86 Aligned_cols=47 Identities=34% Similarity=0.359 Sum_probs=41.1
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
.|+++|..++.+.. +|+|.+|||+.+++|..||+.++.++++||.-.
T Consensus 149 ~lt~re~~vl~~l~-----~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl~~~ 195 (210)
T PRK09935 149 VLSNREVTILRYLV-----SGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLH 195 (210)
T ss_pred cCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCCC
Confidence 38889998887643 669999999999999999999999999998643
No 178
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=96.38 E-value=0.0073 Score=53.70 Aligned_cols=46 Identities=17% Similarity=0.337 Sum_probs=42.0
Q ss_pred hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 046578 316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQ 366 (379)
Q Consensus 316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR 366 (379)
..|+++|.+|+.+.. .|.+.+|||+.+++|.+||+..+++.++||.
T Consensus 142 ~~lt~~E~~vl~~l~-----~g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl~ 187 (204)
T PRK09958 142 DSLSKQEISVMRYIL-----DGKDNNDIAEKMFISNKTVSTYKSRLMEKLE 187 (204)
T ss_pred ccCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 469999999999876 6789999999999999999999999999984
No 179
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=96.32 E-value=0.0087 Score=47.34 Aligned_cols=39 Identities=15% Similarity=0.155 Sum_probs=31.6
Q ss_pred hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578 316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
+.|+++ ..|+.+.- .|+|.+|||+.+|+|++||++ +.|+
T Consensus 35 ~~Ls~R-~~I~~ll~-----~G~S~~eIA~~LgISrsTIyR-i~R~ 73 (88)
T TIGR02531 35 QSLAQR-LQVAKMLK-----QGKTYSDIEAETGASTATISR-VKRC 73 (88)
T ss_pred HhhhHH-HHHHHHHH-----CCCCHHHHHHHHCcCHHHHHH-HHHh
Confidence 358888 77777653 679999999999999999998 4454
No 180
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=96.30 E-value=0.013 Score=40.49 Aligned_cols=41 Identities=22% Similarity=0.279 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578 318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
|++.++.|+....- ..+.|..|||+.+|+|.++|++++++-
T Consensus 1 l~~~~~~Il~~l~~---~~~~t~~ela~~~~is~~tv~~~l~~L 41 (48)
T PF13412_consen 1 LDETQRKILNYLRE---NPRITQKELAEKLGISRSTVNRYLKKL 41 (48)
T ss_dssp --HHHHHHHHHHHH---CTTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH---cCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 56788889876652 366999999999999999998886654
No 181
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=96.29 E-value=0.0041 Score=43.34 Aligned_cols=33 Identities=27% Similarity=0.258 Sum_probs=22.5
Q ss_pred HHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578 324 DILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 324 ~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
.++.++. +|+|.++||+.+|||++||++++++-
T Consensus 9 ~ii~l~~-----~G~s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 9 QIIRLLR-----EGWSIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp -HHHHHH-----HT--HHHHHHHHTS-HHHHHHHHT--
T ss_pred HHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHc
Confidence 3555554 57999999999999999999987663
No 182
>PRK04841 transcriptional regulator MalT; Provisional
Probab=96.27 E-value=0.007 Score=66.95 Aligned_cols=48 Identities=23% Similarity=0.261 Sum_probs=43.9
Q ss_pred hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
..|+++|++|+.+.. +|+|++|||+.|+||.+||+.++++..+||.-.
T Consensus 837 ~~lt~~e~~v~~~~~-----~g~~~~~ia~~l~~s~~tv~~h~~~~~~kl~v~ 884 (903)
T PRK04841 837 SPLTQREWQVLGLIY-----SGYSNEQIAGELDVAATTIKTHIRNLYQKLGIA 884 (903)
T ss_pred CCCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 359999999999976 889999999999999999999999999999643
No 183
>PRK13558 bacterio-opsin activator; Provisional
Probab=96.20 E-value=0.0098 Score=63.68 Aligned_cols=51 Identities=20% Similarity=0.204 Sum_probs=45.3
Q ss_pred HhcCCHHHHHHHHHHhhcCCCCCC-------CHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578 315 LQTLSEREADILRLHFGLDGQTPV-------SCKEIGRLLSLSRERIRQIRGIALTKLQQTN 369 (379)
Q Consensus 315 L~~L~~rer~Vl~l~ygL~g~e~~-------S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l 369 (379)
...|+++|+++|...|. .|| |..|||+.||||++|+++++++|.+||=..+
T Consensus 605 ~~~lt~~q~e~l~~a~~----~gyf~~pr~~~~~e~a~~l~is~~t~~~~lr~a~~~l~~~~ 662 (665)
T PRK13558 605 ENDLTDRQLTALQKAYV----SGYFEWPRRVEGEELAESMGISRSTFHQHLRAAERKLVGAF 662 (665)
T ss_pred hhhCCHHHHHHHHHHHH----cCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 45899999999999883 446 9999999999999999999999999986654
No 184
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=96.15 E-value=0.0098 Score=40.80 Aligned_cols=33 Identities=21% Similarity=0.234 Sum_probs=24.3
Q ss_pred HHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 046578 322 EADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRG 359 (379)
Q Consensus 322 er~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~ 359 (379)
..+|+.|+- +|+|..+||+.+|||++||++.+.
T Consensus 11 ~~~i~~l~~-----~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 11 IEEIKELYA-----EGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHHHH-----TT--HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHh
Confidence 455666664 779999999999999999998763
No 185
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=96.00 E-value=0.0092 Score=58.45 Aligned_cols=36 Identities=19% Similarity=0.314 Sum_probs=31.7
Q ss_pred HHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578 324 DILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT 363 (379)
Q Consensus 324 ~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~ 363 (379)
+|-.||| .+++|++|||++||+|+.+|++++.+|++
T Consensus 20 ~vA~lYY----~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~ 55 (318)
T PRK15418 20 RIAWFYY----HDGLTQSEIGERLGLTRLKVSRLLEKGRQ 55 (318)
T ss_pred HHHHHHH----hcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4566788 37799999999999999999999999976
No 186
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=95.80 E-value=0.039 Score=46.82 Aligned_cols=56 Identities=21% Similarity=0.367 Sum_probs=46.7
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578 308 KQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL 365 (379)
Q Consensus 308 ~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL 365 (379)
.+.+...++.|.+.++.||.++|+ +..++|..+||..|++++.++++....-...+
T Consensus 72 k~~id~~~~~l~de~k~Ii~lry~--~r~~~TW~~IA~~l~i~erta~r~~~~fK~~i 127 (130)
T PF05263_consen 72 KEAIDRWLETLIDEEKRIIKLRYD--RRSRRTWYQIAQKLHISERTARRWRDRFKNDI 127 (130)
T ss_pred HHHHHHHHHhhCHHHHHHHHHHHc--ccccchHHHHHHHhCccHHHHHHHHHHHHHHh
Confidence 456788889999999999999995 22569999999999999999998876655444
No 187
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=95.69 E-value=0.023 Score=41.32 Aligned_cols=26 Identities=23% Similarity=0.194 Sum_probs=24.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
+|++.+|||+.||+++.||++...+-
T Consensus 12 ~G~~~~eIA~~Lg~~~~TV~~W~~r~ 37 (58)
T PF06056_consen 12 QGWSIKEIAEELGVPRSTVYSWKDRY 37 (58)
T ss_pred cCCCHHHHHHHHCCChHHHHHHHHhh
Confidence 67999999999999999999998774
No 188
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=95.54 E-value=0.041 Score=45.45 Aligned_cols=50 Identities=20% Similarity=0.272 Sum_probs=43.0
Q ss_pred HHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578 314 LLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 314 ~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~ 367 (379)
.+..|++.|...+.... .. .=+++|+++.||||..|||.++.+.+++|..
T Consensus 30 ~~~~L~~E~~~Fi~~Fi-~~---rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 30 WFARLSPEQLEFIKLFI-KN---RGNLKEMEKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred hhhcCCHHHHHHHHHHH-Hh---cCCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence 46789999999888765 22 3499999999999999999999999999976
No 189
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=95.30 E-value=0.023 Score=36.15 Aligned_cols=23 Identities=26% Similarity=0.440 Sum_probs=17.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
+|.+|||+.+|+|+++|++.+.+
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~ 25 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKK 25 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHH
T ss_pred cCHHHHHHHhCCcHHHHHHHHHH
Confidence 78999999999999999866544
No 190
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=95.29 E-value=0.059 Score=36.44 Aligned_cols=40 Identities=33% Similarity=0.306 Sum_probs=27.9
Q ss_pred CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
|++.++.||...- -+ ...|+.+||+.+|+|.++|.+++.+
T Consensus 1 lD~~D~~Il~~Lq-~d--~r~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 1 LDELDRKILRLLQ-ED--GRRSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp --HHHHHHHHHHH-H---TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHH-Hc--CCccHHHHHHHHCcCHHHHHHHHHH
Confidence 4556777777654 22 5699999999999999999988665
No 191
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=95.22 E-value=0.034 Score=41.38 Aligned_cols=45 Identities=22% Similarity=0.441 Sum_probs=28.5
Q ss_pred HhcCCHHHHHHHHHH--hhc-CCCCCCCHHHHHHHhCCC-HHHHHHHHHH
Q 046578 315 LQTLSEREADILRLH--FGL-DGQTPVSCKEIGRLLSLS-RERIRQIRGI 360 (379)
Q Consensus 315 L~~L~~rer~Vl~l~--ygL-~g~e~~S~~EIAe~LgiS-~~~Vr~~~~r 360 (379)
+..|+++|++|+... |.- .| -.-|.+|||+.||++ .++|.+.+..
T Consensus 1 M~~LT~rQ~~vL~~I~~~~~~~G-~~Pt~rEIa~~~g~~S~~tv~~~L~~ 49 (65)
T PF01726_consen 1 MKELTERQKEVLEFIREYIEENG-YPPTVREIAEALGLKSTSTVQRHLKA 49 (65)
T ss_dssp -----HHHHHHHHHHHHHHHHHS-S---HHHHHHHHTSSSHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHcC-CCCCHHHHHHHhCCCChHHHHHHHHH
Confidence 457999999999863 211 14 556999999999997 9999877543
No 192
>PF06530 Phage_antitermQ: Phage antitermination protein Q; InterPro: IPR010534 This entry is represented by Bacteriophage 933W, GpQ. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage antitermination protein Q and related bacterial sequences. Phage 993W gene Q encodes a phage-specific positive regulator of late gene expression, thought, by analogy to the corresponding gene of phage lambda, to be a transcription antiterminator. GpQ positively regulates expression of the phage late gene operons. Bacterial host RNA polymerase modified by antitermination proteins transcribes through termination sites that otherwise prevent expression of the regulated genes [, ].; GO: 0003677 DNA binding, 0060567 negative regulation of transcription termination, DNA-dependent
Probab=94.97 E-value=0.16 Score=42.76 Aligned_cols=55 Identities=24% Similarity=0.153 Sum_probs=48.0
Q ss_pred HhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhch
Q 046578 315 LQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN 373 (379)
Q Consensus 315 L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~ 373 (379)
|.+-.|.+-.+|.++|. .+.|...||..+++|..+|++.+.+|-.-+..++...+
T Consensus 60 L~~~~~~~~~ll~~~Yv----~g~s~r~IA~~~~~s~~~ir~~l~~ae~~i~g~l~~~~ 114 (125)
T PF06530_consen 60 LKKRDPEEYDLLILYYV----YGWSKRQIARKLKCSEGKIRKRLQRAEGFIDGCLSMLT 114 (125)
T ss_pred HHccCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHhhhhHhhhhHHhh
Confidence 44578899999999994 67999999999999999999999999999998875444
No 193
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=94.95 E-value=0.048 Score=39.82 Aligned_cols=36 Identities=17% Similarity=0.233 Sum_probs=27.4
Q ss_pred HHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 323 ADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 323 r~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
-..+.++.-.+ ..+++++||+.||||.+||+....+
T Consensus 10 dkA~e~y~~~~--g~i~lkdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 10 DKAFEIYKESN--GKIKLKDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred HHHHHHHHHhC--CCccHHHHHHHHCCCHHHHHHHhhh
Confidence 34555554222 5699999999999999999998765
No 194
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=94.86 E-value=0.068 Score=33.24 Aligned_cols=36 Identities=25% Similarity=0.303 Sum_probs=27.5
Q ss_pred CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHH
Q 046578 318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQI 357 (379)
Q Consensus 318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~ 357 (379)
+++.++..+...+. .+.+..+||+.+|++..+|+++
T Consensus 6 ~~~~~~~~i~~~~~----~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 6 LTPEQIEEARRLLA----AGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHh
Confidence 45556655555552 5589999999999999999875
No 195
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=94.74 E-value=0.041 Score=53.87 Aligned_cols=35 Identities=20% Similarity=0.238 Sum_probs=30.4
Q ss_pred HHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578 325 ILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT 363 (379)
Q Consensus 325 Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~ 363 (379)
+-.+|| .+++|+.|||++||||+.+|++.+.+|++
T Consensus 18 ~A~lYY----~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~ 52 (321)
T COG2390 18 AAWLYY----VEGLTQSEIAERLGISRATVSRLLAKARE 52 (321)
T ss_pred HHHHHH----hcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 445677 48899999999999999999999999875
No 196
>PF13518 HTH_28: Helix-turn-helix domain
Probab=94.65 E-value=0.077 Score=36.89 Aligned_cols=27 Identities=22% Similarity=0.176 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
++.|..+||+.+|||+++|++++.+-.
T Consensus 11 ~g~s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 11 EGESVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred cCCCHHHHHHHHCCCHhHHHHHHHHHH
Confidence 457999999999999999998877654
No 197
>PHA00675 hypothetical protein
Probab=94.55 E-value=0.085 Score=40.21 Aligned_cols=41 Identities=17% Similarity=0.186 Sum_probs=30.8
Q ss_pred hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 046578 316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRG 359 (379)
Q Consensus 316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~ 359 (379)
++|++.|-+.|+..+- .+|.|+.+||+.||+|+++|.++.+
T Consensus 21 AKLt~~qV~~IR~l~~---r~G~s~~~IA~~fGVsrstV~~I~~ 61 (78)
T PHA00675 21 AKLTDAEVERIRELHE---VEGMSYAVLAEKFEQSKGAIAKICR 61 (78)
T ss_pred cccCHHHHHHHHHHHH---hcCccHHHHHHHhCCCHHHHHHHHc
Confidence 3566666555554441 1668999999999999999999865
No 198
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=94.52 E-value=0.036 Score=39.44 Aligned_cols=46 Identities=20% Similarity=0.199 Sum_probs=29.5
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~ 367 (379)
.|+..|+.=+.-.+ ..|.+..+||..|||+.+||+.++.. .+++++
T Consensus 6 ~LTl~eK~~iI~~~----e~g~s~~~ia~~fgv~~sTv~~I~K~-k~~i~~ 51 (53)
T PF04218_consen 6 SLTLEEKLEIIKRL----EEGESKRDIAREFGVSRSTVSTILKN-KDKILE 51 (53)
T ss_dssp S--HHHHHHHHHHH----HCTT-HHHHHHHHT--CCHHHHHHHC-HHHHCC
T ss_pred cCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHh-HHHHHh
Confidence 46666655554455 26689999999999999999998876 444443
No 199
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=94.46 E-value=0.1 Score=37.68 Aligned_cols=44 Identities=14% Similarity=0.135 Sum_probs=33.1
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
.|++.|..||...+.-+ ..++|..|||+.+++++++|++.+.+-
T Consensus 2 glt~~q~~vL~~l~~~~-~~~~t~~~la~~l~~~~~~vs~~v~~L 45 (62)
T PF12802_consen 2 GLTPSQFRVLMALARHP-GEELTQSELAERLGISKSTVSRIVKRL 45 (62)
T ss_dssp TSTHHHHHHHHHHHHST-TSGEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHHCC-CCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 37888888888766422 234899999999999999998876653
No 200
>PF13730 HTH_36: Helix-turn-helix domain
Probab=94.40 E-value=0.16 Score=35.86 Aligned_cols=44 Identities=14% Similarity=0.098 Sum_probs=30.9
Q ss_pred cCCHHHHHHHHHHhhcCCCCC---CCHHHHHHHhCCCHHHHHHHHHH
Q 046578 317 TLSEREADILRLHFGLDGQTP---VSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~---~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.|++.++.|+.......+..+ .|++.||+.+|+|+.||++.+..
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~~ 48 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAIKE 48 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 588888888775432322222 38999999999999999765443
No 201
>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]
Probab=94.30 E-value=0.052 Score=58.71 Aligned_cols=47 Identities=28% Similarity=0.268 Sum_probs=43.3
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
-|+.+|++|+.+.| .|+|.+|||+.+.||..||+.++++.-.||.-.
T Consensus 831 ~Ls~RE~eVL~Lia-----~G~SN~eIa~~L~isl~TVKtH~rniy~KLgV~ 877 (894)
T COG2909 831 PLSQRELEVLGLIA-----QGLSNEEIAQELFISLTTVKTHIRNIYQKLGVA 877 (894)
T ss_pred CccHHHHHHHHHHH-----ccCCHHHHHHHHHHHHHHHHHHHHHHHHHhCcc
Confidence 38999999999998 889999999999999999999999998888544
No 202
>smart00351 PAX Paired Box domain.
Probab=94.11 E-value=0.13 Score=43.32 Aligned_cols=42 Identities=21% Similarity=0.177 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578 318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT 363 (379)
Q Consensus 318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~ 363 (379)
++..+|.-|...|- +|.|..+||+.||||++||++++.+..+
T Consensus 18 ~s~~~R~riv~~~~----~G~s~~~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 18 LPDEERQRIVELAQ----NGVRPCDISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred CCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 55555555555552 6699999999999999999999988643
No 203
>PF02650 HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IPR023054 This domain is found at the C terminus of the sporulation regulator WhiA. It is predicted to form a DNA binding helix-turn-helix structure []. ; PDB: 3HYI_A.
Probab=93.71 E-value=0.17 Score=39.80 Aligned_cols=44 Identities=25% Similarity=0.376 Sum_probs=34.1
Q ss_pred HhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHh--CCCHHHHHHHHHHH
Q 046578 315 LQTLSEREADILRLHFGLDGQTPVSCKEIGRLL--SLSRERIRQIRGIA 361 (379)
Q Consensus 315 L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~L--giS~~~Vr~~~~rA 361 (379)
++.||+..+++..+|.- ..+.|+.|+|+.| .||.++|..++.+.
T Consensus 35 ~~~l~~~l~~~a~lRl~---~Pd~SL~EL~~~~~~~iSKSgvnhrlrKl 80 (85)
T PF02650_consen 35 LDKLPEKLREFAELRLE---NPDASLKELGELLEPPISKSGVNHRLRKL 80 (85)
T ss_dssp GGGS-HHHHHHHHHHHH----TTS-HHHHHHTT--T--HHHHHHHHHHH
T ss_pred cccCCHHHHHHHHHHHH---CccccHHHHHHHHcCcCcHHHHHHHHHHH
Confidence 56899999999999863 4789999999999 99999999887664
No 204
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=93.52 E-value=0.16 Score=46.97 Aligned_cols=46 Identities=15% Similarity=0.127 Sum_probs=35.3
Q ss_pred cCCHHHHHHHHHHh-hcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578 317 TLSEREADILRLHF-GLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT 363 (379)
Q Consensus 317 ~L~~rer~Vl~l~y-gL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~ 363 (379)
.|++++.+++.... +.. .+|+|.+|||+.||+|..||+..+.++..
T Consensus 158 ~Lt~re~~~l~~~i~~~~-~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~ 204 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAHQ-DYEFSTDELANAVNISRVSCRKYLIWLVN 204 (239)
T ss_pred CCCHHHHHHHHHHHHhCC-CCCcCHHHHHHHhCchHHHHHHHHHHHHh
Confidence 48888877765432 111 27899999999999999999999887743
No 205
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=93.47 E-value=0.21 Score=35.27 Aligned_cols=39 Identities=31% Similarity=0.504 Sum_probs=27.5
Q ss_pred HHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578 321 READILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 321 rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
+++.|+.+.. ...+..|.+|||+.||||+.||++.+...
T Consensus 1 R~~~il~~L~--~~~~~it~~eLa~~l~vS~rTi~~~i~~L 39 (55)
T PF08279_consen 1 RQKQILKLLL--ESKEPITAKELAEELGVSRRTIRRDIKEL 39 (55)
T ss_dssp HHHHHHHHHH--HTTTSBEHHHHHHHCTS-HHHHHHHHHHH
T ss_pred CHHHHHHHHH--HcCCCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 4556666543 22245999999999999999998876553
No 206
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 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.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=93.29 E-value=0.25 Score=38.95 Aligned_cols=47 Identities=17% Similarity=0.140 Sum_probs=32.4
Q ss_pred cCCHHHHHHHHHHhhcCC---CCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046578 317 TLSEREADILRLHFGLDG---QTPVSCKEIGRLLSLSRERIRQIRGIALTK 364 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g---~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~k 364 (379)
-++|.|+.-+..|+-+-. .+|+|++|||+.+|+|..||.+ .+|+++.
T Consensus 26 L~T~~E~~~l~~R~~va~~lL~~g~syreIa~~tgvS~aTItR-vsr~Lk~ 75 (87)
T PF01371_consen 26 LCTPDELEALAQRWQVAKELLDEGKSYREIAEETGVSIATITR-VSRCLKY 75 (87)
T ss_dssp HSSHHHHHHHHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHH-HHHHHHH
T ss_pred hCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHH-HHHHHHc
Confidence 377777666554432210 1679999999999999999975 3555554
No 207
>PHA02547 55 RNA polymerase sigma factor; Provisional
Probab=93.05 E-value=0.44 Score=41.92 Aligned_cols=67 Identities=13% Similarity=0.218 Sum_probs=54.8
Q ss_pred HHhHHHHHHHHHhccCCCCC---HHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhc
Q 046578 148 RSYRSLVVSIATGYQGKGLS---LKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKS 214 (379)
Q Consensus 148 ~~y~~lV~~ia~r~~~~~~d---~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~ 214 (379)
...+..+.++.++|.-.+.. .||.+.+|.-..++.+++||+++...+-+|++.++.++..+.++...
T Consensus 44 ~~imkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~kEk 113 (179)
T PHA02547 44 LAIMKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIKKEK 113 (179)
T ss_pred HHHHHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHHHHH
Confidence 34455555666666544554 79999999999999999999999888999999999999999888765
No 208
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=92.84 E-value=0.23 Score=35.49 Aligned_cols=41 Identities=22% Similarity=0.349 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578 318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
|++.|-.+|...+- ..+.+..|||+.+++++++|.+.+.+-
T Consensus 1 lt~~q~~iL~~l~~---~~~~~~~~la~~~~~~~~~~t~~i~~L 41 (59)
T PF01047_consen 1 LTPSQFRILRILYE---NGGITQSELAEKLGISRSTVTRIIKRL 41 (59)
T ss_dssp STHHHHHHHHHHHH---HSSEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH---cCCCCHHHHHHHHCCChhHHHHHHHHH
Confidence 56677777776654 355999999999999999998876654
No 209
>cd00131 PAX Paired Box domain
Probab=92.83 E-value=0.28 Score=41.52 Aligned_cols=41 Identities=15% Similarity=0.079 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
|+...|.-|.+.|- +|+|..+||+.||||+++|.+++.+-.
T Consensus 18 lS~d~R~rIv~~~~----~G~s~~~iA~~~~Vs~~tV~r~i~r~~ 58 (128)
T cd00131 18 LPDSIRQRIVELAQ----SGIRPCDISRQLRVSHGCVSKILNRYY 58 (128)
T ss_pred CCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 45544444444452 679999999999999999999988754
No 210
>PHA02591 hypothetical protein; Provisional
Probab=92.73 E-value=0.14 Score=39.07 Aligned_cols=24 Identities=21% Similarity=0.361 Sum_probs=22.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRG 359 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~ 359 (379)
.|+|.++||+.||+|+.+|++.+.
T Consensus 58 qGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 58 KGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHh
Confidence 669999999999999999998765
No 211
>PRK14082 hypothetical protein; Provisional
Probab=92.56 E-value=0.46 Score=34.94 Aligned_cols=58 Identities=16% Similarity=0.166 Sum_probs=45.6
Q ss_pred ccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhH
Q 046578 138 KERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTY 197 (379)
Q Consensus 138 Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTY 197 (379)
.+....+.++..+.|.|.+-...-. -...|||.||--+.+++.++.++...+.-|.-|
T Consensus 6 ~~~~e~e~ii~~FepkIkKsL~~T~--yqeREDLeQElk~Ki~eK~~~~~~~e~PGF~ef 63 (65)
T PRK14082 6 DDTEEIEHLIENFSPMIKKKLSNTS--YQEREDLEQELKIKIIEKADMLLCQEVPGFWEF 63 (65)
T ss_pred hhHHHHHHHHHHccHHHHHHHhcCC--hhhHHHHHHHHHHHHHHHHHHhhcccCCcHHHh
Confidence 3456778899999999998665542 257899999999999999999987666556544
No 212
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=92.54 E-value=0.35 Score=36.17 Aligned_cols=39 Identities=15% Similarity=0.243 Sum_probs=27.3
Q ss_pred HHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 321 READILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 321 rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.+..|+.+.. -.|.+++|..|||+.+|++..+|++++++
T Consensus 7 ~~~~IL~~L~-~~g~~~~ta~eLa~~lgl~~~~v~r~L~~ 45 (68)
T smart00550 7 LEEKILEFLE-NSGDETSTALQLAKNLGLPKKEVNRVLYS 45 (68)
T ss_pred HHHHHHHHHH-HCCCCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 3445555443 22323699999999999999999877654
No 213
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=92.45 E-value=0.42 Score=32.83 Aligned_cols=37 Identities=22% Similarity=0.298 Sum_probs=27.1
Q ss_pred HHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 320 EREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 320 ~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
|.-..|+.+-. ..+++..||++.+|+|+++|++.+..
T Consensus 2 ~~R~~Il~~L~----~~~~~~~el~~~l~~s~~~vs~hL~~ 38 (47)
T PF01022_consen 2 PTRLRILKLLS----EGPLTVSELAEELGLSQSTVSHHLKK 38 (47)
T ss_dssp HHHHHHHHHHT----TSSEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHH----hCCCchhhHHHhccccchHHHHHHHH
Confidence 34455655544 26799999999999999999988654
No 214
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=92.09 E-value=0.28 Score=42.08 Aligned_cols=27 Identities=15% Similarity=0.193 Sum_probs=24.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
+|+|.+|||+++|+|.+||..+++|-.
T Consensus 20 ~G~S~re~Ak~~gvs~sTvy~wv~r~~ 46 (138)
T COG3415 20 EGLSCREAAKRFGVSISTVYRWVRRYR 46 (138)
T ss_pred cCccHHHHHHHhCccHHHHHHHHHHhc
Confidence 779999999999999999999988754
No 215
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=91.84 E-value=0.85 Score=39.04 Aligned_cols=50 Identities=22% Similarity=0.224 Sum_probs=31.8
Q ss_pred HHHHHhcCCHHHHHHHHHH----hhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 311 LKELLQTLSEREADILRLH----FGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 311 L~~~L~~L~~rer~Vl~l~----ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
+.++-.+|++.|+....+. +...+.+..|+.|||+.+||+++|..++.+.
T Consensus 4 ~~~le~~L~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis~~tLYrWr~~ 57 (142)
T PF13022_consen 4 LKELEAKLTLQQRKAAQLLVENELMPENGERRTQAEIAEEVGISRSTLYRWRQQ 57 (142)
T ss_dssp HHHHHTTS-HHHHHHHHHHHHHHHS------S-HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHcCHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCCHHHHHHHHhc
Confidence 4555678999998854432 1112236799999999999999999999853
No 216
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=91.68 E-value=0.45 Score=36.40 Aligned_cols=53 Identities=17% Similarity=0.151 Sum_probs=36.4
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhh-cCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 308 KQELKELLQTLSEREADILRLHFG-LDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 308 ~~~L~~~L~~L~~rer~Vl~l~yg-L~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
...|......|++.|+.|.....- ......+|..|||+..|+|.++|.+..++
T Consensus 4 ~~~i~~~~~~ls~~e~~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~kk 57 (77)
T PF01418_consen 4 LEKIRSQYNSLSPTEKKIADYILENPDEIAFMSISELAEKAGVSPSTIVRFCKK 57 (77)
T ss_dssp HHHHHHHGGGS-HHHHHHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHHHH
T ss_pred HHHHHHHHhhCCHHHHHHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHHHH
Confidence 356777788999999998875421 01224699999999999999999877654
No 217
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=91.67 E-value=0.46 Score=33.07 Aligned_cols=34 Identities=29% Similarity=0.297 Sum_probs=26.5
Q ss_pred HHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578 323 ADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 323 r~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
+.|+.+.. +..|.++||+.+|+|..||.+++.+.
T Consensus 18 ~~i~~~~~-----~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 18 QYILKLLR-----ESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred HHHHHHHh-----hcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 34555543 33699999999999999999998764
No 218
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=91.64 E-value=0.18 Score=34.80 Aligned_cols=22 Identities=18% Similarity=0.302 Sum_probs=20.1
Q ss_pred CHHHHHHHhCCCHHHHHHHHHH
Q 046578 339 SCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 339 S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
|++|||+..|+|..||++.++.
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~ 22 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNG 22 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTT
T ss_pred CHHHHHHHHCcCHHHHHHHHhC
Confidence 6899999999999999998864
No 219
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=91.58 E-value=0.48 Score=38.30 Aligned_cols=42 Identities=21% Similarity=0.189 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
|++.++.|+....- + ...|+.+||+.+|+|+.+|++++.+-.
T Consensus 1 ld~~D~~il~~L~~-~--~~~~~~~la~~l~~s~~tv~~~l~~L~ 42 (108)
T smart00344 1 LDEIDRKILEELQK-D--ARISLAELAKKVGLSPSTVHNRVKRLE 42 (108)
T ss_pred CCHHHHHHHHHHHH-h--CCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 46778888876542 2 469999999999999999988766543
No 220
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=91.58 E-value=0.51 Score=36.32 Aligned_cols=42 Identities=31% Similarity=0.465 Sum_probs=34.2
Q ss_pred cCCHHHHHHHHHH---hhcCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 046578 317 TLSEREADILRLH---FGLDGQTPVSCKEIGRLLSLSRERIRQIRG 359 (379)
Q Consensus 317 ~L~~rer~Vl~l~---ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~ 359 (379)
.|+++|++||... | ....+...-++||+.+++|..|||+...
T Consensus 1 ~Lt~rq~~IL~alV~~Y-~~~~~PVgSk~ia~~l~~s~aTIRN~M~ 45 (78)
T PF03444_consen 1 MLTERQREILKALVELY-IETGEPVGSKTIAEELGRSPATIRNEMA 45 (78)
T ss_pred CCCHHHHHHHHHHHHHH-HhcCCCcCHHHHHHHHCCChHHHHHHHH
Confidence 3889999988753 3 3445889999999999999999998754
No 221
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=91.54 E-value=1.1 Score=32.50 Aligned_cols=38 Identities=21% Similarity=0.269 Sum_probs=28.5
Q ss_pred HHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 320 EREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 320 ~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
|.-+.|+.+... ..++|..|||+.+|++.++|++.+..
T Consensus 10 p~R~~Il~~L~~---~~~~t~~ela~~l~~~~~t~s~hL~~ 47 (61)
T PF12840_consen 10 PTRLRILRLLAS---NGPMTVSELAEELGISQSTVSYHLKK 47 (61)
T ss_dssp HHHHHHHHHHHH---CSTBEHHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHhc---CCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 666667665521 37899999999999999999887543
No 222
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=91.52 E-value=0.51 Score=36.99 Aligned_cols=43 Identities=12% Similarity=-0.004 Sum_probs=36.7
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
.|+|.-|..|..+. ++ ++.+..++|+.+|||..|+++++.|=+
T Consensus 8 ~Lt~~gR~~lv~~v-v~--~g~~~a~aA~~~gVS~~Ta~kW~~Ryr 50 (85)
T PF13011_consen 8 RLTPRGRLRLVRRV-VE--QGWPVAHAAAEFGVSRRTAYKWLARYR 50 (85)
T ss_pred CCCHHHHHHHHHHH-HH--cCCcHHHHHHHhCCCHHHHHHHHHHHH
Confidence 68999998888876 33 569999999999999999999987744
No 223
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=91.51 E-value=2.7 Score=34.93 Aligned_cols=25 Identities=16% Similarity=0.165 Sum_probs=21.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.+.|+.|||+.||||.++|...+.+
T Consensus 70 pd~tl~Ela~~l~Vs~~ti~~~Lkr 94 (119)
T PF01710_consen 70 PDATLRELAERLGVSPSTIWRALKR 94 (119)
T ss_pred CCcCHHHHHHHcCCCHHHHHHHHHH
Confidence 6799999999999999999765544
No 224
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=91.31 E-value=0.43 Score=34.84 Aligned_cols=43 Identities=28% Similarity=0.410 Sum_probs=28.0
Q ss_pred CCHHHHHHHHHHhhcC-CCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 318 LSEREADILRLHFGLD-GQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 318 L~~rer~Vl~l~ygL~-g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
|++....-|...|-+. +....+..+||+.||+|+++|...+++
T Consensus 2 Lt~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~ 45 (60)
T PF01325_consen 2 LTESEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKR 45 (60)
T ss_dssp CSCHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHH
Confidence 3444444444443333 347799999999999999999766544
No 225
>PRK11083 DNA-binding response regulator CreB; Provisional
Probab=91.26 E-value=0.32 Score=43.58 Aligned_cols=51 Identities=16% Similarity=0.099 Sum_probs=42.7
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCC-----HHHHHHHHHHHHHHHHhH
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLS-----RERIRQIRGIALTKLQQT 368 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS-----~~~Vr~~~~rAl~kLR~~ 368 (379)
.|+++|.+|+.+.. -+.+.++|.+||++.++.+ ..||+.++++.++||...
T Consensus 154 ~Lt~~E~~il~~l~-~~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~l~~Kl~~~ 209 (228)
T PRK11083 154 TLTRYEFLLLKTLL-LSPGRVFSRQQLMDIVWEDAQDSYDRTVDTHIKTLRAKLRAI 209 (228)
T ss_pred ecCHHHHHHHHHHH-hCCCceECHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhccC
Confidence 59999999999876 2222569999999999986 789999999999999743
No 226
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=91.20 E-value=0.49 Score=34.63 Aligned_cols=43 Identities=16% Similarity=0.269 Sum_probs=27.8
Q ss_pred CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
|++.|..||.... ....+++..+||+.++++..+|++.+++..
T Consensus 1 lt~~q~~vL~~l~--~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~ 43 (68)
T PF13463_consen 1 LTRPQWQVLRALA--HSDGPMTQSDLAERLGISKSTVSRIIKKLE 43 (68)
T ss_dssp --HHHHHHHHHHT----TS-BEHHHHHHHTT--HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHH--ccCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4667777776544 124789999999999999999986655543
No 227
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=90.85 E-value=0.66 Score=40.30 Aligned_cols=42 Identities=12% Similarity=0.139 Sum_probs=33.8
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
.|++.++.||..-- -+ ...|+.|||+.+|+|+++|++++.+-
T Consensus 6 ~lD~~D~~Il~~Lq-~d--~R~s~~eiA~~lglS~~tV~~Ri~rL 47 (153)
T PRK11179 6 QIDNLDRGILEALM-EN--ARTPYAELAKQFGVSPGTIHVRVEKM 47 (153)
T ss_pred ccCHHHHHHHHHHH-Hc--CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 47888999988654 23 46999999999999999998876553
No 228
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional
Probab=90.62 E-value=0.34 Score=43.14 Aligned_cols=50 Identities=20% Similarity=0.153 Sum_probs=41.6
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHh
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLS-----LSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~Lg-----iS~~~Vr~~~~rAl~kLR~ 367 (379)
.|+++|.+++.+.. -+.+..+|.++|++.+. ++..+|+..+++.++||..
T Consensus 149 ~Lt~~E~~il~~l~-~~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~lr~Kl~~ 203 (219)
T PRK10336 149 TLKPKEFALLELLM-RNAGRVLPRKLIEEKLYTWDEEVTSNAVEVHVHHLRRKLGS 203 (219)
T ss_pred ecCHHHHHHHHHHH-hCCCccCcHHHHHHHhcCCCCCCCccCHHHHHHHHHHhcCC
Confidence 49999999999765 22224589999999996 9999999999999999863
No 229
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=90.53 E-value=0.26 Score=45.26 Aligned_cols=39 Identities=15% Similarity=0.238 Sum_probs=29.2
Q ss_pred CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
|+++ +|+.+.- .|..|+|.+|||+.||+|+.||++.+..
T Consensus 162 Lt~r--~Vl~~~~--~g~~g~s~~eIa~~l~iS~~Tv~~~~~~ 200 (225)
T PRK10046 162 LTLN--AVRKLFK--EPGVQHTAETVAQALTISRTTARRYLEY 200 (225)
T ss_pred HHHH--HHHHHHH--cCCCCcCHHHHHHHhCccHHHHHHHHHH
Confidence 5554 5666543 2334699999999999999999998753
No 230
>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=90.50 E-value=0.64 Score=40.99 Aligned_cols=42 Identities=14% Similarity=0.152 Sum_probs=34.5
Q ss_pred CHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578 319 SEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT 363 (379)
Q Consensus 319 ~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~ 363 (379)
|+.-|.-++..|.+ +++|+..+|..+|||.+|+++++.+|..
T Consensus 4 ~~e~R~~~R~~YV~---~~~sLe~aA~~~gVs~~TarrWK~~Ak~ 45 (165)
T PF08822_consen 4 PQETRDAVRRAYVF---DRLSLEQAAAKCGVSYATARRWKREAKA 45 (165)
T ss_pred cHHHHHHHHHHHHh---CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 45567777777742 5599999999999999999999998864
No 231
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=90.28 E-value=0.27 Score=36.45 Aligned_cols=41 Identities=27% Similarity=0.351 Sum_probs=30.9
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.|++.|.+|+..-. . ..+.|..|||+.+|+++++|+..+.+
T Consensus 5 gLs~~E~~vy~~Ll--~-~~~~t~~eIa~~l~i~~~~v~~~L~~ 45 (68)
T PF01978_consen 5 GLSENEAKVYLALL--K-NGPATAEEIAEELGISRSTVYRALKS 45 (68)
T ss_dssp CHHHHHHHHHHHHH--H-HCHEEHHHHHHHHTSSHHHHHHHHHH
T ss_pred CcCHHHHHHHHHHH--H-cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 46677777776432 1 25699999999999999999766544
No 232
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=90.01 E-value=1.6 Score=34.75 Aligned_cols=46 Identities=28% Similarity=0.281 Sum_probs=33.7
Q ss_pred HhcCCHHHHHHHHHHh----hcC-CCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 315 LQTLSEREADILRLHF----GLD-GQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 315 L~~L~~rer~Vl~l~y----gL~-g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
...+++++..+|.... |.. ....+|..|||+.+|+++.+|++.+.+
T Consensus 20 ~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~ 70 (95)
T TIGR01610 20 GADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKS 70 (95)
T ss_pred hCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHH
Confidence 3478999998877432 211 236799999999999999998765443
No 233
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=90.01 E-value=0.52 Score=31.65 Aligned_cols=39 Identities=21% Similarity=0.256 Sum_probs=25.9
Q ss_pred CHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 319 SEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 319 ~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
..-|+.+|.-..- ..+-+..+.|+.||||+.++++.+.+
T Consensus 3 ~~~E~~~i~~aL~---~~~gn~~~aA~~Lgisr~tL~~klkk 41 (42)
T PF02954_consen 3 EEFEKQLIRQALE---RCGGNVSKAARLLGISRRTLYRKLKK 41 (42)
T ss_dssp HHHHHHHHHHHHH---HTTT-HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHH---HhCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 3456666665432 13468999999999999999876653
No 234
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=90.00 E-value=0.55 Score=32.93 Aligned_cols=33 Identities=21% Similarity=0.348 Sum_probs=23.7
Q ss_pred HHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 328 LHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 328 l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
+.++-....++|..|||+.+|+++++|.+++..
T Consensus 9 L~~l~~~~~~~t~~eia~~~gl~~stv~r~L~t 41 (52)
T PF09339_consen 9 LEALAESGGPLTLSEIARALGLPKSTVHRLLQT 41 (52)
T ss_dssp HHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 334333346689999999999999999877543
No 235
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=90.00 E-value=0.58 Score=42.45 Aligned_cols=34 Identities=29% Similarity=0.282 Sum_probs=27.3
Q ss_pred HHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 322 EADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 322 er~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
++.|..++- +|+|..+||+.||||++||+++++.
T Consensus 162 ~~~i~~~~~-----~g~s~~~iak~lgis~~Tv~r~~k~ 195 (200)
T PRK13413 162 EEKIKKLLD-----KGTSKSEIARKLGVSRTTLARFLKT 195 (200)
T ss_pred HHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 345666543 6799999999999999999998763
No 236
>PF12728 HTH_17: Helix-turn-helix domain
Probab=89.59 E-value=0.38 Score=33.40 Aligned_cols=24 Identities=25% Similarity=0.342 Sum_probs=21.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
+|.+|+|+.||||+++|+++..+.
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcC
Confidence 789999999999999999988654
No 237
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=89.43 E-value=17 Score=35.46 Aligned_cols=180 Identities=17% Similarity=0.070 Sum_probs=90.1
Q ss_pred HHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcch
Q 046578 144 ERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSM 223 (379)
Q Consensus 144 e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~~ 223 (379)
++-+......|..++.++.-. +-+.|....+++.+.....-+|.+..+.+..++.-++.. .
T Consensus 119 er~l~~a~~~I~~~~~~L~Lp-----~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR~----~---------- 179 (310)
T PRK00423 119 ERNLAFALSELDRIASQLGLP-----RSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRR----C---------- 179 (310)
T ss_pred hHHHHHHHHHHHHHHHHcCCC-----HHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHH----c----------
Confidence 334455557778888777322 345555556666665555556767777766666654432 1
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHHHH
Q 046578 224 AGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQ 303 (379)
Q Consensus 224 ~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~~~ 303 (379)
|-.-+..||++.++++..++........+.+.++.+..+ ...+..-+.+.-. -+.+..
T Consensus 180 ------------------~~prtl~eI~~~~~v~~k~i~~~~~~l~k~L~~~~~~~~--p~~~i~r~~~~L~-L~~~v~- 237 (310)
T PRK00423 180 ------------------KVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPPTD--PIDYVPRFASELG-LSGEVQ- 237 (310)
T ss_pred ------------------CCCcCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCCC--HHHHHHHHHHHcC-CCHHHH-
Confidence 222356677777777777666554432222222221110 0000000000000 011111
Q ss_pred HHHHHHHHHHHHh-cC----CHH--HHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 046578 304 KQLMKQELKELLQ-TL----SER--EADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQ 366 (379)
Q Consensus 304 ~~e~~~~L~~~L~-~L----~~r--er~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR 366 (379)
+.....+..+.+ .| .|. -..+|.+..-+.| .+.|++|||+..|++..||++.++.-.+.|.
T Consensus 238 -~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g-~~~t~keIa~v~~Vs~~tI~~~ykel~~~l~ 305 (310)
T PRK00423 238 -KKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLG-ERRTQREVAEVAGVTEVTVRNRYKELAEKLD 305 (310)
T ss_pred -HHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhC-CCCCHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 111122222221 11 121 1223333322344 6799999999999999999988777666543
No 238
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=89.13 E-value=0.77 Score=40.41 Aligned_cols=41 Identities=20% Similarity=0.121 Sum_probs=32.5
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.|++.+++||..-- -+ ...|+.|||+.+|+|+++|++++.|
T Consensus 11 ~lD~~D~~IL~~Lq-~d--~R~s~~eiA~~lglS~~tv~~Ri~r 51 (164)
T PRK11169 11 DLDRIDRNILNELQ-KD--GRISNVELSKRVGLSPTPCLERVRR 51 (164)
T ss_pred hHHHHHHHHHHHhc-cC--CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 36777888887543 23 5699999999999999999887655
No 239
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=89.12 E-value=0.9 Score=34.99 Aligned_cols=39 Identities=15% Similarity=0.209 Sum_probs=27.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH-H----HHHHHHhHHhhch
Q 046578 335 QTPVSCKEIGRLLSLSRERIRQIRG-I----ALTKLQQTNILNN 373 (379)
Q Consensus 335 ~e~~S~~EIAe~LgiS~~~Vr~~~~-r----Al~kLR~~l~~~~ 373 (379)
..++|++|+|+.+|+|+++|+++.+ + .+.+|.+.+...+
T Consensus 29 ~~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~aLG 72 (80)
T PF13744_consen 29 ERGLTQAELAERLGISQPRVSRLENGKIDDFSLDTLLRYLEALG 72 (80)
T ss_dssp CCT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHHHTT
T ss_pred HcCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHHHcC
Confidence 3679999999999999999999884 2 3666666665544
No 240
>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional
Probab=89.10 E-value=0.61 Score=42.22 Aligned_cols=50 Identities=16% Similarity=0.082 Sum_probs=43.0
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHh
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLS-----LSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~Lg-----iS~~~Vr~~~~rAl~kLR~ 367 (379)
.|+++|++|+.+... +.+++.|.++|++.+. ++..||...+++.++||..
T Consensus 160 ~Lt~~e~~il~~l~~-~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~lr~kl~~ 214 (240)
T PRK10710 160 DLTPAEFRLLKTLSH-EPGKVFSREQLLNHLYDDYRVVTDRTIDSHIKNLRRKLES 214 (240)
T ss_pred ecCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCcCcCCCccCHHHHHHHHHHHhhc
Confidence 499999999998762 3235799999999998 9999999999999999964
No 241
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=89.03 E-value=0.93 Score=31.89 Aligned_cols=39 Identities=31% Similarity=0.354 Sum_probs=24.3
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRG 359 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~ 359 (379)
.|++.||--|.... ..|+++.|||..+|-|+..|++.++
T Consensus 4 ~Lt~~Eqaqid~m~----qlG~s~~~isr~i~RSr~~Ir~yl~ 42 (50)
T PF11427_consen 4 TLTDAEQAQIDVMH----QLGMSLREISRRIGRSRTCIRRYLK 42 (50)
T ss_dssp ---HHHHHHHHHHH----HTT--HHHHHHHHT--HHHHHHHHH
T ss_pred cCCHHHHHHHHHHH----HhchhHHHHHHHhCccHHHHHHHhc
Confidence 46766666665554 2569999999999999999988754
No 242
>PRK12423 LexA repressor; Provisional
Probab=88.84 E-value=0.7 Score=42.15 Aligned_cols=48 Identities=27% Similarity=0.364 Sum_probs=34.0
Q ss_pred hcCCHHHHHHHHHHhh-c-CCCCCCCHHHHHHHhC-CCHHHHHHHHHHHHHHHHh
Q 046578 316 QTLSEREADILRLHFG-L-DGQTPVSCKEIGRLLS-LSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 316 ~~L~~rer~Vl~l~yg-L-~g~e~~S~~EIAe~Lg-iS~~~Vr~~~~rAl~kLR~ 367 (379)
..|++++++|+...-- + .++-..|.+|||+.|| .|+++|+. ++++|++
T Consensus 2 ~~lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~----~l~~L~~ 52 (202)
T PRK12423 2 DTLTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARK----HVQALAE 52 (202)
T ss_pred CcCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHH----HHHHHHH
Confidence 3589999999985421 1 1223459999999999 59999985 4555555
No 243
>PRK15479 transcriptional regulatory protein TctD; Provisional
Probab=88.74 E-value=0.74 Score=40.93 Aligned_cols=50 Identities=26% Similarity=0.252 Sum_probs=41.1
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHh
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLS-----LSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~Lg-----iS~~~Vr~~~~rAl~kLR~ 367 (379)
.|+++|.+|+.+.. -+-+...|.++|++.+. +|..||..++++.++||..
T Consensus 148 ~Lt~~E~~il~~l~-~~~~~~~~~~~i~~~l~~~~~~~~~~tv~~~i~~ir~kl~~ 202 (221)
T PRK15479 148 ALTPREQALLTVLM-YRRTRPVSRQQLFEQVFSLNDEVSPESIELYIHRLRKKLQG 202 (221)
T ss_pred ecCHHHHHHHHHHH-hCCCCcCcHHHHHHHhcCCCCCCCcccHHHHHHHHHHhcCC
Confidence 59999999998765 22114579999999986 9999999999999999863
No 244
>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=88.48 E-value=0.46 Score=31.92 Aligned_cols=25 Identities=24% Similarity=0.282 Sum_probs=22.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
+|..|+|+.+|||+++|+++...+.
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 5789999999999999999987764
No 245
>PF13551 HTH_29: Winged helix-turn helix
Probab=88.45 E-value=0.89 Score=36.53 Aligned_cols=26 Identities=27% Similarity=0.254 Sum_probs=23.2
Q ss_pred CCC-CHHHHHHHhCCCHHHHHHHHHHH
Q 046578 336 TPV-SCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 336 e~~-S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
+|. |..+||+.+|+|+.||++++++-
T Consensus 10 ~g~~~~~~ia~~lg~s~~Tv~r~~~~~ 36 (112)
T PF13551_consen 10 EGVSTIAEIARRLGISRRTVYRWLKRY 36 (112)
T ss_pred cCCCcHHHHHHHHCcCHHHHHHHHHHH
Confidence 668 59999999999999999998873
No 246
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=88.45 E-value=2.2 Score=35.94 Aligned_cols=49 Identities=16% Similarity=0.318 Sum_probs=38.0
Q ss_pred HHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 310 ELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 310 ~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.+..++-.|++.+-+|+....- . ..+.|..|||+.+|++++||++.+++
T Consensus 17 dvl~c~~GLs~~Dv~v~~~LL~-~-~~~~tvdelae~lnr~rStv~rsl~~ 65 (126)
T COG3355 17 DVLKCVYGLSELDVEVYKALLE-E-NGPLTVDELAEILNRSRSTVYRSLQN 65 (126)
T ss_pred HHHHHHhCCcHHHHHHHHHHHh-h-cCCcCHHHHHHHHCccHHHHHHHHHH
Confidence 4667788999999999876531 1 26799999999999999999654443
No 247
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model 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 model 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 (pfam00376).
Probab=88.15 E-value=0.49 Score=31.96 Aligned_cols=24 Identities=13% Similarity=0.299 Sum_probs=21.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
+|.+|+|+.||||+++|+++.+.+
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g 25 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEG 25 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcC
Confidence 789999999999999999988665
No 248
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=88.12 E-value=2.6 Score=34.59 Aligned_cols=41 Identities=20% Similarity=0.243 Sum_probs=33.3
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.|++.|..||..... ..+.|..|||+.+|++.++|.+.+.+
T Consensus 25 ~lt~~q~~iL~~l~~---~~~~t~~ela~~~~~~~~tvs~~l~~ 65 (118)
T TIGR02337 25 GLTEQQWRILRILAE---QGSMEFTQLANQACILRPSLTGILAR 65 (118)
T ss_pred CCCHHHHHHHHHHHH---cCCcCHHHHHHHhCCCchhHHHHHHH
Confidence 689999988876542 35799999999999999999766554
No 249
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=87.94 E-value=0.95 Score=37.78 Aligned_cols=24 Identities=25% Similarity=0.325 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRG 359 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~ 359 (379)
+|+|+.+||+.||+|+..|++.++
T Consensus 21 eG~Sq~~iA~LLGltqaAVS~Yls 44 (119)
T COG2522 21 EGLSQYRIAKLLGLTQAAVSQYLS 44 (119)
T ss_pred cCCcHHHHHHHhCCCHHHHHHHHc
Confidence 579999999999999999999875
No 250
>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB. PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself. It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well.
Probab=87.78 E-value=0.45 Score=42.46 Aligned_cols=50 Identities=14% Similarity=0.155 Sum_probs=41.1
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHH-----HHHhCCCHHHHHHHHHHHHHHHHh
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEI-----GRLLSLSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EI-----Ae~LgiS~~~Vr~~~~rAl~kLR~ 367 (379)
.|+++|.+|+.+..- +-+.++|.++| |+.++++..||+..+++.++||..
T Consensus 154 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~l~~Kl~~ 208 (226)
T TIGR02154 154 SLGPTEFRLLHFFMT-HPERVYSREQLLDRVWGRDVYVEERTVDVHIRRLRKALNP 208 (226)
T ss_pred EcCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCCCCCCCCccHHHHHHHHHHhhcc
Confidence 599999999988752 21246788888 788999999999999999999963
No 251
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=87.71 E-value=1.4 Score=37.81 Aligned_cols=42 Identities=24% Similarity=0.234 Sum_probs=33.7
Q ss_pred hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
..|++.++.||...- -+ -..|+.|||+.+|+|+.+|+.++.+
T Consensus 4 ~~lD~~D~~IL~~L~-~d--~r~~~~eia~~lglS~~~v~~Ri~~ 45 (154)
T COG1522 4 MKLDDIDRRILRLLQ-ED--ARISNAELAERVGLSPSTVLRRIKR 45 (154)
T ss_pred ccccHHHHHHHHHHH-Hh--CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 468888999998653 22 4499999999999999999877554
No 252
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=87.69 E-value=1.8 Score=34.67 Aligned_cols=40 Identities=23% Similarity=0.235 Sum_probs=30.0
Q ss_pred cCCHHHHHHHHHHhhcC---CCCCCCHHHHHHHhCCCHHHHHH
Q 046578 317 TLSEREADILRLHFGLD---GQTPVSCKEIGRLLSLSRERIRQ 356 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~---g~e~~S~~EIAe~LgiS~~~Vr~ 356 (379)
-|+|.||+-+-.|+-+- =..++|++||+..||+|..+|-+
T Consensus 37 lLTpdEReal~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITR 79 (103)
T COG2973 37 LLTPDEREALGTRVRIVEELLRGELSQREIAQKLGVSIATITR 79 (103)
T ss_pred HcCHhHHHHHHHHHHHHHHHHhccccHHHHHHHhCcchhhhcc
Confidence 48888888877765432 01369999999999999988843
No 253
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=87.06 E-value=0.66 Score=32.49 Aligned_cols=25 Identities=32% Similarity=0.377 Sum_probs=20.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.++|++|+|+.+|+|+++|+++++.
T Consensus 8 ~gls~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 8 KGLSQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred cCCCHHHHHHHhCCCcchhHHHhcC
Confidence 5699999999999999999998765
No 254
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=86.83 E-value=2.8 Score=31.04 Aligned_cols=42 Identities=26% Similarity=0.199 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCC-HHHHHHHHHh
Q 046578 226 MVAKIAEANNVLSRRLRRMPTDSEIAEMLNIH-VSTVRLAIER 267 (379)
Q Consensus 226 ~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis-~~~~~~~l~~ 267 (379)
.-.++..+......+.|..||..|||+.+|++ ...+...+..
T Consensus 7 rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~ 49 (65)
T PF01726_consen 7 RQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKA 49 (65)
T ss_dssp HHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence 44566677777888999999999999999997 8888877654
No 255
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=86.79 E-value=1.2 Score=31.99 Aligned_cols=25 Identities=28% Similarity=0.251 Sum_probs=21.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
...|.+|+|+.||+|..||++-+..
T Consensus 13 ~~~s~~ela~~~~VS~~TiRRDl~~ 37 (57)
T PF08220_consen 13 GKVSVKELAEEFGVSEMTIRRDLNK 37 (57)
T ss_pred CCEEHHHHHHHHCcCHHHHHHHHHH
Confidence 5689999999999999999876543
No 256
>CHL00148 orf27 Ycf27; Reviewed
Probab=86.65 E-value=0.96 Score=40.92 Aligned_cols=50 Identities=16% Similarity=0.095 Sum_probs=41.9
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHh-------CCCHHHHHHHHHHHHHHHHh
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLL-------SLSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~L-------giS~~~Vr~~~~rAl~kLR~ 367 (379)
.|+++|.+|+.+.. -+.+.++|.+||++.+ +++..+|..++++.++||..
T Consensus 161 ~Lt~~E~~il~~l~-~~~~~~~s~~~i~~~l~~~~~~~~~~~~tv~~~i~~lr~KL~~ 217 (240)
T CHL00148 161 RLTGMEFSLLELLI-SKSGEIFSRATILKEVWGYTPERHIDTRVVDVHISRLRAKLED 217 (240)
T ss_pred EcCHHHHHHHHHHH-HCCCEEEcHHHHHHHhcCCCcccCCCcccHHHHHHHHHHHhcc
Confidence 49999999998765 2222679999999999 48999999999999999974
No 257
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=86.53 E-value=1.5 Score=31.69 Aligned_cols=37 Identities=22% Similarity=0.316 Sum_probs=27.2
Q ss_pred HHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 321 READILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 321 rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
++-.++.+-+. ...+++.|+|+.+|+|..+|++.+..
T Consensus 6 rq~~Ll~~L~~---~~~~~~~ela~~l~~S~rti~~~i~~ 42 (59)
T PF08280_consen 6 RQLKLLELLLK---NKWITLKELAKKLNISERTIKNDINE 42 (59)
T ss_dssp HHHHHHHHHHH---HTSBBHHHHHHHCTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHc---CCCCcHHHHHHHHCCCHHHHHHHHHH
Confidence 45556665553 46799999999999999999877544
No 258
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=86.53 E-value=0.91 Score=41.05 Aligned_cols=45 Identities=22% Similarity=0.272 Sum_probs=34.0
Q ss_pred hcCCHHHHHHHHHHhh--cCCCCCCCHHHHHHHhCCC-HHHHHHHHHH
Q 046578 316 QTLSEREADILRLHFG--LDGQTPVSCKEIGRLLSLS-RERIRQIRGI 360 (379)
Q Consensus 316 ~~L~~rer~Vl~l~yg--L~g~e~~S~~EIAe~LgiS-~~~Vr~~~~r 360 (379)
..|+++|++|+....- ..+..+.|.+|||+.+|++ ++||+.++.+
T Consensus 2 ~~lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~ 49 (199)
T TIGR00498 2 KPLTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKA 49 (199)
T ss_pred CccCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHH
Confidence 3589999999987541 1123458899999999998 9999876544
No 259
>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator. This model describes a family of DNA-binding response regulator proteins, associated with an adjacent histidine kinase (TIGR03785) to form a two-component system. This system co-occurs with, and often is adjacent to, a proteobacterial variant form of the protein sorting transpeptidase called sortase (TIGR03784), and a single target protein for the sortase. We give this protein the gene symbol pdsR, for Proteobacterial Dedicated Sortase system Response regulator.
Probab=86.49 E-value=1.2 Score=40.12 Aligned_cols=50 Identities=12% Similarity=-0.003 Sum_probs=41.0
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHH--HHHhCCCHHHHHHHHHHHHHHHHh
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEI--GRLLSLSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EI--Ae~LgiS~~~Vr~~~~rAl~kLR~ 367 (379)
.|+++|.+|+.+.. -+.+.-+|.++| |..++++..||+.++.|.++||..
T Consensus 156 ~Lt~~E~~il~~l~-~~~g~v~s~~~i~~~~~~~~~~~tv~~~v~rlr~Kl~~ 207 (227)
T TIGR03787 156 DLTVTEFWMVHALA-KHPGHVKSRQQLMDAAKIVVDDSTITSHIKRIRKKFQA 207 (227)
T ss_pred cCCHHHHHHHHHHH-hCCCccccHHHHHHHhhhcCCccCHHHHHHHHHHHhcc
Confidence 49999999999875 111133599999 888999999999999999999974
No 260
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=86.43 E-value=1.6 Score=30.83 Aligned_cols=51 Identities=12% Similarity=0.171 Sum_probs=38.4
Q ss_pred cCCHHHHHHHHHHhhcCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578 317 TLSEREADILRLHFGLDGQ-TPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~-e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~ 367 (379)
.+++.+..+|...|-.+.. ......+||..+|++...|..+...-+.+.|+
T Consensus 6 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 6 RFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 4678888888888753321 12345679999999999999999988777664
No 261
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=86.26 E-value=3.8 Score=34.97 Aligned_cols=47 Identities=15% Similarity=0.183 Sum_probs=36.6
Q ss_pred HHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 311 LKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 311 L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
+...+. .|++.|..||...+. .++.|..|||+.+|++.++|.+.+.+
T Consensus 29 ~~~~l~~~glt~~q~~vL~~l~~---~~~~t~~eLa~~l~i~~~tvsr~l~~ 77 (144)
T PRK11512 29 LNEYLSPLDITAAQFKVLCSIRC---AACITPVELKKVLSVDLGALTRMLDR 77 (144)
T ss_pred HHHHhcccCCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 444443 589999988886552 35699999999999999999877655
No 262
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=86.17 E-value=8.3 Score=39.24 Aligned_cols=37 Identities=16% Similarity=0.284 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Q 046578 228 AKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLA 264 (379)
Q Consensus 228 ~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~ 264 (379)
..+.+....+..++|++|+..|.|...|++...++..
T Consensus 111 ~~l~~~~~~l~~~~g~~pt~~ewa~~~~~~~~~l~~~ 147 (415)
T PRK07598 111 LRLIEVRERLTSELGHRPSLERWAKTADISLADLKPT 147 (415)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCcHHHHHHh
Confidence 3455666788999999999999997777765555544
No 263
>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=86.09 E-value=0.58 Score=31.87 Aligned_cols=25 Identities=24% Similarity=0.361 Sum_probs=22.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
+|..|+|+.+|||..+|+.+..+++
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999987765
No 264
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=86.09 E-value=1.9 Score=29.36 Aligned_cols=25 Identities=32% Similarity=0.341 Sum_probs=21.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.+.+..+|++.+|+|+.+|++.+.+
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~ 37 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNK 37 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4599999999999999999877654
No 265
>PRK00215 LexA repressor; Validated
Probab=85.91 E-value=1.7 Score=39.48 Aligned_cols=45 Identities=24% Similarity=0.230 Sum_probs=33.8
Q ss_pred CCHHHHHHHHHHh--hcCCCCCCCHHHHHHHhCC-CHHHHHHHHHHHH
Q 046578 318 LSEREADILRLHF--GLDGQTPVSCKEIGRLLSL-SRERIRQIRGIAL 362 (379)
Q Consensus 318 L~~rer~Vl~l~y--gL~g~e~~S~~EIAe~Lgi-S~~~Vr~~~~rAl 362 (379)
|+++|++|+.+.. ...+..+.|++|||+.+|+ ++++|.+++.+-.
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~ 49 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALE 49 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 7889999987543 1122256799999999999 9999988766543
No 266
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=85.22 E-value=0.91 Score=42.53 Aligned_cols=25 Identities=20% Similarity=0.268 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
++|.+.+||+.||||+.||+.+++|
T Consensus 18 ~gmk~~dIAeklGvspntiksWKrr 42 (279)
T COG5484 18 KGMKLKDIAEKLGVSPNTIKSWKRR 42 (279)
T ss_pred hhccHHHHHHHhCCChHHHHHHHHh
Confidence 5699999999999999999999876
No 267
>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]
Probab=84.86 E-value=1.3 Score=39.46 Aligned_cols=40 Identities=23% Similarity=0.156 Sum_probs=32.8
Q ss_pred HHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578 323 ADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 323 r~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~ 367 (379)
+..+.|.- .|+|..|||++||+|++|++.++.|+.++...
T Consensus 9 ~kA~eLk~-----~Glt~gEIAdELNvSreTa~WL~~r~~~~~~~ 48 (203)
T COG0856 9 KKARELKS-----KGLTTGEIADELNVSRETATWLLTRAFKKESV 48 (203)
T ss_pred HHHHHHHH-----CCCcHHHhhhhhhhhHHHHHHHHhhhhhccCC
Confidence 34556664 77999999999999999999999998766543
No 268
>PRK10870 transcriptional repressor MprA; Provisional
Probab=84.67 E-value=5.1 Score=35.63 Aligned_cols=51 Identities=16% Similarity=0.101 Sum_probs=37.2
Q ss_pred HHHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578 310 ELKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 310 ~L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
.+...+. .|++.|..|+...+. .+..+.|..|||+.+|++.++|.+.+.+-
T Consensus 43 ~~~~~l~~~gLt~~q~~iL~~L~~-~~~~~it~~eLa~~l~l~~~tvsr~v~rL 95 (176)
T PRK10870 43 NRNKMLKAQGINETLFMALITLES-QENHSIQPSELSCALGSSRTNATRIADEL 95 (176)
T ss_pred HHHHHHHHCCCCHHHHHHHHHHhc-CCCCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 3455554 478888888876652 22256899999999999999998776553
No 269
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=83.88 E-value=1.9 Score=30.22 Aligned_cols=25 Identities=24% Similarity=0.336 Sum_probs=20.3
Q ss_pred CCC-CHHHHHHHhCCCHHHHHHHHHH
Q 046578 336 TPV-SCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 336 e~~-S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
+.+ |..|||+.+|+|+.+|++.+.+
T Consensus 18 ~~l~s~~~la~~~~vs~~tv~~~l~~ 43 (60)
T smart00345 18 DKLPSERELAAQLGVSRTTVREALSR 43 (60)
T ss_pred CcCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 445 8999999999999999765443
No 270
>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=83.87 E-value=3.9 Score=32.16 Aligned_cols=31 Identities=19% Similarity=0.186 Sum_probs=26.9
Q ss_pred CCCHHHHHHHhC-CCHHHHHHHHHHHHHHHHh
Q 046578 337 PVSCKEIGRLLS-LSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 337 ~~S~~EIAe~Lg-iS~~~Vr~~~~rAl~kLR~ 367 (379)
++|+.+||+.|| .+.+||.....+.-+++.+
T Consensus 44 ~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~~ 75 (90)
T cd06571 44 GLSLPEIGRAFGGRDHSTVLHAVRKIEELLEE 75 (90)
T ss_pred CCCHHHHHHHhCCCCHhHHHHHHHHHHHHHHh
Confidence 599999999999 9999999888777776664
No 271
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=83.84 E-value=1.7 Score=29.24 Aligned_cols=24 Identities=33% Similarity=0.540 Sum_probs=19.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 337 PVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 337 ~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
..|..|||+.+|+|+++|++.+.+
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~ 31 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKR 31 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHH
Confidence 489999999999999999655433
No 272
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=83.66 E-value=3.3 Score=34.46 Aligned_cols=27 Identities=7% Similarity=0.030 Sum_probs=24.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
.|.|..+||+.+||+.++++++..+..
T Consensus 28 ~g~sv~evA~e~gIs~~tl~~W~r~y~ 54 (121)
T PRK09413 28 PGMTVSLVARQHGVAASQLFLWRKQYQ 54 (121)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHh
Confidence 569999999999999999999988753
No 273
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=83.32 E-value=2.3 Score=40.70 Aligned_cols=60 Identities=15% Similarity=0.192 Sum_probs=45.8
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhhcCC---CCCCCHHHHHHHhCCCHHHHHHHHHH----HHHHHHhHHh
Q 046578 309 QELKELLQTLSEREADILRLHFGLDG---QTPVSCKEIGRLLSLSRERIRQIRGI----ALTKLQQTNI 370 (379)
Q Consensus 309 ~~L~~~L~~L~~rer~Vl~l~ygL~g---~e~~S~~EIAe~LgiS~~~Vr~~~~r----Al~kLR~~l~ 370 (379)
..|...+..|++.|+.|.... ++. ...+|..+||+..|+|..||.+..++ +..-||..+.
T Consensus 17 ~~i~~~~~~Lt~~e~~Ia~yi--l~~~~~v~~~si~~lA~~~~vS~aTi~Rf~kkLGf~gf~efk~~l~ 83 (292)
T PRK11337 17 PYIRMKQEGLTPLESRVVEWL--LKPGDLSEATALKDIAEALAVSEAMIVKVAKKLGFSGFRNLRSALE 83 (292)
T ss_pred HHHHHHHhhcCHHHHHHHHHH--HhCHHHHHhcCHHHHHHHhCCChHHHHHHHHHcCCCCHHHHHHHHH
Confidence 468888999999999998854 321 23589999999999999999887665 4455555443
No 274
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=83.32 E-value=1.6 Score=32.74 Aligned_cols=27 Identities=19% Similarity=0.139 Sum_probs=23.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
.|.|..+||..+||+++++++++....
T Consensus 22 ~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 22 SGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp HHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCceEeeecccccccccccHHHHHHh
Confidence 569999999999999999999988876
No 275
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=83.26 E-value=6.2 Score=33.48 Aligned_cols=42 Identities=7% Similarity=0.013 Sum_probs=33.0
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.|++.|..||...+- . .++.|..|||+.+|++.++|.+.+.+
T Consensus 28 glt~~q~~vL~~l~~-~-~~~~t~~eLa~~l~~~~~tvt~~v~~ 69 (144)
T PRK03573 28 ELTQTHWVTLHNIHQ-L-PPEQSQIQLAKAIGIEQPSLVRTLDQ 69 (144)
T ss_pred CCCHHHHHHHHHHHH-c-CCCCCHHHHHHHhCCChhhHHHHHHH
Confidence 688999888876542 1 14689999999999999999876655
No 276
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are 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 as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=83.23 E-value=1.9 Score=33.38 Aligned_cols=36 Identities=14% Similarity=0.211 Sum_probs=27.2
Q ss_pred HHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 321 READILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 321 rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
++.+|+.+.- . ...|.++||+.+|+|.+||++.+..
T Consensus 7 R~~~I~e~l~---~-~~~ti~dvA~~~gvS~~TVsr~L~~ 42 (80)
T TIGR02844 7 RVLEIGKYIV---E-TKATVRETAKVFGVSKSTVHKDVTE 42 (80)
T ss_pred HHHHHHHHHH---H-CCCCHHHHHHHhCCCHHHHHHHhcC
Confidence 5555555443 2 4589999999999999999997753
No 277
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=83.12 E-value=2.3 Score=40.45 Aligned_cols=60 Identities=12% Similarity=0.218 Sum_probs=45.0
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhhcCC---CCCCCHHHHHHHhCCCHHHHHHHHHH----HHHHHHhHHh
Q 046578 309 QELKELLQTLSEREADILRLHFGLDG---QTPVSCKEIGRLLSLSRERIRQIRGI----ALTKLQQTNI 370 (379)
Q Consensus 309 ~~L~~~L~~L~~rer~Vl~l~ygL~g---~e~~S~~EIAe~LgiS~~~Vr~~~~r----Al~kLR~~l~ 370 (379)
..+...+..|+|.|+.|.... ++. ...+|..|||+..|+|.+||.+..++ +..-||..+.
T Consensus 5 ~~i~~~~~~Lt~~e~~Ia~yi--l~n~~~v~~~si~~lA~~~~vS~aTv~Rf~kklG~~gf~e~k~~l~ 71 (284)
T PRK11302 5 EKIQSRLEHLSKSERKVAEVI--LASPQTAIHSSIATLAKMANVSEPTVNRFCRSLDTKGFPDFKLHLA 71 (284)
T ss_pred HHHHHHHhhCCHHHHHHHHHH--HhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence 567888899999999998754 331 13489999999999999999887765 3444444443
No 278
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=83.08 E-value=1.1 Score=35.52 Aligned_cols=24 Identities=21% Similarity=0.141 Sum_probs=17.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRG 359 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~ 359 (379)
.|+|..|||+.+|.|++.|++++.
T Consensus 2 ~G~tq~eIA~~lGks~s~Vs~~l~ 25 (93)
T PF08535_consen 2 FGWTQEEIAKRLGKSRSWVSNHLA 25 (93)
T ss_dssp TT--HHHHHHHTT--HHHHHHHHG
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Confidence 359999999999999999998765
No 279
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 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 dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=83.06 E-value=2.6 Score=34.38 Aligned_cols=42 Identities=21% Similarity=0.287 Sum_probs=27.2
Q ss_pred HHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 321 READILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 321 rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
+.++|...+ .|.+..|+|..+|+|..+|++++++..++-++.
T Consensus 62 R~~~I~~~f------~G~n~~eLA~kyglS~r~I~~Ii~~~~~~~~~~ 103 (108)
T PF08765_consen 62 RNREIRREF------NGMNVRELARKYGLSERQIYRIIKRVRRRERRR 103 (108)
T ss_dssp HHHHHHHH--------SS-HHHHHHHHT--HHHHHHHHHHHHH-----
T ss_pred HHHHHHHHh------CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHh
Confidence 556666643 459999999999999999999999987766554
No 280
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=82.90 E-value=1.7 Score=38.40 Aligned_cols=25 Identities=24% Similarity=0.252 Sum_probs=22.8
Q ss_pred CCCCHHHHHHHhC-CCHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLS-LSRERIRQIRGI 360 (379)
Q Consensus 336 e~~S~~EIAe~Lg-iS~~~Vr~~~~r 360 (379)
+|+|..|||+.|| +|++.|--..+|
T Consensus 17 ~G~SasqIA~~lg~vsRnAViGk~hR 42 (162)
T PF07750_consen 17 EGLSASQIARQLGGVSRNAVIGKAHR 42 (162)
T ss_pred cCCCHHHHHHHhCCcchhhhhhhhhc
Confidence 7899999999999 999999877766
No 281
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=82.74 E-value=5 Score=33.22 Aligned_cols=45 Identities=16% Similarity=0.101 Sum_probs=33.6
Q ss_pred HHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 310 ELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 310 ~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.....-..+.+.+-.-++..+ ++|++++|+.+|+++++|+++.+.
T Consensus 57 ~~~~~~~~~~~~~i~~~r~~~------gltq~~lA~~lg~~~~tis~~e~g 101 (127)
T TIGR03830 57 FYRKVDGLLTPPEIRRIRKKL------GLSQREAAELLGGGVNAFSRYERG 101 (127)
T ss_pred HHHHccCCcCHHHHHHHHHHc------CCCHHHHHHHhCCCHHHHHHHHCC
Confidence 334444567777665565555 399999999999999999998764
No 282
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. 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=82.72 E-value=3.6 Score=37.43 Aligned_cols=45 Identities=27% Similarity=0.224 Sum_probs=35.4
Q ss_pred HHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 313 ELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 313 ~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.....|++++..|+....- ..+.+..|||+.+|+|+++|++.+.+
T Consensus 136 ~~~~~ls~~~~~IL~~l~~---~g~~s~~eia~~l~is~stv~r~L~~ 180 (203)
T TIGR01884 136 PLLAGLSREELKVLEVLKA---EGEKSVKNIAKKLGKSLSTISRHLRE 180 (203)
T ss_pred hhhcCCCHHHHHHHHHHHH---cCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 3455799999988876541 13579999999999999999877665
No 283
>PHA00542 putative Cro-like protein
Probab=82.70 E-value=2.1 Score=33.15 Aligned_cols=25 Identities=20% Similarity=0.102 Sum_probs=22.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.++|..++|+.+|||+++|++++..
T Consensus 30 ~glTq~elA~~lgIs~~tIsr~e~g 54 (82)
T PHA00542 30 AGWSQEQIADATDVSQPTICRIYSG 54 (82)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 5699999999999999999999854
No 284
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=82.68 E-value=2.3 Score=34.46 Aligned_cols=52 Identities=17% Similarity=0.177 Sum_probs=45.3
Q ss_pred hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhh
Q 046578 316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNIL 371 (379)
Q Consensus 316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~ 371 (379)
.+|.+-||-...-+| .+-+|-+|||-.+.+++.+|..+...-+.|.|+.-+.
T Consensus 27 ~QLkELErvF~ETHY----PDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~ 78 (125)
T KOG0484|consen 27 AQLKELERVFAETHY----PDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERA 78 (125)
T ss_pred HHHHHHHHHHHhhcC----CcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHH
Confidence 378888888888888 4679999999999999999999999999999987553
No 285
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=82.68 E-value=3.4 Score=32.09 Aligned_cols=41 Identities=20% Similarity=0.378 Sum_probs=31.9
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.|+..+..||.+.+. ..+++..+||+.++++..+|++.+.+
T Consensus 7 ~l~~~~~~il~~l~~---~~~~~~~~la~~~~~s~~~i~~~l~~ 47 (101)
T smart00347 7 GLTPTQFLVLRILYE---EGPLSVSELAKRLGVSPSTVTRVLDR 47 (101)
T ss_pred CCCHHHHHHHHHHHH---cCCcCHHHHHHHHCCCchhHHHHHHH
Confidence 467778888877663 24589999999999999998765544
No 286
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=82.30 E-value=2.1 Score=31.01 Aligned_cols=25 Identities=28% Similarity=0.434 Sum_probs=21.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
..+|..|||+.+|+|+++|++.+.+
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~ 48 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKE 48 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4689999999999999999766544
No 287
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=82.22 E-value=1.2 Score=34.53 Aligned_cols=32 Identities=22% Similarity=0.128 Sum_probs=25.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~ 367 (379)
+..|..++|+.+++|++++.+.+.+..+.|++
T Consensus 29 ~~~s~~~la~~~~iS~sti~~~i~~l~~~l~~ 60 (87)
T PF05043_consen 29 EYVSIEDLAEELFISRSTIYRDIKKLNKYLKK 60 (87)
T ss_dssp SEEEHHHHHHHHT--HHHHHHHHHHHHHHHHC
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 78999999999999999998887776666654
No 288
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=82.15 E-value=1.4 Score=32.16 Aligned_cols=24 Identities=17% Similarity=0.285 Sum_probs=19.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRG 359 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~ 359 (379)
.++|+.++|+.+|+|.++|+++.+
T Consensus 13 ~gls~~~lA~~~g~s~s~v~~iE~ 36 (64)
T PF13560_consen 13 AGLSQAQLADRLGVSQSTVSRIER 36 (64)
T ss_dssp HTS-HHHHHHHHTS-HHHHHHHHT
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHC
Confidence 569999999999999999999875
No 289
>PF14493 HTH_40: Helix-turn-helix domain
Probab=82.03 E-value=3.6 Score=32.36 Aligned_cols=29 Identities=17% Similarity=0.176 Sum_probs=26.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGIALTK 364 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~rAl~k 364 (379)
+|+|..|||+.-|++.+||..++.++...
T Consensus 12 ~G~si~eIA~~R~L~~sTI~~HL~~~~~~ 40 (91)
T PF14493_consen 12 KGLSIEEIAKIRGLKESTIYGHLAELIES 40 (91)
T ss_pred cCCCHHHHHHHcCCCHHHHHHHHHHHHHh
Confidence 77999999999999999999999887654
No 290
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=81.96 E-value=18 Score=26.59 Aligned_cols=25 Identities=16% Similarity=0.099 Sum_probs=21.0
Q ss_pred CCCHHHHHHHhCC-CHHHHHHHHHHH
Q 046578 337 PVSCKEIGRLLSL-SRERIRQIRGIA 361 (379)
Q Consensus 337 ~~S~~EIAe~Lgi-S~~~Vr~~~~rA 361 (379)
+.+..+||..+|+ +.+...+..++.
T Consensus 50 ~~~~~~ia~~~g~~s~~~f~r~Fk~~ 75 (84)
T smart00342 50 DLSVTEIALRVGFSSQSYFSRAFKKL 75 (84)
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHH
Confidence 5899999999999 988887766543
No 291
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=81.95 E-value=3.4 Score=30.53 Aligned_cols=25 Identities=24% Similarity=0.421 Sum_probs=21.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
...+..|||+.+|+|+.+|++.+.+
T Consensus 12 ~~~~~~eLa~~l~vS~~tv~~~l~~ 36 (69)
T TIGR00122 12 NPFSGEKLGEALGMSRTAVNKHIQT 36 (69)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 3478999999999999999877655
No 292
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=81.91 E-value=1.4 Score=38.88 Aligned_cols=25 Identities=16% Similarity=0.147 Sum_probs=22.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
-++|..|||+.+|.|+.||++++.-
T Consensus 60 ag~Ti~EIAeelG~TeqTir~hlkg 84 (182)
T COG1318 60 AGMTISEIAEELGRTEQTVRNHLKG 84 (182)
T ss_pred ccCcHHHHHHHhCCCHHHHHHHHhc
Confidence 4599999999999999999998764
No 293
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=81.86 E-value=0.79 Score=33.74 Aligned_cols=25 Identities=28% Similarity=0.404 Sum_probs=22.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
||..|+|+.+|||.++|+.+..+.+
T Consensus 1 yti~eva~~~gvs~~tlr~y~~~gl 25 (69)
T PF13411_consen 1 YTIKEVAKLLGVSPSTLRYYEREGL 25 (69)
T ss_dssp EEHHHHHHHTTTTHHHHHHHHHTTS
T ss_pred CcHHHHHHHHCcCHHHHHHHHHhcC
Confidence 5789999999999999999988765
No 294
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=81.61 E-value=4.3 Score=32.99 Aligned_cols=45 Identities=22% Similarity=0.150 Sum_probs=34.8
Q ss_pred cCCHHHHHHHHHHhhcC-CCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578 317 TLSEREADILRLHFGLD-GQTPVSCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~-g~e~~S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
.|++.|..||...+.+. ...+.|..|||+.++++.++|.+.+.+-
T Consensus 22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~L 67 (109)
T TIGR01889 22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKL 67 (109)
T ss_pred CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHH
Confidence 68999999987654111 1256999999999999999998876653
No 295
>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=81.59 E-value=1.6 Score=30.40 Aligned_cols=25 Identities=12% Similarity=0.171 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.++|+.++|+.+|+|+++|+++.+.
T Consensus 14 ~gltq~~lA~~~gvs~~~vs~~e~g 38 (58)
T TIGR03070 14 LGLTQADLADLAGVGLRFIRDVENG 38 (58)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 4599999999999999999998753
No 296
>PRK11564 stationary phase inducible protein CsiE; Provisional
Probab=81.45 E-value=4 Score=41.38 Aligned_cols=51 Identities=16% Similarity=0.101 Sum_probs=39.8
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~ 367 (379)
.+++.||..+.+.+.|...+..|..++|+.|+||++|+.+-+.+..+.|.+
T Consensus 10 ~~s~~ER~~~il~~LL~~~~~v~l~~Lae~l~VSrsTi~~DLk~l~~~L~~ 60 (426)
T PRK11564 10 VLSAPQRRCQILLMLFQPGLTVTLETFSQLNGVDDDTARQDIAETGREIQR 60 (426)
T ss_pred CCCHHHHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 367788777666554554578999999999999999999987777666655
No 297
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=81.30 E-value=4 Score=33.14 Aligned_cols=48 Identities=19% Similarity=0.258 Sum_probs=40.0
Q ss_pred HhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 046578 315 LQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQ 366 (379)
Q Consensus 315 L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR 366 (379)
.+.|++.|-+.+.+++-.. =+++||-..+|+|..+|+..+...+++|-
T Consensus 39 F~~Lt~d~LeFv~lf~r~R----GnlKEvEr~lg~sYptvR~kld~vlramg 86 (122)
T COG3877 39 FEYLTSDQLEFVELFLRCR----GNLKEVERELGISYPTVRTKLDEVLRAMG 86 (122)
T ss_pred ccccCHhHhHHHHHHHHHc----cCHHHHHHHHCCccHHHHHHHHHHHHHcC
Confidence 3568888888888877533 38999999999999999999988888764
No 298
>PHA01976 helix-turn-helix protein
Probab=81.21 E-value=1.8 Score=31.63 Aligned_cols=25 Identities=16% Similarity=0.129 Sum_probs=22.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.++|++|+|+.+|+|+++|+++.+.
T Consensus 14 ~glt~~~lA~~~gvs~~~v~~~e~g 38 (67)
T PHA01976 14 RAWSAPELSRRAGVRHSLIYDFEAD 38 (67)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 5699999999999999999998764
No 299
>PRK15482 transcriptional regulator MurR; Provisional
Probab=81.02 E-value=2.9 Score=39.94 Aligned_cols=59 Identities=17% Similarity=0.273 Sum_probs=44.5
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhhcCC---CCCCCHHHHHHHhCCCHHHHHHHHHH----HHHHHHhHH
Q 046578 309 QELKELLQTLSEREADILRLHFGLDG---QTPVSCKEIGRLLSLSRERIRQIRGI----ALTKLQQTN 369 (379)
Q Consensus 309 ~~L~~~L~~L~~rer~Vl~l~ygL~g---~e~~S~~EIAe~LgiS~~~Vr~~~~r----Al~kLR~~l 369 (379)
..|......|++.|+.|.... ++. ...+|..|||+..|+|.+||-+..++ +...||..+
T Consensus 5 ~~i~~~~~~Lt~~e~~Ia~yI--l~n~~~v~~~si~elA~~~~vS~aTv~Rf~kkLGf~Gf~efk~~l 70 (285)
T PRK15482 5 TKIRNAESEFTENEQKIADFL--RANVSELKSVSSRKMAKQLGISQSSIVKFAQKLGAQGFTELRMAL 70 (285)
T ss_pred HHHHHHHhhcCHHHHHHHHHH--HhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHHhCCCCHHHHHHHH
Confidence 457788889999999998754 331 23599999999999999999887665 344444444
No 300
>PRK10072 putative transcriptional regulator; Provisional
Probab=81.00 E-value=6.9 Score=31.40 Aligned_cols=24 Identities=17% Similarity=0.336 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRG 359 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~ 359 (379)
.++|+.|+|+.+|+|.++|+++.+
T Consensus 45 ~glTQ~elA~~lGvS~~TVs~WE~ 68 (96)
T PRK10072 45 TGLKIDDFARVLGVSVAMVKEWES 68 (96)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHc
Confidence 569999999999999999999976
No 301
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=80.89 E-value=2 Score=32.12 Aligned_cols=27 Identities=37% Similarity=0.721 Sum_probs=21.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578 337 PVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 337 ~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~ 367 (379)
.+|.++||+.+|+|+.+|.+. +++|++
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~----l~~l~~ 54 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRI----LKRLKD 54 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHH----HHHHHH
T ss_pred cCCHHHHHHHHCCCHHHHHHH----HHHHHH
Confidence 489999999999999998665 455544
No 302
>TIGR00647 MG103 conserved hypothetical protein.
Probab=80.71 E-value=3.9 Score=39.31 Aligned_cols=44 Identities=18% Similarity=0.196 Sum_probs=37.8
Q ss_pred HhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhC------CCHHHHHHHHHHH
Q 046578 315 LQTLSEREADILRLHFGLDGQTPVSCKEIGRLLS------LSRERIRQIRGIA 361 (379)
Q Consensus 315 L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~Lg------iS~~~Vr~~~~rA 361 (379)
++.||+.-+++..+|.- .++.|++|+|+.|. +|.+.|..+++|.
T Consensus 225 l~~Lp~~L~~~a~lRl~---~Pd~SL~ELgell~~~~~~~isKSgvnhRlrKl 274 (279)
T TIGR00647 225 FEKLPLNFQRICLLKID---HPDWSLEQIAEFFASKYKVKISRSGIQHRLRKL 274 (279)
T ss_pred cccCCHHHHHHHHHHHh---CcccCHHHHHHHhccCCCCCcCHHHHHHHHHHH
Confidence 46899999999999863 48899999999994 9999999887664
No 303
>PF12116 SpoIIID: Stage III sporulation protein D; 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 [].; PDB: 2L0K_A.
Probab=80.49 E-value=2.9 Score=32.30 Aligned_cols=46 Identities=13% Similarity=0.210 Sum_probs=28.3
Q ss_pred HHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578 322 EADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN 369 (379)
Q Consensus 322 er~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l 369 (379)
+|.+-...|.++ ...|.++.|..||||.+||.+-+..=|.++-..|
T Consensus 6 eR~i~i~~yIi~--~~aTVR~~Ak~FGvSKSTVHkDvteRL~~in~~L 51 (82)
T PF12116_consen 6 ERVIEIANYIIE--TKATVRQAAKVFGVSKSTVHKDVTERLPKINPEL 51 (82)
T ss_dssp HHHHHHHHHHHH--H---HHHHHHHHTS-HHHHHHHHTTHHHHH-HHH
T ss_pred HHHHHHHHHHHH--cccHHHHHHHHHCCcHHHHHHHHHHHHHhcCHHH
Confidence 344444455444 5689999999999999999987766555544433
No 304
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=80.46 E-value=1.7 Score=32.46 Aligned_cols=23 Identities=17% Similarity=0.372 Sum_probs=20.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.|++|||+.+|+|.+||++.++.
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln~ 23 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLNG 23 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCC
Confidence 37899999999999999987754
No 305
>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=80.42 E-value=4.6 Score=29.17 Aligned_cols=37 Identities=24% Similarity=0.376 Sum_probs=26.4
Q ss_pred HHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 320 EREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 320 ~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
..+..|+...+ . .+.+..||++.+|++..+|++.+.+
T Consensus 7 ~~~~~il~~l~--~--~~~~~~ei~~~~~i~~~~i~~~l~~ 43 (78)
T cd00090 7 PTRLRILRLLL--E--GPLTVSELAERLGLSQSTVSRHLKK 43 (78)
T ss_pred hHHHHHHHHHH--H--CCcCHHHHHHHHCcCHhHHHHHHHH
Confidence 34555555433 2 2399999999999999999776555
No 306
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=79.92 E-value=10 Score=35.66 Aligned_cols=51 Identities=24% Similarity=0.317 Sum_probs=37.4
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhh-cCC-CCCCCHHHHHHHhCCCHHHHHHHH
Q 046578 308 KQELKELLQTLSEREADILRLHFG-LDG-QTPVSCKEIGRLLSLSRERIRQIR 358 (379)
Q Consensus 308 ~~~L~~~L~~L~~rer~Vl~l~yg-L~g-~e~~S~~EIAe~LgiS~~~Vr~~~ 358 (379)
...++-++..|+--|.+.+...+- |++ .--.+..+||+.+|+|++.|+..+
T Consensus 167 ka~Vq~Ai~tLSySEleAv~~IL~~L~~~egrlse~eLAerlGVSRs~ireAl 219 (251)
T TIGR02787 167 KAAVQMAINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIVNAL 219 (251)
T ss_pred HHHHHHHHHhccHhHHHHHHHHHHHhccccccccHHHHHHHHCCCHHHHHHHH
Confidence 345788899999887776664422 333 246899999999999999886543
No 307
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=79.69 E-value=6 Score=30.50 Aligned_cols=26 Identities=15% Similarity=0.227 Sum_probs=22.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
.++|..|||+.+|+++++|++.+..-
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l~~L 44 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLNTL 44 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 46999999999999999998876654
No 308
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=79.41 E-value=2.4 Score=30.97 Aligned_cols=23 Identities=17% Similarity=0.258 Sum_probs=20.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
+|..|+|+.+|||.++++++..+
T Consensus 1 ~s~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 57899999999999999998765
No 309
>PRK01905 DNA-binding protein Fis; Provisional
Probab=79.31 E-value=9.2 Score=29.18 Aligned_cols=37 Identities=16% Similarity=0.163 Sum_probs=25.7
Q ss_pred HHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 321 READILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 321 rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
-|+.++...+- ..+-+..+.|+.|||+++++++.+++
T Consensus 37 ~E~~~i~~aL~---~~~gn~s~aAr~LGIsrstL~rklkk 73 (77)
T PRK01905 37 VEKPLLEVVME---QAGGNQSLAAEYLGINRNTLRKKLQQ 73 (77)
T ss_pred HHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 35555554432 13357999999999999998776554
No 310
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=79.09 E-value=1.3 Score=29.18 Aligned_cols=23 Identities=22% Similarity=0.338 Sum_probs=19.0
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHH
Q 046578 339 SCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 339 S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
|..|+|+.+|||..+++.....+
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~G 23 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYEREG 23 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHTT
T ss_pred CHHHHHHHHCCCHHHHHHHHHCC
Confidence 46799999999999999987765
No 311
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=78.51 E-value=3.5 Score=30.91 Aligned_cols=24 Identities=25% Similarity=0.416 Sum_probs=21.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRG 359 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~ 359 (379)
.++|+.|.|+.+|||+.|+..+.+
T Consensus 13 ~~ltQ~elA~~vgVsRQTi~~iEk 36 (68)
T COG1476 13 LGLTQEELAKLVGVSRQTIIAIEK 36 (68)
T ss_pred hCcCHHHHHHHcCcCHHHHHHHHc
Confidence 459999999999999999988764
No 312
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=77.85 E-value=4 Score=28.60 Aligned_cols=26 Identities=15% Similarity=0.194 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
+..|..+|++.+|+|..+|++.+++-
T Consensus 9 ~~~~~~~i~~~l~is~~~v~~~l~~L 34 (66)
T smart00418 9 GELCVCELAEILGLSQSTVSHHLKKL 34 (66)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHH
Confidence 56899999999999999998777553
No 313
>PF13551 HTH_29: Winged helix-turn helix
Probab=77.59 E-value=3.8 Score=32.79 Aligned_cols=23 Identities=39% Similarity=0.286 Sum_probs=20.8
Q ss_pred CHHHHHHHhCCCHHHHHHHHHhc
Q 046578 246 TDSEIAEMLNIHVSTVRLAIERT 268 (379)
Q Consensus 246 t~~eia~~Lgis~~~~~~~l~~~ 268 (379)
+..++|+.+|++..++...+...
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~ 36 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRY 36 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHH
Confidence 79999999999999999988763
No 314
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=77.58 E-value=3.3 Score=39.30 Aligned_cols=58 Identities=7% Similarity=0.131 Sum_probs=42.9
Q ss_pred HHHHHhcCCHHHHHHHHHHhhcCC---CCCCCHHHHHHHhCCCHHHHHHHHHH----HHHHHHhHHh
Q 046578 311 LKELLQTLSEREADILRLHFGLDG---QTPVSCKEIGRLLSLSRERIRQIRGI----ALTKLQQTNI 370 (379)
Q Consensus 311 L~~~L~~L~~rer~Vl~l~ygL~g---~e~~S~~EIAe~LgiS~~~Vr~~~~r----Al~kLR~~l~ 370 (379)
|......|++.|+.|..... +. ...+|..|+|+..|+|..||.+..++ +..-||..+.
T Consensus 3 i~~~~~~Lt~~e~~ia~yil--~n~~~v~~~si~elA~~~~vS~aTv~Rf~kklG~~Gf~efk~~l~ 67 (278)
T PRK11557 3 IRQRYPGLAQSDRKLADYLL--LQPDTARHLSSQQLANEAGVSQSSVVKFAQKLGYKGFPALKLALS 67 (278)
T ss_pred hhHhhhhCCHHHHHHHHHHH--hCHHHHHhcCHHHHHHHhCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence 55677889999999987543 21 13599999999999999999887765 3444444443
No 315
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=77.54 E-value=3.8 Score=38.99 Aligned_cols=43 Identities=28% Similarity=0.314 Sum_probs=35.2
Q ss_pred hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
..|++.|++|+.+.-.=+ -..+++||.+.+|.|+.||++++++
T Consensus 191 ~~L~~~e~~il~~i~~~G--Gri~Q~eL~r~lglsktTvsR~L~~ 233 (258)
T COG2512 191 YDLNEDEKEILDLIRERG--GRITQAELRRALGLSKTTVSRILRR 233 (258)
T ss_pred CCCCHHHHHHHHHHHHhC--CEEeHHHHHHhhCCChHHHHHHHHH
Confidence 469999999999876423 3489999999999999999877655
No 316
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=77.27 E-value=2.7 Score=34.93 Aligned_cols=23 Identities=22% Similarity=0.276 Sum_probs=21.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
||.+|+|+.+|+++.||.+++.+
T Consensus 1 MT~eELA~~tG~srQTINrWvRk 23 (122)
T PF07037_consen 1 MTPEELAELTGYSRQTINRWVRK 23 (122)
T ss_pred CCHHHHHHHhCccHHHHHHHHHh
Confidence 68999999999999999998764
No 317
>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=77.10 E-value=7.6 Score=27.15 Aligned_cols=51 Identities=14% Similarity=0.194 Sum_probs=37.3
Q ss_pred cCCHHHHHHHHHHhhcCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578 317 TLSEREADILRLHFGLDGQ-TPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~-e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~ 367 (379)
.+++.+..+|.-.|..+.. ......+||..+|++...|..+...-+.+.+.
T Consensus 6 ~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 6 RFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 4567777777777743321 22346789999999999999999888777654
No 318
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=77.06 E-value=14 Score=33.39 Aligned_cols=41 Identities=17% Similarity=0.151 Sum_probs=34.1
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.|++.|..||...+. .++.|+++||+.++++.+||.+.+.+
T Consensus 42 gLt~~q~~iL~~L~~---~~~itq~eLa~~l~l~~sTvtr~l~r 82 (185)
T PRK13777 42 DLNINEHHILWIAYH---LKGASISEIAKFGVMHVSTAFNFSKK 82 (185)
T ss_pred CCCHHHHHHHHHHHh---CCCcCHHHHHHHHCCCHhhHHHHHHH
Confidence 689999999877663 35799999999999999998776554
No 319
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=75.89 E-value=3.6 Score=30.16 Aligned_cols=23 Identities=13% Similarity=0.276 Sum_probs=20.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
+|..|+|+.+|||.+|++.+..+
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 57899999999999999998765
No 320
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=75.86 E-value=9.8 Score=25.93 Aligned_cols=23 Identities=13% Similarity=0.192 Sum_probs=17.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
+|+.+.|+.+||+++|++.+++.
T Consensus 17 ~S~r~AA~~ygVp~sTL~~r~~g 39 (45)
T PF05225_consen 17 MSIRKAAKKYGVPRSTLRRRLRG 39 (45)
T ss_dssp S-HHHHHHHHT--HHHHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHcC
Confidence 99999999999999999966554
No 321
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=75.80 E-value=33 Score=33.16 Aligned_cols=121 Identities=17% Similarity=0.065 Sum_probs=60.5
Q ss_pred HHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHHHHHHHHHHHHHHH
Q 046578 235 NVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKEL 314 (379)
Q Consensus 235 ~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~ 314 (379)
.-.....|-.-+.+||++.++++...+..........+.+..+..+. ..+..-+.+.-..+++ + .....+.+..+
T Consensus 148 Y~acR~~~~prtl~eIa~a~~V~~kei~rtyr~~~~~L~l~~~~~~p--~~yi~rf~s~L~l~~~--v-~~~a~ei~~~~ 222 (285)
T COG1405 148 YAACRINGVPRTLDEIAKALGVSKKEIGRTYRLLVRELKLKIPPVDP--SDYIPRFASKLGLSDE--V-RRKAIEIVKKA 222 (285)
T ss_pred HHHHHHcCCCccHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCCCCH--HHHHHHHHHHcCCCHH--H-HHHHHHHHHHH
Confidence 33455556666999999999999988887766433333332221000 0000000010011111 1 11111222222
Q ss_pred Hh-cC----CHH--HHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578 315 LQ-TL----SER--EADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 315 L~-~L----~~r--er~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
.. .+ .|. --..+.+.--+.| ...|++|||+..|+|..||++++..-
T Consensus 223 ~~~g~~~Gk~P~glAaaaiy~as~l~~-~~~tq~eva~v~~vtevTIrnrykel 275 (285)
T COG1405 223 KRAGLTAGKSPAGLAAAAIYLASLLLG-ERRTQKEVAKVAGVTEVTIRNRYKEL 275 (285)
T ss_pred HHhCcccCCCchhHHHHHHHHHHHHhC-CchHHHHHHHHhCCeeeHHHHHHHHH
Confidence 21 11 111 1122222221334 77999999999999999999988443
No 322
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=75.70 E-value=6.3 Score=33.21 Aligned_cols=34 Identities=24% Similarity=0.212 Sum_probs=24.8
Q ss_pred HHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 322 EADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 322 er~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
-+.||.|.. +|.+..+||..|+||.+.|++++.|
T Consensus 23 R~rIvela~-----~G~rp~~Isr~l~Vs~gcVsKIl~R 56 (125)
T PF00292_consen 23 RQRIVELAK-----EGVRPCDISRQLRVSHGCVSKILSR 56 (125)
T ss_dssp HHHHHHHHH-----TT--HHHHHHHHT--HHHHHHHHHH
T ss_pred HHHHHHHhh-----hcCCHHHHHHHHccchhHHHHHHHH
Confidence 345676775 6799999999999999999998776
No 323
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=75.55 E-value=3.3 Score=28.19 Aligned_cols=24 Identities=21% Similarity=0.239 Sum_probs=21.3
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHH
Q 046578 335 QTPVSCKEIGRLLSLSRERIRQIR 358 (379)
Q Consensus 335 ~e~~S~~EIAe~LgiS~~~Vr~~~ 358 (379)
..+.|.++||+..|+|++++.+..
T Consensus 14 ~~~~s~~~Ia~~~gvs~~~~y~~f 37 (47)
T PF00440_consen 14 YEAVSIRDIARRAGVSKGSFYRYF 37 (47)
T ss_dssp TTTSSHHHHHHHHTSCHHHHHHHC
T ss_pred HHhCCHHHHHHHHccchhhHHHHc
Confidence 467999999999999999998754
No 324
>PF12759 HTH_Tnp_IS1: InsA C-terminal domain; InterPro: IPR024431 This entry represents the helix-turn-helix domain found at the C-terminal of InsA.
Probab=75.16 E-value=3.7 Score=28.29 Aligned_cols=38 Identities=13% Similarity=0.217 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
-|.-.++|+.|.+ .|...+++|..|+|+..||-+.++.
T Consensus 7 kpgikeqIvema~-----nG~GiRdtaRvL~I~~nTVlrtLK~ 44 (46)
T PF12759_consen 7 KPGIKEQIVEMAF-----NGSGIRDTARVLKISINTVLRTLKN 44 (46)
T ss_pred CccHHHHHHHHHh-----cCCcchhhHhHhcchHHHHHHHHhc
Confidence 3555668888887 6688999999999999999665543
No 325
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=74.99 E-value=4.5 Score=33.60 Aligned_cols=24 Identities=17% Similarity=0.195 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRG 359 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~ 359 (379)
.|.|..++|..++||.+||.+++.
T Consensus 17 ~g~s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 17 KGKSIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred ccchHHHHHHHhCcHHHHHHHHHH
Confidence 678999999999999999999877
No 326
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=74.51 E-value=6.9 Score=31.86 Aligned_cols=42 Identities=26% Similarity=0.294 Sum_probs=36.5
Q ss_pred HHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 313 ELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 313 ~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.....|++.|-..|+-.++ +|+.+-|..||+|.+||+.+...
T Consensus 39 ~~~~~ls~~eIk~iRe~~~------lSQ~vFA~~L~vs~~Tv~~WEqG 80 (104)
T COG2944 39 LKVKTLSPTEIKAIREKLG------LSQPVFARYLGVSVSTVRKWEQG 80 (104)
T ss_pred ccCCCCCHHHHHHHHHHhC------CCHHHHHHHHCCCHHHHHHHHcC
Confidence 3445799999999988875 99999999999999999999864
No 327
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=74.50 E-value=8.6 Score=32.49 Aligned_cols=44 Identities=20% Similarity=0.401 Sum_probs=34.5
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHh----CCCHHHHHHHHHHHHH
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLL----SLSRERIRQIRGIALT 363 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~L----giS~~~Vr~~~~rAl~ 363 (379)
.|++.|.+|+...+- ..+.|.+||.+.| |++.+||...+.|-.+
T Consensus 1 ~Lt~~E~~VM~vlW~---~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~ 48 (130)
T TIGR02698 1 SISDAEWEVMRVVWT---LGETTSRDIIRILAEKKDWSDSTIKTLLGRLVD 48 (130)
T ss_pred CCCHHHHHHHHHHHc---CCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHH
Confidence 478999999987653 2468999977776 7999999988777544
No 328
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=74.29 E-value=8.6 Score=32.02 Aligned_cols=44 Identities=18% Similarity=0.248 Sum_probs=31.6
Q ss_pred HHHhcCCHHHH-HHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 046578 313 ELLQTLSEREA-DILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRG 359 (379)
Q Consensus 313 ~~L~~L~~rer-~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~ 359 (379)
+.+..|.+.-| .||.+-. + ..+++..||++.+|+|+++|+++++
T Consensus 8 ~~fkaLadptRl~IL~~L~--~-~~~~~v~ela~~l~lsqstvS~HL~ 52 (117)
T PRK10141 8 QLFKILSDETRLGIVLLLR--E-SGELCVCDLCTALDQSQPKISRHLA 52 (117)
T ss_pred HHHHHhCCHHHHHHHHHHH--H-cCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 55566765544 5555432 2 2469999999999999999998853
No 329
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=73.89 E-value=2.5 Score=30.99 Aligned_cols=25 Identities=24% Similarity=0.355 Sum_probs=21.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
+|..|+|+.+|||.++++.+...++
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~~~gl 25 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYERIGL 25 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999876544
No 330
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=73.88 E-value=33 Score=36.36 Aligned_cols=104 Identities=16% Similarity=0.196 Sum_probs=58.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhcCCcc---ccCCccccCCCCcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCC
Q 046578 243 RMPTDSEIAEMLNIHVSTVRLAIERTRHPI---SLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLS 319 (379)
Q Consensus 243 r~pt~~eia~~Lgis~~~~~~~l~~~~~~i---SLd~~~~~~~~~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~ 319 (379)
...|..++|+.+|+|..+++.-+...+..+ .+. ......+..+ .. .++. .+...+..-+
T Consensus 16 ~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~~~~~-~i~~~~Gy~l----~~---~~~~----------~~~~~~~~~~ 77 (584)
T PRK09863 16 QDRSGGELAQQLGVSRRTIVRDIAYINFTLNGKAIG-SISGSAKYHL----EI---LNRR----------SLFQLLQKSD 77 (584)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcchh-heecCCceEE----Ee---CCHH----------HHHHHHhcCC
Confidence 356899999999999999986654321110 000 0000011111 00 0111 1112222223
Q ss_pred HHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578 320 EREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 320 ~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~ 367 (379)
+..+ .+.++. +. .++.+..++|+.|.||++||.+-+.+..+.+.+
T Consensus 78 ~e~~-~il~~L-l~-~~~~~~~~La~~l~vS~sTi~~dl~~v~~~l~~ 122 (584)
T PRK09863 78 NEDR-LLLLRL-LL-NTFTPMAQLASALNLSRTWVAERLPRLNQRYER 122 (584)
T ss_pred HHHH-HHHHHH-HH-cCCccHHHHHHHhCCCHHHHHHHHHHHHHhhhc
Confidence 3333 344444 22 367999999999999999999998888777663
No 331
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=73.66 E-value=6.3 Score=31.53 Aligned_cols=43 Identities=21% Similarity=0.286 Sum_probs=30.4
Q ss_pred cCCHHHHHHHHHHhh-cCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 046578 317 TLSEREADILRLHFG-LDGQTPVSCKEIGRLLSLSRERIRQIRG 359 (379)
Q Consensus 317 ~L~~rer~Vl~l~yg-L~g~e~~S~~EIAe~LgiS~~~Vr~~~~ 359 (379)
.|++.+++|+.+.-- -...+|.+..+|++.|+++...|+..+.
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~ 87 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALD 87 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHH
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHH
Confidence 688888888886543 2345889999999999999998876554
No 332
>TIGR00180 parB_part ParB-like partition proteins. This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.
Probab=73.51 E-value=5.9 Score=35.53 Aligned_cols=43 Identities=16% Similarity=0.247 Sum_probs=32.6
Q ss_pred hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
..|++-|+....... +.. .++|.++||+.+|+|+++|++.+.-
T Consensus 101 ~~lt~~e~a~~~~~l-~~~-~g~s~~~iA~~lg~s~~~V~r~l~l 143 (187)
T TIGR00180 101 EDLSPIEEAQAYKRL-LEK-FSMTQEDLAKKIGKSRAHITNLLRL 143 (187)
T ss_pred cCCCHHHHHHHHHHH-HHH-hCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 378888876665443 221 3599999999999999999987654
No 333
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=73.25 E-value=3.4 Score=29.69 Aligned_cols=26 Identities=19% Similarity=0.289 Sum_probs=19.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
.++|..++|+..|+++++++++.+.-
T Consensus 9 ~~it~~~La~~~gis~~tl~~~~~~~ 34 (63)
T PF13443_consen 9 RGITQKDLARKTGISRSTLSRILNGK 34 (63)
T ss_dssp TT--HHHHHHHHT--HHHHHHHHTTT
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcc
Confidence 45899999999999999999988754
No 334
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=72.80 E-value=9.8 Score=26.40 Aligned_cols=48 Identities=15% Similarity=0.142 Sum_probs=35.3
Q ss_pred CCHHHHHHHHHHhhcCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578 318 LSEREADILRLHFGLDGQ-TPVSCKEIGRLLSLSRERIRQIRGIALTKL 365 (379)
Q Consensus 318 L~~rer~Vl~l~ygL~g~-e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL 365 (379)
+++.+..+|...|..+.. ......+||+.+|++...|..+....+.+.
T Consensus 7 ~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~ 55 (56)
T smart00389 7 FTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKW 55 (56)
T ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhcc
Confidence 677888888877743321 223467899999999999999988766543
No 335
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=72.76 E-value=5.8 Score=26.21 Aligned_cols=26 Identities=8% Similarity=0.105 Sum_probs=19.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
++.++.+||+.+|+|++..++..++.
T Consensus 7 ~~~~l~~iA~~~g~S~~~f~r~Fk~~ 32 (42)
T PF00165_consen 7 QKLTLEDIAEQAGFSPSYFSRLFKKE 32 (42)
T ss_dssp SS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 67999999999999998887776553
No 336
>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional
Probab=72.63 E-value=2.8 Score=37.58 Aligned_cols=46 Identities=20% Similarity=0.135 Sum_probs=38.5
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCC---------HHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578 317 TLSEREADILRLHFGLDGQTPVS---------CKEIGRLLSLSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S---------~~EIAe~LgiS~~~Vr~~~~rAl~kLR~ 367 (379)
.|+++|.+++.+.. .+.+ ..++|..++++..||+.++.+.++||..
T Consensus 156 ~Lt~~E~~~l~~l~-----~~~~~v~sr~~l~~~~~~~~~~~~~~tv~~~i~~lr~Kl~~ 210 (232)
T PRK10955 156 ELTGTEFTLLYLLA-----QHLGQVVSREHLSQEVLGKRLTPFDRAIDMHISNLRRKLPD 210 (232)
T ss_pred cCCHHHHHHHHHHH-----hCCCceEcHHHHHHHHhCCCCCCCCcCHHHHHHHHHHhccc
Confidence 49999999998765 3344 4778888999999999999999999964
No 337
>PRK10161 transcriptional regulator PhoB; Provisional
Probab=72.42 E-value=4.6 Score=36.24 Aligned_cols=50 Identities=8% Similarity=0.047 Sum_probs=39.3
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHH-----HhCCCHHHHHHHHHHHHHHHHh
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGR-----LLSLSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe-----~LgiS~~~Vr~~~~rAl~kLR~ 367 (379)
.|+++|.+++.+.. -+-+++.|.++|.+ .++++..+|+..++|.++||..
T Consensus 154 ~Lt~~E~~ll~~l~-~~~~~~~s~~~l~~~~~~~~~~~~~~tv~~~i~rlr~Kl~~ 208 (229)
T PRK10161 154 EMGPTEFKLLHFFM-THPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEP 208 (229)
T ss_pred EcCHHHHHHHHHHH-hCCCceEcHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhcc
Confidence 49999999998765 22226788777644 6688999999999999999974
No 338
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized 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 uncoded by the upstream member of the gene pair.
Probab=72.24 E-value=4.2 Score=30.53 Aligned_cols=24 Identities=21% Similarity=0.378 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRG 359 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~ 359 (379)
.++|..++|+.+|+|+++|++++.
T Consensus 17 ~~~t~~~lA~~~gis~~tis~~~~ 40 (78)
T TIGR02607 17 LGLSIRALAKALGVSRSTLSRIVN 40 (78)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHc
Confidence 669999999999999999999876
No 339
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=72.00 E-value=4.9 Score=35.67 Aligned_cols=34 Identities=21% Similarity=0.339 Sum_probs=25.6
Q ss_pred HHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 325 ILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 325 Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
|.-.-| +.+ +++|..||++.+|+|+++|++-++.
T Consensus 31 iYgily-ls~-~Pmtl~Ei~E~lg~Sks~vS~~lkk 64 (177)
T COG1510 31 IYGILY-LSR-KPLTLDEIAEALGMSKSNVSMGLKK 64 (177)
T ss_pred Hhhhhe-ecC-CCccHHHHHHHHCCCcchHHHHHHH
Confidence 333334 544 8999999999999999999875443
No 340
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=71.88 E-value=7.8 Score=36.30 Aligned_cols=41 Identities=24% Similarity=0.349 Sum_probs=32.1
Q ss_pred HHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578 320 EREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT 363 (379)
Q Consensus 320 ~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~ 363 (379)
+|++.|+.+..- ....+.+|||+.||+|..||++-+..-..
T Consensus 4 ~R~~~Il~~l~~---~~~~~~~eLa~~l~VS~~TiRRdL~~L~~ 44 (240)
T PRK10411 4 ARQQAIVDLLLN---HTSLTTEALAEQLNVSKETIRRDLNELQT 44 (240)
T ss_pred HHHHHHHHHHHH---cCCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 566666665431 35699999999999999999999987644
No 341
>PHA00738 putative HTH transcription regulator
Probab=71.86 E-value=10 Score=31.12 Aligned_cols=37 Identities=22% Similarity=0.066 Sum_probs=27.4
Q ss_pred HHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 046578 320 EREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRG 359 (379)
Q Consensus 320 ~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~ 359 (379)
|.=+.||.+... .++++..||++.+++|+.+|+++++
T Consensus 12 ptRr~IL~lL~~---~e~~~V~eLae~l~lSQptVS~HLK 48 (108)
T PHA00738 12 ILRRKILELIAE---NYILSASLISHTLLLSYTTVLRHLK 48 (108)
T ss_pred HHHHHHHHHHHH---cCCccHHHHHHhhCCCHHHHHHHHH
Confidence 444556654331 2569999999999999999998853
No 342
>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=71.75 E-value=5.2 Score=28.51 Aligned_cols=22 Identities=27% Similarity=0.348 Sum_probs=18.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRG 359 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~ 359 (379)
.|.++||+.+|+|+.+|++.+.
T Consensus 26 ~~~~~la~~~~is~~~v~~~l~ 47 (66)
T cd07377 26 PSERELAEELGVSRTTVREALR 47 (66)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 4599999999999999875543
No 343
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=71.72 E-value=13 Score=26.69 Aligned_cols=35 Identities=14% Similarity=-0.003 Sum_probs=26.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHh
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNI 370 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~ 370 (379)
.+.+..+.|+.|+|.++||+.++.|+-+.+.-.+.
T Consensus 11 ~~~n~~~tA~~L~iHrNTl~yRl~ki~~l~g~dl~ 45 (59)
T PF13556_consen 11 NNGNISKTARALHIHRNTLRYRLKKIEELLGLDLD 45 (59)
T ss_dssp TTT-HHHHHHHHTS-HHHHHHHHHHHHHHHS--TT
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCcCCC
Confidence 45899999999999999999999888776654443
No 344
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=71.71 E-value=14 Score=28.62 Aligned_cols=29 Identities=21% Similarity=0.337 Sum_probs=23.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
.-.|-++||+.||+|+.+|... +++||+.
T Consensus 18 ~~~SGe~La~~LgiSRtaVwK~----Iq~Lr~~ 46 (79)
T COG1654 18 NFVSGEKLAEELGISRTAVWKH----IQQLREE 46 (79)
T ss_pred CcccHHHHHHHHCccHHHHHHH----HHHHHHh
Confidence 6689999999999999888654 5666643
No 345
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=71.60 E-value=7.2 Score=37.39 Aligned_cols=52 Identities=13% Similarity=0.200 Sum_probs=41.2
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHhhcCC---CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 307 MKQELKELLQTLSEREADILRLHFGLDG---QTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 307 ~~~~L~~~L~~L~~rer~Vl~l~ygL~g---~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
+...|......|++.||.|-.... .. ...+|.+|||+..|||++||-+..++
T Consensus 5 l~~~I~~~~~~Lt~~er~iA~yil--~~~~~~~~~si~elA~~a~VS~aTv~Rf~~k 59 (281)
T COG1737 5 LLERIRERYDSLTKSERKIADYIL--ANPDEVALLSIAELAERAGVSPATVVRFARK 59 (281)
T ss_pred HHHHHHHHHhcCCHHHHHHHHHHH--hCHHHHHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence 345688889999999999987542 21 23589999999999999999887654
No 346
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=71.60 E-value=5.5 Score=28.95 Aligned_cols=25 Identities=20% Similarity=0.266 Sum_probs=18.8
Q ss_pred CCC-CHHHHHHHhCCCHHHHHHHHHH
Q 046578 336 TPV-SCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 336 e~~-S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
+.+ |..+||+.+|+|+.+|+..+.+
T Consensus 22 ~~lps~~~la~~~~vsr~tvr~al~~ 47 (64)
T PF00392_consen 22 DRLPSERELAERYGVSRTTVREALRR 47 (64)
T ss_dssp SBE--HHHHHHHHTS-HHHHHHHHHH
T ss_pred CEeCCHHHHHHHhccCCcHHHHHHHH
Confidence 567 9999999999999999765443
No 347
>PRK10643 DNA-binding transcriptional regulator BasR; Provisional
Probab=71.18 E-value=4.8 Score=35.64 Aligned_cols=47 Identities=15% Similarity=0.005 Sum_probs=35.8
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCH-HHHHHH------hCCCHHHHHHHHHHHHHHHH
Q 046578 317 TLSEREADILRLHFGLDGQTPVSC-KEIGRL------LSLSRERIRQIRGIALTKLQ 366 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~-~EIAe~------LgiS~~~Vr~~~~rAl~kLR 366 (379)
.|+++|.+++.+..- ..|.+. +||+.. ++++..||+.++++.++||.
T Consensus 149 ~Lt~~E~~il~~l~~---~~g~~~~~~~~~~~~~~~~~~~~~~tv~~~i~~lr~Kl~ 202 (222)
T PRK10643 149 ILTPKEFALLSRLML---KAGSPVHREILYQDIYNWDDEPSSNTLEVHIHNLRDKVG 202 (222)
T ss_pred ecCHHHHHHHHHHHh---CCCceEcHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhCC
Confidence 499999999987642 144553 555543 68999999999999999985
No 348
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=70.96 E-value=5.6 Score=27.94 Aligned_cols=25 Identities=24% Similarity=0.401 Sum_probs=19.2
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHH
Q 046578 334 GQTPVSCKEIGRLLSLSRERIRQIR 358 (379)
Q Consensus 334 g~e~~S~~EIAe~LgiS~~~Vr~~~ 358 (379)
|.+..|-.|||+.+|++...||+=+
T Consensus 25 G~~~vSS~~La~~~gi~~~qVRKDl 49 (50)
T PF06971_consen 25 GVERVSSQELAEALGITPAQVRKDL 49 (50)
T ss_dssp T-SEE-HHHHHHHHTS-HHHHHHHH
T ss_pred CCeeECHHHHHHHHCCCHHHhcccC
Confidence 5678899999999999999998743
No 349
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=70.60 E-value=5.6 Score=29.24 Aligned_cols=23 Identities=13% Similarity=0.131 Sum_probs=20.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
++..|+|+.+|||.++++.+..+
T Consensus 1 ~~i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 47899999999999999988665
No 350
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=70.59 E-value=3 Score=28.73 Aligned_cols=21 Identities=19% Similarity=0.251 Sum_probs=18.0
Q ss_pred HHHHHHhCCCHHHHHHHHHHH
Q 046578 341 KEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 341 ~EIAe~LgiS~~~Vr~~~~rA 361 (379)
++||+.+|+|.++|+++++.-
T Consensus 1 ~~lA~~~gvs~~tvs~~l~g~ 21 (52)
T cd01392 1 KDIARAAGVSVATVSRVLNGK 21 (52)
T ss_pred CcHHHHHCcCHHHHHHHHcCC
Confidence 379999999999999987653
No 351
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=70.56 E-value=7.6 Score=29.71 Aligned_cols=24 Identities=17% Similarity=0.278 Sum_probs=21.5
Q ss_pred CCCCHHHHHHHhC------CCHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLS------LSRERIRQIRG 359 (379)
Q Consensus 336 e~~S~~EIAe~Lg------iS~~~Vr~~~~ 359 (379)
-|+|+.++|+.+| +|+++|+++.+
T Consensus 23 lGLTQ~dvA~~lg~~~g~i~SQstISR~Es 52 (75)
T smart00352 23 LGFTQADVGLALGALYGPDFSQTTICRFEA 52 (75)
T ss_pred cCCCHHHHHHHhcccccCcCCHHHHHHHHh
Confidence 4599999999999 59999999765
No 352
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=70.45 E-value=9 Score=30.66 Aligned_cols=41 Identities=17% Similarity=0.284 Sum_probs=32.2
Q ss_pred CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578 318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
|++.|..++...+..+ +.+..+||+.++++.++|.+.+.+-
T Consensus 20 lt~~q~~~L~~l~~~~---~~~~~~la~~l~i~~~~vt~~l~~L 60 (126)
T COG1846 20 LTPPQYQVLLALYEAG---GITVKELAERLGLDRSTVTRLLKRL 60 (126)
T ss_pred CCHHHHHHHHHHHHhC---CCcHHHHHHHHCCCHHHHHHHHHHH
Confidence 9999999998777422 2333999999999999998876653
No 353
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio 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 sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=70.41 E-value=12 Score=28.76 Aligned_cols=24 Identities=42% Similarity=0.520 Sum_probs=18.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 337 PVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 337 ~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
..|.+|||+.+|+|+..|++++.+
T Consensus 25 ~~s~~eiA~~~~i~~~~l~kil~~ 48 (83)
T PF02082_consen 25 PVSSKEIAERLGISPSYLRKILQK 48 (83)
T ss_dssp -BEHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 389999999999999988776443
No 354
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=70.39 E-value=12 Score=28.03 Aligned_cols=25 Identities=24% Similarity=0.300 Sum_probs=19.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
..-|..|||+.||+|...|+.++..
T Consensus 19 r~Pt~eEiA~~lgis~~~v~~~l~~ 43 (78)
T PF04539_consen 19 REPTDEEIAEELGISVEEVRELLQA 43 (78)
T ss_dssp S--BHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCHHHHHHHHcccHHHHHHHHHh
Confidence 6689999999999999999877653
No 355
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=70.16 E-value=5 Score=35.39 Aligned_cols=28 Identities=21% Similarity=0.368 Sum_probs=22.3
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 337 PVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 337 ~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
.+|.+|||+.+|+|+.+|++. +++|++.
T Consensus 143 ~~t~~~iA~~lG~tretvsR~----l~~l~~~ 170 (193)
T TIGR03697 143 RLSHQAIAEAIGSTRVTITRL----LGDLRKK 170 (193)
T ss_pred CCCHHHHHHHhCCcHHHHHHH----HHHHHHC
Confidence 479999999999999998654 5555543
No 356
>PRK09726 antitoxin HipB; Provisional
Probab=70.12 E-value=4.7 Score=31.50 Aligned_cols=25 Identities=8% Similarity=0.187 Sum_probs=22.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.++|+.++|+.+|||+++|+++.+.
T Consensus 24 ~gltq~elA~~~gvs~~tis~~e~g 48 (88)
T PRK09726 24 NGWTQSELAKKIGIKQATISNFENN 48 (88)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 4599999999999999999998774
No 357
>smart00862 Trans_reg_C Transcriptional regulatory protein, C terminal. This domain is almost always found associated with the response regulator receiver domain. It may play a role in DNA binding.
Probab=69.39 E-value=18 Score=26.64 Aligned_cols=50 Identities=18% Similarity=0.183 Sum_probs=35.4
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHh------CCCHHHHHHHHHHHHHHHHh
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLL------SLSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~L------giS~~~Vr~~~~rAl~kLR~ 367 (379)
.|+++|..+|.+.. ..-....|.++|.+.+ +.+..++++.+++.+++|..
T Consensus 5 ~Lt~~e~~lL~~L~-~~~~~~vs~~~l~~~lw~~~~~~~~~~~l~~~i~~LR~~l~~ 60 (78)
T smart00862 5 KLTPKEFRLLELLL-RNPGRVVSREELLEAVWGDDDDDVDDNTLDVHISRLRKKLED 60 (78)
T ss_pred ecCHHHHHHHHHHH-hCCCCccCHHHHHHHHcCCCCCCCccchHHHHHHHHHHHHhc
Confidence 47889999777554 2322568999999976 35667777777777777764
No 358
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=69.36 E-value=8.3 Score=31.37 Aligned_cols=35 Identities=26% Similarity=0.422 Sum_probs=27.0
Q ss_pred HHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 324 DILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 324 ~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
+||.-.| ++. -|+|..+.|+.|||++.+|+.+++-
T Consensus 12 EiL~eef-lep-~glt~~~lA~~lgV~r~~is~ling 46 (104)
T COG3093 12 EILREEF-LEP-LGLTQTELAEALGVTRNTISELING 46 (104)
T ss_pred HHHHHHH-hcc-ccCCHHHHHHHhCCCHHHHHHHHcC
Confidence 4555555 331 3699999999999999999988764
No 359
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=69.02 E-value=5 Score=28.89 Aligned_cols=25 Identities=24% Similarity=0.356 Sum_probs=19.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.++|+.++|+.+|+++++++++.+-
T Consensus 11 ~~lt~~~~a~~~~i~~~~i~~~e~g 35 (64)
T PF12844_consen 11 KGLTQKDLAEKLGISRSTISKIENG 35 (64)
T ss_dssp CT--HHHHHHHHTS-HHHHHHHHTT
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 4699999999999999999998854
No 360
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=68.67 E-value=53 Score=33.00 Aligned_cols=35 Identities=26% Similarity=0.451 Sum_probs=26.3
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Q 046578 231 AEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAI 265 (379)
Q Consensus 231 ~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l 265 (379)
.+....+...+|+.|+..+.|...|++...+...+
T Consensus 97 ~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~ 131 (373)
T PRK07406 97 EELREQFESELGREPSDKEWAELVDMPLPKFRRRL 131 (373)
T ss_pred HHHHHHHHHhcccccchhhHhhhccccHHHHHHHH
Confidence 34456677889999999999998888876555444
No 361
>TIGR00637 ModE_repress ModE molybdate transport repressor domain. ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.
Probab=68.32 E-value=13 Score=29.90 Aligned_cols=46 Identities=9% Similarity=-0.046 Sum_probs=33.3
Q ss_pred CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
++.++-.+|.... +.-|+..-|+.||+|+++|++.+++.-+.|...
T Consensus 2 ~~~~~l~~~~av~-----~~gSis~AA~~L~iS~stvs~~I~~LE~~lg~~ 47 (99)
T TIGR00637 2 ADPRRVALLKAIA-----RMGSISQAAKDAGISYKSAWDYIRAMNNLSGEP 47 (99)
T ss_pred CCHHHHHHHHHHH-----HhCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence 3455556666554 557999999999999999988876655555443
No 362
>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=68.21 E-value=14 Score=28.52 Aligned_cols=50 Identities=14% Similarity=0.123 Sum_probs=36.8
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHh
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLS-----LSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~Lg-----iS~~~Vr~~~~rAl~kLR~ 367 (379)
.|+++|..+|.+.+ ....+..|.++|.+.+. .+..++.+.+++.+++|..
T Consensus 23 ~Lt~~e~~lL~~L~-~~~~~~vs~~~l~~~lw~~~~~~~~~~l~~~I~rLRkkl~~ 77 (95)
T cd00383 23 ELTPKEFELLELLA-RNPGRVLSREQLLEAVWGDDYDVDDRTVDVHISRLRKKLED 77 (95)
T ss_pred EeCHHHHHHHHHHH-hCCCCcCCHHHHHHHhcCCCCCCCcccHHHHHHHHHHHhcc
Confidence 48899999998765 34347899999999884 5666777776666666654
No 363
>PF11662 DUF3263: Protein of unknown function (DUF3263); InterPro: IPR021678 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=68.01 E-value=20 Score=27.53 Aligned_cols=46 Identities=22% Similarity=0.167 Sum_probs=35.0
Q ss_pred cCCHHHHHHHHHHh-hcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578 317 TLSEREADILRLHF-GLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT 363 (379)
Q Consensus 317 ~L~~rer~Vl~l~y-gL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~ 363 (379)
.|+++++.||.+-- ... ..|-+-+.|-+.||+|.....|.++..+.
T Consensus 2 ~Ls~~d~~iL~fE~~ww~-~~GaKe~aIre~fGls~~rYyq~Ln~LiD 48 (77)
T PF11662_consen 2 GLSDRDRAILDFERRWWR-HGGAKEEAIREEFGLSPTRYYQRLNALID 48 (77)
T ss_pred CCCHHHHHHHHHHHHhCc-CCCCcHHHHHHHHCCCHHHHHHHHHHHhC
Confidence 58999999998631 111 13568899999999999999999887653
No 364
>PF05331 DUF742: Protein of unknown function (DUF742); InterPro: IPR007995 This family consists of several uncharacterised Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown.
Probab=67.92 E-value=9.2 Score=31.72 Aligned_cols=40 Identities=28% Similarity=0.287 Sum_probs=35.3
Q ss_pred hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
..|.+.++.|+.+.- ...|..|||..++++.+-|+.+..-
T Consensus 39 ~~l~pE~~~Il~lC~-----~~~SVAEiAA~L~lPlgVvrVLvsD 78 (114)
T PF05331_consen 39 AGLGPEHRAILELCR-----RPLSVAEIAARLGLPLGVVRVLVSD 78 (114)
T ss_pred CCCCHHHHHHHHHHC-----CCccHHHHHHhhCCCchhhhhhHHH
Confidence 469999999999986 5799999999999999999887654
No 365
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=67.63 E-value=13 Score=26.69 Aligned_cols=31 Identities=13% Similarity=0.019 Sum_probs=24.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
-|+...|+.||+|+++|++.+++.-+.|-..
T Consensus 14 gs~~~AA~~l~is~~~vs~~i~~LE~~lg~~ 44 (60)
T PF00126_consen 14 GSISAAAEELGISQSAVSRQIKQLEEELGVP 44 (60)
T ss_dssp SSHHHHHHHCTSSHHHHHHHHHHHHHHHTS-
T ss_pred CCHHHHHHHhhccchHHHHHHHHHHHHhCCe
Confidence 5999999999999999988776655555443
No 366
>PF02787 CPSase_L_D3: Carbamoyl-phosphate synthetase large chain, oligomerisation domain; InterPro: IPR005480 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 oligomerisation domain found in the large subunit of carbamoyl phosphate synthases as well as in certain other carboxy phsophate domain-containing enzymes.; GO: 0006807 nitrogen compound metabolic process; PDB: 1M6V_C 1CS0_C 1C30_E 1C3O_G 1BXR_A 1T36_E 1A9X_A 1KEE_G 1CE8_A 1JDB_H ....
Probab=67.62 E-value=73 Score=26.67 Aligned_cols=43 Identities=30% Similarity=0.392 Sum_probs=25.0
Q ss_pred HHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 311 LKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 311 L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
|......+++. .+....- -|.|-++||..+|++...|+.....
T Consensus 53 L~~~~~~~~~~--~L~~aK~-----~GFsD~~IA~l~~~~e~~vr~~R~~ 95 (123)
T PF02787_consen 53 LKEYLNELDPE--LLRKAKR-----LGFSDRQIARLWGVSEEEVRELRKE 95 (123)
T ss_dssp HHHHGGG--HH--HHHHHHH-----TT--HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHhhccchHH--HHHHHHH-----cCCCHHHHHhccCCCHHHHHHHHHH
Confidence 33334455555 3444443 4599999999999999999876443
No 367
>TIGR02612 mob_myst_A mobile mystery protein A. Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).
Probab=67.42 E-value=13 Score=32.42 Aligned_cols=38 Identities=13% Similarity=0.202 Sum_probs=29.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH------HHHHHHhHHhhch
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGI------ALTKLQQTNILNN 373 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~r------Al~kLR~~l~~~~ 373 (379)
-|+|+.|+|+.+|||+++|+++.+. .+..|.+.....+
T Consensus 37 lGmTq~eLAerlGVS~~tIs~iE~G~~~~~psl~~L~kIA~aLg 80 (150)
T TIGR02612 37 LGMSGAQLAGRLGVTPQRVEALEKSELSGTVTLKTLRAAAEALD 80 (150)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcCCCCCCCCHHHHHHHHHHcC
Confidence 5699999999999999999999884 3445555554433
No 368
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=67.39 E-value=47 Score=27.62 Aligned_cols=41 Identities=7% Similarity=0.031 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh
Q 046578 227 VAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIER 267 (379)
Q Consensus 227 ~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~ 267 (379)
...+.++...+.......++.+++|+.+|+++..+......
T Consensus 8 ~~~i~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 8 AITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 34455666667777778899999999999999998876653
No 369
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=67.12 E-value=14 Score=39.66 Aligned_cols=62 Identities=13% Similarity=0.187 Sum_probs=46.5
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHhhcCC---CCCCCHHHHHHHhCCCHHHHHHHHHH----HHHHHHhHHh
Q 046578 307 MKQELKELLQTLSEREADILRLHFGLDG---QTPVSCKEIGRLLSLSRERIRQIRGI----ALTKLQQTNI 370 (379)
Q Consensus 307 ~~~~L~~~L~~L~~rer~Vl~l~ygL~g---~e~~S~~EIAe~LgiS~~~Vr~~~~r----Al~kLR~~l~ 370 (379)
+.+.|......|++.||.|..+. ++. ...+|..|||+..|+|.+||.+..++ +..-||..+.
T Consensus 343 l~~~I~~~~~~Lt~~E~~IA~yI--l~n~~~v~~~si~eLA~~~~vS~aTV~Rf~kkLGf~Gf~efK~~L~ 411 (638)
T PRK14101 343 VFERIRQMRDALTPAERRVADLA--LNHPRSIINDPIVDIARKADVSQPTVIRFCRSLGCQGLSDFKLKLA 411 (638)
T ss_pred HHHHHHHHHhhcCHHHHHHHHHH--HhCHHHHHhccHHHHHHHhCCCHHHHHHHHHHhCCCCHHHHHHHHH
Confidence 34568889999999999998754 331 23479999999999999999887765 3445554443
No 370
>COG4709 Predicted membrane protein [Function unknown]
Probab=67.05 E-value=18 Score=32.67 Aligned_cols=57 Identities=19% Similarity=0.152 Sum_probs=43.1
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHh---hc-CCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578 305 QLMKQELKELLQTLSEREADILRLHF---GL-DGQTPVSCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 305 ~e~~~~L~~~L~~L~~rer~Vl~l~y---gL-~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
.+....++..|+.||+.+|.=+...| |- .+..|.|-.||++.||-+..-.+..+.+.
T Consensus 4 ~efL~eL~~yL~~Lp~~~r~e~m~dyeehF~~a~~~GksE~EI~~~LG~P~eiA~ei~s~~ 64 (195)
T COG4709 4 TEFLNELEQYLEGLPREERREIMYDYEEHFREAQEAGKSEEEIAKDLGDPKEIAAEILSER 64 (195)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhhhhcCCCHHHHHHHhCCHHHHHHHHHHHc
Confidence 44456799999999999877665443 22 24568899999999999988888776654
No 371
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=66.98 E-value=1.8 Score=38.09 Aligned_cols=48 Identities=21% Similarity=0.282 Sum_probs=0.0
Q ss_pred HHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 046578 310 ELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRG 359 (379)
Q Consensus 310 ~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~ 359 (379)
.|..+...|=..|+..|..- -..-.++|+++||+.+|++.+||++...
T Consensus 24 TL~~v~~~iv~~Q~~ff~~g--~~~l~PLt~~~iA~~lgl~~STVSRav~ 71 (160)
T PF04552_consen 24 TLLRVAQAIVERQKDFFLGG--PGALKPLTMKDIADELGLHESTVSRAVK 71 (160)
T ss_dssp --------------------------------------------------
T ss_pred HHHHHHHHHHHHHHHHHhcC--cccCcCCCHHHHHHHhCCCHhHHHHHHc
Confidence 35555566667777766521 1113679999999999999999998765
No 372
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=66.80 E-value=7.3 Score=27.12 Aligned_cols=24 Identities=29% Similarity=0.392 Sum_probs=19.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
++.+|+++.+|+|++|+.+..+++
T Consensus 4 l~~~ev~~~~g~s~~ti~~~~k~g 27 (51)
T PF05930_consen 4 LRIKEVAELLGVSRSTIYRLIKDG 27 (51)
T ss_dssp E-HHHHHHHHSS-HHHHHHHHHHH
T ss_pred ccHHHHHHHHCCCHHHHHHHHhcc
Confidence 578999999999999999988754
No 373
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=66.67 E-value=14 Score=27.06 Aligned_cols=31 Identities=23% Similarity=0.108 Sum_probs=25.6
Q ss_pred HHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Q 046578 235 NVLSRRLRRMPTDSEIAEMLNIHVSTVRLAI 265 (379)
Q Consensus 235 ~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l 265 (379)
.++...++...+..+||+.||++..+++.--
T Consensus 13 ~e~y~~~~g~i~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 13 FEIYKESNGKIKLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred HHHHHHhCCCccHHHHHHHHCCCHHHHHHHh
Confidence 3455678888999999999999999988543
No 374
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=66.55 E-value=14 Score=26.15 Aligned_cols=21 Identities=19% Similarity=0.256 Sum_probs=17.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIR 358 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~ 358 (379)
++.+|.|+.|||+..+++++-
T Consensus 16 lp~~eAA~~Lgv~~T~LKr~C 36 (52)
T PF02042_consen 16 LPIKEAAKELGVSVTTLKRRC 36 (52)
T ss_pred CCHHHHHHHhCCCHHHHHHHH
Confidence 899999999999988776654
No 375
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=66.52 E-value=7.2 Score=25.61 Aligned_cols=25 Identities=20% Similarity=0.312 Sum_probs=21.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.++|..++|+.+|++..+|+++...
T Consensus 9 ~~~s~~~la~~~~i~~~~i~~~~~~ 33 (56)
T smart00530 9 KGLTQEELAEKLGVSRSTLSRIENG 33 (56)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 4589999999999999999887654
No 376
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=66.40 E-value=6.3 Score=35.10 Aligned_cols=23 Identities=17% Similarity=0.316 Sum_probs=19.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Q 046578 337 PVSCKEIGRLLSLSRERIRQIRG 359 (379)
Q Consensus 337 ~~S~~EIAe~LgiS~~~Vr~~~~ 359 (379)
..|.++||+.+|+|+.+|++.++
T Consensus 149 ~~t~~~iA~~lG~tretvsR~l~ 171 (202)
T PRK13918 149 YATHDELAAAVGSVRETVTKVIG 171 (202)
T ss_pred cCCHHHHHHHhCccHHHHHHHHH
Confidence 47999999999999999976543
No 377
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=66.34 E-value=6.9 Score=28.79 Aligned_cols=25 Identities=28% Similarity=0.276 Sum_probs=20.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.+.+-+|||+.+|+|..+|+..+..
T Consensus 14 ~p~~T~eiA~~~gls~~~aR~yL~~ 38 (62)
T PF04703_consen 14 GPLKTREIADALGLSIYQARYYLEK 38 (62)
T ss_dssp S-EEHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 5699999999999999999887544
No 378
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=66.18 E-value=7.6 Score=39.72 Aligned_cols=24 Identities=21% Similarity=0.391 Sum_probs=22.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRG 359 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~ 359 (379)
.++|+++||+.+|+..+||++..+
T Consensus 317 kPLtlkdiA~~lglheSTVSRav~ 340 (429)
T TIGR02395 317 KPLTLREVAEELGLHESTISRAIN 340 (429)
T ss_pred cCCcHHHHHHHhCCCccchhhhhc
Confidence 789999999999999999998754
No 379
>COG1481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=66.00 E-value=17 Score=35.39 Aligned_cols=49 Identities=22% Similarity=0.350 Sum_probs=38.8
Q ss_pred hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCC--CHHHHHHHHHHHHHHHHhH
Q 046578 316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSL--SRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~Lgi--S~~~Vr~~~~rAl~kLR~~ 368 (379)
+.||+.-+++..+|. + .++.|++|+|+.+.. |.+.|..++.| +++|-..
T Consensus 252 ~~lpe~l~e~a~LRl--~-hpd~SLeeLg~~l~~~iSKSGvnHrlrk-l~kia~~ 302 (308)
T COG1481 252 EKLPEKLREAALLRL--E-HPDASLEELGELLEPPISKSGVNHRLRK-LKKIAER 302 (308)
T ss_pred hhCCHHHHHHHHHhh--c-ChhhhHHHHHHHhcCcccHHHHHHHHHH-HHHHHHH
Confidence 689999999999985 3 488999999999988 88888877655 3444433
No 380
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=65.80 E-value=11 Score=35.58 Aligned_cols=39 Identities=18% Similarity=0.096 Sum_probs=29.0
Q ss_pred HHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578 320 EREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 320 ~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
+|++.|+.+.- .....+.+|+|+.||+|..||++-+..-
T Consensus 5 ~R~~~Il~~l~---~~~~~~~~ela~~l~vS~~TirRdL~~L 43 (251)
T PRK13509 5 QRHQILLELLA---QLGFVTVEKVIERLGISPATARRDINKL 43 (251)
T ss_pred HHHHHHHHHHH---HcCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 34455554332 2356999999999999999999998863
No 381
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=65.70 E-value=13 Score=34.51 Aligned_cols=25 Identities=28% Similarity=0.331 Sum_probs=22.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.++|..|||++||||..+|++++..
T Consensus 24 g~~sa~elA~~Lgis~~avR~HL~~ 48 (218)
T COG2345 24 GPVSADELAEELGISPMAVRRHLDD 48 (218)
T ss_pred CCccHHHHHHHhCCCHHHHHHHHHH
Confidence 5699999999999999999998654
No 382
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=65.69 E-value=14 Score=32.83 Aligned_cols=87 Identities=22% Similarity=0.205 Sum_probs=48.9
Q ss_pred CCCCCHHHHHHHh--CCCHHHHHHHHHhc--CCccccCCccccCCCCcccccCCCCCCCChHHH-HHHHHHHHHHHHHHh
Q 046578 242 RRMPTDSEIAEML--NIHVSTVRLAIERT--RHPISLDGAVTDRGCMTMQDIIPGPDETMPERM-VQKQLMKQELKELLQ 316 (379)
Q Consensus 242 gr~pt~~eia~~L--gis~~~~~~~l~~~--~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~-~~~~e~~~~L~~~L~ 316 (379)
+..+++.+||+.+ +++.++++.++..- -+.+.-+.. +....-...+....+..+... -.+....+.-.++|+
T Consensus 37 ~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~---g~y~~t~~~l~~~~~~~~~avr~~h~q~~~lA~~al~ 113 (171)
T PF14394_consen 37 PFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGD---GKYVQTDKSLTTSSEIPSEAVRSYHKQMLELAQEALD 113 (171)
T ss_pred CCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCC---CcEEEecceeeCCCCCcHHHHHHHHHHHHHHHHHHHH
Confidence 4456899999999 99999999988762 122222211 000011112222222222211 123344455667888
Q ss_pred cCCHHHHHHHHHHhh
Q 046578 317 TLSEREADILRLHFG 331 (379)
Q Consensus 317 ~L~~rer~Vl~l~yg 331 (379)
+.|+.+|.+-.+-++
T Consensus 114 ~~p~~~R~~s~~T~~ 128 (171)
T PF14394_consen 114 RVPPEERDFSGLTMS 128 (171)
T ss_pred hCCccccceeeeEEE
Confidence 899999988777665
No 383
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=65.54 E-value=4.9 Score=35.39 Aligned_cols=23 Identities=39% Similarity=0.452 Sum_probs=0.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHh
Q 046578 245 PTDSEIAEMLNIHVSTVRLAIER 267 (379)
Q Consensus 245 pt~~eia~~Lgis~~~~~~~l~~ 267 (379)
-+..+||+.||+++.++..+...
T Consensus 50 Lt~~~iA~~lgl~~STVSRav~~ 72 (160)
T PF04552_consen 50 LTMKDIADELGLHESTVSRAVKN 72 (160)
T ss_dssp -----------------------
T ss_pred CCHHHHHHHhCCCHhHHHHHHcC
Confidence 37889999999999999987653
No 384
>TIGR01387 cztR_silR_copR heavy metal response regulator. Members of this family contain a response regulator receiver domain (Pfam:PF00072) and an associated transcriptional regulatory region (Pfam:PF00486). This group is separated phylogenetically from related proteins with similar architecture and contains a number of proteins associated with heavy metal resistance efflux systems for copper, silver, cadmium, and/or zinc. Most members encoded by genes adjacent to genes for encoding a member of the heavy metal sensor histidine kinase family (TIGRFAMs:TIGR01386), its partner in the two-component response regulator system.
Probab=65.29 E-value=9.9 Score=33.45 Aligned_cols=50 Identities=16% Similarity=0.145 Sum_probs=40.4
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHHh
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLL-----SLSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~L-----giS~~~Vr~~~~rAl~kLR~ 367 (379)
.|+++|.+|+.+..- +.+.-.|..+|++.+ ..+..+|..+++|.++||..
T Consensus 147 ~Lt~~E~~il~~l~~-~~~~~~sr~~i~~~~~~~~~~~~~~~~~~~i~~lr~kl~~ 201 (218)
T TIGR01387 147 TLTRKEFQLLWLLMR-RTGEVLPRTVIASLVWGMNFDSDTNVVDVAIRRLRAKVDD 201 (218)
T ss_pred eCCHHHHHHHHHHHh-CCCeeEcHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhhcC
Confidence 599999999998762 222558999999999 55678999999998888864
No 385
>PRK11517 transcriptional regulatory protein YedW; Provisional
Probab=64.87 E-value=13 Score=33.02 Aligned_cols=49 Identities=14% Similarity=0.095 Sum_probs=39.4
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHH
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLL-----SLSRERIRQIRGIALTKLQ 366 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~L-----giS~~~Vr~~~~rAl~kLR 366 (379)
.|+++|.+|+.+.. -+-++-+|..+|.+.+ ..+..+|..+++|.++||.
T Consensus 147 ~Lt~~E~~il~~l~-~~~g~~~s~~~i~~~~w~~~~~~~~~tv~~~i~rlr~Kl~ 200 (223)
T PRK11517 147 TLTRKEFQLLWLLA-SRAGEIIPRTVIASEIWGINFDSDTNTVDVAIRRLRAKVD 200 (223)
T ss_pred eCCHHHHHHHHHHH-hCCCccCCHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhhc
Confidence 59999999998765 3322567999999997 4467899999999888886
No 386
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=64.42 E-value=71 Score=25.37 Aligned_cols=79 Identities=10% Similarity=0.006 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHHHHHHHH
Q 046578 228 AKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLM 307 (379)
Q Consensus 228 ~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~~~~~e~ 307 (379)
..+.++...+...+...++.+++|+.+|++...+....... ...+|.+.+
T Consensus 5 ~~~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~~-------------------------~g~s~~~~i----- 54 (107)
T PRK10219 5 KIIQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTV-------------------------THQTLGDYI----- 54 (107)
T ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHH-------------------------HCcCHHHHH-----
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCC
Q 046578 308 KQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLS 350 (379)
Q Consensus 308 ~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS 350 (379)
++..+-....-|.. .+.+..+||..+|.+
T Consensus 55 -------------~~~Rl~~a~~~L~~-~~~~i~~iA~~~Gf~ 83 (107)
T PRK10219 55 -------------RQRRLLLAAVELRT-TERPIFDIAMDLGYV 83 (107)
T ss_pred -------------HHHHHHHHHHHHHc-cCCCHHHHHHHHCCC
No 387
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=64.42 E-value=6.7 Score=33.13 Aligned_cols=25 Identities=16% Similarity=0.163 Sum_probs=22.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.++|+.++|+.+|||+++|+++.+.
T Consensus 17 ~gltq~~lA~~~gvs~~~is~~E~g 41 (135)
T PRK09706 17 LKLSQRSLAKAVKVSHVSISQWERD 41 (135)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 5599999999999999999998754
No 388
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=64.00 E-value=18 Score=28.68 Aligned_cols=24 Identities=25% Similarity=0.293 Sum_probs=21.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRG 359 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~ 359 (379)
-++|.++||+.||+|...|.+.+.
T Consensus 22 ~~ls~~~ia~dL~~s~~~le~vL~ 45 (89)
T PF10078_consen 22 SGLSLEQIAADLGTSPEHLEQVLN 45 (89)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHc
Confidence 459999999999999999988764
No 389
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=63.75 E-value=23 Score=31.46 Aligned_cols=56 Identities=27% Similarity=0.229 Sum_probs=41.5
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHh---hcC-CCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 305 QLMKQELKELLQTLSEREADILRLHF---GLD-GQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 305 ~e~~~~L~~~L~~L~~rer~Vl~l~y---gL~-g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
++-.+.++..|..||+.|++=+.-+| +-+ +.+|.|.+||.+.||=++.-++++...
T Consensus 4 ~efL~~L~~~L~~lp~~e~~e~l~~Y~e~f~d~~~~G~sEeeii~~LG~P~~iA~~i~~~ 63 (181)
T PF08006_consen 4 NEFLNELEKYLKKLPEEEREEILEYYEEYFDDAGEEGKSEEEIIAELGSPKEIAREILAE 63 (181)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhCCCCHHHHHHHcCCHHHHHHHHHHh
Confidence 44556788999999999876555443 222 346789999999999998888877654
No 390
>PF00486 Trans_reg_C: Transcriptional regulatory protein, C terminal; InterPro: IPR001867 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents a domain that is almost always found associated with the response regulator receiver domain (see IPR001789 from INTERPRO). It may play a role in DNA binding [].; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2K4J_A 2JPB_A 1ODD_A 1OPC_A 1KGS_A 2PMU_E 2JZY_A 1GXP_B 1QQI_A 2Z33_A ....
Probab=63.27 E-value=21 Score=26.33 Aligned_cols=51 Identities=22% Similarity=0.184 Sum_probs=39.0
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHhH
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLS-----LSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~Lg-----iS~~~Vr~~~~rAl~kLR~~ 368 (379)
.|++.|..+|.+-. ....+..|.++|.+.+- .+..++.+.+++.+++|...
T Consensus 5 ~Lt~~e~~lL~~L~-~~~~~~vs~~~l~~~~w~~~~~~~~~~l~~~I~rLR~kL~~~ 60 (77)
T PF00486_consen 5 KLTPKEFRLLELLL-RNPGRVVSREELIEALWGDEEDVSDNSLDVHISRLRKKLEDA 60 (77)
T ss_dssp ESSHHHHHHHHHHH-HTTTSEEEHHHHHHHHTSSSSTTCTHHHHHHHHHHHHHHHSS
T ss_pred ecCHHHHHHHHHHH-hCCCCCCCHHHhCChhhhcccccchhhHHHHHHHHHHHHhhc
Confidence 58999999998655 33336789999998764 67778888888877777765
No 391
>PF10654 DUF2481: Protein of unknown function (DUF2481) ; InterPro: IPR018916 This entry is represented by Bacteriophage A500, Gp59. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=63.20 E-value=19 Score=29.75 Aligned_cols=43 Identities=9% Similarity=0.198 Sum_probs=32.5
Q ss_pred HHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHh
Q 046578 323 ADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNI 370 (379)
Q Consensus 323 r~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~ 370 (379)
++.+.||. .|+|...||+.++||.++|-+...+-.+--.+.+.
T Consensus 71 ~Efi~LR~-----AGlt~~aIAd~F~iS~s~~~nft~~n~~eYyr~F~ 113 (126)
T PF10654_consen 71 REFIELRH-----AGLTCYAIADYFKISKSTVFNFTQNNKKEYYRIFD 113 (126)
T ss_pred HHHHHHHh-----cCCChHHHHHHHhHHHHHHHHHHHHhHHHHHHHhh
Confidence 34566665 67999999999999999999887665555544443
No 392
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=63.00 E-value=11 Score=39.12 Aligned_cols=24 Identities=21% Similarity=0.461 Sum_probs=22.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRG 359 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~ 359 (379)
.++++++||+.+|+..+||++..+
T Consensus 368 kPLtlkdVAe~lglHeSTVSRa~~ 391 (481)
T PRK12469 368 KPLVLRDVAEELGLHESTISRATG 391 (481)
T ss_pred cCCcHHHHHHHhCCCcchhhHHhc
Confidence 689999999999999999998754
No 393
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=62.49 E-value=9.7 Score=39.28 Aligned_cols=24 Identities=21% Similarity=0.357 Sum_probs=21.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRG 359 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~ 359 (379)
.++|+++||+.+|+..+||++..+
T Consensus 342 kPLtlkdvAe~lglheSTVSRav~ 365 (455)
T PRK05932 342 KPLVLKDIAEELGMHESTISRATT 365 (455)
T ss_pred cCccHHHHHHHhCCCccchhhhhc
Confidence 689999999999999999998754
No 394
>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=62.27 E-value=10 Score=25.00 Aligned_cols=25 Identities=24% Similarity=0.328 Sum_probs=21.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.++|..++|..+|+++.+|++.+..
T Consensus 11 ~~~s~~~~a~~~~~~~~~v~~~~~g 35 (58)
T cd00093 11 KGLTQEELAEKLGVSRSTISRIENG 35 (58)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHcC
Confidence 4599999999999999999887664
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=62.26 E-value=5.8 Score=31.56 Aligned_cols=25 Identities=24% Similarity=0.404 Sum_probs=22.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
+|..|+|+.+|||..|++.....++
T Consensus 1 ~ti~eva~~~gvs~~tLRyye~~Gl 25 (96)
T cd04768 1 LTIGEFAKLAGVSIRTLRHYDDIGL 25 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999887754
No 396
>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=62.00 E-value=5.7 Score=31.97 Aligned_cols=26 Identities=19% Similarity=0.301 Sum_probs=23.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIALT 363 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rAl~ 363 (379)
++..|+|+.+|||..|++.....++-
T Consensus 2 ~~i~eva~~~gvs~~tLR~ye~~Gll 27 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYESIGLI 27 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 68999999999999999998887653
No 397
>PF13309 HTH_22: HTH domain
Probab=61.95 E-value=5.6 Score=29.32 Aligned_cols=20 Identities=15% Similarity=0.257 Sum_probs=18.2
Q ss_pred CHHHHHHHhCCCHHHHHHHH
Q 046578 339 SCKEIGRLLSLSRERIRQIR 358 (379)
Q Consensus 339 S~~EIAe~LgiS~~~Vr~~~ 358 (379)
+...+|+.||||+.||++.+
T Consensus 44 av~~vA~~L~iS~~TVY~YL 63 (64)
T PF13309_consen 44 AVEYVAEKLGISRATVYRYL 63 (64)
T ss_pred HHHHHHHHHCCCHHHHHHHc
Confidence 78899999999999999864
No 398
>PF11994 DUF3489: Protein of unknown function (DUF3489); InterPro: IPR021880 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 84 to 211 amino acids in length. This protein has a single completely conserved residue W that may be functionally important.
Probab=61.94 E-value=26 Score=26.63 Aligned_cols=41 Identities=15% Similarity=0.133 Sum_probs=32.4
Q ss_pred HHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046578 321 READILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTK 364 (379)
Q Consensus 321 rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~k 364 (379)
++-.||.|..- .+|-|..||++.+|.-..+|+-.+..+++|
T Consensus 11 Kqa~li~mL~r---p~GATi~ei~~atGWq~HTvRgalsg~~kK 51 (72)
T PF11994_consen 11 KQAQLIAMLRR---PEGATIAEICEATGWQPHTVRGALSGLLKK 51 (72)
T ss_pred HHHHHHHHHcC---CCCCCHHHHHHhhCCchhhHHHHHHHHHHH
Confidence 45556665442 477999999999999999999999988544
No 399
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=61.83 E-value=10 Score=36.76 Aligned_cols=42 Identities=17% Similarity=0.093 Sum_probs=35.2
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
.|+..||.-|.... ..++|..|||+.||...+||++-+.|..
T Consensus 7 hLT~~eR~~I~~l~----~~~~S~reIA~~LgRh~sTIsRElkRn~ 48 (318)
T COG2826 7 HLTLFERYEIERLL----KAKMSIREIAKQLNRHHSTISRELKRNR 48 (318)
T ss_pred hCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCcchhhHHHhcCC
Confidence 78888888887544 2689999999999999999998877644
No 400
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=61.58 E-value=6.4 Score=30.80 Aligned_cols=25 Identities=20% Similarity=0.337 Sum_probs=22.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
+|..|+|+.+|||..+++.+..+++
T Consensus 2 ~ti~evA~~~gvs~~tLR~ye~~Gl 26 (88)
T cd01105 2 IGIGEVSKLTGVSPRQLRYWEEKGL 26 (88)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 7999999999999999999877654
No 401
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=61.40 E-value=19 Score=30.06 Aligned_cols=26 Identities=23% Similarity=0.281 Sum_probs=21.9
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 335 QTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 335 ~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
....|..|||+.+|+|+++|++++.+
T Consensus 23 ~~~~s~~eia~~l~is~~~v~~~l~~ 48 (130)
T TIGR02944 23 SQPYSAAEIAEQTGLNAPTVSKILKQ 48 (130)
T ss_pred CCCccHHHHHHHHCcCHHHHHHHHHH
Confidence 35689999999999999999876544
No 402
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=61.28 E-value=15 Score=29.42 Aligned_cols=37 Identities=19% Similarity=0.186 Sum_probs=25.5
Q ss_pred HHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 321 READILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 321 rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
-|+.++...+- ..+-...+.|+.|||+++++++.+.+
T Consensus 55 ~Er~~i~~aL~---~~~gn~s~AAr~LGIsRsTL~rKLkr 91 (95)
T PRK00430 55 VEAPLLDMVMQ---YTRGNQTRAALMLGINRGTLRKKLKK 91 (95)
T ss_pred HHHHHHHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 35555554432 13367999999999999998776554
No 403
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member 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.
Probab=61.00 E-value=16 Score=34.12 Aligned_cols=38 Identities=8% Similarity=0.049 Sum_probs=27.3
Q ss_pred HHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 323 ADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 323 r~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
|-+-.|.++-....++|..|||+.+|++++||.+++.-
T Consensus 10 ral~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~t 47 (248)
T TIGR02431 10 RGLAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLT 47 (248)
T ss_pred HHHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 33334444222236799999999999999999988654
No 404
>PF04645 DUF603: Protein of unknown function, DUF603; InterPro: IPR006739 This family includes several uncharacterised proteins from Borrelia species.
Probab=60.76 E-value=10 Score=33.47 Aligned_cols=25 Identities=28% Similarity=0.339 Sum_probs=21.3
Q ss_pred CC-CCHHHHHHHhCCCHHHHHHHHHH
Q 046578 336 TP-VSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 336 e~-~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
+| ++..|||+.||||+..|.+..++
T Consensus 17 eg~L~d~~Ia~~lgvs~~nV~kmR~K 42 (181)
T PF04645_consen 17 EGRLSDAEIAKELGVSRVNVWKMRQK 42 (181)
T ss_pred cCCccHHHHHHHHCchHHHHHHHHHH
Confidence 55 99999999999999999776544
No 405
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=60.64 E-value=11 Score=33.64 Aligned_cols=27 Identities=33% Similarity=0.624 Sum_probs=21.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578 337 PVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 337 ~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~ 367 (379)
..|.++||+.+|+|+.+|++. +++|++
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR~----l~~l~~ 194 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRV----LKMLED 194 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHHH----HHHHHH
Confidence 488999999999999999765 455554
No 406
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=60.42 E-value=9.5 Score=34.92 Aligned_cols=27 Identities=30% Similarity=0.552 Sum_probs=21.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578 337 PVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 337 ~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~ 367 (379)
.+|.++||+.+|+|+.+|++. +++|++
T Consensus 184 ~lt~~~iA~~lG~sr~tvsR~----l~~l~~ 210 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETISRL----LGRFQK 210 (235)
T ss_pred cccHHHHHHHhCCcHHHHHHH----HHHHHH
Confidence 479999999999999999765 445554
No 407
>PRK11050 manganese transport regulator MntR; Provisional
Probab=60.14 E-value=17 Score=31.39 Aligned_cols=26 Identities=12% Similarity=0.097 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
.+.+..|||+.+|+++++|++.+.+-
T Consensus 50 ~~~t~~eLA~~l~is~stVsr~l~~L 75 (152)
T PRK11050 50 GEARQVDIAARLGVSQPTVAKMLKRL 75 (152)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 57899999999999999998776554
No 408
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=59.30 E-value=14 Score=28.15 Aligned_cols=19 Identities=5% Similarity=0.038 Sum_probs=18.2
Q ss_pred CHHHHHHHhCCCHHHHHHH
Q 046578 339 SCKEIGRLLSLSRERIRQI 357 (379)
Q Consensus 339 S~~EIAe~LgiS~~~Vr~~ 357 (379)
+...+|+.||||.++|+|+
T Consensus 12 s~~kvA~aLGIs~~AVsQW 30 (75)
T PRK09744 12 SKTKLANAAGVRLASVAAW 30 (75)
T ss_pred cHHHHHHHHCCCHHHHHHH
Confidence 7889999999999999998
No 409
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=59.21 E-value=33 Score=30.66 Aligned_cols=39 Identities=18% Similarity=0.237 Sum_probs=28.5
Q ss_pred CHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 319 SEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 319 ~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
++....|+..-. . ....|-.|||+.||++...||+++.+
T Consensus 21 ~~~~~~Vl~~L~--~-~g~~tdeeLA~~Lgi~~~~VRk~L~~ 59 (178)
T PRK06266 21 DEEGFEVLKALI--K-KGEVTDEEIAEQTGIKLNTVRKILYK 59 (178)
T ss_pred CccHhHHHHHHH--H-cCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 444555665432 1 14699999999999999999887665
No 410
>PHA02535 P terminase ATPase subunit; Provisional
Probab=59.20 E-value=12 Score=39.74 Aligned_cols=25 Identities=20% Similarity=0.151 Sum_probs=23.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
+|+|..|||+.||++..+|+++..+
T Consensus 17 ~G~sv~eIA~~LGv~~~Tl~~W~kr 41 (581)
T PHA02535 17 QGWTVAEIAEELGLKSRTIYSWKER 41 (581)
T ss_pred cCCCHHHHHHHhCCChhHHHHHhcc
Confidence 5799999999999999999998765
No 411
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=59.13 E-value=28 Score=24.38 Aligned_cols=46 Identities=20% Similarity=0.157 Sum_probs=28.0
Q ss_pred CCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Q 046578 219 LPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLA 264 (379)
Q Consensus 219 ip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~ 264 (379)
+|.......-...+.-..+..+.-...+..+||+.+|+++.+++.=
T Consensus 3 Ip~~ti~RL~~Y~r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRKD 48 (50)
T PF06971_consen 3 IPKATIRRLPLYLRYLEQLKEEGVERVSSQELAEALGITPAQVRKD 48 (50)
T ss_dssp -SHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHcCCeeECHHHHHHHHCCCHHHhccc
Confidence 4444444455555555555554334568899999999999998853
No 412
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=59.09 E-value=7.1 Score=31.36 Aligned_cols=25 Identities=20% Similarity=0.307 Sum_probs=22.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
+|..|+|+.+|||..|++.....++
T Consensus 1 ~ti~eva~~~gvs~~tlR~ye~~Gl 25 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDEIGL 25 (103)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999998877654
No 413
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=59.08 E-value=20 Score=31.29 Aligned_cols=25 Identities=16% Similarity=0.149 Sum_probs=21.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
......+||+.|||++++|...+++
T Consensus 23 ~~~~~~diA~~L~Vsp~sVt~ml~r 47 (154)
T COG1321 23 GFARTKDIAERLKVSPPSVTEMLKR 47 (154)
T ss_pred CcccHHHHHHHhCCCcHHHHHHHHH
Confidence 5589999999999999999776554
No 414
>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=59.04 E-value=7 Score=31.84 Aligned_cols=25 Identities=20% Similarity=0.349 Sum_probs=22.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
||..|+|+.+|||..|++.....++
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~Gl 25 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEKEGL 25 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999887765
No 415
>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=58.94 E-value=7 Score=30.65 Aligned_cols=25 Identities=12% Similarity=0.169 Sum_probs=22.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
+|..|+|+.+|||..+++.+...++
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye~~Gl 26 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYERLGL 26 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 6899999999999999999877654
No 416
>PRK13698 plasmid-partitioning protein; Provisional
Probab=58.93 E-value=30 Score=34.01 Aligned_cols=48 Identities=13% Similarity=0.071 Sum_probs=32.2
Q ss_pred HHHHHhcCCHHHHHHHH-HHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 311 LKELLQTLSEREADILR-LHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 311 L~~~L~~L~~rer~Vl~-l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
+.+.-..+++.|+-.=. ..+ ++ ..++|++|||+.+|+|+++|.+.+.-
T Consensus 151 iEN~qRels~iE~A~ay~~~L-~~-~~~~tQeeLA~~lG~SRs~Vsn~Lrl 199 (323)
T PRK13698 151 LGNDYRPTSAYERGLRYASRL-QN-EFAGNISALADAENISRKIITRCINT 199 (323)
T ss_pred HHHhccCCCHHHHHHHHHHHH-HH-hcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 33333457888776622 211 11 13589999999999999999887654
No 417
>PF12298 Bot1p: Eukaryotic mitochondrial regulator protein ; InterPro: IPR021036 This entry represents Ribosomal protein S35, which localises to the mitochondria in live cells and co-fractionates with purified mitochondrial ribosomes. This group of proteins have a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery and a role in mitochondrial integrity. Observations also indicate that in Schizosaccharomyces pombe (Fission yeast), alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms [].
Probab=58.85 E-value=23 Score=31.59 Aligned_cols=39 Identities=21% Similarity=0.217 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 046578 318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRG 359 (379)
Q Consensus 318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~ 359 (379)
|++..|.-|...+- .++.|.++||..+||+..+|.-+++
T Consensus 17 lse~~r~~Iy~~~~---~~~~sv~~vS~~ygi~~~RV~AIvr 55 (172)
T PF12298_consen 17 LSEELREQIYEDVM---QDGKSVREVSQKYGIKIQRVEAIVR 55 (172)
T ss_pred CCHHHHHHHHHHHH---hCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 66677766666663 3568999999999999999976654
No 418
>PF06322 Phage_NinH: Phage NinH protein; InterPro: IPR010454 This entry is represented by Bacteriophage 933W, NinH. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=58.83 E-value=15 Score=26.84 Aligned_cols=20 Identities=25% Similarity=0.418 Sum_probs=18.1
Q ss_pred CHHHHHHHhCCCHHHHHHHH
Q 046578 339 SCKEIGRLLSLSRERIRQIR 358 (379)
Q Consensus 339 S~~EIAe~LgiS~~~Vr~~~ 358 (379)
.+.|+|..|+|++.||++..
T Consensus 18 nqtEvaR~l~c~R~TVrKY~ 37 (64)
T PF06322_consen 18 NQTEVARRLGCNRATVRKYS 37 (64)
T ss_pred cHHHHHHHhcccHHHHHHHh
Confidence 78999999999999998764
No 419
>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=58.69 E-value=7.4 Score=30.88 Aligned_cols=25 Identities=24% Similarity=0.345 Sum_probs=22.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
|+..|+|+.+||+..+|+.+...++
T Consensus 1 ~~~~eva~~~gi~~~tlr~~~~~Gl 25 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEEKGL 25 (100)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999877654
No 420
>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=58.61 E-value=7.5 Score=31.62 Aligned_cols=26 Identities=27% Similarity=0.326 Sum_probs=22.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIALT 363 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rAl~ 363 (379)
++..|+|+.+|||.+|++....+++=
T Consensus 1 ~~i~eva~~~gis~~tlR~ye~~GLi 26 (108)
T cd01107 1 FTIGEFAKLSNLSIKALRYYDKIGLL 26 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCC
Confidence 57899999999999999999887653
No 421
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=58.57 E-value=15 Score=26.78 Aligned_cols=19 Identities=16% Similarity=0.291 Sum_probs=17.3
Q ss_pred CHHHHHHHhCCCHHHHHHH
Q 046578 339 SCKEIGRLLSLSRERIRQI 357 (379)
Q Consensus 339 S~~EIAe~LgiS~~~Vr~~ 357 (379)
+...+|+.||||+++|+++
T Consensus 11 ~~~~lAkalGVs~~aVs~W 29 (60)
T PF14549_consen 11 GQSKLAKALGVSPQAVSQW 29 (60)
T ss_dssp SHHHHHHHHTS-HHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHh
Confidence 7899999999999999999
No 422
>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=58.41 E-value=7.6 Score=31.10 Aligned_cols=25 Identities=20% Similarity=0.426 Sum_probs=21.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
++..|+|+.+|||..|++.....++
T Consensus 1 y~i~e~A~~~gvs~~tlR~Ye~~Gl 25 (99)
T cd04772 1 YRTVDLARAIGLSPQTVRNYESLGL 25 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 4788999999999999998876554
No 423
>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=58.39 E-value=7.5 Score=30.97 Aligned_cols=25 Identities=16% Similarity=0.147 Sum_probs=22.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
|+..|+|+.+|+|..+++.....++
T Consensus 1 m~I~eva~~~gvs~~tlR~Ye~~GL 25 (95)
T cd04780 1 MRMSELSKRSGVSVATIKYYLREGL 25 (95)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999998877665
No 424
>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=57.97 E-value=7.7 Score=30.91 Aligned_cols=25 Identities=20% Similarity=0.363 Sum_probs=22.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
+|..|+|+.+|||..|++.....++
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~Gl 25 (97)
T cd04782 1 FTTGEFAKLCGISKQTLFHYDKIGL 25 (97)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999887765
No 425
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=57.87 E-value=45 Score=26.92 Aligned_cols=45 Identities=24% Similarity=0.378 Sum_probs=33.9
Q ss_pred hcCCHHHHHHHHH----HhhcC-CCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 316 QTLSEREADILRL----HFGLD-GQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 316 ~~L~~rer~Vl~l----~ygL~-g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
..|+.+|..|+.. -||.+ ..+-.|..+||+..|+++.+|+..+..
T Consensus 28 ~dls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~~~V~~al~~ 77 (100)
T PF04492_consen 28 ADLSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGLSRDHVSKALNE 77 (100)
T ss_pred ccccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHHCcCHHHHHHHHHH
Confidence 5899999887764 36655 225689999999999999988655443
No 426
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=57.85 E-value=23 Score=30.01 Aligned_cols=25 Identities=12% Similarity=0.147 Sum_probs=21.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
...+..+||+.||+|.++|++.+.+
T Consensus 21 ~~~~~~ela~~l~vs~~svs~~l~~ 45 (142)
T PRK03902 21 GYARVSDIAEALSVHPSSVTKMVQK 45 (142)
T ss_pred CCcCHHHHHHHhCCChhHHHHHHHH
Confidence 4579999999999999999877644
No 427
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=57.82 E-value=30 Score=27.22 Aligned_cols=41 Identities=22% Similarity=0.303 Sum_probs=0.0
Q ss_pred hcCCHHHHHH----HHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 046578 316 QTLSEREADI----LRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRG 359 (379)
Q Consensus 316 ~~L~~rer~V----l~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~ 359 (379)
..|+|.|++. +...|-+.. +|.++||..||+|...+..++.
T Consensus 1 MSLn~eq~~~Tk~elqan~el~~---LS~~~iA~~Ln~t~~~lekil~ 45 (97)
T COG4367 1 MSLNPEQKQRTKQELQANFELCP---LSDEEIATALNWTEVKLEKILQ 45 (97)
T ss_pred CCCCHHHHHHHHHHHHHhhhhcc---ccHHHHHHHhCCCHHHHHHHHH
No 428
>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=57.53 E-value=7.7 Score=30.94 Aligned_cols=25 Identities=20% Similarity=0.417 Sum_probs=21.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
|+..|+|+.+|+|.+|++.+...++
T Consensus 1 ~~I~e~a~~~gvs~~tLR~ye~~Gl 25 (96)
T cd04774 1 YKVDEVAKRLGLTKRTLKYYEEIGL 25 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999876643
No 429
>PRK13503 transcriptional activator RhaS; Provisional
Probab=57.51 E-value=1e+02 Score=28.78 Aligned_cols=38 Identities=8% Similarity=0.152 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh
Q 046578 230 IAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIER 267 (379)
Q Consensus 230 i~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~ 267 (379)
+.+...-+.+......+.+++|+.+|+++..+......
T Consensus 173 i~~~~~~I~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk~ 210 (278)
T PRK13503 173 LNQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQ 210 (278)
T ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 44445555566667789999999999999988877653
No 430
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=56.78 E-value=13 Score=29.73 Aligned_cols=23 Identities=22% Similarity=0.254 Sum_probs=20.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
+|..|+|+.+|||.+|++.+...
T Consensus 1 yti~EvA~~~gVs~~tLR~ye~~ 23 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRYWETE 23 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 57899999999999999998765
No 431
>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=56.76 E-value=8.3 Score=31.06 Aligned_cols=25 Identities=16% Similarity=0.246 Sum_probs=22.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
++..|+|+.+|||..|++.....++
T Consensus 2 ~~i~eva~~~gvs~~tlR~ye~~Gl 26 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEKLGL 26 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 6899999999999999998877654
No 432
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=56.69 E-value=19 Score=33.91 Aligned_cols=38 Identities=29% Similarity=0.239 Sum_probs=28.9
Q ss_pred HHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 320 EREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 320 ~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
+|++.|+.+.-- ....+..|+|+.||||..|||+-+..
T Consensus 5 ~R~~~Il~~l~~---~~~~~~~ela~~l~vS~~TiRRdL~~ 42 (252)
T PRK10906 5 QRHDAIIELVKQ---QGYVSTEELVEHFSVSPQTIRRDLND 42 (252)
T ss_pred HHHHHHHHHHHH---cCCEeHHHHHHHhCCCHHHHHHHHHH
Confidence 466666665431 24589999999999999999996655
No 433
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=56.65 E-value=20 Score=33.87 Aligned_cols=39 Identities=13% Similarity=0.112 Sum_probs=27.1
Q ss_pred HHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 322 EADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 322 er~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
+|-+-.|.++-....++|..|||+.+|+++++|.+++..
T Consensus 11 ~ral~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~t 49 (263)
T PRK09834 11 SRGLMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLET 49 (263)
T ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 344444444222224599999999999999999877654
No 434
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=56.57 E-value=11 Score=31.37 Aligned_cols=25 Identities=12% Similarity=0.064 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.|+|.+|+|+.+|+|+++++++.+.
T Consensus 17 ~Glsq~eLA~~~Gis~~~is~iE~g 41 (120)
T PRK13890 17 RHMTKKELSERSGVSISFLSDLTTG 41 (120)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 5699999999999999999998763
No 435
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=56.51 E-value=14 Score=34.88 Aligned_cols=39 Identities=31% Similarity=0.343 Sum_probs=30.6
Q ss_pred CHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 319 SEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 319 ~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.+|++.|+.+.-- ..-.+.+|+|+.||||..|||+=+..
T Consensus 4 ~eR~~~Il~~l~~---~g~v~v~eLa~~~~VS~~TIRRDL~~ 42 (253)
T COG1349 4 EERHQKILELLKE---KGKVSVEELAELFGVSEMTIRRDLNE 42 (253)
T ss_pred HHHHHHHHHHHHH---cCcEEHHHHHHHhCCCHHHHHHhHHH
Confidence 3577888876542 24589999999999999999996554
No 436
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. 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 characterized.
Probab=56.27 E-value=32 Score=32.98 Aligned_cols=87 Identities=21% Similarity=0.214 Sum_probs=49.0
Q ss_pred CCCCCHHHHHHHhC--CCHHHHHHHHHhc--CCccccCCccccCCCCcccccCCCCCCCChHHH-HHHHHHHHHHHHHHh
Q 046578 242 RRMPTDSEIAEMLN--IHVSTVRLAIERT--RHPISLDGAVTDRGCMTMQDIIPGPDETMPERM-VQKQLMKQELKELLQ 316 (379)
Q Consensus 242 gr~pt~~eia~~Lg--is~~~~~~~l~~~--~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~-~~~~e~~~~L~~~L~ 316 (379)
+..+++++||+.++ |+.++++.++..- -+.+.-+. ++.-..-...+....+..+... --+.+..+.-.++|+
T Consensus 135 ~~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk~~---~g~y~~t~~~l~~~~~~~~~avr~~h~q~l~lA~~al~ 211 (271)
T TIGR02147 135 PFADDPEELAKRCFPKISAEQVKESLDLLERLGLIKKNE---DGFYKQTDKAVSTGDEVIPLAVRQYQKQMIDLAKEALD 211 (271)
T ss_pred CCCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeECC---CCcEEeecceeecCCccchHHHHHHHHHHHHHHHHHHH
Confidence 34557889999998 9999999888752 12222111 1100011112222222222221 123444566778899
Q ss_pred cCCHHHHHHHHHHhh
Q 046578 317 TLSEREADILRLHFG 331 (379)
Q Consensus 317 ~L~~rer~Vl~l~yg 331 (379)
..|+.+|.+-.+-++
T Consensus 212 ~~p~~eR~~S~lT~~ 226 (271)
T TIGR02147 212 ALPPSERDVSTVTFG 226 (271)
T ss_pred hCCccccccceeeEe
Confidence 999999997776664
No 437
>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=56.06 E-value=8.6 Score=31.45 Aligned_cols=25 Identities=24% Similarity=0.287 Sum_probs=22.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
+|..|+|+.+|||..|++.....++
T Consensus 1 ~~i~e~a~~~gvs~~tlr~ye~~gl 25 (113)
T cd01109 1 YTIKEVAEKTGLSADTLRYYEKEGL 25 (113)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999887765
No 438
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=56.04 E-value=16 Score=34.46 Aligned_cols=38 Identities=26% Similarity=0.283 Sum_probs=30.0
Q ss_pred HHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 320 EREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 320 ~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
+|++.|+.+.-- ....+..|+|+.||+|+.|||+-+..
T Consensus 5 eR~~~Il~~L~~---~~~v~v~eLa~~l~VS~~TIRRDL~~ 42 (256)
T PRK10434 5 QRQAAILEYLQK---QGKTSVEELAQYFDTTGTTIRKDLVI 42 (256)
T ss_pred HHHHHHHHHHHH---cCCEEHHHHHHHHCCCHHHHHHHHHH
Confidence 566666665431 24589999999999999999999877
No 439
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=55.89 E-value=26 Score=33.59 Aligned_cols=46 Identities=13% Similarity=0.075 Sum_probs=35.9
Q ss_pred HhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578 315 LQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL 365 (379)
Q Consensus 315 L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL 365 (379)
+++|+-++-++|...+ +.-|+..-|+.|++|+++|++.+++.-+.|
T Consensus 5 ~~~mdl~~L~~f~av~-----e~gs~t~AA~~L~iSQpavS~~I~~LE~~l 50 (319)
T PRK10216 5 LTTLDLNLLLCLQLLM-----QERSVTKAAKRMNVTPSAVSKSLAKLRAWF 50 (319)
T ss_pred hhhcCHHHHHHHHHHH-----HhCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 4667778888888776 667999999999999999987755544443
No 440
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=55.82 E-value=8.6 Score=30.57 Aligned_cols=25 Identities=24% Similarity=0.254 Sum_probs=22.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
|+..|+|+.+|+|..|++.....++
T Consensus 1 m~i~eva~~~gvs~~tlR~ye~~Gl 25 (96)
T cd04788 1 WKIGELARRTGLSVRTLHHYDHIGL 25 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5788999999999999999887654
No 441
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=55.79 E-value=31 Score=28.63 Aligned_cols=25 Identities=36% Similarity=0.446 Sum_probs=21.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
...|.+|||+.+|+++.+|++++..
T Consensus 24 ~~~s~~eia~~~~i~~~~v~~il~~ 48 (132)
T TIGR00738 24 GPVSVKEIAERQGISRSYLEKILRT 48 (132)
T ss_pred CcCcHHHHHHHHCcCHHHHHHHHHH
Confidence 4799999999999999999876544
No 442
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=55.67 E-value=20 Score=26.25 Aligned_cols=25 Identities=8% Similarity=0.250 Sum_probs=21.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
.|.++||+.+|+|...+.+...+..
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~~ 26 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKET 26 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHh
Confidence 6889999999999999988887654
No 443
>PF06970 RepA_N: Replication initiator protein A (RepA) N-terminus; InterPro: IPR010724 This entry represents the N terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids []. Most proteins in this entry are bacterial, but archaeal and eukaryotic members are also included.
Probab=55.22 E-value=12 Score=28.63 Aligned_cols=22 Identities=23% Similarity=0.320 Sum_probs=19.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRG 359 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~ 359 (379)
+|.+|+++.||+|+.+|.+.+.
T Consensus 53 ~s~eel~~~L~~s~~tv~~~~k 74 (76)
T PF06970_consen 53 FSIEELMELLNCSKSTVIKAKK 74 (76)
T ss_pred eeHHHHHHHHCCCHHHHHHHHH
Confidence 7999999999999999987654
No 444
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=54.92 E-value=25 Score=33.45 Aligned_cols=25 Identities=16% Similarity=0.129 Sum_probs=22.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.++|+.|||+.+|++++||.++++-
T Consensus 39 ~~~tl~eIa~~lglpkStv~RlL~t 63 (271)
T PRK10163 39 GSSSVSDISLNLDLPLSTTFRLLKV 63 (271)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 5699999999999999999887654
No 445
>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=54.80 E-value=9.2 Score=31.31 Aligned_cols=25 Identities=16% Similarity=0.161 Sum_probs=22.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
|+..|+|+.+|||..|++.....++
T Consensus 1 m~i~eva~~~gvs~~tlR~Ye~~GL 25 (112)
T cd01282 1 MRIGELAARTGVSVRSLRYYEEQGL 25 (112)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCC
Confidence 5789999999999999999888765
No 446
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=54.73 E-value=23 Score=33.19 Aligned_cols=25 Identities=8% Similarity=0.215 Sum_probs=21.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.++|..|||+.+|+++++|.+++.-
T Consensus 27 ~~l~l~eia~~lgl~kstv~Rll~t 51 (257)
T PRK15090 27 REIGITELSQRVMMSKSTVYRFLQT 51 (257)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 5699999999999999999887654
No 447
>COG3711 BglG Transcriptional antiterminator [Transcription]
Probab=54.59 E-value=21 Score=36.82 Aligned_cols=114 Identities=21% Similarity=0.139 Sum_probs=61.7
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHH
Q 046578 242 RRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSER 321 (379)
Q Consensus 242 gr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~r 321 (379)
...-+..++|+.+|+|..+++.-+........-+........ . .-.+..+ . +...... ...........
T Consensus 17 ~~~~~~~~la~~l~vS~Rti~~~i~~In~~l~~~~~~~~~~~-~-~~~~~~~---~-~~~~~~~-----~~~~~~~~~~~ 85 (491)
T COG3711 17 NPLLTIKELAEQLGVSRRTIRYDIKKINESLEEGGIPIIKRK-G-GGYILEE---D-ERALELE-----ELQELTSYDKD 85 (491)
T ss_pred CCCCCHHHHHHHhCccHHHHHHHHHHHHHHHHhCCceEEecC-C-CcEEecC---c-HHHHHHH-----hcccccccChH
Confidence 344578899999999999998666542211111100000000 0 0011110 0 1101000 00111112256
Q ss_pred HHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578 322 EADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 322 er~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~ 367 (379)
+|..+.+.+-+.+ +..+..++|+.+++|++||.+-+.....+++.
T Consensus 86 er~~~~ll~~~~~-~~~~l~~La~~l~vs~~ti~~dl~~v~~~l~~ 130 (491)
T COG3711 86 ERIIIILLLLLLS-ELLSLHELADELFVSKSTIINDLKDVRLKLLL 130 (491)
T ss_pred HHHHHHHHHHHhc-ChhhHHHHHHHHHhHHHHHHHHHHHHHHHHHh
Confidence 7777776664443 56899999999999999999998875555543
No 448
>PF04814 HNF-1_N: Hepatocyte nuclear factor 1 (HNF-1), N terminus; InterPro: IPR006899 This domain consists of the N terminus of homeobox-containing transcription factor HNF-1. This region contains a dimerisation 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) [].; GO: 0045893 positive regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2GYP_B 1IC8_B 2H8R_B 1G2Y_D 1F93_H 1G39_D 1G2Z_B 1JB6_B.
Probab=54.59 E-value=9.9 Score=34.00 Aligned_cols=51 Identities=20% Similarity=0.248 Sum_probs=34.6
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 309 QELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 309 ~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
..|+++|.+=+-.=++.|..+.. ....++++|++..||+.+.|++++.++.
T Consensus 106 ~~Ve~llr~D~~~VkeeIK~fl~---~h~IsQ~~V~q~TGisQS~lSq~L~kGt 156 (180)
T PF04814_consen 106 AEVEELLRRDPWRVKEEIKAFLQ---QHNISQREVVQVTGISQSHLSQHLNKGT 156 (180)
T ss_dssp HHHHHCTTS-HHHHHHHHHHHHH---HCT--CHHHHHHHT--HHHHHHHHCTB-
T ss_pred HHHHHHHhhCHHHHHHHHHHHHH---HcCCcHHHHHHHhhhhHHHHHHHHHcCC
Confidence 45666665555566777776654 4779999999999999999999987763
No 449
>PF05269 Phage_CII: Bacteriophage CII protein; InterPro: IPR007933 The CII protein is a transcription activator, conserved in bacteriophage lambda and related phages, that plays a key role in the decision between lytic or lysogenic phage development. CII is regulated at multiple levels including transcription, translation initiation, mRNA stability, and proteolysis []. Conditions that stabilise cII favour lysogenic development. The lambda CII protein activates three specific promoters, binding to direct repeat sequences rather than the more usual inverted repeats. Structurally, CII is a homotetramer where each monomer is composed of four alpha helices and a disordered C terminus [, ]. The alpha helical region is responsible for DNA binding and multimerisation. The homotetramer has an unusual spatial arrangement that allows recognition of the direct repeat sequences.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ZS4_C 1ZPQ_C 1XWR_A.
Probab=54.52 E-value=24 Score=28.06 Aligned_cols=33 Identities=12% Similarity=0.178 Sum_probs=26.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHh
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIALTKLQQTNI 370 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~ 370 (379)
.+++.+|+.+||+.++|+++..--+.++-..+.
T Consensus 24 ~gq~~vA~~~Gv~eStISR~k~~~~~~~a~lLa 56 (91)
T PF05269_consen 24 VGQKKVAEAMGVDESTISRWKNDFIEKMAMLLA 56 (91)
T ss_dssp HHHHHHHHHHTSSTTTHHHHHHHHHHHHHHHHH
T ss_pred HhhHHHHHHhCCCHHHHHHHHhhHHHHHHHHHH
Confidence 789999999999999999987665555555444
No 450
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=54.43 E-value=28 Score=28.32 Aligned_cols=44 Identities=14% Similarity=0.134 Sum_probs=31.5
Q ss_pred hcCCHHHH-HHHHHHhhcCCCCCCCHHHHHHHhCC-CHHHHHHHHHHHHH
Q 046578 316 QTLSEREA-DILRLHFGLDGQTPVSCKEIGRLLSL-SRERIRQIRGIALT 363 (379)
Q Consensus 316 ~~L~~rer-~Vl~l~ygL~g~e~~S~~EIAe~Lgi-S~~~Vr~~~~rAl~ 363 (379)
...++..+ +++.++. ..|.|..+||..+|| +.+..+++......
T Consensus 6 r~~s~EfK~~iv~~~~----~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~ 51 (116)
T COG2963 6 KKYSPEFKLEAVALYL----RGGDTVSEVAREFGIVSATQLYKWRIQLQK 51 (116)
T ss_pred ccCCHHHHHHHHHHHH----hcCccHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 34566655 5555554 245899999999996 99999887766554
No 451
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=54.40 E-value=1.9e+02 Score=27.39 Aligned_cols=41 Identities=10% Similarity=-0.017 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh
Q 046578 227 VAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIER 267 (379)
Q Consensus 227 ~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~ 267 (379)
...+.++..-+...+...++.+++|+.+|++...+......
T Consensus 4 ~~~i~~~~~~i~~~~~~~~~l~~lA~~~~~S~~~l~r~F~~ 44 (289)
T PRK15121 4 AGIIRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKD 44 (289)
T ss_pred HHHHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 34566666777778888899999999999999988877653
No 452
>PRK06474 hypothetical protein; Provisional
Probab=54.36 E-value=24 Score=31.43 Aligned_cols=44 Identities=7% Similarity=0.067 Sum_probs=28.4
Q ss_pred hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHh-CCCHHHHHHHHHH
Q 046578 316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLL-SLSRERIRQIRGI 360 (379)
Q Consensus 316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~L-giS~~~Vr~~~~r 360 (379)
+-|...+|..|.-.. ..+.+++|..||++.+ +++..||++.++.
T Consensus 6 ~~La~p~R~~Il~~L-~~~~~~~ta~el~~~l~~is~aTvYrhL~~ 50 (178)
T PRK06474 6 EILMHPVRMKICQVL-MRNKEGLTPLELVKILKDVPQATLYRHLQT 50 (178)
T ss_pred HhhCCHHHHHHHHHH-HhCCCCCCHHHHHHHhcCCCHHHHHHHHHH
Confidence 345545554444332 2222349999999999 7999999876543
No 453
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=53.88 E-value=27 Score=29.70 Aligned_cols=28 Identities=21% Similarity=0.400 Sum_probs=22.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~ 367 (379)
+..|.+|||+.+|+|+..|++. +.+|++
T Consensus 24 ~~~s~~~ia~~~~is~~~vrk~----l~~L~~ 51 (141)
T PRK11014 24 RMTSISEVTEVYGVSRNHMVKI----INQLSR 51 (141)
T ss_pred CccCHHHHHHHHCcCHHHHHHH----HHHHHh
Confidence 5578999999999998888655 555554
No 454
>PF12085 DUF3562: Protein of unknown function (DUF3562); InterPro: IPR021945 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 62 to 84 amino acids in length. This protein has two completely conserved residues (A and Y) that may be functionally important.
Probab=53.37 E-value=28 Score=25.95 Aligned_cols=31 Identities=13% Similarity=0.174 Sum_probs=26.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
-..++||+..|++..+|++.+...+..|+.-
T Consensus 8 e~i~~iA~~t~~P~e~V~~my~dt~~~l~~~ 38 (66)
T PF12085_consen 8 EVIRSIAEETGTPAETVRRMYDDTMRELSSG 38 (66)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHHHHHcC
Confidence 3578999999999999999999888877754
No 455
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=53.35 E-value=9.7 Score=30.44 Aligned_cols=24 Identities=13% Similarity=0.216 Sum_probs=21.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
+|..|+|+.+|||.++++.+...+
T Consensus 2 ~~i~eva~~~gVs~~tLR~ye~~G 25 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVYDRLG 25 (98)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCC
Confidence 689999999999999999986654
No 456
>PRK06424 transcription factor; Provisional
Probab=53.27 E-value=13 Score=32.07 Aligned_cols=24 Identities=13% Similarity=0.127 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRG 359 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~ 359 (379)
.++|+.|+|+.+|+++++|+++.+
T Consensus 96 ~GLSQ~eLA~~iGvs~stIskiE~ 119 (144)
T PRK06424 96 LSMSQADLAAKIFERKNVIASIER 119 (144)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHC
Confidence 569999999999999999999886
No 457
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=52.92 E-value=23 Score=35.07 Aligned_cols=47 Identities=30% Similarity=0.466 Sum_probs=35.8
Q ss_pred hcCCHHHHHHHHH---HhhcCCCCCCCHHHHHHH--hCCCHHHHHHHHHHHHHH
Q 046578 316 QTLSEREADILRL---HFGLDGQTPVSCKEIGRL--LSLSRERIRQIRGIALTK 364 (379)
Q Consensus 316 ~~L~~rer~Vl~l---~ygL~g~e~~S~~EIAe~--LgiS~~~Vr~~~~rAl~k 364 (379)
..|++|+++|+.. .| +...+..+.+++|+. +|+|..|||+-+.. |.+
T Consensus 2 ~~l~~R~~~Il~~IV~~y-i~~~~pv~s~~l~~~~~l~~S~aTIR~dm~~-Le~ 53 (339)
T PRK00082 2 SMLDERQREILRAIVEDY-IATGEPVGSKTLSKRYGLGVSSATIRNDMAD-LEE 53 (339)
T ss_pred CccCHHHHHHHHHHHHHH-HhcCCCcCHHHHHHHhCCCCChHHHHHHHHH-HHh
Confidence 3588999999963 22 333488999999977 99999999988764 444
No 458
>PRK11569 transcriptional repressor IclR; Provisional
Probab=52.86 E-value=28 Score=33.13 Aligned_cols=25 Identities=12% Similarity=0.182 Sum_probs=22.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.++|+.|||+.+|++++||.+++.-
T Consensus 42 ~~~~lseia~~lglpksTv~RlL~t 66 (274)
T PRK11569 42 GSVALTELAQQAGLPNSTTHRLLTT 66 (274)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 5699999999999999999887654
No 459
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=52.74 E-value=10 Score=30.83 Aligned_cols=25 Identities=16% Similarity=0.024 Sum_probs=22.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
+|..|+|+.+|||..|++.....++
T Consensus 1 y~Ige~A~~~gvs~~tlR~ye~~GL 25 (107)
T cd01111 1 YSISQLALDAGVSVHIVRDYLLRGL 25 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999887765
No 460
>COG5625 Predicted transcription regulator containing HTH domain [Transcription]
Probab=52.69 E-value=22 Score=28.76 Aligned_cols=51 Identities=25% Similarity=0.338 Sum_probs=33.4
Q ss_pred HHHHHHhc--CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 310 ELKELLQT--LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 310 ~L~~~L~~--L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
.+..+|.. |.+.+-.|..+-.+. ..+|-.+||+..||||..+|+-...--+
T Consensus 9 ~l~~~L~~~glk~~eI~IY~lLve~--~~~mri~ei~rEl~is~rtvr~~v~~l~ 61 (113)
T COG5625 9 KLGKALEAIGLKKNEIRIYSLLVEK--GRGMRIREIQRELGISERTVRAAVAVLL 61 (113)
T ss_pred HHHHHHHHcCCCcchhhhhhHHHHh--cCCchHHHHHHHHhHHHHHHHHHHHHHH
Confidence 35555554 445454444443322 2679999999999999988877665544
No 461
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=52.68 E-value=29 Score=33.74 Aligned_cols=39 Identities=23% Similarity=0.150 Sum_probs=29.0
Q ss_pred HHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 321 READILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 321 rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
+.+.|+.+.. . ....+..+||+.+|+|+.+|++.+.+-.
T Consensus 5 r~~~il~~L~--~-~~~~s~~~LA~~lgvsr~tV~~~l~~L~ 43 (319)
T PRK11886 5 VMLQLLSLLA--D-GDFHSGEQLGEELGISRAAIWKHIQTLE 43 (319)
T ss_pred HHHHHHHHHH--c-CCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4555665443 1 2568999999999999999998876644
No 462
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=52.56 E-value=44 Score=28.45 Aligned_cols=45 Identities=22% Similarity=0.373 Sum_probs=37.6
Q ss_pred HHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 313 ELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 313 ~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.+...|+|+-+++|.+.-. .+..|..|.|+..|-...+|++-+..
T Consensus 57 ~la~vLsp~nleLl~~Ia~---~~P~Si~ElAe~vgRdv~nvhr~Ls~ 101 (144)
T COG4190 57 DLARVLSPRNLELLELIAQ---EEPASINELAELVGRDVKNVHRTLST 101 (144)
T ss_pred HHHHHhChhHHHHHHHHHh---cCcccHHHHHHHhCcchHHHHHHHHH
Confidence 4455699999999998775 68899999999999999998776543
No 463
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=52.23 E-value=12 Score=29.48 Aligned_cols=27 Identities=19% Similarity=0.359 Sum_probs=22.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
.++++++||+.+||++++|+-....-+
T Consensus 40 ~~l~Q~qiae~lgV~qprvS~l~~gk~ 66 (91)
T COG5606 40 AALSQAQIAELLGVTQPRVSDLARGKI 66 (91)
T ss_pred HHHHHHHHHHHhCCCCchHHHHHhcch
Confidence 458999999999999999998765543
No 464
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=52.20 E-value=48 Score=28.96 Aligned_cols=39 Identities=15% Similarity=0.051 Sum_probs=28.1
Q ss_pred CHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 319 SEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 319 ~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.+....|+..-. .. ..+|-.|||+.||++...||+++.+
T Consensus 13 g~~~v~Vl~aL~-~~--~~~tdEeLa~~Lgi~~~~VRk~L~~ 51 (158)
T TIGR00373 13 EEEVGLVLFSLG-IK--GEFTDEEISLELGIKLNEVRKALYA 51 (158)
T ss_pred ChhHHHHHHHHh-cc--CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 445555665433 12 4699999999999999999877655
No 465
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=52.07 E-value=22 Score=25.24 Aligned_cols=26 Identities=42% Similarity=0.371 Sum_probs=22.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhc
Q 046578 243 RMPTDSEIAEMLNIHVSTVRLAIERT 268 (379)
Q Consensus 243 r~pt~~eia~~Lgis~~~~~~~l~~~ 268 (379)
|..+..|+|+.||++...+..-+.+.
T Consensus 22 R~~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 22 RRITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred CcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 55689999999999999998877653
No 466
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=52.03 E-value=29 Score=32.16 Aligned_cols=30 Identities=13% Similarity=0.128 Sum_probs=24.5
Q ss_pred cCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578 332 LDGQTPVSCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 332 L~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
+++..+.|..|||+.||+|.++|++++.+-
T Consensus 16 l~~~~~IS~~eLA~~L~iS~~Tvsr~Lk~L 45 (217)
T PRK14165 16 VNNTVKISSSEFANHTGTSSKTAARILKQL 45 (217)
T ss_pred cCCCCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 444456899999999999999999887664
No 467
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=52.02 E-value=11 Score=30.45 Aligned_cols=25 Identities=8% Similarity=0.247 Sum_probs=22.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
|+..|+|+.+|+|..|++.....+|
T Consensus 1 m~Ige~a~~~gvs~~tlRyYe~~GL 25 (107)
T cd04777 1 MKIGKFAKKNNITIDTVRHYIDLGL 25 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5788999999999999999888776
No 468
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=51.85 E-value=23 Score=31.79 Aligned_cols=37 Identities=22% Similarity=0.207 Sum_probs=27.8
Q ss_pred HHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 046578 320 EREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRG 359 (379)
Q Consensus 320 ~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~ 359 (379)
++++.|+.+.- .....+..++|+.||+|..|||+-+.
T Consensus 7 ~R~~~Il~~l~---~~~~~~~~~La~~~~vS~~TiRRDl~ 43 (185)
T PRK04424 7 ERQKALQELIE---ENPFITDEELAEKFGVSIQTIRLDRM 43 (185)
T ss_pred HHHHHHHHHHH---HCCCEEHHHHHHHHCcCHHHHHHHHH
Confidence 45556665433 13558999999999999999998765
No 469
>PRK08359 transcription factor; Validated
Probab=51.83 E-value=14 Score=33.06 Aligned_cols=35 Identities=23% Similarity=0.262 Sum_probs=26.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH-------HHHHHHHhHHh
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRG-------IALTKLQQTNI 370 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~-------rAl~kLR~~l~ 370 (379)
.++|++|+|+.+|+++++|+++.+ ..+.+|-+.|.
T Consensus 97 kglSQeeLA~~lgvs~stI~~iE~G~~~Ps~~~l~kLak~l~ 138 (176)
T PRK08359 97 SGLSYEELSHEVGLSVNDLRRIAHGEYEPTIKEAKKLERYFK 138 (176)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCCCcCCCHHHHHHHHHHhC
Confidence 569999999999999999998754 23455555543
No 470
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=51.82 E-value=16 Score=33.51 Aligned_cols=28 Identities=32% Similarity=0.568 Sum_probs=22.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578 337 PVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368 (379)
Q Consensus 337 ~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~ 368 (379)
.+|.++||..+|+++.+|++. +++|++.
T Consensus 179 ~lt~~~IA~~lGisretlsR~----L~~L~~~ 206 (230)
T PRK09391 179 PMSRRDIADYLGLTIETVSRA----LSQLQDR 206 (230)
T ss_pred cCCHHHHHHHHCCCHHHHHHH----HHHHHHC
Confidence 479999999999999998765 4555543
No 471
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=51.50 E-value=79 Score=32.39 Aligned_cols=23 Identities=43% Similarity=0.450 Sum_probs=20.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHh
Q 046578 245 PTDSEIAEMLNIHVSTVRLAIER 267 (379)
Q Consensus 245 pt~~eia~~Lgis~~~~~~~l~~ 267 (379)
-+..+||+.+|+++.+|..+...
T Consensus 319 LtlkdiA~~lglheSTVSRav~~ 341 (429)
T TIGR02395 319 LTLREVAEELGLHESTISRAINN 341 (429)
T ss_pred CcHHHHHHHhCCCccchhhhhcC
Confidence 48899999999999999988754
No 472
>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=51.42 E-value=11 Score=30.98 Aligned_cols=26 Identities=15% Similarity=0.156 Sum_probs=22.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIALT 363 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rAl~ 363 (379)
||..|+|+.+|||..|++.....++=
T Consensus 1 ~~ige~a~~~gvs~~tLryYe~~GLi 26 (116)
T cd04769 1 MYIGELAQQTGVTIKAIRLYEEKGLL 26 (116)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 58899999999999999998877653
No 473
>PRK06030 hypothetical protein; Provisional
Probab=51.26 E-value=59 Score=27.34 Aligned_cols=41 Identities=10% Similarity=0.048 Sum_probs=29.0
Q ss_pred HHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046578 320 EREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTK 364 (379)
Q Consensus 320 ~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~k 364 (379)
+|+-.+...+-. -++|+.+||+.||.+.+||.....+.-+.
T Consensus 56 aRqIAMYL~r~~----~~~sl~~IG~~FGRDHSTV~haikkIe~~ 96 (124)
T PRK06030 56 IRQIAMYVAHVS----LGWPMNEVALAFGRDRTTVGHACHTVEDL 96 (124)
T ss_pred HHHHHHHHHHHH----cCCCHHHHHHHHCCChhHHHHHHHHHHHH
Confidence 344444444442 44999999999999999999887755443
No 474
>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=51.12 E-value=11 Score=31.48 Aligned_cols=25 Identities=20% Similarity=0.291 Sum_probs=21.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
|+..|+|+.+|||..|++.....++
T Consensus 1 m~I~e~a~~~gvs~~tlR~Ye~~GL 25 (126)
T cd04783 1 LTIGELAKAAGVNVETIRYYQRRGL 25 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999998876654
No 475
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=51.02 E-value=49 Score=22.45 Aligned_cols=30 Identities=43% Similarity=0.324 Sum_probs=23.5
Q ss_pred HHHhCCCCCHHHHHHHhCCCHHHHHHHHHh
Q 046578 238 SRRLRRMPTDSEIAEMLNIHVSTVRLAIER 267 (379)
Q Consensus 238 ~~~lgr~pt~~eia~~Lgis~~~~~~~l~~ 267 (379)
.......-|..|||+.+|+|..++......
T Consensus 14 ~~~y~~~~t~~eIa~~lg~s~~~V~~~~~~ 43 (50)
T PF04545_consen 14 RLRYFEGLTLEEIAERLGISRSTVRRILKR 43 (50)
T ss_dssp HHHHTST-SHHHHHHHHTSCHHHHHHHHHH
T ss_pred HHHhcCCCCHHHHHHHHCCcHHHHHHHHHH
Confidence 334466778999999999999999987654
No 476
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=50.97 E-value=28 Score=32.70 Aligned_cols=38 Identities=24% Similarity=0.239 Sum_probs=29.3
Q ss_pred HHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 320 EREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 320 ~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
+|+..|+.+.- .....+..|+|+.||||..|||+=+..
T Consensus 7 eR~~~I~~~l~---~~~~v~v~eLa~~~~VS~~TIRRDL~~ 44 (252)
T PRK10681 7 ERIGQLLQALK---RSDKLHLKDAAALLGVSEMTIRRDLNA 44 (252)
T ss_pred HHHHHHHHHHH---HcCCCcHHHHHHHhCCCHHHHHHHHHH
Confidence 45666665432 235689999999999999999998886
No 477
>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=50.93 E-value=12 Score=31.07 Aligned_cols=26 Identities=23% Similarity=0.330 Sum_probs=22.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIALT 363 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rAl~ 363 (379)
||..|+|+.+|||..|++.....++=
T Consensus 1 ~~I~eva~~~gvs~~tLRyYe~~GLl 26 (123)
T cd04770 1 MKIGELAKAAGVSPDTIRYYERIGLL 26 (123)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999988776654
No 478
>PF07506 RepB: RepB plasmid partitioning protein; InterPro: IPR011111 This family includes proteins with sequence similarity to the RepB partitioning protein of the large Ti (tumour-inducing) plasmids of Agrobacterium tumefaciens [, ].
Probab=50.89 E-value=37 Score=30.30 Aligned_cols=41 Identities=17% Similarity=0.203 Sum_probs=33.9
Q ss_pred hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 046578 316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRG 359 (379)
Q Consensus 316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~ 359 (379)
..|+..|+..+..+.- + .|++.++|+..||++.+.|++.+.
T Consensus 3 ~~Ls~IE~~~fa~~l~-~--~G~~~~~I~~aL~id~~~ls~~~~ 43 (185)
T PF07506_consen 3 RDLSFIERARFARRLE-E--RGFSREEIAAALGIDKSYLSRMLS 43 (185)
T ss_pred ccCcHHHHHHHHHHHH-H--cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4688888888877762 2 579999999999999999988755
No 479
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe
Probab=50.86 E-value=11 Score=31.45 Aligned_cols=26 Identities=19% Similarity=0.234 Sum_probs=22.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIALT 363 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rAl~ 363 (379)
++..|+|+.+|||..|++....+++-
T Consensus 2 ysI~eVA~~~GVs~~TLR~wE~~GLl 27 (120)
T cd04767 2 YPIGVVAELLNIHPETLRIWERHGLI 27 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 68999999999999999988776543
No 480
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=50.65 E-value=15 Score=32.68 Aligned_cols=25 Identities=20% Similarity=0.197 Sum_probs=22.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
.++|++|+|+.+|+|+++|+++.+.
T Consensus 19 ~glt~~elA~~~gis~~~is~~E~g 43 (185)
T PRK09943 19 QGLSQRRAAELSGLTHSAISTIEQD 43 (185)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHcC
Confidence 5599999999999999999998864
No 481
>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=50.12 E-value=12 Score=31.00 Aligned_cols=25 Identities=20% Similarity=0.272 Sum_probs=22.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
|+..|+|+.+|||..|++.....++
T Consensus 1 m~IgevA~~~gvs~~tlRyYe~~GL 25 (120)
T cd04781 1 LDIAEVARQSGLPASTLRYYEEKGL 25 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999998887754
No 482
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=49.93 E-value=45 Score=24.77 Aligned_cols=30 Identities=13% Similarity=0.095 Sum_probs=25.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGIALTKL 365 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL 365 (379)
...|..|.|+.+|++..+|+++...=++.|
T Consensus 12 ~~~s~~~Aa~~lG~~~~~v~~wv~~fR~wl 41 (65)
T PF05344_consen 12 QQISVAQAADRLGTDPGTVRRWVRMFRQWL 41 (65)
T ss_pred ccccHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 779999999999999999999876655444
No 483
>PRK09836 DNA-binding transcriptional activator CusR; Provisional
Probab=49.37 E-value=26 Score=31.19 Aligned_cols=50 Identities=14% Similarity=0.126 Sum_probs=39.1
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHHh
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLL-----SLSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~L-----giS~~~Vr~~~~rAl~kLR~ 367 (379)
.|+++|.+++.+..- +.+.-.|.++|.+.+ ..+..+|..++++-++||..
T Consensus 150 ~Lt~~E~~ll~~l~~-~~g~~~sr~~l~~~~w~~~~~~~~~~v~~~i~~lR~Kl~~ 204 (227)
T PRK09836 150 TLTSKEFTLLEFFLR-HQGEVLPRSLIASQVWDMNFDSDTNAIDVAVKRLRGKIDN 204 (227)
T ss_pred ecCHHHHHHHHHHHh-CCCeeEcHHHHHHHHcCCCCCCCcCCHHHHHHHHHHHhCC
Confidence 499999999987662 212448999999998 45678899999888888853
No 484
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=49.36 E-value=51 Score=22.43 Aligned_cols=27 Identities=33% Similarity=0.414 Sum_probs=21.9
Q ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHHh
Q 046578 241 LRRMPTDSEIAEMLNIHVSTVRLAIER 267 (379)
Q Consensus 241 lgr~pt~~eia~~Lgis~~~~~~~l~~ 267 (379)
+...++..++|+.+|++..++..++.+
T Consensus 24 ~~~~~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 24 LRESRSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred HhhcCCHHHHHHHHCCCHHHHHHHHHh
Confidence 333468899999999999999988754
No 485
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=49.21 E-value=13 Score=30.88 Aligned_cols=25 Identities=16% Similarity=0.274 Sum_probs=21.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
++..|+|+.+|||..|++.....++
T Consensus 1 ~~Igeva~~~gvs~~tlRyYe~~GL 25 (118)
T cd04776 1 YTISELAREFDVTPRTLRFYEDKGL 25 (118)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5788999999999999998877654
No 486
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=49.01 E-value=34 Score=27.94 Aligned_cols=43 Identities=16% Similarity=0.253 Sum_probs=31.9
Q ss_pred CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCC----HHHHHHHHHHHHH
Q 046578 318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLS----RERIRQIRGIALT 363 (379)
Q Consensus 318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS----~~~Vr~~~~rAl~ 363 (379)
|++.|.+|+...+-. .+.|.+||.+.++=. .+||...+.|-.+
T Consensus 1 Ls~~E~~IM~~lW~~---~~~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~ 47 (115)
T PF03965_consen 1 LSDLELEIMEILWES---GEATVREIHEALPEERSWAYSTVQTLLNRLVE 47 (115)
T ss_dssp --HHHHHHHHHHHHH---SSEEHHHHHHHHCTTSS--HHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHhC---CCCCHHHHHHHHHhccccchhHHHHHHHHHHh
Confidence 678899999877632 339999999998754 8899888777554
No 487
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=48.91 E-value=31 Score=32.84 Aligned_cols=38 Identities=24% Similarity=0.285 Sum_probs=27.5
Q ss_pred HHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 320 EREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 320 ~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
+|+..|+.+.-- ....+..|+|+.||+|..|||+-+..
T Consensus 17 eR~~~Il~~L~~---~~~vtv~eLa~~l~VS~~TIRRDL~~ 54 (269)
T PRK09802 17 ERREQIIQRLRQ---QGSVQVNDLSALYGVSTVTIRNDLAF 54 (269)
T ss_pred HHHHHHHHHHHH---cCCEeHHHHHHHHCCCHHHHHHHHHH
Confidence 455566654321 24589999999999999999877654
No 488
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=48.85 E-value=44 Score=31.47 Aligned_cols=26 Identities=23% Similarity=0.242 Sum_probs=22.4
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 335 QTPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 335 ~e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
+....++|||+.||||.+.|+..++.
T Consensus 23 qp~v~q~eIA~~lgiT~QaVsehiK~ 48 (260)
T COG1497 23 QPRVKQKEIAKKLGITLQAVSEHIKE 48 (260)
T ss_pred CCCCCHHHHHHHcCCCHHHHHHHHHH
Confidence 36789999999999999999887654
No 489
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=48.78 E-value=16 Score=32.66 Aligned_cols=25 Identities=16% Similarity=0.170 Sum_probs=21.9
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHH
Q 046578 334 GQTPVSCKEIGRLLSLSRERIRQIR 358 (379)
Q Consensus 334 g~e~~S~~EIAe~LgiS~~~Vr~~~ 358 (379)
|.++.|.++||+..|+|++++++..
T Consensus 28 G~~~~ti~~Ia~~agvsk~t~Y~~F 52 (213)
T PRK09975 28 GVSNTTLNDIADAANVTRGAIYWHF 52 (213)
T ss_pred CcccCCHHHHHHHcCCCHHHHHHHc
Confidence 3577999999999999999998754
No 490
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=48.75 E-value=17 Score=31.74 Aligned_cols=24 Identities=13% Similarity=0.195 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRG 359 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~ 359 (379)
.++|++++|+.+|+++++|+++.+
T Consensus 81 ~glSqeeLA~~lgvs~s~IsriE~ 104 (154)
T TIGR00270 81 RGWSQEQLAKKIQEKESLIKKIEN 104 (154)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHC
Confidence 569999999999999999999985
No 491
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=48.53 E-value=62 Score=30.92 Aligned_cols=49 Identities=14% Similarity=0.053 Sum_probs=38.3
Q ss_pred HHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578 312 KELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL 365 (379)
Q Consensus 312 ~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL 365 (379)
..+|..++-++-++|.... +.-|+..-|+.||+|+.+|++.+++-=+.|
T Consensus 8 ~~~~~~~~l~~L~~f~~va-----~~gs~s~AA~~L~iSQpavS~~I~~LE~~l 56 (311)
T PRK10086 8 NRLLNGWQLSKLHTFEVAA-----RHQSFALAADELSLTPSAVSHRINQLEEEL 56 (311)
T ss_pred HhhhcCCcHHHHHHHHHHH-----HcCCHHHHHHHHCCCHHHHHHHHHHHHHHh
Confidence 4567788888877777665 667999999999999999988766544444
No 492
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=48.42 E-value=19 Score=26.60 Aligned_cols=25 Identities=24% Similarity=0.280 Sum_probs=19.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGI 360 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~r 360 (379)
...|..|||..||+++.+|...+..
T Consensus 13 ~~~S~~eLa~~~~~s~~~ve~mL~~ 37 (69)
T PF09012_consen 13 GRVSLAELAREFGISPEAVEAMLEQ 37 (69)
T ss_dssp -SEEHHHHHHHTT--HHHHHHHHHH
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 5589999999999999999887654
No 493
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=48.20 E-value=14 Score=30.27 Aligned_cols=25 Identities=20% Similarity=0.260 Sum_probs=21.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578 338 VSCKEIGRLLSLSRERIRQIRGIAL 362 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr~~~~rAl 362 (379)
|+..|+|+.+|||..|++.....++
T Consensus 1 ~~I~eva~~~gvs~~tLRyYE~~GL 25 (124)
T COG0789 1 YTIGEVAKLTGVSVRTLRFYERKGL 25 (124)
T ss_pred CcHHHHHHHhCCCHHHHHHHHHcCC
Confidence 5789999999999999998876654
No 494
>PRK13832 plasmid partitioning protein; Provisional
Probab=48.02 E-value=39 Score=35.27 Aligned_cols=53 Identities=15% Similarity=0.110 Sum_probs=35.4
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH--HHHHHHhHHhhc
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI--ALTKLQQTNILN 372 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r--Al~kLR~~l~~~ 372 (379)
.|+|-|+.--..+. + ..|+|.++||+.+|+|+..|++++.- ..-.|...+...
T Consensus 101 dL~PiEea~AfkrL-i--e~G~T~EeIA~~lG~S~~~V~rlllLA~L~P~lLdal~~G 155 (520)
T PRK13832 101 PLNPVDQWRAIERL-V--ALGWTEEAIAVALALPVRQIRKLRLLANVLPAMLDHMAKG 155 (520)
T ss_pred CCCHHHHHHHHHHH-H--hcCCCHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHcC
Confidence 67877765554444 2 26799999999999999999984332 123444444433
No 495
>PF06413 Neugrin: Neugrin; InterPro: IPR010487 This family contains 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 []. Homologues of neugrin are found in fungi suggesting they have a alternative role or more than one function.
Probab=48.01 E-value=36 Score=31.73 Aligned_cols=42 Identities=21% Similarity=0.271 Sum_probs=31.6
Q ss_pred cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 046578 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRG 359 (379)
Q Consensus 317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~ 359 (379)
.|+..+.+-|++..-.+ .+.+|...+|+.|+||+..|+++++
T Consensus 10 ~Ls~~~~~~ir~L~~~~-p~~~t~~~Lae~F~vspe~irrILk 51 (225)
T PF06413_consen 10 KLSREAMEQIRYLHKED-PEEWTVERLAESFKVSPEAIRRILK 51 (225)
T ss_pred CCCHHHHHHHHHHHHhC-ccccCHHHHHhhCCCCHHHHHHHHh
Confidence 46666666666544222 3568999999999999999999875
No 496
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=47.94 E-value=6.6 Score=28.95 Aligned_cols=23 Identities=22% Similarity=0.268 Sum_probs=18.1
Q ss_pred CCHHHHHHHhCCCHHHHH-HHHHH
Q 046578 338 VSCKEIGRLLSLSRERIR-QIRGI 360 (379)
Q Consensus 338 ~S~~EIAe~LgiS~~~Vr-~~~~r 360 (379)
.+.+|+|+.+|||+++|+ ....|
T Consensus 13 ~~~~~lA~~lgis~st~s~~~~~r 36 (66)
T PF07022_consen 13 KSDKELAERLGISKSTLSNNWKKR 36 (66)
T ss_dssp SSCHHHHCCTT--HHHHH-HHHHS
T ss_pred CCHHHHHHHhCcCHHHhhHHHHhC
Confidence 477899999999999999 77665
No 497
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=47.93 E-value=18 Score=33.03 Aligned_cols=45 Identities=9% Similarity=0.038 Sum_probs=28.3
Q ss_pred CHHHHHHHHHHhhcC-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578 319 SEREADILRLHFGLD-GQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 319 ~~rer~Vl~l~ygL~-g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~ 367 (379)
+.++|-+-.+...-+ +.-..|.+|||+.+|+|+.+|++. +++|++
T Consensus 150 ~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~----L~~L~~ 195 (226)
T PRK10402 150 PLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYV----LAQFIQ 195 (226)
T ss_pred hHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHH----HHHHHH
Confidence 555555444432111 112368999999999999999764 555554
No 498
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=47.89 E-value=41 Score=27.96 Aligned_cols=26 Identities=12% Similarity=0.221 Sum_probs=23.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGIA 361 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~rA 361 (379)
+..|.+++|+.+|+|+.++.++.++.
T Consensus 24 ~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 24 SPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 66999999999999999999988876
No 499
>COG2411 Uncharacterized conserved protein [Function unknown]
Probab=47.74 E-value=87 Score=27.94 Aligned_cols=48 Identities=33% Similarity=0.434 Sum_probs=36.5
Q ss_pred HhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCC--CHHHHHHHHHHHHHHHHh
Q 046578 315 LQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSL--SRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 315 L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~Lgi--S~~~Vr~~~~rAl~kLR~ 367 (379)
+..|+++++.|+.+.. +.=|++.-|..+|= .+..|++.+.+|..-|.+
T Consensus 135 l~~Ls~~~~~iL~~~~-----~~gslRkaA~klgg~~kr~~ir~vLrKay~~L~~ 184 (188)
T COG2411 135 LDNLSERDKRILELFV-----EEGSLRKAAKKLGGLEKRGRIRRVLRKAYHELKK 184 (188)
T ss_pred cccCCHHHHHHHHHHH-----HcCcHHHHHHHhcCcchhhHHHHHHHHHHHHHHh
Confidence 4459999999999875 44599999999986 346777777777666654
No 500
>PRK02277 orotate phosphoribosyltransferase-like protein; Provisional
Probab=47.70 E-value=15 Score=33.35 Aligned_cols=32 Identities=25% Similarity=0.139 Sum_probs=27.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578 336 TPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367 (379)
Q Consensus 336 e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~ 367 (379)
.+++..|||++||||+.|+..++.++-.+...
T Consensus 17 ~~~~~~~ia~el~vs~~t~~~l~~~~~~~~~~ 48 (200)
T PRK02277 17 KGLSTGEIADELNVSRETATWLLTRAKKLEKA 48 (200)
T ss_pred cCCChhhhhhhhcchHHHHHHHHhcccCCCCC
Confidence 67999999999999999999999887754433
Done!