Query 012567
Match_columns 460
No_of_seqs 360 out of 2143
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 04:00:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012567.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012567hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK07598 RNA polymerase sigma 100.0 5.4E-47 1.2E-51 393.9 27.0 230 209-439 57-329 (415)
2 PRK07406 RNA polymerase sigma 100.0 1.8E-44 4E-49 371.9 27.2 229 210-439 61-290 (373)
3 TIGR02997 Sig70-cyanoRpoD RNA 100.0 5.7E-44 1.2E-48 358.6 25.9 226 212-438 1-227 (298)
4 PRK05949 RNA polymerase sigma 100.0 1E-43 2.2E-48 361.3 27.2 228 210-438 16-244 (327)
5 PRK07405 RNA polymerase sigma 100.0 1.4E-42 3.1E-47 351.6 27.0 227 211-438 7-234 (317)
6 PRK05901 RNA polymerase sigma 100.0 1.2E-40 2.7E-45 353.9 21.3 223 206-442 205-428 (509)
7 COG0568 RpoD DNA-directed RNA 100.0 2.1E-40 4.6E-45 335.3 20.1 234 210-444 7-261 (342)
8 PRK07921 RNA polymerase sigma 100.0 1.9E-39 4.1E-44 329.6 23.6 217 210-440 24-241 (324)
9 PRK09210 RNA polymerase sigma 100.0 3E-35 6.6E-40 303.6 21.9 191 209-440 93-284 (367)
10 PRK05658 RNA polymerase sigma 100.0 2E-33 4.4E-38 307.5 20.7 159 284-442 379-537 (619)
11 PRK07500 rpoH2 RNA polymerase 100.0 4.2E-30 9.1E-35 257.5 21.7 189 211-439 5-202 (289)
12 PRK07122 RNA polymerase sigma 100.0 1.1E-29 2.3E-34 251.5 20.1 154 284-437 39-196 (264)
13 PRK06596 RNA polymerase factor 100.0 2.6E-29 5.6E-34 251.2 21.7 187 210-438 12-204 (284)
14 TIGR02393 RpoD_Cterm RNA polym 100.0 7.4E-30 1.6E-34 248.3 16.3 155 286-440 1-155 (238)
15 TIGR02392 rpoH_proteo alternat 100.0 6.7E-29 1.5E-33 246.2 20.6 184 213-438 2-192 (270)
16 PRK07408 RNA polymerase sigma 100.0 2.2E-28 4.8E-33 240.8 20.4 156 284-439 24-184 (256)
17 PRK05657 RNA polymerase sigma 100.0 5.3E-28 1.1E-32 246.1 22.0 188 211-439 52-240 (325)
18 TIGR02850 spore_sigG RNA polym 100.0 1.3E-27 2.8E-32 234.8 20.5 178 221-439 10-189 (254)
19 PRK08215 sporulation sigma fac 99.9 3.4E-26 7.5E-31 225.0 20.3 176 222-438 14-191 (258)
20 TIGR02394 rpoS_proteo RNA poly 99.9 9E-25 1.9E-29 218.2 22.0 191 207-438 8-199 (285)
21 PRK05911 RNA polymerase sigma 99.9 3.7E-25 8.1E-30 218.2 18.8 154 284-440 22-184 (257)
22 COG1191 FliA DNA-directed RNA 99.9 5.4E-25 1.2E-29 215.5 17.2 158 276-435 14-175 (247)
23 TIGR02885 spore_sigF RNA polym 99.9 1.6E-24 3.6E-29 209.2 17.8 156 281-437 6-164 (231)
24 PRK06288 RNA polymerase sigma 99.9 2.2E-24 4.8E-29 213.5 18.6 179 220-440 5-191 (268)
25 TIGR02980 SigBFG RNA polymeras 99.9 1.4E-23 3.1E-28 202.0 17.3 154 284-437 2-159 (227)
26 TIGR02941 Sigma_B RNA polymera 99.9 5.3E-23 1.2E-27 201.8 20.6 165 225-428 8-174 (255)
27 PRK05572 sporulation sigma fac 99.9 3.2E-22 7E-27 196.2 20.6 178 222-440 9-188 (252)
28 PRK07670 RNA polymerase sigma 99.9 6.5E-22 1.4E-26 194.0 18.4 152 273-427 8-166 (251)
29 PRK08583 RNA polymerase sigma 99.9 1.9E-21 4.1E-26 191.1 20.2 166 223-427 6-173 (257)
30 PRK12427 flagellar biosynthesi 99.9 1.3E-21 2.8E-26 190.3 16.9 138 286-427 16-158 (231)
31 TIGR02479 FliA_WhiG RNA polyme 99.9 2E-21 4.3E-26 187.1 15.7 146 290-438 1-152 (224)
32 PRK06986 fliA flagellar biosyn 99.8 1.1E-19 2.4E-24 176.4 16.9 143 282-427 5-152 (236)
33 PRK05803 sporulation sigma fac 99.8 6.1E-19 1.3E-23 171.1 16.1 161 213-414 17-221 (233)
34 PRK08301 sporulation sigma fac 99.7 7.6E-17 1.7E-21 156.1 15.0 131 284-414 51-224 (234)
35 TIGR02895 spore_sigI RNA polym 99.7 7.2E-17 1.6E-21 156.1 13.9 128 279-406 3-141 (218)
36 TIGR02846 spore_sigmaK RNA pol 99.7 1.4E-16 3.1E-21 154.0 15.4 131 284-414 47-220 (227)
37 TIGR02835 spore_sigmaE RNA pol 99.7 6.8E-16 1.5E-20 150.0 15.0 131 284-414 51-224 (234)
38 TIGR02859 spore_sigH RNA polym 99.7 8.2E-16 1.8E-20 144.0 12.6 145 271-415 4-192 (198)
39 PRK05602 RNA polymerase sigma 99.7 8.6E-16 1.9E-20 143.2 12.6 144 271-415 5-171 (186)
40 PRK08295 RNA polymerase factor 99.6 1.9E-15 4.1E-20 142.7 13.7 145 271-415 9-197 (208)
41 PRK09646 RNA polymerase sigma 99.6 1.4E-15 3E-20 143.1 11.9 143 272-415 16-185 (194)
42 PRK12513 RNA polymerase sigma 99.6 2.8E-15 6.1E-20 140.6 12.6 143 271-415 11-182 (194)
43 PRK06811 RNA polymerase factor 99.6 3.6E-15 7.9E-20 139.7 12.8 144 271-415 3-174 (189)
44 PRK09648 RNA polymerase sigma 99.6 5.8E-15 1.2E-19 137.9 12.9 140 274-414 12-181 (189)
45 PRK13919 putative RNA polymera 99.6 5.3E-15 1.1E-19 137.5 11.7 144 271-415 8-178 (186)
46 PRK06759 RNA polymerase factor 99.6 4.8E-15 1E-19 133.4 10.8 129 284-414 3-148 (154)
47 TIGR02954 Sig70_famx3 RNA poly 99.6 7.8E-15 1.7E-19 134.5 12.1 143 271-415 1-162 (169)
48 PRK09640 RNA polymerase sigma 99.6 9.1E-15 2E-19 136.8 12.8 144 270-415 7-177 (188)
49 PRK12514 RNA polymerase sigma 99.6 6.7E-15 1.4E-19 136.2 11.7 143 272-415 5-172 (179)
50 PRK12537 RNA polymerase sigma 99.6 7.7E-15 1.7E-19 136.6 11.5 144 271-415 8-176 (182)
51 PRK12524 RNA polymerase sigma 99.6 7.2E-15 1.6E-19 138.5 11.4 145 271-416 11-180 (196)
52 PRK11922 RNA polymerase sigma 99.6 1.2E-14 2.5E-19 141.0 13.0 130 284-415 29-192 (231)
53 PRK09641 RNA polymerase sigma 99.6 1E-14 2.2E-19 135.2 11.4 142 272-415 4-179 (187)
54 PRK09638 RNA polymerase sigma 99.6 1.9E-14 4E-19 132.5 13.1 143 271-415 3-169 (176)
55 TIGR02948 SigW_bacill RNA poly 99.6 1.2E-14 2.5E-19 134.8 11.5 140 274-415 6-179 (187)
56 TIGR02952 Sig70_famx2 RNA poly 99.6 1.3E-14 2.8E-19 132.3 11.6 135 279-414 4-164 (170)
57 PRK09643 RNA polymerase sigma 99.6 2E-14 4.4E-19 135.3 12.7 144 271-416 12-178 (192)
58 PRK12538 RNA polymerase sigma 99.6 2.1E-14 4.6E-19 140.0 12.3 144 272-416 49-215 (233)
59 PRK12534 RNA polymerase sigma 99.6 1.4E-14 3.1E-19 134.9 10.7 142 273-415 12-180 (187)
60 PRK12531 RNA polymerase sigma 99.6 1.8E-14 3.9E-19 135.6 11.1 141 274-415 15-184 (194)
61 TIGR02939 RpoE_Sigma70 RNA pol 99.6 3.3E-14 7.1E-19 132.1 12.6 142 272-415 6-181 (190)
62 PRK12519 RNA polymerase sigma 99.6 2.5E-14 5.4E-19 134.0 11.8 142 272-415 15-184 (194)
63 PRK09652 RNA polymerase sigma 99.5 2.5E-14 5.3E-19 131.0 10.7 134 280-415 4-171 (182)
64 PRK12526 RNA polymerase sigma 99.5 4.3E-14 9.3E-19 134.6 12.1 139 276-415 28-196 (206)
65 PRK12536 RNA polymerase sigma 99.5 6.9E-14 1.5E-18 130.1 12.3 140 274-415 9-172 (181)
66 PRK11923 algU RNA polymerase s 99.5 7.4E-14 1.6E-18 130.7 12.5 141 273-415 7-181 (193)
67 PRK12542 RNA polymerase sigma 99.5 2.9E-14 6.3E-19 132.9 8.9 134 283-416 7-166 (185)
68 PRK12539 RNA polymerase sigma 99.5 9.9E-14 2.2E-18 129.4 12.4 141 273-415 8-174 (184)
69 COG1595 RpoE DNA-directed RNA 99.5 1.8E-13 3.9E-18 127.6 13.3 134 280-415 10-170 (182)
70 TIGR03001 Sig-70_gmx1 RNA poly 99.5 1.2E-13 2.5E-18 135.8 12.3 145 269-415 22-204 (244)
71 PRK12515 RNA polymerase sigma 99.5 1.3E-13 2.9E-18 128.9 12.1 144 271-416 7-175 (189)
72 TIGR02989 Sig-70_gvs1 RNA poly 99.5 8.9E-14 1.9E-18 125.6 10.2 128 286-415 2-154 (159)
73 PRK09649 RNA polymerase sigma 99.5 1.3E-13 2.7E-18 129.2 11.1 141 274-417 12-175 (185)
74 TIGR02999 Sig-70_X6 RNA polyme 99.5 1.2E-13 2.6E-18 127.9 10.7 140 274-415 5-177 (183)
75 PRK12522 RNA polymerase sigma 99.5 1.6E-13 3.4E-18 126.5 10.4 129 285-415 3-162 (173)
76 PRK12512 RNA polymerase sigma 99.5 3.5E-13 7.5E-18 125.3 12.7 138 276-415 12-174 (184)
77 PRK12520 RNA polymerase sigma 99.5 1.4E-13 3E-18 129.0 9.7 129 286-416 3-175 (191)
78 PRK09645 RNA polymerase sigma 99.5 2.4E-13 5.3E-18 124.9 10.5 132 283-415 7-161 (173)
79 TIGR02937 sigma70-ECF RNA poly 99.5 1.9E-13 4.1E-18 119.7 9.3 127 286-414 2-152 (158)
80 PRK11924 RNA polymerase sigma 99.5 2.4E-13 5.1E-18 124.2 10.3 137 277-415 4-168 (179)
81 PRK12543 RNA polymerase sigma 99.5 2.5E-13 5.4E-18 126.2 9.9 130 284-415 6-160 (179)
82 TIGR02947 SigH_actino RNA poly 99.5 2.5E-13 5.4E-18 127.4 10.0 131 284-416 10-175 (193)
83 PRK12516 RNA polymerase sigma 99.5 3.6E-13 7.8E-18 126.6 11.0 131 283-415 8-159 (187)
84 PRK09415 RNA polymerase factor 99.5 3.7E-13 8E-18 125.1 10.7 130 284-415 15-170 (179)
85 TIGR02983 SigE-fam_strep RNA p 99.4 5.8E-13 1.2E-17 121.0 10.6 131 283-415 4-153 (162)
86 PRK08241 RNA polymerase factor 99.4 1E-12 2.3E-17 133.8 12.3 141 274-416 7-197 (339)
87 PRK12518 RNA polymerase sigma 99.4 1E-12 2.3E-17 120.8 11.0 133 280-415 5-163 (175)
88 PRK12547 RNA polymerase sigma 99.4 1E-12 2.3E-17 120.3 10.9 130 284-415 5-155 (164)
89 TIGR02985 Sig70_bacteroi1 RNA 99.4 5.2E-13 1.1E-17 119.7 8.2 127 286-414 2-155 (161)
90 PRK12535 RNA polymerase sigma 99.4 1.4E-12 3.1E-17 123.6 11.5 137 275-414 14-175 (196)
91 PRK12529 RNA polymerase sigma 99.4 8.7E-13 1.9E-17 122.7 9.8 131 284-414 12-169 (178)
92 PRK12533 RNA polymerase sigma 99.4 1.2E-12 2.6E-17 126.4 11.0 132 282-416 15-178 (216)
93 TIGR02984 Sig-70_plancto1 RNA 99.4 1.3E-12 2.8E-17 121.1 10.7 131 284-414 6-182 (189)
94 PRK12541 RNA polymerase sigma 99.4 1.4E-12 2.9E-17 118.8 10.5 129 284-415 4-155 (161)
95 PRK09644 RNA polymerase sigma 99.4 1.2E-12 2.7E-17 119.7 9.4 126 287-415 3-151 (165)
96 PRK08311 putative RNA polymera 99.4 1.3E-11 2.9E-16 121.0 16.5 89 272-360 4-95 (237)
97 TIGR02960 SigX5 RNA polymerase 99.4 1.8E-12 4E-17 130.8 10.6 130 284-415 4-185 (324)
98 PRK12523 RNA polymerase sigma 99.4 1.7E-12 3.6E-17 119.7 9.3 131 282-415 6-162 (172)
99 PRK09642 RNA polymerase sigma 99.4 1.2E-12 2.6E-17 118.8 7.4 121 292-415 2-149 (160)
100 PRK12540 RNA polymerase sigma 99.4 3.6E-12 7.9E-17 119.4 10.7 130 285-416 5-155 (182)
101 PRK12528 RNA polymerase sigma 99.4 4.4E-12 9.4E-17 115.4 10.7 128 284-414 3-155 (161)
102 PRK12532 RNA polymerase sigma 99.3 3.2E-12 6.9E-17 120.1 9.5 126 288-415 8-179 (195)
103 PRK09647 RNA polymerase sigma 99.3 4.7E-12 1E-16 120.8 10.8 130 284-416 27-182 (203)
104 PRK12545 RNA polymerase sigma 99.3 3.1E-12 6.8E-17 121.4 9.0 126 289-416 12-183 (201)
105 PRK09639 RNA polymerase sigma 99.3 4.3E-12 9.4E-17 115.6 9.4 127 284-415 2-154 (166)
106 PRK12530 RNA polymerase sigma 99.3 5.3E-12 1.1E-16 118.6 9.5 126 288-415 10-177 (189)
107 PRK12517 RNA polymerase sigma 99.3 8.8E-12 1.9E-16 117.2 10.8 133 281-415 19-171 (188)
108 TIGR02943 Sig70_famx1 RNA poly 99.3 5.3E-12 1.2E-16 118.6 9.3 127 288-416 5-175 (188)
109 PRK12544 RNA polymerase sigma 99.3 6.7E-12 1.4E-16 120.0 9.8 127 287-415 20-191 (206)
110 PRK09637 RNA polymerase sigma 99.3 1E-11 2.3E-16 116.0 10.8 126 287-414 3-148 (181)
111 TIGR02950 SigM_subfam RNA poly 99.3 4.6E-12 1E-16 113.8 8.0 120 292-414 2-147 (154)
112 TIGR02959 SigZ RNA polymerase 99.3 7.3E-12 1.6E-16 115.6 9.1 122 292-415 2-143 (170)
113 PF04542 Sigma70_r2: Sigma-70 99.3 7.7E-12 1.7E-16 97.9 7.6 70 290-359 1-70 (71)
114 PRK12546 RNA polymerase sigma 99.3 1.4E-11 3.1E-16 116.1 10.7 129 284-415 7-156 (188)
115 PRK12511 RNA polymerase sigma 99.3 1.7E-11 3.8E-16 114.8 9.6 127 287-415 6-154 (182)
116 PRK09651 RNA polymerase sigma 99.2 4.9E-11 1.1E-15 110.2 10.7 128 284-414 9-161 (172)
117 PRK06704 RNA polymerase factor 99.2 5.1E-11 1.1E-15 116.2 9.6 133 278-416 11-160 (228)
118 PRK07037 extracytoplasmic-func 99.2 5.4E-11 1.2E-15 108.2 9.0 123 289-414 2-151 (163)
119 PRK12527 RNA polymerase sigma 99.2 5.4E-11 1.2E-15 108.0 8.1 121 292-415 2-148 (159)
120 PRK12525 RNA polymerase sigma 99.2 1.6E-10 3.5E-15 106.2 11.2 128 284-414 8-160 (168)
121 PRK09636 RNA polymerase sigma 99.1 4.2E-10 9E-15 112.9 10.2 127 286-416 5-159 (293)
122 PRK09635 sigI RNA polymerase s 99.0 5.6E-10 1.2E-14 112.5 8.7 128 285-416 5-162 (290)
123 TIGR03209 P21_Cbot clostridium 99.0 1E-09 2.3E-14 97.9 9.3 113 287-406 1-141 (142)
124 PRK09191 two-component respons 99.0 7.1E-10 1.5E-14 107.2 8.6 121 286-414 2-130 (261)
125 PF04539 Sigma70_r3: Sigma-70 99.0 7.3E-10 1.6E-14 89.7 6.1 76 369-444 1-76 (78)
126 TIGR02957 SigX4 RNA polymerase 99.0 1.7E-09 3.6E-14 108.2 9.7 124 289-416 1-152 (281)
127 PRK09047 RNA polymerase factor 98.9 2.3E-09 4.9E-14 97.0 6.9 106 307-415 2-149 (161)
128 PF07638 Sigma70_ECF: ECF sigm 98.4 3.7E-06 8.1E-11 79.1 12.6 141 274-414 5-177 (185)
129 PF00140 Sigma70_r1_2: Sigma-7 98.1 1.3E-06 2.9E-11 61.7 1.3 32 211-243 1-33 (37)
130 PRK05658 RNA polymerase sigma 97.8 0.00066 1.4E-08 75.5 16.4 32 210-242 102-134 (619)
131 TIGR02393 RpoD_Cterm RNA polym 96.3 0.05 1.1E-06 53.1 11.9 130 244-414 88-222 (238)
132 PRK07670 RNA polymerase sigma 96.0 0.036 7.7E-07 54.6 9.4 30 385-414 214-243 (251)
133 PRK05901 RNA polymerase sigma 95.9 0.12 2.5E-06 56.6 13.1 132 244-412 359-491 (509)
134 PRK07122 RNA polymerase sigma 95.4 0.13 2.8E-06 51.3 10.8 34 244-277 128-161 (264)
135 PRK09210 RNA polymerase sigma 95.4 0.15 3.2E-06 53.4 11.4 128 244-412 217-349 (367)
136 PRK07921 RNA polymerase sigma 95.3 0.25 5.3E-06 51.0 12.7 132 244-412 174-306 (324)
137 PRK07408 RNA polymerase sigma 95.2 0.03 6.4E-07 55.5 5.2 34 244-277 114-147 (256)
138 PRK06288 RNA polymerase sigma 95.1 0.29 6.2E-06 48.7 12.1 132 244-414 119-254 (268)
139 PRK07598 RNA polymerase sigma 95.0 0.16 3.5E-06 54.2 10.5 35 244-278 263-297 (415)
140 COG1191 FliA DNA-directed RNA 95.0 0.33 7.1E-06 48.4 11.9 144 216-411 92-235 (247)
141 PRK05911 RNA polymerase sigma 94.9 0.21 4.6E-06 49.5 10.3 30 385-414 218-247 (257)
142 TIGR02997 Sig70-cyanoRpoD RNA 94.8 0.21 4.6E-06 50.5 10.5 29 386-414 267-295 (298)
143 PRK05949 RNA polymerase sigma 94.8 0.24 5.1E-06 51.2 10.8 28 387-414 285-312 (327)
144 PRK07500 rpoH2 RNA polymerase 94.8 0.26 5.6E-06 49.9 10.9 28 387-414 244-271 (289)
145 TIGR02479 FliA_WhiG RNA polyme 94.6 0.28 6.1E-06 47.2 10.2 30 385-414 188-217 (224)
146 PRK07406 RNA polymerase sigma 94.5 0.48 1E-05 49.9 12.4 34 244-277 224-257 (373)
147 PF04539 Sigma70_r3: Sigma-70 94.3 0.094 2E-06 42.1 5.3 37 243-279 4-40 (78)
148 PRK07405 RNA polymerase sigma 94.3 0.37 8.1E-06 49.4 10.9 34 244-277 169-202 (317)
149 PF12645 HTH_16: Helix-turn-he 93.9 0.26 5.6E-06 39.2 6.8 56 276-331 3-65 (65)
150 TIGR02850 spore_sigG RNA polym 93.6 0.8 1.7E-05 45.1 11.3 34 245-278 122-155 (254)
151 TIGR02941 Sigma_B RNA polymera 93.2 0.4 8.6E-06 47.2 8.5 30 385-414 218-247 (255)
152 PRK06986 fliA flagellar biosyn 93.2 0.62 1.4E-05 45.2 9.8 30 385-414 197-226 (236)
153 PF08281 Sigma70_r4_2: Sigma-7 92.7 0.061 1.3E-06 40.2 1.5 30 384-413 22-51 (54)
154 TIGR02885 spore_sigF RNA polym 92.5 0.95 2.1E-05 43.7 9.9 32 246-277 100-131 (231)
155 PRK08215 sporulation sigma fac 91.6 2.3 5E-05 42.0 11.6 33 245-277 125-157 (258)
156 PRK12427 flagellar biosynthesi 91.2 2.3 4.9E-05 41.6 11.0 33 245-277 103-135 (231)
157 TIGR02394 rpoS_proteo RNA poly 91.2 1.9 4.2E-05 43.2 10.8 30 386-415 240-269 (285)
158 PRK06596 RNA polymerase factor 90.9 2.6 5.5E-05 42.5 11.3 26 387-412 247-272 (284)
159 PRK05572 sporulation sigma fac 90.4 2 4.3E-05 42.3 9.8 28 386-413 216-243 (252)
160 PF01726 LexA_DNA_bind: LexA D 90.4 0.92 2E-05 36.0 6.0 42 369-410 6-48 (65)
161 TIGR02980 SigBFG RNA polymeras 90.3 2.2 4.8E-05 41.0 9.8 29 386-414 192-220 (227)
162 PRK05657 RNA polymerase sigma 89.2 3.2 6.9E-05 42.8 10.6 31 386-416 280-310 (325)
163 PHA02547 55 RNA polymerase sig 88.7 1.2 2.7E-05 41.8 6.4 62 297-358 49-113 (179)
164 PF04545 Sigma70_r4: Sigma-70, 88.4 0.88 1.9E-05 33.5 4.3 30 383-412 15-44 (50)
165 COG0568 RpoD DNA-directed RNA 82.1 19 0.0004 37.8 11.9 36 241-276 187-222 (342)
166 TIGR02392 rpoH_proteo alternat 80.3 17 0.00036 36.2 10.6 27 386-412 234-260 (270)
167 TIGR03879 near_KaiC_dom probab 80.2 2.2 4.7E-05 34.8 3.5 26 386-411 30-55 (73)
168 PRK08583 RNA polymerase sigma 78.1 1.6 3.4E-05 43.0 2.5 30 385-414 218-247 (257)
169 PF10668 Phage_terminase: Phag 77.2 5.4 0.00012 31.4 4.7 31 380-410 14-44 (60)
170 PRK06930 positive control sigm 77.1 1.7 3.8E-05 40.7 2.4 30 385-414 127-156 (170)
171 PF06971 Put_DNA-bind_N: Putat 76.8 5.6 0.00012 30.1 4.6 45 363-407 3-47 (50)
172 PHA02591 hypothetical protein; 76.0 3.7 8E-05 34.0 3.6 25 387-411 58-82 (83)
173 PF13936 HTH_38: Helix-turn-he 71.2 6.5 0.00014 28.5 3.6 26 385-410 17-42 (44)
174 PRK00118 putative DNA-binding 70.7 5.5 0.00012 34.6 3.7 30 385-414 30-59 (104)
175 PF13542 HTH_Tnp_ISL3: Helix-t 69.1 11 0.00024 27.5 4.7 27 385-411 24-50 (52)
176 cd06171 Sigma70_r4 Sigma70, re 69.0 7.1 0.00015 27.4 3.5 28 386-413 24-51 (55)
177 PF02796 HTH_7: Helix-turn-hel 68.8 7.3 0.00016 28.2 3.5 24 387-410 20-43 (45)
178 PF08279 HTH_11: HTH domain; 67.6 12 0.00025 27.8 4.5 25 387-411 14-38 (55)
179 PRK04217 hypothetical protein; 67.4 4.8 0.0001 35.3 2.7 29 387-415 57-85 (110)
180 smart00421 HTH_LUXR helix_turn 66.0 6.3 0.00014 28.4 2.8 27 387-413 17-43 (58)
181 PF00325 Crp: Bacterial regula 65.5 8.2 0.00018 26.6 3.0 22 389-410 3-24 (32)
182 COG4941 Predicted RNA polymera 65.4 15 0.00032 38.6 6.1 126 288-415 8-163 (415)
183 PF13404 HTH_AsnC-type: AsnC-t 65.2 18 0.00038 26.2 4.9 24 387-410 16-39 (42)
184 COG4367 Uncharacterized protei 65.0 16 0.00035 31.0 5.2 37 376-412 10-47 (97)
185 PF04967 HTH_10: HTH DNA bindi 64.6 7 0.00015 29.9 2.8 26 387-412 22-47 (53)
186 PF13384 HTH_23: Homeodomain-l 62.9 8.4 0.00018 27.9 2.9 26 388-413 17-42 (50)
187 cd06170 LuxR_C_like C-terminal 62.1 8.3 0.00018 27.9 2.8 27 387-413 14-40 (57)
188 cd00092 HTH_CRP helix_turn_hel 61.4 26 0.00057 26.4 5.6 25 387-411 24-48 (67)
189 PF13412 HTH_24: Winged helix- 60.2 28 0.00061 25.0 5.3 24 387-410 16-39 (48)
190 PF00196 GerE: Bacterial regul 59.4 11 0.00024 28.4 3.2 29 384-412 14-42 (58)
191 TIGR00721 tfx DNA-binding prot 59.1 6.3 0.00014 36.0 2.0 29 386-414 19-47 (137)
192 PF12728 HTH_17: Helix-turn-he 59.1 12 0.00026 27.3 3.2 24 389-412 2-25 (51)
193 PF13744 HTH_37: Helix-turn-he 59.0 24 0.00051 28.7 5.2 36 386-421 29-64 (80)
194 PF13730 HTH_36: Helix-turn-he 58.8 12 0.00026 27.7 3.2 24 387-410 24-47 (55)
195 PF06056 Terminase_5: Putative 58.2 23 0.00051 27.4 4.7 26 387-412 12-37 (58)
196 PF00356 LacI: Bacterial regul 57.6 13 0.00028 27.5 3.0 23 390-412 1-23 (46)
197 PF03444 HrcA_DNA-bdg: Winged 54.6 44 0.00096 27.7 6.0 41 371-411 6-46 (78)
198 TIGR01764 excise DNA binding d 53.0 23 0.00051 24.8 3.8 24 389-412 2-25 (49)
199 PF04297 UPF0122: Putative hel 52.6 20 0.00043 31.1 3.9 34 381-414 26-59 (101)
200 PRK03975 tfx putative transcri 51.2 9.5 0.00021 35.0 1.8 28 386-413 19-46 (141)
201 COG2197 CitB Response regulato 50.9 21 0.00046 34.3 4.3 30 383-412 158-187 (211)
202 PRK11511 DNA-binding transcrip 50.4 44 0.00095 29.4 5.9 39 372-410 9-47 (127)
203 PF01325 Fe_dep_repress: Iron 50.1 40 0.00087 26.1 4.9 35 376-411 11-45 (60)
204 PRK15411 rcsA colanic acid cap 48.6 25 0.00054 33.6 4.3 33 380-412 144-176 (207)
205 TIGR03826 YvyF flagellar opero 48.5 57 0.0012 29.8 6.4 46 373-418 31-76 (137)
206 smart00550 Zalpha Z-DNA-bindin 48.4 53 0.0012 25.9 5.5 27 384-410 17-44 (68)
207 PF10078 DUF2316: Uncharacteri 48.3 42 0.00092 28.5 5.1 36 377-412 11-47 (89)
208 smart00345 HTH_GNTR helix_turn 48.1 23 0.0005 25.8 3.2 23 389-411 21-43 (60)
209 cd04762 HTH_MerR-trunc Helix-T 47.6 32 0.00069 23.8 3.8 23 390-412 2-24 (49)
210 PRK10840 transcriptional regul 47.2 28 0.00061 32.5 4.5 32 382-413 159-190 (216)
211 PRK10430 DNA-binding transcrip 47.0 30 0.00066 33.1 4.7 32 383-414 173-204 (239)
212 PF01726 LexA_DNA_bind: LexA D 46.2 60 0.0013 25.6 5.5 19 254-272 20-38 (65)
213 PRK14082 hypothetical protein; 45.8 66 0.0014 25.7 5.5 56 284-341 8-63 (65)
214 PRK13870 transcriptional regul 44.3 13 0.00028 36.5 1.7 30 386-415 186-215 (234)
215 COG0856 Orotate phosphoribosyl 44.2 26 0.00057 33.5 3.6 35 386-420 16-50 (203)
216 PRK11475 DNA-binding transcrip 43.5 34 0.00074 32.8 4.4 31 382-412 143-173 (207)
217 PF09339 HTH_IclR: IclR helix- 43.5 29 0.00063 25.6 3.1 26 385-410 15-40 (52)
218 PF14502 HTH_41: Helix-turn-he 43.2 31 0.00066 26.0 3.1 33 387-419 5-39 (48)
219 PRK13719 conjugal transfer tra 43.1 36 0.00079 33.4 4.5 35 380-414 150-184 (217)
220 PRK15201 fimbriae regulatory p 42.4 39 0.00085 32.5 4.4 32 382-413 142-173 (198)
221 COG4566 TtrR Response regulato 41.8 27 0.00059 33.8 3.3 23 386-408 155-177 (202)
222 PRK10219 DNA-binding transcrip 41.5 74 0.0016 26.7 5.8 37 374-410 7-43 (107)
223 PRK12423 LexA repressor; Provi 41.1 72 0.0016 30.4 6.2 39 372-410 9-48 (202)
224 PF14711 Nitr_red_bet_C: Respi 40.7 60 0.0013 27.2 4.8 52 213-273 31-82 (83)
225 TIGR00498 lexA SOS regulatory 40.3 72 0.0016 30.0 6.0 39 372-410 9-48 (199)
226 COG2771 CsgD DNA-binding HTH d 39.8 67 0.0015 23.8 4.8 27 386-412 17-43 (65)
227 TIGR03541 reg_near_HchA LuxR f 39.8 16 0.00034 35.6 1.5 28 387-414 185-212 (232)
228 PF01381 HTH_3: Helix-turn-hel 39.4 37 0.0008 24.8 3.1 25 387-411 8-32 (55)
229 cd00569 HTH_Hin_like Helix-tur 39.3 61 0.0013 19.9 3.9 21 388-408 21-41 (42)
230 PRK10188 DNA-binding transcrip 39.0 17 0.00037 35.7 1.6 30 386-415 192-221 (240)
231 PF04703 FaeA: FaeA-like prote 38.2 42 0.00092 26.4 3.4 25 386-410 13-37 (62)
232 cd04761 HTH_MerR-SF Helix-Turn 37.7 43 0.00092 23.7 3.2 23 390-412 2-24 (49)
233 PRK10572 DNA-binding transcrip 37.7 3.4E+02 0.0074 26.6 10.7 38 373-410 184-221 (290)
234 smart00419 HTH_CRP helix_turn_ 37.1 46 0.001 23.3 3.3 24 388-411 8-31 (48)
235 PRK10046 dpiA two-component re 37.1 43 0.00093 31.8 4.0 25 387-411 176-200 (225)
236 TIGR03020 EpsA transcriptional 36.9 38 0.00083 33.7 3.7 29 386-414 203-231 (247)
237 PF04218 CENP-B_N: CENP-B N-te 36.7 26 0.00057 26.4 2.0 26 385-410 19-44 (53)
238 PF08280 HTH_Mga: M protein tr 36.6 87 0.0019 23.9 4.9 26 386-411 17-42 (59)
239 COG1522 Lrp Transcriptional re 36.4 70 0.0015 28.4 5.1 23 389-411 23-45 (154)
240 PRK10100 DNA-binding transcrip 36.3 57 0.0012 31.5 4.7 29 385-413 167-195 (216)
241 PF05225 HTH_psq: helix-turn-h 35.4 1.2E+02 0.0025 22.2 5.1 35 373-410 4-38 (45)
242 TIGR02844 spore_III_D sporulat 35.3 1.5E+02 0.0031 24.6 6.3 25 387-411 18-42 (80)
243 TIGR02531 yecD_yerC TrpR-relat 35.3 92 0.002 26.2 5.2 25 386-410 48-72 (88)
244 PF08784 RPA_C: Replication pr 34.6 55 0.0012 27.5 3.8 25 386-410 63-87 (102)
245 COG2344 AT-rich DNA-binding pr 34.4 82 0.0018 30.6 5.3 49 362-410 6-54 (211)
246 PRK13239 alkylmercury lyase; P 34.1 84 0.0018 30.7 5.4 29 385-413 33-61 (206)
247 PRK00215 LexA repressor; Valid 33.4 1.1E+02 0.0024 28.8 6.2 36 375-410 10-46 (205)
248 PF00392 GntR: Bacterial regul 33.4 46 0.001 25.5 3.0 24 388-411 24-47 (64)
249 smart00354 HTH_LACI helix_turn 33.4 47 0.001 26.2 3.0 23 389-411 1-23 (70)
250 PF13443 HTH_26: Cro/C1-type H 33.3 44 0.00096 25.1 2.8 33 387-419 9-41 (63)
251 COG1318 Predicted transcriptio 33.2 81 0.0017 30.1 4.9 25 387-411 60-84 (182)
252 PRK15369 two component system 33.2 41 0.00089 29.8 3.0 31 386-416 162-192 (211)
253 PRK12469 RNA polymerase factor 32.7 2.4E+02 0.0052 31.0 9.2 36 387-422 368-408 (481)
254 PF00376 MerR: MerR family reg 32.6 35 0.00077 24.0 1.9 22 390-411 1-22 (38)
255 PRK09483 response regulator; P 32.5 34 0.00074 31.2 2.5 32 385-416 160-191 (217)
256 PF00440 TetR_N: Bacterial reg 32.4 1.1E+02 0.0025 21.8 4.7 33 376-408 4-36 (47)
257 smart00346 HTH_ICLR helix_turn 32.3 1.2E+02 0.0026 24.3 5.4 25 387-411 19-43 (91)
258 PRK15320 transcriptional activ 32.1 33 0.00071 33.6 2.3 32 380-411 171-202 (251)
259 PRK11161 fumarate/nitrate redu 31.5 1.8E+02 0.0038 27.6 7.3 24 388-411 184-207 (235)
260 PRK11169 leucine-responsive tr 31.3 89 0.0019 28.7 5.0 25 387-411 27-51 (164)
261 COG3413 Predicted DNA binding 31.1 40 0.00087 32.4 2.7 28 387-414 177-204 (215)
262 PRK10403 transcriptional regul 30.5 48 0.001 29.8 3.0 33 386-418 166-198 (215)
263 PRK11179 DNA-binding transcrip 30.3 85 0.0018 28.5 4.6 26 387-412 22-47 (153)
264 TIGR02337 HpaR homoprotocatech 30.2 1.5E+02 0.0033 25.3 6.0 24 387-410 41-64 (118)
265 PRK13918 CRP/FNR family transc 30.0 2.1E+02 0.0045 26.3 7.3 24 388-411 149-172 (202)
266 PF13545 HTH_Crp_2: Crp-like h 29.8 65 0.0014 25.1 3.3 24 388-411 28-51 (76)
267 PF01371 Trp_repressor: Trp re 29.5 87 0.0019 26.4 4.1 24 385-408 46-69 (87)
268 TIGR03070 couple_hipB transcri 29.3 71 0.0015 23.0 3.3 24 387-410 14-37 (58)
269 PF02082 Rrf2: Transcriptional 28.6 71 0.0015 25.8 3.4 22 389-410 26-47 (83)
270 PRK11511 DNA-binding transcrip 28.6 2.9E+02 0.0062 24.2 7.6 37 246-282 12-48 (127)
271 cd07377 WHTH_GntR Winged helix 28.6 1E+02 0.0022 22.8 4.1 23 389-411 26-48 (66)
272 PRK09464 pdhR transcriptional 28.5 1.3E+02 0.0029 29.1 6.0 23 389-411 35-57 (254)
273 PF13518 HTH_28: Helix-turn-he 28.4 1.1E+02 0.0024 21.8 4.1 23 389-411 13-35 (52)
274 PRK15044 transcriptional regul 28.3 2E+02 0.0043 29.7 7.2 39 373-411 193-231 (295)
275 TIGR02297 HpaA 4-hydroxyphenyl 28.3 5.6E+02 0.012 24.9 10.4 37 374-410 188-224 (287)
276 PF04760 IF2_N: Translation in 28.0 48 0.001 24.7 2.1 35 389-423 4-40 (54)
277 PRK15418 transcriptional regul 27.8 37 0.00081 34.9 2.0 39 385-423 26-68 (318)
278 COG4977 Transcriptional regula 27.7 1.3E+02 0.0028 31.4 5.9 71 340-410 186-258 (328)
279 PF01978 TrmB: Sugar-specific 27.6 59 0.0013 25.1 2.7 24 387-410 21-44 (68)
280 PF13551 HTH_29: Winged helix- 27.5 1.5E+02 0.0033 24.4 5.4 24 388-411 80-110 (112)
281 PF00165 HTH_AraC: Bacterial r 27.3 82 0.0018 22.0 3.1 26 385-410 5-30 (42)
282 PRK09935 transcriptional regul 27.1 52 0.0011 29.6 2.6 32 386-417 162-193 (210)
283 PF02001 DUF134: Protein of un 27.0 33 0.00072 30.0 1.2 30 387-416 56-85 (106)
284 PRK10219 DNA-binding transcrip 26.8 3.1E+02 0.0067 22.8 7.2 37 246-282 8-44 (107)
285 TIGR03764 ICE_PFGI_1_parB inte 26.7 5.9E+02 0.013 25.8 10.1 91 224-331 110-222 (258)
286 PHA01976 helix-turn-helix prot 26.7 1E+02 0.0022 23.4 3.9 24 387-410 14-37 (67)
287 PF12324 HTH_15: Helix-turn-he 26.6 1.1E+02 0.0024 25.3 4.1 27 386-412 36-62 (77)
288 smart00420 HTH_DEOR helix_turn 26.4 95 0.0021 21.8 3.4 25 387-411 13-37 (53)
289 TIGR00373 conserved hypothetic 26.3 73 0.0016 29.5 3.5 25 387-411 27-51 (158)
290 PRK10651 transcriptional regul 26.1 69 0.0015 28.8 3.2 34 385-418 167-200 (216)
291 PF09012 FeoC: FeoC like trans 25.9 62 0.0013 25.4 2.5 25 386-410 12-36 (69)
292 PF13411 MerR_1: MerR HTH fami 25.7 73 0.0016 24.4 2.9 23 390-412 2-24 (69)
293 PF08535 KorB: KorB domain; I 25.3 71 0.0015 26.5 2.9 31 388-418 3-33 (93)
294 PF13560 HTH_31: Helix-turn-he 24.9 82 0.0018 24.0 3.0 24 387-410 13-36 (64)
295 PF12802 MarR_2: MarR family; 24.8 1.1E+02 0.0024 22.7 3.6 23 388-410 21-43 (62)
296 PRK09975 DNA-binding transcrip 24.7 1.5E+02 0.0032 27.5 5.4 40 368-407 10-50 (213)
297 PRK09726 antitoxin HipB; Provi 24.7 1.9E+02 0.0042 23.6 5.4 25 387-411 24-48 (88)
298 cd01104 HTH_MlrA-CarA Helix-Tu 24.5 90 0.0019 23.8 3.2 22 390-411 2-23 (68)
299 TIGR01321 TrpR trp operon repr 24.2 63 0.0014 27.7 2.3 24 387-410 54-77 (94)
300 COG2390 DeoR Transcriptional r 24.1 1E+02 0.0022 32.0 4.4 39 385-423 23-65 (321)
301 COG2524 Predicted transcriptio 24.0 1.5E+02 0.0032 30.3 5.2 41 372-412 9-49 (294)
302 smart00422 HTH_MERR helix_turn 23.6 96 0.0021 23.6 3.2 21 390-410 2-22 (70)
303 PF13022 HTH_Tnp_1_2: Helix-tu 23.5 91 0.002 28.7 3.4 31 380-410 26-56 (142)
304 PHA02943 hypothetical protein; 23.4 2.5E+02 0.0054 26.4 6.2 24 387-410 23-46 (165)
305 TIGR03697 NtcA_cyano global ni 23.2 1.9E+02 0.0042 26.2 5.7 25 388-412 143-167 (193)
306 smart00342 HTH_ARAC helix_turn 23.1 3.3E+02 0.0072 20.5 6.7 35 373-410 38-73 (84)
307 PRK09390 fixJ response regulat 23.1 1E+02 0.0022 27.2 3.7 30 387-416 155-184 (202)
308 PF08220 HTH_DeoR: DeoR-like h 23.0 95 0.0021 23.5 3.0 25 386-410 12-36 (57)
309 PRK09480 slmA division inhibit 23.0 1.7E+02 0.0037 26.5 5.3 39 369-407 10-49 (194)
310 PRK06424 transcription factor; 22.9 2.7E+02 0.0059 25.5 6.5 40 369-410 80-119 (144)
311 TIGR02944 suf_reg_Xantho FeS a 22.8 1.4E+02 0.0031 26.0 4.5 26 386-411 23-48 (130)
312 cd04764 HTH_MlrA-like_sg1 Heli 22.6 82 0.0018 24.2 2.6 22 390-411 2-23 (67)
313 TIGR00270 conserved hypothetic 22.4 1.8E+02 0.0038 27.0 5.2 24 387-410 81-104 (154)
314 PRK09391 fixK transcriptional 21.9 3.8E+02 0.0083 25.6 7.7 24 388-411 179-202 (230)
315 PRK09480 slmA division inhibit 21.9 5.9E+02 0.013 22.9 9.6 72 254-325 25-96 (194)
316 smart00530 HTH_XRE Helix-turn- 21.6 1.3E+02 0.0027 20.2 3.2 24 387-410 9-32 (56)
317 PF15545 Toxin_67: Putative to 21.4 98 0.0021 25.0 2.8 31 337-367 6-36 (70)
318 PRK03837 transcriptional regul 21.4 2.6E+02 0.0056 26.7 6.4 24 388-411 37-60 (241)
319 smart00418 HTH_ARSR helix_turn 21.3 1.3E+02 0.0029 21.5 3.5 26 386-411 8-33 (66)
320 PRK15121 right oriC-binding tr 21.1 2E+02 0.0043 28.6 5.7 38 372-409 5-42 (289)
321 PRK10072 putative transcriptio 20.7 1.4E+02 0.0031 25.5 3.9 26 387-412 45-70 (96)
322 smart00342 HTH_ARAC helix_turn 20.7 2E+02 0.0044 21.7 4.6 23 259-281 1-23 (84)
323 TIGR03613 RutR pyrimidine util 20.6 2.2E+02 0.0047 26.2 5.5 38 368-405 7-45 (202)
324 TIGR02607 antidote_HigA addict 20.6 1.2E+02 0.0026 23.7 3.3 24 387-410 17-40 (78)
325 TIGR02147 Fsuc_second hypothet 20.6 8.9E+02 0.019 24.5 14.0 34 377-410 126-161 (271)
326 PRK09393 ftrA transcriptional 20.5 1.9E+02 0.004 29.3 5.4 40 372-411 218-257 (322)
327 PRK09685 DNA-binding transcrip 20.3 3E+02 0.0064 27.2 6.8 77 296-401 201-277 (302)
328 KOG3758 Uncharacterized conser 20.2 2.9E+02 0.0063 31.3 7.0 159 208-379 278-445 (655)
329 PRK08359 transcription factor; 20.1 2.1E+02 0.0045 27.3 5.2 40 369-410 81-120 (176)
330 COG1916 Uncharacterized homolo 20.1 5E+02 0.011 27.7 8.4 122 212-333 47-181 (388)
331 PF11176 DUF2962: Protein of u 20.0 6.2E+02 0.013 23.4 8.3 87 214-333 51-141 (155)
No 1
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=100.00 E-value=5.4e-47 Score=393.87 Aligned_cols=230 Identities=37% Similarity=0.651 Sum_probs=217.3
Q ss_pred CCCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHH--------------------HHhHHHHHhhhcCCCCcHHHHHH
Q 012567 209 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLK--------------------LEGLREVLSERCGGSPTFAQWAA 267 (460)
Q Consensus 209 ~~~d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~--------------------le~~~~~L~~~~g~~pt~~ewA~ 267 (460)
.++|+++ ||++| |++||||++||++|+++||.++. |++++..|.+++|++||..|||.
T Consensus 57 ~~~d~v~~yl~~i-gr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~ 135 (415)
T PRK07598 57 RSTDLVRLYLQEI-GRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAK 135 (415)
T ss_pred CCCChHHHHHHhc-ccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHH
Confidence 3479999 99999 99999999999999999999999 99999999999999999999995
Q ss_pred HhC----------------------CCHHHHHHHHhccHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHH
Q 012567 268 AAG----------------------VDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVR 325 (460)
Q Consensus 268 a~g----------------------~de~~L~~~l~~G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLir 325 (460)
++| ++..+|+..++.|..|+++||.+|+++|+++|++|.++|++++||+|||++|||+
T Consensus 136 ~~~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~r 215 (415)
T PRK07598 136 TADISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLER 215 (415)
T ss_pred HhCCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHH
Confidence 555 5566666777889999999999999999999999999999999999999999999
Q ss_pred HHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHH
Q 012567 326 GAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRL 405 (460)
Q Consensus 326 AiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~V 405 (460)
|+++|||.+|++|+||++||||++|.++++++++++++|.++.+.+++++++...|..++|+.|+..|||+.|||++++|
T Consensus 216 avekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~v 295 (415)
T PRK07598 216 AVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQV 295 (415)
T ss_pred HHHHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhCCCCCcccccccccCCCCCcccccccCCC
Q 012567 406 HAVLLSPKAPRSLDQKIGINQNLKPSVCFILNLA 439 (460)
Q Consensus 406 k~~l~~ar~~lSLD~~v~~e~d~tl~Eli~D~~~ 439 (460)
+.++..++.++|||.+++++++.++.|+++++..
T Consensus 296 r~~l~~~~~~~SLd~~vg~~~d~~l~d~l~~~~~ 329 (415)
T PRK07598 296 REVLLRVPRSVSLETKVGKDKDTELGDLLETDDI 329 (415)
T ss_pred HHHHHHccCCcccccccCCCccccHHHhccCCCC
Confidence 9999999999999999998888889998876543
No 2
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=1.8e-44 Score=371.92 Aligned_cols=229 Identities=43% Similarity=0.721 Sum_probs=221.6
Q ss_pred CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHH
Q 012567 210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD 288 (460)
Q Consensus 210 ~~d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e 288 (460)
..|++. ||+++ +++|+||+|||++|+++|++++.+++++.+|++.+|++|+..+||.++|++..+|..++..|..|++
T Consensus 61 ~~d~l~~Yl~~i-~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~ 139 (373)
T PRK07406 61 TEDSIRVYLQEI-GRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKE 139 (373)
T ss_pred CCCHHHHHHHHh-cccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHH
Confidence 368899 99999 9999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchH
Q 012567 289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV 368 (460)
Q Consensus 289 ~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~ 368 (460)
.||..|+++|+++|++|.++|.+++||+|||++|||+++++|||.+|++|+|||+||||++|.++|+++++++|+|.++.
T Consensus 140 ~Li~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~~ 219 (373)
T PRK07406 140 KMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLY 219 (373)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCCCCcccccccCCC
Q 012567 369 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSVCFILNLA 439 (460)
Q Consensus 369 e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d~tl~Eli~D~~~ 439 (460)
+.+++++++...|...+|+.||.+|||+.||+++++|..++..+...+|||.+++++++.++.|+++|+..
T Consensus 220 ~~~~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~~~l~d~l~d~~~ 290 (373)
T PRK07406 220 ETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADGE 290 (373)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCcccHHHhcCCCCC
Confidence 99999999999999999999999999999999999999999888889999999988878889999987643
No 3
>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=5.7e-44 Score=358.60 Aligned_cols=226 Identities=42% Similarity=0.727 Sum_probs=217.3
Q ss_pred CHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHHH
Q 012567 212 DPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKM 290 (460)
Q Consensus 212 d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~L 290 (460)
|++. ||+++ +++|+||+|||.+|+++++.++.+++++..|+++.|++||..+||+++|++..+|+..++.|..|++.|
T Consensus 1 ~~~~~yl~~~-~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~L 79 (298)
T TIGR02997 1 DLVRLYLQEI-GRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKM 79 (298)
T ss_pred CcHHHHHHHc-cccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHH
Confidence 4678 99999 999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHHH
Q 012567 291 ITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEA 370 (460)
Q Consensus 291 I~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e~ 370 (460)
|.+|+++|+++|++|.++|.+++||+||||+|||+|+++|||.+|++|+||++||||++|.+++.++++++|+|.++...
T Consensus 80 v~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~I~r~i~~~~r~vr~p~~~~~~ 159 (298)
T TIGR02997 80 IKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEK 159 (298)
T ss_pred HHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHHHHHHHHhcCCCeeCcHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCCCCcccccccCC
Q 012567 371 TYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSVCFILNL 438 (460)
Q Consensus 371 i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d~tl~Eli~D~~ 438 (460)
+++++++...+...+|+.||.+|||+.||+++++|..++......+|||.+++++++.++.++++|+.
T Consensus 160 ~~~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~~~ 227 (298)
T TIGR02997 160 LNKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDDG 227 (298)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCcchHHHhccCCC
Confidence 99999999999999999999999999999999999999998889999999998776677888887743
No 4
>PRK05949 RNA polymerase sigma factor; Validated
Probab=100.00 E-value=1e-43 Score=361.34 Aligned_cols=228 Identities=37% Similarity=0.647 Sum_probs=221.3
Q ss_pred CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHH
Q 012567 210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD 288 (460)
Q Consensus 210 ~~d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e 288 (460)
.+|++. ||+++ +++|+||++||++|+++|+.++.+++.+..|.+.+|++|+..+|+.++++++.+|+..++.|..|++
T Consensus 16 ~~d~~~~yl~~i-~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~ 94 (327)
T PRK05949 16 SADMVRTYLHEI-GRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQ 94 (327)
T ss_pred CCCHHHHHHHHc-CCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHH
Confidence 478999 99999 9999999999999999999999999999999999999999999999999999999999999989999
Q ss_pred HHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchH
Q 012567 289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV 368 (460)
Q Consensus 289 ~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~ 368 (460)
.||..|+++|+++|++|.+++.+++||+||||+|||+++++|||++|++|+|||+||||++|.++|+++++++|+|.++.
T Consensus 95 ~Li~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~~~~ 174 (327)
T PRK05949 95 KMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHIT 174 (327)
T ss_pred HHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCCCCcccccccCC
Q 012567 369 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSVCFILNL 438 (460)
Q Consensus 369 e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d~tl~Eli~D~~ 438 (460)
+.+++++++...+..++|+.|+.+|||+.+|+++++|..++..+..++|||.+++++++.++.++++|+.
T Consensus 175 ~~~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~l~d~~ 244 (327)
T PRK05949 175 EKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEG 244 (327)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCccHHhhcCCCC
Confidence 9999999999999999999999999999999999999999998899999999998887788899998764
No 5
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=1.4e-42 Score=351.65 Aligned_cols=227 Identities=41% Similarity=0.661 Sum_probs=220.1
Q ss_pred CCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHH
Q 012567 211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDK 289 (460)
Q Consensus 211 ~d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~ 289 (460)
+|++. ||+++ +++|+||+|||++|+++|++++.+++++..|.+++|++|+..+||.++++++..|+..++.|..|++.
T Consensus 7 ~~~~~~yl~~i-~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~~ 85 (317)
T PRK07405 7 TDLVRTYLREI-GRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRK 85 (317)
T ss_pred CcHHHHHHHHc-cccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHHH
Confidence 68899 99999 99999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHH
Q 012567 290 MITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVE 369 (460)
Q Consensus 290 LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e 369 (460)
||..|+++|+++|++|.+++.+++||+||||+|||+++++|||.+|++|+||++||||++|.++|.++++++|+|.++..
T Consensus 86 L~~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir~p~~~~~ 165 (317)
T PRK07405 86 MVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITE 165 (317)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCccCChHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCCCCcccccccCC
Q 012567 370 ATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSVCFILNL 438 (460)
Q Consensus 370 ~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d~tl~Eli~D~~ 438 (460)
.+++++++...+...+|+.||.+|||+.+|+++++|..++......+|||.+++++.+.++.++++|+.
T Consensus 166 ~~~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~~~d~~ 234 (317)
T PRK07405 166 KLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTG 234 (317)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCccHHHhhcCCC
Confidence 999999999999999999999999999999999999999988888999999998877788889988764
No 6
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=100.00 E-value=1.2e-40 Score=353.92 Aligned_cols=223 Identities=36% Similarity=0.594 Sum_probs=198.4
Q ss_pred CCCCCCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccH
Q 012567 206 QEVDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGI 284 (460)
Q Consensus 206 ~~~~~~d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~ 284 (460)
......|+++ ||+++ +++|+||++||++|+++|+.+..++. .+.+ ..+|+. .....|...++.|.
T Consensus 205 ~~~~~~d~l~~YL~~i-~~~~lLt~eEE~~La~~i~~g~~~~~---~~~~-------~~~~~~---~~~~~l~~~~~~g~ 270 (509)
T PRK05901 205 KLTATADPVKAYLKQI-GKVKLLNAEEEVELAKRIEAGLYAEE---LLAE-------GEKLDP---ELRRDLQWIGRDGK 270 (509)
T ss_pred hccccccHHHHHHHHh-ccCCCCCHHHHHHHHHHHHhCCchhh---hhhh-------cccchh---hhhhhhhhhccchH
Confidence 3344678999 99999 99999999999999999997633322 1111 112332 24567888899999
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccC
Q 012567 285 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP 364 (460)
Q Consensus 285 ~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP 364 (460)
.|+++||.+|+|||+++|++|.++|++++||||||+||||+|+++|||++|++|+|||+||||++|.++|+++.+.+|+|
T Consensus 271 ~Ar~~LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP 350 (509)
T PRK05901 271 RAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIP 350 (509)
T ss_pred HHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCCCCcccccccCCCcch
Q 012567 365 FHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSVCFILNLADSL 442 (460)
Q Consensus 365 ~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d~tl~Eli~D~~~ds~ 442 (460)
.++.+.++++.++.+.|...+|+.||.+|||+.||+++++|..++.....++|||.+++++++.++.++|+|+...++
T Consensus 351 ~~~~e~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~~p 428 (509)
T PRK05901 351 VHMVETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSP 428 (509)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCcccHHHhccCCCCCCH
Confidence 999999999999999999999999999999999999999999999988899999999988878889999998755433
No 7
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=100.00 E-value=2.1e-40 Score=335.33 Aligned_cols=234 Identities=38% Similarity=0.609 Sum_probs=213.3
Q ss_pred CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhh-hcCCCCcHH---------------HHHHHhCCC
Q 012567 210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSE-RCGGSPTFA---------------QWAAAAGVD 272 (460)
Q Consensus 210 ~~d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~-~~g~~pt~~---------------ewA~a~g~d 272 (460)
..|.+. |+.++ +..+++++++|..+.+.++....+..+...|.. ..|..|+.. +|+..+..+
T Consensus 7 ~~d~~~~~l~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 85 (342)
T COG0568 7 SADAVRAYLDEI-GRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPE 85 (342)
T ss_pred chhHHHHHHHHh-cchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChH
Confidence 467888 99999 999999999999999999887767677777776 667888876 555555554
Q ss_pred H-HHHHHHHhccH---HHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHH
Q 012567 273 Q-RELRRRLNYGI---LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQ 348 (460)
Q Consensus 273 e-~~L~~~l~~G~---~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~ 348 (460)
+ ..|..++..|. .|+.+||.+|++||++||++|.|+|+++.||||||++|||+|++||||.+|++|||||+||||+
T Consensus 86 Ee~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAVekFdp~rG~kFsTYA~wWIrq 165 (342)
T COG0568 86 EEKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQ 165 (342)
T ss_pred HHHHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHHHHhcCcccCCcchhHHHHHHHH
Confidence 4 66888888884 5999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhcCcccccCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCCC
Q 012567 349 AVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNL 428 (460)
Q Consensus 349 aI~~~Lrk~~r~iriP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d~ 428 (460)
+|.++|.+++++||+|.|+.+.++++.++.+.|.+.+|++|+++|||+.||++.++|..++.++..++|||.|++++++.
T Consensus 166 aI~raI~~q~rtIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd~~ig~ded~ 245 (342)
T COG0568 166 AITRAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDDEDS 245 (342)
T ss_pred HHHHHHHHhcchhhHhHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccCCcCCCCccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcccccccCCCcchhh
Q 012567 429 KPSVCFILNLADSLII 444 (460)
Q Consensus 429 tl~Eli~D~~~ds~~~ 444 (460)
.+.|+++|+...++..
T Consensus 246 ~l~d~leD~~~~~p~~ 261 (342)
T COG0568 246 ELGDFLEDDKSVSPED 261 (342)
T ss_pred HHHHHhhcCCcCCHHH
Confidence 9999999997654443
No 8
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=100.00 E-value=1.9e-39 Score=329.65 Aligned_cols=217 Identities=38% Similarity=0.629 Sum_probs=196.3
Q ss_pred CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHH
Q 012567 210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD 288 (460)
Q Consensus 210 ~~d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e 288 (460)
.+|++. ||+++ +++|+||+|||.+|+++|+.+..++.. |+..+|+... ....|...++.|..|++
T Consensus 24 ~~~~~~~Yl~~i-~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~~ 89 (324)
T PRK07921 24 AADLVRVYLNGI-GKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAARR 89 (324)
T ss_pred CCChHHHHHHHh-cccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHHH
Confidence 468999 99999 999999999999999999987655533 2223332111 45678889999999999
Q ss_pred HHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchH
Q 012567 289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV 368 (460)
Q Consensus 289 ~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~ 368 (460)
.||..|+++|+++|++|.+++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++|+++++.+++|.++.
T Consensus 90 ~Lv~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~~~~ 169 (324)
T PRK07921 90 HLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLV 169 (324)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCCCCcccccccCCCc
Q 012567 369 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSVCFILNLAD 440 (460)
Q Consensus 369 e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d~tl~Eli~D~~~d 440 (460)
+.++++.++...|...+|+.||.+|||+.||+++++|..++..+...+|||.+++++++.++.|+++|+...
T Consensus 170 ~~~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~ 241 (324)
T PRK07921 170 EQVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEAT 241 (324)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCchHHHHhcCCCCC
Confidence 999999999999999999999999999999999999999998888899999999887777899999986543
No 9
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=3e-35 Score=303.63 Aligned_cols=191 Identities=41% Similarity=0.687 Sum_probs=180.5
Q ss_pred CCCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHH
Q 012567 209 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCK 287 (460)
Q Consensus 209 ~~~d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~ 287 (460)
...|+++ ||++| +++|+||+++|.+|+++++.+ +..|+
T Consensus 93 ~~~d~~~~yl~~i-~~~~~l~~~ee~~L~~~~~~G----------------------------------------d~~A~ 131 (367)
T PRK09210 93 KINDPVRMYLKEI-GRVPLLTAEEEIELAKRIEEG----------------------------------------DEEAK 131 (367)
T ss_pred ccCcHHHHHHHHh-hccCCCCHHHHHHHHHHHHhh----------------------------------------HHHHH
Confidence 3478999 99999 999999999999999888752 26799
Q ss_pred HHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcch
Q 012567 288 DKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHM 367 (460)
Q Consensus 288 e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~ 367 (460)
+.||..|+++|+++|++|.+++.+++||+||||+|||+|+++|||.+|++|+|||+||||++|.++|+++.+.+|+|.++
T Consensus 132 ~~Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~~~ 211 (367)
T PRK09210 132 QRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 211 (367)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCCCCcccccccCCCc
Q 012567 368 VEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSVCFILNLAD 440 (460)
Q Consensus 368 ~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d~tl~Eli~D~~~d 440 (460)
.+.++++.++.+.|..++|+.||.+|||+.||+++++|..++..+..++|||.+++++++.++.|+++|+...
T Consensus 212 ~~~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~i~d~~~~ 284 (367)
T PRK09210 212 VETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDAT 284 (367)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCCCcchhhhhccCCCCC
Confidence 9999999999999999999999999999999999999999999888899999999988788899999987644
No 10
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=2e-33 Score=307.46 Aligned_cols=159 Identities=40% Similarity=0.695 Sum_probs=152.5
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccccc
Q 012567 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL 363 (460)
Q Consensus 284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iri 363 (460)
..|+++||.+|++||++||++|.++|++++||||||+||||+|+++|||.+|++|+|||+||||++|.++|+++.+++|+
T Consensus 379 ~~a~~~Li~~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA~~wIr~aI~~~i~~~~r~iri 458 (619)
T PRK05658 379 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 458 (619)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCchHHHhHHHHHHHHHHHHHHcCCceec
Confidence 36899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCCCCcccccccCCCcch
Q 012567 364 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSVCFILNLADSL 442 (460)
Q Consensus 364 P~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d~tl~Eli~D~~~ds~ 442 (460)
|.++.+.++++.++...|.+++|+.||.+|||+.||+++++|..++..+..++|||.|++++++.++.|+++|+...++
T Consensus 459 p~~~~~~~~k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~Sld~~i~~~~~~~l~d~i~d~~~~~p 537 (619)
T PRK05658 459 PVHMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELP 537 (619)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCcCCCCCCCCCCCchhhhcCCCCCCCh
Confidence 9999999999999999999999999999999999999999999999999999999999998888899999998765443
No 11
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=99.97 E-value=4.2e-30 Score=257.53 Aligned_cols=189 Identities=23% Similarity=0.377 Sum_probs=161.8
Q ss_pred CCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHH
Q 012567 211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDK 289 (460)
Q Consensus 211 ~d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~ 289 (460)
.+.++ ||+++ +++|+||+++|.+|+.+++.. ++..|++.
T Consensus 5 ~~~~~~y~~~~-~~~~~l~~~~e~~L~~~~~~~---------------------------------------gd~~A~~~ 44 (289)
T PRK07500 5 ASADRSMIRSA-MKAPYLEREEEHALAYRWKDH---------------------------------------RDEDALHR 44 (289)
T ss_pred hhHHHHHHHHH-hcCCCCCHHHHHHHHHHHHHC---------------------------------------CCHHHHHH
Confidence 34667 99999 999999999999999876531 23789999
Q ss_pred HHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHH
Q 012567 290 MITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVE 369 (460)
Q Consensus 290 LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e 369 (460)
||..|+++|+++|++|.+++.+++||+||||+|||+++++|||.+|.+|+|||+||||++|.++|+++.+.+|+|.+...
T Consensus 45 Lv~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I~~~lr~~~~~iR~p~~~~~ 124 (289)
T PRK07500 45 IISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQ 124 (289)
T ss_pred HHHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHCCCceecCccHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999988654
Q ss_pred --HHHHHHHHHHHHHH---HhCCCCCHHHHHHHhCCCHHHHHHHHh-CCCCCcccccccccCCCC--CcccccccCCC
Q 012567 370 --ATYRVKEARKQLYS---ENGRHPNNEEVAEATGLSMKRLHAVLL-SPKAPRSLDQKIGINQNL--KPSVCFILNLA 439 (460)
Q Consensus 370 --~i~kl~ka~~~L~~---~~gr~pS~eEIAe~LGIS~e~Vk~~l~-~ar~~lSLD~~v~~e~d~--tl~Eli~D~~~ 439 (460)
...++++....+.. .+|+.||.+|||+.||+++++|..+.. .....+|||.+++++++. ++.|+++|+..
T Consensus 125 ~~~~~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~i~d~~~ 202 (289)
T PRK07500 125 KALFFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDDSP 202 (289)
T ss_pred HHHHHHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCCCCCCcccHHHhccCCCC
Confidence 33455555554444 678999999999999999999988753 455799999999765543 68899987643
No 12
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=99.97 E-value=1.1e-29 Score=251.50 Aligned_cols=154 Identities=25% Similarity=0.349 Sum_probs=142.0
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccccc
Q 012567 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL 363 (460)
Q Consensus 284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iri 363 (460)
..++++||..|++||+++|++|.++|++++||||+|+|||++|+++|||++|++|+|||+||||++|.++++++.+.+++
T Consensus 39 ~~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~iGLi~AierFDp~~G~~FsTYA~~~Irg~I~~~lr~~~~~ir~ 118 (264)
T PRK07122 39 QRQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKV 118 (264)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHcCCcccc
Confidence 45899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhC--CCCCcccccccccCCC--CCcccccccC
Q 012567 364 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLS--PKAPRSLDQKIGINQN--LKPSVCFILN 437 (460)
Q Consensus 364 P~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~--ar~~lSLD~~v~~e~d--~tl~Eli~D~ 437 (460)
|.++.+.+++++++...|..++|+.||.+|||+.||+++++|..++.. ...++|||.+++++++ ..+.+.++|+
T Consensus 119 Pr~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~~~d~~~~~ 196 (264)
T PRK07122 119 PRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSGDDDARAIADTLGDV 196 (264)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccccccCCCCCcccchhccCCc
Confidence 999999999999999999999999999999999999999999998863 4568999999875433 3566777665
No 13
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=99.97 E-value=2.6e-29 Score=251.19 Aligned_cols=187 Identities=25% Similarity=0.397 Sum_probs=157.6
Q ss_pred CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHH
Q 012567 210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD 288 (460)
Q Consensus 210 ~~d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e 288 (460)
+.+++. |++++ ++.|+||.++|.+|+.+++.. ++..|++
T Consensus 12 ~~~~~~~y~~~~-~~~~~l~~~~e~~l~~~~~~~---------------------------------------Gd~~a~~ 51 (284)
T PRK06596 12 PEGNLDAYIQAV-NKIPMLTAEEEYMLAKRLREH---------------------------------------GDLEAAK 51 (284)
T ss_pred CccHHHHHHHHH-hccCCCCHHHHHHHHHHHHHc---------------------------------------CCHHHHH
Confidence 457889 99999 999999999999998875420 2378999
Q ss_pred HHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchH
Q 012567 289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV 368 (460)
Q Consensus 289 ~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~ 368 (460)
.||..|+++|+++|++|.+++.+++||+|||++||++|+++|||++|++|+|||+|||+++|.++++++++.+++|.+..
T Consensus 52 ~Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~~~l~~~~~~vr~p~~~~ 131 (284)
T PRK06596 52 QLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKA 131 (284)
T ss_pred HHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHcCCeeeccchHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999888889998753
Q ss_pred --HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhC-CCCCcccccccccCC--CCCcccccccCC
Q 012567 369 --EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLS-PKAPRSLDQKIGINQ--NLKPSVCFILNL 438 (460)
Q Consensus 369 --e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~-ar~~lSLD~~v~~e~--d~tl~Eli~D~~ 438 (460)
....++.+....+. .++.|+.+|||+.||+++++|..++.. ....+|||.++++++ +.++.++++|+.
T Consensus 132 ~~~~~~~~~~~~~~l~--~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~~~l~d~~ 204 (284)
T PRK06596 132 QRKLFFNLRKAKKRLG--WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLEDKS 204 (284)
T ss_pred HHHHHHHHHHHHHHhc--cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCCCCCcchHHHHcCCCC
Confidence 23334444444443 348999999999999999999998753 346899999987553 346788888864
No 14
>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=99.97 E-value=7.4e-30 Score=248.25 Aligned_cols=155 Identities=41% Similarity=0.719 Sum_probs=147.2
Q ss_pred HHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCc
Q 012567 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF 365 (460)
Q Consensus 286 A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~ 365 (460)
|+++||..|+++|+++|++|.+++.+++||+|||++||++|+++|||.+|++|+|||+||||++|.++++++.+.+++|.
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 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCCCCcccccccCCCc
Q 012567 366 HMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSVCFILNLAD 440 (460)
Q Consensus 366 ~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d~tl~Eli~D~~~d 440 (460)
++.+.++++.++...|...+|+.||.+|||+.||+++++|..++......+|||.+++++++.++.|+++|+...
T Consensus 81 ~~~~~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~ 155 (238)
T TIGR02393 81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDTSIE 155 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCCCCCCcccHHHHhcCCCCC
Confidence 999999999999999999999999999999999999999999998777899999999877777888999887543
No 15
>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=99.96 E-value=6.7e-29 Score=246.17 Aligned_cols=184 Identities=25% Similarity=0.467 Sum_probs=152.4
Q ss_pred HHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHHHH
Q 012567 213 PLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMI 291 (460)
Q Consensus 213 ~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~LI 291 (460)
++. ||+++ +++|+|+.++|.+|+.++.. .++..|++.||
T Consensus 2 ~~~~yl~~~-~~~~~l~~~~e~~l~~~~~~---------------------------------------~gd~~a~~~Lv 41 (270)
T TIGR02392 2 SLDAYIRAV-NRIPMLTPEEEYQLAKRLRE---------------------------------------HGDLDAAKKLV 41 (270)
T ss_pred hHHHHHHHH-hcCCCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHHHH
Confidence 567 99999 99999999999999887432 02378999999
Q ss_pred HHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchH--H
Q 012567 292 TSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV--E 369 (460)
Q Consensus 292 ~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~--e 369 (460)
..|+++|+++|++|.+++.+++||+|+|++||++++++|||++|++|+|||.|||+++|.++++++++.+|+|.+.. +
T Consensus 42 ~~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA~~~Ir~~i~~~l~~~~~~ir~p~~~~~~~ 121 (270)
T TIGR02392 42 LSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRK 121 (270)
T ss_pred HHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhhHHHHHHHHHHHHHHcCCceecCchHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999887889997643 3
Q ss_pred HHHHHHHHHHHHHHHhCCCC-CHHHHHHHhCCCHHHHHHHHhCC-CCCcccccccccCCC--CCcccccccCC
Q 012567 370 ATYRVKEARKQLYSENGRHP-NNEEVAEATGLSMKRLHAVLLSP-KAPRSLDQKIGINQN--LKPSVCFILNL 438 (460)
Q Consensus 370 ~i~kl~ka~~~L~~~~gr~p-S~eEIAe~LGIS~e~Vk~~l~~a-r~~lSLD~~v~~e~d--~tl~Eli~D~~ 438 (460)
...++.++...+. ..+.| +.+|||+.||+++++|..++... ...+|||.+++++++ .++.++++|+.
T Consensus 122 ~~~~~~~~~~~~~--~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~l~d~~ 192 (270)
T TIGR02392 122 LFFNLRKMKKRLQ--GWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDDEDDGGAPIAYLVDKT 192 (270)
T ss_pred HHHHHHHHHHHHh--cCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCCCCCccccHHHHhcCCC
Confidence 3444555544442 12445 69999999999999999986533 348999999976544 35778887764
No 16
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=99.96 E-value=2.2e-28 Score=240.83 Aligned_cols=156 Identities=29% Similarity=0.471 Sum_probs=142.9
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCC-CCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccc
Q 012567 284 ILCKDKMITSNIRLVISIAKNYQGA-GMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR 362 (460)
Q Consensus 284 ~~A~e~LI~~nlrLV~~IAkry~~~-g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~ir 362 (460)
..|+++||..|+++|+++|++|.+. +.+++||+|+|++|||+|+++|||++|++|+||++|||+|+|.+++|++...+|
T Consensus 24 ~~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~~~vr 103 (256)
T PRK07408 24 IALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTVR 103 (256)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHHcCCeee
Confidence 7899999999999999999999875 667999999999999999999999999999999999999999999999999999
Q ss_pred cCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHh--CCCCCcccccccccCCC--CCcccccccCC
Q 012567 363 LPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL--SPKAPRSLDQKIGINQN--LKPSVCFILNL 438 (460)
Q Consensus 363 iP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~--~ar~~lSLD~~v~~e~d--~tl~Eli~D~~ 438 (460)
+|.++.+.++++.++...|...+|+.||.+|||+.||+++++|..++. .....+|||.+++++++ .++.+.++|+.
T Consensus 104 ~pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~~~d~~ 183 (256)
T PRK07408 104 IPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQDEDGSTSLGDLLPDPR 183 (256)
T ss_pred eCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCCCCCCccccccccCCcc
Confidence 999999999999999999999999999999999999999999999864 44568999999865443 36778888765
Q ss_pred C
Q 012567 439 A 439 (460)
Q Consensus 439 ~ 439 (460)
.
T Consensus 184 ~ 184 (256)
T PRK07408 184 Y 184 (256)
T ss_pred c
Confidence 4
No 17
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=99.96 E-value=5.3e-28 Score=246.14 Aligned_cols=188 Identities=35% Similarity=0.557 Sum_probs=174.0
Q ss_pred CCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHH
Q 012567 211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDK 289 (460)
Q Consensus 211 ~d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~ 289 (460)
.|..+ ||++| +..|+||+++|..|..+++. ++..|++.
T Consensus 52 ~~~~~~y~~~~-~~~~~l~~~ee~~li~~~~~----------------------------------------Gd~~A~~~ 90 (325)
T PRK05657 52 LDATQLYLNEI-GYSPLLTAEEEVYFARRALR----------------------------------------GDFAARQR 90 (325)
T ss_pred ccHHHHHHHHH-hcCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHH
Confidence 67888 99999 99999999999999887764 23789999
Q ss_pred HHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHH
Q 012567 290 MITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVE 369 (460)
Q Consensus 290 LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e 369 (460)
||..|.++|+++|++|.+++.+++||+||||+|+|+++++||+.+|++|+||++||||+.|.++++++.+.+++|.++..
T Consensus 91 Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~~i~~~~r~ir~p~~~~~ 170 (325)
T PRK05657 91 MIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVK 170 (325)
T ss_pred HHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHcCCccccCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999988
Q ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCCCCcccccccCCC
Q 012567 370 ATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSVCFILNLA 439 (460)
Q Consensus 370 ~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d~tl~Eli~D~~~ 439 (460)
.++.+.++...|...+|+.|+.+|||+.||+++++|..++.......|||.+++.+...++.+.++|+..
T Consensus 171 ~l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~~~~~~~~l~d~l~d~~~ 240 (325)
T PRK05657 171 ELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQE 240 (325)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCCCCCCCcchhhhccCCCC
Confidence 8888888989999999999999999999999999999999877778999999987777788888887653
No 18
>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=99.96 E-value=1.3e-27 Score=234.82 Aligned_cols=178 Identities=28% Similarity=0.397 Sum_probs=160.7
Q ss_pred hcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHHHHHHhHHHHHH
Q 012567 221 TSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVIS 300 (460)
Q Consensus 221 ~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~LI~~nlrLV~~ 300 (460)
++++|+||+++|.+|+.+++. ++..|++.|+..|+++|++
T Consensus 10 ~~~~~~l~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~~~~~~~v~~ 49 (254)
T TIGR02850 10 TSKLPVLKNQEMRELFIRMQS----------------------------------------GDTTAREKLINGNLRLVLS 49 (254)
T ss_pred ccCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHHHH
Confidence 377999999999988877663 1367999999999999999
Q ss_pred HHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHHHHHHHHHHHHH
Q 012567 301 IAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQ 380 (460)
Q Consensus 301 IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e~i~kl~ka~~~ 380 (460)
+|++|.+++.+++||+||||+|||+++++|||.+|.+|+||+++||+|.|.+++|++. .+++|.++.+...++.++...
T Consensus 50 ~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~~lr~~~-~ir~p~~~~~~~~~~~~~~~~ 128 (254)
T TIGR02850 50 VIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRDK 128 (254)
T ss_pred HHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CccCchHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999976 789999999999999999999
Q ss_pred HHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCC--CCcccccccCCC
Q 012567 381 LYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQN--LKPSVCFILNLA 439 (460)
Q Consensus 381 L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d--~tl~Eli~D~~~ 439 (460)
+..++|+.||.+|||+.||+++++|..++.....++|||.++.++++ .++.+.++|+..
T Consensus 129 l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~~~d~~~ 189 (254)
T TIGR02850 129 LISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDEKN 189 (254)
T ss_pred HHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCCCCCcchhhhhcCCccc
Confidence 99999999999999999999999999999888888999999864443 357788877643
No 19
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=99.94 E-value=3.4e-26 Score=225.03 Aligned_cols=176 Identities=28% Similarity=0.399 Sum_probs=158.8
Q ss_pred cCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHHHHHHhHHHHHHH
Q 012567 222 SSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI 301 (460)
Q Consensus 222 ~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~LI~~nlrLV~~I 301 (460)
.++|+|+++++..|+.+++. ++..+++.|+..|+++|+++
T Consensus 14 ~~~~~l~~~~~~~l~~~~~~----------------------------------------gd~~a~~~l~~~~~~~v~~~ 53 (258)
T PRK08215 14 SKLPVLKNEEMRELFERMQN----------------------------------------GDKEAREKLINGNLRLVLSV 53 (258)
T ss_pred CCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHHHHHHHHH
Confidence 56789999999988877663 23679999999999999999
Q ss_pred HHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHHHHHHHHHHHHHH
Q 012567 302 AKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQL 381 (460)
Q Consensus 302 Akry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e~i~kl~ka~~~L 381 (460)
|++|.+++.+++||+|||++|||+++++||+.+|.+|+||+++||+|+|.++++++. .+++|.+......++.++...+
T Consensus 54 a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~~~lr~~~-~vrip~~~~~~~~~~~~~~~~l 132 (258)
T PRK08215 54 IQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVREKL 132 (258)
T ss_pred HHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-ceEecHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999986 7899999999999999999999
Q ss_pred HHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCCC--CcccccccCC
Q 012567 382 YSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNL--KPSVCFILNL 438 (460)
Q Consensus 382 ~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d~--tl~Eli~D~~ 438 (460)
..++|+.|+..|||+.||+++++|...+.....+.|||.++.++++. ++.+.++|+.
T Consensus 133 ~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~ 191 (258)
T PRK08215 133 INENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQISDEK 191 (258)
T ss_pred HHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCCCCcchhhhhhccCcc
Confidence 99999999999999999999999999988777888999998655433 4667777664
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=99.93 E-value=9e-25 Score=218.17 Aligned_cols=191 Identities=37% Similarity=0.569 Sum_probs=172.2
Q ss_pred CCCCCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHH
Q 012567 207 EVDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 285 (460)
Q Consensus 207 ~~~~~d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~ 285 (460)
+....|.++ ||.+| +.+|.||.++|.+|..+++. | +..
T Consensus 8 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~~li~~~~~---------------g-------------------------d~~ 46 (285)
T TIGR02394 8 ETRVADVTQLYLREI-GFKPLLTAEEEIAYARRALA---------------G-------------------------DFE 46 (285)
T ss_pred ccCcchHHHHHHHHH-hccCCCCHHHHHHHHHHHHc---------------C-------------------------CHH
Confidence 345678999 99999 99999999999999887764 1 378
Q ss_pred HHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCc
Q 012567 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF 365 (460)
Q Consensus 286 A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~ 365 (460)
|++.|+..|.++|+.+|++|.+++.+++||+||||+|||+++++||+.+|++|+||+.|||+.++.++++++.+.+++|.
T Consensus 47 a~~~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ain~~i~~~~~~~~~p~ 126 (285)
T TIGR02394 47 ARKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPV 126 (285)
T ss_pred HHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHHHHHHHHcCCceeCcH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCCCCcccccccCC
Q 012567 366 HMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSVCFILNL 438 (460)
Q Consensus 366 ~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d~tl~Eli~D~~ 438 (460)
.+....+.+.+..+.+...+|+.|+..++|+.||++++.|..++..+...+|+|.++..+...++.+.++++.
T Consensus 127 ~~~~~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~~ 199 (285)
T TIGR02394 127 HVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQ 199 (285)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCCCCCCCcchhhhhcCCC
Confidence 9998888888888778888899999999999999999999999988888999999887666556666666554
No 21
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=99.93 E-value=3.7e-25 Score=218.15 Aligned_cols=154 Identities=25% Similarity=0.369 Sum_probs=137.0
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccC---CCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcc
Q 012567 284 ILCKDKMITSNIRLVISIAKNYQG---AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT 360 (460)
Q Consensus 284 ~~A~e~LI~~nlrLV~~IAkry~~---~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~ 360 (460)
..|++.||..|+++|+++|++|.+ .+.+.+||+|+|++|||+|+++|||++|++|+||+.||||++|.+++|++.+
T Consensus 22 ~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~~- 100 (257)
T PRK05911 22 IEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQDW- 100 (257)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCC-
Confidence 789999999999999999999862 4568999999999999999999999999999999999999999999998764
Q ss_pred cccCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCC--CCccccccccc--C--CCCCccccc
Q 012567 361 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPK--APRSLDQKIGI--N--QNLKPSVCF 434 (460)
Q Consensus 361 iriP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar--~~lSLD~~v~~--e--~d~tl~Eli 434 (460)
+|.++.+..+++.++...|...+|+.|+.+|||+.||+++++|..++..++ ..+|||.++.. + .+.++.+.+
T Consensus 101 --~pr~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~Sld~~~~~~~~~~~~~~l~~~l 178 (257)
T PRK05911 101 --VPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPCQSDDEAGLALEERI 178 (257)
T ss_pred --CCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHHhhccceeeccccCCCCCCCccccchhhhc
Confidence 899999999999999999999999999999999999999999999887554 36899988743 2 234678888
Q ss_pred ccCCCc
Q 012567 435 ILNLAD 440 (460)
Q Consensus 435 ~D~~~d 440 (460)
+|+...
T Consensus 179 ~d~~~~ 184 (257)
T PRK05911 179 ADERAE 184 (257)
T ss_pred cCCCCC
Confidence 886544
No 22
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=99.93 E-value=5.4e-25 Score=215.48 Aligned_cols=158 Identities=30% Similarity=0.446 Sum_probs=140.7
Q ss_pred HHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCC-CcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHH
Q 012567 276 LRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGM-NLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKS 353 (460)
Q Consensus 276 L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~-d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~ 353 (460)
+....+.| ..++ .||+.|+|||.++|++|.+++. +.+||+|.|+|||++|+++|||++|.+|+|||..+|+++|+++
T Consensus 14 ~~~~~~~g~~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d~ 92 (247)
T COG1191 14 LLEYYAEGDEEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILDY 92 (247)
T ss_pred HHHHHHhcCHHHH-HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHHH
Confidence 34444556 7888 9999999999999999998887 9999999999999999999999999999999999999999999
Q ss_pred hhhcCcccccCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCC--CCcccccccccCCCCCcc
Q 012567 354 LSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPK--APRSLDQKIGINQNLKPS 431 (460)
Q Consensus 354 Lrk~~r~iriP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar--~~lSLD~~v~~e~d~tl~ 431 (460)
+|++. .+++|..+.+..+++..++..|..++|++||..|||+.|||+.++|...+.... ..+|+|..+..+++....
T Consensus 93 LR~~~-~v~vpR~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~d~~~~ 171 (247)
T COG1191 93 LRKND-SVKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDDDVD 171 (247)
T ss_pred HHhCC-CccCcHHHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhccccccchh
Confidence 99999 899999999999999999999999999999999999999999999999987553 688999877654444344
Q ss_pred cccc
Q 012567 432 VCFI 435 (460)
Q Consensus 432 Eli~ 435 (460)
+.+.
T Consensus 172 ~~~~ 175 (247)
T COG1191 172 DQIE 175 (247)
T ss_pred hccc
Confidence 4443
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=99.92 E-value=1.6e-24 Score=209.22 Aligned_cols=156 Identities=33% Similarity=0.473 Sum_probs=143.7
Q ss_pred hcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCc
Q 012567 281 NYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSR 359 (460)
Q Consensus 281 ~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r 359 (460)
+.| ..|++.|+..|.++|+++|++|.+++.+++||+|||++|||+++++||+..|.+|+||+++||+|.|.+++|++.
T Consensus 6 ~~gd~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~lr~~~- 84 (231)
T TIGR02885 6 QNGDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDDG- 84 (231)
T ss_pred HcCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-
Confidence 344 889999999999999999999999999999999999999999999999999999999999999999999999986
Q ss_pred ccccCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCC--CCcccccccC
Q 012567 360 TIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQN--LKPSVCFILN 437 (460)
Q Consensus 360 ~iriP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d--~tl~Eli~D~ 437 (460)
.+++|.++.....++.++...|..++|+.||.+|||+.||+++++|..++..+....|||.+++++++ .++.|.++|+
T Consensus 85 ~i~~p~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~~ 164 (231)
T TIGR02885 85 IIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPIYLLDQIADK 164 (231)
T ss_pred CeECCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCCCCCcchhhhhcCCC
Confidence 78999999999999999999999999999999999999999999999998877788999998875543 2566777776
No 24
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=99.92 E-value=2.2e-24 Score=213.47 Aligned_cols=179 Identities=22% Similarity=0.269 Sum_probs=153.9
Q ss_pred hhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHHHHHHhHHHHH
Q 012567 220 TTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVI 299 (460)
Q Consensus 220 ~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~LI~~nlrLV~ 299 (460)
|+|++|+||.++|.+|+..++.. ++..+++.++..|.++|+
T Consensus 5 ~~~~~~~~~~~~e~~l~~~~~~~---------------------------------------~d~~a~~~l~~~y~~lv~ 45 (268)
T PRK06288 5 MSGKIPKYAQQDETELWREYKKT---------------------------------------GDPKIREYLILKYSPLVK 45 (268)
T ss_pred ccCCCccccchHHHHHHHHHHHc---------------------------------------CCHHHHHHHHHHHHHHHH
Confidence 46899999999999999887641 237799999999999999
Q ss_pred HHHHHcc-C--CCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHHHHHHHHH
Q 012567 300 SIAKNYQ-G--AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKE 376 (460)
Q Consensus 300 ~IAkry~-~--~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e~i~kl~k 376 (460)
.+|++|. + .+.+++||+||||+|||+++++||+.+|.+|+||+++||+|.|++++|+.. ++|.++.....++++
T Consensus 46 ~~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i~d~~R~~~---~~p~~~~~~~~~i~~ 122 (268)
T PRK06288 46 YVAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSID---WIPRSVRQKARQIER 122 (268)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC---ccCHHHHHHHHHHHH
Confidence 9999986 2 567899999999999999999999998999999999999999999999754 589999888999999
Q ss_pred HHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCC--CCCcccccccccCC---CCCcccccccCCCc
Q 012567 377 ARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSP--KAPRSLDQKIGINQ---NLKPSVCFILNLAD 440 (460)
Q Consensus 377 a~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~a--r~~lSLD~~v~~e~---d~tl~Eli~D~~~d 440 (460)
+...|...+++.||.+|||+.+|++.+.|..++... ...+|||.++..++ ..++.+.++++..+
T Consensus 123 ~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~l~~~~~~~~~~ 191 (268)
T PRK06288 123 AIAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGDEVSLMDTLESPAAL 191 (268)
T ss_pred HHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhccCCCcccchhhhhccCCCCC
Confidence 999999999999999999999999999999988643 45789998874222 23677778765444
No 25
>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=99.91 E-value=1.4e-23 Score=202.00 Aligned_cols=154 Identities=29% Similarity=0.420 Sum_probs=140.3
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccccc
Q 012567 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL 363 (460)
Q Consensus 284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iri 363 (460)
..|++.|+..|.++|+++|++|.+++.+.+||+|||++||++++++||+.+|.+|+||+++||+|.|.++++++.+.+++
T Consensus 2 ~~a~~~lv~~y~~~v~~~a~~~~~~~~~~eDl~Qe~~i~l~~a~~~f~~~~~~~F~ty~~~~i~~~~~~~~r~~~~~~ri 81 (227)
T TIGR02980 2 KEAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTWAVRV 81 (227)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCcHHHHHHHHHHHHHHHHHHcCCceec
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCC--CcccccccccCC--CCCcccccccC
Q 012567 364 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKA--PRSLDQKIGINQ--NLKPSVCFILN 437 (460)
Q Consensus 364 P~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~--~lSLD~~v~~e~--d~tl~Eli~D~ 437 (460)
|.++.+...+++++...+...+|+.|+..|+|+.||+++++|..++..... ..|||.++.+++ +.++.+.++++
T Consensus 82 ~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~d~~~~~ 159 (227)
T TIGR02980 82 PRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIEDDDGDPIALLDTLGDE 159 (227)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCCCCCCCcccccccCCc
Confidence 999999999999999999999999999999999999999999998875554 899999986332 23466666654
No 26
>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=99.91 E-value=5.3e-23 Score=201.81 Aligned_cols=165 Identities=26% Similarity=0.321 Sum_probs=149.3
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHHHHHHhHHHHHHHHHH
Q 012567 225 RLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKN 304 (460)
Q Consensus 225 ~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~LI~~nlrLV~~IAkr 304 (460)
|.||+++|.+|..+++.. ++..|+++|+..|.++|+.+|++
T Consensus 8 ~~l~~~~~~~li~~~~~~---------------------------------------gd~~a~~~l~~~y~~~v~~~a~~ 48 (255)
T TIGR02941 8 TNLTKEDVIQWIAEFQQN---------------------------------------QNGEAQEKLVDHYQNLVYSIAYK 48 (255)
T ss_pred CCCCHHHHHHHHHHHHHC---------------------------------------CCHHHHHHHHHHhHHHHHHHHHH
Confidence 678999988888776641 12789999999999999999999
Q ss_pred ccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHHHHHHHHHHHHHHHHH
Q 012567 305 YQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSE 384 (460)
Q Consensus 305 y~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e~i~kl~ka~~~L~~~ 384 (460)
|.+++.+++||+||||+|||+++++|++..|.+|.||+++||+|.|.++++++...+++|.++.+...+++++...+...
T Consensus 49 ~~~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~iri~~~~~~~~~~~~~~~~~l~~~ 128 (255)
T TIGR02941 49 YSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAIDELTDH 128 (255)
T ss_pred HhcCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999889999999999999999999999999
Q ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHhC--CCCCcccccccccCCCC
Q 012567 385 NGRHPNNEEVAEATGLSMKRLHAVLLS--PKAPRSLDQKIGINQNL 428 (460)
Q Consensus 385 ~gr~pS~eEIAe~LGIS~e~Vk~~l~~--ar~~lSLD~~v~~e~d~ 428 (460)
+|+.|+..|||+.||++.+.+..++.. .....|||.+++.+++.
T Consensus 129 ~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~ 174 (255)
T TIGR02941 129 LQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSDG 174 (255)
T ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCCCCC
Confidence 999999999999999999999888753 34578999998765443
No 27
>PRK05572 sporulation sigma factor SigF; Validated
Probab=99.90 E-value=3.2e-22 Score=196.24 Aligned_cols=178 Identities=26% Similarity=0.397 Sum_probs=156.3
Q ss_pred cCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHHHHHHhHHHHHHH
Q 012567 222 SSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI 301 (460)
Q Consensus 222 ~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~LI~~nlrLV~~I 301 (460)
...|.||.+++.+|..+++. ++..|++.|+..|.++|+.+
T Consensus 9 ~~~~~l~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~~~y~~~v~~~ 48 (252)
T PRK05572 9 KKKPQLKDEENKELIKKSQD----------------------------------------GDQEARDTLVEKNLRLVWSV 48 (252)
T ss_pred cCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHHHHH
Confidence 45789999998888766543 23679999999999999999
Q ss_pred HHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHHHHHHHHHHHHHH
Q 012567 302 AKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQL 381 (460)
Q Consensus 302 Akry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e~i~kl~ka~~~L 381 (460)
|++|.+++.+++||+||||+++|+++++|++.+|.+|.||+++||+|.|.+++|+.. .+++|..+.....++.++...+
T Consensus 49 a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~~lr~~~-~~r~~~~~~~~~~~~~~~~~~l 127 (252)
T PRK05572 49 VQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANKIRKDKDEL 127 (252)
T ss_pred HHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CCCCCHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999988889999999999999999999885 7899999999999999999999
Q ss_pred HHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCCC--CcccccccCCCc
Q 012567 382 YSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNL--KPSVCFILNLAD 440 (460)
Q Consensus 382 ~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d~--tl~Eli~D~~~d 440 (460)
..++|+.|+..|||+.||++++.|..++.......||+.++.+++.. ++.|.++++...
T Consensus 128 ~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~~~~~ 188 (252)
T PRK05572 128 SKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGDPITLLDQIADQSEE 188 (252)
T ss_pred HHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCcccCCCCcchhhhhcCCCchh
Confidence 99999999999999999999999999888777889999988654432 355666665443
No 28
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=99.88 E-value=6.5e-22 Score=194.00 Aligned_cols=152 Identities=27% Similarity=0.319 Sum_probs=135.5
Q ss_pred HHHHHHH-Hhcc-HHHHHHHHHHhHHHHHHHHHHccC---CCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHH
Q 012567 273 QRELRRR-LNYG-ILCKDKMITSNIRLVISIAKNYQG---AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIK 347 (460)
Q Consensus 273 e~~L~~~-l~~G-~~A~e~LI~~nlrLV~~IAkry~~---~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr 347 (460)
+..|..+ ...| ..|++.|+..|.++|+++|++|.+ ++.+.+||+||||+|||+++++||+.+|.+|+||+++||+
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 4455555 4444 899999999999999999999965 6889999999999999999999999999999999999999
Q ss_pred HHHHHHhhhcCcccccCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHh--CCCCCcccccccccC
Q 012567 348 QAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL--SPKAPRSLDQKIGIN 425 (460)
Q Consensus 348 ~aI~~~Lrk~~r~iriP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~--~ar~~lSLD~~v~~e 425 (460)
|.|++++|++. ++|..+.+.+.+++++...+.+.+|+.|+.+|||+.||+++++|..++. .....+|||.++.++
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 99999999876 4899888999999999999999999999999999999999999999975 455689999998654
Q ss_pred CC
Q 012567 426 QN 427 (460)
Q Consensus 426 ~d 427 (460)
++
T Consensus 165 ~~ 166 (251)
T PRK07670 165 DD 166 (251)
T ss_pred CC
Confidence 44
No 29
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=99.88 E-value=1.9e-21 Score=191.08 Aligned_cols=166 Identities=25% Similarity=0.323 Sum_probs=148.3
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHHHHHHhHHHHHHHH
Q 012567 223 SSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIA 302 (460)
Q Consensus 223 ~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~LI~~nlrLV~~IA 302 (460)
..|.|++++|.+|..+++.. ++..|++.|+..|.++|+++|
T Consensus 6 ~~~~l~~~e~~~li~~~~~~---------------------------------------gd~~a~~~l~~~~~~~v~~~a 46 (257)
T PRK08583 6 QPTKLTKEEVNKWIAEYQEN---------------------------------------QDEEAQEKLVKHYKNLVESLA 46 (257)
T ss_pred cCCcCChHHHHHHHHHHHHc---------------------------------------CCHHHHHHHHHHHHHHHHHHH
Confidence 34789999998887766531 237899999999999999999
Q ss_pred HHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHHHHHHHHHHHHHHH
Q 012567 303 KNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLY 382 (460)
Q Consensus 303 kry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e~i~kl~ka~~~L~ 382 (460)
++|.+++.+++||+||||+|||+++++||+..|.+|+||+++||+|.|.+++|++...+++|.+..+..++++.+...+.
T Consensus 47 ~~~~~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~~~i~r~~~~~~~~~~~~~~~~~ 126 (257)
T PRK08583 47 YKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELT 126 (257)
T ss_pred HHHhcCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHHHHHHHhcCCCcCCCHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999998889999999999999999999999899999999999999999999999
Q ss_pred HHhCCCCCHHHHHHHhCCCHHHHHHHHhCC--CCCcccccccccCCC
Q 012567 383 SENGRHPNNEEVAEATGLSMKRLHAVLLSP--KAPRSLDQKIGINQN 427 (460)
Q Consensus 383 ~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~a--r~~lSLD~~v~~e~d 427 (460)
..+++.|+.+|+|+.+|++.+.+...+... ...+|+|.+++.+.+
T Consensus 127 ~~~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~~~ 173 (257)
T PRK08583 127 TELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSD 173 (257)
T ss_pred HHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCCCC
Confidence 999999999999999999999998877643 357899998865443
No 30
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=99.88 E-value=1.3e-21 Score=190.31 Aligned_cols=138 Identities=20% Similarity=0.337 Sum_probs=123.2
Q ss_pred HHHHHHHHhHHHHHHHHHHccC---CCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccc
Q 012567 286 CKDKMITSNIRLVISIAKNYQG---AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR 362 (460)
Q Consensus 286 A~e~LI~~nlrLV~~IAkry~~---~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~ir 362 (460)
-...|+..|+++|.+++++|.+ .+.+.+||+|||++|||+|+++||+.+| +|+||++|||+|+|.+++++...
T Consensus 16 ~~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~il~~lr~~~~--- 91 (231)
T PRK12427 16 EEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELRELDW--- 91 (231)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHHHHhcCC---
Confidence 4567999999999999999874 4679999999999999999999998665 89999999999999999998653
Q ss_pred cCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHh--CCCCCcccccccccCCC
Q 012567 363 LPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL--SPKAPRSLDQKIGINQN 427 (460)
Q Consensus 363 iP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~--~ar~~lSLD~~v~~e~d 427 (460)
.|..+....++++++...|..++|+.||.+|||+.||+++++|..++. .+....|||.+++++++
T Consensus 92 ~~r~vr~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~ 158 (231)
T PRK12427 92 RPRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALEAH 158 (231)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccCCCc
Confidence 688888889999999999999999999999999999999999999875 34568999999876544
No 31
>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=99.87 E-value=2e-21 Score=187.07 Aligned_cols=146 Identities=27% Similarity=0.375 Sum_probs=128.4
Q ss_pred HHHHhHHHHHHHHHHccC---CCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcc
Q 012567 290 MITSNIRLVISIAKNYQG---AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFH 366 (460)
Q Consensus 290 LI~~nlrLV~~IAkry~~---~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~ 366 (460)
|+..|.++|+++|++|.+ ++.+++||+|||++|||+++++|||.+|.+|+||+++||+|.|++++|+.. ++|..
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 578999999999999986 789999999999999999999999999999999999999999999999865 48888
Q ss_pred hHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHh--CCCCCcccccccccC-CCCCcccccccCC
Q 012567 367 MVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL--SPKAPRSLDQKIGIN-QNLKPSVCFILNL 438 (460)
Q Consensus 367 ~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~--~ar~~lSLD~~v~~e-~d~tl~Eli~D~~ 438 (460)
....++++.++...|...+|+.|+.+|||+.||++++.|..++. .....+|+|....++ ++.++.++++++.
T Consensus 78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~ 152 (224)
T TIGR02479 78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLIDRIEDDK 152 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcccCCCccchhhhhccccc
Confidence 88999999999999999999999999999999999999999985 344578898876543 3346666666433
No 32
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=99.83 E-value=1.1e-19 Score=176.44 Aligned_cols=143 Identities=31% Similarity=0.451 Sum_probs=127.3
Q ss_pred ccHHHHHHHHHHhHHHHHHHHHHcc---CCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcC
Q 012567 282 YGILCKDKMITSNIRLVISIAKNYQ---GAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS 358 (460)
Q Consensus 282 ~G~~A~e~LI~~nlrLV~~IAkry~---~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~ 358 (460)
.|.-+++.|+..|.++|+++|++|. +++.+++||+||||+|||+++++||+..|.+|+||+++||+|.|++++|++.
T Consensus 5 ~~~~~~~~L~~~~~~~v~~~a~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~~~lR~~~ 84 (236)
T PRK06986 5 EGKMDQDELVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLD 84 (236)
T ss_pred cccccHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHcC
Confidence 4677899999999999999999997 6789999999999999999999999998999999999999999999999976
Q ss_pred cccccCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhC--CCCCcccccccccCCC
Q 012567 359 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLS--PKAPRSLDQKIGINQN 427 (460)
Q Consensus 359 r~iriP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~--ar~~lSLD~~v~~e~d 427 (460)
+ +|..+.....++.++...+...++++|+.+|||+.||++.++|..++.. ....+|++..++++++
T Consensus 85 ~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~~ 152 (236)
T PRK06986 85 W---VPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGD 152 (236)
T ss_pred C---CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccccCCCc
Confidence 4 6777777777888899999999999999999999999999999988863 3456789988765444
No 33
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=99.81 E-value=6.1e-19 Score=171.05 Aligned_cols=161 Identities=25% Similarity=0.357 Sum_probs=129.3
Q ss_pred HHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHHHH
Q 012567 213 PLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMI 291 (460)
Q Consensus 213 ~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~LI 291 (460)
.+. |+.++ +..|+||+++|..|...++. ++..|++.|+
T Consensus 17 ~~~~~~~~~-~~~~~~~~~~e~~l~~~~~~----------------------------------------gd~~a~~~l~ 55 (233)
T PRK05803 17 FLVSYVKNN-SFPQPLSEEEERKYLELMKE----------------------------------------GDEEARNILI 55 (233)
T ss_pred HHHHHHHHh-cccCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHH
Confidence 345 99999 88999999999888776653 2378999999
Q ss_pred HHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccc---cc-----
Q 012567 292 TSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI---RL----- 363 (460)
Q Consensus 292 ~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~i---ri----- 363 (460)
..|.++|++++.+|.+++.+++|++|||++++|+++++|++.+|.+|.||+++|++|.+++++|+..+.. ..
T Consensus 56 ~~y~~~l~~~a~~~~~~~~daeDlvQE~fi~l~~~~~~f~~~~~~~f~~wl~~i~rn~~id~~Rk~~~~~~~~~~~~~~~ 135 (233)
T PRK05803 56 ERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRNLKKTKKEVSLQDPIG 135 (233)
T ss_pred HHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHHhccccCCCcccccc
Confidence 9999999999999999999999999999999999999999988889999999999999999998754311 00
Q ss_pred --------------Cc---ch------HHHHHHHHHHHHHHHHH--------h----CCCCCHHHHHHHhCCCHHHHHHH
Q 012567 364 --------------PF---HM------VEATYRVKEARKQLYSE--------N----GRHPNNEEVAEATGLSMKRLHAV 408 (460)
Q Consensus 364 --------------P~---~~------~e~i~kl~ka~~~L~~~--------~----gr~pS~eEIAe~LGIS~e~Vk~~ 408 (460)
+. .. ......+.+++..|+.. + ..+.|++|||+.||+|.++|+..
T Consensus 136 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~ 215 (233)
T PRK05803 136 VDKEGNEISLIDILGSEEDDVIEQVELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRI 215 (233)
T ss_pred CCCCcCcccHHHHccCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHH
Confidence 00 00 01223466666666553 2 35679999999999999999999
Q ss_pred HhCCCC
Q 012567 409 LLSPKA 414 (460)
Q Consensus 409 l~~ar~ 414 (460)
++++..
T Consensus 216 ~~rA~~ 221 (233)
T PRK05803 216 EKRALK 221 (233)
T ss_pred HHHHHH
Confidence 876654
No 34
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=99.72 E-value=7.6e-17 Score=156.10 Aligned_cols=131 Identities=25% Similarity=0.413 Sum_probs=107.6
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccc-
Q 012567 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR- 362 (460)
Q Consensus 284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~ir- 362 (460)
..|++.++..|.++|+.+|++|.+++.+++|++||+|+++|+++++|++..+++|.||++++++|.|++++|++.+...
T Consensus 51 ~~af~~l~~~y~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~~d~lRk~~~~~~~ 130 (234)
T PRK08301 51 EAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLRRNNKVKAE 130 (234)
T ss_pred HHHHHHHHHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHHHHHHhccccc
Confidence 7899999999999999999999999999999999999999999999998877889999999999999999997543210
Q ss_pred --c--C-----------------c--ch-------HHHHHHHHHHHHHHHHH--------h----CCCCCHHHHHHHhCC
Q 012567 363 --L--P-----------------F--HM-------VEATYRVKEARKQLYSE--------N----GRHPNNEEVAEATGL 400 (460)
Q Consensus 363 --i--P-----------------~--~~-------~e~i~kl~ka~~~L~~~--------~----gr~pS~eEIAe~LGI 400 (460)
+ + . .. ......+.+++..|+.+ + -.+.|++|||+.||+
T Consensus 131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgi 210 (234)
T PRK08301 131 VSFDEPLNIDWDGNELLLSDVLGTDNDIIYKDIEDEVDRKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGI 210 (234)
T ss_pred cccccccccccCCCcccHHHhccCcccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCC
Confidence 0 0 0 00 01123467777777654 2 368899999999999
Q ss_pred CHHHHHHHHhCCCC
Q 012567 401 SMKRLHAVLLSPKA 414 (460)
Q Consensus 401 S~e~Vk~~l~~ar~ 414 (460)
|+++|+..+++++.
T Consensus 211 s~~tVk~~~~rA~~ 224 (234)
T PRK08301 211 SQSYISRLEKRIIK 224 (234)
T ss_pred CHHHHHHHHHHHHH
Confidence 99999999887754
No 35
>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=99.72 E-value=7.2e-17 Score=156.10 Aligned_cols=128 Identities=16% Similarity=0.216 Sum_probs=109.8
Q ss_pred HHhccHHHHHHHHHHhHHHHHHHHHHccCCC--CCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhh
Q 012567 279 RLNYGILCKDKMITSNIRLVISIAKNYQGAG--MNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD 356 (460)
Q Consensus 279 ~l~~G~~A~e~LI~~nlrLV~~IAkry~~~g--~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk 356 (460)
.++.|...++.||..|.|+|.++|++|.+++ .+.+|++|+|++|||+|+++||+++|.+|.||+.+||++.|++++|+
T Consensus 3 ~~~~gd~~~e~LI~~Y~plI~~~a~~~~~~~~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~sya~~~Ir~~i~dylRk 82 (218)
T TIGR02895 3 PIQPGNEEREELIRQYKPFIAKIVSSVCGRYIDTKSDDELSIGLIAFNEAIESYDSNKGKSFLSFAKLIIKRRLIDYIRK 82 (218)
T ss_pred hhhcCChHHHHHHHHhHHHHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence 3556744499999999999999999998765 58999999999999999999999999999999999999999999998
Q ss_pred cC---cccccCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHH------HhCCCHHHHH
Q 012567 357 QS---RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAE------ATGLSMKRLH 406 (460)
Q Consensus 357 ~~---r~iriP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe------~LGIS~e~Vk 406 (460)
.. ..+++|....+....+..+..++..+.++.|+.+||+. ..|||.+++-
T Consensus 83 ~~k~~~~v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~~~~~L~~~gi~~~dLv 141 (218)
T TIGR02895 83 NQKYQNLLYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILEYKKLLKQFGIEFVELV 141 (218)
T ss_pred cccccCeeeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcCCcHHHHh
Confidence 76 45678876666666788888888889999999999996 3578766653
No 36
>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=99.71 E-value=1.4e-16 Score=154.00 Aligned_cols=131 Identities=23% Similarity=0.360 Sum_probs=106.6
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccc-
Q 012567 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR- 362 (460)
Q Consensus 284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~ir- 362 (460)
..|++.|+..|.++|+++|.+|.++..+++|++||+|+++|+++++|++..+.+|.||++++++|.|++++|+..+..+
T Consensus 47 ~~af~~l~~~y~~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~~d~~Rk~~r~~~~ 126 (227)
T TIGR02846 47 EEARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEILMHLRALKKTKGE 126 (227)
T ss_pred HHHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHHHHHHHHHhccccc
Confidence 7899999999999999999999999999999999999999999999999888889999999999999999987543210
Q ss_pred c---------------------Cc---c------hHHHHHHHHHHHHHHHHH--------h----CCCCCHHHHHHHhCC
Q 012567 363 L---------------------PF---H------MVEATYRVKEARKQLYSE--------N----GRHPNNEEVAEATGL 400 (460)
Q Consensus 363 i---------------------P~---~------~~e~i~kl~ka~~~L~~~--------~----gr~pS~eEIAe~LGI 400 (460)
. +. . ..+....+.+++..|+.. + ..+.|++|||+.||+
T Consensus 127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgi 206 (227)
T TIGR02846 127 VSLQDPIGVDKEGNEISLIDILGSDGDSVIEQVELNLEIKKLYKKLSVLDGREREVIEMRYGLGDGRRKTQREIAKILGI 206 (227)
T ss_pred eeccccccCCcccCcccHHHHhcCCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCC
Confidence 0 00 0 011223466666666553 2 256899999999999
Q ss_pred CHHHHHHHHhCCCC
Q 012567 401 SMKRLHAVLLSPKA 414 (460)
Q Consensus 401 S~e~Vk~~l~~ar~ 414 (460)
|+++|+..++++..
T Consensus 207 s~~tV~~~~~rAl~ 220 (227)
T TIGR02846 207 SRSYVSRIEKRALM 220 (227)
T ss_pred CHHHHHHHHHHHHH
Confidence 99999999887654
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=99.68 E-value=6.8e-16 Score=149.97 Aligned_cols=131 Identities=25% Similarity=0.379 Sum_probs=107.6
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccc-
Q 012567 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR- 362 (460)
Q Consensus 284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~ir- 362 (460)
..|++.++..|.+.|+.+|++|.+++.+++|++||+|+++|+++++|++..+++|.||++++++|.+++++|++.+...
T Consensus 51 ~~a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~~d~~Rk~~r~~~~ 130 (234)
T TIGR02835 51 ESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEILMYLRRNNKTRSE 130 (234)
T ss_pred HHHHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHhccccCc
Confidence 7899999999999999999999999999999999999999999999998877889999999999999999997654210
Q ss_pred cC----------------------c-----ch---HHHHHHHHHHHHHHHHH--------h----CCCCCHHHHHHHhCC
Q 012567 363 LP----------------------F-----HM---VEATYRVKEARKQLYSE--------N----GRHPNNEEVAEATGL 400 (460)
Q Consensus 363 iP----------------------~-----~~---~e~i~kl~ka~~~L~~~--------~----gr~pS~eEIAe~LGI 400 (460)
.+ . .. ......+.+++..|+.+ + ..+.|++|||+.||+
T Consensus 131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgi 210 (234)
T TIGR02835 131 VSFDEPLNVDWDGNELLLSDVLGTDSDIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGTEKTQKEVADMLGI 210 (234)
T ss_pred ccccccccCCCCCCcchHHHhcCCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCC
Confidence 00 0 00 01223477777777653 2 257899999999999
Q ss_pred CHHHHHHHHhCCCC
Q 012567 401 SMKRLHAVLLSPKA 414 (460)
Q Consensus 401 S~e~Vk~~l~~ar~ 414 (460)
|+++|+..+++++.
T Consensus 211 s~~tV~~~l~ra~~ 224 (234)
T TIGR02835 211 SQSYISRLEKRILK 224 (234)
T ss_pred CHHHHHHHHHHHHH
Confidence 99999999887654
No 38
>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=99.66 E-value=8.2e-16 Score=143.96 Aligned_cols=145 Identities=19% Similarity=0.258 Sum_probs=113.7
Q ss_pred CCHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHH
Q 012567 271 VDQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA 349 (460)
Q Consensus 271 ~de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a 349 (460)
|++..|+..+..| ..|++.|+..|.+.|+.+|+++.++..+++|++||+|+++|+++.+|++..+..|.||++.+|++.
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 4567778888888 999999999999999999999999999999999999999999999999887779999999999999
Q ss_pred HHHHhhhcCcccc--------------------------------cCcch---HHHHHHHHHHHHHHHHH--------hC
Q 012567 350 VRKSLSDQSRTIR--------------------------------LPFHM---VEATYRVKEARKQLYSE--------NG 386 (460)
Q Consensus 350 I~~~Lrk~~r~ir--------------------------------iP~~~---~e~i~kl~ka~~~L~~~--------~g 386 (460)
+++++++..+..+ -|... .+....+.+++..|+.. +-
T Consensus 84 ~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~~~~~ 163 (198)
T TIGR02859 84 IITAIKTATRQKHIPLNSYVSLNKPIYDEESDRTLLDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVLQSYL 163 (198)
T ss_pred HHHHHHHHHHhcccchhhhcCcccccccccccchHHHHhhccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence 9888864211000 00000 11223355566654322 22
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLLSPKAP 415 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~ 415 (460)
.+.|++|||+.||+|+++|+..+++++..
T Consensus 164 ~~~s~~eIA~~l~~s~~tV~~~l~r~r~~ 192 (198)
T TIGR02859 164 DGKSYQEIACDLNRHVKSIDNALQRVKRK 192 (198)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 78899999999999999999999877653
No 39
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=99.66 E-value=8.6e-16 Score=143.17 Aligned_cols=144 Identities=17% Similarity=0.207 Sum_probs=117.2
Q ss_pred CCHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHH
Q 012567 271 VDQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA 349 (460)
Q Consensus 271 ~de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a 349 (460)
+++..|+..+..| ..|++.|+..|.++|+.+|++|.+++.+++|++||+|+++|+++.+|++. +..|.+|++.+++|.
T Consensus 5 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n~ 83 (186)
T PRK05602 5 DPDEELLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLNL 83 (186)
T ss_pred ccHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHHH
Confidence 4566777777777 99999999999999999999999999999999999999999999999975 458999999999999
Q ss_pred HHHHhhhcCcccc--cCc---------c---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHH
Q 012567 350 VRKSLSDQSRTIR--LPF---------H---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHA 407 (460)
Q Consensus 350 I~~~Lrk~~r~ir--iP~---------~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~ 407 (460)
+.+++|++..... ++. . ..+....+.+++..|+.+.+ .+.+++|||+.||+|..+|+.
T Consensus 84 ~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~ 163 (186)
T PRK05602 84 CYDRLRRRREVPVEDAPDVPDPAPGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALES 163 (186)
T ss_pred HHHHHHhcCCCCcccccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHhcCCCHHHHHHHhCcCHHHHHH
Confidence 9999997653211 110 0 01233456677776665433 788999999999999999999
Q ss_pred HHhCCCCC
Q 012567 408 VLLSPKAP 415 (460)
Q Consensus 408 ~l~~ar~~ 415 (460)
.+++++..
T Consensus 164 ~l~Rar~~ 171 (186)
T PRK05602 164 LLARGRRA 171 (186)
T ss_pred HHHHHHHH
Confidence 99988754
No 40
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=99.64 E-value=1.9e-15 Score=142.72 Aligned_cols=145 Identities=21% Similarity=0.267 Sum_probs=111.9
Q ss_pred CCHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHH
Q 012567 271 VDQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA 349 (460)
Q Consensus 271 ~de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a 349 (460)
++...|+..++.| ..+++.|+..|.++|+.+|++|.++..+++|++||++++||+++.+|++.++.+|.||++.+++|.
T Consensus 9 ~~~~~l~~~~~~~d~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~~n~ 88 (208)
T PRK08295 9 LEDEELVELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQ 88 (208)
T ss_pred CChHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHH
Confidence 4566677777777 999999999999999999999999999999999999999999999999987789999999999999
Q ss_pred HHHHhhhcCcccccC-----------------------------cch------HHHHHHHH-HHHHHHHHH-------hC
Q 012567 350 VRKSLSDQSRTIRLP-----------------------------FHM------VEATYRVK-EARKQLYSE-------NG 386 (460)
Q Consensus 350 I~~~Lrk~~r~iriP-----------------------------~~~------~e~i~kl~-ka~~~L~~~-------~g 386 (460)
+++++++..+..+.+ ... .+....+. .+...|+.. +-
T Consensus 89 ~~d~~r~~~r~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~~r~vl~l~~ 168 (208)
T PRK08295 89 IITAIKTANRQKHIPLNSYVSLDKPIYDEESDRTLLDVISEAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLELYL 168 (208)
T ss_pred HHHHHHHhhhhccccccceeecCCcccCCccchhHHHHhcCcccCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence 999987532211110 000 00111221 222333322 34
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLLSPKAP 415 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~ 415 (460)
.+.+++|||+.||+|+++|+..+++++..
T Consensus 169 e~~s~~EIA~~lgis~~tV~~~l~rar~~ 197 (208)
T PRK08295 169 DGKSYQEIAEELNRHVKSIDNALQRVKRK 197 (208)
T ss_pred ccCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 78999999999999999999999887654
No 41
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=99.64 E-value=1.4e-15 Score=143.15 Aligned_cols=143 Identities=14% Similarity=0.102 Sum_probs=115.0
Q ss_pred CHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHH
Q 012567 272 DQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAV 350 (460)
Q Consensus 272 de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI 350 (460)
+...|+..+..| ..+++.|+..|.++|+++|.+|.++..+++|++||+|+++|+.+.+|++.+| .|.+|++.+++|.+
T Consensus 16 ~~~~li~~~~~g~~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi~l~~~~~~~~~~~~-~~~~wl~~ia~n~~ 94 (194)
T PRK09646 16 DLDALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SALAWLLTLAHRRA 94 (194)
T ss_pred cHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCcccc-cHHHHHHHHHHHHH
Confidence 455677777777 9999999999999999999999999999999999999999999999998655 79999999999999
Q ss_pred HHHhhhcCccccc---------Cc---ch------HHHHHHHHHHHHHHHHHh--------CCCCCHHHHHHHhCCCHHH
Q 012567 351 RKSLSDQSRTIRL---------PF---HM------VEATYRVKEARKQLYSEN--------GRHPNNEEVAEATGLSMKR 404 (460)
Q Consensus 351 ~~~Lrk~~r~iri---------P~---~~------~e~i~kl~ka~~~L~~~~--------gr~pS~eEIAe~LGIS~e~ 404 (460)
++++|++.+..+. .. .. .+....+..++..|+... -.+.+++|||+.||+|+++
T Consensus 95 ~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~EIA~~Lgis~~t 174 (194)
T PRK09646 95 VDRVRSEQAASQREVRYGARNVDPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAYYGGLTYREVAERLAVPLGT 174 (194)
T ss_pred HHHHHhhccccccccccccccccccccchHHHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCChHh
Confidence 9999976431111 00 00 112234666666665542 3789999999999999999
Q ss_pred HHHHHhCCCCC
Q 012567 405 LHAVLLSPKAP 415 (460)
Q Consensus 405 Vk~~l~~ar~~ 415 (460)
|+..+++++..
T Consensus 175 Vk~~l~ra~~~ 185 (194)
T PRK09646 175 VKTRMRDGLIR 185 (194)
T ss_pred HHHHHHHHHHH
Confidence 99999887653
No 42
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=99.63 E-value=2.8e-15 Score=140.61 Aligned_cols=143 Identities=14% Similarity=0.152 Sum_probs=116.5
Q ss_pred CCHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHH
Q 012567 271 VDQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA 349 (460)
Q Consensus 271 ~de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a 349 (460)
+++..|+..++.| ..|++.|+..|.+.|+++|+++.++..+.+|++||+|+++|+++.+|++. ..|.+|++++++|.
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 4566777777777 99999999999999999999999999999999999999999999999964 47999999999999
Q ss_pred HHHHhhhcCcccccCc-----------------c---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCC
Q 012567 350 VRKSLSDQSRTIRLPF-----------------H---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLS 401 (460)
Q Consensus 350 I~~~Lrk~~r~iriP~-----------------~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS 401 (460)
+++++|+..+....+. . ..+....+..++..|+...+ .+.|++|||+.||+|
T Consensus 89 ~~~~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis 168 (194)
T PRK12513 89 LIDHWRRHGARQAPSLDADEQLHALADDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVP 168 (194)
T ss_pred HHHHHHHhccccccccccchhhhhcCCCCCCHHHHHHHHHHHHHHHHHHHhCCHhHhhheeeehccCCCHHHHHHHHCCC
Confidence 9999997654322110 0 01123446677777766533 678999999999999
Q ss_pred HHHHHHHHhCCCCC
Q 012567 402 MKRLHAVLLSPKAP 415 (460)
Q Consensus 402 ~e~Vk~~l~~ar~~ 415 (460)
+++|+..+++++..
T Consensus 169 ~~tV~~~l~ra~~~ 182 (194)
T PRK12513 169 EETVKSRLRYALQK 182 (194)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999877654
No 43
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=99.62 E-value=3.6e-15 Score=139.75 Aligned_cols=144 Identities=15% Similarity=0.154 Sum_probs=115.0
Q ss_pred CCHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCC---CCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHH
Q 012567 271 VDQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAG---MNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWI 346 (460)
Q Consensus 271 ~de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g---~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wI 346 (460)
+++..|+..+..| ..|++.|+..|.+.|++++.++.+++ .+++|++||+++++|+++++|++..+ .|.+|++.++
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 5677788888888 89999999999999999999998753 47999999999999999999997544 7999999999
Q ss_pred HHHHHHHhhhcCcccccC---c-------c------hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCH
Q 012567 347 KQAVRKSLSDQSRTIRLP---F-------H------MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSM 402 (460)
Q Consensus 347 r~aI~~~Lrk~~r~iriP---~-------~------~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~ 402 (460)
+|.+++++|++.+..... . . ..+....+.+++..|+.+.+ .+.+++|||+.||+|.
T Consensus 82 rn~~~d~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIAe~lgis~ 161 (189)
T PRK06811 82 KYKAIDYKRKLTKNNEIDSIDEFILISEESIENEIILKENKEEILKLINDLEKLDREIFIRRYLLGEKIEEIAKKLGLTR 161 (189)
T ss_pred HHHHHHHHHHhccccccccchhhhhcccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHccCCHHHHHHHHCCCH
Confidence 999999999765422111 0 0 11223346666666655422 7899999999999999
Q ss_pred HHHHHHHhCCCCC
Q 012567 403 KRLHAVLLSPKAP 415 (460)
Q Consensus 403 e~Vk~~l~~ar~~ 415 (460)
.+|+..+++++..
T Consensus 162 ~~V~~~l~Ra~~~ 174 (189)
T PRK06811 162 SAIDNRLSRGRKK 174 (189)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999877653
No 44
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=99.61 E-value=5.8e-15 Score=137.95 Aligned_cols=140 Identities=19% Similarity=0.209 Sum_probs=111.5
Q ss_pred HHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCC----CCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHH
Q 012567 274 RELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGA----GMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQ 348 (460)
Q Consensus 274 ~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~----g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~ 348 (460)
..|+..+..| ..|++.|+..|.+.|+.+|.++.++ +.+++|++||+|+++|+++.+|++. +..|.+|++.+++|
T Consensus 12 ~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~~~~wl~~i~~n 90 (189)
T PRK09648 12 DALVAEAVAGDRRALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITALPRYRDQ-GRPFLAFVYGIAAH 90 (189)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHHHHHHhcc-CCcHHHHHHHHHHH
Confidence 4466777777 9999999999999999999998764 4689999999999999999999864 45899999999999
Q ss_pred HHHHHhhhcCccccc-----Cc------c------hHHHHHHHHHHHHHHHHHh--------CCCCCHHHHHHHhCCCHH
Q 012567 349 AVRKSLSDQSRTIRL-----PF------H------MVEATYRVKEARKQLYSEN--------GRHPNNEEVAEATGLSMK 403 (460)
Q Consensus 349 aI~~~Lrk~~r~iri-----P~------~------~~e~i~kl~ka~~~L~~~~--------gr~pS~eEIAe~LGIS~e 403 (460)
.+++++|++.+.... +. . ..+....+.+++..|+... -.+.+++|||+.||+|+.
T Consensus 91 ~~~d~~r~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~ 170 (189)
T PRK09648 91 KVADAHRAAGRDKAVPTEEVPERPSDDAGPEERALRSESSNRMRELLDTLPEKQREILILRVVVGLSAEETAEAVGSTPG 170 (189)
T ss_pred HHHHHHHHhCCCccccccccccccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHH
Confidence 999999986642211 10 0 1122334667777766643 378999999999999999
Q ss_pred HHHHHHhCCCC
Q 012567 404 RLHAVLLSPKA 414 (460)
Q Consensus 404 ~Vk~~l~~ar~ 414 (460)
+|+..+++++.
T Consensus 171 tV~~~l~Ra~~ 181 (189)
T PRK09648 171 AVRVAQHRALA 181 (189)
T ss_pred HHHHHHHHHHH
Confidence 99999987754
No 45
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=99.60 E-value=5.3e-15 Score=137.52 Aligned_cols=144 Identities=17% Similarity=0.139 Sum_probs=114.9
Q ss_pred CCHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHH
Q 012567 271 VDQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA 349 (460)
Q Consensus 271 ~de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a 349 (460)
+++..|...++.| ..+++.|+..|.+.|+.++++|.+++.+++|++||+++++|+++++|++.. ..|.+|++++++|.
T Consensus 8 ~~~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~-~~~~~wl~~ia~n~ 86 (186)
T PRK13919 8 LSDEALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRR-GSARAWLLALAHHA 86 (186)
T ss_pred cCHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCccc-cchHHHHHHHHHHH
Confidence 3566777777777 999999999999999999999999999999999999999999999998654 36999999999999
Q ss_pred HHHHhhhcCcccc-c------C------cc-----hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHH
Q 012567 350 VRKSLSDQSRTIR-L------P------FH-----MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMK 403 (460)
Q Consensus 350 I~~~Lrk~~r~ir-i------P------~~-----~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e 403 (460)
+++++|++.+... + + .. .......+.+++..|+...+ .+.+++|||+.||+|++
T Consensus 87 ~~d~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~ 166 (186)
T PRK13919 87 AVDHVRRRAARPQPLEPDEREPEAFDLPGPGLDEEGHLDRTRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLG 166 (186)
T ss_pred HHHHHHhhhcccccccccccccccccCCCccccHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHH
Confidence 9999997543210 1 0 00 01112346677777665433 78899999999999999
Q ss_pred HHHHHHhCCCCC
Q 012567 404 RLHAVLLSPKAP 415 (460)
Q Consensus 404 ~Vk~~l~~ar~~ 415 (460)
+|+..+++++..
T Consensus 167 ~V~~~l~ra~~~ 178 (186)
T PRK13919 167 TLKTRARRALSR 178 (186)
T ss_pred HHHHHHHHHHHH
Confidence 999999887653
No 46
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=99.60 E-value=4.8e-15 Score=133.38 Aligned_cols=129 Identities=16% Similarity=0.155 Sum_probs=104.2
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcc---
Q 012567 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT--- 360 (460)
Q Consensus 284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~--- 360 (460)
..+++.|+..|.++|+.+++++ ++..+++|++||+++++|+++++|++..+ .|.+|++.+++|.+++++|++.+.
T Consensus 3 ~~af~~l~~~y~~~l~~~~~~~-~~~~~aeDi~Qe~~l~l~~~~~~~~~~~~-~f~~wl~~i~~n~~ld~~rk~~~~~~~ 80 (154)
T PRK06759 3 PATFTEAVVLYEGLIVNQIKKL-GIYQDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYILERLKKEFAVQEK 80 (154)
T ss_pred cccHHHHHHHHHHHHHHHHHHh-CCcccHHHHHHHHHHHHHHHHHHhCccCC-chHHHHHHHHHHHHHHHHHHHHhhccc
Confidence 3579999999999999999986 56679999999999999999999997666 799999999999999999986421
Q ss_pred ---cccCcc---hHHHHHHHHHHHHHHHHH--------hCCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567 361 ---IRLPFH---MVEATYRVKEARKQLYSE--------NGRHPNNEEVAEATGLSMKRLHAVLLSPKA 414 (460)
Q Consensus 361 ---iriP~~---~~e~i~kl~ka~~~L~~~--------~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~ 414 (460)
...|.. ..+....+..++..|+.. +..+.|++|||+.||+|+++|+..+++++.
T Consensus 81 ~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~ii~l~~~~~~s~~EIA~~l~is~~tV~~~~~ra~~ 148 (154)
T PRK06759 81 CVCVGEYEDHFHFEDVEMKVKDFMSVLDEKEKYIIFERFFVGKTMGEIALETEMTYYQVRWIYRQALE 148 (154)
T ss_pred ccccCCCcccccHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 111221 223345577777776554 347899999999999999999999987654
No 47
>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=99.60 E-value=7.8e-15 Score=134.53 Aligned_cols=143 Identities=14% Similarity=0.138 Sum_probs=115.0
Q ss_pred CCHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHH
Q 012567 271 VDQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA 349 (460)
Q Consensus 271 ~de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a 349 (460)
|++..++..+..| ..|++.++..|.+.|++++.++.++..+++|++||+++.+|+.+++|++. ..|.+|++.+++|.
T Consensus 1 ~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~--~~~~~wl~~i~~n~ 78 (169)
T TIGR02954 1 MNDEELVKKAKRGNKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHP--KYFNTWLTRILINE 78 (169)
T ss_pred CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCc--cccHHHHHHHHHHH
Confidence 4556677777777 99999999999999999999999999999999999999999999999964 37999999999999
Q ss_pred HHHHhhhcCcccccCcc----------hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhC
Q 012567 350 VRKSLSDQSRTIRLPFH----------MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 350 I~~~Lrk~~r~iriP~~----------~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
+++++|+..+....+.. ..+....+..+...|+...+ .+.+++|||+.||+|+++|+..+++
T Consensus 79 ~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eiA~~lgis~~tv~~~l~R 158 (169)
T TIGR02954 79 CIDLLKKKKKVIPFDPNTSIEKGECETHADSRLDLYKAIDTLNDKYQTAIILRYYHDLTIKEIAEVMNKPEGTVKTYLHR 158 (169)
T ss_pred HHHHHHhcCCcCccccccccccchhhhchHHHHHHHHHHHhCCHHHhHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 99999986643222110 01112246666666655433 7889999999999999999999988
Q ss_pred CCCC
Q 012567 412 PKAP 415 (460)
Q Consensus 412 ar~~ 415 (460)
++..
T Consensus 159 a~~~ 162 (169)
T TIGR02954 159 ALKK 162 (169)
T ss_pred HHHH
Confidence 7653
No 48
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=99.60 E-value=9.1e-15 Score=136.81 Aligned_cols=144 Identities=14% Similarity=0.149 Sum_probs=116.5
Q ss_pred CCCHHHHHHHHhc----cHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHH
Q 012567 270 GVDQRELRRRLNY----GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWW 345 (460)
Q Consensus 270 g~de~~L~~~l~~----G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~w 345 (460)
.+++..|+..++. +..|++.|+..|.+.|+.++.+|.++..+++|++||+|+++|+++++|++ ...|.+|++++
T Consensus 7 ~~~~~~li~~~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~~~~~~~~--~~~~~~wl~~i 84 (188)
T PRK09640 7 ELNDEELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEG--KSKFKTWLYSI 84 (188)
T ss_pred CCCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHH
Confidence 3566777777763 39999999999999999999999999999999999999999999999985 34799999999
Q ss_pred HHHHHHHHhhhcCcccccC---------c---c---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCH
Q 012567 346 IKQAVRKSLSDQSRTIRLP---------F---H---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSM 402 (460)
Q Consensus 346 Ir~aI~~~Lrk~~r~iriP---------~---~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~ 402 (460)
++|.+++++|+..+..... . . ..+....+.++...|+...+ .+.+++|||+.||+|.
T Consensus 85 a~n~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~lgis~ 164 (188)
T PRK09640 85 TYNECITQYRKERRKRRLMDALSLDPLEEASEEKAPKPEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMGL 164 (188)
T ss_pred HHHHHHHHHHHhcccccCcchhhhcccccccccccccHHHHHHHHHHHHhcChhheeeeeeHHhcCCCHHHHHHHHCCCH
Confidence 9999999999754321110 0 0 11233557777777776543 6789999999999999
Q ss_pred HHHHHHHhCCCCC
Q 012567 403 KRLHAVLLSPKAP 415 (460)
Q Consensus 403 e~Vk~~l~~ar~~ 415 (460)
++|+..+++++..
T Consensus 165 ~tV~~~l~Ra~~~ 177 (188)
T PRK09640 165 SATKMRYKRALDK 177 (188)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999887653
No 49
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=99.60 E-value=6.7e-15 Score=136.21 Aligned_cols=143 Identities=13% Similarity=0.122 Sum_probs=113.6
Q ss_pred CHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHH
Q 012567 272 DQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAV 350 (460)
Q Consensus 272 de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI 350 (460)
+...|+..+..| ..++..|+..|.+.|+.+|.++.++..+++|++||+|+++|+++++|++.. ..|.||++..++|.+
T Consensus 5 ~~~~li~~~~~g~~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~~-~~~~~wl~~ia~n~~ 83 (179)
T PRK12514 5 DIEKLIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSG-LSPMTWLITIARNHA 83 (179)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHH
Confidence 445566666666 899999999999999999999999999999999999999999999998654 469999999999999
Q ss_pred HHHhhhcCccc-cc------------Ccch---HHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHH
Q 012567 351 RKSLSDQSRTI-RL------------PFHM---VEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLH 406 (460)
Q Consensus 351 ~~~Lrk~~r~i-ri------------P~~~---~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk 406 (460)
++++|++.+.. .+ |... .+....+..++..|+...+ .+.|++|||+.||+|+++|+
T Consensus 84 ~d~~R~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tV~ 163 (179)
T PRK12514 84 IDRLRARKAVAVDIDEAHDLADPSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMR 163 (179)
T ss_pred HHHHHhcCCcccccccchhccccCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCChHHHH
Confidence 99998765321 00 0000 1122346666666665433 68899999999999999999
Q ss_pred HHHhCCCCC
Q 012567 407 AVLLSPKAP 415 (460)
Q Consensus 407 ~~l~~ar~~ 415 (460)
..+++++..
T Consensus 164 ~~l~Rar~~ 172 (179)
T PRK12514 164 TWLRRSLLK 172 (179)
T ss_pred HHHHHHHHH
Confidence 999987653
No 50
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=99.59 E-value=7.7e-15 Score=136.62 Aligned_cols=144 Identities=13% Similarity=0.131 Sum_probs=115.9
Q ss_pred CCHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHH
Q 012567 271 VDQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA 349 (460)
Q Consensus 271 ~de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a 349 (460)
++...|+..+..| ..+++.|+..|.+.|+.+++++.++..+.+|++||+|+.+|+.+++|++.. ..|.+|++.+++|.
T Consensus 8 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~-~~~~~wL~~iarn~ 86 (182)
T PRK12537 8 FDYEACLLACARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPAR-GSARGWIYSVTRHL 86 (182)
T ss_pred hhHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCccc-ccHHHHHHHHHHHH
Confidence 3445677777777 999999999999999999999999999999999999999999999998643 47999999999999
Q ss_pred HHHHhhhcCcccccCc----------c------hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHH
Q 012567 350 VRKSLSDQSRTIRLPF----------H------MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRL 405 (460)
Q Consensus 350 I~~~Lrk~~r~iriP~----------~------~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~V 405 (460)
+++++|++.+...... . ..+....+.+++..|+.+.+ .+.+++|||+.||+|+++|
T Consensus 87 ~~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~~~s~~eIA~~lgis~~tV 166 (182)
T PRK12537 87 ALNVLRDTRREVVLDDDAEETAQTLHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTV 166 (182)
T ss_pred HHHHHHhccccCccccchhhhcccccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCChhhH
Confidence 9999998764321110 0 01223456667776665433 7889999999999999999
Q ss_pred HHHHhCCCCC
Q 012567 406 HAVLLSPKAP 415 (460)
Q Consensus 406 k~~l~~ar~~ 415 (460)
+..+++++..
T Consensus 167 ~~~l~ra~~~ 176 (182)
T PRK12537 167 KAWIKRSLKA 176 (182)
T ss_pred HHHHHHHHHH
Confidence 9999877643
No 51
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=99.59 E-value=7.2e-15 Score=138.53 Aligned_cols=145 Identities=17% Similarity=0.151 Sum_probs=117.2
Q ss_pred CCHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHH
Q 012567 271 VDQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA 349 (460)
Q Consensus 271 ~de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a 349 (460)
+++..|+..+..| ..|++.|+..|.+.|+.+|.++.++..+++|++||+++++|+.+.+|++. ...|.+|++..++|.
T Consensus 11 ~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~-~~~~~~wl~~ia~n~ 89 (196)
T PRK12524 11 VSDEALLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQG-EARVSTWLYRVVCNL 89 (196)
T ss_pred cCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhccccc-cchHHHHHHHHHHHH
Confidence 4667788877877 99999999999999999999999999999999999999999999999853 347999999999999
Q ss_pred HHHHhhhcCcc-ccc---C---------cc---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHH
Q 012567 350 VRKSLSDQSRT-IRL---P---------FH---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRL 405 (460)
Q Consensus 350 I~~~Lrk~~r~-iri---P---------~~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~V 405 (460)
+++++|++.+. ..+ + .. ..+....+.+++..|+.+.+ .+.+++|||+.||+|..+|
T Consensus 90 ~~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~L~~~~g~s~~eIA~~lgis~~tV 169 (196)
T PRK12524 90 CTDRLRRRRRASVDLDDAPEPADAAPGAEEALIEGDRMRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAV 169 (196)
T ss_pred HHHHHHhhcCCCCCccccccccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHH
Confidence 99999975432 110 0 00 11223456667777665433 7899999999999999999
Q ss_pred HHHHhCCCCCc
Q 012567 406 HAVLLSPKAPR 416 (460)
Q Consensus 406 k~~l~~ar~~l 416 (460)
+..+++++..+
T Consensus 170 ~~~l~Ra~~~L 180 (196)
T PRK12524 170 ESLTARGKRAL 180 (196)
T ss_pred HHHHHHHHHHH
Confidence 99999887654
No 52
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=99.59 E-value=1.2e-14 Score=140.98 Aligned_cols=130 Identities=18% Similarity=0.154 Sum_probs=107.3
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccccc
Q 012567 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL 363 (460)
Q Consensus 284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iri 363 (460)
..+++.|+..|.+.|+.+++++.+++.+++|++||+|+++|+.+++|++. ..|.+|++..++|.+++++|+..+....
T Consensus 29 ~~a~~~l~~~y~~~l~~~a~~~~~~~~~AEDlvQE~fi~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~Rk~~r~~~~ 106 (231)
T PRK11922 29 EAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGD--ASLSTWLSRIVLNEALGRLRRRRRLVNL 106 (231)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHhcCCC--chhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 78999999999999999999999999999999999999999999999975 4799999999999999999976542221
Q ss_pred Cc-----------------------c---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHH
Q 012567 364 PF-----------------------H---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVL 409 (460)
Q Consensus 364 P~-----------------------~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l 409 (460)
+. . ..+....+.+++..|+...+ .+.+++|||+.||+|.++|+..+
T Consensus 107 ~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIAe~lgis~~tVk~~l 186 (231)
T PRK11922 107 AEMVMASTIAGGERTPLADPAEDPERAAARREIRALLERAIDALPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRL 186 (231)
T ss_pred hhcccccccccccccccCcccCChHHHHHHHHHHHHHHHHHHhCCHHHhhhheeehhcCCCHHHHHHHHCcCHHHHHHHH
Confidence 10 0 01223456777777766533 67899999999999999999999
Q ss_pred hCCCCC
Q 012567 410 LSPKAP 415 (460)
Q Consensus 410 ~~ar~~ 415 (460)
++++..
T Consensus 187 ~Rar~k 192 (231)
T PRK11922 187 HRARRL 192 (231)
T ss_pred HHHHHH
Confidence 987754
No 53
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=99.58 E-value=1e-14 Score=135.19 Aligned_cols=142 Identities=15% Similarity=0.142 Sum_probs=113.1
Q ss_pred CHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHH
Q 012567 272 DQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAV 350 (460)
Q Consensus 272 de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI 350 (460)
+...|+..++.| ..+++.++..|.++|+++|+++.++..+++|++||++++||+++.+|++.. .|.+|++.+++|.+
T Consensus 4 ~~~~li~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn~~ 81 (187)
T PRK09641 4 LIKRLIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATNLT 81 (187)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHHHH
Confidence 345666777777 999999999999999999999999999999999999999999999999753 79999999999999
Q ss_pred HHHhhhcCccccc----------------Cc------c---hHHHHHHHHHHHHHHHHHh--------CCCCCHHHHHHH
Q 012567 351 RKSLSDQSRTIRL----------------PF------H---MVEATYRVKEARKQLYSEN--------GRHPNNEEVAEA 397 (460)
Q Consensus 351 ~~~Lrk~~r~iri----------------P~------~---~~e~i~kl~ka~~~L~~~~--------gr~pS~eEIAe~ 397 (460)
++++|++.+.... +. . ..+....+..+...|+... -.+.+++|||+.
T Consensus 82 ~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~~~~~s~~eIA~~ 161 (187)
T PRK09641 82 IDRLRKRKPDYYLDAEVAGTEGLTMYSQLAADDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEI 161 (187)
T ss_pred HHHHHhcCccccccccccCCcchhhhcccccCcCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHhhCCCHHHHHHH
Confidence 9999986532111 00 0 0111234666666665532 278899999999
Q ss_pred hCCCHHHHHHHHhCCCCC
Q 012567 398 TGLSMKRLHAVLLSPKAP 415 (460)
Q Consensus 398 LGIS~e~Vk~~l~~ar~~ 415 (460)
||+|+++|+..+++++..
T Consensus 162 lgis~~~v~~~l~Rar~~ 179 (187)
T PRK09641 162 LDLPVGTVKTRIHRGREA 179 (187)
T ss_pred HCCCHHHHHHHHHHHHHH
Confidence 999999999999877653
No 54
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=99.58 E-value=1.9e-14 Score=132.54 Aligned_cols=143 Identities=16% Similarity=0.097 Sum_probs=115.4
Q ss_pred CCHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHH
Q 012567 271 VDQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA 349 (460)
Q Consensus 271 ~de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a 349 (460)
|++..+...+..| ..+++.|+..|.+.|+.++++|.++..+++|++||+|+++|+++++|++. .+|.+|++..++|.
T Consensus 3 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~--~~~~~wl~~i~~n~ 80 (176)
T PRK09638 3 MDEKELIQKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGR--SKFSTWLISIASRL 80 (176)
T ss_pred ccHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHH
Confidence 4566677777777 99999999999999999999999999999999999999999999999864 48999999999999
Q ss_pred HHHHhhhcCcccccCc------------c---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHH
Q 012567 350 VRKSLSDQSRTIRLPF------------H---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLH 406 (460)
Q Consensus 350 I~~~Lrk~~r~iriP~------------~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk 406 (460)
+++++|+..+...... . .......+.+++..|+...+ .+.+++|||+.||+|+.+|+
T Consensus 81 ~~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l~is~~~V~ 160 (176)
T PRK09638 81 YKDHLRKQKREKLRLQRAKEETLRKEKWEAAIKGAEWSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVK 160 (176)
T ss_pred HHHHHHHhccccchhhhcccccCCccchHHHHHhhhHHHHHHHHHcCCHHHhheeeehhhcCCCHHHHHHHHCCChhHHH
Confidence 9999997653221110 0 11233456666666666533 67899999999999999999
Q ss_pred HHHhCCCCC
Q 012567 407 AVLLSPKAP 415 (460)
Q Consensus 407 ~~l~~ar~~ 415 (460)
..+++++..
T Consensus 161 ~~l~ra~~~ 169 (176)
T PRK09638 161 SRVHHGIKQ 169 (176)
T ss_pred HHHHHHHHH
Confidence 999877643
No 55
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=99.58 E-value=1.2e-14 Score=134.79 Aligned_cols=140 Identities=12% Similarity=0.140 Sum_probs=111.0
Q ss_pred HHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHH
Q 012567 274 RELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRK 352 (460)
Q Consensus 274 ~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~ 352 (460)
..|+..+..| ..++..|+..|.++|+.+|++|.+++.+++|++||+++++|+++.+|++.. .|.+|++.+++|.+++
T Consensus 6 ~~li~~~~~gd~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~~ 83 (187)
T TIGR02948 6 KKRIKEVRKGDENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQR--KFSTWLYRIATNLTID 83 (187)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHHHH
Confidence 3455666666 899999999999999999999999999999999999999999999999764 6999999999999999
Q ss_pred HhhhcCcccccC----------------------cc-h--HHHHHHHHHHHHHHHHHh--------CCCCCHHHHHHHhC
Q 012567 353 SLSDQSRTIRLP----------------------FH-M--VEATYRVKEARKQLYSEN--------GRHPNNEEVAEATG 399 (460)
Q Consensus 353 ~Lrk~~r~iriP----------------------~~-~--~e~i~kl~ka~~~L~~~~--------gr~pS~eEIAe~LG 399 (460)
++|+..+..... .. + .+....+.+++..|+... -.+.+++|||+.||
T Consensus 84 ~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lg 163 (187)
T TIGR02948 84 RLRKRKPDFYLDDEVQGTDGLTMESQLAADEAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKYMEDLSLKEISEILD 163 (187)
T ss_pred HHHhhcccccccccccCccccccccccccCcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhHHhcCCCHHHHHHHHC
Confidence 998754321100 00 0 011233556666665532 36789999999999
Q ss_pred CCHHHHHHHHhCCCCC
Q 012567 400 LSMKRLHAVLLSPKAP 415 (460)
Q Consensus 400 IS~e~Vk~~l~~ar~~ 415 (460)
+|+++|+..+++++..
T Consensus 164 is~~~v~~~l~Rar~~ 179 (187)
T TIGR02948 164 LPVGTVKTRIHRGREA 179 (187)
T ss_pred CCHHHHHHHHHHHHHH
Confidence 9999999999887653
No 56
>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=99.58 E-value=1.3e-14 Score=132.31 Aligned_cols=135 Identities=16% Similarity=0.132 Sum_probs=108.1
Q ss_pred HHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhc
Q 012567 279 RLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQ 357 (460)
Q Consensus 279 ~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~ 357 (460)
.+++| ..|++.|+..|.+.+++++.++.++..+++|++||+++++|+.+++|+...+ .|.+|++.+++|.+++++|++
T Consensus 4 ~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~~R~~ 82 (170)
T TIGR02952 4 RAQDREEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVNDYFRGS 82 (170)
T ss_pred HHHccCHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHHHHHhc
Confidence 34455 8999999999999999999999998899999999999999999999996544 899999999999999999986
Q ss_pred CcccccC--------------cch---HHHHHHHHHHHHHHHHH--------hCCCCCHHHHHHHhCCCHHHHHHHHhCC
Q 012567 358 SRTIRLP--------------FHM---VEATYRVKEARKQLYSE--------NGRHPNNEEVAEATGLSMKRLHAVLLSP 412 (460)
Q Consensus 358 ~r~iriP--------------~~~---~e~i~kl~ka~~~L~~~--------~gr~pS~eEIAe~LGIS~e~Vk~~l~~a 412 (460)
.+....+ ... .+....+.++...|+.. +-.+.+++|||+.||+|+++|+..++++
T Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~eIA~~l~is~~tv~~~l~ra 162 (170)
T TIGR02952 83 KRHPLFSLDVFKELLSNEPNPEEAILKEEANEKLLKALKILTPKQQHVIALRFGQNLPIAEVARILGKTEGAVKILQFRA 162 (170)
T ss_pred CCCCCCcHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 5332211 000 11233466666666553 2378999999999999999999999877
Q ss_pred CC
Q 012567 413 KA 414 (460)
Q Consensus 413 r~ 414 (460)
+.
T Consensus 163 ~~ 164 (170)
T TIGR02952 163 IK 164 (170)
T ss_pred HH
Confidence 54
No 57
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=99.57 E-value=2e-14 Score=135.31 Aligned_cols=144 Identities=17% Similarity=0.168 Sum_probs=117.9
Q ss_pred CCHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHH
Q 012567 271 VDQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA 349 (460)
Q Consensus 271 ~de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a 349 (460)
+++..++..+..| ..+++.|+..|.+.|++++.++.++..+++|++||+|+.+|+.+++|++. ..|.+|++.+++|.
T Consensus 12 ~~~~~l~~~~~~gd~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~--~~f~~wL~~i~rn~ 89 (192)
T PRK09643 12 RSDAELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGD--AAVSSWLHRIVVNA 89 (192)
T ss_pred cCHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCC--CccHHHHHHHHHHH
Confidence 4566777777777 99999999999999999999999999999999999999999999999964 36999999999999
Q ss_pred HHHHhhhcCcccccC-----------cc---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHH
Q 012567 350 VRKSLSDQSRTIRLP-----------FH---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHA 407 (460)
Q Consensus 350 I~~~Lrk~~r~iriP-----------~~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~ 407 (460)
+++++|+.++....+ .. ..+....+..++..|+...+ .+.+++|||+.||+|..+|+.
T Consensus 90 ~~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~i~~l~~~~g~s~~EIA~~lg~s~~tV~~ 169 (192)
T PRK09643 90 CLDRLRRAKARPTVPLDDVYPVAQLERDPTARVETALAVQRALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKS 169 (192)
T ss_pred HHHHHHccccCCCCCccccccccCCcccHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHH
Confidence 999999765322111 01 12334557777777766433 788999999999999999999
Q ss_pred HHhCCCCCc
Q 012567 408 VLLSPKAPR 416 (460)
Q Consensus 408 ~l~~ar~~l 416 (460)
.+++++..+
T Consensus 170 rl~rar~~L 178 (192)
T PRK09643 170 RCARGRARL 178 (192)
T ss_pred HHHHHHHHH
Confidence 998877643
No 58
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=99.56 E-value=2.1e-14 Score=139.97 Aligned_cols=144 Identities=17% Similarity=0.177 Sum_probs=115.4
Q ss_pred CHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHH
Q 012567 272 DQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAV 350 (460)
Q Consensus 272 de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI 350 (460)
++..|+..+..| ..+++.|+..|.+.|+.+++++.++..+.+|++||+|+++|+.+++|++..+ .|.+|++.+++|.+
T Consensus 49 ~d~~Li~~~~~gd~~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN~~ 127 (233)
T PRK12538 49 EDEELLDRLATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSNRC 127 (233)
T ss_pred cHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHHHH
Confidence 456677777777 8999999999999999999999999999999999999999999999986444 79999999999999
Q ss_pred HHHhhhcCccc--cc-------Ccc-----hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHH
Q 012567 351 RKSLSDQSRTI--RL-------PFH-----MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAV 408 (460)
Q Consensus 351 ~~~Lrk~~r~i--ri-------P~~-----~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~ 408 (460)
++++|++.+.. .. +.. ..+....+..++..|+...+ .+.+++|||+.||+|+++|+..
T Consensus 128 id~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~L~~Lp~~~R~v~~L~~~eg~s~~EIA~~Lgis~~tVk~~ 207 (233)
T PRK12538 128 IDLRRKPRTENVDAVPEVADGKPDAVSVIERNELSDLLEAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESL 207 (233)
T ss_pred HHHHHhhcccccccccccccCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHhcCCCHHHHHHHHCcCHHHHHHH
Confidence 99998754211 00 110 01222346677777766433 7889999999999999999999
Q ss_pred HhCCCCCc
Q 012567 409 LLSPKAPR 416 (460)
Q Consensus 409 l~~ar~~l 416 (460)
+++++..+
T Consensus 208 l~RAr~kL 215 (233)
T PRK12538 208 LKRGRQQL 215 (233)
T ss_pred HHHHHHHH
Confidence 99887643
No 59
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=99.56 E-value=1.4e-14 Score=134.88 Aligned_cols=142 Identities=12% Similarity=0.079 Sum_probs=112.7
Q ss_pred HHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHH
Q 012567 273 QRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVR 351 (460)
Q Consensus 273 e~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~ 351 (460)
...+...+..| ..+++.|+..|.+.|+.++++|.++..+.+|++||+|+++|+.+++|++.++ .|.+|++.+++|.++
T Consensus 12 ~~~l~~~~~~~~~~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~~n~~~ 90 (187)
T PRK12534 12 TGRLLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIARNKAI 90 (187)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHH
Confidence 34445554556 8999999999999999999999999999999999999999999999997644 689999999999999
Q ss_pred HHhhhcCcccc------cC---------cc---hHHHHHHHHHHHHHHHHHh--------CCCCCHHHHHHHhCCCHHHH
Q 012567 352 KSLSDQSRTIR------LP---------FH---MVEATYRVKEARKQLYSEN--------GRHPNNEEVAEATGLSMKRL 405 (460)
Q Consensus 352 ~~Lrk~~r~ir------iP---------~~---~~e~i~kl~ka~~~L~~~~--------gr~pS~eEIAe~LGIS~e~V 405 (460)
+++|++.+... .+ .. ..+....+..++..|+... -.+.+++|||+.||+|+++|
T Consensus 91 d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~~v 170 (187)
T PRK12534 91 DHLRANAPQRRNVALDDAGELRAADASPLERTERASTRRRIDHCLAELEPPRSELIRTAFFEGITYEELAARTDTPIGTV 170 (187)
T ss_pred HHHHhcccccccccccchhhhccccCChhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCChhHH
Confidence 99997643110 00 00 1223445666777765543 27899999999999999999
Q ss_pred HHHHhCCCCC
Q 012567 406 HAVLLSPKAP 415 (460)
Q Consensus 406 k~~l~~ar~~ 415 (460)
+..+++++..
T Consensus 171 ~~~l~Rar~~ 180 (187)
T PRK12534 171 KSWIRRGLAK 180 (187)
T ss_pred HHHHHHHHHH
Confidence 9999987653
No 60
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=99.56 E-value=1.8e-14 Score=135.57 Aligned_cols=141 Identities=16% Similarity=0.101 Sum_probs=111.5
Q ss_pred HHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHH
Q 012567 274 RELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRK 352 (460)
Q Consensus 274 ~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~ 352 (460)
..++..+..| ..+++.|+..|.+.|+.+|.++.++..+++|++||+|+.+|+.+.+|++..+ .|.+|++.+++|.+++
T Consensus 15 ~~li~~~~~~d~~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l~l~~~~~~~~~~~~-~~~~wL~~iarn~~ld 93 (194)
T PRK12531 15 LECMEKVKSRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYTIIRNLCFD 93 (194)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-hHHHHHHHHHHHHHHH
Confidence 3455666667 8999999999999999999999999889999999999999999999996443 7999999999999999
Q ss_pred HhhhcCccc-cc------Cc---------c-h---HHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHH
Q 012567 353 SLSDQSRTI-RL------PF---------H-M---VEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKR 404 (460)
Q Consensus 353 ~Lrk~~r~i-ri------P~---------~-~---~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~ 404 (460)
++|+..+.. .. +. . . ......+.+++..|+.+.+ .+.+++|||+.||+|+++
T Consensus 94 ~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~l~~~l~~Lp~~~r~v~~l~~~eg~s~~EIA~~lgis~~t 173 (194)
T PRK12531 94 LLRKQKGKDLHIHADDIWPSDYYPPDLVDHYSPEQDMLKEQVMKFLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGT 173 (194)
T ss_pred HHHHhcccccccchhhcccccccccccccccCHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCcCHHH
Confidence 999854311 10 00 0 0 0112346666666665433 788999999999999999
Q ss_pred HHHHHhCCCCC
Q 012567 405 LHAVLLSPKAP 415 (460)
Q Consensus 405 Vk~~l~~ar~~ 415 (460)
|+..+++++..
T Consensus 174 Vk~rl~ra~~~ 184 (194)
T PRK12531 174 VKSRLRLAVEK 184 (194)
T ss_pred HHHHHHHHHHH
Confidence 99999877653
No 61
>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=99.56 E-value=3.3e-14 Score=132.08 Aligned_cols=142 Identities=17% Similarity=0.183 Sum_probs=113.1
Q ss_pred CHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHH
Q 012567 272 DQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAV 350 (460)
Q Consensus 272 de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI 350 (460)
++..|+..+..| ..+++.|+..|.+.|+.+|+++.++..+++|++||+|+++|+.+.+|++. ..|.+|++.+.+|.+
T Consensus 6 ~d~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~--~~~~~wl~~iarn~~ 83 (190)
T TIGR02939 6 LDLELVERVQRGEKQAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGD--SAFYTWLYRIAVNTA 83 (190)
T ss_pred cHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCC--CccHhHHHHHHHHHH
Confidence 455677777777 89999999999999999999999999999999999999999999999964 479999999999999
Q ss_pred HHHhhhcCccccc----------------------Ccc---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHH
Q 012567 351 RKSLSDQSRTIRL----------------------PFH---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEA 397 (460)
Q Consensus 351 ~~~Lrk~~r~iri----------------------P~~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~ 397 (460)
+++++++.+.... |.. ..+....+..+...|+.... .+.+++|||+.
T Consensus 84 ~~~~r~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~EIA~~ 163 (190)
T TIGR02939 84 KNHLVAQGRRPPTSDVEIEDAEHFEGADRLREIDTPERLLLSRELEQTVMRAVEALPEDLRTAITLRELEGLSYEDIARI 163 (190)
T ss_pred HHHHHHhccCCCcccccccchhhhcccccccccCChHHHHHHHHHHHHHHHHHHcCCHHHhhhhhhhhhcCCCHHHHHHH
Confidence 9999764432110 000 01122346666666665433 67899999999
Q ss_pred hCCCHHHHHHHHhCCCCC
Q 012567 398 TGLSMKRLHAVLLSPKAP 415 (460)
Q Consensus 398 LGIS~e~Vk~~l~~ar~~ 415 (460)
||+|+.+|+..+++++..
T Consensus 164 lgis~~tv~~~l~rar~~ 181 (190)
T TIGR02939 164 MDCPVGTVRSRIFRAREA 181 (190)
T ss_pred HCcCHHHHHHHHHHHHHH
Confidence 999999999999987654
No 62
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=99.56 E-value=2.5e-14 Score=134.03 Aligned_cols=142 Identities=22% Similarity=0.242 Sum_probs=111.9
Q ss_pred CHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHH
Q 012567 272 DQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAV 350 (460)
Q Consensus 272 de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI 350 (460)
+...|+..+..| ..+++.|+..|.+.|+.+++++.++..+.+|++||+|+++|+. ..|++..+ .|.||++.+++|.+
T Consensus 15 ~~~~l~~~~~~gd~~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn~~ 92 (194)
T PRK12519 15 SDAELFSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRSRA 92 (194)
T ss_pred cHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHHHH
Confidence 455677766777 9999999999999999999999999999999999999999976 67886554 79999999999999
Q ss_pred HHHhhhcCccccc------------Cc-c------hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHH
Q 012567 351 RKSLSDQSRTIRL------------PF-H------MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMK 403 (460)
Q Consensus 351 ~~~Lrk~~r~iri------------P~-~------~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e 403 (460)
++++|++.+.... +. . ..+....+..++..|+.+.+ .+.+++|||+.||+|+.
T Consensus 93 ~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~~~g~s~~EIA~~lgis~~ 172 (194)
T PRK12519 93 IDRLRSRRSRQRLLERWQQELLGEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLG 172 (194)
T ss_pred HHHHHhcccccchhhhhhhhhcccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhhhcCCCHHHHHHHhCCCHH
Confidence 9999976532110 00 0 01123446666666665433 68899999999999999
Q ss_pred HHHHHHhCCCCC
Q 012567 404 RLHAVLLSPKAP 415 (460)
Q Consensus 404 ~Vk~~l~~ar~~ 415 (460)
+|+..+++++..
T Consensus 173 tV~~~l~Ra~~~ 184 (194)
T PRK12519 173 TVKARARQGLLK 184 (194)
T ss_pred HHHHHHHHHHHH
Confidence 999999877643
No 63
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=99.55 E-value=2.5e-14 Score=131.04 Aligned_cols=134 Identities=19% Similarity=0.184 Sum_probs=106.5
Q ss_pred Hhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcC
Q 012567 280 LNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS 358 (460)
Q Consensus 280 l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~ 358 (460)
++.| ..|++.|+..|.++|+.++++|.+++.+.+|++||++++||+++.+|+ .+.+|.+|++.++++.+.+.+|+..
T Consensus 4 ~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~r~~~ 81 (182)
T PRK09652 4 VQRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR--GGAAFYTWLYRIARNTAINYLRKQG 81 (182)
T ss_pred hhcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHHHHHHHHccc
Confidence 3445 889999999999999999999999999999999999999999999999 4568999999999999999998754
Q ss_pred cccccC----------------------cch---HHHHHHHHHHHHHHHHH--------hCCCCCHHHHHHHhCCCHHHH
Q 012567 359 RTIRLP----------------------FHM---VEATYRVKEARKQLYSE--------NGRHPNNEEVAEATGLSMKRL 405 (460)
Q Consensus 359 r~iriP----------------------~~~---~e~i~kl~ka~~~L~~~--------~gr~pS~eEIAe~LGIS~e~V 405 (460)
+....+ ... ......+..+...|+.. +..+.+++|||+.||+|+.+|
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~tV 161 (182)
T PRK09652 82 RRPPASDVDAEEAEDFDLADALRDISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTV 161 (182)
T ss_pred CCCCccccccccccccccccccccccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHH
Confidence 432111 000 11234455555555443 237889999999999999999
Q ss_pred HHHHhCCCCC
Q 012567 406 HAVLLSPKAP 415 (460)
Q Consensus 406 k~~l~~ar~~ 415 (460)
+..+++++..
T Consensus 162 ~~~l~ra~~~ 171 (182)
T PRK09652 162 RSRIFRAREA 171 (182)
T ss_pred HHHHHHHHHH
Confidence 9998876543
No 64
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=99.54 E-value=4.3e-14 Score=134.61 Aligned_cols=139 Identities=14% Similarity=0.088 Sum_probs=109.3
Q ss_pred HHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHh
Q 012567 276 LRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSL 354 (460)
Q Consensus 276 L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~L 354 (460)
|...+..| ..+++.|+..|.+.|+.++.++.++..+++|++||+|+.+|+.+.+|++.++ .|.+|++.+++|.+++++
T Consensus 28 l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wl~~I~rn~~~d~~ 106 (206)
T PRK12526 28 LILVAISRDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYTVMRNAAFDML 106 (206)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCccc-chhHHHHHHHHHHHHHHH
Confidence 44444555 8999999999999999999999999899999999999999999999997654 699999999999999999
Q ss_pred hhcCccccc-------Cc---------chHH-----HHHHHHHHHHHHHHH--------hCCCCCHHHHHHHhCCCHHHH
Q 012567 355 SDQSRTIRL-------PF---------HMVE-----ATYRVKEARKQLYSE--------NGRHPNNEEVAEATGLSMKRL 405 (460)
Q Consensus 355 rk~~r~iri-------P~---------~~~e-----~i~kl~ka~~~L~~~--------~gr~pS~eEIAe~LGIS~e~V 405 (460)
|++.+.... |. .... ....+.+++..|+.+ +-.+.|++|||+.||+|+.+|
T Consensus 107 Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~EIA~~lgis~~tV 186 (206)
T PRK12526 107 RKIKAKKEQNLGDDIWPIEQALAESQSESEEFSDHLMDKQILSYIEKLPEAQQTVVKGVYFQELSQEQLAQQLNVPLGTV 186 (206)
T ss_pred HHhccccccccccccchhhhhcccccCchHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHH
Confidence 875432110 00 0000 112356666666554 337899999999999999999
Q ss_pred HHHHhCCCCC
Q 012567 406 HAVLLSPKAP 415 (460)
Q Consensus 406 k~~l~~ar~~ 415 (460)
+..+++++..
T Consensus 187 ~~~l~Ra~~~ 196 (206)
T PRK12526 187 KSRLRLALAK 196 (206)
T ss_pred HHHHHHHHHH
Confidence 9999877654
No 65
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=99.53 E-value=6.9e-14 Score=130.10 Aligned_cols=140 Identities=17% Similarity=0.113 Sum_probs=109.6
Q ss_pred HHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccC-CCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHH
Q 012567 274 RELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQG-AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVR 351 (460)
Q Consensus 274 ~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~-~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~ 351 (460)
..++..+..| ..|++.|+..|.+.|+.++.++.+ +..+.+|++||+|+.+|+.++.|++. ..|.+|++.+++|.++
T Consensus 9 ~~~~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~--~~~~~wl~~iarN~~~ 86 (181)
T PRK12536 9 RALLLRGLAGDAAAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRAD--QPLTAWVHAIARYKLM 86 (181)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCC--CchHHHHHHHHHHHHH
Confidence 3455555555 899999999999999999988664 57899999999999999999999964 4799999999999999
Q ss_pred HHhhhcCcccccC--------------cchHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHH
Q 012567 352 KSLSDQSRTIRLP--------------FHMVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVL 409 (460)
Q Consensus 352 ~~Lrk~~r~iriP--------------~~~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l 409 (460)
+++|++.+..... ....+....+.+++..|+...+ .+.+++|||+.||+|+++|+..+
T Consensus 87 d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tV~~~l 166 (181)
T PRK12536 87 DFLRSRARREALHDPLDDESELFATSDDEAAEARRDLGKLLEQLPDRQRLPIVHVKLEGLSVAETAQLTGLSESAVKVGI 166 (181)
T ss_pred HHHHHHhccccccCCccchhhhcCCCCcchHHHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 9999854321100 0112233456677776655322 78899999999999999999999
Q ss_pred hCCCCC
Q 012567 410 LSPKAP 415 (460)
Q Consensus 410 ~~ar~~ 415 (460)
++++..
T Consensus 167 ~rar~~ 172 (181)
T PRK12536 167 HRGLKA 172 (181)
T ss_pred HHHHHH
Confidence 877653
No 66
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=99.53 E-value=7.4e-14 Score=130.73 Aligned_cols=141 Identities=15% Similarity=0.172 Sum_probs=111.9
Q ss_pred HHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHH
Q 012567 273 QRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVR 351 (460)
Q Consensus 273 e~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~ 351 (460)
...|+..++.| ..+++.|+..|.+.|+.+++++.++..+.+|++||+|+++|+++.+|++.. .|.+|++.+++|.++
T Consensus 7 ~~~ll~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~l~~~~~~~~~~~--~~~~wl~~ia~n~~~ 84 (193)
T PRK11923 7 DQQLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDS--AFYTWLYRIAINTAK 84 (193)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHhCcCCCC--ccHhHHHHHHHHHHH
Confidence 44566667777 899999999999999999999999999999999999999999999999763 599999999999999
Q ss_pred HHhhhcCcccc-----c-----------------Ccc---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHh
Q 012567 352 KSLSDQSRTIR-----L-----------------PFH---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEAT 398 (460)
Q Consensus 352 ~~Lrk~~r~ir-----i-----------------P~~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~L 398 (460)
+++|++.+... + |.. ..+....+..++..|+...+ .+.+++|||+.|
T Consensus 85 d~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l 164 (193)
T PRK11923 85 NHLVSRGRRPPDSDVSSEDAEFYDGDHALKDIESPERALLRDEIEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVM 164 (193)
T ss_pred HHHHHhcCCCccccccccchhhhcccccccCcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHHhhHHhcCCCHHHHHHHH
Confidence 99986443211 0 000 01122345566666655433 678999999999
Q ss_pred CCCHHHHHHHHhCCCCC
Q 012567 399 GLSMKRLHAVLLSPKAP 415 (460)
Q Consensus 399 GIS~e~Vk~~l~~ar~~ 415 (460)
|+|.++|+..+++++..
T Consensus 165 gis~~tv~~~l~Rar~~ 181 (193)
T PRK11923 165 QCPVGTVRSRIFRAREA 181 (193)
T ss_pred CCCHHHHHHHHHHHHHH
Confidence 99999999999887653
No 67
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=99.52 E-value=2.9e-14 Score=132.92 Aligned_cols=134 Identities=13% Similarity=0.099 Sum_probs=108.6
Q ss_pred cHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccc
Q 012567 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR 362 (460)
Q Consensus 283 G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~ir 362 (460)
+..++..|+..|.+.++.+|.++.++..+++|++||.|+.+|+.+.+|+...+..|.||++.+++|.+++++|++.+...
T Consensus 7 d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn~~~d~~Rk~~~~~~ 86 (185)
T PRK12542 7 DYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRKNKRHET 86 (185)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Confidence 38899999999999999999999999999999999999999999999986544589999999999999999998654221
Q ss_pred cC------------cch------HHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCCc
Q 012567 363 LP------------FHM------VEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAPR 416 (460)
Q Consensus 363 iP------------~~~------~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~l 416 (460)
.. ... ......+.+++..|+...+ .+.+++|||+.||+|+++|++.+++++..+
T Consensus 87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~L 166 (185)
T PRK12542 87 FLEEYERESIEAVDENIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARKRV 166 (185)
T ss_pred hhhhccccchhhhhccHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 10 000 1112346667777666433 789999999999999999999999877543
No 68
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=99.52 E-value=9.9e-14 Score=129.37 Aligned_cols=141 Identities=13% Similarity=0.107 Sum_probs=111.8
Q ss_pred HHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHH----HccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHH
Q 012567 273 QRELRRRLNYG-ILCKDKMITSNIRLVISIAK----NYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIK 347 (460)
Q Consensus 273 e~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAk----ry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr 347 (460)
...|+..+..| ..|++.|+..|.+.|+.+++ ++.++..+.+|++||+++.+|+.+.+|++. ..|.+|++.+++
T Consensus 8 ~~~l~~~~~~gd~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~--~~f~~wl~~i~~ 85 (184)
T PRK12539 8 LKALMLASLDGDAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPE--QPLTPWVYAIAR 85 (184)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCC--CChHHHHHHHHH
Confidence 44566666666 89999999999999999976 556788999999999999999999999974 369999999999
Q ss_pred HHHHHHhhhcCcc-cccC---------c---chHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHH
Q 012567 348 QAVRKSLSDQSRT-IRLP---------F---HMVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLH 406 (460)
Q Consensus 348 ~aI~~~Lrk~~r~-iriP---------~---~~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk 406 (460)
|.+++++|+..+. ...+ . ...+....+..++..|+...+ .+.+++|||+.||+|+++|+
T Consensus 86 n~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~ 165 (184)
T PRK12539 86 YKLIDHLRRTRASLADVPIDDADELVAHDDHAAVESTLDLGRLLARLPEKMRLAIQAVKLEGLSVAEAATRSGMSESAVK 165 (184)
T ss_pred HHHHHHHHHHhccccccChhhhccccCCcHHhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCcHHHHHHHHCcCHHHHH
Confidence 9999999985431 1111 0 112334557777777766533 78899999999999999999
Q ss_pred HHHhCCCCC
Q 012567 407 AVLLSPKAP 415 (460)
Q Consensus 407 ~~l~~ar~~ 415 (460)
..+++++..
T Consensus 166 ~~l~ra~~~ 174 (184)
T PRK12539 166 VSVHRGLKA 174 (184)
T ss_pred HHHHHHHHH
Confidence 999877653
No 69
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=99.51 E-value=1.8e-13 Score=127.59 Aligned_cols=134 Identities=18% Similarity=0.169 Sum_probs=111.4
Q ss_pred HhccHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCc
Q 012567 280 LNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSR 359 (460)
Q Consensus 280 l~~G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r 359 (460)
......++..++..|.+.++.+++++.++..+.+||+||+|+.+|+++..| .. +..|.||++.+++|.+++++|+.++
T Consensus 10 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~-~~~~~~wl~~Ia~n~~iD~~R~~~r 87 (182)
T COG1595 10 LRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RG-RSSFKAWLYRIARNLAIDRLRKRKR 87 (182)
T ss_pred HhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CC-CCchHHHHHHHHHHHHHHHHHHhcc
Confidence 344488999999999999999999999998899999999999999999999 33 4589999999999999999997654
Q ss_pred cccc-C-------------cch-----HHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCC
Q 012567 360 TIRL-P-------------FHM-----VEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSP 412 (460)
Q Consensus 360 ~iri-P-------------~~~-----~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~a 412 (460)
.... + ... .+....+.+++..|+.+++ .+.|++|||+.||||+++|++.++++
T Consensus 88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~~~gls~~EIA~~l~i~~~tVks~l~ra 167 (182)
T COG1595 88 RRARVEEADLLPEEADPAPDLAELLLAEEELERLRRALARLPPRQREAFLLRYLEGLSYEEIAEILGISVGTVKSRLHRA 167 (182)
T ss_pred cccccccccccccccCcccccchHHHHHHHHHHHHHHHHhCCHHHhHHhhhHhhcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 3221 0 001 2344668888888887655 78999999999999999999999987
Q ss_pred CCC
Q 012567 413 KAP 415 (460)
Q Consensus 413 r~~ 415 (460)
+..
T Consensus 168 ~~~ 170 (182)
T COG1595 168 RKK 170 (182)
T ss_pred HHH
Confidence 653
No 70
>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=99.51 E-value=1.2e-13 Score=135.80 Aligned_cols=145 Identities=6% Similarity=-0.008 Sum_probs=117.0
Q ss_pred hCCCHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHH-------HHhhcCCCCCCchHh
Q 012567 269 AGVDQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVR-------GAEKFDASKGFKFST 340 (460)
Q Consensus 269 ~g~de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLir-------AiekFDp~kG~rFST 340 (460)
++.++..|+..++.| ..|+..|+..|.+.|+.++.++.++..+++|++||.|+.+|. .+.+|++. ..|.|
T Consensus 22 ~~~~d~~Li~~~~~gd~~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~--~~~~t 99 (244)
T TIGR03001 22 LHAADLYLACACAQGEPAALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGR--GPLLS 99 (244)
T ss_pred ccccHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccchhhhhhccCCC--CchHh
Confidence 445677788888888 899999999999999999999999999999999999999994 78889863 47999
Q ss_pred HHHHHHHHHHHHHhhhcCcccccC---------------cch-H------HHHHHHHHHHHHHHHHhC--------CCCC
Q 012567 341 YAHWWIKQAVRKSLSDQSRTIRLP---------------FHM-V------EATYRVKEARKQLYSENG--------RHPN 390 (460)
Q Consensus 341 YA~~wIr~aI~~~Lrk~~r~iriP---------------~~~-~------e~i~kl~ka~~~L~~~~g--------r~pS 390 (460)
|++.+++|.+++++|++.+...+. ... . +....+.+++.+|+...+ .+.|
T Consensus 100 WL~~Ia~N~~id~lRk~~r~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~e~~~~l~~aL~~Lp~~~R~v~~L~~~eg~S 179 (244)
T TIGR03001 100 WVRIVATRIALELQAQERRHSPVEEPTELAALPAPGSDPELDLLRERYRQDFRQALREALAALSERERHLLRLHFVDGLS 179 (244)
T ss_pred HHHHHHHHHHHHHHHHhcccCccccccccccccCCCCCHHHHHHHHhhHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCC
Confidence 999999999999999755321110 000 0 122346777777777543 7899
Q ss_pred HHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567 391 NEEVAEATGLSMKRLHAVLLSPKAP 415 (460)
Q Consensus 391 ~eEIAe~LGIS~e~Vk~~l~~ar~~ 415 (460)
++|||+.||||+++|+..+++++..
T Consensus 180 ~~EIA~~Lgis~~TVk~rl~RAr~~ 204 (244)
T TIGR03001 180 MDRIGAMYQVHRSTVSRWVAQARER 204 (244)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 9999999999999999999887653
No 71
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=99.51 E-value=1.3e-13 Score=128.86 Aligned_cols=144 Identities=14% Similarity=0.110 Sum_probs=115.4
Q ss_pred CCHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHH
Q 012567 271 VDQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA 349 (460)
Q Consensus 271 ~de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a 349 (460)
+++..|...+..| ..+++.|+..|.+.++.++.++.++..+.+|++||+|+.+|+.+.+|++. ..|.+|++..++|.
T Consensus 7 ~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~~~~~~~--~~~~~wl~~i~~n~ 84 (189)
T PRK12515 7 TTDEMLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIARFK 84 (189)
T ss_pred cCHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CChHHHHHHHHHHH
Confidence 4667777777777 89999999999999999999999999999999999999999999999963 47999999999999
Q ss_pred HHHHhhhcCccccc-------Cc------c---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHH
Q 012567 350 VRKSLSDQSRTIRL-------PF------H---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRL 405 (460)
Q Consensus 350 I~~~Lrk~~r~iri-------P~------~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~V 405 (460)
+++++++..+.... +. . ..+....+.++...|+.+.+ .+.+++|||+.||+|+++|
T Consensus 85 ~~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~tV 164 (189)
T PRK12515 85 ALSALRRRKHEEIDDEAAAAIEDGADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTV 164 (189)
T ss_pred HHHHHHccCCCCCccccccccCCCCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHH
Confidence 99999975432110 00 0 01122345666666655433 7899999999999999999
Q ss_pred HHHHhCCCCCc
Q 012567 406 HAVLLSPKAPR 416 (460)
Q Consensus 406 k~~l~~ar~~l 416 (460)
+..+++++..+
T Consensus 165 ~~~l~Rar~~L 175 (189)
T PRK12515 165 KTRMFYARKKL 175 (189)
T ss_pred HHHHHHHHHHH
Confidence 99999887543
No 72
>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=99.50 E-value=8.9e-14 Score=125.62 Aligned_cols=128 Identities=13% Similarity=0.121 Sum_probs=103.9
Q ss_pred HHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccC-
Q 012567 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP- 364 (460)
Q Consensus 286 A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP- 364 (460)
+++.++..|.+.|+.+++++.++..+.+|++||+++.+|+++++|++.. .|.+|++..++|.+++++|++.+.....
T Consensus 2 ~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~~~~ 79 (159)
T TIGR02989 2 AFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRDRLVFD 79 (159)
T ss_pred HHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhcccccccC
Confidence 7899999999999999999999999999999999999999999999753 6999999999999999999865432110
Q ss_pred cc----------------hHHHHHHHHHHHHHHHHHh--------CCCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567 365 FH----------------MVEATYRVKEARKQLYSEN--------GRHPNNEEVAEATGLSMKRLHAVLLSPKAP 415 (460)
Q Consensus 365 ~~----------------~~e~i~kl~ka~~~L~~~~--------gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~ 415 (460)
.. ..+....+.+++..|+... -.+.+++|||+.||||.++|+..+++++..
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~v~~l~~~~g~~~~eIA~~l~is~~tv~~~l~Rar~~ 154 (159)
T TIGR02989 80 DELLEALAAEAEATEADRSEDELQALEGCLEKLPERQRELLQLRYQRGVSLTALAEQLGRTVNAVYKALSRLRVR 154 (159)
T ss_pred HHHHHHHHhhcccchHhhHHHHHHHHHHHHHHCCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 00 0112233566666665542 278899999999999999999999887654
No 73
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=99.50 E-value=1.3e-13 Score=129.17 Aligned_cols=141 Identities=15% Similarity=0.112 Sum_probs=112.7
Q ss_pred HHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHH
Q 012567 274 RELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRK 352 (460)
Q Consensus 274 ~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~ 352 (460)
..|+..+..| ..+++.|+..|.+.++.++. +.++..+++|++||.|+.+|+.+++|++. ..|.+|++.+++|.+++
T Consensus 12 ~~l~~~~~~gd~~af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~flkl~~~~~~~~~~--~~~~~Wl~~Iarn~~~d 88 (185)
T PRK09649 12 TALALSAAKGNGRALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVAD 88 (185)
T ss_pred HHHHHHHHccCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHhccccCcc--chHHHHHHHHHHHHHHH
Confidence 3456666666 89999999999999999995 67888899999999999999999999964 47999999999999999
Q ss_pred HhhhcCccccc-----Ccc---------hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 353 SLSDQSRTIRL-----PFH---------MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 353 ~Lrk~~r~iri-----P~~---------~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
++|++.+..+. +.. ..+....+.+++..|+.+++ .+.|++|||+.||+|+++|+..++
T Consensus 89 ~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~ 168 (185)
T PRK09649 89 HIRHVRSRPRTTRGARPEHLIDGDRHARGFEDLVEVTTMIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVA 168 (185)
T ss_pred HHHHhccccccccccchhhccChhhhhhhHHHHHHHHHHHHhCCHHHhHHhhhHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 99975432111 110 01223457777777776544 788999999999999999999999
Q ss_pred CCCCCcc
Q 012567 411 SPKAPRS 417 (460)
Q Consensus 411 ~ar~~lS 417 (460)
+++..+.
T Consensus 169 Rar~~Lr 175 (185)
T PRK09649 169 RARDALL 175 (185)
T ss_pred HHHHHHH
Confidence 8877554
No 74
>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=99.49 E-value=1.2e-13 Score=127.89 Aligned_cols=140 Identities=18% Similarity=0.190 Sum_probs=106.9
Q ss_pred HHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCC-----CcccHHhHHHHHHHH-HHhhcCCCCCCchHhHHHHHH
Q 012567 274 RELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGM-----NLQDLVQEGCRGLVR-GAEKFDASKGFKFSTYAHWWI 346 (460)
Q Consensus 274 ~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~-----d~eDLiQEG~IGLir-AiekFDp~kG~rFSTYA~~wI 346 (460)
..|+..+..| ..|++.|+..|.+.++.+|++|.++.. +++|++||+|+.+|+ ...+|++. ..|.+|++.++
T Consensus 5 ~~li~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~--~~~~~wl~~i~ 82 (183)
T TIGR02999 5 TELLQQWQNGDAAARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR--AHFFAAAAKAM 82 (183)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCCch--HHHHHHHHHHH
Confidence 4456666667 899999999999999999999998877 899999999999998 78888753 37999999999
Q ss_pred HHHHHHHhhhcCcccc------c------Cc---chHHHHHHHHHHHHH---HHHHhC--------CCCCHHHHHHHhCC
Q 012567 347 KQAVRKSLSDQSRTIR------L------PF---HMVEATYRVKEARKQ---LYSENG--------RHPNNEEVAEATGL 400 (460)
Q Consensus 347 r~aI~~~Lrk~~r~ir------i------P~---~~~e~i~kl~ka~~~---L~~~~g--------r~pS~eEIAe~LGI 400 (460)
+|.+++++|++.+..+ . +. ...+....+..+... |+.+++ .+.|++|||+.|||
T Consensus 83 ~n~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgi 162 (183)
T TIGR02999 83 RRILVDHARRRRAQKRGGGAVRVPLDEVLPDAEADLDEELLDLDDALDKLAQVDPRQAEVVELRFFAGLTVEEIAELLGV 162 (183)
T ss_pred HHHHHHHHHHHHHHhccCCccccccccccCCCCccHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHcCCCHHHHHHHhCC
Confidence 9999999987432111 0 10 111222223333333 555433 78999999999999
Q ss_pred CHHHHHHHHhCCCCC
Q 012567 401 SMKRLHAVLLSPKAP 415 (460)
Q Consensus 401 S~e~Vk~~l~~ar~~ 415 (460)
|+++|+..+++++..
T Consensus 163 s~~tVk~~l~Rar~~ 177 (183)
T TIGR02999 163 SVRTVERDWRFARAW 177 (183)
T ss_pred CHHHHHHHHHHHHHH
Confidence 999999999987653
No 75
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=99.48 E-value=1.6e-13 Score=126.54 Aligned_cols=129 Identities=9% Similarity=0.047 Sum_probs=104.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccccc-
Q 012567 285 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL- 363 (460)
Q Consensus 285 ~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iri- 363 (460)
..+++|+..|.++|+.+|++|.++..+++|++||+++.+|+.+++|++. .+|.+|++..++|.+++++|++.+....
T Consensus 3 ~~~~~l~~~y~~~i~~~~~~~~~~~~daeDvvQe~~i~l~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~Rk~~~~~~~~ 80 (173)
T PRK12522 3 EKVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYV--ENYKKWITTICVRTFYDFYRKKKRWKDRI 80 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcCCc--cchHHHHHHHHHHHHHHHHHHhccccccc
Confidence 4589999999999999999999999999999999999999999999974 3799999999999999999876532110
Q ss_pred --------------------Ccc--hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCC
Q 012567 364 --------------------PFH--MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPK 413 (460)
Q Consensus 364 --------------------P~~--~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar 413 (460)
|.. ..+....+.+++..|+.... .+.+++|||+.||+|+++|+..+++++
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~~~s~~EIA~~lgis~~tV~~~l~Ra~ 160 (173)
T PRK12522 81 LDLFHKEDGGEIEFADDVNISEEFIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAK 160 (173)
T ss_pred ccccchhhhhhhccccCCCChHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 000 01223346666666666433 788999999999999999999999876
Q ss_pred CC
Q 012567 414 AP 415 (460)
Q Consensus 414 ~~ 415 (460)
..
T Consensus 161 ~~ 162 (173)
T PRK12522 161 KQ 162 (173)
T ss_pred HH
Confidence 54
No 76
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=99.48 E-value=3.5e-13 Score=125.26 Aligned_cols=138 Identities=15% Similarity=0.139 Sum_probs=108.7
Q ss_pred HHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccC----CCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHH
Q 012567 276 LRRRLNYG-ILCKDKMITSNIRLVISIAKNYQG----AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAV 350 (460)
Q Consensus 276 L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~----~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI 350 (460)
++..+..| ..|++.|+..|.+.|+.+++++.+ +..+++|++||+++.+|...++|+.. ..|.+|++.+++|.+
T Consensus 12 l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~--~~~~~wl~~i~rn~~ 89 (184)
T PRK12512 12 LMRSANAGDAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWLFAIARNKL 89 (184)
T ss_pred HHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCcc--ccHHHHHHHHHHHHH
Confidence 44455555 999999999999999999998875 34689999999999999999999863 479999999999999
Q ss_pred HHHhhhcCccccc---------Ccc---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 351 RKSLSDQSRTIRL---------PFH---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 351 ~~~Lrk~~r~iri---------P~~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
.+++|++.+.... |.. .......+.++...|+...+ .+.+++|||+.||+|..+|+..++
T Consensus 90 ~d~~Rr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l~is~~tV~~~l~ 169 (184)
T PRK12512 90 IDALRRRGRRVFVDIDDFAETLPAEPATETLPAGDVGRHLETLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVRVALH 169 (184)
T ss_pred HHHHHhhcccccCCchhccccccccchhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 9999876543221 110 11223456667776666433 788999999999999999999998
Q ss_pred CCCCC
Q 012567 411 SPKAP 415 (460)
Q Consensus 411 ~ar~~ 415 (460)
+++..
T Consensus 170 ra~~~ 174 (184)
T PRK12512 170 RGLAA 174 (184)
T ss_pred HHHHH
Confidence 77653
No 77
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=99.48 E-value=1.4e-13 Score=129.03 Aligned_cols=129 Identities=14% Similarity=0.161 Sum_probs=105.2
Q ss_pred HHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCc
Q 012567 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF 365 (460)
Q Consensus 286 A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~ 365 (460)
+++.|+..|.+.|+.+|.++.++..+++|++||.|+.+|+.+.+|++. .+|.+|++.+++|.+++++|++.+....+.
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 379999999999999999998654321110
Q ss_pred ------------------------------c------hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCC
Q 012567 366 ------------------------------H------MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLS 401 (460)
Q Consensus 366 ------------------------------~------~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS 401 (460)
. ..+....+..++..|+...+ .+.|++|||+.||+|
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis 160 (191)
T PRK12520 81 DDADEQSDDDLFDALFAADGHYREPPSDWGDPDAALSRREFFEVLQACVDRLPPRTGRVFMMREWLELETEEICQELQIT 160 (191)
T ss_pred cccccchhhhhhhhhcccccccccCccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCC
Confidence 0 01122346677777766543 688999999999999
Q ss_pred HHHHHHHHhCCCCCc
Q 012567 402 MKRLHAVLLSPKAPR 416 (460)
Q Consensus 402 ~e~Vk~~l~~ar~~l 416 (460)
+++|+..+++++..+
T Consensus 161 ~~tV~~~l~Rar~~L 175 (191)
T PRK12520 161 ATNAWVLLYRARMRL 175 (191)
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999999887643
No 78
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=99.47 E-value=2.4e-13 Score=124.94 Aligned_cols=132 Identities=14% Similarity=0.062 Sum_probs=106.1
Q ss_pred cHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccc
Q 012567 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR 362 (460)
Q Consensus 283 G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~ir 362 (460)
+..+++.|+..|.+.|+.++.++.++..+++|++||.|+.+|+..++|++.. ..|.+|++.+++|.+++++|++.+...
T Consensus 7 ~~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~~~~~~~~~~-~~~~~wL~~iarn~~~d~~Rk~~~~~~ 85 (173)
T PRK09645 7 EAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTG-RSARAWLFTVARNLVIDERRSARARPV 85 (173)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHHHHHHHhhccccc
Confidence 4789999999999999999999999989999999999999999999997532 479999999999999999997543211
Q ss_pred --------cC-----cch--HHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567 363 --------LP-----FHM--VEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAP 415 (460)
Q Consensus 363 --------iP-----~~~--~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~ 415 (460)
.+ ... ......+..++..|+...+ .+.+++|||+.||+|+++|+..+++++..
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~ 161 (173)
T PRK09645 86 EGGDDVLGVPEQSAPDEVDRALDRLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRA 161 (173)
T ss_pred ccccccccCCCCCCchHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 01 111 1112346677777766433 78999999999999999999999877653
No 79
>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=99.47 E-value=1.9e-13 Score=119.73 Aligned_cols=127 Identities=21% Similarity=0.291 Sum_probs=101.7
Q ss_pred HHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCc------
Q 012567 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSR------ 359 (460)
Q Consensus 286 A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r------ 359 (460)
|++.++..|.++|+++++++.+++.+.+|++|+|+++++++++.|++. ..|.+|+.+++++.+.++++++.+
T Consensus 2 a~~~l~~~~~~~v~~~~~~~~~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~rk~~~~~~~~~ 79 (158)
T TIGR02937 2 AFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRRLRRELD 79 (158)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHHHHHHHHhccCCcchh
Confidence 689999999999999999999999999999999999999999999987 689999999999999999998763
Q ss_pred c-ccc------Ccc---hHHHHHHHHHHHHHHHHH--------hCCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567 360 T-IRL------PFH---MVEATYRVKEARKQLYSE--------NGRHPNNEEVAEATGLSMKRLHAVLLSPKA 414 (460)
Q Consensus 360 ~-iri------P~~---~~e~i~kl~ka~~~L~~~--------~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~ 414 (460)
. ... |.. .......+.++...|+.. +..+.+..|||+.+|+|..+|...+.+++.
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~ii~~~~~~g~s~~eIA~~l~~s~~~v~~~~~~~~~ 152 (158)
T TIGR02937 80 LLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARK 152 (158)
T ss_pred hhhhcccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 0 000 000 112233455555555432 246789999999999999999999886543
No 80
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=99.47 E-value=2.4e-13 Score=124.19 Aligned_cols=137 Identities=15% Similarity=0.075 Sum_probs=108.1
Q ss_pred HHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhh
Q 012567 277 RRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLS 355 (460)
Q Consensus 277 ~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lr 355 (460)
...+..| ..|++.++..|.+.|+.+++++.++..+.+|++||++++||+.+.+|+ .+..|.+|++.++++.++++++
T Consensus 4 ~~~~~~~~~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~~~d~~r 81 (179)
T PRK11924 4 MPVDATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNVCYDLLR 81 (179)
T ss_pred HHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHHHHHHHH
Confidence 3444555 899999999999999999999999999999999999999999999998 3458999999999999999998
Q ss_pred hcCcccccCc-------------c------hHHHHHHHHHHHHHHHHH--------hCCCCCHHHHHHHhCCCHHHHHHH
Q 012567 356 DQSRTIRLPF-------------H------MVEATYRVKEARKQLYSE--------NGRHPNNEEVAEATGLSMKRLHAV 408 (460)
Q Consensus 356 k~~r~iriP~-------------~------~~e~i~kl~ka~~~L~~~--------~gr~pS~eEIAe~LGIS~e~Vk~~ 408 (460)
+..+...... . ..+....+..++..|+.. +..+.+.+|||+.||+|..+|+..
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~~~~~~eIA~~lgis~~tv~~~ 161 (179)
T PRK11924 82 RRRREKAVLSDDALEPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSR 161 (179)
T ss_pred hcccccccCcccccccccCCccCCHHHHHhhHHHHHHHHHHHHhCCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHHH
Confidence 7544222110 0 112233455555555443 236889999999999999999999
Q ss_pred HhCCCCC
Q 012567 409 LLSPKAP 415 (460)
Q Consensus 409 l~~ar~~ 415 (460)
+++++..
T Consensus 162 ~~ra~~~ 168 (179)
T PRK11924 162 LRRARQL 168 (179)
T ss_pred HHHHHHH
Confidence 9877643
No 81
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=99.46 E-value=2.5e-13 Score=126.16 Aligned_cols=130 Identities=13% Similarity=0.127 Sum_probs=106.2
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccc-
Q 012567 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR- 362 (460)
Q Consensus 284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~ir- 362 (460)
..++..|+..|.+.|+.+++.|.++..+.+|++||+|+.+|+++.+|++.. .|.+|++.+++|.+.+++++..+..+
T Consensus 6 ~~af~~l~~~~~~~l~~~~~~~~~~~~daeDl~Qevfl~l~~~~~~~~~~~--~f~~wl~~iarn~~~~~~r~~~~~~~~ 83 (179)
T PRK12543 6 QEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNR--PFRFWLIGLVIKQIHSWRRKRWRRFRI 83 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--ChHHHHHHHHHHHHHHHHHhhcccccc
Confidence 789999999999999999999999999999999999999999999999763 69999999999999999876432111
Q ss_pred --------------cCcch--HHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567 363 --------------LPFHM--VEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAP 415 (460)
Q Consensus 363 --------------iP~~~--~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~ 415 (460)
.|... .+....+.++...|+...+ .+.+++|||+.||||+++|+..+++++..
T Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~i~~l~~~e~~s~~EIA~~lgis~~tV~~~l~ra~~~ 160 (179)
T PRK12543 84 FEKAEEQRKPVSIDFSEDVLSKESNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKK 160 (179)
T ss_pred ccccccccccccccChHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHccCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 11111 1234556677777766433 78899999999999999999999877654
No 82
>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=99.46 E-value=2.5e-13 Score=127.44 Aligned_cols=131 Identities=15% Similarity=0.098 Sum_probs=107.4
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccccc
Q 012567 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL 363 (460)
Q Consensus 284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iri 363 (460)
..+|+.|+..|.+.|+.+++++.++..+++|++||.|+.+|+.+.+|++. ..|.+|++.+++|.+++++|++.+....
T Consensus 10 ~~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~~~~~~~~~--~~~~~wL~~iarN~~~d~~Rk~~~~~~~ 87 (193)
T TIGR02947 10 AQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPG--TNLKAWLYRILTNTYINSYRKAQRRPQQ 87 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcccCCC--CcchHHHHHHHHHHHHHHHHHhcCCccc
Confidence 78899999999999999999999999999999999999999999999863 4799999999999999999976532111
Q ss_pred C--------------cc------h-------HHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHH
Q 012567 364 P--------------FH------M-------VEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAV 408 (460)
Q Consensus 364 P--------------~~------~-------~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~ 408 (460)
. .. . ......+..++..|+...+ .+.|++|||+.||+|+++|+..
T Consensus 88 ~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~r~i~~L~~~~g~s~~EIA~~lgis~~tVk~~ 167 (193)
T TIGR02947 88 SDDDDIEDWQLAKAASHTSNGLRSAELEALDGLPDQDIKDALQGLPEEFRQAVYLADVEGFAYKEIAEIMGTPIGTVMSR 167 (193)
T ss_pred ccchhhhhhhhccccccccccccchhHHHHhhhhHHHHHHHHHhCCHHHhhheeehhhcCCCHHHHHHHHCCCHHHHHHH
Confidence 0 00 0 0112456777777777544 6789999999999999999999
Q ss_pred HhCCCCCc
Q 012567 409 LLSPKAPR 416 (460)
Q Consensus 409 l~~ar~~l 416 (460)
+++++..+
T Consensus 168 l~Rar~~L 175 (193)
T TIGR02947 168 LHRGRKQL 175 (193)
T ss_pred HHHHHHHH
Confidence 99887643
No 83
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=99.46 E-value=3.6e-13 Score=126.65 Aligned_cols=131 Identities=13% Similarity=0.117 Sum_probs=107.8
Q ss_pred cHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccc
Q 012567 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR 362 (460)
Q Consensus 283 G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~ir 362 (460)
+..++..|+..|.+.++.+|+++.++..+++|++||.|+.+|+...+|+.. ..|.+|++++++|.+++++|++.+...
T Consensus 8 ~~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~awL~~Ia~n~~~d~~R~~~~~~~ 85 (187)
T PRK12516 8 GTPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVG--TNMKAWLFTILRNEFYSQMRKRGREVQ 85 (187)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCc--ccHHHHHHHHHHHHHHHHHHhhcCCcc
Confidence 378999999999999999999999999999999999999999999999854 369999999999999999998654221
Q ss_pred cCc-------------chHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567 363 LPF-------------HMVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAP 415 (460)
Q Consensus 363 iP~-------------~~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~ 415 (460)
... ........+..++..|+...+ .+.+++|||+.||+|+++|+..+++++..
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~i~~L~~~~g~s~~EIA~~Lgis~~tVk~~l~Rar~~ 159 (187)
T PRK12516 86 DTDGMFTEQLAVHPSQYGTLDLQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQR 159 (187)
T ss_pred ccccccccccCCCcchhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 100 011123457777777776533 78999999999999999999999987754
No 84
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=99.45 E-value=3.7e-13 Score=125.14 Aligned_cols=130 Identities=15% Similarity=0.081 Sum_probs=105.9
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccccc
Q 012567 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL 363 (460)
Q Consensus 284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iri 363 (460)
..|++.|+..|.+.|+++++++.++..+++|++||+|+.+|+++.+|++. ..|.+|++.+++|.+++++|+..+....
T Consensus 15 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~--~~~~awl~~ia~n~~~d~~Rk~~~~~~~ 92 (179)
T PRK09415 15 EDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGK--SSLKTWLYRIAINHCKDYLKSWHNKKVI 92 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--cccHHHHHHHHHHHHHHHHHhhcccccc
Confidence 78999999999999999999999999999999999999999999999864 3799999999999999999874321110
Q ss_pred C---------------cc---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567 364 P---------------FH---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAP 415 (460)
Q Consensus 364 P---------------~~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~ 415 (460)
+ .. ..+....+.+++..|+...+ .+.|++|||+.||||+++|+..+++++..
T Consensus 93 ~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tv~~~l~Ra~~~ 170 (179)
T PRK09415 93 VTEDIFTYMESQKESVEEEVIQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKEL 170 (179)
T ss_pred ccccccccccccccCcHHHHHHHHHHHHHHHHHHhCCHHHhhHhHhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 0 00 12233456666667766543 68899999999999999999999987654
No 85
>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=99.44 E-value=5.8e-13 Score=121.02 Aligned_cols=131 Identities=17% Similarity=0.095 Sum_probs=106.3
Q ss_pred cHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccc
Q 012567 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR 362 (460)
Q Consensus 283 G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~ir 362 (460)
+..+++.++..|.+.|+.++..+.++..+.+|++||+|+.+|+.+++|+. ...|.+|++..++|.+++++|++.+...
T Consensus 4 ~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~--~~~~~~wl~~i~~n~~~d~~rk~~~~~~ 81 (162)
T TIGR02983 4 TEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRD--PDAPDAYVRRVLVNLARSRWRRRRLLEL 81 (162)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCC--cccHHHHHHHHHHHHHHHHHHhhccccc
Confidence 48899999999999999999999999999999999999999999999964 3489999999999999999997653110
Q ss_pred ----cC-----c--chHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567 363 ----LP-----F--HMVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAP 415 (460)
Q Consensus 363 ----iP-----~--~~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~ 415 (460)
.+ . ........+..++..|+...+ .+.+++|||+.||+|+++|+..+.+++..
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ra~~~ 153 (162)
T TIGR02983 82 PTRELPDAAAPDPAPDVALRAALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALAR 153 (162)
T ss_pred cccccCcccCCccchhHHHHHHHHHHHHhCCHHHHHHhhhHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 00 0 012234456666666665433 67899999999999999999999877653
No 86
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=99.42 E-value=1e-12 Score=133.79 Aligned_cols=141 Identities=19% Similarity=0.162 Sum_probs=112.1
Q ss_pred HHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHH
Q 012567 274 RELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRK 352 (460)
Q Consensus 274 ~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~ 352 (460)
.+|+..+..| ..+++.|+..|.+.|+.+|+++.++..+.+|++||.|+.+|+.+.+|++. ..|.+|++.+++|.+++
T Consensus 7 ~~l~~~~~~gd~~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d 84 (339)
T PRK08241 7 AALLARAAAGDRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGR--SSLRTWLYRIATNVCLD 84 (339)
T ss_pred HHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhhhccccc--cchHHHHHHHHHHHHHH
Confidence 3566666777 89999999999999999999999999999999999999999999999853 47999999999999999
Q ss_pred HhhhcCcccc---c-----------------------Cc-----------ch---HHH-HHHHHHHHHHHHHHhC-----
Q 012567 353 SLSDQSRTIR---L-----------------------PF-----------HM---VEA-TYRVKEARKQLYSENG----- 386 (460)
Q Consensus 353 ~Lrk~~r~ir---i-----------------------P~-----------~~---~e~-i~kl~ka~~~L~~~~g----- 386 (460)
++|++.+... . +. .. .+. ...+..++..|+.+++
T Consensus 85 ~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L 164 (339)
T PRK08241 85 ALEGRARRPLPTDLGAPAADPVDELVERPEVPWLEPYPDALLDPAAADPAARVVARESVRLAFVAALQHLPPRQRAVLIL 164 (339)
T ss_pred HHHhhccccCccccCCCcCcccccccccccccccCCCCcccccccCCChHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhh
Confidence 9997543210 0 00 00 011 1236667777766544
Q ss_pred ---CCCCHHHHHHHhCCCHHHHHHHHhCCCCCc
Q 012567 387 ---RHPNNEEVAEATGLSMKRLHAVLLSPKAPR 416 (460)
Q Consensus 387 ---r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~l 416 (460)
.+.+++|||+.||+|+++|+..+++++..+
T Consensus 165 ~~~~g~s~~EIA~~lgis~~tVk~~l~RAr~~L 197 (339)
T PRK08241 165 RDVLGWSAAEVAELLDTSVAAVNSALQRARATL 197 (339)
T ss_pred HHhhCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 678999999999999999999998776544
No 87
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=99.42 E-value=1e-12 Score=120.80 Aligned_cols=133 Identities=17% Similarity=0.109 Sum_probs=103.7
Q ss_pred Hhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcC
Q 012567 280 LNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS 358 (460)
Q Consensus 280 l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~ 358 (460)
++.| ..+++.++..|.+.|+.+++++.+ ..+++|++||+|+.+|+.+++|++. ..|.+|++.+++|.+++++|+..
T Consensus 5 ~~~gd~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~~~ 81 (175)
T PRK12518 5 CQRGDRQSFRQLYRRYQQKVRSTLYQLCG-RELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATDARRQFA 81 (175)
T ss_pred HHcCCHHHHHHHHHHHHHHHHHHHHHHcC-HhHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHHHHHHhh
Confidence 4455 899999999999999999999875 4689999999999999999999964 47999999999999999998753
Q ss_pred ccc----ccC-----------cch--HHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCC
Q 012567 359 RTI----RLP-----------FHM--VEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPK 413 (460)
Q Consensus 359 r~i----riP-----------~~~--~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar 413 (460)
+.. ..+ ... .+....+.++...|+...+ .+.+++|||+.||+|+++|+..+++++
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~eIA~~lg~s~~tv~~~l~Rar 161 (175)
T PRK12518 82 QRPSRIQDDSLNDQPSRPSDTPDLMQLHYQDLVQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYAR 161 (175)
T ss_pred ccccchhcccccccccCCCCcHHHHHHHHHHHHHHHHHhCCHHHeeeeeehHhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 211 000 000 1111235566666666433 678999999999999999999999876
Q ss_pred CC
Q 012567 414 AP 415 (460)
Q Consensus 414 ~~ 415 (460)
..
T Consensus 162 ~~ 163 (175)
T PRK12518 162 RQ 163 (175)
T ss_pred HH
Confidence 54
No 88
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=99.42 E-value=1e-12 Score=120.30 Aligned_cols=130 Identities=11% Similarity=0.106 Sum_probs=105.2
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccccc
Q 012567 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL 363 (460)
Q Consensus 284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iri 363 (460)
...+..++..|.+.|+.+|+++.++..+++|++||.|+.+|+...+|++. ..|.+|++..++|.+++++|++++....
T Consensus 5 ~~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R~~~~~~~~ 82 (164)
T PRK12547 5 SKNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMG--TNLKAWLFTILRNEFYSQMRKRGREVQD 82 (164)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCc--ccHHHHHHHHHHHHHHHHHHhhcccccc
Confidence 46789999999999999999999999999999999999999999999853 3699999999999999999975432111
Q ss_pred C---------cc----hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567 364 P---------FH----MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAP 415 (460)
Q Consensus 364 P---------~~----~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~ 415 (460)
. .. .......+..++..|+...+ .+.+++|||+.||+|+++|+..+++++..
T Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~~ 155 (164)
T PRK12547 83 SDGVFTARVAVHPAQYGSLDLQDFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNR 155 (164)
T ss_pred ccccccccCCCCchhhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 0 00 11123456677777766433 78999999999999999999999987653
No 89
>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=99.41 E-value=5.2e-13 Score=119.65 Aligned_cols=127 Identities=17% Similarity=0.164 Sum_probs=100.4
Q ss_pred HHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccccc--
Q 012567 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL-- 363 (460)
Q Consensus 286 A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iri-- 363 (460)
|++.|+..|.+.|+.+++++.++..+.+|++||+++++|+.+.+|++. .+|.+|++.++++.+.+++++..+....
T Consensus 2 a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~--~~~~~wl~~i~r~~~~d~~r~~~~~~~~~~ 79 (161)
T TIGR02985 2 AFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEV--ESFKAYLFTIVKNRSLNYLRHKQVEEKYQE 79 (161)
T ss_pred hHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc--ccHHHHHHHHHHHHHHHHHHHHHhHhHHHH
Confidence 789999999999999999999998999999999999999999999863 4799999999999999999875432110
Q ss_pred --------------Ccc---hHHHHHHHHHHHHHHHHH--------hCCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567 364 --------------PFH---MVEATYRVKEARKQLYSE--------NGRHPNNEEVAEATGLSMKRLHAVLLSPKA 414 (460)
Q Consensus 364 --------------P~~---~~e~i~kl~ka~~~L~~~--------~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~ 414 (460)
|.. ..+....+..+...|+.. +-.+.+..|||+.||+|..+|+..+++++.
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~il~l~~~~~~~~~eIA~~lgis~~tv~~~~~ra~~ 155 (161)
T TIGR02985 80 EILEIEVDELSENDPEEELEAKELQLIIYKAIEKLPEQCRKIFILSRFEGKSYKEIAEELGISVKTVEYHISKALK 155 (161)
T ss_pred HHHhhcccccCCCCcHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 000 012223355555544432 236889999999999999999999987654
No 90
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=99.41 E-value=1.4e-12 Score=123.57 Aligned_cols=137 Identities=15% Similarity=0.069 Sum_probs=108.4
Q ss_pred HHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHH
Q 012567 275 ELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKS 353 (460)
Q Consensus 275 ~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~ 353 (460)
+|+..+..| ..+++.++..|.+.++.+++ +.++..+++|++||.|+.+|+..++|++. ..|.+|++.+++|.++++
T Consensus 14 ~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~-~~~~~~~AEDivQevflkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~ 90 (196)
T PRK12535 14 DLALAAGRGDRAALTEFIRETQDDVWRLLA-HLGGHDIADDLTQETYLRVMSALPRFAAR--SSARTWLLSLARRVWVDN 90 (196)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHHhhhcCCc--ccHHHHHHHHHHHHHHHH
Confidence 455555566 89999999999999999975 56888899999999999999999999863 379999999999999999
Q ss_pred hhhcCccccc--------------Cc--chHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHH
Q 012567 354 LSDQSRTIRL--------------PF--HMVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVL 409 (460)
Q Consensus 354 Lrk~~r~iri--------------P~--~~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l 409 (460)
+|++.+..+. |. ...+....+.+++..|+...+ .+.+++|||+.||+|+++|+..+
T Consensus 91 ~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIAe~lgis~~tV~~~l 170 (196)
T PRK12535 91 IRHDMARPRKSATEYEDAAATTASNETTGSWSEWIDVRTLIDALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSRV 170 (196)
T ss_pred HHhhccCCCcccccccccccccCCcchhHHHHHHHHHHHHHHcCCHHHHHHhhhHHHhCCCHHHHHHHhCCCHHHHHHHH
Confidence 9975432110 00 011223456777777766543 77899999999999999999999
Q ss_pred hCCCC
Q 012567 410 LSPKA 414 (460)
Q Consensus 410 ~~ar~ 414 (460)
++++.
T Consensus 171 ~Rar~ 175 (196)
T PRK12535 171 ARARA 175 (196)
T ss_pred HHHHH
Confidence 87765
No 91
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=99.41 E-value=8.7e-13 Score=122.67 Aligned_cols=131 Identities=9% Similarity=0.004 Sum_probs=104.0
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccC--CCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccc
Q 012567 284 ILCKDKMITSNIRLVISIAKNYQG--AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI 361 (460)
Q Consensus 284 ~~A~e~LI~~nlrLV~~IAkry~~--~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~i 361 (460)
..++..|+..|.+.|+.++..+.+ +..+++|++||.|+.+|+...+|+......|.||++.+++|.+++++|++.+..
T Consensus 12 ~~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~~Rk~~~~~ 91 (178)
T PRK12529 12 RDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSWRRRQSLEL 91 (178)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 889999999999999998765555 467899999999999999999997544457999999999999999998753211
Q ss_pred -------cc-------Ccc---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567 362 -------RL-------PFH---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKA 414 (460)
Q Consensus 362 -------ri-------P~~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~ 414 (460)
.. |.. ..+....|.+++..|+.+++ .+.|++|||+.||+|+++|+..++++..
T Consensus 92 ~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~rAl~ 169 (178)
T PRK12529 92 AWLEALATLPEPLHPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQAYV 169 (178)
T ss_pred hhhhHhhhccCcCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 00 111 12234457778888877654 6899999999999999999999986643
No 92
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=99.41 E-value=1.2e-12 Score=126.37 Aligned_cols=132 Identities=14% Similarity=0.124 Sum_probs=107.1
Q ss_pred ccHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccc
Q 012567 282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI 361 (460)
Q Consensus 282 ~G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~i 361 (460)
....++..|+..|.+.++.+++++.++..+.+|++||+|+.+|+.+.+|++ + .|.+|++++++|.+++++|++++..
T Consensus 15 ~~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~--~-~~~aWL~~IarN~~~d~~Rk~~~~~ 91 (216)
T PRK12533 15 ARGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRG--D-NARPWLLAIVRHTWYSEWRRRANAH 91 (216)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCc--c-chHhHHHHHHHHHHHHHHHhhcccc
Confidence 347899999999999999999999999999999999999999999999985 2 5999999999999999998764311
Q ss_pred c------cCc------------c------hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHH
Q 012567 362 R------LPF------------H------MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVL 409 (460)
Q Consensus 362 r------iP~------------~------~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l 409 (460)
. +.. . ..+....+.+++..|+...+ .+.+++|||+.||||+++|+..+
T Consensus 92 ~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y~eg~s~~EIAe~LgiS~~tVk~~L 171 (216)
T PRK12533 92 EVAAPDTLDDADSLDDWQPAGEDPLALLLRAEDVRLVNAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRL 171 (216)
T ss_pred cccccccccccccccccccCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHhHhhhHHhcCCCHHHHHHHHCCCHHHHHHHH
Confidence 0 000 0 11234557777777766533 78899999999999999999999
Q ss_pred hCCCCCc
Q 012567 410 LSPKAPR 416 (460)
Q Consensus 410 ~~ar~~l 416 (460)
++++..+
T Consensus 172 ~RAr~~L 178 (216)
T PRK12533 172 ARARRRL 178 (216)
T ss_pred HHHHHHH
Confidence 9877643
No 93
>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=99.40 E-value=1.3e-12 Score=121.09 Aligned_cols=131 Identities=19% Similarity=0.161 Sum_probs=102.3
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcc----CCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcC-
Q 012567 284 ILCKDKMITSNIRLVISIAKNYQ----GAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS- 358 (460)
Q Consensus 284 ~~A~e~LI~~nlrLV~~IAkry~----~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~- 358 (460)
..|++.|+..|.+.|+.++++|. ++..+++|++||+++.+|+++.+|+...+..|.+|++..++|.++++++++.
T Consensus 6 ~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r~~~~ 85 (189)
T TIGR02984 6 QEALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNVLADALRRHLG 85 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHHHHHHHHHH
Confidence 88999999999999999999874 3567899999999999999999998765568999999999999999998641
Q ss_pred ---ccc----cc-----------------------Ccc---hHHHHHHHHHHHHHHHHH--------hCCCCCHHHHHHH
Q 012567 359 ---RTI----RL-----------------------PFH---MVEATYRVKEARKQLYSE--------NGRHPNNEEVAEA 397 (460)
Q Consensus 359 ---r~i----ri-----------------------P~~---~~e~i~kl~ka~~~L~~~--------~gr~pS~eEIAe~ 397 (460)
+.. .+ |.. ..+....+.+++..|+.. +-.+.+++|||+.
T Consensus 86 ~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vi~l~~~~g~s~~eIA~~ 165 (189)
T TIGR02984 86 AQKRDIRREQSLDAGGRLDESSVRLAAQLAADGPSPSQVAARREAAVRLAQALAKLPEDYREVILLRHLEGLSFAEVAER 165 (189)
T ss_pred HHhhhcccccCCCcccccCCcchhHHHHccCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCHHHHHHH
Confidence 100 00 000 011223455666655543 3378899999999
Q ss_pred hCCCHHHHHHHHhCCCC
Q 012567 398 TGLSMKRLHAVLLSPKA 414 (460)
Q Consensus 398 LGIS~e~Vk~~l~~ar~ 414 (460)
||||+++|+..+++++.
T Consensus 166 lgis~~~v~~~l~Ra~~ 182 (189)
T TIGR02984 166 MDRSEGAVSMLWVRGLA 182 (189)
T ss_pred HCcCHHHHHHHHHHHHH
Confidence 99999999999987754
No 94
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=99.40 E-value=1.4e-12 Score=118.77 Aligned_cols=129 Identities=13% Similarity=0.126 Sum_probs=103.2
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccccc
Q 012567 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL 363 (460)
Q Consensus 284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iri 363 (460)
..+++.++..|.+.|+.++.++.++..+++|++||+++.+|+.+++|++. .|.||++.+++|.+++++|++.+....
T Consensus 4 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDv~Qe~f~~~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~~~~ 80 (161)
T PRK12541 4 KQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE---EIRPWLFTIAYNAFIDWYRKEKKYKTT 80 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhHHHccCC---ChHHHHHHHHHHHHHHHHHhccccccc
Confidence 57899999999999999999999999999999999999999999999853 599999999999999999985532111
Q ss_pred ----------Ccc-----hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567 364 ----------PFH-----MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAP 415 (460)
Q Consensus 364 ----------P~~-----~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~ 415 (460)
+.. ..+....+..+...|+.+.+ .+.+++|||+.||+|+++|+..+++++..
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~Rar~~ 155 (161)
T PRK12541 81 TIEEFHLPNVPSTEHEYFIKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKE 155 (161)
T ss_pred chhhhhccCCCCcHHHHHHHhHHHHHHHHHHHCCHHHHHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 000 01122334455556655433 78899999999999999999999887653
No 95
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=99.39 E-value=1.2e-12 Score=119.67 Aligned_cols=126 Identities=12% Similarity=0.056 Sum_probs=101.5
Q ss_pred HHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccC--
Q 012567 287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP-- 364 (460)
Q Consensus 287 ~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP-- 364 (460)
++.|+..|.+.|+.+|+++.++..+++|++||+++.+|+.+.+|++. .|.+|++.+++|.+++++|+.++.....
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wL~~i~~n~~~d~~R~~~~~~~~~~~ 79 (165)
T PRK09644 3 IEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYHTFIDFVRKEKKVSFVGTD 79 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc---chHHHHHHHHHHHHHHHHHhhhhccccchh
Confidence 67899999999999999999999999999999999999999999863 6999999999999999999865421111
Q ss_pred ----------cc---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567 365 ----------FH---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAP 415 (460)
Q Consensus 365 ----------~~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~ 415 (460)
.. ..+....+.++...|+...+ .+.+++|||+.||+|+++|+..+++++..
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Rar~~ 151 (165)
T PRK09644 80 EIEAIQAESTEEYVVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKR 151 (165)
T ss_pred HHhhhcccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 11 01222445566666655422 77899999999999999999999987653
No 96
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=99.38 E-value=1.3e-11 Score=120.99 Aligned_cols=89 Identities=15% Similarity=0.280 Sum_probs=79.7
Q ss_pred CHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCC--CcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHH
Q 012567 272 DQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGM--NLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQ 348 (460)
Q Consensus 272 de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~--d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~ 348 (460)
+...|+..++.| ..|++.|+..|.++|+++|.+|+++.. +.+|++|+|++++|+++++|++.+|..|.+|+.++|+|
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 345566777777 889999999999999999999998775 58999999999999999999998888899999999999
Q ss_pred HHHHHhhhcCcc
Q 012567 349 AVRKSLSDQSRT 360 (460)
Q Consensus 349 aI~~~Lrk~~r~ 360 (460)
.+++++|++.+.
T Consensus 84 ~~iDylRk~~~~ 95 (237)
T PRK08311 84 RLIDYFRKESKH 95 (237)
T ss_pred HHHHHHHHhhcc
Confidence 999999986653
No 97
>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=99.38 E-value=1.8e-12 Score=130.84 Aligned_cols=130 Identities=20% Similarity=0.154 Sum_probs=105.0
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccc-
Q 012567 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR- 362 (460)
Q Consensus 284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~ir- 362 (460)
..+++.|+..|.+.|+.+|+++.++..+.+|++||.|+.+|+.+.+|++. ..|.+|++.+++|.+++++|++.+...
T Consensus 4 ~~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~~~~~~ 81 (324)
T TIGR02960 4 GAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGR--SSVRTWLYRIATNACLDALEARQRRPRP 81 (324)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCcc--cchHHHHHHHHHHHHHHHHHhccCCcCc
Confidence 78999999999999999999999999999999999999999999999864 479999999999999999997543210
Q ss_pred -------------------------cCc--------------ch---HH-HHHHHHHHHHHHHHHhC--------CCCCH
Q 012567 363 -------------------------LPF--------------HM---VE-ATYRVKEARKQLYSENG--------RHPNN 391 (460)
Q Consensus 363 -------------------------iP~--------------~~---~e-~i~kl~ka~~~L~~~~g--------r~pS~ 391 (460)
++. .. .+ ....+..++..|+.+.+ .+.++
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~ 161 (324)
T TIGR02960 82 VGLGAPSADGTAAASEAAEVTWLEPLPDLTLDLDDPAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRDVLGWRA 161 (324)
T ss_pred cccCCCCCcccccccccccccccCCCCccccccccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHHhCCCH
Confidence 000 00 11 11235667777766533 67899
Q ss_pred HHHHHHhCCCHHHHHHHHhCCCCC
Q 012567 392 EEVAEATGLSMKRLHAVLLSPKAP 415 (460)
Q Consensus 392 eEIAe~LGIS~e~Vk~~l~~ar~~ 415 (460)
+|||+.||+|+++|++.+++++..
T Consensus 162 ~EIA~~lgis~~tV~~~l~Rar~~ 185 (324)
T TIGR02960 162 AETAELLGTSTASVNSALQRARAT 185 (324)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHH
Confidence 999999999999999999877653
No 98
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=99.37 E-value=1.7e-12 Score=119.70 Aligned_cols=131 Identities=12% Similarity=0.089 Sum_probs=103.4
Q ss_pred cc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcc
Q 012567 282 YG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT 360 (460)
Q Consensus 282 ~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~ 360 (460)
.| ..++..|+..|.+.|+.++.++.++..+.+|++||.|+.+|+. ..|... ..|.+|++.+++|.+++++|++.+.
T Consensus 6 ~~~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~~~d~~Rk~~~~ 82 (172)
T PRK12523 6 SPHSELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRRAALE 82 (172)
T ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45 8899999999999999999999999999999999999999986 456542 4799999999999999999975421
Q ss_pred c----c---c-------Ccc---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567 361 I----R---L-------PFH---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAP 415 (460)
Q Consensus 361 i----r---i-------P~~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~ 415 (460)
. . . |.. ..+....+.+++..|+.+.+ .+.+++|||+.||+|+++|+..++++...
T Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~ 162 (172)
T PRK12523 83 QAYLAELALVPEAEQPSPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGLRQ 162 (172)
T ss_pred HHHHHHHhhcccccCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 1 0 0 011 01223456677777766433 78999999999999999999999877653
No 99
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=99.36 E-value=1.2e-12 Score=118.81 Aligned_cols=121 Identities=10% Similarity=0.083 Sum_probs=96.8
Q ss_pred HHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccc-c-------
Q 012567 292 TSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR-L------- 363 (460)
Q Consensus 292 ~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~ir-i------- 363 (460)
+.|.+.|+.+|.++.++..+++|++||+|+.+|+++.+|++. .|.+|++.+++|.+++++|++.+... .
T Consensus 2 ~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~~~~~~~ 78 (160)
T PRK09642 2 QTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFR---GLKTWMARIATNHAIDYKRKKARENEELSLCKETE 78 (160)
T ss_pred chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcccccccc---hhHHHHHHHHHHHHHHHHHHhcccccccccchhhh
Confidence 568899999999999999999999999999999999999852 59999999999999999997543211 0
Q ss_pred --------Ccch---HHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567 364 --------PFHM---VEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAP 415 (460)
Q Consensus 364 --------P~~~---~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~ 415 (460)
|... .+....+..++..|+...+ .+.|++|||+.||+|+++|+..+++++..
T Consensus 79 ~~~~~~~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~ 149 (160)
T PRK09642 79 ENIKSSHNIEDLLLTKEQKLLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKW 149 (160)
T ss_pred hhccCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 0000 1122346677777766533 78999999999999999999999987654
No 100
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=99.36 E-value=3.6e-12 Score=119.35 Aligned_cols=130 Identities=14% Similarity=0.152 Sum_probs=105.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccccc-
Q 012567 285 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL- 363 (460)
Q Consensus 285 ~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iri- 363 (460)
.++..++..|.+.|+.+|.++.++..+++|++||.|+.+|+.+++|++. ..|.+|++.+++|.+++++|++.+....
T Consensus 5 ~~~~~~~~~~~~~l~~~~~~~~~~~~~AEDivQevflkl~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~~~~~~~ 82 (182)
T PRK12540 5 DSLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPG--SNLPAWLFTILRNLFRSDYRKRRREVEDA 82 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCC--chHHHHHHHHHHHHHHHHHHhcccccccc
Confidence 5678899999999999999999999999999999999999999999865 3699999999999999999876542211
Q ss_pred -----------Ccc-hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCCc
Q 012567 364 -----------PFH-MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAPR 416 (460)
Q Consensus 364 -----------P~~-~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~l 416 (460)
+.. .......+..++..|+..++ .+.|++|||+.||+|+++|+..+++++..+
T Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RAr~~L 155 (182)
T PRK12540 83 DGSYAKTLKSQPGQNAHLEFEEFRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKL 155 (182)
T ss_pred cccccccccCCCchHHHHHHHHHHHHHHhCCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 000 11123456777777766533 788999999999999999999999887643
No 101
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=99.36 E-value=4.4e-12 Score=115.44 Aligned_cols=128 Identities=13% Similarity=0.109 Sum_probs=101.9
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccc--
Q 012567 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI-- 361 (460)
Q Consensus 284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~i-- 361 (460)
..+++.|+..|.+.|+.++.++.++..+.+|++||.|+.+|+....|++ ..|.+|++++++|.+++++|++.+..
T Consensus 3 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~---~~~~~wl~~i~~n~~~d~~R~~~~~~~~ 79 (161)
T PRK12528 3 SATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQI---IEPRAFLTTIAKRVLCNHYRRQDLERAY 79 (161)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhccccccc---cCHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3689999999999999999999999999999999999999999888764 26999999999999999999753211
Q ss_pred -----ccCc----c------hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567 362 -----RLPF----H------MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKA 414 (460)
Q Consensus 362 -----riP~----~------~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~ 414 (460)
..+. . ..+....+.+++..|+...+ .+.+++|||+.||+|+++|+..++++..
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~~g~s~~EIA~~l~is~~tV~~~l~ra~~ 155 (161)
T PRK12528 80 LEALAQLPERVAPSEEERAIILETLVELDQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAM 155 (161)
T ss_pred HHHhhccccccCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 0110 0 01223456666666666433 7899999999999999999999987643
No 102
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=99.35 E-value=3.2e-12 Score=120.15 Aligned_cols=126 Identities=14% Similarity=0.178 Sum_probs=99.6
Q ss_pred HHHHHHhHHHHHHHHHHccCCCCC-cccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccC--
Q 012567 288 DKMITSNIRLVISIAKNYQGAGMN-LQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP-- 364 (460)
Q Consensus 288 e~LI~~nlrLV~~IAkry~~~g~d-~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP-- 364 (460)
+..+..|.+.|+.+|+++.++..+ ++|++||+|+.+|+++.+|++. ..|.+|++.+++|.+++++|++++.....
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 457788999999999999999888 9999999999999999999863 47999999999999999999865321110
Q ss_pred --------------------------------cc---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCC
Q 012567 365 --------------------------------FH---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLS 401 (460)
Q Consensus 365 --------------------------------~~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS 401 (460)
.. ..+....+.+++..|+...+ .+.|++|||+.||+|
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~L~~~~g~s~~EIA~~lgis 165 (195)
T PRK12532 86 LDDELLDEAFESHFSQNGHWTPEGQPQHWNTPEKSLNNNEFQKILQSCLYNLPENTARVFTLKEILGFSSDEIQQMCGIS 165 (195)
T ss_pred ccccccchhhhhhhccccccccccCccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHHhCCCHHHHHHHHCCC
Confidence 00 01122346666666665432 688999999999999
Q ss_pred HHHHHHHHhCCCCC
Q 012567 402 MKRLHAVLLSPKAP 415 (460)
Q Consensus 402 ~e~Vk~~l~~ar~~ 415 (460)
+++|+..+++++..
T Consensus 166 ~~tVk~~l~Rar~~ 179 (195)
T PRK12532 166 TSNYHTIMHRARES 179 (195)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999987653
No 103
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=99.35 E-value=4.7e-12 Score=120.83 Aligned_cols=130 Identities=16% Similarity=0.216 Sum_probs=105.3
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcc--c
Q 012567 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT--I 361 (460)
Q Consensus 284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~--i 361 (460)
..++..|+..|.+.++.++.++.++..+.+|++||+|+.+|+...+|++ + .|.+|++.+++|.+++++|+..+. .
T Consensus 27 ~~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~~~d~~Rk~~~~~~~ 103 (203)
T PRK09647 27 MPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNLFLDMVRRRARIRME 103 (203)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHHHHHHHHhcccCccc
Confidence 8899999999999999999999999999999999999999999999985 3 699999999999999999986431 1
Q ss_pred ccC-----------c--c---hHHHHHHHHHHHHHHHHHh--------CCCCCHHHHHHHhCCCHHHHHHHHhCCCCCc
Q 012567 362 RLP-----------F--H---MVEATYRVKEARKQLYSEN--------GRHPNNEEVAEATGLSMKRLHAVLLSPKAPR 416 (460)
Q Consensus 362 riP-----------~--~---~~e~i~kl~ka~~~L~~~~--------gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~l 416 (460)
..+ . . ..+....+..++..|+... -.+.+++|||+.||||+++|+..+++++..+
T Consensus 104 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~L~~~~r~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RArk~L 182 (203)
T PRK09647 104 ALPEDYDRVPGDEPNPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQL 182 (203)
T ss_pred cccccccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 000 0 0 0122344566666665542 3788999999999999999999999887543
No 104
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=99.34 E-value=3.1e-12 Score=121.37 Aligned_cols=126 Identities=12% Similarity=0.083 Sum_probs=100.0
Q ss_pred HHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccC---c
Q 012567 289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP---F 365 (460)
Q Consensus 289 ~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP---~ 365 (460)
.++..|.+.++.+|+++.++..+++|++||.|+.+|+.+++|++. ..|.+|++.+++|.+++++|++.+....+ .
T Consensus 12 ~~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~~~ 89 (201)
T PRK12545 12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQ--SAHKTWVFGILRNKLIDTLRARQRTVNLSALDA 89 (201)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhcccc--chHHHHHHHHHHHHHHHHHHhhccccccccccc
Confidence 348889999999999999999999999999999999999999965 36999999999999999999865432110 0
Q ss_pred -----------------------------ch------HHHHHHHHHHHHHHHHHh--------CCCCCHHHHHHHhCCCH
Q 012567 366 -----------------------------HM------VEATYRVKEARKQLYSEN--------GRHPNNEEVAEATGLSM 402 (460)
Q Consensus 366 -----------------------------~~------~e~i~kl~ka~~~L~~~~--------gr~pS~eEIAe~LGIS~ 402 (460)
.. .+....+.+++..|+... -.+.+++|||+.||+|+
T Consensus 90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~v~~L~~~eg~s~~EIA~~lgis~ 169 (201)
T PRK12545 90 ELDGEALLDRELFKDNGHWAAHAKPRPWPKPETILQQQQFWTLFETCLDHLPEQIGRVFMMREFLDFEIDDICTELTLTA 169 (201)
T ss_pred ccchhhhhhhhhhcccccccccccCcCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCH
Confidence 00 011124566666666543 37889999999999999
Q ss_pred HHHHHHHhCCCCCc
Q 012567 403 KRLHAVLLSPKAPR 416 (460)
Q Consensus 403 e~Vk~~l~~ar~~l 416 (460)
++|+..+++++..+
T Consensus 170 ~tVk~~l~RAr~~L 183 (201)
T PRK12545 170 NHCSVLLYRARTRL 183 (201)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999877643
No 105
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=99.33 E-value=4.3e-12 Score=115.56 Aligned_cols=127 Identities=16% Similarity=0.054 Sum_probs=101.2
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccccc
Q 012567 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL 363 (460)
Q Consensus 284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iri 363 (460)
..+++.|+..|.+.|+.+|+++.++..+.+|++||+|+.+|++ .|+. +..|.+|++.+++|.+++++|+..+....
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 3579999999999999999999999999999999999999999 6763 34799999999999999999886542211
Q ss_pred C---------------cc---hHHHHHHHHHHHHHHHH--------HhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567 364 P---------------FH---MVEATYRVKEARKQLYS--------ENGRHPNNEEVAEATGLSMKRLHAVLLSPKAP 415 (460)
Q Consensus 364 P---------------~~---~~e~i~kl~ka~~~L~~--------~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~ 415 (460)
. .. ..+....+.++...|+. .+ .+.+++|||+.||+|+.+|+..+++++..
T Consensus 78 ~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~-~g~s~~eIA~~lgis~~tV~~~i~ra~~~ 154 (166)
T PRK09639 78 ILGEFQWQEVDNEPSPEEIWIRKEEITKVQEVLAKMTERDRTVLLLRF-SGYSYKEIAEALGIKESSVGTTLARAKKK 154 (166)
T ss_pred ccchhhhhhccCCCChHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 0 00 01223345666665554 35 88999999999999999999999877653
No 106
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=99.32 E-value=5.3e-12 Score=118.60 Aligned_cols=126 Identities=14% Similarity=0.135 Sum_probs=99.9
Q ss_pred HHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccC---
Q 012567 288 DKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP--- 364 (460)
Q Consensus 288 e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP--- 364 (460)
+..|..|.+.++.+|.++.++..+++|++||.|+.+|+.+.+|++. .+|.+|++++++|.+++++|++.+.....
T Consensus 10 ~~~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~~~~ 87 (189)
T PRK12530 10 SLEIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQ--SALKTWIFAILKNKIIDLIRYRKRFVNESELI 87 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCC--ccHHHHHHHHHHHHHHHHHHhhccCCCccccc
Confidence 3457788999999999999999999999999999999999999864 36999999999999999999765421110
Q ss_pred ----------------------cc---------hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHH
Q 012567 365 ----------------------FH---------MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRL 405 (460)
Q Consensus 365 ----------------------~~---------~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~V 405 (460)
.. ..+....+..++..|+...+ .+.|++|||+.||+|+++|
T Consensus 88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tV 167 (189)
T PRK12530 88 EEDSPNSFFDEKGHWKPEYYEPSEWQEVENTVYKEEFWLIFEACLNHLPAQQARVFMMREYLELSSEQICQECDISTSNL 167 (189)
T ss_pred ccccchhhhcccccccccccCCccccCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHhHHHHcCCCHHHHHHHHCCCHHHH
Confidence 00 00112235677777766533 6889999999999999999
Q ss_pred HHHHhCCCCC
Q 012567 406 HAVLLSPKAP 415 (460)
Q Consensus 406 k~~l~~ar~~ 415 (460)
+..+++++..
T Consensus 168 k~~l~RAr~~ 177 (189)
T PRK12530 168 HVLLYRARLQ 177 (189)
T ss_pred HHHHHHHHHH
Confidence 9999987653
No 107
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=99.32 E-value=8.8e-12 Score=117.25 Aligned_cols=133 Identities=11% Similarity=0.028 Sum_probs=106.2
Q ss_pred hccHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcc
Q 012567 281 NYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT 360 (460)
Q Consensus 281 ~~G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~ 360 (460)
.....+++.++..|.+.|+.+|+++.++..+++|++||.|+.+|+.+..|++. ..|.+|++.+++|.+++..+++.+.
T Consensus 19 ~~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~--~~~~~wL~~Iarn~~~~~~r~~~~~ 96 (188)
T PRK12517 19 LSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDE--KAAKAWLITILRRENARRFERKQFD 96 (188)
T ss_pred hccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCc--cchHHHHHHHHHHHHHHHHHHhccC
Confidence 34588999999999999999999999999999999999999999999999864 3799999999999988877654321
Q ss_pred c-c-----cC-----c-chHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567 361 I-R-----LP-----F-HMVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAP 415 (460)
Q Consensus 361 i-r-----iP-----~-~~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~ 415 (460)
. . .+ . ........+..++..|+...+ .+.+++|||+.||||+++|+..+++++..
T Consensus 97 ~~~~~~~~~~~~~~~~~e~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~ 171 (188)
T PRK12517 97 LVDIEDDSIEDDASHSSEEEMEQEWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARNQ 171 (188)
T ss_pred ccCcccccccCccccChhHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 1 0 00 0 011122346777777776533 78899999999999999999999987654
No 108
>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=99.32 E-value=5.3e-12 Score=118.59 Aligned_cols=127 Identities=13% Similarity=0.109 Sum_probs=100.6
Q ss_pred HHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccC---
Q 012567 288 DKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP--- 364 (460)
Q Consensus 288 e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP--- 364 (460)
.+++..|.+.|+.+++++.++..+++|++||+|+.+|+...+|++. .+|.+|++.+++|.+++++|++.+....+
T Consensus 5 ~~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R~~~r~~~~~~~~ 82 (188)
T TIGR02943 5 PQELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKNKIIDALRAKGREVKVSDLD 82 (188)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHHHHHHHHHhhcccCCccccc
Confidence 3578889999999999999999999999999999999999999864 48999999999999999999765422111
Q ss_pred ------------------------c------c---hHHHHHHHHHHHHHHHHHh--------CCCCCHHHHHHHhCCCHH
Q 012567 365 ------------------------F------H---MVEATYRVKEARKQLYSEN--------GRHPNNEEVAEATGLSMK 403 (460)
Q Consensus 365 ------------------------~------~---~~e~i~kl~ka~~~L~~~~--------gr~pS~eEIAe~LGIS~e 403 (460)
. . ..+....+.+++..|+... -.+.+++|||+.||+|++
T Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~lgis~~ 162 (188)
T TIGR02943 83 DELDDEAFNALFTQNGHWAQHGQPQHWNTPEKQLENKEFWEVFEACLYHLPEQTARVFMMREVLGFESDEICQELEISTS 162 (188)
T ss_pred cccccchhhhhhccccchhccccccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHhCCCHH
Confidence 0 0 0111234566666665532 378899999999999999
Q ss_pred HHHHHHhCCCCCc
Q 012567 404 RLHAVLLSPKAPR 416 (460)
Q Consensus 404 ~Vk~~l~~ar~~l 416 (460)
+|+..+.+++..+
T Consensus 163 tvk~rl~Rar~~L 175 (188)
T TIGR02943 163 NCHVLLYRARLSL 175 (188)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999876543
No 109
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=99.31 E-value=6.7e-12 Score=120.05 Aligned_cols=127 Identities=17% Similarity=0.170 Sum_probs=100.8
Q ss_pred HHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccC--
Q 012567 287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP-- 364 (460)
Q Consensus 287 ~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP-- 364 (460)
-..++..|.+.|+.+|+++.++..+++|++||+|+.+|+.+.+|+.. .+|.+|++++++|.+++++|++.+....+
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 35688899999999999999999999999999999999999999854 47999999999999999999765422111
Q ss_pred --------------------------------cch---HHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCC
Q 012567 365 --------------------------------FHM---VEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLS 401 (460)
Q Consensus 365 --------------------------------~~~---~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS 401 (460)
... .+....+..++..|+.+.+ .+.+++|||+.||+|
T Consensus 98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~L~~L~~~~r~v~~L~~~~g~s~~EIAe~lgis 177 (206)
T PRK12544 98 LRDEEEEEDFEELFDESGHWQKDERPQAWGNPEESLEQEQFWRIFEACLDGLPAKYARVFMMREFIELETNEICHAVDLS 177 (206)
T ss_pred ccccchhhHHHHhhcccccccccccccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcC
Confidence 000 1111235556666655433 788999999999999
Q ss_pred HHHHHHHHhCCCCC
Q 012567 402 MKRLHAVLLSPKAP 415 (460)
Q Consensus 402 ~e~Vk~~l~~ar~~ 415 (460)
+++|+..+++++..
T Consensus 178 ~~tV~~~l~RAr~~ 191 (206)
T PRK12544 178 VSNLNVLLYRARLR 191 (206)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999988764
No 110
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=99.31 E-value=1e-11 Score=116.04 Aligned_cols=126 Identities=13% Similarity=0.105 Sum_probs=100.8
Q ss_pred HHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCc-
Q 012567 287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF- 365 (460)
Q Consensus 287 ~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~- 365 (460)
++.|+..|.+.|+.++.++.++..+++|++||.++.+|+.+..|++ +..|.+|++.+++|.+++++|++.+....+.
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~aeDi~QEvflkl~~~~~~~~~--~~~~~~wL~~i~~n~~~d~~Rk~~~~~~~~~~ 80 (181)
T PRK09637 3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKD--GSSIKSWLYQIANNTIIDFYRKKNRSEELPDD 80 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHhHHHhcc--ccchHHHHHHHHHHHHHHHHHhccccCCcchh
Confidence 6789999999999999999999999999999999999999999985 3479999999999999999997654322211
Q ss_pred -------c----hHHHHHHHHHHHHHHHHHh--------CCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567 366 -------H----MVEATYRVKEARKQLYSEN--------GRHPNNEEVAEATGLSMKRLHAVLLSPKA 414 (460)
Q Consensus 366 -------~----~~e~i~kl~ka~~~L~~~~--------gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~ 414 (460)
. ..+....+..+...|+... -.+.+.+|||+.||+|.++|+..+.+++.
T Consensus 81 ~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~~~~EIA~~lgis~~tV~~~l~Rar~ 148 (181)
T PRK09637 81 LLFEDEEREENAKKELAPCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRV 148 (181)
T ss_pred hhccCCChhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 0 1122233555555555432 27889999999999999999999987765
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=99.31 E-value=4.6e-12 Score=113.82 Aligned_cols=120 Identities=13% Similarity=0.116 Sum_probs=96.3
Q ss_pred HHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccccc--------
Q 012567 292 TSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL-------- 363 (460)
Q Consensus 292 ~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iri-------- 363 (460)
..|.+.|+.++.++.++..+++|++||+++.+|+.+++|++ .+|.+|++..+++.++++++++.+....
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~~~d~~r~~~~~~~~~~~~~~~~ 78 (154)
T TIGR02950 2 REYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNAFIDWYRKDKKIQTIDDDAIGDL 78 (154)
T ss_pred chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHHHHHHHHHhhhhccccHhhhhhc
Confidence 57889999999999999899999999999999999999996 4799999999999999999875432111
Q ss_pred -------Ccch---HHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567 364 -------PFHM---VEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKA 414 (460)
Q Consensus 364 -------P~~~---~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~ 414 (460)
|... .+....+.+++..|+.... .+.+++|||+.||+|+++|+..+++++.
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~ 147 (154)
T TIGR02950 79 EQHPVESPEHHLLIKIEQEEITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARK 147 (154)
T ss_pred cccccCChhHHHHHHHHHHHHHHHHHhCCHhheeeeeehhhccCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 0100 1122456777777766432 6789999999999999999999987754
No 112
>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=99.30 E-value=7.3e-12 Score=115.61 Aligned_cols=122 Identities=18% Similarity=0.200 Sum_probs=97.2
Q ss_pred HHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcc-----
Q 012567 292 TSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFH----- 366 (460)
Q Consensus 292 ~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~----- 366 (460)
..|.+.++.+++++.++..+++|++||+|+.+|+++.+|+. +.+|.+|++.+++|.+++++|+..+...++..
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~l~~~~~~~~~--~~~f~~wl~~iarn~~~d~~Rk~~~~~~~~~~~~~~~ 79 (170)
T TIGR02959 2 DEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKD--GQKIQSWLYQIARNTIIDFYRSKSRSVELPESLLAAD 79 (170)
T ss_pred chHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCC--cccHHHHHHHHHHHHHHHHHHhccCccccchhhcccC
Confidence 46788999999999999999999999999999999999996 35899999999999999999987653332211
Q ss_pred -------hHHHHHHHHHHHHHHHHH--------hCCCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567 367 -------MVEATYRVKEARKQLYSE--------NGRHPNNEEVAEATGLSMKRLHAVLLSPKAP 415 (460)
Q Consensus 367 -------~~e~i~kl~ka~~~L~~~--------~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~ 415 (460)
..+....+.+++..|+.. .-.+.+.+|||+.||+|+.+|+..+++++..
T Consensus 80 ~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~~ 143 (170)
T TIGR02959 80 SAREETFVKELSQCIPPMIKELPDEYREAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQRGRKK 143 (170)
T ss_pred CccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 111223355555555543 2378899999999999999999999887754
No 113
>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=99.30 E-value=7.7e-12 Score=97.93 Aligned_cols=70 Identities=23% Similarity=0.377 Sum_probs=67.0
Q ss_pred HHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCc
Q 012567 290 MITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSR 359 (460)
Q Consensus 290 LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r 359 (460)
|++.|.++|++++++|.+++.+.+|++||++++||+++.+||++.+..|.+|++.+++|.++++++++++
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 6889999999999999999999999999999999999999999999899999999999999999998764
No 114
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=99.29 E-value=1.4e-11 Score=116.10 Aligned_cols=129 Identities=17% Similarity=0.151 Sum_probs=102.3
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccccc
Q 012567 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL 363 (460)
Q Consensus 284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iri 363 (460)
.++++.|.. |.+.|+.+|+.+.++..+.+|++||.|+.+|+.+..|+.. ..|.+|++.+++|.+++++|++.+....
T Consensus 7 ~~~~~~l~~-~~~~l~~~a~~~l~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n~~~d~~Rk~~r~~~~ 83 (188)
T PRK12546 7 RDPRDELVE-HLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSDRRKHKREVPD 83 (188)
T ss_pred hhHHHHHHH-HHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHHHHHHHHHHhcccccC
Confidence 456666665 7799999999999999999999999999999999999853 4799999999999999999986542111
Q ss_pred C------------cc-hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567 364 P------------FH-MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAP 415 (460)
Q Consensus 364 P------------~~-~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~ 415 (460)
. .. .......+..++..|+.... .+.+.+|||+.||||+.+|+..+++++..
T Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~v~~L~~~~g~s~~EIA~~LgiS~~tVk~~l~Rar~~ 156 (188)
T PRK12546 84 PEGVHAASLAVKPAHDGRLAMSDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARAR 156 (188)
T ss_pred cccccccccccCCcchhHHHHHHHHHHHHhCCHHHhHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 0 00 01122456677777766533 78899999999999999999999987753
No 115
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=99.27 E-value=1.7e-11 Score=114.85 Aligned_cols=127 Identities=14% Similarity=0.129 Sum_probs=101.2
Q ss_pred HHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccC--
Q 012567 287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP-- 364 (460)
Q Consensus 287 ~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP-- 364 (460)
++..+..+++.|+.++.++.++..+.+|++||.|+.+|+.+..|+.. ..|.+|++.+++|.+++++|++.+.....
T Consensus 6 ~~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~Rk~~~~~~~~~~ 83 (182)
T PRK12511 6 KRFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSG--GNLRTWLMSILHNAFIDELRRRRVEARRADE 83 (182)
T ss_pred hhhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCc--cchHHHHHHHHHHHHHHHHHhhccccccccc
Confidence 44557889999999999999999999999999999999999999853 47999999999999999999865321110
Q ss_pred ----------cc--hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567 365 ----------FH--MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAP 415 (460)
Q Consensus 365 ----------~~--~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~ 415 (460)
.. .......+.+++..|+...+ .+.+++|||+.||||+++|+..+++++..
T Consensus 84 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~eg~s~~EIA~~lgis~~tV~~~l~Rar~~ 154 (182)
T PRK12511 84 LAVLADASLPAAQEHAVRLAQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAA 154 (182)
T ss_pred hhhccccCCCcchHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHHHH
Confidence 00 11223446677777766533 78899999999999999999999887754
No 116
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=99.24 E-value=4.9e-11 Score=110.23 Aligned_cols=128 Identities=10% Similarity=0.089 Sum_probs=101.2
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccc--
Q 012567 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI-- 361 (460)
Q Consensus 284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~i-- 361 (460)
..++..++..|.+.++.++.++.++..+++|++||.|+.+|+. ..|++- ..|.+|++.+++|.+++++|++.+..
T Consensus 9 ~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~-~~~~~~--~~~~~wL~~iarn~~~d~~R~~~~~~~~ 85 (172)
T PRK09651 9 SLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTI--RDPRSFLCTIAKRVMVDLFRRNALEKAY 85 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhh-cccccc--cCHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 6789999999999999999999999999999999999999997 456533 26899999999999999998653211
Q ss_pred -----cc-----Cc--ch---HHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567 362 -----RL-----PF--HM---VEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKA 414 (460)
Q Consensus 362 -----ri-----P~--~~---~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~ 414 (460)
.+ +. .. .+....+..++..|+.+.+ .+.+++|||+.||+|+++|+..++++..
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~ 161 (172)
T PRK09651 86 LEMLALMPEGGAPSPEERESQLETLQLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKATE 161 (172)
T ss_pred hhHHhhccccCCCChHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhhhccCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 00 11 01 1233456677777766533 7889999999999999999999987654
No 117
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=99.20 E-value=5.1e-11 Score=116.21 Aligned_cols=133 Identities=10% Similarity=0.041 Sum_probs=101.5
Q ss_pred HHHhccHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhc
Q 012567 278 RRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQ 357 (460)
Q Consensus 278 ~~l~~G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~ 357 (460)
+.+.....+++.+++.| +.++.++.++.++..+.+|++||.|+.+|+. |+.. ..|.+|++.+++|.+++++|++
T Consensus 11 ~~~~~~~~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~~---~~~~--~~~~~WL~~IarN~~id~~Rk~ 84 (228)
T PRK06704 11 NHIDMNHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQK---YSNK--DICMTLVYKIARNRWLDQIKSK 84 (228)
T ss_pred cccCCCHHHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH---cCcc--ccHHHHHHHHHHHHHHHHHhcc
Confidence 33444477888777766 7899999999999999999999999999976 5533 3599999999999999999986
Q ss_pred CcccccCc---------chHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCCc
Q 012567 358 SRTIRLPF---------HMVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAPR 416 (460)
Q Consensus 358 ~r~iriP~---------~~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~l 416 (460)
.+...+.. ...+....+..+...|+.+.+ .+.|++|||+.||+|+++|+..+++++..+
T Consensus 85 k~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~R~v~lL~~~eg~S~~EIAe~LgiS~~tVksrL~Rark~L 160 (228)
T PRK06704 85 SVHEKIRDQITFEEPHEKIADLHEMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRL 160 (228)
T ss_pred ccccccccccccCChHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHhhCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 54221111 011223345666666666433 678999999999999999999999888754
No 118
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=99.20 E-value=5.4e-11 Score=108.19 Aligned_cols=123 Identities=15% Similarity=0.193 Sum_probs=95.4
Q ss_pred HHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccc------
Q 012567 289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR------ 362 (460)
Q Consensus 289 ~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~ir------ 362 (460)
.++..|.+.++.+|.++.++..+++|++||+++++|+....|++. .|.+|++.+++|.+++++|++.+...
T Consensus 2 ~~~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~---~~~~wl~~iarn~~~d~~R~~~~~~~~~~~~~ 78 (163)
T PRK07037 2 DVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVK---QPVAYLFRIVRNLAIDHYRRQALENKYHGDEE 78 (163)
T ss_pred hHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhccccCCcc---cHHHHHHHHHHHHHHHHHHhhccccccccccc
Confidence 367789999999999999999999999999999999988877653 58999999999999999987543111
Q ss_pred ----cCc---c------hHHHHHHHHHHHHHHHHHh--------CCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567 363 ----LPF---H------MVEATYRVKEARKQLYSEN--------GRHPNNEEVAEATGLSMKRLHAVLLSPKA 414 (460)
Q Consensus 363 ----iP~---~------~~e~i~kl~ka~~~L~~~~--------gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~ 414 (460)
.+. . ..+....+..+...|+.+. -.+.+++|||+.||+|.++|+..+.+++.
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~EIA~~lgis~~tV~~~l~ra~~ 151 (163)
T PRK07037 79 DGLDVPSPEASPEAALINRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALV 151 (163)
T ss_pred cccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 110 0 1122344566666665542 27889999999999999999999887654
No 119
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=99.18 E-value=5.4e-11 Score=108.03 Aligned_cols=121 Identities=9% Similarity=0.042 Sum_probs=94.8
Q ss_pred HHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccccc--------
Q 012567 292 TSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL-------- 363 (460)
Q Consensus 292 ~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iri-------- 363 (460)
..|.+.++.++.++.++..+++|++||.|+.+|+....|++ .+|.+|++.+++|.+++++|++......
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~---~~~~~wL~~ia~n~~~d~~R~~~~~~~~~~~~~~~~ 78 (159)
T PRK12527 2 ENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQI---EHPRAFLYRTALNLVVDRHRRHRVRQAEPLEVLDEE 78 (159)
T ss_pred hhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhccccccc---cchHHHHHHHHHHHHHHHHHHHhcccccchhhhhcc
Confidence 56888899999999999899999999999999999999874 2799999999999999999865321100
Q ss_pred -----C--cc---hHHHHHHHHHHHHHHHHHh--------CCCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567 364 -----P--FH---MVEATYRVKEARKQLYSEN--------GRHPNNEEVAEATGLSMKRLHAVLLSPKAP 415 (460)
Q Consensus 364 -----P--~~---~~e~i~kl~ka~~~L~~~~--------gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~ 415 (460)
| .. ..+....+..++..|+.+. ..+.+++|||+.||+|+++|+..+.+++..
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~ra~~~ 148 (159)
T PRK12527 79 ERLHSPSPQTRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKH 148 (159)
T ss_pred ccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 0 00 1122335667777776643 378899999999999999999999877653
No 120
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=99.18 E-value=1.6e-10 Score=106.19 Aligned_cols=128 Identities=11% Similarity=0.094 Sum_probs=99.8
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccc--
Q 012567 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI-- 361 (460)
Q Consensus 284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~i-- 361 (460)
..++..++..|.+.++.++.++.++..+.+|++||.|+.+|+....++. ..|.+|++++++|.+++++|+.....
T Consensus 8 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~~---~~~~~wl~~Iarn~~~d~~Rr~~~~~~~ 84 (168)
T PRK12525 8 NTLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEGWRRQDLERAY 84 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCcccc---cCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5789999999999999999999999999999999999999986555442 37999999999999999998643110
Q ss_pred -----c-------cCcc---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567 362 -----R-------LPFH---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKA 414 (460)
Q Consensus 362 -----r-------iP~~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~ 414 (460)
. .|.. ..+....+.+++..|+...+ .+.|++|||+.||+|+++|+..+.++..
T Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~eg~s~~EIA~~l~is~~tV~~~l~ra~~ 160 (168)
T PRK12525 85 LQSLAEAPEAVQPSPEEQWMVIETLLAIDRLLDGLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAFK 160 (168)
T ss_pred HHHHhcccccccCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 0 1110 11223446666666665433 7889999999999999999999987653
No 121
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=99.09 E-value=4.2e-10 Score=112.91 Aligned_cols=127 Identities=14% Similarity=0.061 Sum_probs=98.1
Q ss_pred HHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcc--c--
Q 012567 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT--I-- 361 (460)
Q Consensus 286 A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~--i-- 361 (460)
....++..|.+.++.+|+++.++..+++|++||.++. |.....|+ ...|.+|++++++|.|++++|++.+. .
T Consensus 5 ~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~-~~~~~~~~---~~~~~~WL~~Ia~n~~~d~lR~~~~~~~~~~ 80 (293)
T PRK09636 5 DAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQ---IRDPRAWLTRVVTRLCLDRLRSARHRRETYV 80 (293)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHhccccc---ccCHHHHHHHHHHHHHHHHHHhhhccccccc
Confidence 4678999999999999999999999999999999999 55667775 34799999999999999999975421 0
Q ss_pred --ccCcc----------h---HHH-HHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCCc
Q 012567 362 --RLPFH----------M---VEA-TYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAPR 416 (460)
Q Consensus 362 --riP~~----------~---~e~-i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~l 416 (460)
.++.. . .+. ...+..++..|+.+.+ .+.+++|||+.||+|+.+|++.+++++..+
T Consensus 81 ~~~~~e~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~R~v~~L~~~~g~s~~EIA~~lg~s~~tVk~~l~RAr~~L 159 (293)
T PRK09636 81 GPWLPEPVVEELDDPLEAVVAAEDLSLALMLALERLSPLERAAFLLHDVFGVPFDEIASTLGRSPAACRQLASRARKHV 159 (293)
T ss_pred CCcCCcCCCCCCCChHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 01110 0 111 1235666666665433 788999999999999999999999877644
No 122
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=99.04 E-value=5.6e-10 Score=112.47 Aligned_cols=128 Identities=10% Similarity=-0.045 Sum_probs=98.4
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcc-c--
Q 012567 285 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT-I-- 361 (460)
Q Consensus 285 ~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~-i-- 361 (460)
..+..++..|.+.++.+|+++.++..+.+|++||.|+.+|++...+ ...|.+|++.+.+|.|++++|+..+. .
T Consensus 5 ~~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~----~~~~~aWL~~Ia~n~~id~lRk~~~rr~~~ 80 (290)
T PRK09635 5 DPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGD----IDDERGWLIVVTSRLCLDHIKSASTRRERP 80 (290)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCccc----cccHHHHHHHHHHHHHHHHHhhhhccCcCc
Confidence 5688899999999999999999999999999999999999986543 13699999999999999999874311 0
Q ss_pred -----ccC----------cch----HHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567 362 -----RLP----------FHM----VEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKA 414 (460)
Q Consensus 362 -----riP----------~~~----~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~ 414 (460)
..| ... .+....+..++..|+...+ .+.+++|||+.||+|+.+|++.+++++.
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~al~~~L~~L~p~~R~vf~L~~~~g~s~~EIA~~Lgis~~tVr~~l~RAr~ 160 (290)
T PRK09635 81 QDIAAWHDGDASVSSVDPADRVTLDDEVRLALLIMLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARR 160 (290)
T ss_pred ccccccCccccCCCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHHhCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 001 000 1112345556666655433 6789999999999999999999988776
Q ss_pred Cc
Q 012567 415 PR 416 (460)
Q Consensus 415 ~l 416 (460)
.+
T Consensus 161 ~L 162 (290)
T PRK09635 161 KI 162 (290)
T ss_pred HH
Confidence 44
No 123
>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=99.03 E-value=1e-09 Score=97.88 Aligned_cols=113 Identities=10% Similarity=0.062 Sum_probs=85.3
Q ss_pred HHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhh-----cCCCCCCchHhHHHHHHHHHHHHHhhhcCccc
Q 012567 287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEK-----FDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI 361 (460)
Q Consensus 287 ~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiek-----FDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~i 361 (460)
++.++..|.++++.+|++|... +| +||.++.+|....+ |++ ...|.||++.+++|.+++++|++.+..
T Consensus 1 f~~~~~~y~~~l~~~~~~~~~~----~~-~qdvf~~~w~~~~~~~~~~~~~--~~~~~~wL~~iarN~~id~~Rk~~~~~ 73 (142)
T TIGR03209 1 FEEIYMNFKNTIDIFTRKYNLY----YD-YNDILYHLWIILKKIDLNKFNT--ENDLEKYISTSLKRYCLDICNKKNRDK 73 (142)
T ss_pred ChHHHHHHHHHHHHHHHHhcch----hh-HHHHHHHHHHHHHHhhhhhcCc--hhHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 3679999999999999999662 24 49999999999865 553 247999999999999999999764321
Q ss_pred cc------------C-cc--hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHH
Q 012567 362 RL------------P-FH--MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLH 406 (460)
Q Consensus 362 ri------------P-~~--~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk 406 (460)
.. + .. ..+....+.+++..|+..++ .+.|++|||+.||||+++|+
T Consensus 74 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~~~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 74 KIIYNSEITDIKLSLINVYSSNDLEFEFNDLISILPNKQKKIIYMKFFEDMKEIDIAKKLHISRQSVY 141 (142)
T ss_pred hhhhhhhhhccccchhHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHhhc
Confidence 11 0 00 11123457777777777544 78899999999999999986
No 124
>PRK09191 two-component response regulator; Provisional
Probab=99.02 E-value=7.1e-10 Score=107.23 Aligned_cols=121 Identities=14% Similarity=0.078 Sum_probs=95.6
Q ss_pred HHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCc
Q 012567 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF 365 (460)
Q Consensus 286 A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~ 365 (460)
++..|+..|.+.|+.+|.++.++..+.+|++||+|+.+|+...+|++. ..|.+|+++++++........... ...+
T Consensus 2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~--~~~~~wl~~~~~~~~~~~~~~~~~-~~~~- 77 (261)
T PRK09191 2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEA--SSPRVGLYRLFHRLWSSAGANDPE-PGSP- 77 (261)
T ss_pred chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCC--cchhhHHHHHHHHHhccccccCCC-CCCC-
Confidence 578899999999999999999999999999999999999999999864 469999999998876443222110 0011
Q ss_pred chHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567 366 HMVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKA 414 (460)
Q Consensus 366 ~~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~ 414 (460)
....+.+++..|+...+ .+.|++|||+.||+|+++|+..+++++.
T Consensus 78 ----~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~l~~s~~tV~~~l~ra~~ 130 (261)
T PRK09191 78 ----FEARAERRLAGLTPLPRQAFLLTALEGFSVEEAAEILGVDPAEAEALLDDARA 130 (261)
T ss_pred ----chHHHHHHHHhCCHHHhHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 11256777777766544 6889999999999999999999886654
No 125
>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=98.99 E-value=7.3e-10 Score=89.71 Aligned_cols=76 Identities=29% Similarity=0.389 Sum_probs=64.9
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCCCCcccccccCCCcchhh
Q 012567 369 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSVCFILNLADSLII 444 (460)
Q Consensus 369 e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d~tl~Eli~D~~~ds~~~ 444 (460)
+.+++|.++...|.+++|+.||.+|||+.|||++++|..++..++..+||+.+++.+++.++.++|+|+...++..
T Consensus 1 E~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~~~~l~~~i~d~~~~~P~e 76 (78)
T PF04539_consen 1 EKLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDEDDSTLGDFIEDDDAPSPEE 76 (78)
T ss_dssp HHHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSSSEEGGGSSB-SSS--HHH
T ss_pred ChHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCCCCchhheecCCCCCChhh
Confidence 4578999999999999999999999999999999999999999999999999999888899999999997776643
No 126
>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=98.98 E-value=1.7e-09 Score=108.16 Aligned_cols=124 Identities=16% Similarity=0.053 Sum_probs=92.6
Q ss_pred HHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccc------c
Q 012567 289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI------R 362 (460)
Q Consensus 289 ~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~i------r 362 (460)
+++..|.+.++.+|+++.++..+.+|++||+++.+++. .|+. ...|.+|++++++|.+++++|+..+.. .
T Consensus 1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~--~~~~~awL~~Ia~n~~ld~lR~~~~~~~~~~~~~ 76 (281)
T TIGR02957 1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQ--IENPKAYLTKVVTRRCIDVLRSARARREVYVGPW 76 (281)
T ss_pred ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Cccc--ccCHHHHHHHHHHHHHHHHHHHhhhcccccCCCC
Confidence 36889999999999999999999999999999997765 5543 237999999999999999998753210 1
Q ss_pred cCcc----------hH---HHH-HHHHHHHHHHHHHh--------CCCCCHHHHHHHhCCCHHHHHHHHhCCCCCc
Q 012567 363 LPFH----------MV---EAT-YRVKEARKQLYSEN--------GRHPNNEEVAEATGLSMKRLHAVLLSPKAPR 416 (460)
Q Consensus 363 iP~~----------~~---e~i-~kl~ka~~~L~~~~--------gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~l 416 (460)
+|.. .. +.+ ..+..++..|+... -.+.+++|||+.||+|+.+|++.+++++..+
T Consensus 77 ~~e~~~~~~~~~~~~~~~~e~~~~~l~~~l~~L~~~~R~v~~L~~~~g~s~~EIA~~lg~s~~tVr~~l~RAr~~L 152 (281)
T TIGR02957 77 LPEPLLTTSADPAESVELAESLSMAYLLLLERLSPLERAVFVLREVFDYPYEEIASIVGKSEANCRQLVSRARRHL 152 (281)
T ss_pred CCcccCCCCCChHHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 1110 01 111 12344555555432 2788999999999999999999998877644
No 127
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=98.91 E-value=2.3e-09 Score=97.01 Aligned_cols=106 Identities=12% Similarity=0.050 Sum_probs=79.0
Q ss_pred CCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccC----------------------
Q 012567 307 GAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP---------------------- 364 (460)
Q Consensus 307 ~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP---------------------- 364 (460)
++..+++|++||+|+.+|+.+..+ + +..|.+|++.+++|.+++++|++.+..+..
T Consensus 2 ~~~~~AeDivQe~fl~~~~~~~~~-~--~~~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 78 (161)
T PRK09047 2 RDDDAALDIVQDAMIKLAEKYGDR-P--AAEWPPLFQRILQNRIHDWFRRQKVRNTWVSLFSSFSDDDDDDDFDPLETLD 78 (161)
T ss_pred CCHHHHHHHHHHHHHHHHHHHhhc-c--cCchHHHHHHHHHHHHHHHHHhhcccccccccccccccccccccccHHHHhc
Confidence 345678999999999999998863 2 457999999999999999998754321110
Q ss_pred ------cc------hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567 365 ------FH------MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAP 415 (460)
Q Consensus 365 ------~~------~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~ 415 (460)
.. ..+....+.+++..|+..++ .+.+++|||+.||+|+++|+..+++++..
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~ 149 (161)
T PRK09047 79 SADEGAESPADKLERAQVLQLIEEAIQKLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATHA 149 (161)
T ss_pred cccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 00 01123446667777766533 78899999999999999999999877653
No 128
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=98.40 E-value=3.7e-06 Score=79.11 Aligned_cols=141 Identities=21% Similarity=0.200 Sum_probs=96.8
Q ss_pred HHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCC---CCCccc--HHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHH
Q 012567 274 RELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGA---GMNLQD--LVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIK 347 (460)
Q Consensus 274 ~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~---g~d~eD--LiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr 347 (460)
..|+..++.| ..|.+.|+..|++-+..+|+++.+. +.+.+| |+++.|+.+++.-...+......|..|+...++
T Consensus 5 t~ll~~~~~GD~~A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~~lv~ea~lrl~~~~~~~~~~~~~~f~~~~~~~~r 84 (185)
T PF07638_consen 5 TELLDRWRQGDEAALDQLFERYYPELRRLARRRLRRERRGHDLQDTALVHEAFLRLARRGRFVQFSDRRHFWALLARIMR 84 (185)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHhccccCCchhHHHHHHHHHHHHhccccccCCCCHHHHHHHHHHHHH
Confidence 3566777888 9999999999999999999876532 345555 466777777763332233333469999999999
Q ss_pred HHHHHHhhhcCcccc------cC---------cchHHHHHHHHHHHHHHHH-----------HhCCCCCHHHHHHHhCCC
Q 012567 348 QAVRKSLSDQSRTIR------LP---------FHMVEATYRVKEARKQLYS-----------ENGRHPNNEEVAEATGLS 401 (460)
Q Consensus 348 ~aI~~~Lrk~~r~ir------iP---------~~~~e~i~kl~ka~~~L~~-----------~~gr~pS~eEIAe~LGIS 401 (460)
+.+++..|++....| .+ ....+..-.+.++...|.. ..-.+.|.+|||+.||||
T Consensus 85 r~lid~~R~~~a~KRg~~~~~~~l~~~~~~~~~~~~~~~~~l~e~l~~L~~l~~~~~~~v~l~~~~Gls~~EIA~~lgiS 164 (185)
T PF07638_consen 85 RKLIDHARRRQAQKRGGDQVRVELDERADSGDEPSPEELLELEEALERLLALDPRQRRVVELRFFEGLSVEEIAERLGIS 164 (185)
T ss_pred HHHHHHHHHHHHHhcCCCCcccchhhhhccccCCCHHHHHHHHHHHHHHHccCHHHHHHHHHHHHCCCCHHHHHHHHCcC
Confidence 999999986443222 11 0112223334444443322 122678999999999999
Q ss_pred HHHHHHHHhCCCC
Q 012567 402 MKRLHAVLLSPKA 414 (460)
Q Consensus 402 ~e~Vk~~l~~ar~ 414 (460)
+.+|+..+..++.
T Consensus 165 ~~tV~r~l~~aR~ 177 (185)
T PF07638_consen 165 ERTVRRRLRRARA 177 (185)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999887663
No 129
>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPro: IPR009042 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 [, ]. ; 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: 1SMY_F 1IW7_P 1SIG_A 3IYD_F 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P 3DXJ_P ....
Probab=98.07 E-value=1.3e-06 Score=61.67 Aligned_cols=32 Identities=44% Similarity=0.559 Sum_probs=28.5
Q ss_pred CCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHH
Q 012567 211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLL 243 (460)
Q Consensus 211 ~d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~ 243 (460)
+|+++ ||++| +++||||++||++|+++|+.+.
T Consensus 1 ~D~l~~Yl~ei-~~~~LLt~eeE~~LA~~i~~g~ 33 (37)
T PF00140_consen 1 SDSLRLYLKEI-GRYPLLTAEEEIELARRIRKGD 33 (37)
T ss_dssp HHHHHHHHHHH-HHS-EETTHHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHH-cCCCCCCHHHHHHHHHHHHHhH
Confidence 37899 99999 9999999999999999999863
No 130
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=97.77 E-value=0.00066 Score=75.47 Aligned_cols=32 Identities=34% Similarity=0.583 Sum_probs=30.8
Q ss_pred CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHH
Q 012567 210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDL 242 (460)
Q Consensus 210 ~~d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~ 242 (460)
++||++ ||++| |++||||+|+|++|+++|+.+
T Consensus 102 t~DPVRMYLREM-G~V~LLTREgEIeIAKRIE~G 134 (619)
T PRK05658 102 TDDPVRMYLREM-GTVELLTREGEIEIAKRIEAG 134 (619)
T ss_pred CCChHHHHHHHh-ccCcCCCcHHHHHHHHHHHHH
Confidence 589999 99999 999999999999999999986
No 131
>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=96.30 E-value=0.05 Score=53.11 Aligned_cols=130 Identities=20% Similarity=0.151 Sum_probs=69.9
Q ss_pred HHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHH-HHH
Q 012567 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEG-CRG 322 (460)
Q Consensus 244 ~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG-~IG 322 (460)
++.+....|....|++||..|.|+.+|++...+..... .. ....++++.++++ -..
T Consensus 88 ~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~-------------------~~----~~~~SLd~~~~~~~~~~ 144 (238)
T TIGR02393 88 KLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKK-------------------IA----QEPISLETPIGEEEDSF 144 (238)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH-------------------Hh----ccCCCcCCCCCCCCccc
Confidence 34455677778889999999999999999876542211 00 1122223322211 112
Q ss_pred HHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHHHHHHHHHHHHHHHHHh----CCCCCHHHHHHHh
Q 012567 323 LVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSEN----GRHPNNEEVAEAT 398 (460)
Q Consensus 323 LirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e~i~kl~ka~~~L~~~~----gr~pS~eEIAe~L 398 (460)
+...+.. +..............+..+..++.. +|..-.. -|...+ ..+.|.+|||+.|
T Consensus 145 l~d~l~d--~~~~~p~~~~~~~~~~~~l~~~l~~------L~~~er~----------vl~l~ygl~~~~~~t~~EIA~~l 206 (238)
T TIGR02393 145 LGDFIED--TSIESPDDYAAKELLREQLDEVLET------LTERERK----------VLRMRYGLLDGRPHTLEEVGKEF 206 (238)
T ss_pred HHHHhcC--CCCCChHHHHHHHHHHHHHHHHHHh------CCHHHHH----------HHHHHhCCCCCCCccHHHHHHHH
Confidence 2222221 1111122333333334444444431 3322111 112223 3678999999999
Q ss_pred CCCHHHHHHHHhCCCC
Q 012567 399 GLSMKRLHAVLLSPKA 414 (460)
Q Consensus 399 GIS~e~Vk~~l~~ar~ 414 (460)
|+|.++|+++...+..
T Consensus 207 gis~~~V~q~~~~al~ 222 (238)
T TIGR02393 207 NVTRERIRQIESKALR 222 (238)
T ss_pred CCCHHHHHHHHHHHHH
Confidence 9999999999876544
No 132
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=96.03 E-value=0.036 Score=54.56 Aligned_cols=30 Identities=13% Similarity=0.107 Sum_probs=26.3
Q ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567 385 NGRHPNNEEVAEATGLSMKRLHAVLLSPKA 414 (460)
Q Consensus 385 ~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~ 414 (460)
+..+.|++|||+.||+|+++|+..+++++.
T Consensus 214 ~~~~~s~~EIA~~lgis~~tV~~~~~ra~~ 243 (251)
T PRK07670 214 YKEELTLTEIGQVLNLSTSRISQIHSKALF 243 (251)
T ss_pred HhcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 357889999999999999999999987654
No 133
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=95.86 E-value=0.12 Score=56.57 Aligned_cols=132 Identities=17% Similarity=0.230 Sum_probs=72.0
Q ss_pred HHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHh-HHHHH
Q 012567 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ-EGCRG 322 (460)
Q Consensus 244 ~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQ-EG~IG 322 (460)
++.+.+.+|...+|++||..|.|+.+|++...+....+ +....+++++.+. ++...
T Consensus 359 kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~-----------------------~~~~~~SLD~~i~~d~~~~ 415 (509)
T PRK05901 359 KLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQK-----------------------YNREPISLDKTIGKEGDSQ 415 (509)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH-----------------------hcCCCcccccccccCCccc
Confidence 45567788888899999999999999999876543211 1122233333332 11112
Q ss_pred HHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCH
Q 012567 323 LVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSM 402 (460)
Q Consensus 323 LirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~ 402 (460)
+..-+.. +........+.....+..+...|.. ++..- ..|-..+--| ..+.+.|.+|||+.||||.
T Consensus 416 l~d~l~D--~~~~~p~~~~~~~~l~~~L~~aL~~------L~eRE----r~VI~lRyGL--~~~e~~TL~EIa~~lGVSr 481 (509)
T PRK05901 416 FGDFIED--SEAVSPVDAVSFTLLQDQLQEVLET------LSERE----AGVIRMRFGL--TDGQPKTLDEIGQVYGVTR 481 (509)
T ss_pred HHHhccC--CCCCCHHHHHHHHHHHHHHHHHHhh------CCHHH----HHHHHHHhhc--cCCCCCCHHHHHHHHCCCH
Confidence 2222211 1111223333444445455554432 22221 1111111101 1136789999999999999
Q ss_pred HHHHHHHhCC
Q 012567 403 KRLHAVLLSP 412 (460)
Q Consensus 403 e~Vk~~l~~a 412 (460)
++|+++...+
T Consensus 482 ERVRQIe~kA 491 (509)
T PRK05901 482 ERIRQIESKT 491 (509)
T ss_pred HHHHHHHHHH
Confidence 9999987644
No 134
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=95.44 E-value=0.13 Score=51.34 Aligned_cols=34 Identities=35% Similarity=0.502 Sum_probs=27.7
Q ss_pred HHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHH
Q 012567 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELR 277 (460)
Q Consensus 244 ~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~ 277 (460)
++.+...+|...+|++||..|.|+.+|++...+.
T Consensus 128 ~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~ 161 (264)
T PRK07122 128 RLGRATAELSQRLGRAPTASELAAELGMDREEVV 161 (264)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHH
Confidence 3445566777888999999999999999987654
No 135
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=95.37 E-value=0.15 Score=53.42 Aligned_cols=128 Identities=22% Similarity=0.203 Sum_probs=72.6
Q ss_pred HHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHh-HHHHH
Q 012567 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ-EGCRG 322 (460)
Q Consensus 244 ~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQ-EG~IG 322 (460)
++.+...+|...+|++||..|.|+.+|++...+...+.. +. ...++++.+. ++-..
T Consensus 217 ~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~-------------------~~----~~~SLd~~~~~~~~~~ 273 (367)
T PRK09210 217 KLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKI-------------------AQ----EPVSLETPIGEEDDSH 273 (367)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHH-------------------hc----CCCCcCCCCCCCCcch
Confidence 345667778888999999999999999998766433221 11 1122222221 11111
Q ss_pred HHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHHHHHHHHHHHHHHHHHh----CCCCCHHHHHHHh
Q 012567 323 LVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSEN----GRHPNNEEVAEAT 398 (460)
Q Consensus 323 LirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e~i~kl~ka~~~L~~~~----gr~pS~eEIAe~L 398 (460)
+..-+. |+.............++..+.++|.. +|..-.. | |.-.+ |.+.|.+|||+.|
T Consensus 274 l~d~i~--d~~~~~p~~~~~~~~~~~~l~~~l~~------L~~rEr~----V------l~lrygl~~~~~~tl~EIa~~l 335 (367)
T PRK09210 274 LGDFIE--DQDATSPADHAAYELLKEQLEDVLDT------LTDREEN----V------LRLRFGLDDGRTRTLEEVGKVF 335 (367)
T ss_pred hhhhcc--CCCCCCHHHHHHHHHHHHHHHHHHHh------CCHHHHH----H------HHHHhccCCCCCccHHHHHHHH
Confidence 222221 11112234444555566666665532 3332111 1 11223 3678999999999
Q ss_pred CCCHHHHHHHHhCC
Q 012567 399 GLSMKRLHAVLLSP 412 (460)
Q Consensus 399 GIS~e~Vk~~l~~a 412 (460)
|+|.++|+++...+
T Consensus 336 gvs~erVrQi~~~A 349 (367)
T PRK09210 336 GVTRERIRQIEAKA 349 (367)
T ss_pred CCCHHHHHHHHHHH
Confidence 99999999987644
No 136
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=95.33 E-value=0.25 Score=51.02 Aligned_cols=132 Identities=17% Similarity=0.179 Sum_probs=69.9
Q ss_pred HHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHh-HHHHH
Q 012567 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ-EGCRG 322 (460)
Q Consensus 244 ~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQ-EG~IG 322 (460)
++.+.+..|...+|++||..|.|+.+|++...+..... .+ ....++++.+. ++-..
T Consensus 174 ~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~-------------------~~----~~~~SLd~~~~~~~~~~ 230 (324)
T PRK07921 174 KLARIKRELHQQLGREATDEELAEESGIPEEKIADLLE-------------------HS----RDPVSLDMPVGSDEEAP 230 (324)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHH-------------------Hc----CCCceecCCCCCCCCch
Confidence 45566778888899999999999999999866543211 01 11122222221 11112
Q ss_pred HHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCH
Q 012567 323 LVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSM 402 (460)
Q Consensus 323 LirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~ 402 (460)
|...+..-+ .......+...-.+..+...|.. +|..- ..|-...--| ..+.+.|.+|||+.||||.
T Consensus 231 l~d~l~d~~--~~~pe~~~~~~~~~~~l~~~L~~------L~eRE----r~Vl~~rygl--~~~~~~Tl~eIa~~lgvS~ 296 (324)
T PRK07921 231 LGDFIEDSE--ATSAENAVIAGLLHTDIRSVLAT------LDERE----QQVIRLRFGL--DDGQPRTLDQIGKLFGLSR 296 (324)
T ss_pred HHHHhcCCC--CCCHHHHHHHHHHHHHHHHHHHh------CCHHH----HHHHHHHHhc--CCCCCcCHHHHHHHHCCCH
Confidence 333332211 11123334444444445554431 23221 1111111000 1135679999999999999
Q ss_pred HHHHHHHhCC
Q 012567 403 KRLHAVLLSP 412 (460)
Q Consensus 403 e~Vk~~l~~a 412 (460)
+.|+++...+
T Consensus 297 eRVrQIe~~A 306 (324)
T PRK07921 297 ERVRQIEREV 306 (324)
T ss_pred HHHHHHHHHH
Confidence 9999987654
No 137
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=95.17 E-value=0.03 Score=55.51 Aligned_cols=34 Identities=24% Similarity=0.320 Sum_probs=28.1
Q ss_pred HHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHH
Q 012567 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELR 277 (460)
Q Consensus 244 ~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~ 277 (460)
++.+.+.+|...+|++||..|.|+.+|++...+.
T Consensus 114 ~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~ 147 (256)
T PRK07408 114 QAKKVRQELRQELGRQPTDQEIAQALDISLEEWQ 147 (256)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHH
Confidence 3455677788889999999999999999987654
No 138
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=95.12 E-value=0.29 Score=48.70 Aligned_cols=132 Identities=17% Similarity=0.118 Sum_probs=70.1
Q ss_pred HHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHh----HH
Q 012567 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ----EG 319 (460)
Q Consensus 244 ~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQ----EG 319 (460)
++.+.+..|+..+|++||..+.|..+|++...+...... + ....-.+++|.+. +.
T Consensus 119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~-------------------~--~~~~~~sld~~~~~~~~~~ 177 (268)
T PRK06288 119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYNSLLSK-------------------L--SGTSVVSLNDLWFGGDEGD 177 (268)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHH-------------------H--hcccccchhhhhccCCCcc
Confidence 455667778888999999999999999987654322110 0 0111122223221 00
Q ss_pred HHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhC
Q 012567 320 CRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATG 399 (460)
Q Consensus 320 ~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LG 399 (460)
.+.++..+..- ........+...-....+..++. .+|...... +...+..+.|++|||+.||
T Consensus 178 ~~~l~~~~~~~--~~~~pe~~~~~~e~~~~l~~~l~------~L~~~~r~v----------l~l~~~~~~s~~eIA~~lg 239 (268)
T PRK06288 178 EVSLMDTLESP--AALNPDEIAEREEIKRVIVEAIK------TLPEREKKV----------LILYYYEDLTLKEIGKVLG 239 (268)
T ss_pred cchhhhhccCC--CCCCHHHHHHHHHHHHHHHHHHH------hCCHHHHHH----------HHHHHHcCCCHHHHHHHHC
Confidence 12222222221 11112333333333333433332 234332211 1122346889999999999
Q ss_pred CCHHHHHHHHhCCCC
Q 012567 400 LSMKRLHAVLLSPKA 414 (460)
Q Consensus 400 IS~e~Vk~~l~~ar~ 414 (460)
+|+++|+..++++..
T Consensus 240 is~~tV~~~~~ra~~ 254 (268)
T PRK06288 240 VTESRISQLHTKAVL 254 (268)
T ss_pred cCHHHHHHHHHHHHH
Confidence 999999988876543
No 139
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=95.03 E-value=0.16 Score=54.15 Aligned_cols=35 Identities=20% Similarity=0.351 Sum_probs=29.9
Q ss_pred HHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHH
Q 012567 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR 278 (460)
Q Consensus 244 ~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~ 278 (460)
++.+.+..|...+|+.||..|.|+++|++...+..
T Consensus 263 ~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~ 297 (415)
T PRK07598 263 KIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVRE 297 (415)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 56677788888899999999999999999877654
No 140
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=94.96 E-value=0.33 Score=48.37 Aligned_cols=144 Identities=19% Similarity=0.190 Sum_probs=79.6
Q ss_pred HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHHHHHHhH
Q 012567 216 YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNI 295 (460)
Q Consensus 216 YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~LI~~nl 295 (460)
|||+- . +.--+.-=.+++. ++++...+|+..+|++||..|.|+..|++.+++...+..+ +-
T Consensus 92 ~LR~~-~--~v~vpR~~~~~~~------~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~----------~~ 152 (247)
T COG1191 92 YLRKN-D--SVKVPRSLRELGR------RIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAI----------NG 152 (247)
T ss_pred HHHhC-C--CccCcHHHHHHHH------HHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHh----------cc
Confidence 77776 4 2222333333333 3445677888899999999999999999987665333222 11
Q ss_pred HHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHHHHHHHH
Q 012567 296 RLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVK 375 (460)
Q Consensus 296 rLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e~i~kl~ 375 (460)
.....+--..... +| |. -+...+..+..+-.+...+.+...+.. +|..-. .
T Consensus 153 ~~~~sld~~~~~~----~d----~~---------~~~~~~~~~~~~~~~~~~~~l~~ai~~------L~EREk----~-- 203 (247)
T COG1191 153 SQLLSLDEDVLKD----DD----DD---------VDDQIENPDDGVEKEELLEILKEAIEP------LPEREK----L-- 203 (247)
T ss_pred ccccchhhhhccc----cc----cc---------hhhccccchhHHHHHHHHHHHHHHHHc------cCHHHH----H--
Confidence 1111111111110 01 11 111123345556666666666666541 222110 1
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhC
Q 012567 376 EARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 376 ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
-+.-.+..+.|..|||+.||||...|..+...
T Consensus 204 ----Vl~l~y~eelt~kEI~~~LgISes~VSql~kk 235 (247)
T COG1191 204 ----VLVLRYKEELTQKEIAEVLGISESRVSRLHKK 235 (247)
T ss_pred ----HHHHHHHhccCHHHHHHHhCccHHHHHHHHHH
Confidence 11122346789999999999999999877653
No 141
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=94.85 E-value=0.21 Score=49.51 Aligned_cols=30 Identities=13% Similarity=0.073 Sum_probs=25.8
Q ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567 385 NGRHPNNEEVAEATGLSMKRLHAVLLSPKA 414 (460)
Q Consensus 385 ~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~ 414 (460)
+..+.|.+|||+.||+|.++|+.+++++..
T Consensus 218 y~e~~t~~EIA~~lgis~~~V~~~~~ral~ 247 (257)
T PRK05911 218 YYEELVLKEIGKILGVSESRVSQIHSKALL 247 (257)
T ss_pred HhcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 346889999999999999999999886643
No 142
>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=94.84 E-value=0.21 Score=50.51 Aligned_cols=29 Identities=17% Similarity=0.193 Sum_probs=25.4
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567 386 GRHPNNEEVAEATGLSMKRLHAVLLSPKA 414 (460)
Q Consensus 386 gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~ 414 (460)
+.+.|.+|||+.||+|.++|+++++++..
T Consensus 267 ~~~~Tl~EIa~~lgiS~erVrq~~~rAl~ 295 (298)
T TIGR02997 267 GEPLTLAEIGRRLNLSRERVRQIEAKALR 295 (298)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 36789999999999999999999987643
No 143
>PRK05949 RNA polymerase sigma factor; Validated
Probab=94.81 E-value=0.24 Score=51.18 Aligned_cols=28 Identities=21% Similarity=0.197 Sum_probs=25.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLLSPKA 414 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~~ar~ 414 (460)
.+.|++|||+.||+|.++|++++.++..
T Consensus 285 e~~Tl~EIa~~lgiS~erVrq~~~rAl~ 312 (327)
T PRK05949 285 KELSLAKVGERLNLSRERVRQLEHQALA 312 (327)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 6789999999999999999999887654
No 144
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=94.78 E-value=0.26 Score=49.86 Aligned_cols=28 Identities=18% Similarity=0.236 Sum_probs=25.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLLSPKA 414 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~~ar~ 414 (460)
.+.|.+|||+.||+|.++|+++++.+..
T Consensus 244 ~~~t~~EIa~~lgvs~~~V~q~~~~Al~ 271 (289)
T PRK07500 244 DGATLEALGEELGISKERVRQIEARALE 271 (289)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6789999999999999999999886654
No 145
>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=94.58 E-value=0.28 Score=47.22 Aligned_cols=30 Identities=20% Similarity=0.203 Sum_probs=25.7
Q ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567 385 NGRHPNNEEVAEATGLSMKRLHAVLLSPKA 414 (460)
Q Consensus 385 ~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~ 414 (460)
+..+.|++|||+.||+|.++|+..++++..
T Consensus 188 y~~~~s~~eIA~~lgis~~tV~~~~~ra~~ 217 (224)
T TIGR02479 188 YYEELNLKEIGEVLGLTESRVSQIHSQALK 217 (224)
T ss_pred HhCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 356789999999999999999998876643
No 146
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=94.50 E-value=0.48 Score=49.90 Aligned_cols=34 Identities=26% Similarity=0.393 Sum_probs=27.9
Q ss_pred HHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHH
Q 012567 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELR 277 (460)
Q Consensus 244 ~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~ 277 (460)
++.+....|...+|++||..|.|+.+|++...+.
T Consensus 224 ~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~ 257 (373)
T PRK07406 224 RIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLR 257 (373)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHH
Confidence 4555677788888999999999999999986653
No 147
>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=94.32 E-value=0.094 Score=42.09 Aligned_cols=37 Identities=30% Similarity=0.390 Sum_probs=28.6
Q ss_pred HHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHH
Q 012567 243 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRR 279 (460)
Q Consensus 243 ~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~ 279 (460)
.++.+.+.+|...+||+||..|.|+.+|++...+...
T Consensus 4 ~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~ 40 (78)
T PF04539_consen 4 RKIERARRELEQELGREPTDEEIAEELGISVEEVREL 40 (78)
T ss_dssp HHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHH
Confidence 3567788899999999999999999999998776543
No 148
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=94.31 E-value=0.37 Score=49.42 Aligned_cols=34 Identities=21% Similarity=0.375 Sum_probs=27.4
Q ss_pred HHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHH
Q 012567 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELR 277 (460)
Q Consensus 244 ~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~ 277 (460)
++.+.+..+...+|+.||..+.|+++|++...+.
T Consensus 169 ~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~ 202 (317)
T PRK07405 169 KIKKAQRQLSQQLGRAATIGELAEELELTPKQVR 202 (317)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHH
Confidence 4555667777788999999999999999876543
No 149
>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=93.88 E-value=0.26 Score=39.17 Aligned_cols=56 Identities=16% Similarity=0.173 Sum_probs=45.3
Q ss_pred HHHHHhcc-HHHHHHHHHHhHHHHHHHHHHcc----C--CCCCcccHHhHHHHHHHHHHhhcC
Q 012567 276 LRRRLNYG-ILCKDKMITSNIRLVISIAKNYQ----G--AGMNLQDLVQEGCRGLVRGAEKFD 331 (460)
Q Consensus 276 L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~----~--~g~d~eDLiQEG~IGLirAiekFD 331 (460)
++..+..| ..|.+++++.|.+++.+.+.+-. + ++.--+|+-|+--..|++++-+|+
T Consensus 3 vI~~A~~GD~~A~~~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kLi~~I~~F~ 65 (65)
T PF12645_consen 3 VIKAAKQGDPEAMEEILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKLIEAILKFE 65 (65)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHHHHHHHccC
Confidence 34445566 99999999999999999987622 1 244558999999999999999996
No 150
>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=93.56 E-value=0.8 Score=45.15 Aligned_cols=34 Identities=24% Similarity=0.197 Sum_probs=27.2
Q ss_pred HHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHH
Q 012567 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR 278 (460)
Q Consensus 245 le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~ 278 (460)
+.+...+|...+|++||..|.|+.+|++.+.+..
T Consensus 122 ~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~ 155 (254)
T TIGR02850 122 ALQVRDKLISENSKEPTVSEIAKELKVPQEEVVF 155 (254)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHH
Confidence 3445566777789999999999999999876654
No 151
>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=93.22 E-value=0.4 Score=47.16 Aligned_cols=30 Identities=13% Similarity=0.139 Sum_probs=25.6
Q ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567 385 NGRHPNNEEVAEATGLSMKRLHAVLLSPKA 414 (460)
Q Consensus 385 ~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~ 414 (460)
+..+.|++|||+.||+|.++|+..++++..
T Consensus 218 ~~~g~s~~eIA~~lgis~~~V~~~~~ra~~ 247 (255)
T TIGR02941 218 FEENLSQKETGERLGISQMHVSRLQRQAIS 247 (255)
T ss_pred HcCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 356889999999999999999999876543
No 152
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=93.22 E-value=0.62 Score=45.24 Aligned_cols=30 Identities=17% Similarity=0.180 Sum_probs=26.0
Q ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567 385 NGRHPNNEEVAEATGLSMKRLHAVLLSPKA 414 (460)
Q Consensus 385 ~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~ 414 (460)
+..+.|++|||+.||+|+++|+..++++..
T Consensus 197 ~~~g~s~~EIA~~lgis~~tV~~~~~ra~~ 226 (236)
T PRK06986 197 YQEELNLKEIGAVLGVSESRVSQIHSQAIK 226 (236)
T ss_pred hccCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 346789999999999999999999887654
No 153
>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=92.70 E-value=0.061 Score=40.16 Aligned_cols=30 Identities=20% Similarity=0.174 Sum_probs=22.5
Q ss_pred HhCCCCCHHHHHHHhCCCHHHHHHHHhCCC
Q 012567 384 ENGRHPNNEEVAEATGLSMKRLHAVLLSPK 413 (460)
Q Consensus 384 ~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar 413 (460)
.+..+.|+.|||+.+|+|+++|+..+++++
T Consensus 22 ~~~~g~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 22 RYFQGMSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp HHTS---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHHCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 356889999999999999999999988654
No 154
>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=92.49 E-value=0.95 Score=43.69 Aligned_cols=32 Identities=34% Similarity=0.482 Sum_probs=25.6
Q ss_pred HhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHH
Q 012567 246 EGLREVLSERCGGSPTFAQWAAAAGVDQRELR 277 (460)
Q Consensus 246 e~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~ 277 (460)
.+....|...+|+.||..|.|+.+|++...+.
T Consensus 100 ~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~ 131 (231)
T TIGR02885 100 RYMKEELSKELGREPTINELAEALGVSPEEIV 131 (231)
T ss_pred HHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHH
Confidence 33456677778999999999999999987654
No 155
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=91.56 E-value=2.3 Score=41.96 Aligned_cols=33 Identities=24% Similarity=0.231 Sum_probs=26.7
Q ss_pred HHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHH
Q 012567 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELR 277 (460)
Q Consensus 245 le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~ 277 (460)
+.+...++....|++|+..|.|..+|++...+.
T Consensus 125 ~~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~ 157 (258)
T PRK08215 125 ALQVREKLINENSKEPTVEEIAKELEVPREEVV 157 (258)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHH
Confidence 334556677788999999999999999987764
No 156
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=91.20 E-value=2.3 Score=41.58 Aligned_cols=33 Identities=18% Similarity=0.336 Sum_probs=26.9
Q ss_pred HHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHH
Q 012567 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELR 277 (460)
Q Consensus 245 le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~ 277 (460)
+.+....|...+|++||..|.|+.+|++...+.
T Consensus 103 i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~ 135 (231)
T PRK12427 103 TNDAIREIAKRLGHEPNFEEISAELNLTAEEYQ 135 (231)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHH
Confidence 344566777788999999999999999987654
No 157
>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=91.18 E-value=1.9 Score=43.21 Aligned_cols=30 Identities=23% Similarity=0.283 Sum_probs=26.6
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567 386 GRHPNNEEVAEATGLSMKRLHAVLLSPKAP 415 (460)
Q Consensus 386 gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~ 415 (460)
-.+.|++|||+.||+|+++|+.+++++...
T Consensus 240 ~e~~s~~EIA~~Lgis~~tVk~~l~rAlkk 269 (285)
T TIGR02394 240 YEPATLEEVAAEVGLTRERVRQIQVEALKK 269 (285)
T ss_pred CCCccHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 467899999999999999999999877654
No 158
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=90.86 E-value=2.6 Score=42.55 Aligned_cols=26 Identities=19% Similarity=0.299 Sum_probs=23.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHhCC
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLLSP 412 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~~a 412 (460)
.+.|.+|||+.||+|.++|+++...+
T Consensus 247 ~~~Tl~EIA~~lgvS~~rVrqi~~~A 272 (284)
T PRK06596 247 DKSTLQELAAEYGVSAERVRQIEKNA 272 (284)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 57899999999999999999988754
No 159
>PRK05572 sporulation sigma factor SigF; Validated
Probab=90.41 E-value=2 Score=42.28 Aligned_cols=28 Identities=18% Similarity=0.134 Sum_probs=24.4
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHhCCC
Q 012567 386 GRHPNNEEVAEATGLSMKRLHAVLLSPK 413 (460)
Q Consensus 386 gr~pS~eEIAe~LGIS~e~Vk~~l~~ar 413 (460)
..+.|..|||+.+|+|..+|..+.+++.
T Consensus 216 ~~~~s~~eIA~~lgis~~~V~~~~~ral 243 (252)
T PRK05572 216 FKDKTQSEVAKRLGISQVQVSRLEKKIL 243 (252)
T ss_pred hCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4678999999999999999999887654
No 160
>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=90.36 E-value=0.92 Score=35.98 Aligned_cols=42 Identities=33% Similarity=0.389 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCC-HHHHHHHHh
Q 012567 369 EATYRVKEARKQLYSENGRHPNNEEVAEATGLS-MKRLHAVLL 410 (460)
Q Consensus 369 e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS-~e~Vk~~l~ 410 (460)
+...+|..++.....+.|..||..|||+.+|++ ..+|...+.
T Consensus 6 ~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~ 48 (65)
T PF01726_consen 6 ERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLK 48 (65)
T ss_dssp HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHH
Confidence 344567777888888999999999999999997 899988775
No 161
>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=90.25 E-value=2.2 Score=40.99 Aligned_cols=29 Identities=21% Similarity=0.222 Sum_probs=25.2
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567 386 GRHPNNEEVAEATGLSMKRLHAVLLSPKA 414 (460)
Q Consensus 386 gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~ 414 (460)
..+.|++|||+.||+|..+|...++++..
T Consensus 192 ~~~~s~~eIA~~lgis~~~v~~~~~ra~~ 220 (227)
T TIGR02980 192 FEDKTQSEIAERLGISQMHVSRLLRRALK 220 (227)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 46789999999999999999999886643
No 162
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=89.17 E-value=3.2 Score=42.79 Aligned_cols=31 Identities=19% Similarity=0.236 Sum_probs=26.9
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHhCCCCCc
Q 012567 386 GRHPNNEEVAEATGLSMKRLHAVLLSPKAPR 416 (460)
Q Consensus 386 gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~l 416 (460)
..+.|.+|||+.||+|.++|+++++++...+
T Consensus 280 ~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kL 310 (325)
T PRK05657 280 YEAATLEDVAREIGLTRERVRQIQVEALRRL 310 (325)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 3678999999999999999999998776543
No 163
>PHA02547 55 RNA polymerase sigma factor; Provisional
Probab=88.68 E-value=1.2 Score=41.83 Aligned_cols=62 Identities=15% Similarity=0.260 Sum_probs=49.1
Q ss_pred HHHHHHHHccCCCCC---cccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcC
Q 012567 297 LVISIAKNYQGAGMN---LQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS 358 (460)
Q Consensus 297 LV~~IAkry~~~g~d---~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~ 358 (460)
.+..+.++|--+|.. -+|+|.+|.-.+++.+..||+++...+-.|....+-++..+.|.+..
T Consensus 49 Ia~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~kEk 113 (179)
T PHA02547 49 IAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIKKEK 113 (179)
T ss_pred HHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHHHHH
Confidence 344455555434443 68999999999999999999999988999999999998888776543
No 164
>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=88.38 E-value=0.88 Score=33.47 Aligned_cols=30 Identities=23% Similarity=0.191 Sum_probs=25.0
Q ss_pred HHhCCCCCHHHHHHHhCCCHHHHHHHHhCC
Q 012567 383 SENGRHPNNEEVAEATGLSMKRLHAVLLSP 412 (460)
Q Consensus 383 ~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~a 412 (460)
..+..+.|..|||+.||+|.++|+.+...+
T Consensus 15 ~~y~~~~t~~eIa~~lg~s~~~V~~~~~~a 44 (50)
T PF04545_consen 15 LRYFEGLTLEEIAERLGISRSTVRRILKRA 44 (50)
T ss_dssp HHHTST-SHHHHHHHHTSCHHHHHHHHHHH
T ss_pred HHhcCCCCHHHHHHHHCCcHHHHHHHHHHH
Confidence 345788999999999999999999988754
No 165
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=82.15 E-value=19 Score=37.76 Aligned_cols=36 Identities=25% Similarity=0.317 Sum_probs=29.6
Q ss_pred HHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHH
Q 012567 241 DLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQREL 276 (460)
Q Consensus 241 ~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L 276 (460)
-.-+|.+++.+|....|++|+..+.|+.+|+++..+
T Consensus 187 ~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V 222 (342)
T COG0568 187 LINKLRRVKRELLQELGREPTPEEIAEELGVSPDKV 222 (342)
T ss_pred HHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHH
Confidence 334667788888888999999999999999987543
No 166
>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=80.27 E-value=17 Score=36.24 Aligned_cols=27 Identities=19% Similarity=0.268 Sum_probs=23.4
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHhCC
Q 012567 386 GRHPNNEEVAEATGLSMKRLHAVLLSP 412 (460)
Q Consensus 386 gr~pS~eEIAe~LGIS~e~Vk~~l~~a 412 (460)
..+.|.+|||+.||+|.++|+++...+
T Consensus 234 ~~~~t~~eIA~~lgvS~~~V~q~~~~A 260 (270)
T TIGR02392 234 DDKLTLQELAAEYGVSAERIRQIEKNA 260 (270)
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 347899999999999999999887654
No 167
>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=80.23 E-value=2.2 Score=34.85 Aligned_cols=26 Identities=19% Similarity=0.207 Sum_probs=23.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHhC
Q 012567 386 GRHPNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 386 gr~pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
-.+.|+.|||+.||+|+.+|+..+..
T Consensus 30 ~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 30 EAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 36889999999999999999999874
No 168
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=78.08 E-value=1.6 Score=43.00 Aligned_cols=30 Identities=13% Similarity=0.081 Sum_probs=26.0
Q ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567 385 NGRHPNNEEVAEATGLSMKRLHAVLLSPKA 414 (460)
Q Consensus 385 ~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~ 414 (460)
+..+.|.+|||+.||||.++|+..++++..
T Consensus 218 ~~~g~s~~eIA~~l~is~~tV~~~~~ra~~ 247 (257)
T PRK08583 218 FIENLSQKETGERLGISQMHVSRLQRQAIK 247 (257)
T ss_pred HhCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 357889999999999999999999886654
No 169
>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=77.21 E-value=5.4 Score=31.38 Aligned_cols=31 Identities=19% Similarity=0.304 Sum_probs=26.4
Q ss_pred HHHHHhCCCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 380 QLYSENGRHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 380 ~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
+|..+++...+..+||+.||++..+|+.--.
T Consensus 14 e~y~~~~g~i~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 14 EIYKESNGKIKLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred HHHHHhCCCccHHHHHHHHCCCHHHHHHHhh
Confidence 4556678899999999999999999987654
No 170
>PRK06930 positive control sigma-like factor; Validated
Probab=77.12 E-value=1.7 Score=40.70 Aligned_cols=30 Identities=10% Similarity=0.200 Sum_probs=26.4
Q ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567 385 NGRHPNNEEVAEATGLSMKRLHAVLLSPKA 414 (460)
Q Consensus 385 ~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~ 414 (460)
+..+.|+.|||+.||+|+++|+..+.+++.
T Consensus 127 ~~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~ 156 (170)
T PRK06930 127 RGYGLSYSEIADYLNIKKSTVQSMIERAEK 156 (170)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 457899999999999999999999987654
No 171
>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=76.83 E-value=5.6 Score=30.06 Aligned_cols=45 Identities=20% Similarity=0.211 Sum_probs=31.5
Q ss_pred cCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Q 012567 363 LPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHA 407 (460)
Q Consensus 363 iP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~ 407 (460)
+|....+.+....++.+.|..+.-...+..|||+.+|++..+|+.
T Consensus 3 Ip~~ti~RL~~Y~r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRK 47 (50)
T PF06971_consen 3 IPKATIRRLPLYLRYLEQLKEEGVERVSSQELAEALGITPAQVRK 47 (50)
T ss_dssp -SHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHcCCeeECHHHHHHHHCCCHHHhcc
Confidence 565555666666677777776655677999999999999999975
No 172
>PHA02591 hypothetical protein; Provisional
Probab=75.99 E-value=3.7 Score=33.96 Aligned_cols=25 Identities=24% Similarity=0.341 Sum_probs=22.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHhC
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
++.|.++||+.||++..+|+..++.
T Consensus 58 qGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 58 KGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 5899999999999999999998763
No 173
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=71.16 E-value=6.5 Score=28.51 Aligned_cols=26 Identities=19% Similarity=0.087 Sum_probs=18.1
Q ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 385 NGRHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 385 ~gr~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
+..+.|..+||+.||++..+|...++
T Consensus 17 ~~~G~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 17 LEQGMSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp HCS---HHHHHHHTT--HHHHHHHHH
T ss_pred HHcCCCHHHHHHHHCcCcHHHHHHHh
Confidence 45679999999999999999987765
No 174
>PRK00118 putative DNA-binding protein; Validated
Probab=70.73 E-value=5.5 Score=34.64 Aligned_cols=30 Identities=13% Similarity=0.012 Sum_probs=26.1
Q ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567 385 NGRHPNNEEVAEATGLSMKRLHAVLLSPKA 414 (460)
Q Consensus 385 ~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~ 414 (460)
+..+.|+.|||+.+|+|..+|...+.+++.
T Consensus 30 y~eg~S~~EIAe~lGIS~~TV~r~L~RArk 59 (104)
T PRK00118 30 YLDDYSLGEIAEEFNVSRQAVYDNIKRTEK 59 (104)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 346899999999999999999999987654
No 175
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=69.14 E-value=11 Score=27.53 Aligned_cols=27 Identities=15% Similarity=0.176 Sum_probs=22.8
Q ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHhC
Q 012567 385 NGRHPNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 385 ~gr~pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
+....|..+||+.+|++..+|..++..
T Consensus 24 ~~~~~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 24 LRESRSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred HhhcCCHHHHHHHHCCCHHHHHHHHHh
Confidence 344479999999999999999998763
No 176
>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=69.04 E-value=7.1 Score=27.43 Aligned_cols=28 Identities=29% Similarity=0.324 Sum_probs=24.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHhCCC
Q 012567 386 GRHPNNEEVAEATGLSMKRLHAVLLSPK 413 (460)
Q Consensus 386 gr~pS~eEIAe~LGIS~e~Vk~~l~~ar 413 (460)
..+.+..+||+.+|++..+|...++.++
T Consensus 24 ~~~~~~~~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 24 GEGLSYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4678999999999999999998887543
No 177
>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=68.81 E-value=7.3 Score=28.24 Aligned_cols=24 Identities=21% Similarity=0.145 Sum_probs=18.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
.+.+..+||+.+|||..+|..++.
T Consensus 20 ~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 20 EGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp TT--HHHHHHHTTS-HHHHHHHHC
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHh
Confidence 348999999999999999988764
No 178
>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=67.64 E-value=12 Score=27.78 Aligned_cols=25 Identities=20% Similarity=0.274 Sum_probs=20.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHhC
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
...|.+|||+.||+|..+|...+..
T Consensus 14 ~~it~~eLa~~l~vS~rTi~~~i~~ 38 (55)
T PF08279_consen 14 EPITAKELAEELGVSRRTIRRDIKE 38 (55)
T ss_dssp TSBEHHHHHHHCTS-HHHHHHHHHH
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHH
Confidence 3489999999999999999888763
No 179
>PRK04217 hypothetical protein; Provisional
Probab=67.40 E-value=4.8 Score=35.34 Aligned_cols=29 Identities=21% Similarity=0.240 Sum_probs=25.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLLSPKAP 415 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~ 415 (460)
.+.|++|||+.+|+|..+|...+++++..
T Consensus 57 eGlS~~EIAk~LGIS~sTV~r~L~RArkk 85 (110)
T PRK04217 57 EGLTQEEAGKRMGVSRGTVWRALTSARKK 85 (110)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 57799999999999999999999876553
No 180
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=65.98 E-value=6.3 Score=28.38 Aligned_cols=27 Identities=30% Similarity=0.315 Sum_probs=23.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHhCCC
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLLSPK 413 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~~ar 413 (460)
.+.+..|||+.+|+|..+|...+.++.
T Consensus 17 ~g~s~~eia~~l~is~~tv~~~~~~~~ 43 (58)
T smart00421 17 EGLTNKEIAERLGISEKTVKTHLSNIM 43 (58)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 457999999999999999999987553
No 181
>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=65.48 E-value=8.2 Score=26.57 Aligned_cols=22 Identities=18% Similarity=0.379 Sum_probs=17.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHh
Q 012567 389 PNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 389 pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
.|.+|||..+|++.++|...+.
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~ 24 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILK 24 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHH
T ss_pred cCHHHHHHHhCCcHHHHHHHHH
Confidence 4679999999999999988775
No 182
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=65.37 E-value=15 Score=38.59 Aligned_cols=126 Identities=10% Similarity=0.033 Sum_probs=79.2
Q ss_pred HHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcch
Q 012567 288 DKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHM 367 (460)
Q Consensus 288 e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~ 367 (460)
+..+..-.+.+..-.-+|.++-.-.||.+|+.|+..++..-+=-|-+ .-..|++..-||.-+|.+|++.+....|.+.
T Consensus 8 e~~~r~~~~r~~a~L~r~~rd~dlAEEa~~dA~~~Ale~WPr~G~P~--~PaAWL~~v~R~~aiD~~Rr~~~~~~~~~el 85 (415)
T COG4941 8 EAAARIERPRAMAALARYLRDLDLAEEALQDAFAAALERWPRAGPPR--NPAAWLIAVGRNRAIDRVRRRARRDAAPPEL 85 (415)
T ss_pred HHHHHHhhhHHHHHHHHHhcccchHHHHHHHHHHHHHHhCcccCCCC--ChHHHHHHHHhhhHHHHHHHHHHhccCChhh
Confidence 33444444555555556777766789999999876555444433333 4689999999999999999876544443332
Q ss_pred HHHH--HHHHHH----------------------------HHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567 368 VEAT--YRVKEA----------------------------RKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAP 415 (460)
Q Consensus 368 ~e~i--~kl~ka----------------------------~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~ 415 (460)
.... ..+..+ .-.|.-..-.+.|..|||...=+++.++.+.+.+++..
T Consensus 86 ~~~~e~~e~~~a~~~~d~~i~Dd~LRLiFvccHPal~~~~riALtLR~v~GLs~~eIArAFLv~e~am~QRivRAK~r 163 (415)
T COG4941 86 LLSDEDEEMEEAEALDDEHIRDDRLRLIFVCCHPALPPEQRIALTLRLVGGLSTAEIARAFLVPEAAMAQRIVRAKAR 163 (415)
T ss_pred cccccchhhhccccccccccchhhHHhhhhhcCCCCChhhHHHHHHHHHcCCcHHHHHHHHcCCcHHHHHHHHHHHHH
Confidence 1111 001000 01122222367789999999999999999888776653
No 183
>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=65.23 E-value=18 Score=26.15 Aligned_cols=24 Identities=25% Similarity=0.271 Sum_probs=19.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
...++.+||+.+|+|..+|...++
T Consensus 16 ~r~s~~~la~~lglS~~~v~~Ri~ 39 (42)
T PF13404_consen 16 GRRSYAELAEELGLSESTVRRRIR 39 (42)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHH
T ss_pred CCccHHHHHHHHCcCHHHHHHHHH
Confidence 346799999999999999998875
No 184
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=64.99 E-value=16 Score=30.95 Aligned_cols=37 Identities=19% Similarity=0.248 Sum_probs=27.9
Q ss_pred HHHHHHHHHhC-CCCCHHHHHHHhCCCHHHHHHHHhCC
Q 012567 376 EARKQLYSENG-RHPNNEEVAEATGLSMKRLHAVLLSP 412 (460)
Q Consensus 376 ka~~~L~~~~g-r~pS~eEIAe~LGIS~e~Vk~~l~~a 412 (460)
...++|..... ...|+++||+.||+++.+++.++...
T Consensus 10 ~Tk~elqan~el~~LS~~~iA~~Ln~t~~~lekil~~t 47 (97)
T COG4367 10 RTKQELQANFELCPLSDEEIATALNWTEVKLEKILQVT 47 (97)
T ss_pred HHHHHHHHhhhhccccHHHHHHHhCCCHHHHHHHHHHh
Confidence 34445544332 46799999999999999999999754
No 185
>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=64.55 E-value=7 Score=29.89 Aligned_cols=26 Identities=31% Similarity=0.328 Sum_probs=23.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHhCC
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLLSP 412 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~~a 412 (460)
++.+..|||+.||||..++...++++
T Consensus 22 R~~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 22 RRITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred CcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 67799999999999999999988765
No 186
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=62.85 E-value=8.4 Score=27.93 Aligned_cols=26 Identities=15% Similarity=0.077 Sum_probs=19.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHhCCC
Q 012567 388 HPNNEEVAEATGLSMKRLHAVLLSPK 413 (460)
Q Consensus 388 ~pS~eEIAe~LGIS~e~Vk~~l~~ar 413 (460)
+.|..+||+.||+|..+|...++..+
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT---
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHcc
Confidence 78899999999999999999987543
No 187
>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=62.07 E-value=8.3 Score=27.91 Aligned_cols=27 Identities=26% Similarity=0.321 Sum_probs=23.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHhCCC
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLLSPK 413 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~~ar 413 (460)
.+.+..+||+.+|+|..+|...++++.
T Consensus 14 ~~~s~~eia~~l~~s~~tv~~~~~~~~ 40 (57)
T cd06170 14 EGKTNKEIADILGISEKTVKTHLRNIM 40 (57)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 467999999999999999999987553
No 188
>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=61.41 E-value=26 Score=26.43 Aligned_cols=25 Identities=20% Similarity=0.264 Sum_probs=21.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHhC
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
...+..+||+.+|++..+|...+..
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~ 48 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKE 48 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4578999999999999999988763
No 189
>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=60.20 E-value=28 Score=25.03 Aligned_cols=24 Identities=25% Similarity=0.310 Sum_probs=19.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
...|..|||+.+|+|..+|...++
T Consensus 16 ~~~t~~ela~~~~is~~tv~~~l~ 39 (48)
T PF13412_consen 16 PRITQKELAEKLGISRSTVNRYLK 39 (48)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Confidence 448999999999999999998876
No 190
>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=59.39 E-value=11 Score=28.39 Aligned_cols=29 Identities=24% Similarity=0.193 Sum_probs=23.4
Q ss_pred HhCCCCCHHHHHHHhCCCHHHHHHHHhCC
Q 012567 384 ENGRHPNNEEVAEATGLSMKRLHAVLLSP 412 (460)
Q Consensus 384 ~~gr~pS~eEIAe~LGIS~e~Vk~~l~~a 412 (460)
-...+.+..|||+.||+++.+|+..+...
T Consensus 14 ~l~~G~~~~eIA~~l~is~~tV~~~~~~i 42 (58)
T PF00196_consen 14 LLAQGMSNKEIAEELGISEKTVKSHRRRI 42 (58)
T ss_dssp HHHTTS-HHHHHHHHTSHHHHHHHHHHHH
T ss_pred HHHhcCCcchhHHhcCcchhhHHHHHHHH
Confidence 34568899999999999999999887643
No 191
>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=59.10 E-value=6.3 Score=35.95 Aligned_cols=29 Identities=10% Similarity=0.096 Sum_probs=24.8
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567 386 GRHPNNEEVAEATGLSMKRLHAVLLSPKA 414 (460)
Q Consensus 386 gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~ 414 (460)
..+.|++|||+.||+|..+|+.+.++++.
T Consensus 19 ~~GlTq~EIAe~LgiS~stV~~~e~ra~k 47 (137)
T TIGR00721 19 EKGLSQKEIAKELKTTRANVSAIEKRAME 47 (137)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHhHHH
Confidence 46889999999999999999988776544
No 192
>PF12728 HTH_17: Helix-turn-helix domain
Probab=59.07 E-value=12 Score=27.33 Aligned_cols=24 Identities=21% Similarity=0.138 Sum_probs=21.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHhCC
Q 012567 389 PNNEEVAEATGLSMKRLHAVLLSP 412 (460)
Q Consensus 389 pS~eEIAe~LGIS~e~Vk~~l~~a 412 (460)
.|.+|+|+.|||+..+|...++..
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcC
Confidence 478999999999999999998744
No 193
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=59.03 E-value=24 Score=28.68 Aligned_cols=36 Identities=28% Similarity=0.232 Sum_probs=24.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccc
Q 012567 386 GRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQK 421 (460)
Q Consensus 386 gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~ 421 (460)
.++.|..|+|+.||++..+|..+++--...+|++.-
T Consensus 29 ~~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L 64 (80)
T PF13744_consen 29 ERGLTQAELAERLGISQPRVSRLENGKIDDFSLDTL 64 (80)
T ss_dssp CCT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHHH
T ss_pred HcCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHHH
Confidence 478999999999999999999988644455777654
No 194
>PF13730 HTH_36: Helix-turn-helix domain
Probab=58.78 E-value=12 Score=27.71 Aligned_cols=24 Identities=21% Similarity=0.401 Sum_probs=21.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
--||.+.||+.+|++..+|...+.
T Consensus 24 ~~pS~~~la~~~g~s~~Tv~~~i~ 47 (55)
T PF13730_consen 24 CFPSQETLAKDLGVSRRTVQRAIK 47 (55)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHH
Confidence 568999999999999999998876
No 195
>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=58.16 E-value=23 Score=27.40 Aligned_cols=26 Identities=15% Similarity=0.022 Sum_probs=22.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHhCC
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLLSP 412 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~~a 412 (460)
.+.++.|||+.||++..+|..-..+.
T Consensus 12 ~G~~~~eIA~~Lg~~~~TV~~W~~r~ 37 (58)
T PF06056_consen 12 QGWSIKEIAEELGVPRSTVYSWKDRY 37 (58)
T ss_pred cCCCHHHHHHHHCCChHHHHHHHHhh
Confidence 47899999999999999999887644
No 196
>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=57.59 E-value=13 Score=27.52 Aligned_cols=23 Identities=26% Similarity=0.444 Sum_probs=20.5
Q ss_pred CHHHHHHHhCCCHHHHHHHHhCC
Q 012567 390 NNEEVAEATGLSMKRLHAVLLSP 412 (460)
Q Consensus 390 S~eEIAe~LGIS~e~Vk~~l~~a 412 (460)
|.++||+.+|+|..+|..+++-.
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~~ 23 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNGP 23 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTTC
T ss_pred CHHHHHHHHCcCHHHHHHHHhCC
Confidence 57899999999999999999844
No 197
>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=54.56 E-value=44 Score=27.68 Aligned_cols=41 Identities=22% Similarity=0.297 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhC
Q 012567 371 TYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 371 i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
...|-+++-++..+.++....++||+.+|++..+|++.|..
T Consensus 6 q~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~ 46 (78)
T PF03444_consen 6 QREILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMAD 46 (78)
T ss_pred HHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHH
Confidence 34555666666777788889999999999999999998863
No 198
>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=53.00 E-value=23 Score=24.76 Aligned_cols=24 Identities=25% Similarity=0.218 Sum_probs=21.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHhCC
Q 012567 389 PNNEEVAEATGLSMKRLHAVLLSP 412 (460)
Q Consensus 389 pS~eEIAe~LGIS~e~Vk~~l~~a 412 (460)
.|.+|+|+.||++..++...++..
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g 25 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEG 25 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcC
Confidence 478999999999999999998754
No 199
>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=52.65 E-value=20 Score=31.13 Aligned_cols=34 Identities=18% Similarity=0.130 Sum_probs=24.4
Q ss_pred HHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567 381 LYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKA 414 (460)
Q Consensus 381 L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~ 414 (460)
+...+..+.|..|||+.+|||...|...++++..
T Consensus 26 l~lyy~eDlSlsEIAe~~~iSRqaV~d~ikr~~~ 59 (101)
T PF04297_consen 26 LELYYEEDLSLSEIAEELGISRQAVYDSIKRAEK 59 (101)
T ss_dssp HHHHCTS---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred HHHHHccCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3344668999999999999999999999887653
No 200
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=51.23 E-value=9.5 Score=34.96 Aligned_cols=28 Identities=18% Similarity=0.266 Sum_probs=23.6
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHhCCC
Q 012567 386 GRHPNNEEVAEATGLSMKRLHAVLLSPK 413 (460)
Q Consensus 386 gr~pS~eEIAe~LGIS~e~Vk~~l~~ar 413 (460)
..+.|.+|||+.||+|..+|+.+.+.++
T Consensus 19 ~~GlTq~EIAe~LGiS~~tVs~ie~ra~ 46 (141)
T PRK03975 19 ERGLTQQEIADILGTSRANVSSIEKRAR 46 (141)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3689999999999999999988776443
No 201
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=50.86 E-value=21 Score=34.25 Aligned_cols=30 Identities=23% Similarity=0.170 Sum_probs=25.3
Q ss_pred HHhCCCCCHHHHHHHhCCCHHHHHHHHhCC
Q 012567 383 SENGRHPNNEEVAEATGLSMKRLHAVLLSP 412 (460)
Q Consensus 383 ~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~a 412 (460)
.-+.++.|.+|||+.|++|++||+......
T Consensus 158 ~lla~G~snkeIA~~L~iS~~TVk~h~~~i 187 (211)
T COG2197 158 RLLAEGLSNKEIAEELNLSEKTVKTHVSNI 187 (211)
T ss_pred HHHHCCCCHHHHHHHHCCCHhHHHHHHHHH
Confidence 345678999999999999999999877643
No 202
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=50.44 E-value=44 Score=29.41 Aligned_cols=39 Identities=15% Similarity=0.124 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 372 YRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 372 ~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
..+.++...+.......++.++||+.+|+++..+....+
T Consensus 9 ~~i~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk 47 (127)
T PRK11511 9 ITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFK 47 (127)
T ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 345566667777777889999999999999999877765
No 203
>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=50.09 E-value=40 Score=26.09 Aligned_cols=35 Identities=23% Similarity=0.295 Sum_probs=26.6
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhC
Q 012567 376 EARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 376 ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
+++-.|.. -+...+..+||+.||++..+|-.++++
T Consensus 11 ~~Iy~l~~-~~~~v~~~~iA~~L~vs~~tvt~ml~~ 45 (60)
T PF01325_consen 11 KAIYELSE-EGGPVRTKDIAERLGVSPPTVTEMLKR 45 (60)
T ss_dssp HHHHHHHH-CTSSBBHHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHc-CCCCccHHHHHHHHCCChHHHHHHHHH
Confidence 44445554 467889999999999999999888763
No 204
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=48.65 E-value=25 Score=33.58 Aligned_cols=33 Identities=3% Similarity=-0.042 Sum_probs=26.6
Q ss_pred HHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCC
Q 012567 380 QLYSENGRHPNNEEVAEATGLSMKRLHAVLLSP 412 (460)
Q Consensus 380 ~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~a 412 (460)
+.......+.|.+|||+.||+|+.+|+..+...
T Consensus 144 eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~I 176 (207)
T PRK15411 144 SMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNI 176 (207)
T ss_pred HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHH
Confidence 333445678999999999999999999887644
No 205
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=48.54 E-value=57 Score=29.79 Aligned_cols=46 Identities=20% Similarity=0.220 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCccc
Q 012567 373 RVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSL 418 (460)
Q Consensus 373 kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSL 418 (460)
...+...-|...-++..|..||++.+|++++.|...++-.|-.++=
T Consensus 31 ~f~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~IreGRL~~~~ 76 (137)
T TIGR03826 31 EFEKVYKFLRKHENRQATVSEIVEETGVSEKLILKFIREGRLQLKH 76 (137)
T ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCCeeccC
Confidence 3334444444444566899999999999999999999876654443
No 206
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=48.43 E-value=53 Score=25.88 Aligned_cols=27 Identities=26% Similarity=0.422 Sum_probs=22.9
Q ss_pred HhCC-CCCHHHHHHHhCCCHHHHHHHHh
Q 012567 384 ENGR-HPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 384 ~~gr-~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
..|. ..+..|||+.||++..+|...+.
T Consensus 17 ~~g~~~~ta~eLa~~lgl~~~~v~r~L~ 44 (68)
T smart00550 17 NSGDETSTALQLAKNLGLPKKEVNRVLY 44 (68)
T ss_pred HCCCCCcCHHHHHHHHCCCHHHHHHHHH
Confidence 3344 48999999999999999999886
No 207
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=48.34 E-value=42 Score=28.47 Aligned_cols=36 Identities=25% Similarity=0.232 Sum_probs=28.0
Q ss_pred HHHHHHHHhC-CCCCHHHHHHHhCCCHHHHHHHHhCC
Q 012567 377 ARKQLYSENG-RHPNNEEVAEATGLSMKRLHAVLLSP 412 (460)
Q Consensus 377 a~~~L~~~~g-r~pS~eEIAe~LGIS~e~Vk~~l~~a 412 (460)
...+|...+. .+.|.++||..||+|.+.|..++..-
T Consensus 11 T~~ELq~nf~~~~ls~~~ia~dL~~s~~~le~vL~l~ 47 (89)
T PF10078_consen 11 TRQELQANFELSGLSLEQIAADLGTSPEHLEQVLNLK 47 (89)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC
Confidence 3445555433 57899999999999999999998743
No 208
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=48.11 E-value=23 Score=25.84 Aligned_cols=23 Identities=26% Similarity=0.423 Sum_probs=20.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHhC
Q 012567 389 PNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 389 pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
||..+||+.+|+|..+|...+..
T Consensus 21 ~s~~~la~~~~vs~~tv~~~l~~ 43 (60)
T smart00345 21 PSERELAAQLGVSRTTVREALSR 43 (60)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHH
Confidence 48999999999999999998864
No 209
>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=47.60 E-value=32 Score=23.84 Aligned_cols=23 Identities=26% Similarity=0.251 Sum_probs=20.4
Q ss_pred CHHHHHHHhCCCHHHHHHHHhCC
Q 012567 390 NNEEVAEATGLSMKRLHAVLLSP 412 (460)
Q Consensus 390 S~eEIAe~LGIS~e~Vk~~l~~a 412 (460)
+..|+|+.||++..+|.......
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~g 24 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKEG 24 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcC
Confidence 67899999999999999988754
No 210
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=47.22 E-value=28 Score=32.54 Aligned_cols=32 Identities=16% Similarity=-0.019 Sum_probs=26.0
Q ss_pred HHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCC
Q 012567 382 YSENGRHPNNEEVAEATGLSMKRLHAVLLSPK 413 (460)
Q Consensus 382 ~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar 413 (460)
......+.|.+|||+.||+|..||+..+....
T Consensus 159 l~~~~~G~s~~eIA~~l~iS~~TV~~h~~~i~ 190 (216)
T PRK10840 159 LRLFAEGFLVTEIAKKLNRSIKTISSQKKSAM 190 (216)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 33445789999999999999999998876443
No 211
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=46.99 E-value=30 Score=33.05 Aligned_cols=32 Identities=16% Similarity=0.116 Sum_probs=26.8
Q ss_pred HHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567 383 SENGRHPNNEEVAEATGLSMKRLHAVLLSPKA 414 (460)
Q Consensus 383 ~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~ 414 (460)
..+..+.|.+|||+.||+|..+|+..+.+...
T Consensus 173 ~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~ 204 (239)
T PRK10430 173 AHQDYEFSTDELANAVNISRVSCRKYLIWLVN 204 (239)
T ss_pred hCCCCCcCHHHHHHHhCchHHHHHHHHHHHHh
Confidence 34568899999999999999999999875533
No 212
>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=46.25 E-value=60 Score=25.61 Aligned_cols=19 Identities=37% Similarity=0.478 Sum_probs=14.0
Q ss_pred hhcCCCCcHHHHHHHhCCC
Q 012567 254 ERCGGSPTFAQWAAAAGVD 272 (460)
Q Consensus 254 ~~~g~~pt~~ewA~a~g~d 272 (460)
...|.+||.+|.++++|+.
T Consensus 20 ~~~G~~Pt~rEIa~~~g~~ 38 (65)
T PF01726_consen 20 EENGYPPTVREIAEALGLK 38 (65)
T ss_dssp HHHSS---HHHHHHHHTSS
T ss_pred HHcCCCCCHHHHHHHhCCC
Confidence 4579999999999999985
No 213
>PRK14082 hypothetical protein; Provisional
Probab=45.82 E-value=66 Score=25.74 Aligned_cols=56 Identities=14% Similarity=0.051 Sum_probs=41.7
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhH
Q 012567 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTY 341 (460)
Q Consensus 284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTY 341 (460)
....+.+|..+.+.+.+-... .+..+.+||.||--+.+++-+..++-..+.-|-.|
T Consensus 8 ~~e~e~ii~~FepkIkKsL~~--T~yqeREDLeQElk~Ki~eK~~~~~~~e~PGF~ef 63 (65)
T PRK14082 8 TEEIEHLIENFSPMIKKKLSN--TSYQEREDLEQELKIKIIEKADMLLCQEVPGFWEF 63 (65)
T ss_pred HHHHHHHHHHccHHHHHHHhc--CChhhHHHHHHHHHHHHHHHHHHhhcccCCcHHHh
Confidence 445677888888877765543 23457899999999999999999987665556554
No 214
>PRK13870 transcriptional regulator TraR; Provisional
Probab=44.34 E-value=13 Score=36.46 Aligned_cols=30 Identities=17% Similarity=0.219 Sum_probs=25.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567 386 GRHPNNEEVAEATGLSMKRLHAVLLSPKAP 415 (460)
Q Consensus 386 gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~ 415 (460)
..+.|..|||.+||||+.+|+..++.++..
T Consensus 186 A~GKT~~EIa~ILgISe~TV~~Hl~na~~K 215 (234)
T PRK13870 186 AVGKTMEEIADVEGVKYNSVRVKLREAMKR 215 (234)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 468899999999999999999988766543
No 215
>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]
Probab=44.22 E-value=26 Score=33.50 Aligned_cols=35 Identities=14% Similarity=0.121 Sum_probs=28.2
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHhCCCCCccccc
Q 012567 386 GRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQ 420 (460)
Q Consensus 386 gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~ 420 (460)
.++++..|||+.|++|.+++.-++.++....+--.
T Consensus 16 ~~Glt~gEIAdELNvSreTa~WL~~r~~~~~~~~~ 50 (203)
T COG0856 16 SKGLTTGEIADELNVSRETATWLLTRAFKKESVPA 50 (203)
T ss_pred HCCCcHHHhhhhhhhhHHHHHHHHhhhhhccCCCC
Confidence 46899999999999999999999887655444433
No 216
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=43.46 E-value=34 Score=32.84 Aligned_cols=31 Identities=16% Similarity=0.088 Sum_probs=25.5
Q ss_pred HHHhCCCCCHHHHHHHhCCCHHHHHHHHhCC
Q 012567 382 YSENGRHPNNEEVAEATGLSMKRLHAVLLSP 412 (460)
Q Consensus 382 ~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~a 412 (460)
......+.|.+|||+.|+||+.||+......
T Consensus 143 L~ll~~G~snkeIA~~L~iS~~TV~~h~~~I 173 (207)
T PRK11475 143 LRFMSRGYSMPQIAEQLERNIKTIRAHKFNV 173 (207)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 3344578999999999999999999887644
No 217
>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=43.45 E-value=29 Score=25.61 Aligned_cols=26 Identities=31% Similarity=0.415 Sum_probs=21.5
Q ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 385 NGRHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 385 ~gr~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
.+...+..|||+.+|++..++..++.
T Consensus 15 ~~~~~t~~eia~~~gl~~stv~r~L~ 40 (52)
T PF09339_consen 15 SGGPLTLSEIARALGLPKSTVHRLLQ 40 (52)
T ss_dssp TBSCEEHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34556899999999999999998876
No 218
>PF14502 HTH_41: Helix-turn-helix domain
Probab=43.21 E-value=31 Score=26.05 Aligned_cols=33 Identities=24% Similarity=0.272 Sum_probs=26.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHhCC--CCCcccc
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLLSP--KAPRSLD 419 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~~a--r~~lSLD 419 (460)
|-|++.|.++.++++.++|+..+..- ...++|.
T Consensus 5 Ri~tI~e~~~~~~vs~GtiQ~Alk~Le~~gaI~Le 39 (48)
T PF14502_consen 5 RIPTISEYSEKFGVSRGTIQNALKFLEENGAIKLE 39 (48)
T ss_pred ccCCHHHHHHHhCcchhHHHHHHHHHHHCCcEEee
Confidence 67899999999999999999998742 2344444
No 219
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=43.11 E-value=36 Score=33.42 Aligned_cols=35 Identities=6% Similarity=-0.009 Sum_probs=27.8
Q ss_pred HHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567 380 QLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKA 414 (460)
Q Consensus 380 ~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~ 414 (460)
+...-+.++.|.+|||+.|++++.+|+..+.....
T Consensus 150 eVL~Lia~G~SnkEIA~~L~IS~~TVk~hvs~I~~ 184 (217)
T PRK13719 150 DVFILYSFGFSHEYIAQLLNITVGSSKNKISEILK 184 (217)
T ss_pred HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 33444567899999999999999999998765433
No 220
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=42.38 E-value=39 Score=32.49 Aligned_cols=32 Identities=16% Similarity=-0.044 Sum_probs=26.0
Q ss_pred HHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCC
Q 012567 382 YSENGRHPNNEEVAEATGLSMKRLHAVLLSPK 413 (460)
Q Consensus 382 ~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar 413 (460)
..-...+.|.+|||+.||+|..+|+..+....
T Consensus 142 LrLLAqGkTnKEIAe~L~IS~rTVkth~srIm 173 (198)
T PRK15201 142 LKLIASGYHLSETAALLSLSEEQTKSLRRSIM 173 (198)
T ss_pred HHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 33446789999999999999999998876443
No 221
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=41.77 E-value=27 Score=33.80 Aligned_cols=23 Identities=22% Similarity=0.195 Sum_probs=20.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHH
Q 012567 386 GRHPNNEEVAEATGLSMKRLHAV 408 (460)
Q Consensus 386 gr~pS~eEIAe~LGIS~e~Vk~~ 408 (460)
-++...++||..||||+.||+..
T Consensus 155 V~G~~NKqIA~dLgiS~rTVe~H 177 (202)
T COG4566 155 VRGLMNKQIAFDLGISERTVELH 177 (202)
T ss_pred HcCcccHHHHHHcCCchhhHHHH
Confidence 37788899999999999999754
No 222
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=41.45 E-value=74 Score=26.66 Aligned_cols=37 Identities=16% Similarity=0.109 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 374 VKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 374 l~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
+.++..-+...+...++.++||+.+|+|...+..+.+
T Consensus 7 ~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~ 43 (107)
T PRK10219 7 IQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFR 43 (107)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4445555666677789999999999999998877765
No 223
>PRK12423 LexA repressor; Provisional
Probab=41.11 E-value=72 Score=30.42 Aligned_cols=39 Identities=18% Similarity=0.219 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCC-CHHHHHHHHh
Q 012567 372 YRVKEARKQLYSENGRHPNNEEVAEATGL-SMKRLHAVLL 410 (460)
Q Consensus 372 ~kl~ka~~~L~~~~gr~pS~eEIAe~LGI-S~e~Vk~~l~ 410 (460)
..+-..+.....+.|..||..|||+.+|+ +...|+..+.
T Consensus 9 ~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~ 48 (202)
T PRK12423 9 AAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQ 48 (202)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHH
Confidence 34444455555566778999999999995 8888877664
No 224
>PF14711 Nitr_red_bet_C: Respiratory nitrate reductase beta C-terminal; PDB: 3IR7_B 1Y5N_B 1R27_D 3EGW_B 1Y5I_B 1Q16_B 1Y4Z_B 1Y5L_B 3IR6_B 3IR5_B ....
Probab=40.66 E-value=60 Score=27.16 Aligned_cols=52 Identities=23% Similarity=0.418 Sum_probs=30.7
Q ss_pred HHHHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCH
Q 012567 213 PLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQ 273 (460)
Q Consensus 213 ~l~YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de 273 (460)
|++||..+ ||+-.|..+-.-++.++.+....+.. ..|++ ...++.+++|+++
T Consensus 31 Pi~YLAnL------ftAGd~~~V~~~L~rL~AmR~ymR~~--~v~~~-~~~~~l~~~glt~ 82 (83)
T PF14711_consen 31 PIEYLANL------FTAGDEEPVRRALKRLLAMRSYMRAK--NVGGE-PDEEVLEAVGLTE 82 (83)
T ss_dssp -HHHHHHH------HSTT-HHHHHHHHHHHHHHHHHHHHH--HTT-S----HHHHHTT--H
T ss_pred cHHHHHHH------HccCChHHHHHHHHHHHHHHHHHHHH--HhCCC-CcHHHHHHcCCCC
Confidence 88899997 88888887777777665554444432 34544 4478888888875
No 225
>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=40.28 E-value=72 Score=30.01 Aligned_cols=39 Identities=23% Similarity=0.243 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCC-HHHHHHHHh
Q 012567 372 YRVKEARKQLYSENGRHPNNEEVAEATGLS-MKRLHAVLL 410 (460)
Q Consensus 372 ~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS-~e~Vk~~l~ 410 (460)
.+|...+.....+.+..||..|||+.+|++ ..+|...+.
T Consensus 9 ~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~ 48 (199)
T TIGR00498 9 QEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLK 48 (199)
T ss_pred HHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHH
Confidence 344445555555667789999999999998 899988775
No 226
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=39.84 E-value=67 Score=23.83 Aligned_cols=27 Identities=22% Similarity=0.310 Sum_probs=23.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHhCC
Q 012567 386 GRHPNNEEVAEATGLSMKRLHAVLLSP 412 (460)
Q Consensus 386 gr~pS~eEIAe~LGIS~e~Vk~~l~~a 412 (460)
..+.+..|||..+|++..+|...+...
T Consensus 17 ~~G~s~~eia~~l~is~~tV~~h~~~i 43 (65)
T COG2771 17 AQGKSNKEIARILGISEETVKTHLRNI 43 (65)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 456899999999999999999877643
No 227
>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=39.79 E-value=16 Score=35.61 Aligned_cols=28 Identities=18% Similarity=0.252 Sum_probs=24.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLLSPKA 414 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~~ar~ 414 (460)
.+.|..|||+.||+|+.+|+..+..+..
T Consensus 185 ~G~t~~eIa~~l~is~~Tv~~~l~~~~~ 212 (232)
T TIGR03541 185 LGRRQADIAAILGISERTVENHLRSARR 212 (232)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 6789999999999999999999886644
No 228
>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=39.35 E-value=37 Score=24.78 Aligned_cols=25 Identities=20% Similarity=0.282 Sum_probs=20.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHhC
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
.+.|..++|+.+|++..+|..+..-
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 5788999999999999999998874
No 229
>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=39.27 E-value=61 Score=19.93 Aligned_cols=21 Identities=24% Similarity=0.213 Sum_probs=17.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHH
Q 012567 388 HPNNEEVAEATGLSMKRLHAV 408 (460)
Q Consensus 388 ~pS~eEIAe~LGIS~e~Vk~~ 408 (460)
+.+..+||+.+|++..+|...
T Consensus 21 ~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 21 GESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCCHHHHHHHHCCCHHHHHHh
Confidence 458999999999999988754
No 230
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=39.02 E-value=17 Score=35.73 Aligned_cols=30 Identities=10% Similarity=0.039 Sum_probs=25.4
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567 386 GRHPNNEEVAEATGLSMKRLHAVLLSPKAP 415 (460)
Q Consensus 386 gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~ 415 (460)
..+.|..|||++||||+.+|+..+..+...
T Consensus 192 a~G~t~~eIa~~l~is~~TV~~h~~~~~~K 221 (240)
T PRK10188 192 AEGKTSAEIAMILSISENTVNFHQKNMQKK 221 (240)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 467899999999999999999988765443
No 231
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=38.18 E-value=42 Score=26.45 Aligned_cols=25 Identities=28% Similarity=0.303 Sum_probs=20.6
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 386 GRHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 386 gr~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
...++-.|||+.+|++..+++..|.
T Consensus 13 ~~p~~T~eiA~~~gls~~~aR~yL~ 37 (62)
T PF04703_consen 13 NGPLKTREIADALGLSIYQARYYLE 37 (62)
T ss_dssp TS-EEHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 5667889999999999999998876
No 232
>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=37.72 E-value=43 Score=23.74 Aligned_cols=23 Identities=26% Similarity=0.121 Sum_probs=20.1
Q ss_pred CHHHHHHHhCCCHHHHHHHHhCC
Q 012567 390 NNEEVAEATGLSMKRLHAVLLSP 412 (460)
Q Consensus 390 S~eEIAe~LGIS~e~Vk~~l~~a 412 (460)
+..|+|+.+|++..+|+......
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHHCC
Confidence 67899999999999999887644
No 233
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=37.69 E-value=3.4e+02 Score=26.64 Aligned_cols=38 Identities=29% Similarity=0.270 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 373 RVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 373 kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
.+.++...+...+....+.+++|+.+|+|...+..+.+
T Consensus 184 ~i~~~~~~i~~~~~~~isl~~lA~~~~lS~~~l~r~Fk 221 (290)
T PRK10572 184 RVREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFR 221 (290)
T ss_pred HHHHHHHHHHhcccCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 45566666667777899999999999999988877665
No 234
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=37.11 E-value=46 Score=23.26 Aligned_cols=24 Identities=25% Similarity=0.326 Sum_probs=20.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHhC
Q 012567 388 HPNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 388 ~pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
..+..+||+.+|++..++...+..
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~ 31 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKR 31 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHH
Confidence 467899999999999999888763
No 235
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=37.07 E-value=43 Score=31.76 Aligned_cols=25 Identities=24% Similarity=0.129 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHhC
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
.+.|.+|||+.||||..||+..+.+
T Consensus 176 ~g~s~~eIa~~l~iS~~Tv~~~~~~ 200 (225)
T PRK10046 176 VQHTAETVAQALTISRTTARRYLEY 200 (225)
T ss_pred CCcCHHHHHHHhCccHHHHHHHHHH
Confidence 3689999999999999999998864
No 236
>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=36.87 E-value=38 Score=33.73 Aligned_cols=29 Identities=24% Similarity=0.180 Sum_probs=25.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567 386 GRHPNNEEVAEATGLSMKRLHAVLLSPKA 414 (460)
Q Consensus 386 gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~ 414 (460)
..+.|..|||+.||||+.+|+..++.+..
T Consensus 203 a~G~s~~eIA~~L~IS~~TVk~hl~~i~~ 231 (247)
T TIGR03020 203 RDGKTNEEIAAILGISSLTVKNHLQHIFK 231 (247)
T ss_pred HCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 46799999999999999999999875543
No 237
>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=36.70 E-value=26 Score=26.40 Aligned_cols=26 Identities=15% Similarity=0.248 Sum_probs=19.7
Q ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 385 NGRHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 385 ~gr~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
+..+++..+||..+||+..+|..++.
T Consensus 19 ~e~g~s~~~ia~~fgv~~sTv~~I~K 44 (53)
T PF04218_consen 19 LEEGESKRDIAREFGVSRSTVSTILK 44 (53)
T ss_dssp HHCTT-HHHHHHHHT--CCHHHHHHH
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 34566999999999999999999886
No 238
>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=36.60 E-value=87 Score=23.87 Aligned_cols=26 Identities=12% Similarity=0.153 Sum_probs=21.9
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHhC
Q 012567 386 GRHPNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 386 gr~pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
....+..|||+.||+|..+++..+..
T Consensus 17 ~~~~~~~ela~~l~~S~rti~~~i~~ 42 (59)
T PF08280_consen 17 NKWITLKELAKKLNISERTIKNDINE 42 (59)
T ss_dssp HTSBBHHHHHHHCTS-HHHHHHHHHH
T ss_pred CCCCcHHHHHHHHCCCHHHHHHHHHH
Confidence 46789999999999999999988763
No 239
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=36.44 E-value=70 Score=28.39 Aligned_cols=23 Identities=30% Similarity=0.306 Sum_probs=20.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHhC
Q 012567 389 PNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 389 pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
.++.|||+.+|+|..+|..++..
T Consensus 23 ~~~~eia~~lglS~~~v~~Ri~~ 45 (154)
T COG1522 23 ISNAELAERVGLSPSTVLRRIKR 45 (154)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Confidence 78999999999999999988763
No 240
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=36.34 E-value=57 Score=31.50 Aligned_cols=29 Identities=17% Similarity=0.072 Sum_probs=24.6
Q ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHhCCC
Q 012567 385 NGRHPNNEEVAEATGLSMKRLHAVLLSPK 413 (460)
Q Consensus 385 ~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar 413 (460)
...+.|.+|||+.||+|+.+|+..+....
T Consensus 167 ~~~G~s~~eIA~~L~iS~~TVk~~~~~i~ 195 (216)
T PRK10100 167 LRIGASNNEIARSLFISENTVKTHLYNLF 195 (216)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 34578999999999999999999887543
No 241
>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=35.42 E-value=1.2e+02 Score=22.18 Aligned_cols=35 Identities=20% Similarity=0.264 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 373 RVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 373 kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
.|..|+..+. .|. .|..+.|+..|||..++...++
T Consensus 4 ~l~~Ai~~v~--~g~-~S~r~AA~~ygVp~sTL~~r~~ 38 (45)
T PF05225_consen 4 DLQKAIEAVK--NGK-MSIRKAAKKYGVPRSTLRRRLR 38 (45)
T ss_dssp HHHHHHHHHH--TTS-S-HHHHHHHHT--HHHHHHHHH
T ss_pred HHHHHHHHHH--hCC-CCHHHHHHHHCcCHHHHHHHHc
Confidence 4556665554 334 9999999999999999997765
No 242
>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=35.33 E-value=1.5e+02 Score=24.64 Aligned_cols=25 Identities=20% Similarity=0.252 Sum_probs=22.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHhC
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
...+..+||+.+|+|..+|...+..
T Consensus 18 ~~~ti~dvA~~~gvS~~TVsr~L~~ 42 (80)
T TIGR02844 18 TKATVRETAKVFGVSKSTVHKDVTE 42 (80)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHhcC
Confidence 5678999999999999999998763
No 243
>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=35.26 E-value=92 Score=26.23 Aligned_cols=25 Identities=16% Similarity=0.182 Sum_probs=21.7
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 386 GRHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 386 gr~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
..+.|..+||+.+|+|..+|..+.+
T Consensus 48 ~~G~S~~eIA~~LgISrsTIyRi~R 72 (88)
T TIGR02531 48 KQGKTYSDIEAETGASTATISRVKR 72 (88)
T ss_pred HCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3567999999999999999998654
No 244
>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=34.62 E-value=55 Score=27.54 Aligned_cols=25 Identities=20% Similarity=0.272 Sum_probs=21.3
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 386 GRHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 386 gr~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
..+.+..+|++.||++..+|+.++.
T Consensus 63 ~~Gv~v~~I~~~l~~~~~~v~~al~ 87 (102)
T PF08784_consen 63 EEGVHVDEIAQQLGMSENEVRKALD 87 (102)
T ss_dssp TTTEEHHHHHHHSTS-HHHHHHHHH
T ss_pred CCcccHHHHHHHhCcCHHHHHHHHH
Confidence 4567899999999999999999876
No 245
>COG2344 AT-rich DNA-binding protein [General function prediction only]
Probab=34.43 E-value=82 Score=30.63 Aligned_cols=49 Identities=12% Similarity=0.142 Sum_probs=40.2
Q ss_pred ccCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 362 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 362 riP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
.+|......+....+..+.|..+.-...|.+|||+.+|++..+|+.=+.
T Consensus 6 ~IP~AT~kRL~~YyR~le~l~a~~v~rvsS~els~~~~vdsatIRrDfS 54 (211)
T COG2344 6 KIPKATAKRLPLYYRVLERLHASGVERVSSKELSEALGVDSATIRRDFS 54 (211)
T ss_pred cCCHHHHHHhHHHHHHHHHHHHcCCceecHHHHHHHhCCCHHHHhhhhH
Confidence 5787777777777788888877766778999999999999999986554
No 246
>PRK13239 alkylmercury lyase; Provisional
Probab=34.07 E-value=84 Score=30.66 Aligned_cols=29 Identities=28% Similarity=0.344 Sum_probs=26.3
Q ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHhCCC
Q 012567 385 NGRHPNNEEVAEATGLSMKRLHAVLLSPK 413 (460)
Q Consensus 385 ~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar 413 (460)
.|+.+|..+||+.+|+++++|+.+|+...
T Consensus 33 ~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 33 KGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 68999999999999999999999998543
No 247
>PRK00215 LexA repressor; Validated
Probab=33.41 E-value=1.1e+02 Score=28.82 Aligned_cols=36 Identities=31% Similarity=0.414 Sum_probs=27.8
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHhCC-CHHHHHHHHh
Q 012567 375 KEARKQLYSENGRHPNNEEVAEATGL-SMKRLHAVLL 410 (460)
Q Consensus 375 ~ka~~~L~~~~gr~pS~eEIAe~LGI-S~e~Vk~~l~ 410 (460)
.+.+.+...+.+..++..|||+.+|+ +..++..++.
T Consensus 10 l~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~ 46 (205)
T PRK00215 10 LDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLK 46 (205)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHH
Confidence 33334444566788999999999999 9999988865
No 248
>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=33.38 E-value=46 Score=25.49 Aligned_cols=24 Identities=29% Similarity=0.414 Sum_probs=18.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHhC
Q 012567 388 HPNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 388 ~pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
-|+..+||+.+|+|..+|+.++..
T Consensus 24 lps~~~la~~~~vsr~tvr~al~~ 47 (64)
T PF00392_consen 24 LPSERELAERYGVSRTTVREALRR 47 (64)
T ss_dssp E--HHHHHHHHTS-HHHHHHHHHH
T ss_pred eCCHHHHHHHhccCCcHHHHHHHH
Confidence 359999999999999999998863
No 249
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=33.38 E-value=47 Score=26.16 Aligned_cols=23 Identities=26% Similarity=0.319 Sum_probs=19.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHhC
Q 012567 389 PNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 389 pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
++..+||+.+|+|..+|..+++-
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln~ 23 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLNG 23 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCC
Confidence 36789999999999999998863
No 250
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=33.27 E-value=44 Score=25.14 Aligned_cols=33 Identities=30% Similarity=0.395 Sum_probs=20.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccc
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLD 419 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD 419 (460)
++.|..++|+.+|++..++..+++.-...++++
T Consensus 9 ~~it~~~La~~~gis~~tl~~~~~~~~~~~~~~ 41 (63)
T PF13443_consen 9 RGITQKDLARKTGISRSTLSRILNGKPSNPSLD 41 (63)
T ss_dssp TT--HHHHHHHHT--HHHHHHHHTTT-----HH
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcccccccHH
Confidence 456899999999999999999988443345554
No 251
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=33.22 E-value=81 Score=30.07 Aligned_cols=25 Identities=20% Similarity=0.169 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHhC
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
-+.|+.|||+.||.|+.+|++.+.-
T Consensus 60 ag~Ti~EIAeelG~TeqTir~hlkg 84 (182)
T COG1318 60 AGMTISEIAEELGRTEQTVRNHLKG 84 (182)
T ss_pred ccCcHHHHHHHhCCCHHHHHHHHhc
Confidence 4678999999999999999999873
No 252
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=33.21 E-value=41 Score=29.84 Aligned_cols=31 Identities=19% Similarity=0.185 Sum_probs=25.4
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHhCCCCCc
Q 012567 386 GRHPNNEEVAEATGLSMKRLHAVLLSPKAPR 416 (460)
Q Consensus 386 gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~l 416 (460)
..+.+.+|||+.|+++..+|+..+...+..+
T Consensus 162 ~~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl 192 (211)
T PRK15369 162 TEGYTNRDIAEQLSISIKTVETHRLNMMRKL 192 (211)
T ss_pred HCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 4567899999999999999999887655444
No 253
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=32.67 E-value=2.4e+02 Score=31.04 Aligned_cols=36 Identities=17% Similarity=0.194 Sum_probs=26.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHh-----CCCCCccccccc
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLL-----SPKAPRSLDQKI 422 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~-----~ar~~lSLD~~v 422 (460)
+.++.++||+.+|+.+.||..+.. +.+..+.|-..+
T Consensus 368 kPLtlkdVAe~lglHeSTVSRa~~~KY~~tp~GifeLK~FF 408 (481)
T PRK12469 368 KPLVLRDVAEELGLHESTISRATGNKYMATPRGTFEFKHFF 408 (481)
T ss_pred cCCcHHHHHHHhCCCcchhhHHhcCceeecCCceEeHHHhh
Confidence 567999999999999999987764 444455555444
No 254
>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=32.59 E-value=35 Score=24.04 Aligned_cols=22 Identities=27% Similarity=0.187 Sum_probs=18.0
Q ss_pred CHHHHHHHhCCCHHHHHHHHhC
Q 012567 390 NNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 390 S~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
|+.|+|+.+|+++.+++-.-..
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~ 22 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYERE 22 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHT
T ss_pred CHHHHHHHHCCCHHHHHHHHHC
Confidence 4679999999999999988764
No 255
>PRK09483 response regulator; Provisional
Probab=32.50 E-value=34 Score=31.23 Aligned_cols=32 Identities=16% Similarity=0.075 Sum_probs=26.1
Q ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCc
Q 012567 385 NGRHPNNEEVAEATGLSMKRLHAVLLSPKAPR 416 (460)
Q Consensus 385 ~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~l 416 (460)
...+.+.+|||+.|++|..+|+..++.....+
T Consensus 160 ~~~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl 191 (217)
T PRK09483 160 ITKGQKVNEISEQLNLSPKTVNSYRYRMFSKL 191 (217)
T ss_pred HHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 34678999999999999999999887554444
No 256
>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=32.40 E-value=1.1e+02 Score=21.84 Aligned_cols=33 Identities=12% Similarity=0.086 Sum_probs=23.9
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Q 012567 376 EARKQLYSENGRHPNNEEVAEATGLSMKRLHAV 408 (460)
Q Consensus 376 ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~ 408 (460)
.+.+.+.++--...|..+||+.+|++...+-..
T Consensus 4 aa~~l~~~~G~~~~s~~~Ia~~~gvs~~~~y~~ 36 (47)
T PF00440_consen 4 AALELFAEKGYEAVSIRDIARRAGVSKGSFYRY 36 (47)
T ss_dssp HHHHHHHHHHTTTSSHHHHHHHHTSCHHHHHHH
T ss_pred HHHHHHHHhCHHhCCHHHHHHHHccchhhHHHH
Confidence 344444444447899999999999999887643
No 257
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=32.27 E-value=1.2e+02 Score=24.27 Aligned_cols=25 Identities=32% Similarity=0.296 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHhC
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
...+..+||+.+|++..+|...+..
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l~~ 43 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLNT 43 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHH
Confidence 4789999999999999999988863
No 258
>PRK15320 transcriptional activator SprB; Provisional
Probab=32.10 E-value=33 Score=33.59 Aligned_cols=32 Identities=19% Similarity=0.058 Sum_probs=25.7
Q ss_pred HHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhC
Q 012567 380 QLYSENGRHPNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 380 ~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
++...+..+.|.+|||+.|++|.++|+..+.+
T Consensus 171 EVL~LLAkG~SNKEIAekL~LS~KTVSTYKnR 202 (251)
T PRK15320 171 ALLILLSSGHPAIELAKKFGLGTKTVSIYRKK 202 (251)
T ss_pred HHHHHHHcCCCHHHHHHHhccchhhHHHHHHH
Confidence 34444567899999999999999999887653
No 259
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=31.47 E-value=1.8e+02 Score=27.63 Aligned_cols=24 Identities=13% Similarity=0.264 Sum_probs=20.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHhC
Q 012567 388 HPNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 388 ~pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
..|.++||+.||++.++|...++.
T Consensus 184 ~lt~~~iA~~lG~sr~tvsR~l~~ 207 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETISRLLGR 207 (235)
T ss_pred cccHHHHHHHhCCcHHHHHHHHHH
Confidence 368899999999999999888763
No 260
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=31.29 E-value=89 Score=28.73 Aligned_cols=25 Identities=20% Similarity=0.142 Sum_probs=21.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHhC
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
...+..|||+.+|+|..+|..++++
T Consensus 27 ~R~s~~eiA~~lglS~~tv~~Ri~r 51 (164)
T PRK11169 27 GRISNVELSKRVGLSPTPCLERVRR 51 (164)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3457899999999999999998864
No 261
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=31.06 E-value=40 Score=32.38 Aligned_cols=28 Identities=21% Similarity=0.285 Sum_probs=25.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLLSPKA 414 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~~ar~ 414 (460)
|..+.++||+.||||..++...|+++..
T Consensus 177 R~~~l~dLA~~lGISkst~~ehLRrAe~ 204 (215)
T COG3413 177 RRVSLKDLAKELGISKSTLSEHLRRAER 204 (215)
T ss_pred ccCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 7779999999999999999999987644
No 262
>PRK10403 transcriptional regulator NarP; Provisional
Probab=30.47 E-value=48 Score=29.77 Aligned_cols=33 Identities=9% Similarity=0.123 Sum_probs=26.8
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHhCCCCCccc
Q 012567 386 GRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSL 418 (460)
Q Consensus 386 gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSL 418 (460)
..+.+.++||+.||+|..+|+..+.+.+..+.+
T Consensus 166 ~~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~ 198 (215)
T PRK10403 166 AQGLSNKQIASVLNISEQTVKVHIRNLLRKLNV 198 (215)
T ss_pred HCCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 356899999999999999999988766555444
No 263
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=30.29 E-value=85 Score=28.46 Aligned_cols=26 Identities=19% Similarity=0.193 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHhCC
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLLSP 412 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~~a 412 (460)
...++.+||+.||+|..+|..++++.
T Consensus 22 ~R~s~~eiA~~lglS~~tV~~Ri~rL 47 (153)
T PRK11179 22 ARTPYAELAKQFGVSPGTIHVRVEKM 47 (153)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 44679999999999999999988743
No 264
>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=30.24 E-value=1.5e+02 Score=25.27 Aligned_cols=24 Identities=13% Similarity=0.108 Sum_probs=20.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
...+..+||+.+|++..+|...+.
T Consensus 41 ~~~t~~ela~~~~~~~~tvs~~l~ 64 (118)
T TIGR02337 41 GSMEFTQLANQACILRPSLTGILA 64 (118)
T ss_pred CCcCHHHHHHHhCCCchhHHHHHH
Confidence 467899999999999999987765
No 265
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=29.95 E-value=2.1e+02 Score=26.29 Aligned_cols=24 Identities=21% Similarity=0.260 Sum_probs=21.1
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHhC
Q 012567 388 HPNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 388 ~pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
..|.++||..+|++.++|...++.
T Consensus 149 ~~t~~~iA~~lG~tretvsR~l~~ 172 (202)
T PRK13918 149 YATHDELAAAVGSVRETVTKVIGE 172 (202)
T ss_pred cCCHHHHHHHhCccHHHHHHHHHH
Confidence 458999999999999999888764
No 266
>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=29.77 E-value=65 Score=25.06 Aligned_cols=24 Identities=25% Similarity=0.375 Sum_probs=21.1
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHhC
Q 012567 388 HPNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 388 ~pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
..|.++||..+|++..+|...++.
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~ 51 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKR 51 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHH
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHH
Confidence 458899999999999999988863
No 267
>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=29.45 E-value=87 Score=26.38 Aligned_cols=24 Identities=29% Similarity=0.396 Sum_probs=19.8
Q ss_pred hCCCCCHHHHHHHhCCCHHHHHHH
Q 012567 385 NGRHPNNEEVAEATGLSMKRLHAV 408 (460)
Q Consensus 385 ~gr~pS~eEIAe~LGIS~e~Vk~~ 408 (460)
+..+.|+.||++.+|+|.-+|-..
T Consensus 46 L~~g~syreIa~~tgvS~aTItRv 69 (87)
T PF01371_consen 46 LDEGKSYREIAEETGVSIATITRV 69 (87)
T ss_dssp HHTTSSHHHHHHHHTSTHHHHHHH
T ss_pred HHCCCCHHHHHHHhCCCHHHHHHH
Confidence 346789999999999999887543
No 268
>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=29.28 E-value=71 Score=23.03 Aligned_cols=24 Identities=13% Similarity=0.225 Sum_probs=21.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
.+.|..++|+.+|++..+|..+.+
T Consensus 14 ~gltq~~lA~~~gvs~~~vs~~e~ 37 (58)
T TIGR03070 14 LGLTQADLADLAGVGLRFIRDVEN 37 (58)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHC
Confidence 478899999999999999999876
No 269
>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=28.65 E-value=71 Score=25.84 Aligned_cols=22 Identities=32% Similarity=0.443 Sum_probs=19.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHh
Q 012567 389 PNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 389 pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
.+.+|||+.+|++...+..++.
T Consensus 26 ~s~~eiA~~~~i~~~~l~kil~ 47 (83)
T PF02082_consen 26 VSSKEIAERLGISPSYLRKILQ 47 (83)
T ss_dssp BEHHHHHHHHTS-HHHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 7999999999999999998886
No 270
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=28.60 E-value=2.9e+02 Score=24.17 Aligned_cols=37 Identities=8% Similarity=0.211 Sum_probs=28.2
Q ss_pred HhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhc
Q 012567 246 EGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY 282 (460)
Q Consensus 246 e~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~ 282 (460)
.++..-+......+++..++|+.+|+++..|.+.++.
T Consensus 12 ~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 12 HSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3444455666778899999999999999888766654
No 271
>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=28.59 E-value=1e+02 Score=22.79 Aligned_cols=23 Identities=30% Similarity=0.482 Sum_probs=20.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHhC
Q 012567 389 PNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 389 pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
++..+||+.+|+|..+|...+..
T Consensus 26 ~~~~~la~~~~is~~~v~~~l~~ 48 (66)
T cd07377 26 PSERELAEELGVSRTTVREALRE 48 (66)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Confidence 56999999999999999988764
No 272
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=28.55 E-value=1.3e+02 Score=29.11 Aligned_cols=23 Identities=22% Similarity=0.319 Sum_probs=21.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHhC
Q 012567 389 PNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 389 pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
|+..+||+.+|+|-..|+.++..
T Consensus 35 psE~eLa~~lgVSRtpVREAL~~ 57 (254)
T PRK09464 35 PPERELAKQFDVSRPSLREAIQR 57 (254)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Confidence 58999999999999999999873
No 273
>PF13518 HTH_28: Helix-turn-helix domain
Probab=28.44 E-value=1.1e+02 Score=21.83 Aligned_cols=23 Identities=17% Similarity=0.184 Sum_probs=20.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHhC
Q 012567 389 PNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 389 pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
-|..+||..+||+..+|...+..
T Consensus 13 ~s~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 13 ESVREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred CCHHHHHHHHCCCHhHHHHHHHH
Confidence 39999999999999999888763
No 274
>PRK15044 transcriptional regulator SirC; Provisional
Probab=28.33 E-value=2e+02 Score=29.65 Aligned_cols=39 Identities=21% Similarity=0.146 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhC
Q 012567 373 RVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 373 kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
...++..-+.....+.++.++||+.+|+|..++....+.
T Consensus 193 ~~~kV~~~I~~nl~~~~SLeeLA~~lgmS~~tL~R~Fk~ 231 (295)
T PRK15044 193 TKEKVYNIIISDLTRKWSQAEVAGKLFMSVSSLKRKLAA 231 (295)
T ss_pred HHHHHHHHHHhCcccCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 345566666777788999999999999999999988764
No 275
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=28.26 E-value=5.6e+02 Score=24.92 Aligned_cols=37 Identities=19% Similarity=0.178 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 374 VKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 374 l~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
+.++...+.+.+....|.++||+.+|+|...+..+.+
T Consensus 188 ~~~~~~~I~~~~~~~~sl~~lA~~~~~S~~~l~r~Fk 224 (287)
T TIGR02297 188 FNRFNFLIEENYKQHLRLPEYADRLGISESRLNDICR 224 (287)
T ss_pred HHHHHHHHHHhhccCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3445555556667788999999999999998877665
No 276
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=28.03 E-value=48 Score=24.73 Aligned_cols=35 Identities=17% Similarity=0.189 Sum_probs=21.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHH-h-CCCCCcccccccc
Q 012567 389 PNNEEVAEATGLSMKRLHAVL-L-SPKAPRSLDQKIG 423 (460)
Q Consensus 389 pS~eEIAe~LGIS~e~Vk~~l-~-~ar~~lSLD~~v~ 423 (460)
.+..|||+.||++..+|-..+ . ..-...+..+.++
T Consensus 4 i~V~elAk~l~v~~~~ii~~l~~~~Gi~~~~~~~~ld 40 (54)
T PF04760_consen 4 IRVSELAKELGVPSKEIIKKLFKELGIMVKSINSSLD 40 (54)
T ss_dssp E-TTHHHHHHSSSHHHHHHHH-HHHTS---SSSS-EE
T ss_pred eEHHHHHHHHCcCHHHHHHHHHHhCCcCcCCCCCcCC
Confidence 356899999999999998888 4 2222245544443
No 277
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=27.79 E-value=37 Score=34.94 Aligned_cols=39 Identities=13% Similarity=0.215 Sum_probs=31.5
Q ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHhCCCC----Ccccccccc
Q 012567 385 NGRHPNNEEVAEATGLSMKRLHAVLLSPKA----PRSLDQKIG 423 (460)
Q Consensus 385 ~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~----~lSLD~~v~ 423 (460)
+-.+.|..|||+.||+|--+|..+|..|+. .+.++.|..
T Consensus 26 Y~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~I~I~~~~~ 68 (318)
T PRK15418 26 YHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQINSRFE 68 (318)
T ss_pred HhcCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEEEEEeCCCc
Confidence 346899999999999999999999988775 355655543
No 278
>COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]
Probab=27.74 E-value=1.3e+02 Score=31.38 Aligned_cols=71 Identities=21% Similarity=0.240 Sum_probs=48.6
Q ss_pred hHHHHHHHHHHHHHhhhcCcccccCcc--hHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 340 TYAHWWIKQAVRKSLSDQSRTIRLPFH--MVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 340 TYA~~wIr~aI~~~Lrk~~r~iriP~~--~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
+.+....++-+.+.+|......++|.. .-..-.+|.+++..+.....+..+.++||+.+|+|..++..+.+
T Consensus 186 ~~a~~va~~lv~~~~R~~~~~Q~~~~~~~~~~~~~~l~~~i~~me~nle~plsl~~LA~~~~~S~R~leRlF~ 258 (328)
T COG4977 186 ALANRVARQLVVDPIRSGGDRQRLPLLGRLGHRDPRLLRAIELMEANLEEPLSLEELADRAGLSRRQLERLFR 258 (328)
T ss_pred HHHHHHHHHhhhccccCCCccccccccccCCCCCHHHHHHHHHHHHhhcCCcCHHHHHHHhCCCHHHHHHHHH
Confidence 556666666677766653222222222 12233567788888888888999999999999999998877654
No 279
>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=27.65 E-value=59 Score=25.12 Aligned_cols=24 Identities=29% Similarity=0.338 Sum_probs=21.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
...|..|||+.+|++..+|...+.
T Consensus 21 ~~~t~~eIa~~l~i~~~~v~~~L~ 44 (68)
T PF01978_consen 21 GPATAEEIAEELGISRSTVYRALK 44 (68)
T ss_dssp CHEEHHHHHHHHTSSHHHHHHHHH
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHH
Confidence 467899999999999999998876
No 280
>PF13551 HTH_29: Winged helix-turn helix
Probab=27.54 E-value=1.5e+02 Score=24.43 Aligned_cols=24 Identities=25% Similarity=0.174 Sum_probs=18.0
Q ss_pred CCCHHHHHHHh-------CCCHHHHHHHHhC
Q 012567 388 HPNNEEVAEAT-------GLSMKRLHAVLLS 411 (460)
Q Consensus 388 ~pS~eEIAe~L-------GIS~e~Vk~~l~~ 411 (460)
..+..+|++.| .+|..+|..+++.
T Consensus 80 ~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~~ 110 (112)
T PF13551_consen 80 RWTLEELAEWLIEEEFGIDVSPSTIRRILKR 110 (112)
T ss_pred cccHHHHHHHHHHhccCccCCHHHHHHHHHH
Confidence 45677887755 6888899888874
No 281
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=27.30 E-value=82 Score=22.00 Aligned_cols=26 Identities=19% Similarity=0.241 Sum_probs=18.5
Q ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 385 NGRHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 385 ~gr~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
+....+.++||+.+|+|........+
T Consensus 5 ~~~~~~l~~iA~~~g~S~~~f~r~Fk 30 (42)
T PF00165_consen 5 LQQKLTLEDIAEQAGFSPSYFSRLFK 30 (42)
T ss_dssp T-SS--HHHHHHHHTS-HHHHHHHHH
T ss_pred ccCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 45668899999999999988877765
No 282
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=27.15 E-value=52 Score=29.63 Aligned_cols=32 Identities=22% Similarity=0.041 Sum_probs=27.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcc
Q 012567 386 GRHPNNEEVAEATGLSMKRLHAVLLSPKAPRS 417 (460)
Q Consensus 386 gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lS 417 (460)
..+.+.+|||+.|+++..+|+..+.+.+..+.
T Consensus 162 ~~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl~ 193 (210)
T PRK09935 162 VSGLSNKEIADQLLLSNKTVSAHKSNIYGKLG 193 (210)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 34699999999999999999999887766554
No 283
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=27.02 E-value=33 Score=30.00 Aligned_cols=30 Identities=27% Similarity=0.304 Sum_probs=26.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHhCCCCCc
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLLSPKAPR 416 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~l 416 (460)
.+.+.+|-|+.||||-.|+..++..++..+
T Consensus 56 egl~QeeaA~~MgVSR~T~~ril~~ARkKi 85 (106)
T PF02001_consen 56 EGLSQEEAAERMGVSRPTFQRILESARKKI 85 (106)
T ss_pred cCCCHHHHHHHcCCcHHHHHHHHHHHHHHH
Confidence 578999999999999999999998887643
No 284
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=26.78 E-value=3.1e+02 Score=22.84 Aligned_cols=37 Identities=16% Similarity=0.138 Sum_probs=28.7
Q ss_pred HhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhc
Q 012567 246 EGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY 282 (460)
Q Consensus 246 e~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~ 282 (460)
+++..-+.+....+++..++|..+|++...|.+.++.
T Consensus 8 ~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~ 44 (107)
T PRK10219 8 QTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRT 44 (107)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3444556666788899999999999999888776665
No 285
>TIGR03764 ICE_PFGI_1_parB integrating conjugative element, PFGI_1 class, ParB family protein. Members of this protein family carry the ParB-type nuclease domain and are found in integrating conjugative elements (ICE) in the same class as PFGI-1 of Pseudomonas fluorescens Pf-5.
Probab=26.75 E-value=5.9e+02 Score=25.79 Aligned_cols=91 Identities=19% Similarity=0.201 Sum_probs=46.6
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCC-----CH--------------HHHHHHHhcc-
Q 012567 224 SRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGV-----DQ--------------RELRRRLNYG- 283 (460)
Q Consensus 224 ~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~-----de--------------~~L~~~l~~G- 283 (460)
..-||+=|+..-.+++.+ -+++.+|..-|-.+.|+.+|. +. ..+...+..|
T Consensus 110 R~dLsfIE~A~~~~~l~~---------l~e~~~g~~ltq~ela~~lgk~g~~isrs~Isn~lrll~~L~~~i~~~l~~gl 180 (258)
T TIGR03764 110 RGDLTFIEKALGVQKARA---------LYEKELGESLSQRELARRLSADGYPISQSHISRMGDTVEYLYPAIPNLLYSGL 180 (258)
T ss_pred hcCCCHHHHHHHHHHHHH---------HHHhhccCCCCHHHHHHHhcccCCCCCHHHHHHHHHHHHhChHHHHHHHHccC
Confidence 456888777655444433 233344555666666666654 32 2233344444
Q ss_pred -HHHHHHHHHHhHHHHHHHHHHc-cCCCCCcccHHhHHHHHHHHHHhhcC
Q 012567 284 -ILCKDKMITSNIRLVISIAKNY-QGAGMNLQDLVQEGCRGLVRGAEKFD 331 (460)
Q Consensus 284 -~~A~e~LI~~nlrLV~~IAkry-~~~g~d~eDLiQEG~IGLirAiekFD 331 (460)
..-...|..-. +-..++-.+| .+...+|++++|+. +.+||
T Consensus 181 Gr~~~~~L~~L~-~~a~~~w~~~~~~~~~~f~~~f~~~-------~~~~d 222 (258)
T TIGR03764 181 GRPQIEKLLSLR-KAAEKIWNRYSSGVEVDFEEVFQEV-------LARFD 222 (258)
T ss_pred ChHHHHHHHHHH-HHHHHHHHHHccccCCCHHHHHHHH-------HHhcC
Confidence 33334443311 1122232333 34457889988875 46788
No 286
>PHA01976 helix-turn-helix protein
Probab=26.71 E-value=1e+02 Score=23.43 Aligned_cols=24 Identities=13% Similarity=0.101 Sum_probs=21.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
++.|..++|+.+|++..+|..+..
T Consensus 14 ~glt~~~lA~~~gvs~~~v~~~e~ 37 (67)
T PHA01976 14 RAWSAPELSRRAGVRHSLIYDFEA 37 (67)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHc
Confidence 568899999999999999998775
No 287
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=26.57 E-value=1.1e+02 Score=25.30 Aligned_cols=27 Identities=26% Similarity=0.372 Sum_probs=20.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHhCC
Q 012567 386 GRHPNNEEVAEATGLSMKRLHAVLLSP 412 (460)
Q Consensus 386 gr~pS~eEIAe~LGIS~e~Vk~~l~~a 412 (460)
|+..|..++|..+|+++++|..++...
T Consensus 36 G~PVt~~~LA~a~g~~~e~v~~~L~~~ 62 (77)
T PF12324_consen 36 GQPVTVEQLAAALGWPVEEVRAALAAM 62 (77)
T ss_dssp TS-B-HHHHHHHHT--HHHHHHHHHH-
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHhC
Confidence 788899999999999999999999754
No 288
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=26.41 E-value=95 Score=21.80 Aligned_cols=25 Identities=28% Similarity=0.228 Sum_probs=22.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHhC
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
..++..+|++.+|++..++...+..
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~ 37 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNK 37 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4589999999999999999888764
No 289
>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=26.29 E-value=73 Score=29.48 Aligned_cols=25 Identities=16% Similarity=0.352 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHhC
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
...|.+|||+.|||+...|+.++..
T Consensus 27 ~~~tdEeLa~~Lgi~~~~VRk~L~~ 51 (158)
T TIGR00373 27 GEFTDEEISLELGIKLNEVRKALYA 51 (158)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3689999999999999999999863
No 290
>PRK10651 transcriptional regulator NarL; Provisional
Probab=26.08 E-value=69 Score=28.81 Aligned_cols=34 Identities=9% Similarity=0.010 Sum_probs=26.9
Q ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCccc
Q 012567 385 NGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSL 418 (460)
Q Consensus 385 ~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSL 418 (460)
+..+.+.++||+.|+++..+|+..+...+..+.+
T Consensus 167 l~~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl~~ 200 (216)
T PRK10651 167 IAQGLPNKMIARRLDITESTVKVHVKHMLKKMKL 200 (216)
T ss_pred HHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 3456789999999999999999988766554433
No 291
>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=25.91 E-value=62 Score=25.36 Aligned_cols=25 Identities=24% Similarity=0.240 Sum_probs=19.9
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 386 GRHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 386 gr~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
+...|..+||..+|++++.|+.++.
T Consensus 12 ~~~~S~~eLa~~~~~s~~~ve~mL~ 36 (69)
T PF09012_consen 12 RGRVSLAELAREFGISPEAVEAMLE 36 (69)
T ss_dssp S-SEEHHHHHHHTT--HHHHHHHHH
T ss_pred cCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 4567899999999999999999986
No 292
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=25.72 E-value=73 Score=24.35 Aligned_cols=23 Identities=26% Similarity=0.147 Sum_probs=20.4
Q ss_pred CHHHHHHHhCCCHHHHHHHHhCC
Q 012567 390 NNEEVAEATGLSMKRLHAVLLSP 412 (460)
Q Consensus 390 S~eEIAe~LGIS~e~Vk~~l~~a 412 (460)
|..|+|+.+|+|..+|+......
T Consensus 2 ti~eva~~~gvs~~tlr~y~~~g 24 (69)
T PF13411_consen 2 TIKEVAKLLGVSPSTLRYYEREG 24 (69)
T ss_dssp EHHHHHHHTTTTHHHHHHHHHTT
T ss_pred cHHHHHHHHCcCHHHHHHHHHhc
Confidence 56899999999999999998754
No 293
>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=25.29 E-value=71 Score=26.54 Aligned_cols=31 Identities=23% Similarity=0.199 Sum_probs=20.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHhCCCCCccc
Q 012567 388 HPNNEEVAEATGLSMKRLHAVLLSPKAPRSL 418 (460)
Q Consensus 388 ~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSL 418 (460)
+.|..|||+.||.|...|..++....-+-.+
T Consensus 3 G~tq~eIA~~lGks~s~Vs~~l~Ll~lP~~i 33 (93)
T PF08535_consen 3 GWTQEEIAKRLGKSRSWVSNHLALLDLPEEI 33 (93)
T ss_dssp T--HHHHHHHTT--HHHHHHHHGGGS--HHH
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHcCCHHH
Confidence 5688999999999999999999865443333
No 294
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=24.91 E-value=82 Score=23.98 Aligned_cols=24 Identities=13% Similarity=0.177 Sum_probs=20.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
.+.|..++|+.+|++..+|..+.+
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 468999999999999999999887
No 295
>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=24.83 E-value=1.1e+02 Score=22.71 Aligned_cols=23 Identities=22% Similarity=0.333 Sum_probs=19.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHh
Q 012567 388 HPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 388 ~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
..+..|||+.+|++..+|..++.
T Consensus 21 ~~t~~~la~~l~~~~~~vs~~v~ 43 (62)
T PF12802_consen 21 ELTQSELAERLGISKSTVSRIVK 43 (62)
T ss_dssp GEEHHHHHHHHTS-HHHHHHHHH
T ss_pred CcCHHHHHHHHCcCHHHHHHHHH
Confidence 37999999999999999988876
No 296
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=24.68 E-value=1.5e+02 Score=27.53 Aligned_cols=40 Identities=10% Similarity=0.189 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHHHHHHhC-CCCCHHHHHHHhCCCHHHHHH
Q 012567 368 VEATYRVKEARKQLYSENG-RHPNNEEVAEATGLSMKRLHA 407 (460)
Q Consensus 368 ~e~i~kl~ka~~~L~~~~g-r~pS~eEIAe~LGIS~e~Vk~ 407 (460)
.+...+|.++..++..+.| ...|.++||+..|+|.+++-.
T Consensus 10 ~~~r~~Il~aa~~lf~~~G~~~~ti~~Ia~~agvsk~t~Y~ 50 (213)
T PRK09975 10 LKTRQELIETAIAQFALRGVSNTTLNDIADAANVTRGAIYW 50 (213)
T ss_pred HHHHHHHHHHHHHHHHHcCcccCCHHHHHHHcCCCHHHHHH
Confidence 4445667777777777777 678999999999999998854
No 297
>PRK09726 antitoxin HipB; Provisional
Probab=24.67 E-value=1.9e+02 Score=23.63 Aligned_cols=25 Identities=12% Similarity=0.118 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHhC
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
.+.|.+++|+.+|++..+|..+.+-
T Consensus 24 ~gltq~elA~~~gvs~~tis~~e~g 48 (88)
T PRK09726 24 NGWTQSELAKKIGIKQATISNFENN 48 (88)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 4789999999999999999998873
No 298
>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=24.52 E-value=90 Score=23.77 Aligned_cols=22 Identities=32% Similarity=0.185 Sum_probs=19.5
Q ss_pred CHHHHHHHhCCCHHHHHHHHhC
Q 012567 390 NNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 390 S~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
+..|+|+.+|++..+++...+.
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh
Confidence 6789999999999999988763
No 299
>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=24.15 E-value=63 Score=27.72 Aligned_cols=24 Identities=17% Similarity=0.188 Sum_probs=20.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
.+.|+.|||+.+|||..+|-..-+
T Consensus 54 ~~~tQrEIa~~lGiS~atIsR~sn 77 (94)
T TIGR01321 54 GNMSQREIASKLGVSIATITRGSN 77 (94)
T ss_pred CCCCHHHHHHHhCCChhhhhHHHh
Confidence 578999999999999988865533
No 300
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=24.06 E-value=1e+02 Score=32.02 Aligned_cols=39 Identities=18% Similarity=0.244 Sum_probs=31.3
Q ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHhCCCC----Ccccccccc
Q 012567 385 NGRHPNNEEVAEATGLSMKRLHAVLLSPKA----PRSLDQKIG 423 (460)
Q Consensus 385 ~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~----~lSLD~~v~ 423 (460)
+-.+.|..|||+.||||.-+|..++..++. .++++.++.
T Consensus 23 Y~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I~i~~~~~ 65 (321)
T COG2390 23 YVEGLTQSEIAERLGISRATVSRLLAKAREEGIVKISINSPVE 65 (321)
T ss_pred HhcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEEEeCCCCc
Confidence 446889999999999999999999987775 355655554
No 301
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=24.00 E-value=1.5e+02 Score=30.28 Aligned_cols=41 Identities=22% Similarity=0.212 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCC
Q 012567 372 YRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSP 412 (460)
Q Consensus 372 ~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~a 412 (460)
..+..+.-.|..+.++...-+|||+.+|..+++|++.++.-
T Consensus 9 keIL~aLi~LY~~~~r~IKgeeIA~~l~rnpGTVRNqmq~L 49 (294)
T COG2524 9 KEILQALINLYRRKKRPIKGEEIAEVLNRNPGTVRNQMQSL 49 (294)
T ss_pred HHHHHHHHHHHHhcCCCcchHHHHHHHccCcchHHHHHHHH
Confidence 44556666677777777778999999999999999998743
No 302
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=23.58 E-value=96 Score=23.64 Aligned_cols=21 Identities=29% Similarity=0.286 Sum_probs=19.1
Q ss_pred CHHHHHHHhCCCHHHHHHHHh
Q 012567 390 NNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 390 S~eEIAe~LGIS~e~Vk~~l~ 410 (460)
+..|+|+.+|++..+++....
T Consensus 2 s~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 678999999999999998876
No 303
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=23.48 E-value=91 Score=28.72 Aligned_cols=31 Identities=32% Similarity=0.415 Sum_probs=18.4
Q ss_pred HHHHHhCCCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 380 QLYSENGRHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 380 ~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
++....+..+|..|||+.+||+..++-...+
T Consensus 26 e~~~~~~~r~T~~eiAee~Gis~~tLYrWr~ 56 (142)
T PF13022_consen 26 ELMPENGERRTQAEIAEEVGISRSTLYRWRQ 56 (142)
T ss_dssp HHS------S-HHHHHHHHTS-HHHHHHHHH
T ss_pred HHhhhccccchHHHHHHHhCCCHHHHHHHHh
Confidence 3444445779999999999999998866553
No 304
>PHA02943 hypothetical protein; Provisional
Probab=23.41 E-value=2.5e+02 Score=26.39 Aligned_cols=24 Identities=17% Similarity=0.200 Sum_probs=20.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
...|..|||+.||+|-+.++.++.
T Consensus 23 G~~TtseIAkaLGlS~~qa~~~Ly 46 (165)
T PHA02943 23 GCKTTSRIANKLGVSHSMARNALY 46 (165)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHH
Confidence 345789999999999999998876
No 305
>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=23.15 E-value=1.9e+02 Score=26.15 Aligned_cols=25 Identities=20% Similarity=0.227 Sum_probs=21.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHhCC
Q 012567 388 HPNNEEVAEATGLSMKRLHAVLLSP 412 (460)
Q Consensus 388 ~pS~eEIAe~LGIS~e~Vk~~l~~a 412 (460)
..|.++||..+|++.++|-.+++..
T Consensus 143 ~~t~~~iA~~lG~tretvsR~l~~l 167 (193)
T TIGR03697 143 RLSHQAIAEAIGSTRVTITRLLGDL 167 (193)
T ss_pred CCCHHHHHHHhCCcHHHHHHHHHHH
Confidence 4688999999999999999888643
No 306
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=23.13 E-value=3.3e+02 Score=20.48 Aligned_cols=35 Identities=23% Similarity=0.293 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCC-CHHHHHHHHh
Q 012567 373 RVKEARKQLYSENGRHPNNEEVAEATGL-SMKRLHAVLL 410 (460)
Q Consensus 373 kl~ka~~~L~~~~gr~pS~eEIAe~LGI-S~e~Vk~~l~ 410 (460)
++..+...|... +.+..+||..+|+ +........+
T Consensus 38 r~~~a~~~l~~~---~~~~~~ia~~~g~~s~~~f~r~Fk 73 (84)
T smart00342 38 RLERARRLLRDT---DLSVTEIALRVGFSSQSYFSRAFK 73 (84)
T ss_pred HHHHHHHHHHcC---CCCHHHHHHHhCCCChHHHHHHHH
Confidence 455555555432 6899999999999 8887766654
No 307
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=23.08 E-value=1e+02 Score=27.16 Aligned_cols=30 Identities=10% Similarity=0.036 Sum_probs=24.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHhCCCCCc
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLLSPKAPR 416 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~l 416 (460)
.+.+.++||+.+|++..+|+..+.+++..+
T Consensus 155 ~~~~~~~ia~~l~~s~~tv~~~~~~~~~kl 184 (202)
T PRK09390 155 AGLSNKVIARDLDISPRTVEVYRANVMTKM 184 (202)
T ss_pred ccCchHHHHHHcCCCHHHHHHHHHHHHHHH
Confidence 356799999999999999998887655443
No 308
>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=23.02 E-value=95 Score=23.54 Aligned_cols=25 Identities=24% Similarity=0.185 Sum_probs=21.4
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 386 GRHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 386 gr~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
....+.+|||+.+|+|..+|+.-+.
T Consensus 12 ~~~~s~~ela~~~~VS~~TiRRDl~ 36 (57)
T PF08220_consen 12 KGKVSVKELAEEFGVSEMTIRRDLN 36 (57)
T ss_pred cCCEEHHHHHHHHCcCHHHHHHHHH
Confidence 3567899999999999999987665
No 309
>PRK09480 slmA division inhibitor protein; Provisional
Probab=22.99 E-value=1.7e+02 Score=26.50 Aligned_cols=39 Identities=23% Similarity=0.258 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHH-HHhCCCCCHHHHHHHhCCCHHHHHH
Q 012567 369 EATYRVKEARKQLY-SENGRHPNNEEVAEATGLSMKRLHA 407 (460)
Q Consensus 369 e~i~kl~ka~~~L~-~~~gr~pS~eEIAe~LGIS~e~Vk~ 407 (460)
....+|.++...|. .+.|...|..+||+..|++.+++-.
T Consensus 10 ~~r~~Il~aa~~l~~~~~G~~~ti~~Ia~~agvs~gt~Y~ 49 (194)
T PRK09480 10 ERREQILQALAQMLESPPGERITTAKLAARVGVSEAALYR 49 (194)
T ss_pred hHHHHHHHHHHHHHHhcCCCccCHHHHHHHhCCCHhHHHH
Confidence 33445556655554 4446889999999999999888743
No 310
>PRK06424 transcription factor; Provisional
Probab=22.95 E-value=2.7e+02 Score=25.52 Aligned_cols=40 Identities=8% Similarity=-0.061 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 369 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 369 e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
+....+...++.+..+ .+.|.+++|+.+|++..+|..+.+
T Consensus 80 ~~~~~~g~~Ir~lRe~--~GLSQ~eLA~~iGvs~stIskiE~ 119 (144)
T PRK06424 80 DIVEDYAELVKNARER--LSMSQADLAAKIFERKNVIASIER 119 (144)
T ss_pred HHHHHHHHHHHHHHHH--cCCCHHHHHHHhCCCHHHHHHHHC
Confidence 3334444444444333 678999999999999999999876
No 311
>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=22.84 E-value=1.4e+02 Score=25.99 Aligned_cols=26 Identities=27% Similarity=0.382 Sum_probs=22.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHhC
Q 012567 386 GRHPNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 386 gr~pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
+...+..|||+.+|+|...|..++..
T Consensus 23 ~~~~s~~eia~~l~is~~~v~~~l~~ 48 (130)
T TIGR02944 23 SQPYSAAEIAEQTGLNAPTVSKILKQ 48 (130)
T ss_pred CCCccHHHHHHHHCcCHHHHHHHHHH
Confidence 45679999999999999999988863
No 312
>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=22.55 E-value=82 Score=24.19 Aligned_cols=22 Identities=23% Similarity=0.188 Sum_probs=19.1
Q ss_pred CHHHHHHHhCCCHHHHHHHHhC
Q 012567 390 NNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 390 S~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
+..|+|+.+|++..+++.....
T Consensus 2 ~i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 2 TIKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh
Confidence 6789999999999999987653
No 313
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=22.38 E-value=1.8e+02 Score=26.98 Aligned_cols=24 Identities=13% Similarity=0.032 Sum_probs=21.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
++.|.+++|+.+|++...|..+.+
T Consensus 81 ~glSqeeLA~~lgvs~s~IsriE~ 104 (154)
T TIGR00270 81 RGWSQEQLAKKIQEKESLIKKIEN 104 (154)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHC
Confidence 678999999999999999988775
No 314
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=21.91 E-value=3.8e+02 Score=25.58 Aligned_cols=24 Identities=17% Similarity=0.339 Sum_probs=20.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHhC
Q 012567 388 HPNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 388 ~pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
..|.++||..||++.++|-.+++.
T Consensus 179 ~lt~~~IA~~lGisretlsR~L~~ 202 (230)
T PRK09391 179 PMSRRDIADYLGLTIETVSRALSQ 202 (230)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHH
Confidence 368899999999999999888763
No 315
>PRK09480 slmA division inhibitor protein; Provisional
Probab=21.86 E-value=5.9e+02 Score=22.88 Aligned_cols=72 Identities=17% Similarity=0.005 Sum_probs=44.3
Q ss_pred hhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHH
Q 012567 254 ERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVR 325 (460)
Q Consensus 254 ~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLir 325 (460)
++-|...|..+.|+.+|++...+-.-..+..+-+..++..+..-+............+..+.++..+-.++.
T Consensus 25 ~~~G~~~ti~~Ia~~agvs~gt~Y~~F~~K~~L~~~v~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ 96 (194)
T PRK09480 25 SPPGERITTAKLAARVGVSEAALYRHFPSKARMFEGLIEFIEESLFSRINQILKDEKDTLARARLILLLLLG 96 (194)
T ss_pred hcCCCccCHHHHHHHhCCCHhHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHccCCCHHHHHHHHHHHHHH
Confidence 344778899999999999998888777766666666666555444433333332223344444444433333
No 316
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=21.57 E-value=1.3e+02 Score=20.23 Aligned_cols=24 Identities=29% Similarity=0.318 Sum_probs=20.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
...+..++|+.+|++..+|.....
T Consensus 9 ~~~s~~~la~~~~i~~~~i~~~~~ 32 (56)
T smart00530 9 KGLTQEELAEKLGVSRSTLSRIEN 32 (56)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHC
Confidence 467899999999999999988765
No 317
>PF15545 Toxin_67: Putative toxin 67
Probab=21.40 E-value=98 Score=24.98 Aligned_cols=31 Identities=26% Similarity=0.521 Sum_probs=25.5
Q ss_pred chHhHHHHHHHHHHHHHhhhcCcccccCcch
Q 012567 337 KFSTYAHWWIKQAVRKSLSDQSRTIRLPFHM 367 (460)
Q Consensus 337 rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~ 367 (460)
+-+.|+.-||+|.|...-+.+...+|+|...
T Consensus 6 kq~~~vRGwiknEi~~i~~~~r~~iRlPpG~ 36 (70)
T PF15545_consen 6 KQPSWVRGWIKNEINRIKTGRRKSIRLPPGK 36 (70)
T ss_pred cchHHHHHHHHHHHHHHHhCccceecCCCch
Confidence 4578999999999998877777789998653
No 318
>PRK03837 transcriptional regulator NanR; Provisional
Probab=21.36 E-value=2.6e+02 Score=26.75 Aligned_cols=24 Identities=17% Similarity=0.279 Sum_probs=21.3
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHhC
Q 012567 388 HPNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 388 ~pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
-|+..+||+.+|+|-..|++++..
T Consensus 37 Lp~E~~Lae~~gVSRt~VREAL~~ 60 (241)
T PRK03837 37 LPSERELMAFFGVGRPAVREALQA 60 (241)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHH
Confidence 348999999999999999999873
No 319
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=21.31 E-value=1.3e+02 Score=21.54 Aligned_cols=26 Identities=27% Similarity=0.144 Sum_probs=22.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHhC
Q 012567 386 GRHPNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 386 gr~pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
....+..+|++.+|++..++...++.
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~ 33 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKK 33 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHH
Confidence 34568899999999999999988864
No 320
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=21.10 E-value=2e+02 Score=28.63 Aligned_cols=38 Identities=16% Similarity=0.102 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Q 012567 372 YRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVL 409 (460)
Q Consensus 372 ~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l 409 (460)
..+.++..-+...+...++.++||+.+|+|...+..+.
T Consensus 5 ~~i~~~~~~i~~~~~~~~~l~~lA~~~~~S~~~l~r~F 42 (289)
T PRK15121 5 GIIRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMF 42 (289)
T ss_pred HHHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHH
Confidence 45666666677777778888999988888877665543
No 321
>PRK10072 putative transcriptional regulator; Provisional
Probab=20.73 E-value=1.4e+02 Score=25.47 Aligned_cols=26 Identities=12% Similarity=0.068 Sum_probs=22.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHhCC
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLLSP 412 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~~a 412 (460)
.+.|..++|+.+|++..+|.....--
T Consensus 45 ~glTQ~elA~~lGvS~~TVs~WE~G~ 70 (96)
T PRK10072 45 TGLKIDDFARVLGVSVAMVKEWESRR 70 (96)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcCC
Confidence 47889999999999999999988733
No 322
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=20.69 E-value=2e+02 Score=21.72 Aligned_cols=23 Identities=30% Similarity=0.447 Sum_probs=18.7
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHh
Q 012567 259 SPTFAQWAAAAGVDQRELRRRLN 281 (460)
Q Consensus 259 ~pt~~ewA~a~g~de~~L~~~l~ 281 (460)
+++..++|..+|++...|.+.+.
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~ 23 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFK 23 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Confidence 36788999999999888876665
No 323
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=20.64 E-value=2.2e+02 Score=26.18 Aligned_cols=38 Identities=24% Similarity=0.274 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHHhC-CCCCHHHHHHHhCCCHHHH
Q 012567 368 VEATYRVKEARKQLYSENG-RHPNNEEVAEATGLSMKRL 405 (460)
Q Consensus 368 ~e~i~kl~ka~~~L~~~~g-r~pS~eEIAe~LGIS~e~V 405 (460)
.....+|..+..++..+.| ...|..+||+..|+|.+.+
T Consensus 7 ~~~r~~Il~aA~~lf~e~G~~~~s~~~IA~~agvs~~~l 45 (202)
T TIGR03613 7 EAKRKAILSAALDTFSRFGFHGTSLEQIAELAGVSKTNL 45 (202)
T ss_pred HHHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCCCHHHH
No 324
>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=20.63 E-value=1.2e+02 Score=23.67 Aligned_cols=24 Identities=21% Similarity=0.182 Sum_probs=21.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 387 RHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 387 r~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
.+.|..++|+.+|++..+|..++.
T Consensus 17 ~~~t~~~lA~~~gis~~tis~~~~ 40 (78)
T TIGR02607 17 LGLSIRALAKALGVSRSTLSRIVN 40 (78)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHc
Confidence 567899999999999999999887
No 325
>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=20.57 E-value=8.9e+02 Score=24.48 Aligned_cols=34 Identities=18% Similarity=0.121 Sum_probs=25.5
Q ss_pred HHHHHHHHhCCCCCHHHHHHHhC--CCHHHHHHHHh
Q 012567 377 ARKQLYSENGRHPNNEEVAEATG--LSMKRLHAVLL 410 (460)
Q Consensus 377 a~~~L~~~~gr~pS~eEIAe~LG--IS~e~Vk~~l~ 410 (460)
++++|..-.+..++..+||+.|+ ||.++|++.+.
T Consensus 126 virel~~~~~~~~~~~~ia~~l~p~is~~ev~~sL~ 161 (271)
T TIGR02147 126 VIRELLGVMPFADDPEELAKRCFPKISAEQVKESLD 161 (271)
T ss_pred HHHHHhhcCCCCCCHHHHHHHhCCCCCHHHHHHHHH
Confidence 34444444455667889999999 99999998886
No 326
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=20.51 E-value=1.9e+02 Score=29.27 Aligned_cols=40 Identities=8% Similarity=0.007 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhC
Q 012567 372 YRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLS 411 (460)
Q Consensus 372 ~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ 411 (460)
..+.++...+...+...++.++||+.+|+|...+....+.
T Consensus 218 ~~~~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~ 257 (322)
T PRK09393 218 DRLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEA 257 (322)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3466666667777778899999999999999999887663
No 327
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=20.33 E-value=3e+02 Score=27.17 Aligned_cols=77 Identities=16% Similarity=0.133 Sum_probs=0.0
Q ss_pred HHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHHHHHHHH
Q 012567 296 RLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVK 375 (460)
Q Consensus 296 rLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e~i~kl~ 375 (460)
+.+..|...|....+..+++.+.-.+..-.-..-|... |..|..|+.. .+|.
T Consensus 201 ~~~~~I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk~~-G~T~~~yi~~---------------------------~RL~ 252 (302)
T PRK09685 201 KVVALIDQSIQEEILRPEWIAGELGISVRSLYRLFAEQ-GLVVAQYIRN---------------------------RRLD 252 (302)
T ss_pred HHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHc-CCCHHHHHHH---------------------------HHHH
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHhCCC
Q 012567 376 EARKQLYSENGRHPNNEEVAEATGLS 401 (460)
Q Consensus 376 ka~~~L~~~~gr~pS~eEIAe~LGIS 401 (460)
++...| .......++.|||..+|.+
T Consensus 253 ~A~~lL-~~~~~~~sI~eIA~~~GF~ 277 (302)
T PRK09685 253 RCADDL-RPAADDEKITSIAYKWGFS 277 (302)
T ss_pred HHHHHh-hhhccCCCHHHHHHHhCCC
No 328
>KOG3758 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.20 E-value=2.9e+02 Score=31.33 Aligned_cols=159 Identities=19% Similarity=0.225 Sum_probs=76.2
Q ss_pred CCCCCHHHHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhcc----
Q 012567 208 VDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYG---- 283 (460)
Q Consensus 208 ~~~~d~l~YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G---- 283 (460)
....||+||+-+|-+ +=-=+-..|++|.+.+-+. + ..+++. . .-+..+....+|-...-|...+-.|
T Consensus 278 l~ahDPlRyIGDmLa-wlHq~ia~Ekelv~aLfd~-~----~~d~q~--n-~~~~en~~~vl~~~dn~lld~i~~gvcrP 348 (655)
T KOG3758|consen 278 LHAHDPLRYIGDMLA-WLHQAIANEKELVEALFDF-K----KEDLQD--N-ISISENLPNVLGGIDNKLLDDILEGVCRP 348 (655)
T ss_pred ccCCChHHHHHHHHH-HHHHHhhhHHHHHHHHhcc-h----hhhhcc--C-CCchhHhHHHHhchhhhHHHHHHHHhcch
Confidence 456799999988811 1112345677887766532 1 111111 1 1122334444442222222222233
Q ss_pred -HHHHHHHHHHhHH--HHHHHHHHccCCCCCcccHHhHHH--HHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcC
Q 012567 284 -ILCKDKMITSNIR--LVISIAKNYQGAGMNLQDLVQEGC--RGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS 358 (460)
Q Consensus 284 -~~A~e~LI~~nlr--LV~~IAkry~~~g~d~eDLiQEG~--IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~ 358 (460)
.--.++++..--. ..++|.+-..-+...++++||.+. +-.++.++++-. .+|.+|+....++-+...+.-..
T Consensus 349 lkvRvEqil~~e~~~Iilfki~nlL~FY~~~fs~~v~~ds~l~~~l~~L~d~s~---q~~~~~l~~~~~~l~~~~l~p~~ 425 (655)
T KOG3758|consen 349 LKVRVEQILQAEKNAIILFKISNLLKFYRVTFSKLVQDDSALLNTLKELEDISK---QRFIGYLEDHVKKLMRKELSPPS 425 (655)
T ss_pred hHHHHHHHHHcCcCceeehhHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHhcCCCcc
Confidence 1122333322211 223333322223345678888554 445555666642 36888888877777766443322
Q ss_pred cccccCcchHHHHHHHHHHHH
Q 012567 359 RTIRLPFHMVEATYRVKEARK 379 (460)
Q Consensus 359 r~iriP~~~~e~i~kl~ka~~ 379 (460)
..-.|..+.+.++.+.+...
T Consensus 426 -DLlPpp~v~~~l~ll~ei~~ 445 (655)
T KOG3758|consen 426 -DLLPPPAVREYLNLLVEIFE 445 (655)
T ss_pred -ccCCCHHHHHHHHHHHHHHH
Confidence 22234556666666555554
No 329
>PRK08359 transcription factor; Validated
Probab=20.14 E-value=2.1e+02 Score=27.25 Aligned_cols=40 Identities=18% Similarity=0.170 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHh
Q 012567 369 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL 410 (460)
Q Consensus 369 e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~ 410 (460)
+.+..+...++++.. .++.|.+|+|+.+|++...|..+-.
T Consensus 81 elv~dy~~rIkeaRe--~kglSQeeLA~~lgvs~stI~~iE~ 120 (176)
T PRK08359 81 DIVEDYAERVYEAIQ--KSGLSYEELSHEVGLSVNDLRRIAH 120 (176)
T ss_pred HHHHHHHHHHHHHHH--HcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 444444444444433 3589999999999999999987644
No 330
>COG1916 Uncharacterized homolog of PrgY (pheromone shutdown protein) [Function unknown]
Probab=20.11 E-value=5e+02 Score=27.74 Aligned_cols=122 Identities=19% Similarity=0.210 Sum_probs=68.3
Q ss_pred CHHHHHHHhhcCCCCCCHHHHHHHHHHHH--HHHHHHhHHHHHhhhcCCCCcHH-----HHHHHhCCCHHHHHHHHhcc-
Q 012567 212 DPLRYLRATTSSSRLLTANEEMQLSAGIQ--DLLKLEGLREVLSERCGGSPTFA-----QWAAAAGVDQRELRRRLNYG- 283 (460)
Q Consensus 212 d~l~YL~~~~~~~~lLT~EEE~eL~~~Iq--~~~~le~~~~~L~~~~g~~pt~~-----ewA~a~g~de~~L~~~l~~G- 283 (460)
|+-||+.=..+...-|+-.+.....+... ...-|...|..|.++.|-+|-.+ |-|...|.+...+-+-++--
T Consensus 47 d~~R~~sLl~~~~~~ldl~~vlk~Gk~~~~l~~~lLa~~Qrklg~~~Gv~PGsEmk~AIe~A~e~ga~V~lIDRdI~vTl 126 (388)
T COG1916 47 DEARLLSLLGGSREELDLAQVLKEGKAFFLLAGLLLAYFQRKLGKELGVKPGSEMKAAIEAARELGAPVALIDRDIGVTL 126 (388)
T ss_pred cHHHHHHHhcCCcccCCHHHHHHcCchHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHcCCCEEEecccHHHHH
Confidence 45556544411122355555554333332 22456778889999999998644 45555554422111111111
Q ss_pred HHHHHHH-HHHhHHHHHHHHHHccCCC---CCcccHHhHHHHH-HHHHHhhcCCC
Q 012567 284 ILCKDKM-ITSNIRLVISIAKNYQGAG---MNLQDLVQEGCRG-LVRGAEKFDAS 333 (460)
Q Consensus 284 ~~A~e~L-I~~nlrLV~~IAkry~~~g---~d~eDLiQEG~IG-LirAiekFDp~ 333 (460)
+++..++ +-.-+++...++......| .+.++|.|+..+. +++-+.+|-|.
T Consensus 127 ~R~~~~~~~~EKlK~~~~L~~~~~~~g~~e~ei~~l~~~D~~~al~~efr~~~P~ 181 (388)
T COG1916 127 RRAWAKMPFWEKLKLISSLISGLLFPGQSEIEIDELKQEDVLSALMQEFRRFSPT 181 (388)
T ss_pred HHHHHhCCHHHHHHHHHHHHHhcccCCCchHHHHHHhhhhHHHHHHHHHHHhChh
Confidence 2222222 2234566777777543343 5788999988887 99999999885
No 331
>PF11176 DUF2962: Protein of unknown function (DUF2962); InterPro: IPR021346 This eukaryotic family of proteins has no known function. ; PDB: 2KKM_A.
Probab=20.03 E-value=6.2e+02 Score=23.41 Aligned_cols=87 Identities=20% Similarity=0.344 Sum_probs=42.3
Q ss_pred HHHHHHh-hc-CCCCCCHHHHHHHHHHHH--HHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHH
Q 012567 214 LRYLRAT-TS-SSRLLTANEEMQLSAGIQ--DLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDK 289 (460)
Q Consensus 214 l~YL~~~-~~-~~~lLT~EEE~eL~~~Iq--~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~ 289 (460)
+.|+.+. .. ....+|.++=.+|....= ..-.|++++.+ ..-||+|+-.| .
T Consensus 51 ~~wFq~~i~~~~~~~~t~~e~~~lI~~yl~R~DeEleql~~~--rR~gRp~s~re------------------------~ 104 (155)
T PF11176_consen 51 LKWFQEAIDEKDKKPFTLEEIHELIERYLHRFDEELEQLKKE--RRKGRPPSNRE------------------------D 104 (155)
T ss_dssp HHHHHHHHHSTT-----HHHHHHHHHHHHHHHHHHHHHHHHH--GGGT---TTHH------------------------H
T ss_pred HHHHHHHccccCCCCCCHHHHHHHHHHHHhcCHHHHHHHHHh--hcCCCCCchHH------------------------H
Confidence 3355554 22 467899998888776532 11234444433 34588877333 3
Q ss_pred HHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCC
Q 012567 290 MITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDAS 333 (460)
Q Consensus 290 LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~ 333 (460)
+++.- +-.-...|. .|+...||..+.++.+++. +|.+
T Consensus 105 ~L~~~---~~~E~~ey~-~G~~vPDLtd~~nv~~Lr~---W~G~ 141 (155)
T PF11176_consen 105 LLEQK---IEREEEEYK-TGFEVPDLTDEKNVKLLRE---WNGD 141 (155)
T ss_dssp HHHHH---HHHHHHHHH-TTEEEE-S--HHHHHHHHT----SS-
T ss_pred HHHHH---HHHHHHHHh-hCeeCCCCCCHHHHHHHHh---cCCC
Confidence 33321 233445676 8999999999999988876 5543
Done!