Query 011577
Match_columns 482
No_of_seqs 346 out of 2022
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 02:55:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011577.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011577hhsearch_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 1.4E-47 2.9E-52 401.0 28.7 228 253-480 58-327 (415)
2 TIGR02997 Sig70-cyanoRpoD RNA 100.0 6.4E-45 1.4E-49 366.6 27.8 226 255-480 1-226 (298)
3 PRK05949 RNA polymerase sigma 100.0 8E-45 1.7E-49 371.2 28.8 228 253-480 16-243 (327)
4 PRK07406 RNA polymerase sigma 100.0 1.4E-44 3E-49 375.0 28.2 227 254-480 62-288 (373)
5 PRK07405 RNA polymerase sigma 100.0 1.4E-43 3.1E-48 360.4 28.4 227 254-480 7-233 (317)
6 COG0568 RpoD DNA-directed RNA 100.0 9.5E-41 2.1E-45 340.6 21.9 228 254-481 8-255 (342)
7 PRK05901 RNA polymerase sigma 100.0 1E-40 2.2E-45 356.8 22.7 216 253-481 209-424 (509)
8 PRK07921 RNA polymerase sigma 100.0 1.3E-39 2.7E-44 332.7 24.1 214 254-480 25-238 (324)
9 PRK09210 RNA polymerase sigma 100.0 2.7E-36 5.8E-41 312.7 23.2 192 250-481 91-282 (367)
10 PRK05658 RNA polymerase sigma 100.0 4.7E-34 1E-38 313.5 21.2 154 328-481 380-533 (619)
11 PRK07500 rpoH2 RNA polymerase 100.0 2.3E-31 5E-36 267.7 21.2 188 254-480 5-200 (289)
12 PRK06596 RNA polymerase factor 100.0 1.9E-30 4.1E-35 260.4 21.6 186 253-480 12-203 (284)
13 PRK07122 RNA polymerase sigma 100.0 9.5E-31 2.1E-35 260.0 18.8 153 328-480 40-196 (264)
14 TIGR02393 RpoD_Cterm RNA polym 100.0 1.2E-30 2.7E-35 254.4 17.8 153 329-481 1-153 (238)
15 TIGR02392 rpoH_proteo alternat 100.0 3.6E-30 7.8E-35 256.0 20.8 184 256-480 2-191 (270)
16 PRK05657 RNA polymerase sigma 100.0 2.1E-29 4.6E-34 257.5 22.8 188 253-480 51-238 (325)
17 PRK07408 RNA polymerase sigma 100.0 1.4E-29 3E-34 250.2 20.2 157 325-481 21-183 (256)
18 TIGR02850 spore_sigG RNA polym 100.0 1.4E-28 3E-33 242.3 22.0 176 264-480 10-187 (254)
19 PRK08215 sporulation sigma fac 100.0 1.7E-27 3.8E-32 234.9 21.8 176 264-480 13-190 (258)
20 TIGR02394 rpoS_proteo RNA poly 99.9 2.8E-26 6E-31 229.7 22.9 191 250-480 8-198 (285)
21 PRK05911 RNA polymerase sigma 99.9 2.4E-26 5.1E-31 227.5 19.5 153 325-480 19-181 (257)
22 TIGR02885 spore_sigF RNA polym 99.9 4.9E-26 1.1E-30 220.3 18.5 158 322-480 4-164 (231)
23 COG1191 FliA DNA-directed RNA 99.9 8.2E-26 1.8E-30 223.0 18.2 160 318-479 13-176 (247)
24 PRK06288 RNA polymerase sigma 99.9 8.9E-25 1.9E-29 216.9 20.3 175 264-480 6-188 (268)
25 TIGR02980 SigBFG RNA polymeras 99.9 9.6E-25 2.1E-29 210.5 18.9 154 327-480 2-159 (227)
26 TIGR02941 Sigma_B RNA polymera 99.9 3.1E-24 6.7E-29 211.1 21.4 144 327-470 28-173 (255)
27 PRK05572 sporulation sigma fac 99.9 2E-23 4.3E-28 205.4 22.3 177 263-480 7-185 (252)
28 PRK07670 RNA polymerase sigma 99.9 1.8E-23 4E-28 205.5 19.1 152 316-470 8-166 (251)
29 PRK08583 RNA polymerase sigma 99.9 6E-23 1.3E-27 202.1 21.0 143 327-469 28-172 (257)
30 PRK12427 flagellar biosynthesi 99.9 1.5E-22 3.3E-27 197.6 18.1 138 329-470 16-158 (231)
31 TIGR02479 FliA_WhiG RNA polyme 99.9 2.7E-22 5.9E-27 193.5 16.9 143 333-478 1-149 (224)
32 PRK06986 fliA flagellar biosyn 99.9 1E-20 2.2E-25 184.1 18.3 143 325-470 5-152 (236)
33 PRK05803 sporulation sigma fac 99.9 1.7E-20 3.7E-25 182.4 17.2 162 256-457 17-221 (233)
34 PRK08301 sporulation sigma fac 99.8 4.3E-18 9.3E-23 165.2 17.0 141 318-458 41-225 (234)
35 TIGR02846 spore_sigmaK RNA pol 99.8 5.2E-18 1.1E-22 164.6 16.7 134 324-457 43-220 (227)
36 PRK08295 RNA polymerase factor 99.8 1.1E-17 2.3E-22 158.3 14.7 146 313-458 8-197 (208)
37 TIGR02859 spore_sigH RNA polym 99.8 1.1E-17 2.4E-22 156.7 14.7 145 314-458 4-192 (198)
38 TIGR02895 spore_sigI RNA polym 99.7 1.5E-17 3.3E-22 161.9 14.5 128 322-449 3-141 (218)
39 TIGR02835 spore_sigmaE RNA pol 99.7 2.1E-17 4.6E-22 161.0 15.1 143 315-457 38-224 (234)
40 PRK05602 RNA polymerase sigma 99.7 3.4E-17 7.4E-22 152.9 13.6 145 313-458 4-171 (186)
41 PRK12513 RNA polymerase sigma 99.7 9.3E-17 2E-21 150.9 14.2 143 314-458 11-182 (194)
42 PRK09646 RNA polymerase sigma 99.7 9.3E-17 2E-21 151.5 13.4 143 315-458 16-185 (194)
43 PRK06811 RNA polymerase factor 99.7 1.2E-16 2.5E-21 150.3 13.9 143 314-457 3-173 (189)
44 TIGR02954 Sig70_famx3 RNA poly 99.7 1.8E-16 4E-21 145.6 13.4 143 314-458 1-162 (169)
45 PRK13919 putative RNA polymera 99.7 2E-16 4.3E-21 147.4 13.4 144 314-458 8-178 (186)
46 TIGR02948 SigW_bacill RNA poly 99.7 1.7E-16 3.8E-21 147.1 12.7 141 316-458 5-179 (187)
47 PRK09640 RNA polymerase sigma 99.7 3E-16 6.4E-21 147.2 14.1 145 312-458 6-177 (188)
48 PRK09648 RNA polymerase sigma 99.7 3.5E-16 7.5E-21 146.5 14.4 141 317-458 12-182 (189)
49 PRK12537 RNA polymerase sigma 99.7 2.2E-16 4.7E-21 147.4 12.9 144 314-458 8-176 (182)
50 PRK12524 RNA polymerase sigma 99.7 3.4E-16 7.4E-21 147.9 13.4 146 313-459 10-180 (196)
51 PRK12514 RNA polymerase sigma 99.7 3.3E-16 7.2E-21 145.2 13.0 144 314-458 4-172 (179)
52 TIGR02952 Sig70_famx2 RNA poly 99.7 4.1E-16 9E-21 142.3 13.4 138 320-458 2-165 (170)
53 PRK06759 RNA polymerase factor 99.7 5.7E-16 1.2E-20 139.6 13.2 129 328-458 4-149 (154)
54 PRK09643 RNA polymerase sigma 99.7 9.7E-16 2.1E-20 144.7 14.2 144 314-459 12-178 (192)
55 PRK09641 RNA polymerase sigma 99.7 7.5E-16 1.6E-20 142.9 13.1 142 315-458 4-179 (187)
56 PRK09638 RNA polymerase sigma 99.7 9.6E-16 2.1E-20 141.3 13.5 143 314-458 3-169 (176)
57 PRK12538 RNA polymerase sigma 99.7 8E-16 1.7E-20 150.6 13.3 144 314-458 48-214 (233)
58 TIGR02939 RpoE_Sigma70 RNA pol 99.7 1.1E-15 2.4E-20 142.1 13.5 143 314-458 5-181 (190)
59 PRK12534 RNA polymerase sigma 99.7 6.8E-16 1.5E-20 144.0 12.0 142 316-458 12-180 (187)
60 PRK12526 RNA polymerase sigma 99.7 1.3E-15 2.8E-20 145.5 13.7 140 319-459 28-197 (206)
61 PRK12531 RNA polymerase sigma 99.7 9.2E-16 2E-20 144.7 12.6 141 317-458 15-184 (194)
62 PRK09652 RNA polymerase sigma 99.7 8.8E-16 1.9E-20 140.6 11.9 134 323-458 4-171 (182)
63 PRK12519 RNA polymerase sigma 99.7 1.2E-15 2.6E-20 143.2 13.1 143 314-458 14-184 (194)
64 PRK11923 algU RNA polymerase s 99.6 2E-15 4.2E-20 141.6 13.7 142 315-458 6-181 (193)
65 PRK11922 RNA polymerase sigma 99.6 1.9E-15 4.1E-20 147.0 13.5 143 314-458 15-192 (231)
66 PRK12539 RNA polymerase sigma 99.6 3.7E-15 7.9E-20 139.4 13.9 141 316-458 8-174 (184)
67 PRK12536 RNA polymerase sigma 99.6 3.8E-15 8.1E-20 139.0 13.7 141 316-458 8-172 (181)
68 PRK12515 RNA polymerase sigma 99.6 3.6E-15 7.8E-20 139.8 13.4 144 313-458 6-174 (189)
69 PRK12542 RNA polymerase sigma 99.6 1.6E-15 3.5E-20 141.7 9.9 135 325-459 5-166 (185)
70 TIGR03001 Sig-70_gmx1 RNA poly 99.6 6.6E-15 1.4E-19 145.3 13.6 144 312-457 22-203 (244)
71 TIGR02999 Sig-70_X6 RNA polyme 99.6 5.3E-15 1.2E-19 137.2 11.8 141 316-458 4-177 (183)
72 PRK09649 RNA polymerase sigma 99.6 8.2E-15 1.8E-19 137.6 12.1 141 317-460 12-175 (185)
73 TIGR02989 Sig-70_gvs1 RNA poly 99.6 1.1E-14 2.4E-19 131.7 12.5 130 328-459 1-155 (159)
74 PRK11924 RNA polymerase sigma 99.6 1.5E-14 3.3E-19 132.1 13.0 138 319-458 3-168 (179)
75 PRK12512 RNA polymerase sigma 99.6 2.2E-14 4.9E-19 133.5 14.1 139 318-458 11-174 (184)
76 COG1595 RpoE DNA-directed RNA 99.6 2.5E-14 5.3E-19 133.8 14.0 132 325-458 12-170 (182)
77 PRK12522 RNA polymerase sigma 99.6 2.1E-14 4.6E-19 132.6 12.4 129 328-458 3-162 (173)
78 PRK12543 RNA polymerase sigma 99.6 2E-14 4.4E-19 133.8 12.3 132 325-458 3-160 (179)
79 PRK12520 RNA polymerase sigma 99.6 1.8E-14 4E-19 135.2 11.7 129 329-459 3-175 (191)
80 TIGR02937 sigma70-ECF RNA poly 99.6 3E-14 6.4E-19 124.6 11.8 126 329-457 2-152 (158)
81 TIGR02947 SigH_actino RNA poly 99.6 1.8E-14 3.9E-19 135.5 10.6 129 328-458 11-174 (193)
82 PRK09645 RNA polymerase sigma 99.6 3.9E-14 8.4E-19 130.5 12.5 132 326-458 7-161 (173)
83 PRK09415 RNA polymerase factor 99.5 4.1E-14 8.8E-19 132.0 12.3 129 328-458 16-170 (179)
84 PRK12518 RNA polymerase sigma 99.5 5E-14 1.1E-18 129.8 12.6 135 321-458 3-163 (175)
85 PRK12516 RNA polymerase sigma 99.5 5.6E-14 1.2E-18 132.6 12.8 130 327-458 9-159 (187)
86 TIGR02985 Sig70_bacteroi1 RNA 99.5 4.2E-14 9.1E-19 126.8 10.7 129 328-458 1-156 (161)
87 PRK08241 RNA polymerase factor 99.5 1.2E-13 2.6E-18 141.0 15.4 141 317-459 7-197 (339)
88 TIGR02984 Sig-70_plancto1 RNA 99.5 5.8E-14 1.3E-18 130.3 12.0 134 325-458 3-183 (189)
89 TIGR02983 SigE-fam_strep RNA p 99.5 1.1E-13 2.4E-18 126.0 12.3 131 326-458 4-153 (162)
90 PRK12529 RNA polymerase sigma 99.5 8.9E-14 1.9E-18 129.7 11.8 134 324-457 8-169 (178)
91 PRK12547 RNA polymerase sigma 99.5 1.5E-13 3.2E-18 126.3 12.8 130 327-458 5-155 (164)
92 PRK12541 RNA polymerase sigma 99.5 1.4E-13 3E-18 125.6 12.3 128 328-458 5-155 (161)
93 PRK12535 RNA polymerase sigma 99.5 1.5E-13 3.2E-18 130.8 12.8 138 317-457 13-175 (196)
94 TIGR02960 SigX5 RNA polymerase 99.5 1.1E-13 2.3E-18 140.0 11.8 129 328-458 5-185 (324)
95 PRK12533 RNA polymerase sigma 99.5 2E-13 4.4E-18 132.4 13.0 132 324-458 14-177 (216)
96 PRK09644 RNA polymerase sigma 99.5 1.8E-13 3.9E-18 125.5 11.5 126 330-458 3-151 (165)
97 PRK12523 RNA polymerase sigma 99.5 1.3E-13 2.7E-18 127.5 10.5 132 324-458 5-162 (172)
98 PRK08311 putative RNA polymera 99.5 4.9E-13 1.1E-17 131.9 15.0 91 315-405 4-97 (237)
99 PRK09642 RNA polymerase sigma 99.5 2E-13 4.3E-18 124.2 9.5 122 334-458 1-149 (160)
100 PRK12545 RNA polymerase sigma 99.5 3.9E-13 8.4E-18 128.0 11.8 124 333-458 13-182 (201)
101 PRK09639 RNA polymerase sigma 99.5 5.1E-13 1.1E-17 121.9 11.6 126 328-458 3-154 (166)
102 PRK12540 RNA polymerase sigma 99.5 6.1E-13 1.3E-17 125.1 12.5 129 328-458 5-154 (182)
103 PRK09647 RNA polymerase sigma 99.5 5.6E-13 1.2E-17 127.8 12.3 131 325-458 24-181 (203)
104 PRK12528 RNA polymerase sigma 99.4 9.4E-13 2E-17 120.1 12.9 127 328-457 4-155 (161)
105 PRK12532 RNA polymerase sigma 99.4 5.8E-13 1.2E-17 125.5 11.2 125 331-457 8-178 (195)
106 PRK09637 RNA polymerase sigma 99.4 1.4E-12 2.9E-17 122.5 13.0 126 330-457 3-148 (181)
107 TIGR02943 Sig70_famx1 RNA poly 99.4 8.5E-13 1.8E-17 124.4 11.5 127 331-459 5-175 (188)
108 PRK12544 RNA polymerase sigma 99.4 9.4E-13 2E-17 126.5 12.0 128 329-458 19-191 (206)
109 PRK12517 RNA polymerase sigma 99.4 1.3E-12 2.9E-17 123.3 12.7 132 325-458 20-171 (188)
110 PRK12530 RNA polymerase sigma 99.4 8.4E-13 1.8E-17 124.4 11.3 126 331-458 10-177 (189)
111 TIGR02950 SigM_subfam RNA poly 99.4 8.3E-13 1.8E-17 118.8 10.3 122 334-458 1-148 (154)
112 PF04542 Sigma70_r2: Sigma-70 99.4 7.7E-13 1.7E-17 104.0 8.2 70 333-402 1-70 (71)
113 PRK12546 RNA polymerase sigma 99.4 2.1E-12 4.6E-17 122.2 12.6 128 328-458 8-156 (188)
114 TIGR02959 SigZ RNA polymerase 99.4 1.9E-12 4E-17 120.0 11.2 122 335-458 2-143 (170)
115 PRK09651 RNA polymerase sigma 99.4 7.9E-12 1.7E-16 115.9 12.8 128 327-457 9-161 (172)
116 PRK12511 RNA polymerase sigma 99.4 5E-12 1.1E-16 119.0 11.5 127 330-458 6-154 (182)
117 PRK06704 RNA polymerase factor 99.3 1.1E-11 2.4E-16 121.7 11.2 132 322-459 11-160 (228)
118 PRK07037 extracytoplasmic-func 99.3 1.4E-11 3E-16 112.3 11.0 123 332-457 2-151 (163)
119 PRK12527 RNA polymerase sigma 99.3 1.3E-11 2.8E-16 112.4 10.3 122 334-458 1-148 (159)
120 PRK12525 RNA polymerase sigma 99.3 4E-11 8.6E-16 110.6 13.5 127 328-457 9-160 (168)
121 PRK09636 RNA polymerase sigma 99.3 4.6E-11 1E-15 120.2 12.6 127 328-458 4-158 (293)
122 PRK09635 sigI RNA polymerase s 99.2 9.2E-11 2E-15 118.7 10.7 128 328-459 5-162 (290)
123 TIGR02957 SigX4 RNA polymerase 99.2 1.9E-10 4.1E-15 115.4 12.2 124 332-459 1-152 (281)
124 PRK09191 two-component respons 99.2 1.4E-10 3E-15 112.1 10.6 127 329-458 2-131 (261)
125 TIGR03209 P21_Cbot clostridium 99.1 4.1E-10 8.8E-15 100.9 9.9 113 330-449 1-141 (142)
126 PRK09047 RNA polymerase factor 99.1 4.8E-10 1E-14 101.6 8.9 106 350-458 2-149 (161)
127 PF04539 Sigma70_r3: Sigma-70 99.0 5.8E-10 1.3E-14 90.9 7.4 71 412-482 1-71 (78)
128 PF07638 Sigma70_ECF: ECF sigm 98.8 6.4E-08 1.4E-12 91.5 12.0 141 317-457 5-177 (185)
129 PF00140 Sigma70_r1_2: Sigma-7 97.9 2.5E-06 5.5E-11 61.2 0.6 34 254-287 1-34 (37)
130 PRK05658 RNA polymerase sigma 97.3 0.0073 1.6E-07 67.6 16.2 35 253-287 102-136 (619)
131 PF12645 HTH_16: Helix-turn-he 96.2 0.015 3.2E-07 46.9 6.4 56 319-374 3-65 (65)
132 PRK07670 RNA polymerase sigma 96.1 0.049 1.1E-06 53.9 11.0 30 429-458 215-244 (251)
133 PRK07408 RNA polymerase sigma 96.1 0.015 3.2E-07 58.0 7.1 34 287-320 114-147 (256)
134 TIGR02393 RpoD_Cterm RNA polym 96.1 0.053 1.1E-06 53.2 10.8 34 287-320 88-121 (238)
135 COG1191 FliA DNA-directed RNA 96.0 0.21 4.5E-06 50.3 14.8 149 256-455 88-236 (247)
136 PRK05911 RNA polymerase sigma 96.0 0.046 9.9E-07 54.6 10.0 29 429-457 219-247 (257)
137 PRK06288 RNA polymerase sigma 95.9 0.097 2.1E-06 52.3 11.7 34 287-320 119-152 (268)
138 PRK07122 RNA polymerase sigma 95.7 0.068 1.5E-06 53.7 10.0 35 287-321 128-162 (264)
139 PRK07500 rpoH2 RNA polymerase 95.6 0.15 3.3E-06 51.8 12.3 29 430-458 244-272 (289)
140 PRK05949 RNA polymerase sigma 95.6 0.071 1.5E-06 55.4 9.8 35 287-321 179-213 (327)
141 PRK09210 RNA polymerase sigma 95.6 0.19 4.2E-06 52.9 13.2 133 287-456 217-350 (367)
142 PRK05901 RNA polymerase sigma 95.3 0.33 7E-06 53.6 14.0 35 287-321 359-393 (509)
143 PRK07598 RNA polymerase sigma 95.2 0.2 4.2E-06 54.0 11.7 36 287-322 263-298 (415)
144 TIGR02885 spore_sigF RNA polym 95.0 0.11 2.3E-06 50.5 8.4 32 289-320 100-131 (231)
145 TIGR02479 FliA_WhiG RNA polyme 94.8 0.28 6E-06 47.5 10.8 34 287-320 84-117 (224)
146 TIGR02997 Sig70-cyanoRpoD RNA 94.7 0.42 9.1E-06 48.7 12.3 34 287-320 162-195 (298)
147 PRK07921 RNA polymerase sigma 94.6 0.64 1.4E-05 48.4 13.5 34 287-320 174-207 (324)
148 TIGR02941 Sigma_B RNA polymera 94.4 0.095 2.1E-06 51.8 6.7 29 429-457 219-247 (255)
149 PRK07405 RNA polymerase sigma 94.4 0.21 4.5E-06 51.7 9.3 34 287-320 169-202 (317)
150 PF04539 Sigma70_r3: Sigma-70 94.3 0.096 2.1E-06 42.4 5.4 38 286-323 4-41 (78)
151 PRK06986 fliA flagellar biosyn 94.1 0.46 1E-05 46.4 10.6 30 429-458 198-227 (236)
152 TIGR02850 spore_sigG RNA polym 94.0 0.34 7.5E-06 48.0 9.6 35 288-322 122-156 (254)
153 COG0568 RpoD DNA-directed RNA 93.8 1.3 2.7E-05 46.7 13.5 33 253-285 65-97 (342)
154 PRK07406 RNA polymerase sigma 93.7 0.71 1.5E-05 49.1 11.8 34 287-320 224-257 (373)
155 PF08281 Sigma70_r4_2: Sigma-7 92.9 0.15 3.2E-06 38.5 3.8 30 428-457 23-52 (54)
156 TIGR02980 SigBFG RNA polymeras 92.8 0.17 3.7E-06 48.9 5.2 28 430-457 193-220 (227)
157 TIGR02394 rpoS_proteo RNA poly 92.6 0.25 5.4E-06 49.9 6.2 31 429-459 240-270 (285)
158 PF04545 Sigma70_r4: Sigma-70, 92.2 0.36 7.9E-06 36.0 5.2 30 427-456 16-45 (50)
159 PRK08215 sporulation sigma fac 92.1 2.2 4.7E-05 42.4 12.1 33 289-321 126-158 (258)
160 PRK08583 RNA polymerase sigma 91.9 0.41 8.8E-06 47.4 6.6 29 429-457 219-247 (257)
161 PRK12427 flagellar biosynthesi 91.6 1.5 3.2E-05 43.2 10.2 34 288-321 103-136 (231)
162 PRK05572 sporulation sigma fac 91.6 1.6 3.4E-05 43.2 10.5 28 430-457 217-244 (252)
163 PHA02547 55 RNA polymerase sig 91.3 0.57 1.2E-05 44.7 6.5 67 335-401 44-113 (179)
164 PF01726 LexA_DNA_bind: LexA D 90.3 0.92 2E-05 36.5 6.0 42 413-454 7-49 (65)
165 PF13404 HTH_AsnC-type: AsnC-t 89.0 1.4 3E-05 32.4 5.6 35 419-454 6-40 (42)
166 PRK06596 RNA polymerase factor 86.8 14 0.00031 37.4 13.5 27 430-456 247-273 (284)
167 TIGR03879 near_KaiC_dom probab 86.0 1.4 2.9E-05 36.6 4.5 25 430-454 31-55 (73)
168 cd06171 Sigma70_r4 Sigma70, re 85.8 1.5 3.3E-05 31.3 4.3 28 430-457 25-52 (55)
169 PF10668 Phage_terminase: Phag 84.4 2 4.3E-05 34.4 4.6 31 424-454 15-45 (60)
170 PF06971 Put_DNA-bind_N: Putat 84.0 3 6.6E-05 32.1 5.3 47 405-451 2-48 (50)
171 PRK06930 positive control sigm 84.0 1 2.2E-05 42.7 3.3 30 429-458 128-157 (170)
172 COG4941 Predicted RNA polymera 83.4 4.2 9.2E-05 43.0 7.8 125 331-457 8-162 (415)
173 PF13412 HTH_24: Winged helix- 82.1 4.8 0.0001 29.5 5.7 29 425-454 12-40 (48)
174 PF04967 HTH_10: HTH DNA bindi 81.5 1.2 2.7E-05 34.6 2.4 28 430-457 22-49 (53)
175 PRK05657 RNA polymerase sigma 81.1 1.5 3.2E-05 45.6 3.6 30 429-458 280-309 (325)
176 PRK00118 putative DNA-binding 80.6 2.6 5.6E-05 37.2 4.3 28 430-457 32-59 (104)
177 smart00421 HTH_LUXR helix_turn 80.5 2.3 4.9E-05 31.1 3.5 29 431-459 18-46 (58)
178 PRK04217 hypothetical protein; 80.0 1.8 4E-05 38.5 3.3 28 431-458 58-85 (110)
179 cd06170 LuxR_C_like C-terminal 77.5 2.8 6E-05 30.8 3.2 27 431-457 15-41 (57)
180 PF13936 HTH_38: Helix-turn-he 76.5 4.4 9.5E-05 29.9 3.9 26 429-454 18-43 (44)
181 PF08279 HTH_11: HTH domain; 76.0 6.8 0.00015 29.4 5.0 33 422-455 7-39 (55)
182 PF06056 Terminase_5: Putative 75.6 7.1 0.00015 30.8 5.1 26 431-456 13-38 (58)
183 PHA02591 hypothetical protein; 74.4 6.6 0.00014 33.1 4.8 23 431-453 59-81 (83)
184 PF00196 GerE: Bacterial regul 73.9 4.7 0.0001 30.9 3.7 29 430-458 17-45 (58)
185 PF00325 Crp: Bacterial regula 73.1 5 0.00011 28.2 3.2 24 432-455 3-26 (32)
186 PF13542 HTH_Tnp_ISL3: Helix-t 73.0 8.7 0.00019 28.5 4.8 24 431-454 27-50 (52)
187 TIGR00721 tfx DNA-binding prot 72.9 2.6 5.6E-05 38.9 2.3 29 430-458 20-48 (137)
188 PF02796 HTH_7: Helix-turn-hel 71.2 5.8 0.00013 29.2 3.5 23 431-453 21-43 (45)
189 PRK03975 tfx putative transcri 70.1 3.3 7.1E-05 38.4 2.3 28 430-457 20-47 (141)
190 cd00092 HTH_CRP helix_turn_hel 68.5 17 0.00038 27.7 5.8 25 431-455 25-49 (67)
191 PF01325 Fe_dep_repress: Iron 68.3 18 0.00038 28.5 5.8 37 418-455 10-46 (60)
192 TIGR02392 rpoH_proteo alternat 67.9 9.3 0.0002 38.3 5.3 27 430-456 235-261 (270)
193 PRK11179 DNA-binding transcrip 67.7 10 0.00022 34.9 5.1 39 417-456 10-48 (153)
194 PF13384 HTH_23: Homeodomain-l 67.4 5.5 0.00012 29.3 2.7 25 431-455 17-41 (50)
195 PF04297 UPF0122: Putative hel 66.8 11 0.00025 33.0 4.9 34 424-457 26-59 (101)
196 PF13744 HTH_37: Helix-turn-he 66.7 10 0.00022 31.2 4.4 34 430-463 30-63 (80)
197 COG2197 CitB Response regulato 65.4 7.4 0.00016 37.7 3.9 35 427-461 159-193 (211)
198 PF12728 HTH_17: Helix-turn-he 65.1 8.1 0.00018 28.6 3.2 24 432-455 2-25 (51)
199 PF09012 FeoC: FeoC like trans 65.0 12 0.00026 29.8 4.4 33 422-455 6-38 (69)
200 COG4367 Uncharacterized protei 65.0 18 0.00038 31.3 5.5 27 431-457 23-49 (97)
201 PF00356 LacI: Bacterial regul 64.8 6.9 0.00015 29.4 2.7 23 433-455 1-23 (46)
202 PRK11169 leucine-responsive tr 64.6 14 0.0003 34.4 5.4 41 414-455 12-52 (164)
203 PRK10840 transcriptional regul 64.1 8.7 0.00019 36.2 4.0 34 428-461 162-195 (216)
204 PRK15411 rcsA colanic acid cap 63.8 10 0.00023 36.5 4.5 38 423-460 144-181 (207)
205 smart00550 Zalpha Z-DNA-bindin 63.5 23 0.00049 28.4 5.7 34 422-455 12-46 (68)
206 PRK14082 hypothetical protein; 62.9 27 0.00058 28.5 5.8 55 328-384 9-63 (65)
207 TIGR03020 EpsA transcriptional 62.4 8.7 0.00019 38.7 3.8 30 430-459 204-233 (247)
208 PF13730 HTH_36: Helix-turn-he 62.3 10 0.00022 28.4 3.3 26 429-454 23-48 (55)
209 PF08220 HTH_DeoR: DeoR-like h 62.0 18 0.00039 28.0 4.7 28 426-454 10-37 (57)
210 COG1522 Lrp Transcriptional re 61.6 17 0.00036 32.7 5.2 39 416-455 8-46 (154)
211 TIGR01764 excise DNA binding d 61.4 12 0.00027 26.5 3.6 25 432-456 2-26 (49)
212 PF01710 HTH_Tnp_IS630: Transp 61.2 32 0.0007 30.4 6.9 34 422-456 63-96 (119)
213 PRK13719 conjugal transfer tra 61.1 9.8 0.00021 37.8 3.8 39 423-461 150-188 (217)
214 PRK11475 DNA-binding transcrip 60.6 10 0.00022 36.8 3.8 35 427-461 145-179 (207)
215 PRK13870 transcriptional regul 60.2 9.3 0.0002 37.8 3.6 30 430-459 187-216 (234)
216 PF01978 TrmB: Sugar-specific 59.3 20 0.00044 28.1 4.7 24 431-454 22-45 (68)
217 PF09339 HTH_IclR: IclR helix- 58.7 15 0.00033 27.5 3.8 28 427-454 14-41 (52)
218 TIGR02844 spore_III_D sporulat 57.7 25 0.00054 29.6 5.2 30 423-454 13-42 (80)
219 PF14502 HTH_41: Helix-turn-he 57.5 15 0.00032 28.2 3.4 36 428-463 3-40 (48)
220 PRK10188 DNA-binding transcrip 57.3 10 0.00023 37.5 3.4 30 430-459 193-222 (240)
221 PF03444 HrcA_DNA-bdg: Winged 57.1 38 0.00083 28.5 6.1 41 415-455 7-47 (78)
222 smart00345 HTH_GNTR helix_turn 56.8 15 0.00032 27.2 3.4 25 431-455 20-44 (60)
223 PRK15201 fimbriae regulatory p 56.8 13 0.00028 36.2 3.8 32 428-459 145-176 (198)
224 TIGR03541 reg_near_HchA LuxR f 56.8 11 0.00023 37.1 3.3 30 430-459 185-214 (232)
225 COG2771 CsgD DNA-binding HTH d 56.4 24 0.00053 26.6 4.6 27 431-457 19-45 (65)
226 cd04762 HTH_MerR-trunc Helix-T 55.8 18 0.00039 25.5 3.6 24 433-456 2-25 (49)
227 PRK10430 DNA-binding transcrip 55.4 22 0.00048 34.2 5.2 33 427-459 174-206 (239)
228 PRK10046 dpiA two-component re 55.1 21 0.00046 34.1 5.0 41 424-464 170-212 (225)
229 PRK09483 response regulator; P 55.0 16 0.00035 33.6 4.0 32 430-461 162-193 (217)
230 PRK15369 two component system 54.3 15 0.00033 32.7 3.7 32 430-461 163-194 (211)
231 PF04703 FaeA: FaeA-like prote 53.6 21 0.00044 28.7 3.8 27 429-455 13-39 (62)
232 TIGR03826 YvyF flagellar opero 53.0 50 0.0011 30.6 6.8 35 428-462 43-77 (137)
233 COG3413 Predicted DNA binding 52.9 11 0.00024 36.6 2.7 30 429-458 176-205 (215)
234 PRK11511 DNA-binding transcrip 52.6 41 0.00089 29.9 6.1 40 416-455 10-49 (127)
235 PF01381 HTH_3: Helix-turn-hel 52.3 25 0.00055 26.0 4.1 24 431-454 9-32 (55)
236 COG1318 Predicted transcriptio 52.2 25 0.00055 33.9 4.8 24 431-454 61-84 (182)
237 PRK00423 tfb transcription ini 52.1 1.2E+02 0.0027 31.3 10.3 28 428-455 273-300 (310)
238 PRK10100 DNA-binding transcrip 52.0 22 0.00048 34.7 4.6 29 431-459 170-198 (216)
239 PRK10403 transcriptional regul 51.9 19 0.00041 32.5 3.9 34 430-463 167-200 (215)
240 PF00440 TetR_N: Bacterial reg 51.4 35 0.00076 24.9 4.6 33 419-451 4-36 (47)
241 TIGR02337 HpaR homoprotocatech 51.0 74 0.0016 27.5 7.4 65 382-455 2-66 (118)
242 PF08784 RPA_C: Replication pr 50.9 17 0.00036 31.1 3.2 27 429-455 63-89 (102)
243 PRK12423 LexA repressor; Provi 50.7 44 0.00095 32.2 6.4 39 416-454 10-49 (202)
244 smart00420 HTH_DEOR helix_turn 50.2 50 0.0011 23.6 5.3 25 431-455 14-38 (53)
245 TIGR03070 couple_hipB transcri 50.2 40 0.00086 24.7 4.8 23 431-453 15-37 (58)
246 TIGR02531 yecD_yerC TrpR-relat 50.0 36 0.00078 29.1 5.0 23 431-453 50-72 (88)
247 PRK09935 transcriptional regul 50.0 21 0.00046 32.3 4.0 32 430-461 163-194 (210)
248 COG0856 Orotate phosphoribosyl 48.7 22 0.00047 34.6 3.8 35 430-464 17-51 (203)
249 PHA02943 hypothetical protein; 48.5 57 0.0012 31.0 6.4 27 427-454 21-47 (165)
250 cd00569 HTH_Hin_like Helix-tur 48.4 33 0.00071 21.5 3.7 21 431-451 21-41 (42)
251 PRK10651 transcriptional regul 48.3 23 0.00049 32.1 3.9 33 430-462 169-201 (216)
252 PRK10219 DNA-binding transcrip 47.4 57 0.0012 27.6 6.0 37 418-454 8-44 (107)
253 smart00419 HTH_CRP helix_turn_ 47.2 28 0.0006 24.7 3.5 25 431-455 8-32 (48)
254 PF13518 HTH_28: Helix-turn-he 47.1 36 0.00077 24.8 4.1 25 432-456 13-37 (52)
255 smart00344 HTH_ASNC helix_turn 47.1 37 0.0008 28.8 4.7 25 431-455 17-41 (108)
256 PF04218 CENP-B_N: CENP-B N-te 46.7 19 0.00041 27.6 2.6 24 430-453 21-44 (53)
257 smart00346 HTH_ICLR helix_turn 46.5 58 0.0013 26.4 5.7 25 431-455 20-44 (91)
258 TIGR00498 lexA SOS regulatory 46.4 45 0.00099 31.6 5.7 37 419-455 13-50 (199)
259 PRK09390 fixJ response regulat 46.3 68 0.0015 28.3 6.6 30 431-460 156-185 (202)
260 PRK15320 transcriptional activ 46.2 18 0.00039 35.9 2.9 34 424-457 172-205 (251)
261 PF08280 HTH_Mga: M protein tr 45.4 68 0.0015 24.8 5.6 27 430-456 18-44 (59)
262 PRK10572 DNA-binding transcrip 44.8 2.6E+02 0.0056 27.7 11.1 39 417-455 185-223 (290)
263 PRK09685 DNA-binding transcrip 44.5 2.4E+02 0.0052 28.0 10.9 49 339-388 201-249 (302)
264 PF04760 IF2_N: Translation in 44.0 21 0.00046 27.1 2.5 37 432-468 4-42 (54)
265 cd04761 HTH_MerR-SF Helix-Turn 43.7 31 0.00066 24.8 3.2 24 433-456 2-25 (49)
266 PRK06424 transcription factor; 43.5 81 0.0018 29.3 6.7 43 409-453 77-119 (144)
267 COG2390 DeoR Transcriptional r 43.3 39 0.00084 35.5 5.1 37 430-466 25-65 (321)
268 PHA01976 helix-turn-helix prot 43.0 62 0.0013 25.0 5.1 23 431-453 15-37 (67)
269 PF00392 GntR: Bacterial regul 42.7 30 0.00064 26.9 3.2 26 430-455 23-48 (64)
270 PF13443 HTH_26: Cro/C1-type H 42.6 29 0.00063 26.5 3.1 32 431-462 10-41 (63)
271 PF00376 MerR: MerR family reg 42.0 24 0.00052 25.4 2.3 23 433-455 1-23 (38)
272 PF02001 DUF134: Protein of un 41.6 32 0.0007 30.5 3.5 29 431-459 57-85 (106)
273 PRK09726 antitoxin HipB; Provi 41.3 62 0.0013 26.9 5.1 23 431-453 25-47 (88)
274 cd07377 WHTH_GntR Winged helix 41.1 1.1E+02 0.0024 22.8 6.1 24 432-455 26-49 (66)
275 PF07374 DUF1492: Protein of u 41.0 1E+02 0.0022 26.5 6.5 30 427-456 67-96 (100)
276 PRK15418 transcriptional regul 40.9 35 0.00076 35.5 4.3 36 430-465 28-67 (318)
277 PF02082 Rrf2: Transcriptional 40.5 47 0.001 27.3 4.2 24 432-455 26-49 (83)
278 TIGR02147 Fsuc_second hypothet 40.4 2.1E+02 0.0046 29.3 9.7 25 431-455 137-163 (271)
279 PF12324 HTH_15: Helix-turn-he 40.1 63 0.0014 27.2 4.8 27 429-455 36-62 (77)
280 PRK13239 alkylmercury lyase; P 40.0 62 0.0014 32.0 5.6 29 428-456 33-61 (206)
281 smart00354 HTH_LACI helix_turn 39.7 29 0.00064 27.7 2.8 22 432-453 1-22 (70)
282 PF05225 HTH_psq: helix-turn-h 39.7 94 0.002 23.0 5.3 36 416-454 4-39 (45)
283 PF13545 HTH_Crp_2: Crp-like h 39.6 40 0.00086 26.6 3.6 24 432-455 29-52 (76)
284 PRK11161 fumarate/nitrate redu 39.2 1.1E+02 0.0024 29.2 7.3 26 431-456 184-209 (235)
285 PF12802 MarR_2: MarR family; 39.1 56 0.0012 24.6 4.2 24 432-455 22-45 (62)
286 PRK14101 bifunctional glucokin 39.0 1.6E+02 0.0035 33.3 9.6 23 431-453 374-396 (638)
287 PRK09958 DNA-binding transcrip 39.0 39 0.00084 30.7 3.9 32 430-461 157-188 (204)
288 PF13560 HTH_31: Helix-turn-he 38.5 59 0.0013 25.1 4.3 24 431-454 14-37 (64)
289 COG2344 AT-rich DNA-binding pr 38.2 77 0.0017 31.3 5.8 51 404-454 5-55 (211)
290 PF01371 Trp_repressor: Trp re 38.1 79 0.0017 27.1 5.3 23 430-452 48-70 (87)
291 PF05138 PaaA_PaaC: Phenylacet 37.9 1.8E+02 0.0039 29.6 8.7 115 264-398 4-119 (263)
292 PF13551 HTH_29: Winged helix- 37.7 86 0.0019 26.2 5.6 25 431-455 80-111 (112)
293 PRK00215 LexA repressor; Valid 37.6 90 0.002 29.7 6.3 34 422-455 14-48 (205)
294 PF01726 LexA_DNA_bind: LexA D 37.6 1.1E+02 0.0024 24.5 5.8 19 297-315 20-38 (65)
295 PF10078 DUF2316: Uncharacteri 36.0 36 0.00079 29.3 2.9 25 431-455 23-47 (89)
296 PF13309 HTH_22: HTH domain 35.7 64 0.0014 25.7 4.1 20 433-452 44-63 (64)
297 TIGR03697 NtcA_cyano global ni 35.5 2E+02 0.0044 26.2 8.1 26 431-456 143-168 (193)
298 PRK10072 putative transcriptio 35.4 67 0.0015 27.9 4.5 25 431-455 46-70 (96)
299 PF13411 MerR_1: MerR HTH fami 34.5 45 0.00098 25.8 3.1 24 433-456 2-25 (69)
300 PRK10219 DNA-binding transcrip 34.5 1.9E+02 0.0041 24.4 7.2 42 349-390 18-59 (107)
301 PRK15044 transcriptional regul 34.2 2.4E+02 0.0053 29.4 9.1 60 257-325 172-231 (295)
302 PF00165 HTH_AraC: Bacterial r 34.2 60 0.0013 23.1 3.4 28 428-455 5-32 (42)
303 PRK13918 CRP/FNR family transc 34.0 1.7E+02 0.0038 27.0 7.5 26 431-456 149-174 (202)
304 PRK15044 transcriptional regul 33.9 1.5E+02 0.0033 30.8 7.6 38 417-454 194-231 (295)
305 TIGR01321 TrpR trp operon repr 33.8 84 0.0018 27.4 4.8 24 430-453 54-77 (94)
306 COG4566 TtrR Response regulato 33.6 1.2E+02 0.0025 30.0 6.2 42 412-453 138-179 (202)
307 PF13022 HTH_Tnp_1_2: Helix-tu 33.2 50 0.0011 30.8 3.5 30 424-453 27-56 (142)
308 PRK03902 manganese transport t 33.2 1.1E+02 0.0024 27.5 5.8 36 419-455 11-46 (142)
309 PRK10360 DNA-binding transcrip 32.8 55 0.0012 29.5 3.8 30 431-460 152-181 (196)
310 COG3355 Predicted transcriptio 32.5 87 0.0019 28.7 4.9 24 431-454 42-65 (126)
311 TIGR00180 parB_part ParB-like 32.0 98 0.0021 29.4 5.5 33 431-463 120-152 (187)
312 TIGR00373 conserved hypothetic 31.8 54 0.0012 30.7 3.7 25 431-455 28-52 (158)
313 COG2524 Predicted transcriptio 31.6 82 0.0018 32.5 5.0 41 415-455 9-49 (294)
314 TIGR02944 suf_reg_Xantho FeS a 31.5 90 0.0019 27.6 4.9 28 428-455 22-49 (130)
315 PRK05472 redox-sensing transcr 31.3 1.4E+02 0.003 28.8 6.5 50 405-454 6-55 (213)
316 PF08765 Mor: Mor transcriptio 31.2 1.2E+02 0.0025 26.4 5.4 26 431-456 72-97 (108)
317 TIGR01610 phage_O_Nterm phage 31.2 1.3E+02 0.0027 25.6 5.5 26 429-454 45-70 (95)
318 PF09862 DUF2089: Protein of u 31.0 64 0.0014 29.0 3.7 38 421-461 42-79 (113)
319 PRK09464 pdhR transcriptional 31.0 81 0.0017 30.9 4.9 26 430-455 33-58 (254)
320 PRK09975 DNA-binding transcrip 30.9 1.1E+02 0.0024 28.6 5.6 41 410-450 9-50 (213)
321 cd01104 HTH_MlrA-CarA Helix-Tu 30.7 58 0.0012 25.2 3.1 23 433-455 2-24 (68)
322 TIGR02607 antidote_HigA addict 30.7 96 0.0021 24.5 4.5 31 431-462 18-48 (78)
323 smart00753 PAM PCI/PINT associ 30.4 93 0.002 25.3 4.5 44 421-465 15-58 (88)
324 smart00088 PINT motif in prote 30.4 93 0.002 25.3 4.5 44 421-465 15-58 (88)
325 PRK08359 transcription factor; 30.3 1.4E+02 0.0029 28.9 6.1 41 410-452 79-119 (176)
326 PRK11753 DNA-binding transcrip 29.8 2.8E+02 0.006 25.8 8.2 26 431-456 168-193 (211)
327 PRK04841 transcriptional regul 29.7 53 0.0012 37.9 3.9 32 429-460 851-882 (903)
328 smart00351 PAX Paired Box doma 29.6 85 0.0018 28.0 4.4 31 431-461 33-63 (125)
329 smart00342 HTH_ARAC helix_turn 29.5 1.6E+02 0.0034 22.6 5.5 61 302-364 1-62 (84)
330 PF13551 HTH_29: Winged helix- 29.4 61 0.0013 27.1 3.3 24 433-456 14-37 (112)
331 PF08535 KorB: KorB domain; I 29.4 54 0.0012 27.6 2.9 28 431-458 3-30 (93)
332 smart00418 HTH_ARSR helix_turn 29.1 81 0.0017 22.9 3.6 25 431-455 10-34 (66)
333 COG2207 AraC AraC-type DNA-bin 29.0 1.9E+02 0.0042 24.0 6.4 51 348-398 32-82 (127)
334 TIGR00270 conserved hypothetic 28.8 1.9E+02 0.0042 27.1 6.7 41 411-453 64-104 (154)
335 PRK11511 DNA-binding transcrip 28.8 2.3E+02 0.0049 25.1 7.0 49 350-398 23-71 (127)
336 PF12840 HTH_20: Helix-turn-he 28.8 1.6E+02 0.0035 22.5 5.3 26 429-454 22-47 (61)
337 PF02954 HTH_8: Bacterial regu 28.6 2.2E+02 0.0047 20.5 5.6 22 433-454 20-41 (42)
338 TIGR03830 CxxCG_CxxCG_HTH puta 28.3 1.8E+02 0.0039 25.2 6.2 24 431-454 78-101 (127)
339 PRK11512 DNA-binding transcrip 28.1 3E+02 0.0065 24.6 7.8 25 431-455 54-78 (144)
340 PRK06266 transcription initiat 28.0 1E+02 0.0022 29.6 4.8 25 431-455 36-60 (178)
341 TIGR02297 HpaA 4-hydroxyphenyl 27.6 5.9E+02 0.013 24.9 10.6 33 422-454 193-225 (287)
342 PRK03573 transcriptional regul 27.4 3.5E+02 0.0076 24.0 8.0 25 431-455 46-70 (144)
343 smart00422 HTH_MERR helix_turn 27.0 73 0.0016 24.6 3.1 22 433-454 2-23 (70)
344 TIGR03613 RutR pyrimidine util 26.8 94 0.002 28.8 4.4 32 417-448 14-45 (202)
345 TIGR02325 C_P_lyase_phnF phosp 26.7 1.6E+02 0.0034 28.4 6.0 27 428-454 29-55 (238)
346 PRK10411 DNA-binding transcrip 26.7 1.2E+02 0.0025 30.2 5.2 28 427-455 15-42 (240)
347 COG1476 Predicted transcriptio 26.4 1.2E+02 0.0027 24.9 4.3 23 431-453 14-36 (68)
348 cd00090 HTH_ARSR Arsenical Res 26.3 1.9E+02 0.0041 21.5 5.3 24 432-455 21-44 (78)
349 PRK10681 DNA-binding transcrip 25.9 1.2E+02 0.0026 30.2 5.1 31 423-454 14-44 (252)
350 cd04764 HTH_MlrA-like_sg1 Heli 25.7 71 0.0015 24.9 2.8 22 433-454 2-23 (67)
351 smart00530 HTH_XRE Helix-turn- 25.5 99 0.0021 21.0 3.3 23 431-453 10-32 (56)
352 smart00342 HTH_ARAC helix_turn 25.4 3.1E+02 0.0067 20.9 7.8 36 416-454 38-74 (84)
353 PRK09480 slmA division inhibit 25.2 1.6E+02 0.0034 26.9 5.5 38 413-450 11-49 (194)
354 PRK14999 histidine utilization 25.2 1.7E+02 0.0036 28.6 6.0 27 428-454 33-59 (241)
355 COG1321 TroR Mn-dependent tran 25.1 1.5E+02 0.0032 27.7 5.3 38 417-455 11-48 (154)
356 PF07022 Phage_CI_repr: Bacter 25.1 55 0.0012 25.9 2.1 30 424-454 6-36 (66)
357 TIGR00738 rrf2_super rrf2 fami 25.1 1.4E+02 0.0029 26.2 4.9 25 431-455 25-49 (132)
358 COG3415 Transposase and inacti 25.0 1.6E+02 0.0034 27.4 5.3 32 430-461 20-51 (138)
359 COG4977 Transcriptional regula 24.5 1.2E+02 0.0026 32.0 5.1 72 384-455 187-260 (328)
360 PRK10371 DNA-binding transcrip 24.5 4.6E+02 0.0099 26.6 9.2 60 339-399 195-254 (302)
361 PRK11050 manganese transport r 24.5 2.4E+02 0.0052 25.9 6.5 26 431-456 51-76 (152)
362 PRK13502 transcriptional activ 24.5 5.6E+02 0.012 25.1 9.6 29 415-446 228-256 (282)
363 PF12844 HTH_19: Helix-turn-he 24.3 1.4E+02 0.0031 22.7 4.3 24 431-454 12-35 (64)
364 PRK09393 ftrA transcriptional 24.3 1.5E+02 0.0033 30.1 5.7 40 416-455 219-258 (322)
365 COG1342 Predicted DNA-binding 24.2 80 0.0017 27.8 3.0 28 431-458 49-76 (99)
366 PRK13509 transcriptional repre 24.2 1.4E+02 0.0029 29.9 5.2 28 426-454 15-42 (251)
367 KOG0037 Ca2+-binding protein, 24.2 6.8E+02 0.015 25.2 9.8 97 260-377 101-203 (221)
368 PRK10434 srlR DNA-bindng trans 24.0 1.3E+02 0.0027 30.2 4.9 29 425-454 14-42 (256)
369 PRK10079 phosphonate metabolis 23.8 1.2E+02 0.0027 29.5 4.7 27 428-454 32-58 (241)
370 PRK09391 fixK transcriptional 23.8 3.1E+02 0.0067 26.4 7.5 26 431-456 179-204 (230)
371 PHA00675 hypothetical protein 23.8 1.7E+02 0.0038 24.7 4.8 23 432-454 40-62 (78)
372 TIGR02404 trehalos_R_Bsub treh 23.7 1.8E+02 0.004 28.0 5.9 27 428-454 21-47 (233)
373 TIGR02702 SufR_cyano iron-sulf 23.6 1.6E+02 0.0034 28.2 5.3 27 428-455 13-39 (203)
374 PRK00430 fis global DNA-bindin 23.5 4.8E+02 0.01 22.4 9.5 67 385-455 24-92 (95)
375 PF01022 HTH_5: Bacterial regu 23.5 2.2E+02 0.0048 20.7 5.0 24 431-454 15-38 (47)
376 TIGR02018 his_ut_repres histid 23.4 1.9E+02 0.0042 27.9 6.0 27 428-454 22-48 (230)
377 PF01418 HTH_6: Helix-turn-hel 23.3 2.2E+02 0.0047 23.1 5.4 24 431-454 34-57 (77)
378 smart00531 TFIIE Transcription 23.1 93 0.002 28.6 3.5 27 431-457 15-41 (147)
379 KOG1597 Transcription initiati 23.0 2.3E+02 0.0049 29.7 6.5 24 431-454 260-283 (308)
380 PRK13558 bacterio-opsin activa 23.0 50 0.0011 36.9 2.0 28 430-457 629-656 (665)
381 TIGR00122 birA_repr_reg BirA b 23.0 1.8E+02 0.0039 22.8 4.7 25 431-455 13-37 (69)
382 PRK09764 DNA-binding transcrip 22.9 2.1E+02 0.0044 28.0 6.1 27 428-454 26-52 (240)
383 cd00131 PAX Paired Box domain 22.8 1.3E+02 0.0028 27.1 4.3 32 431-462 33-64 (128)
384 PRK09940 transcriptional regul 22.5 3.6E+02 0.0077 27.4 7.8 57 340-397 138-194 (253)
385 PF06970 RepA_N: Replication i 22.4 94 0.002 25.8 3.0 21 433-453 54-74 (76)
386 TIGR02431 pcaR_pcaU beta-ketoa 22.4 1.8E+02 0.0039 28.5 5.6 27 428-454 21-47 (248)
387 PRK13413 mpi multiple promoter 22.4 3.6E+02 0.0078 25.6 7.5 24 431-454 172-195 (200)
388 COG2345 Predicted transcriptio 22.4 1.4E+02 0.0031 29.7 4.8 31 423-454 18-48 (218)
389 PRK10906 DNA-binding transcrip 22.2 1.4E+02 0.003 29.9 4.8 28 425-453 14-41 (252)
390 PRK13503 transcriptional activ 22.2 2E+02 0.0043 28.1 5.9 38 417-454 173-210 (278)
391 COG1725 Predicted transcriptio 22.1 1.1E+02 0.0024 28.0 3.6 27 428-454 32-58 (125)
392 COG2188 PhnF Transcriptional r 22.1 1.9E+02 0.0042 28.3 5.8 27 428-454 28-54 (236)
393 PRK15121 right oriC-binding tr 22.1 2E+02 0.0043 28.9 5.9 40 415-454 5-44 (289)
394 cd01392 HTH_LacI Helix-turn-he 22.1 67 0.0015 23.4 1.9 18 436-453 2-19 (52)
395 PF05344 DUF746: Domain of Unk 22.1 1.3E+02 0.0028 24.6 3.6 36 423-458 5-40 (65)
396 PRK01381 Trp operon repressor; 21.9 1.1E+02 0.0024 26.9 3.5 21 431-451 55-75 (99)
397 PF02002 TFIIE_alpha: TFIIE al 21.9 1.1E+02 0.0024 26.2 3.5 25 431-455 27-51 (105)
398 PRK15008 HTH-type transcriptio 21.8 1.3E+02 0.0029 28.5 4.4 38 413-450 19-57 (212)
399 PRK09480 slmA division inhibit 21.8 6E+02 0.013 23.0 10.6 75 296-370 24-98 (194)
400 PRK09706 transcriptional repre 21.8 1.8E+02 0.004 25.9 5.1 23 431-453 18-40 (135)
401 PRK11402 DNA-binding transcrip 21.6 2.2E+02 0.0047 27.8 5.9 26 428-453 30-55 (241)
402 PRK10163 DNA-binding transcrip 21.6 1.5E+02 0.0032 29.8 4.9 29 427-455 36-64 (271)
403 PRK09978 DNA-binding transcrip 21.5 8.9E+02 0.019 24.8 10.6 122 331-453 56-180 (274)
404 cd04763 HTH_MlrA-like Helix-Tu 21.4 1.1E+02 0.0023 23.9 3.1 22 433-454 2-23 (68)
405 TIGR03384 betaine_BetI transcr 21.4 1.3E+02 0.0029 27.2 4.2 33 419-451 16-48 (189)
406 PRK10402 DNA-binding transcrip 21.1 2.3E+02 0.0051 27.1 6.0 25 432-456 170-194 (226)
407 PRK09943 DNA-binding transcrip 21.1 1.5E+02 0.0032 27.8 4.5 21 432-452 21-41 (185)
408 smart00389 HOX Homeodomain. DN 21.0 1.8E+02 0.004 21.3 4.2 23 433-455 29-51 (56)
409 PF01527 HTH_Tnp_1: Transposas 21.0 1.9E+02 0.0041 22.7 4.5 26 431-456 23-48 (76)
410 COG2522 Predicted transcriptio 20.8 2.8E+02 0.0061 25.2 5.9 27 431-457 22-48 (119)
411 TIGR02395 rpoN_sigma RNA polym 20.7 2.3E+02 0.005 30.9 6.4 24 430-453 317-340 (429)
412 PF00046 Homeobox: Homeobox do 20.7 1.2E+02 0.0027 22.6 3.2 21 433-453 29-49 (57)
413 PF08221 HTH_9: RNA polymerase 20.6 3.3E+02 0.0073 21.4 5.7 27 426-453 23-49 (62)
414 PRK13503 transcriptional activ 20.5 3.8E+02 0.0081 26.1 7.4 37 350-386 185-221 (278)
415 cd00093 HTH_XRE Helix-turn-hel 20.5 1.3E+02 0.0029 20.4 3.2 23 431-453 12-34 (58)
416 PHA00542 putative Cro-like pro 20.3 1.1E+02 0.0024 25.3 3.1 25 431-455 31-55 (82)
417 PRK11534 DNA-binding transcrip 20.3 1.4E+02 0.003 28.6 4.3 27 429-455 28-54 (224)
418 COG1405 SUA7 Transcription ini 20.3 9.7E+02 0.021 24.8 11.8 24 431-454 251-274 (285)
419 PRK11014 transcriptional repre 20.3 1.6E+02 0.0034 26.6 4.4 27 429-455 23-49 (141)
420 PF15545 Toxin_67: Putative to 20.2 99 0.0021 25.5 2.6 30 380-409 6-35 (70)
421 PF14394 DUF4423: Domain of un 20.2 1.8E+02 0.0038 27.7 4.8 25 431-455 39-65 (171)
422 PF01399 PCI: PCI domain; Int 20.1 1.7E+02 0.0038 23.8 4.3 32 423-455 53-84 (105)
423 PF13613 HTH_Tnp_4: Helix-turn 20.1 1.8E+02 0.004 21.9 4.0 28 427-454 15-42 (53)
No 1
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=100.00 E-value=1.4e-47 Score=400.96 Aligned_cols=228 Identities=39% Similarity=0.646 Sum_probs=218.0
Q ss_pred CCcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHH--------------------HHHHHHHHHhhhCCCCcHHHHHH--
Q 011577 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR--------------------LEKEKSKLQSQFGREPTLIEWAK-- 310 (482)
Q Consensus 253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~--------------------le~~~~~l~~~~g~~pt~~ewA~-- 310 (482)
.+|+++.||++|++.||||++||++|+++||.+++ |++++..|++++|++||..|||.
T Consensus 58 ~~d~v~~yl~~igr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~~~ 137 (415)
T PRK07598 58 STDLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKTA 137 (415)
T ss_pred CCChHHHHHHhcccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHHHh
Confidence 47999999999999999999999999999999999 89999999999999999999994
Q ss_pred --------------------HhcCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhH
Q 011577 311 --------------------AIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSV 370 (482)
Q Consensus 311 --------------------a~gmdd~eLi~~l~~Gd~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAi 370 (482)
++||++++|+..++.|..|+++||.+|+++|+++|++|.++|++++||||||+||||+|+
T Consensus 138 ~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~rav 217 (415)
T PRK07598 138 DISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAV 217 (415)
T ss_pred CCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHH
Confidence 455677778888899999999999999999999999999999999999999999999999
Q ss_pred HhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHH
Q 011577 371 EKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLER 450 (482)
Q Consensus 371 ekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~ 450 (482)
++|||.+|++|+||++||||++|.+++++++++|++|.++.+.+++++++.+.|...+|+.|+.+|||+.|||++++|+.
T Consensus 218 ekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~ 297 (415)
T PRK07598 218 EKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVRE 297 (415)
T ss_pred HHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHcCCCccCcccCCCCCCCcccccccCC
Q 011577 451 LIFITRMPLSMQQPVWADQDTTFQSTFLDA 480 (482)
Q Consensus 451 ~L~~ar~~lSLD~~i~~d~~~~l~d~i~D~ 480 (482)
++..++.++|||.+++++++..+.|+++|+
T Consensus 298 ~l~~~~~~~SLd~~vg~~~d~~l~d~l~~~ 327 (415)
T PRK07598 298 VLLRVPRSVSLETKVGKDKDTELGDLLETD 327 (415)
T ss_pred HHHHccCCcccccccCCCccccHHHhccCC
Confidence 999999999999999988888888888764
No 2
>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=6.4e-45 Score=366.57 Aligned_cols=226 Identities=43% Similarity=0.726 Sum_probs=216.9
Q ss_pred cHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHHHH
Q 011577 255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLI 334 (482)
Q Consensus 255 d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~LI 334 (482)
|++..||++++++|+||++||.+|+++++.++++++++..|+++.|++|+..+||+++|+++.+|+.+++.|..|+++||
T Consensus 1 ~~~~~yl~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Lv 80 (298)
T TIGR02997 1 DLVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMI 80 (298)
T ss_pred CcHHHHHHHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHHH
Confidence 36788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHHH
Q 011577 335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL 414 (482)
Q Consensus 335 ~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~e~l 414 (482)
.+|+++|+++|++|.++|.+++|||||||+|||+|+++|||.+|++|+||++||||++|.+++.++.+.+++|.++...+
T Consensus 81 ~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~I~r~i~~~~r~vr~p~~~~~~~ 160 (298)
T TIGR02997 81 KANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKL 160 (298)
T ss_pred HHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHHHHHHHHhcCCCeeCcHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCCCcccccccCC
Q 011577 415 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDA 480 (482)
Q Consensus 415 ~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~~l~d~i~D~ 480 (482)
++++++...+...+|+.|+.+|||+.+|+++++|..++..+...+|||.+++++++.++.++++|+
T Consensus 161 ~~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~~ 226 (298)
T TIGR02997 161 NKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDD 226 (298)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCcchHHHhccCC
Confidence 999999999999999999999999999999999999999999999999999876666777777653
No 3
>PRK05949 RNA polymerase sigma factor; Validated
Probab=100.00 E-value=8e-45 Score=371.20 Aligned_cols=228 Identities=38% Similarity=0.653 Sum_probs=221.1
Q ss_pred CCcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHH
Q 011577 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 332 (482)
Q Consensus 253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~ 332 (482)
.+|++..||++|+++|+||++||++|+++|+.++.+++.+..|+..+|++|+..+||.+++|++.+|+..++.|+.|++.
T Consensus 16 ~~d~~~~yl~~i~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~~ 95 (327)
T PRK05949 16 SADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQK 95 (327)
T ss_pred CCCHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHHH
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHH
Q 011577 333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 412 (482)
Q Consensus 333 LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~e 412 (482)
||..|+++|+++|++|.+++.+++|||||||||||+++++|||++|++|+|||+||||++|.++|+++++.|++|.++..
T Consensus 96 Li~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~~~~~ 175 (327)
T PRK05949 96 MIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITE 175 (327)
T ss_pred HHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCCCcccccccCC
Q 011577 413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDA 480 (482)
Q Consensus 413 ~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~~l~d~i~D~ 480 (482)
.++++.++.+.+...+|+.|+.+|||+.+||++++|..++..++.++|||.|++++++.++.|+++|+
T Consensus 176 ~~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~l~d~ 243 (327)
T PRK05949 176 KLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDE 243 (327)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCccHHhhcCCC
Confidence 99999999999999999999999999999999999999999999999999999887777888888775
No 4
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=1.4e-44 Score=375.00 Aligned_cols=227 Identities=37% Similarity=0.703 Sum_probs=220.6
Q ss_pred CcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHHH
Q 011577 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL 333 (482)
Q Consensus 254 ~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~L 333 (482)
.|++..||++|+++|+||++||++|+++|++++.+++++.+|+...|++|+..+||.++|++..+|..++..|..|++.|
T Consensus 62 ~d~l~~Yl~~i~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~L 141 (373)
T PRK07406 62 EDSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEKM 141 (373)
T ss_pred CCHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHHHH
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHH
Q 011577 334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTL 413 (482)
Q Consensus 334 I~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~e~ 413 (482)
|.+|+++|+++|++|.++|.+++||+||||||||+|+++||+.+|++|+|||+||||++|.++|+++++.|++|.++...
T Consensus 142 i~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~~~~ 221 (373)
T PRK07406 142 VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYET 221 (373)
T ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCCCcccccccCC
Q 011577 414 LSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDA 480 (482)
Q Consensus 414 l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~~l~d~i~D~ 480 (482)
++++.++...|.+.+|+.||.+|||+.||+++++|..++..+..++|||.|++++++.++.|+++|+
T Consensus 222 ~~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~~~l~d~l~d~ 288 (373)
T PRK07406 222 ISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEAD 288 (373)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCcccHHHhcCCC
Confidence 9999999999999999999999999999999999999999888999999999887777888988874
No 5
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=1.4e-43 Score=360.44 Aligned_cols=227 Identities=40% Similarity=0.644 Sum_probs=220.1
Q ss_pred CcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHHH
Q 011577 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL 333 (482)
Q Consensus 254 ~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~L 333 (482)
+|++..||++|+++|+||++||.+|+++|++++.+++++..|++++|++|+..+||.++++++.+|+..++.|+.|++.|
T Consensus 7 ~~~~~~yl~~i~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~~L 86 (317)
T PRK07405 7 TDLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRKM 86 (317)
T ss_pred CcHHHHHHHHccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHHHH
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHH
Q 011577 334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTL 413 (482)
Q Consensus 334 I~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~e~ 413 (482)
|..|+++|+++|++|.+++.+++||+||||+|||+++++|||.+|++|+|||+||||++|.++|.++++.+++|.++...
T Consensus 87 ~~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir~p~~~~~~ 166 (317)
T PRK07405 87 VEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEK 166 (317)
T ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCccCChHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCCCcccccccCC
Q 011577 414 LSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDA 480 (482)
Q Consensus 414 l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~~l~d~i~D~ 480 (482)
+++++++...+...+|+.|+.+|||+.+|+++++|..++...+..+|||.|++++++.++.++++|+
T Consensus 167 ~~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~~~d~ 233 (317)
T PRK07405 167 LNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDT 233 (317)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCccHHHhhcCC
Confidence 9999999999999999999999999999999999999999889999999999887777888888764
No 6
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=100.00 E-value=9.5e-41 Score=340.57 Aligned_cols=228 Identities=36% Similarity=0.626 Sum_probs=211.0
Q ss_pred CcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHh-hhCCCCcHH---------------HHHHHhcCCH-
Q 011577 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQS-QFGREPTLI---------------EWAKAIGLSC- 316 (482)
Q Consensus 254 ~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~-~~g~~pt~~---------------ewA~a~gmdd- 316 (482)
.|.+..|+.+++..++++.++|.++.+.++....+......+.. ..|..|+.. +|+..+..++
T Consensus 8 ~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Ee 87 (342)
T COG0568 8 ADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEEE 87 (342)
T ss_pred hhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHHH
Confidence 57899999999999999999999999999887777667777777 677888876 6665555554
Q ss_pred HHHHHHHhhc--H-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHH
Q 011577 317 RDLKSELHSG--N-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 393 (482)
Q Consensus 317 ~eLi~~l~~G--d-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI 393 (482)
..|..++..| + .|..+||.+|++||++||++|.|+|+.+.||||||+||||+|++||||++|++|+|||+||||++|
T Consensus 88 ~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAVekFdp~rG~kFsTYA~wWIrqaI 167 (342)
T COG0568 88 KALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQAI 167 (342)
T ss_pred HHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHHHHhcCcccCCcchhHHHHHHHHHH
Confidence 6688888888 4 699999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhcCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCCCcc
Q 011577 394 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 473 (482)
Q Consensus 394 ~~~Lrkq~r~irlP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~~l 473 (482)
.++|.++.|+|++|.|+.+.++++.+..+.+.+.++++|+.+|||+.||++.++|+.++.++..++|||.|+|++++..+
T Consensus 168 ~raI~~q~rtIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd~~ig~ded~~l 247 (342)
T COG0568 168 TRAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDDEDSEL 247 (342)
T ss_pred HHHHHHhcchhhHhHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccCCcCCCCcccHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999988899
Q ss_pred cccccCCC
Q 011577 474 QSTFLDAA 481 (482)
Q Consensus 474 ~d~i~D~~ 481 (482)
+|+++|..
T Consensus 248 ~d~leD~~ 255 (342)
T COG0568 248 GDFLEDDK 255 (342)
T ss_pred HHHhhcCC
Confidence 99999975
No 7
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=100.00 E-value=1e-40 Score=356.81 Aligned_cols=216 Identities=36% Similarity=0.579 Sum_probs=195.1
Q ss_pred CCcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHH
Q 011577 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 332 (482)
Q Consensus 253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~ 332 (482)
..|+++.||++|+++|+||++||++|+++|+.+..++.. +. ....|+. ....+|...+..|..|+++
T Consensus 209 ~~d~l~~YL~~i~~~~lLt~eEE~~La~~i~~g~~~~~~---~~-------~~~~~~~---~~~~~l~~~~~~g~~Ar~~ 275 (509)
T PRK05901 209 TADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEEL---LA-------EGEKLDP---ELRRDLQWIGRDGKRAKNH 275 (509)
T ss_pred cccHHHHHHHHhccCCCCCHHHHHHHHHHHHhCCchhhh---hh-------hcccchh---hhhhhhhhhccchHHHHHH
Confidence 468999999999999999999999999999886433321 11 1122432 2456788888899999999
Q ss_pred HHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHH
Q 011577 333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 412 (482)
Q Consensus 333 LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~e 412 (482)
||.+|+|||++||++|.++|++++||||||+||||+|+++|||++|++|+|||+||||++|.++|+++.+.+++|.++.+
T Consensus 276 LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP~~~~e 355 (509)
T PRK05901 276 LLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE 355 (509)
T ss_pred HHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCCCcccccccCCC
Q 011577 413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDAA 481 (482)
Q Consensus 413 ~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~~l~d~i~D~~ 481 (482)
.++++.++.+.|...+|+.||.+|||+.|||++++|..++...+.++|||.+++++++.++.|+++|+.
T Consensus 356 ~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~l~d~l~D~~ 424 (509)
T PRK05901 356 TINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSE 424 (509)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCcccHHHhccCCC
Confidence 999999999999999999999999999999999999999999999999999998887778999998864
No 8
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=100.00 E-value=1.3e-39 Score=332.66 Aligned_cols=214 Identities=36% Similarity=0.596 Sum_probs=194.4
Q ss_pred CcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHHH
Q 011577 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL 333 (482)
Q Consensus 254 ~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~L 333 (482)
+|++..||++++++|+||++||.+|+++|+.+..++.. |+..+|+... ...+|...++.|..|+++|
T Consensus 25 ~~~~~~Yl~~i~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~~~L 91 (324)
T PRK07921 25 ADLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAARRHL 91 (324)
T ss_pred CChHHHHHHHhcccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHHHHH
Confidence 57899999999999999999999999999987665543 1122232111 3467888999999999999
Q ss_pred HHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHH
Q 011577 334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTL 413 (482)
Q Consensus 334 I~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~e~ 413 (482)
|..|+++|+++|++|.+++.+++||+|||+||||+|+++|||++|++|+|||+||||++|.++|+++.+.+++|.++.+.
T Consensus 92 v~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~~~~~~ 171 (324)
T PRK07921 92 LEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ 171 (324)
T ss_pred HHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCCCcccccccCC
Q 011577 414 LSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDA 480 (482)
Q Consensus 414 l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~~l~d~i~D~ 480 (482)
++++.++...|...+|+.||.+|||+.||+++++|..++..+...+|||.|++++++.++.|+++|+
T Consensus 172 ~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~ 238 (324)
T PRK07921 172 VNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDS 238 (324)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCchHHHHhcCC
Confidence 9999999999999999999999999999999999999998888999999999877777889999875
No 9
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=2.7e-36 Score=312.71 Aligned_cols=192 Identities=39% Similarity=0.707 Sum_probs=180.3
Q ss_pred CCCCCcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHH
Q 011577 250 GFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSS 329 (482)
Q Consensus 250 ~~~~~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~A 329 (482)
+...+|+++.||++|+++|+||++||.+|+++++. ++..|
T Consensus 91 ~~~~~d~~~~yl~~i~~~~~l~~~ee~~L~~~~~~----------------------------------------Gd~~A 130 (367)
T PRK09210 91 GVKINDPVRMYLKEIGRVPLLTAEEEIELAKRIEE----------------------------------------GDEEA 130 (367)
T ss_pred ccccCcHHHHHHHHhhccCCCCHHHHHHHHHHHHh----------------------------------------hHHHH
Confidence 33457899999999999999999999999987764 12389
Q ss_pred HHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchh
Q 011577 330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 409 (482)
Q Consensus 330 re~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~ 409 (482)
++.||..|+++|+++|++|.+++.+++||+||||||||+|+++|||.+|++|+|||+||||++|.++|+++.+.+++|.+
T Consensus 131 ~~~Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~~ 210 (367)
T PRK09210 131 KQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVH 210 (367)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCCCcccccccCCC
Q 011577 410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDAA 481 (482)
Q Consensus 410 v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~~l~d~i~D~~ 481 (482)
+.+.++++.++.+.|...+|+.||.+|||+.|||++++|+.++..++.++|||.|++++++..+.|+++|+.
T Consensus 211 ~~~~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~i~d~~ 282 (367)
T PRK09210 211 MVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQD 282 (367)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCCCcchhhhhccCCC
Confidence 999999999999999999999999999999999999999999999989999999999877788999998864
No 10
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=4.7e-34 Score=313.48 Aligned_cols=154 Identities=36% Similarity=0.737 Sum_probs=149.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc
Q 011577 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 407 (482)
Q Consensus 328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP 407 (482)
.|+++||.+|++||++||++|.++|++++||||||+||||+|+++|||.+|++|+|||+||||++|.++|+++.++|++|
T Consensus 380 ~a~~~Li~~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA~~wIr~aI~~~i~~~~r~irip 459 (619)
T PRK05658 380 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 459 (619)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCchHHHhHHHHHHHHHHHHHHcCCceecC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCCCcccccccCCC
Q 011577 408 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDAA 481 (482)
Q Consensus 408 ~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~~l~d~i~D~~ 481 (482)
.++.+.++++.++.+.+.+++|+.||.+|||+.||+++++|+.++..+..++|||.|++++++.++.|+++|+.
T Consensus 460 ~~~~~~~~k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~Sld~~i~~~~~~~l~d~i~d~~ 533 (619)
T PRK05658 460 VHMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKN 533 (619)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCcCCCCCCCCCCCchhhhcCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999888888999998863
No 11
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=99.98 E-value=2.3e-31 Score=267.67 Aligned_cols=188 Identities=22% Similarity=0.413 Sum_probs=159.4
Q ss_pred CcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHHH
Q 011577 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL 333 (482)
Q Consensus 254 ~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~L 333 (482)
.+..+.||+++.++|+||+++|.+|+++++. .++..|+++|
T Consensus 5 ~~~~~~y~~~~~~~~~l~~~~e~~L~~~~~~---------------------------------------~gd~~A~~~L 45 (289)
T PRK07500 5 ASADRSMIRSAMKAPYLEREEEHALAYRWKD---------------------------------------HRDEDALHRI 45 (289)
T ss_pred hhHHHHHHHHHhcCCCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHHH
Confidence 3567889999999999999999999997643 1234899999
Q ss_pred HHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHH-
Q 011577 334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT- 412 (482)
Q Consensus 334 I~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~e- 412 (482)
|..|+++|+++|++|.+++.+++||+||||+|||+++++||+.+|.+|+|||+||||++|.++|+++.+.+++|.+...
T Consensus 46 v~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I~~~lr~~~~~iR~p~~~~~~ 125 (289)
T PRK07500 46 ISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQK 125 (289)
T ss_pred HHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHCCCceecCccHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999987544
Q ss_pred ----HHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHH-HcCCCccCcccCCCCCCC--cccccccCC
Q 011577 413 ----LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF-ITRMPLSMQQPVWADQDT--TFQSTFLDA 480 (482)
Q Consensus 413 ----~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~-~ar~~lSLD~~i~~d~~~--~l~d~i~D~ 480 (482)
.+.++..........+++.|+.+|||+.||+++++|..+.. .....+|||.+++++++. ++.|+++|+
T Consensus 126 ~~~~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~i~d~ 200 (289)
T PRK07500 126 ALFFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDD 200 (289)
T ss_pred HHHHHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCCCCCCcccHHHhccCC
Confidence 33333333333334678899999999999999999988754 345789999999765543 678888775
No 12
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=99.97 E-value=1.9e-30 Score=260.40 Aligned_cols=186 Identities=27% Similarity=0.489 Sum_probs=156.7
Q ss_pred CCcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcH-HHHH
Q 011577 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGN-SSRE 331 (482)
Q Consensus 253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd-~Are 331 (482)
+.+++..|++++++.|+||.++|.+|+..++. .|+ .|++
T Consensus 12 ~~~~~~~y~~~~~~~~~l~~~~e~~l~~~~~~----------------------------------------~Gd~~a~~ 51 (284)
T PRK06596 12 PEGNLDAYIQAVNKIPMLTAEEEYMLAKRLRE----------------------------------------HGDLEAAK 51 (284)
T ss_pred CccHHHHHHHHHhccCCCCHHHHHHHHHHHHH----------------------------------------cCCHHHHH
Confidence 45789999999999999999999999886432 234 8999
Q ss_pred HHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHH
Q 011577 332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY 411 (482)
Q Consensus 332 ~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~ 411 (482)
.||..|+++|+++|++|.+.+.+++||+|||++||++|+++|||++|++|+|||+|||+++|.++|+++.+.+++|.+..
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 99999999999999999999999999999999999999999999999999999999999999999999887889998653
Q ss_pred H--HHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHc-CCCccCcccCCCCC--CCcccccccCC
Q 011577 412 T--LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT-RMPLSMQQPVWADQ--DTTFQSTFLDA 480 (482)
Q Consensus 412 e--~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~a-r~~lSLD~~i~~d~--~~~l~d~i~D~ 480 (482)
. ...++.+...++. .++.|+.+|||+.||+++++|..++... ...+|||.++++++ +.++.++++|+
T Consensus 132 ~~~~~~~~~~~~~~l~--~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~~~l~d~ 203 (284)
T PRK06596 132 QRKLFFNLRKAKKRLG--WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLEDK 203 (284)
T ss_pred HHHHHHHHHHHHHHhc--cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCCCCCcchHHHHcCCC
Confidence 2 2333444444442 3478999999999999999999987643 46899999987553 24577888775
No 13
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=99.97 E-value=9.5e-31 Score=260.03 Aligned_cols=153 Identities=23% Similarity=0.384 Sum_probs=141.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc
Q 011577 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 407 (482)
Q Consensus 328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP 407 (482)
.++++||..|++||++||++|.++|++++||||||+|||++|+++|||++|++|+|||+||||++|.++|+++.+.+++|
T Consensus 40 ~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~iGLi~AierFDp~~G~~FsTYA~~~Irg~I~~~lr~~~~~ir~P 119 (264)
T PRK07122 40 RQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVP 119 (264)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHcCCccccC
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH--cCCCccCcccCCCCCC--CcccccccCC
Q 011577 408 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI--TRMPLSMQQPVWADQD--TTFQSTFLDA 480 (482)
Q Consensus 408 ~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~--ar~~lSLD~~i~~d~~--~~l~d~i~D~ 480 (482)
.++.+.+.+++++...|.+.+|+.||.+|||+.||+++++|.+++.. ...++|||.+++++++ ..+.|.++|+
T Consensus 120 r~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~~~d~~~~~ 196 (264)
T PRK07122 120 RRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSGDDDARAIADTLGDV 196 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccccccCCCCCcccchhccCCc
Confidence 99999999999999999999999999999999999999999998864 4568999999875433 3566777665
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=1.2e-30 Score=254.40 Aligned_cols=153 Identities=40% Similarity=0.757 Sum_probs=145.8
Q ss_pred HHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccch
Q 011577 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE 408 (482)
Q Consensus 329 Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~ 408 (482)
|+++||..|+++|+++|++|.+++.+++||+|||+|||++|+++|||++|++|+|||+||||++|.++++++.+.+++|.
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 hHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCCCcccccccCCC
Q 011577 409 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDAA 481 (482)
Q Consensus 409 ~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~~l~d~i~D~~ 481 (482)
++...++++.++...+...+|+.||.+|||+.||+++++|..++......+|||.+++++++.++.|+++|++
T Consensus 81 ~~~~~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~ 153 (238)
T TIGR02393 81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDTS 153 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCCCCCCcccHHHHhcCCC
Confidence 9999999999999999999999999999999999999999999988888999999998777767888888764
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=99.97 E-value=3.6e-30 Score=256.05 Aligned_cols=184 Identities=26% Similarity=0.516 Sum_probs=151.4
Q ss_pred HHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHHHHH
Q 011577 256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 335 (482)
Q Consensus 256 ~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~LI~ 335 (482)
++..||++++++|+|++++|.+|+.++.. .++..|++.||.
T Consensus 2 ~~~~yl~~~~~~~~l~~~~e~~l~~~~~~---------------------------------------~gd~~a~~~Lv~ 42 (270)
T TIGR02392 2 SLDAYIRAVNRIPMLTPEEEYQLAKRLRE---------------------------------------HGDLDAAKKLVL 42 (270)
T ss_pred hHHHHHHHHhcCCCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHHHHH
Confidence 57889999999999999999999886432 123489999999
Q ss_pred HHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHH--HH
Q 011577 336 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY--TL 413 (482)
Q Consensus 336 snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~--e~ 413 (482)
.|+++|+++|++|.+++.+++||+||||+||++|+++|||++|++|+|||+|||+++|.++|+++.+.+++|.+.. ..
T Consensus 43 ~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA~~~Ir~~i~~~l~~~~~~ir~p~~~~~~~~ 122 (270)
T TIGR02392 43 SHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRKL 122 (270)
T ss_pred HhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhhHHHHHHHHHHHHHHcCCceecCchHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999877789886543 33
Q ss_pred HHHHHHHHHHHHHhcCCCC-cHHHHHHHhCCCHHHHHHHHHHcC-CCccCcccCCCCCC--CcccccccCC
Q 011577 414 LSKVLEAKRLYIQEGNHSP-DKEDLARRVGITVEKLERLIFITR-MPLSMQQPVWADQD--TTFQSTFLDA 480 (482)
Q Consensus 414 l~kI~ka~~eL~~e~gr~p-S~eEIAe~LGIS~etVk~~L~~ar-~~lSLD~~i~~d~~--~~l~d~i~D~ 480 (482)
..++.+....+. ..+.| +.+|||+.||+++++|..++.... ..+|||.+++++++ .++.|.++|.
T Consensus 123 ~~~~~~~~~~~~--~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~l~d~ 191 (270)
T TIGR02392 123 FFNLRKMKKRLQ--GWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDDEDDGGAPIAYLVDK 191 (270)
T ss_pred HHHHHHHHHHHh--cCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCCCCCccccHHHHhcCC
Confidence 344444444332 21345 699999999999999999876443 47999999876543 3566777664
No 16
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=99.97 E-value=2.1e-29 Score=257.55 Aligned_cols=188 Identities=36% Similarity=0.630 Sum_probs=173.5
Q ss_pred CCcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHH
Q 011577 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 332 (482)
Q Consensus 253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~ 332 (482)
..|.++.||++|+..|+||+++|..|+.+++. ++..|++.
T Consensus 51 ~~~~~~~y~~~~~~~~~l~~~ee~~li~~~~~----------------------------------------Gd~~A~~~ 90 (325)
T PRK05657 51 VLDATQLYLNEIGYSPLLTAEEEVYFARRALR----------------------------------------GDFAARQR 90 (325)
T ss_pred cccHHHHHHHHHhcCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHH
Confidence 46789999999999999999999999887653 22389999
Q ss_pred HHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHH
Q 011577 333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 412 (482)
Q Consensus 333 LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~e 412 (482)
||..|.++|+++|++|.+++.+++||+||||||||+++++||+.+|++|+||++||||..|.++++++.+.+++|.++..
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 HHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCCCcccccccCC
Q 011577 413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDA 480 (482)
Q Consensus 413 ~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~~l~d~i~D~ 480 (482)
.++.+.++...|...+++.|+.+|||+.||++++.|+.++.......|||.++..+...++.|.++|+
T Consensus 171 ~l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~~~~~~~~l~d~l~d~ 238 (325)
T PRK05657 171 ELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADE 238 (325)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCCCCCCCcchhhhccCC
Confidence 88888888888988899999999999999999999999998877889999998877777788888765
No 17
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=99.97 E-value=1.4e-29 Score=250.22 Aligned_cols=157 Identities=28% Similarity=0.505 Sum_probs=142.6
Q ss_pred hcH-HHHHHHHHHHHHHHHHHHHHccCC-CCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcC
Q 011577 325 SGN-SSREKLINANLRLVVHVAKQYQGR-GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR 402 (482)
Q Consensus 325 ~Gd-~Are~LI~snlrLV~sIAkrY~~~-g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r 402 (482)
+|+ .|+++||..|+++|+++|++|.+. +.+++||+|||+||||+|+++|||++|++|+|||+|||+|+|++++|++..
T Consensus 21 ~gd~~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~~ 100 (256)
T PRK07408 21 NPSIALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSP 100 (256)
T ss_pred CCCHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHHcCC
Confidence 455 899999999999999999999876 667999999999999999999999999999999999999999999999999
Q ss_pred CcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHH--HcCCCccCcccCCCCCC--Cccccccc
Q 011577 403 TIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF--ITRMPLSMQQPVWADQD--TTFQSTFL 478 (482)
Q Consensus 403 ~irlP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~--~ar~~lSLD~~i~~d~~--~~l~d~i~ 478 (482)
.+++|+++...++++.++...|.+.+|+.|+.+|||+.||+++++|..++. .....+|||.+++++++ .++.+.++
T Consensus 101 ~vr~pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~~~ 180 (256)
T PRK07408 101 TVRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQDEDGSTSLGDLLP 180 (256)
T ss_pred eeeeCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCCCCCCccccccccC
Confidence 999999999999999999999999999999999999999999999999865 34568999999865443 35777777
Q ss_pred CCC
Q 011577 479 DAA 481 (482)
Q Consensus 479 D~~ 481 (482)
|+.
T Consensus 181 d~~ 183 (256)
T PRK07408 181 DPR 183 (256)
T ss_pred Ccc
Confidence 763
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=1.4e-28 Score=242.34 Aligned_cols=176 Identities=27% Similarity=0.469 Sum_probs=158.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHHHHHHHHHHHHH
Q 011577 264 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH 343 (482)
Q Consensus 264 i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~LI~snlrLV~s 343 (482)
..++|+||++||.+|+..++. ++..|++.||..|.++|++
T Consensus 10 ~~~~~~l~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~~~~~~~v~~ 49 (254)
T TIGR02850 10 TSKLPVLKNQEMRELFIRMQS----------------------------------------GDTTAREKLINGNLRLVLS 49 (254)
T ss_pred ccCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHHHH
Confidence 467899999999888876553 2237999999999999999
Q ss_pred HHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHHHHHHHHHHHH
Q 011577 344 VAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRL 423 (482)
Q Consensus 344 IAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~e~l~kI~ka~~e 423 (482)
+|++|.+++.+++||+||||+|||+++++||+.+|.+|+||+++||+|.|++++|++. .+++|.++.....++.++...
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 9999999999999999999999999999999999999999999999999999999975 789999999999999999999
Q ss_pred HHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCC--CcccccccCC
Q 011577 424 YIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD--TTFQSTFLDA 480 (482)
Q Consensus 424 L~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~--~~l~d~i~D~ 480 (482)
+..++++.|+.+|||+.||+++++|..++.....++|||.++.++++ .++.+.+.|+
T Consensus 129 l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~~~d~ 187 (254)
T TIGR02850 129 LISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDE 187 (254)
T ss_pred HHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCCCCCcchhhhhcCCc
Confidence 99999999999999999999999999999988889999999864443 3467777664
No 19
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=99.96 E-value=1.7e-27 Score=234.86 Aligned_cols=176 Identities=27% Similarity=0.486 Sum_probs=157.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHHHHHHHHHHHHH
Q 011577 264 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH 343 (482)
Q Consensus 264 i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~LI~snlrLV~s 343 (482)
..++|+|+++|+..|+.+++. ++..|++.||..|.++|++
T Consensus 13 ~~~~~~l~~~~~~~l~~~~~~----------------------------------------gd~~a~~~l~~~~~~~v~~ 52 (258)
T PRK08215 13 TSKLPVLKNEEMRELFERMQN----------------------------------------GDKEAREKLINGNLRLVLS 52 (258)
T ss_pred CCCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHHHHHHHH
Confidence 466789999999888876553 2348999999999999999
Q ss_pred HHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHHHHHHHHHHHH
Q 011577 344 VAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRL 423 (482)
Q Consensus 344 IAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~e~l~kI~ka~~e 423 (482)
+|++|.+++.+++||+|||++|||+++++||+.+|.+|+||+++||+|.|.+++++.. .+++|+++.....++.++...
T Consensus 53 ~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~~~lr~~~-~vrip~~~~~~~~~~~~~~~~ 131 (258)
T PRK08215 53 VIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVREK 131 (258)
T ss_pred HHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-ceEecHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999985 789999999999999999999
Q ss_pred HHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCC--CcccccccCC
Q 011577 424 YIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD--TTFQSTFLDA 480 (482)
Q Consensus 424 L~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~--~~l~d~i~D~ 480 (482)
+...+++.|+.+|||+.|||++++|...+.....++|||.+++++++ .++.|.++|+
T Consensus 132 l~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~ 190 (258)
T PRK08215 132 LINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQISDE 190 (258)
T ss_pred HHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCCCCcchhhhhhccCc
Confidence 99999999999999999999999999999887888999999865543 2456777665
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=99.95 E-value=2.8e-26 Score=229.72 Aligned_cols=191 Identities=36% Similarity=0.597 Sum_probs=171.0
Q ss_pred CCCCCcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHH
Q 011577 250 GFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSS 329 (482)
Q Consensus 250 ~~~~~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~A 329 (482)
.....|.+++||++|..+|.||.++|.+|+..++. ++..|
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~----------------------------------------gd~~a 47 (285)
T TIGR02394 8 ETRVADVTQLYLREIGFKPLLTAEEEIAYARRALA----------------------------------------GDFEA 47 (285)
T ss_pred ccCcchHHHHHHHHHhccCCCCHHHHHHHHHHHHc----------------------------------------CCHHH
Confidence 34457899999999999999999999999887654 22489
Q ss_pred HHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchh
Q 011577 330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 409 (482)
Q Consensus 330 re~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~ 409 (482)
++.||..|.++|+++|++|.+++.+++||+||||||||+++++||+.+|++|+||+.|||+.++.++++++.+.+++|..
T Consensus 48 ~~~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ain~~i~~~~~~~~~p~~ 127 (285)
T TIGR02394 48 RKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVH 127 (285)
T ss_pred HHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHHHHHHHHcCCceeCcHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCCCcccccccCC
Q 011577 410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDA 480 (482)
Q Consensus 410 v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~~l~d~i~D~ 480 (482)
+...++.+.+..+.+....++.|+..|+|+.||+++..|..++..+...+|+|.++..++..++.+.+.++
T Consensus 128 ~~~~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~ 198 (285)
T TIGR02394 128 VIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADE 198 (285)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCCCCCCCcchhhhhcCC
Confidence 99999888887777777788899999999999999999999999888899999988766555555555543
No 21
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=99.94 E-value=2.4e-26 Score=227.54 Aligned_cols=153 Identities=23% Similarity=0.373 Sum_probs=135.8
Q ss_pred hcH-HHHHHHHHHHHHHHHHHHHHcc---CCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHh
Q 011577 325 SGN-SSREKLINANLRLVVHVAKQYQ---GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH 400 (482)
Q Consensus 325 ~Gd-~Are~LI~snlrLV~sIAkrY~---~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq 400 (482)
.|+ .|+++||..|+++|+++|++|. ..+.+++||+|||+||||+|+++|||++|++|+|||+||||++|.+++|++
T Consensus 19 ~~~~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~ 98 (257)
T PRK05911 19 TQEIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQ 98 (257)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhc
Confidence 455 8999999999999999999985 235689999999999999999999999999999999999999999999998
Q ss_pred cCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcC--CCccCcccCCC--CC--CCccc
Q 011577 401 SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR--MPLSMQQPVWA--DQ--DTTFQ 474 (482)
Q Consensus 401 ~r~irlP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar--~~lSLD~~i~~--d~--~~~l~ 474 (482)
. ++|+++.+.++++.++...|...+|+.|+.+|||+.||+++++|..++..++ ..+|||.++.. ++ +.++.
T Consensus 99 ~---~~pr~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~Sld~~~~~~~~~~~~~~l~ 175 (257)
T PRK05911 99 D---WVPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPCQSDDEAGLALE 175 (257)
T ss_pred C---CCCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHHhhccceeeccccCCCCCCCccccchh
Confidence 6 4899999999999999999999999999999999999999999999987664 46899998643 21 34577
Q ss_pred ccccCC
Q 011577 475 STFLDA 480 (482)
Q Consensus 475 d~i~D~ 480 (482)
|.++|+
T Consensus 176 ~~l~d~ 181 (257)
T PRK05911 176 ERIADE 181 (257)
T ss_pred hhccCC
Confidence 888775
No 22
>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=99.94 E-value=4.9e-26 Score=220.28 Aligned_cols=158 Identities=27% Similarity=0.432 Sum_probs=144.2
Q ss_pred HHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHh
Q 011577 322 ELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH 400 (482)
Q Consensus 322 ~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq 400 (482)
+++.|+ .|++.||..|.++|+++|++|.+++.+++||+||||+|||+++++||+.+|.+|.||+++||+|.|.+++|++
T Consensus 4 ~~~~gd~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~lr~~ 83 (231)
T TIGR02885 4 LAQNGDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDD 83 (231)
T ss_pred HHHcCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhC
Confidence 344556 8999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred cCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCC--Cccccccc
Q 011577 401 SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD--TTFQSTFL 478 (482)
Q Consensus 401 ~r~irlP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~--~~l~d~i~ 478 (482)
. .+++|+++.....++.++...+...+++.||.+|||+.||+++++|..++..+....|||.+++++++ .++.|.+.
T Consensus 84 ~-~i~~p~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~ 162 (231)
T TIGR02885 84 G-IIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPIYLLDQIA 162 (231)
T ss_pred C-CeECCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCCCCCcchhhhhcC
Confidence 6 78999999999999999999999999999999999999999999999999888889999999876543 24667776
Q ss_pred CC
Q 011577 479 DA 480 (482)
Q Consensus 479 D~ 480 (482)
|+
T Consensus 163 ~~ 164 (231)
T TIGR02885 163 DK 164 (231)
T ss_pred CC
Confidence 65
No 23
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=99.94 E-value=8.2e-26 Score=222.99 Aligned_cols=160 Identities=27% Similarity=0.484 Sum_probs=142.5
Q ss_pred HHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCC-CHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHH
Q 011577 318 DLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGI-SLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK 395 (482)
Q Consensus 318 eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~-d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~ 395 (482)
.+....+.|+ +++ .||+.|+|||.++|++|.+++. +.+||+|.|+|||++|+++|||++|.+|+|||..+|+++|++
T Consensus 13 ~~~~~~~~g~~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d 91 (247)
T COG1191 13 KLLEYYAEGDEEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILD 91 (247)
T ss_pred HHHHHHHhcCHHHH-HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHH
Confidence 3455556677 788 9999999999999999998887 999999999999999999999999999999999999999999
Q ss_pred HHHHhcCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcC--CCccCcccCCCCCCCcc
Q 011577 396 AIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR--MPLSMQQPVWADQDTTF 473 (482)
Q Consensus 396 ~Lrkq~r~irlP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar--~~lSLD~~i~~d~~~~l 473 (482)
++|++. .+++|+.+.+..+++..+..+|..+++|+||..|||+.|||+.++|...+.... ..+|+|..+..+++...
T Consensus 92 ~LR~~~-~v~vpR~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~d~~~ 170 (247)
T COG1191 92 YLRKND-SVKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDDDV 170 (247)
T ss_pred HHHhCC-CccCcHHHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhccccccch
Confidence 999999 999999999999999999999999999999999999999999999999998664 68999887664443334
Q ss_pred cccccC
Q 011577 474 QSTFLD 479 (482)
Q Consensus 474 ~d~i~D 479 (482)
.+.+.+
T Consensus 171 ~~~~~~ 176 (247)
T COG1191 171 DDQIEN 176 (247)
T ss_pred hhcccc
Confidence 444433
No 24
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=99.93 E-value=8.9e-25 Score=216.92 Aligned_cols=175 Identities=21% Similarity=0.334 Sum_probs=150.4
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHHHHHHHHHHHHH
Q 011577 264 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH 343 (482)
Q Consensus 264 i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~LI~snlrLV~s 343 (482)
.+++|+||.++|.+|+..++. .++..|++.|+..|.++|+.
T Consensus 6 ~~~~~~~~~~~e~~l~~~~~~---------------------------------------~~d~~a~~~l~~~y~~lv~~ 46 (268)
T PRK06288 6 SGKIPKYAQQDETELWREYKK---------------------------------------TGDPKIREYLILKYSPLVKY 46 (268)
T ss_pred cCCCccccchHHHHHHHHHHH---------------------------------------cCCHHHHHHHHHHHHHHHHH
Confidence 378999999999999987654 12337999999999999999
Q ss_pred HHHHcc-C--CCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHHHHHHHHH
Q 011577 344 VAKQYQ-G--RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEA 420 (482)
Q Consensus 344 IAkrY~-~--~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~e~l~kI~ka 420 (482)
+|++|. + .+.+++||+||||+|||+++++||+.+|++|+||+++||||.|.+++|+.. ++|+++.....++.++
T Consensus 47 ~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i~d~~R~~~---~~p~~~~~~~~~i~~~ 123 (268)
T PRK06288 47 VAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSID---WIPRSVRQKARQIERA 123 (268)
T ss_pred HHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC---ccCHHHHHHHHHHHHH
Confidence 999986 2 567899999999999999999999998999999999999999999999754 6899999989999999
Q ss_pred HHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHc--CCCccCcccCCCCC---CCcccccccCC
Q 011577 421 KRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQ---DTTFQSTFLDA 480 (482)
Q Consensus 421 ~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~a--r~~lSLD~~i~~d~---~~~l~d~i~D~ 480 (482)
...|...+++.||.+|||+.+|++.+.|..++... ...+|||.++..++ ..++.+.++|+
T Consensus 124 ~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~l~~~~~~~ 188 (268)
T PRK06288 124 IAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGDEVSLMDTLESP 188 (268)
T ss_pred HHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhccCCCcccchhhhhccCC
Confidence 99999999999999999999999999999998754 45799999874222 23566666554
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=99.93 E-value=9.6e-25 Score=210.53 Aligned_cols=154 Identities=27% Similarity=0.465 Sum_probs=140.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc
Q 011577 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 406 (482)
Q Consensus 327 d~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irl 406 (482)
..|++.||..|.++|+++|++|.+++.+++||+|||++|||+|+++||+.+|.+|+||+++||+|.|.++++++...+++
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 36999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCC--CccCcccCCCCC--CCcccccccCC
Q 011577 407 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRM--PLSMQQPVWADQ--DTTFQSTFLDA 480 (482)
Q Consensus 407 P~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~--~lSLD~~i~~d~--~~~l~d~i~D~ 480 (482)
|.++.....+++++...+...+++.|+.+|||+.||+++++|..++..... .+|||.++.+++ +.++.|.++++
T Consensus 82 ~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~d~~~~~ 159 (227)
T TIGR02980 82 PRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIEDDDGDPIALLDTLGDE 159 (227)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCCCCCCCcccccccCCc
Confidence 999999999999999999999999999999999999999999998886654 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=99.93 E-value=3.1e-24 Score=211.06 Aligned_cols=144 Identities=23% Similarity=0.364 Sum_probs=134.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc
Q 011577 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 406 (482)
Q Consensus 327 d~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irl 406 (482)
..|+++||..|.++|+.+|++|.+++.+++||+||||+|||+++++||++.|.+|.||+++||+|.|.+++++....+++
T Consensus 28 ~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~iri 107 (255)
T TIGR02941 28 GEAQEKLVDHYQNLVYSIAYKYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEIKRYLRDKTWSVHV 107 (255)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHHHHHHHHHcCCCcCC
Confidence 38999999999999999999999999999999999999999999999999999999999999999999999999888999
Q ss_pred chhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHc--CCCccCcccCCCCCC
Q 011577 407 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQD 470 (482)
Q Consensus 407 P~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~a--r~~lSLD~~i~~d~~ 470 (482)
|.++.....++.++...+...+++.|+.+|||+.||++.+.+..++... ...+|||.+++.+++
T Consensus 108 ~~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~~~ 173 (255)
T TIGR02941 108 PRRIKELGPKIKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSD 173 (255)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCCCC
Confidence 9999999999999999999999999999999999999999999887654 467999999875543
No 27
>PRK05572 sporulation sigma factor SigF; Validated
Probab=99.92 E-value=2e-23 Score=205.37 Aligned_cols=177 Identities=27% Similarity=0.425 Sum_probs=154.8
Q ss_pred cCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHHHHHHHHHHHH
Q 011577 263 GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVV 342 (482)
Q Consensus 263 ~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~LI~snlrLV~ 342 (482)
.-+..|.||.+++.+|+..++. ++..|++.||..|.++|+
T Consensus 7 ~~~~~~~l~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~~~y~~~v~ 46 (252)
T PRK05572 7 NKKKKPQLKDEENKELIKKSQD----------------------------------------GDQEARDTLVEKNLRLVW 46 (252)
T ss_pred cCcCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHHH
Confidence 3467799999988888765432 224899999999999999
Q ss_pred HHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHHHHHHHHHHH
Q 011577 343 HVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKR 422 (482)
Q Consensus 343 sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~e~l~kI~ka~~ 422 (482)
.+|++|.+++.+++||+||||+++|+++++|++.+|.+|.||+++||+|.|.+++|+.. .+++|+.+.....++.++..
T Consensus 47 ~~a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~~lr~~~-~~r~~~~~~~~~~~~~~~~~ 125 (252)
T PRK05572 47 SVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANKIRKDKD 125 (252)
T ss_pred HHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CCCCCHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999988889999999999999999999885 78999999999999999999
Q ss_pred HHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCC--CcccccccCC
Q 011577 423 LYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD--TTFQSTFLDA 480 (482)
Q Consensus 423 eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~--~~l~d~i~D~ 480 (482)
.+...+++.|+..|||+.||++++.|..++.......||+.++.+++. .++.|.++++
T Consensus 126 ~l~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~~ 185 (252)
T PRK05572 126 ELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGDPITLLDQIADQ 185 (252)
T ss_pred HHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCcccCCCCcchhhhhcCCC
Confidence 998888899999999999999999999998887888999998865443 2345555554
No 28
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=99.91 E-value=1.8e-23 Score=205.49 Aligned_cols=152 Identities=22% Similarity=0.310 Sum_probs=135.8
Q ss_pred HHHHHHH-HhhcH-HHHHHHHHHHHHHHHHHHHHccC---CCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHH
Q 011577 316 CRDLKSE-LHSGN-SSREKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVR 390 (482)
Q Consensus 316 d~eLi~~-l~~Gd-~Are~LI~snlrLV~sIAkrY~~---~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIR 390 (482)
+.+|+.+ ..+|+ .|++.||..|.++|+.+|++|.+ ++.+.+||+||||+|||+++++||+.+|.+|+||+++||+
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 4556666 34456 89999999999999999999965 6889999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhcCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHH--HcCCCccCcccCCCC
Q 011577 391 QTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF--ITRMPLSMQQPVWAD 468 (482)
Q Consensus 391 naI~~~Lrkq~r~irlP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~--~ar~~lSLD~~i~~d 468 (482)
|.|++++|++. ++|..+.+.+.+++++...+.+.+++.|+.+|||+.||+++++|+.++. .....+|||.++.++
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 6999999999999999999999999999999999999999999999986 345789999998654
Q ss_pred CC
Q 011577 469 QD 470 (482)
Q Consensus 469 ~~ 470 (482)
++
T Consensus 165 ~~ 166 (251)
T PRK07670 165 DD 166 (251)
T ss_pred CC
Confidence 43
No 29
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=99.91 E-value=6e-23 Score=202.13 Aligned_cols=143 Identities=24% Similarity=0.375 Sum_probs=132.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc
Q 011577 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 406 (482)
Q Consensus 327 d~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irl 406 (482)
..|++.||..|.++|+++|++|.+++.+++||+||||+|||+++++||+.+|.+|.||+++||+|.|.+++|++...+++
T Consensus 28 ~~a~~~l~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~~~i 107 (257)
T PRK08583 28 EEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVHV 107 (257)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHHHHHHHhcCCCcCC
Confidence 38999999999999999999999999999999999999999999999999888999999999999999999999989999
Q ss_pred chhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHc--CCCccCcccCCCCC
Q 011577 407 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQ 469 (482)
Q Consensus 407 P~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~a--r~~lSLD~~i~~d~ 469 (482)
|+++....+++..+...+...+++.|+.+|+|+.+|++.+.|...+... ...+|+|.+++.++
T Consensus 108 ~r~~~~~~~~~~~~~~~~~~~~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~~ 172 (257)
T PRK08583 108 PRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADS 172 (257)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCCC
Confidence 9999999999999999998888899999999999999999998887654 35789999886544
No 30
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=99.90 E-value=1.5e-22 Score=197.61 Aligned_cols=138 Identities=22% Similarity=0.310 Sum_probs=123.6
Q ss_pred HHHHHHHHHHHHHHHHHHHccC---CCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcc
Q 011577 329 SREKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR 405 (482)
Q Consensus 329 Are~LI~snlrLV~sIAkrY~~---~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~ir 405 (482)
-...|+..|+++|.++|++|.+ .+.+.+||+|||+||||+|+++||+.+| +|+||++|||||+|.++|++.. +
T Consensus 16 ~~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~il~~lr~~~---~ 91 (231)
T PRK12427 16 EEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELRELD---W 91 (231)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHHHHhcC---C
Confidence 4457899999999999999874 4679999999999999999999998665 8999999999999999999865 5
Q ss_pred cchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH--cCCCccCcccCCCCCC
Q 011577 406 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI--TRMPLSMQQPVWADQD 470 (482)
Q Consensus 406 lP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~--ar~~lSLD~~i~~d~~ 470 (482)
.|+.+.....+++++...+.+.+|+.|+.+|||+.||+++++|..++.. +...+|||.+++++++
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 7999999999999999999999999999999999999999999998764 4568999999876554
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=99.89 E-value=2.7e-22 Score=193.52 Aligned_cols=143 Identities=20% Similarity=0.362 Sum_probs=126.6
Q ss_pred HHHHHHHHHHHHHHHccC---CCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchh
Q 011577 333 LINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 409 (482)
Q Consensus 333 LI~snlrLV~sIAkrY~~---~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~ 409 (482)
||..|.++|+++|++|.+ ++.+++||+||||+|||+++++||+.+|++|+||+++||+|.|++++|+.. ++|..
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 688999999999999986 789999999999999999999999999999999999999999999999865 68999
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHc--CCCccCcccCCCC-CCCccccccc
Q 011577 410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWAD-QDTTFQSTFL 478 (482)
Q Consensus 410 v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~a--r~~lSLD~~i~~d-~~~~l~d~i~ 478 (482)
+...++++.++...+...+++.|+.+|||+.||++++.|..++..+ ...+|+|.++.++ +..++.+.++
T Consensus 78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~ 149 (224)
T TIGR02479 78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLIDRIE 149 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcccCCCccchhhhhcc
Confidence 9999999999999999999999999999999999999999998644 4568898876543 2334555554
No 32
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=99.86 E-value=1e-20 Score=184.10 Aligned_cols=143 Identities=21% Similarity=0.389 Sum_probs=127.8
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHHcc---CCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhc
Q 011577 325 SGNSSREKLINANLRLVVHVAKQYQ---GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS 401 (482)
Q Consensus 325 ~Gd~Are~LI~snlrLV~sIAkrY~---~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~ 401 (482)
.|.-++++||..|.++|+.+|++|. +++.+++||+||||+|||+++++||+.+|.+|+||+++||+|.|.+++|++.
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 4667999999999999999999997 6789999999999999999999999998999999999999999999999976
Q ss_pred CCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHc--CCCccCcccCCCCCC
Q 011577 402 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQD 470 (482)
Q Consensus 402 r~irlP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~a--r~~lSLD~~i~~d~~ 470 (482)
++|..+.....++.++...+...+++.|+.+|||+.||+++++|..++... ...+|++.+++++++
T Consensus 85 ---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~~ 152 (236)
T PRK06986 85 ---WVPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGD 152 (236)
T ss_pred ---CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccccCCCc
Confidence 368888888788888888888889999999999999999999999988743 356789988765443
No 33
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=99.85 E-value=1.7e-20 Score=182.45 Aligned_cols=162 Identities=22% Similarity=0.345 Sum_probs=127.2
Q ss_pred HHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHHHHH
Q 011577 256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 335 (482)
Q Consensus 256 ~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~LI~ 335 (482)
.|..|+.+++..|+||+++|..|+..++. ++..|++.|+.
T Consensus 17 ~~~~~~~~~~~~~~~~~~~e~~l~~~~~~----------------------------------------gd~~a~~~l~~ 56 (233)
T PRK05803 17 FLVSYVKNNSFPQPLSEEEERKYLELMKE----------------------------------------GDEEARNILIE 56 (233)
T ss_pred HHHHHHHHhcccCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHH
Confidence 57789999999999999999888775543 23489999999
Q ss_pred HHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCc---cc------
Q 011577 336 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI---RL------ 406 (482)
Q Consensus 336 snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~i---rl------ 406 (482)
.|.++|+++|.+|.+++.+++||+|||||++|+++++||+++|.+|.||+++|++|.+++++|+..+.. .+
T Consensus 57 ~y~~~l~~~a~~~~~~~~daeDlvQE~fi~l~~~~~~f~~~~~~~f~~wl~~i~rn~~id~~Rk~~~~~~~~~~~~~~~~ 136 (233)
T PRK05803 57 RNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRNLKKTKKEVSLQDPIGV 136 (233)
T ss_pred HhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHHhccccCCCccccccC
Confidence 999999999999999999999999999999999999999988889999999999999999999765321 00
Q ss_pred -------------------chhH-H--HHHHHHHHHHHHHH--------Hhc----CCCCcHHHHHHHhCCCHHHHHHHH
Q 011577 407 -------------------PENI-Y--TLLSKVLEAKRLYI--------QEG----NHSPDKEDLARRVGITVEKLERLI 452 (482)
Q Consensus 407 -------------------P~~v-~--e~l~kI~ka~~eL~--------~e~----gr~pS~eEIAe~LGIS~etVk~~L 452 (482)
|... . .....+.++...|. ..+ ..+.|++|||+.||+|.++|+..+
T Consensus 137 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~ 216 (233)
T PRK05803 137 DKEGNEISLIDILGSEEDDVIEQVELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIE 216 (233)
T ss_pred CCCcCcccHHHHccCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHH
Confidence 0000 0 11112333332221 112 356799999999999999999998
Q ss_pred HHcCC
Q 011577 453 FITRM 457 (482)
Q Consensus 453 ~~ar~ 457 (482)
++++.
T Consensus 217 ~rA~~ 221 (233)
T PRK05803 217 KRALK 221 (233)
T ss_pred HHHHH
Confidence 88764
No 34
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=99.78 E-value=4.3e-18 Score=165.23 Aligned_cols=141 Identities=25% Similarity=0.392 Sum_probs=108.5
Q ss_pred HHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHH
Q 011577 318 DLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKA 396 (482)
Q Consensus 318 eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~ 396 (482)
.|+.+++.|+ .|++.|+..|.++|+.+|++|.+++.+++||+||+|+++|+++++|++..+++|.||++++++|.|+++
T Consensus 41 ~L~~~~~~gd~~af~~l~~~y~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~~d~ 120 (234)
T PRK08301 41 YLLNKLPKGDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMY 120 (234)
T ss_pred HHHHHHHccCHHHHHHHHHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHH
Confidence 3444444556 899999999999999999999999999999999999999999999999888899999999999999999
Q ss_pred HHHhcCCcc---c--c--------------------h---hHH---HHHHHHHHHHHHHHH--------hc----CCCCc
Q 011577 397 IFQHSRTIR---L--P--------------------E---NIY---TLLSKVLEAKRLYIQ--------EG----NHSPD 433 (482)
Q Consensus 397 Lrkq~r~ir---l--P--------------------~---~v~---e~l~kI~ka~~eL~~--------e~----gr~pS 433 (482)
+|++.+... + + . ... .....+.++...|+. .+ ..+.|
T Consensus 121 lRk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~v~~L~y~l~~~eg~s 200 (234)
T PRK08301 121 LRRNNKVKAEVSFDEPLNIDWDGNELLLSDVLGTDNDIIYKDIEDEVDRKLLKKALKKLSDREKQIMELRFGLNGGEEKT 200 (234)
T ss_pred HHHHhccccccccccccccccCCCcccHHHhccCcccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCC
Confidence 997654211 0 0 0 000 011123334333321 12 35889
Q ss_pred HHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 434 KEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 434 ~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
++|||+.||+|+++|+..+++++..
T Consensus 201 ~~EIA~~lgis~~tVk~~~~rA~~~ 225 (234)
T PRK08301 201 QKEVADMLGISQSYISRLEKRIIKR 225 (234)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 9999999999999999999988653
No 35
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=99.78 E-value=5.2e-18 Score=164.60 Aligned_cols=134 Identities=25% Similarity=0.436 Sum_probs=104.5
Q ss_pred hhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcC
Q 011577 324 HSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR 402 (482)
Q Consensus 324 ~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r 402 (482)
+.|+ .|++.|+..|.++|+++|.+|.++..+++||+||+|+++|+++++|+++++.+|.||+++|++|.|++++|+..+
T Consensus 43 ~~gd~~af~~l~~~y~~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~~d~~Rk~~r 122 (227)
T TIGR02846 43 KEGDEEARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEILMHLRALKK 122 (227)
T ss_pred HcCCHHHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHHHHHHHHHhc
Confidence 3455 899999999999999999999999999999999999999999999999888899999999999999999998754
Q ss_pred Ccc-c----------------------c-----hh---HHHHHHHHHHHHHHHH--------Hhc----CCCCcHHHHHH
Q 011577 403 TIR-L----------------------P-----EN---IYTLLSKVLEAKRLYI--------QEG----NHSPDKEDLAR 439 (482)
Q Consensus 403 ~ir-l----------------------P-----~~---v~e~l~kI~ka~~eL~--------~e~----gr~pS~eEIAe 439 (482)
... . + .. .......+.+++..|. ..+ ..+.|++|||+
T Consensus 123 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~il~l~y~~~~~e~~S~~EIAe 202 (227)
T TIGR02846 123 TKGEVSLQDPIGVDKEGNEISLIDILGSDGDSVIEQVELNLEIKKLYKKLSVLDGREREVIEMRYGLGDGRRKTQREIAK 202 (227)
T ss_pred cccceeccccccCCcccCcccHHHHhcCCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHcCCCCCCcCHHHHHH
Confidence 211 0 0 00 0011122333333222 112 25789999999
Q ss_pred HhCCCHHHHHHHHHHcCC
Q 011577 440 RVGITVEKLERLIFITRM 457 (482)
Q Consensus 440 ~LGIS~etVk~~L~~ar~ 457 (482)
+||+++++|+.++++++.
T Consensus 203 ~lgis~~tV~~~~~rAl~ 220 (227)
T TIGR02846 203 ILGISRSYVSRIEKRALM 220 (227)
T ss_pred HHCCCHHHHHHHHHHHHH
Confidence 999999999999988764
No 36
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=99.76 E-value=1.1e-17 Score=158.28 Aligned_cols=146 Identities=22% Similarity=0.286 Sum_probs=113.4
Q ss_pred cCCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHH
Q 011577 313 GLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ 391 (482)
Q Consensus 313 gmdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRn 391 (482)
.+++..|+..++.|+ .|++.|+..|.++|+.+|++|.++..+++||+||+|++||+++.+||+.+|.+|.||++.+++|
T Consensus 8 ~~~~~~l~~~~~~~d~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~~n 87 (208)
T PRK08295 8 ELEDEELVELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITR 87 (208)
T ss_pred CCChHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHH
Confidence 456778888888888 8999999999999999999999999999999999999999999999998878999999999999
Q ss_pred HHHHHHHHhcCCccc--------------------------------chh-H--HHHH--------HHHHHHHHHHHHhc
Q 011577 392 TIRKAIFQHSRTIRL--------------------------------PEN-I--YTLL--------SKVLEAKRLYIQEG 428 (482)
Q Consensus 392 aI~~~Lrkq~r~irl--------------------------------P~~-v--~e~l--------~kI~ka~~eL~~e~ 428 (482)
.+.+++++..+..+. |.. + .... ..+....+.+...+
T Consensus 88 ~~~d~~r~~~r~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~~r~vl~l~ 167 (208)
T PRK08295 88 QIITAIKTANRQKHIPLNSYVSLDKPIYDEESDRTLLDVISEAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLELY 167 (208)
T ss_pred HHHHHHHHhhhhccccccceeecCCcccCCccchhHHHHhcCcccCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence 999999864332111 000 0 0011 11111112221114
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 429 NHSPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
..+.+++|||+.||+|+++|+..+++++..
T Consensus 168 ~e~~s~~EIA~~lgis~~tV~~~l~rar~~ 197 (208)
T PRK08295 168 LDGKSYQEIAEELNRHVKSIDNALQRVKRK 197 (208)
T ss_pred HccCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 457899999999999999999999988754
No 37
>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=99.76 E-value=1.1e-17 Score=156.74 Aligned_cols=145 Identities=22% Similarity=0.288 Sum_probs=112.8
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011577 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (482)
Q Consensus 314 mdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRna 392 (482)
|++.+|+..++.|+ .|++.||..|.+.|+.+|+++.++..+++||+||+|+++|+++.+|++..+..|.||++.+|++.
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 56788999999988 89999999999999999999999999999999999999999999999987779999999999999
Q ss_pred HHHHHHHhcCCcc--------------------------------cchhH---HHHHHHHHHHHHH--------HHHhcC
Q 011577 393 IRKAIFQHSRTIR--------------------------------LPENI---YTLLSKVLEAKRL--------YIQEGN 429 (482)
Q Consensus 393 I~~~Lrkq~r~ir--------------------------------lP~~v---~e~l~kI~ka~~e--------L~~e~g 429 (482)
|++++++..+..+ -|... .+....+.++... +...+-
T Consensus 84 ~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~~~~~ 163 (198)
T TIGR02859 84 IITAIKTATRQKHIPLNSYVSLNKPIYDEESDRTLLDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVLQSYL 163 (198)
T ss_pred HHHHHHHHHHhcccchhhhcCcccccccccccchHHHHhhccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence 9888874311100 01110 0111112223322 222233
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 430 HSPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
.+.|++|||+.||+|+++|+..+++++..
T Consensus 164 ~~~s~~eIA~~l~~s~~tV~~~l~r~r~~ 192 (198)
T TIGR02859 164 DGKSYQEIACDLNRHVKSIDNALQRVKRK 192 (198)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 47899999999999999999999988754
No 38
>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=99.75 E-value=1.5e-17 Score=161.92 Aligned_cols=128 Identities=19% Similarity=0.281 Sum_probs=109.0
Q ss_pred HHhhcHHHHHHHHHHHHHHHHHHHHHccCCC--CCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHH
Q 011577 322 ELHSGNSSREKLINANLRLVVHVAKQYQGRG--ISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQ 399 (482)
Q Consensus 322 ~l~~Gd~Are~LI~snlrLV~sIAkrY~~~g--~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrk 399 (482)
.++.|+..+++||..|.|+|.++|++|.++. .+.+|++|+|+||||+|+++||+++|.+|.|||.+||+++|++++|+
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 4567886699999999999999999998775 58999999999999999999999999999999999999999999999
Q ss_pred hcC---CcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHH------hCCCHHHHH
Q 011577 400 HSR---TIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARR------VGITVEKLE 449 (482)
Q Consensus 400 q~r---~irlP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~------LGIS~etVk 449 (482)
..+ .+++|+...+...++..+..++....++.++.+||+.. .||+.+.+-
T Consensus 83 ~~k~~~~v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~~~~~L~~~gi~~~dLv 141 (218)
T TIGR02895 83 NQKYQNLLYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILEYKKLLKQFGIEFVELV 141 (218)
T ss_pred cccccCeeeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcCCcHHHHh
Confidence 873 45788766665667777777888888889999999864 377766553
No 39
>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=99.75 E-value=2.1e-17 Score=161.02 Aligned_cols=143 Identities=24% Similarity=0.371 Sum_probs=112.8
Q ss_pred CHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHH
Q 011577 315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 393 (482)
Q Consensus 315 dd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI 393 (482)
.+.+|+..+..|+ .|++.|+..|.+.|+.+|++|.+++.+++||+||+|+++|+++++|++..+++|.||++++++|.+
T Consensus 38 ~~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~ 117 (234)
T TIGR02835 38 EEEALLQKLTQGDESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEI 117 (234)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHH
Confidence 3566777888877 899999999999999999999999999999999999999999999998877889999999999999
Q ss_pred HHHHHHhcCCcc-cc----------------------h-----hH---HHHHHHHHHHHHHHHH--------hc----CC
Q 011577 394 RKAIFQHSRTIR-LP----------------------E-----NI---YTLLSKVLEAKRLYIQ--------EG----NH 430 (482)
Q Consensus 394 ~~~Lrkq~r~ir-lP----------------------~-----~v---~e~l~kI~ka~~eL~~--------e~----gr 430 (482)
++++|+..+... .+ . .. ......+.+++..|.. .+ ..
T Consensus 118 ~d~~Rk~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~e 197 (234)
T TIGR02835 118 LMYLRRNNKTRSEVSFDEPLNVDWDGNELLLSDVLGTDSDIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGT 197 (234)
T ss_pred HHHHHHhccccCcccccccccCCCCCCcchHHHhcCCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCC
Confidence 999998664211 00 0 00 0011224444433321 12 25
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577 431 SPDKEDLARRVGITVEKLERLIFITRM 457 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (482)
+.|++|||+.||+|+++|+..+++++.
T Consensus 198 g~s~~EIA~~Lgis~~tV~~~l~ra~~ 224 (234)
T TIGR02835 198 EKTQKEVADMLGISQSYISRLEKRILK 224 (234)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 789999999999999999999988754
No 40
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=99.73 E-value=3.4e-17 Score=152.89 Aligned_cols=145 Identities=17% Similarity=0.178 Sum_probs=114.5
Q ss_pred cCCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHH
Q 011577 313 GLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ 391 (482)
Q Consensus 313 gmdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRn 391 (482)
.++++.|+..++.|+ .|++.|+..|.++|+.+|++|.+++.+++|++||+|+++|+++.+|++. +..|.+|++.+++|
T Consensus 4 ~~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n 82 (186)
T PRK05602 4 ADPDEELLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLN 82 (186)
T ss_pred cccHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHH
Confidence 356788999988888 8999999999999999999999999999999999999999999999975 45899999999999
Q ss_pred HHHHHHHHhcCCcc--c---------chhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHH
Q 011577 392 TIRKAIFQHSRTIR--L---------PENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLE 449 (482)
Q Consensus 392 aI~~~Lrkq~r~ir--l---------P~~v---~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk 449 (482)
.+.+++|++..... + |... .+....+.++...|. ..+..+.+++|||+.||+|.++|+
T Consensus 83 ~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~ 162 (186)
T PRK05602 83 LCYDRLRRRREVPVEDAPDVPDPAPGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALE 162 (186)
T ss_pred HHHHHHHhcCCCCcccccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHhcCCCHHHHHHHhCcCHHHHH
Confidence 99999997754211 0 1110 011122333333222 223347899999999999999999
Q ss_pred HHHHHcCCC
Q 011577 450 RLIFITRMP 458 (482)
Q Consensus 450 ~~L~~ar~~ 458 (482)
..+++++..
T Consensus 163 ~~l~Rar~~ 171 (186)
T PRK05602 163 SLLARGRRA 171 (186)
T ss_pred HHHHHHHHH
Confidence 999998754
No 41
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=99.72 E-value=9.3e-17 Score=150.91 Aligned_cols=143 Identities=15% Similarity=0.188 Sum_probs=114.1
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011577 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (482)
Q Consensus 314 mdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRna 392 (482)
+++..|+..++.|+ .|++.|+..|.+.|+++|.++.++..+++|++||+|+++|+++++|++. ..|.+|++++++|.
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 56788999999888 8999999999999999999999999999999999999999999999974 46999999999999
Q ss_pred HHHHHHHhcCCcccc-----------------hhH---HHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCC
Q 011577 393 IRKAIFQHSRTIRLP-----------------ENI---YTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGIT 444 (482)
Q Consensus 393 I~~~Lrkq~r~irlP-----------------~~v---~e~l~kI~ka~~eL~~e--------~gr~pS~eEIAe~LGIS 444 (482)
+++++|+..+....+ ... ......+.++...|... +..+.+++|||+.||+|
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 999999876533221 000 01112244444443322 23467999999999999
Q ss_pred HHHHHHHHHHcCCC
Q 011577 445 VEKLERLIFITRMP 458 (482)
Q Consensus 445 ~etVk~~L~~ar~~ 458 (482)
+++|+..+++++..
T Consensus 169 ~~tV~~~l~ra~~~ 182 (194)
T PRK12513 169 EETVKSRLRYALQK 182 (194)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999988754
No 42
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=99.71 E-value=9.3e-17 Score=151.51 Aligned_cols=143 Identities=8% Similarity=0.067 Sum_probs=111.8
Q ss_pred CHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHH
Q 011577 315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 393 (482)
Q Consensus 315 dd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI 393 (482)
++.+|+..+..|+ .|++.|+..|.++|+.+|.+|.++..+++|++||+|+++|+++++||+.+| .|.+|++.+++|.+
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 4567888888888 899999999999999999999999999999999999999999999998655 79999999999999
Q ss_pred HHHHHHhcCCccc---------------chh-H--HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHH
Q 011577 394 RKAIFQHSRTIRL---------------PEN-I--YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEK 447 (482)
Q Consensus 394 ~~~Lrkq~r~irl---------------P~~-v--~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~et 447 (482)
++++|++.+..+. +.. + .+....+.+++..|. ..+..+.+++|||+.||+++++
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 9999986532110 000 0 011122333333221 2233478999999999999999
Q ss_pred HHHHHHHcCCC
Q 011577 448 LERLIFITRMP 458 (482)
Q Consensus 448 Vk~~L~~ar~~ 458 (482)
|+..+++++..
T Consensus 175 Vk~~l~ra~~~ 185 (194)
T PRK09646 175 VKTRMRDGLIR 185 (194)
T ss_pred HHHHHHHHHHH
Confidence 99999988754
No 43
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=99.71 E-value=1.2e-16 Score=150.29 Aligned_cols=143 Identities=15% Similarity=0.229 Sum_probs=111.2
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCC---CCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHH
Q 011577 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRG---ISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWV 389 (482)
Q Consensus 314 mdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g---~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wI 389 (482)
++++.|+..+..|+ .|++.|+..|.++|+.++.++.+++ .+++|++||+++++|+++++|++..+ .|.||++.++
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 67788999999988 8999999999999999999998753 57999999999999999999987544 7999999999
Q ss_pred HHHHHHHHHHhcCCcccc-------------hh----------HHHHHHHHHHHHHHHH-HhcCCCCcHHHHHHHhCCCH
Q 011577 390 RQTIRKAIFQHSRTIRLP-------------EN----------IYTLLSKVLEAKRLYI-QEGNHSPDKEDLARRVGITV 445 (482)
Q Consensus 390 RnaI~~~Lrkq~r~irlP-------------~~----------v~e~l~kI~ka~~eL~-~e~gr~pS~eEIAe~LGIS~ 445 (482)
+|.+++++|++.+..... .. +...+.++....+.+. ..+..+.+++|||+.||+|.
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 999999999876432211 00 1111222222222221 12334789999999999999
Q ss_pred HHHHHHHHHcCC
Q 011577 446 EKLERLIFITRM 457 (482)
Q Consensus 446 etVk~~L~~ar~ 457 (482)
.+|+..+++++.
T Consensus 162 ~~V~~~l~Ra~~ 173 (189)
T PRK06811 162 SAIDNRLSRGRK 173 (189)
T ss_pred HHHHHHHHHHHH
Confidence 999999998864
No 44
>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=99.70 E-value=1.8e-16 Score=145.62 Aligned_cols=143 Identities=14% Similarity=0.161 Sum_probs=113.2
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011577 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (482)
Q Consensus 314 mdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRna 392 (482)
|++++|+..+..|+ .|++.|+..|.+.|++++.++.++..+++|++||+|+.+|+.+++|++. ..|.+|++.+++|.
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 45778888888888 8999999999999999999999999999999999999999999999875 36999999999999
Q ss_pred HHHHHHHhcCCcccch-----------------hHHHHHHHHHHHHHHHH-HhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 393 IRKAIFQHSRTIRLPE-----------------NIYTLLSKVLEAKRLYI-QEGNHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 393 I~~~Lrkq~r~irlP~-----------------~v~e~l~kI~ka~~eL~-~e~gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
+++++|+..+...++. .+...+.++....+++. ..+..+.+++|||+.||+|+++|+..+.+
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 9999998765432211 01122222222222221 22334789999999999999999999998
Q ss_pred cCCC
Q 011577 455 TRMP 458 (482)
Q Consensus 455 ar~~ 458 (482)
++..
T Consensus 159 a~~~ 162 (169)
T TIGR02954 159 ALKK 162 (169)
T ss_pred HHHH
Confidence 8654
No 45
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=99.70 E-value=2e-16 Score=147.36 Aligned_cols=144 Identities=14% Similarity=0.118 Sum_probs=112.4
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011577 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (482)
Q Consensus 314 mdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRna 392 (482)
+++.+|+..++.|+ .|++.|+..|.+.|+.++++|.+++.+++|++||+|+++|+++++|++.. ..|.+|++++++|.
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 46788888888888 89999999999999999999999999999999999999999999998754 36999999999999
Q ss_pred HHHHHHHhcCCcc-c------------c-----hhHHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHH
Q 011577 393 IRKAIFQHSRTIR-L------------P-----ENIYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVE 446 (482)
Q Consensus 393 I~~~Lrkq~r~ir-l------------P-----~~v~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~e 446 (482)
+++++|+..+... + + .........+.++...|. ..+..+.+++|||+.||++++
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 9999998653211 0 0 000011112333333322 223347899999999999999
Q ss_pred HHHHHHHHcCCC
Q 011577 447 KLERLIFITRMP 458 (482)
Q Consensus 447 tVk~~L~~ar~~ 458 (482)
+|+..+++++..
T Consensus 167 ~V~~~l~ra~~~ 178 (186)
T PRK13919 167 TLKTRARRALSR 178 (186)
T ss_pred HHHHHHHHHHHH
Confidence 999999988754
No 46
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=99.69 E-value=1.7e-16 Score=147.13 Aligned_cols=141 Identities=12% Similarity=0.189 Sum_probs=109.6
Q ss_pred HHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHH
Q 011577 316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR 394 (482)
Q Consensus 316 d~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~ 394 (482)
+++|+..++.|+ .|+++|+..|.++|+.+|.+|.+++.+++|++||+|+++|+++.+|++.. .|.+|++.+++|.++
T Consensus 5 ~~~li~~~~~gd~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~ 82 (187)
T TIGR02948 5 IKKRIKEVRKGDENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQR--KFSTWLYRIATNLTI 82 (187)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHHH
Confidence 456777888888 89999999999999999999999999999999999999999999999864 699999999999999
Q ss_pred HHHHHhcCCccc----------------------chhH-H--HHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHh
Q 011577 395 KAIFQHSRTIRL----------------------PENI-Y--TLLSKVLEAKRLYI--------QEGNHSPDKEDLARRV 441 (482)
Q Consensus 395 ~~Lrkq~r~irl----------------------P~~v-~--e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~L 441 (482)
+++|+..+.... |... . +....+.++...|. ..+..+.+++|||+.|
T Consensus 83 ~~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l 162 (187)
T TIGR02948 83 DRLRKRKPDFYLDDEVQGTDGLTMESQLAADEAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKYMEDLSLKEISEIL 162 (187)
T ss_pred HHHHhhcccccccccccCccccccccccccCcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhHHhcCCCHHHHHHHH
Confidence 999986542110 0000 0 01112333333221 1133467999999999
Q ss_pred CCCHHHHHHHHHHcCCC
Q 011577 442 GITVEKLERLIFITRMP 458 (482)
Q Consensus 442 GIS~etVk~~L~~ar~~ 458 (482)
|+++++|+..+++++..
T Consensus 163 gis~~~v~~~l~Rar~~ 179 (187)
T TIGR02948 163 DLPVGTVKTRIHRGREA 179 (187)
T ss_pred CCCHHHHHHHHHHHHHH
Confidence 99999999999988754
No 47
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=99.69 E-value=3e-16 Score=147.20 Aligned_cols=145 Identities=13% Similarity=0.081 Sum_probs=114.2
Q ss_pred hcCCHHHHHHHHhh---cH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHH
Q 011577 312 IGLSCRDLKSELHS---GN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYW 387 (482)
Q Consensus 312 ~gmdd~eLi~~l~~---Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~ 387 (482)
..+++++|+..++. |+ .|++.|+..|.+.|+.+|.+|.++..+++|++||+|++||+++++|++. ..|.+|+++
T Consensus 6 ~~~~~~~li~~~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~~~~~~~~~--~~~~~wl~~ 83 (188)
T PRK09640 6 RELNDEELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGK--SKFKTWLYS 83 (188)
T ss_pred CCCCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHHHhcCC--CcchHHHHH
Confidence 45778889988885 35 8999999999999999999999999999999999999999999999863 479999999
Q ss_pred HHHHHHHHHHHHhcCCcccc-h-----------h---HHHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCC
Q 011577 388 WVRQTIRKAIFQHSRTIRLP-E-----------N---IYTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGIT 444 (482)
Q Consensus 388 wIRnaI~~~Lrkq~r~irlP-~-----------~---v~e~l~kI~ka~~eL~~e--------~gr~pS~eEIAe~LGIS 444 (482)
+++|.+++++|+..+..... . . ..+....+.++...|... +..+.+++|||+.||||
T Consensus 84 ia~n~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~lgis 163 (188)
T PRK09640 84 ITYNECITQYRKERRKRRLMDALSLDPLEEASEEKAPKPEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMG 163 (188)
T ss_pred HHHHHHHHHHHHhcccccCcchhhhcccccccccccccHHHHHHHHHHHHhcChhheeeeeeHHhcCCCHHHHHHHHCCC
Confidence 99999999999765322211 0 0 011123344444444332 22367999999999999
Q ss_pred HHHHHHHHHHcCCC
Q 011577 445 VEKLERLIFITRMP 458 (482)
Q Consensus 445 ~etVk~~L~~ar~~ 458 (482)
.++|+..+++++..
T Consensus 164 ~~tV~~~l~Ra~~~ 177 (188)
T PRK09640 164 LSATKMRYKRALDK 177 (188)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999988653
No 48
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=99.69 E-value=3.5e-16 Score=146.48 Aligned_cols=141 Identities=18% Similarity=0.213 Sum_probs=108.3
Q ss_pred HHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCC----CCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHH
Q 011577 317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGR----GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ 391 (482)
Q Consensus 317 ~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~----g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRn 391 (482)
..|+..+..|+ .|++.|+..|.+.|+.+|.++.++ +.+++|++||+|++||+++.+|++. +..|.+|++.+++|
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 45778888888 899999999999999999998765 4689999999999999999999864 45799999999999
Q ss_pred HHHHHHHHhcCCcccc--------------hhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHH
Q 011577 392 TIRKAIFQHSRTIRLP--------------ENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVE 446 (482)
Q Consensus 392 aI~~~Lrkq~r~irlP--------------~~v---~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~e 446 (482)
.+++++|++.+....+ ... .+....+.+++..|. ..+..+.+++|||+.||++++
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 9999999877532211 000 111112333333222 223347899999999999999
Q ss_pred HHHHHHHHcCCC
Q 011577 447 KLERLIFITRMP 458 (482)
Q Consensus 447 tVk~~L~~ar~~ 458 (482)
+|+..+++++..
T Consensus 171 tV~~~l~Ra~~~ 182 (189)
T PRK09648 171 AVRVAQHRALAR 182 (189)
T ss_pred HHHHHHHHHHHH
Confidence 999999988643
No 49
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=99.69 E-value=2.2e-16 Score=147.42 Aligned_cols=144 Identities=11% Similarity=0.150 Sum_probs=113.4
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011577 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (482)
Q Consensus 314 mdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRna 392 (482)
+++.+|+..+..|+ .|++.|+..|.+.|+.++.++.++..+++|++||+|+.+|+.+++|++.. ..|.+|++.+++|.
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 45677888888888 89999999999999999999999999999999999999999999998643 47999999999999
Q ss_pred HHHHHHHhcCCcccc-------------hh---HHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHH
Q 011577 393 IRKAIFQHSRTIRLP-------------EN---IYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKL 448 (482)
Q Consensus 393 I~~~Lrkq~r~irlP-------------~~---v~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etV 448 (482)
+++++|+..+..... .. ..+....+.++...|. ..+..+.+++|||+.||||+++|
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 999999886532211 00 0011222333333322 22334789999999999999999
Q ss_pred HHHHHHcCCC
Q 011577 449 ERLIFITRMP 458 (482)
Q Consensus 449 k~~L~~ar~~ 458 (482)
+..+++++..
T Consensus 167 ~~~l~ra~~~ 176 (182)
T PRK12537 167 KAWIKRSLKA 176 (182)
T ss_pred HHHHHHHHHH
Confidence 9999988653
No 50
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=99.68 E-value=3.4e-16 Score=147.90 Aligned_cols=146 Identities=17% Similarity=0.155 Sum_probs=114.2
Q ss_pred cCCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHH
Q 011577 313 GLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ 391 (482)
Q Consensus 313 gmdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRn 391 (482)
.+++..|+.++..|+ .|++.|+..|.+.|+.+|.++.++..+++|++||+++++|+.+.+|++. ...|.||++.+++|
T Consensus 10 ~~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~-~~~~~~wl~~ia~n 88 (196)
T PRK12524 10 DVSDEALLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQG-EARVSTWLYRVVCN 88 (196)
T ss_pred CcCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhccccc-cchHHHHHHHHHHH
Confidence 456788999999888 8999999999999999999999999999999999999999999999853 34799999999999
Q ss_pred HHHHHHHHhcCCc-cc------------chhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHH
Q 011577 392 TIRKAIFQHSRTI-RL------------PENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEK 447 (482)
Q Consensus 392 aI~~~Lrkq~r~i-rl------------P~~v---~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~et 447 (482)
.+++++|++.+.. .+ |... .+....+.++...|. ..+..+.+++|||+.||+|+++
T Consensus 89 ~~~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~L~~~~g~s~~eIA~~lgis~~t 168 (196)
T PRK12524 89 LCTDRLRRRRRASVDLDDAPEPADAAPGAEEALIEGDRMRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEA 168 (196)
T ss_pred HHHHHHHhhcCCCCCccccccccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHH
Confidence 9999999755421 10 0110 011122333333222 2233578999999999999999
Q ss_pred HHHHHHHcCCCc
Q 011577 448 LERLIFITRMPL 459 (482)
Q Consensus 448 Vk~~L~~ar~~l 459 (482)
|+..+++++..+
T Consensus 169 V~~~l~Ra~~~L 180 (196)
T PRK12524 169 VESLTARGKRAL 180 (196)
T ss_pred HHHHHHHHHHHH
Confidence 999999997654
No 51
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=99.68 E-value=3.3e-16 Score=145.19 Aligned_cols=144 Identities=9% Similarity=0.051 Sum_probs=111.0
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011577 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (482)
Q Consensus 314 mdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRna 392 (482)
++...|+..+..|+ .|++.|+..|.+.|+.+|.++.++..+++|++||+|+++|+++++|++.. ..|.||++.+++|.
T Consensus 4 ~~~~~li~~~~~g~~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~~-~~~~~wl~~ia~n~ 82 (179)
T PRK12514 4 DDIEKLIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSG-LSPMTWLITIARNH 82 (179)
T ss_pred hHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHH
Confidence 34566777777787 89999999999999999999999999999999999999999999998653 46999999999999
Q ss_pred HHHHHHHhcCCcc-c------------chhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHH
Q 011577 393 IRKAIFQHSRTIR-L------------PENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKL 448 (482)
Q Consensus 393 I~~~Lrkq~r~ir-l------------P~~v---~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etV 448 (482)
+++++|+..+... + |... .+....+..+...|. ..+..+.+++|||+.||+|+++|
T Consensus 83 ~~d~~R~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tV 162 (179)
T PRK12514 83 AIDRLRARKAVAVDIDEAHDLADPSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTM 162 (179)
T ss_pred HHHHHHhcCCcccccccchhccccCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCChHHH
Confidence 9999998664210 0 1110 011112333333222 22334789999999999999999
Q ss_pred HHHHHHcCCC
Q 011577 449 ERLIFITRMP 458 (482)
Q Consensus 449 k~~L~~ar~~ 458 (482)
+..+++++..
T Consensus 163 ~~~l~Rar~~ 172 (179)
T PRK12514 163 RTWLRRSLLK 172 (179)
T ss_pred HHHHHHHHHH
Confidence 9999988754
No 52
>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=99.68 E-value=4.1e-16 Score=142.28 Aligned_cols=138 Identities=15% Similarity=0.149 Sum_probs=106.8
Q ss_pred HHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHH
Q 011577 320 KSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIF 398 (482)
Q Consensus 320 i~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lr 398 (482)
+.++++|+ .|++.|+..|.+.++.++.++.++..+++|++||+|+++|+++++|+...+ .|.+|++.+++|.+++++|
T Consensus 2 i~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~~R 80 (170)
T TIGR02952 2 LERAQDREEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVNDYFR 80 (170)
T ss_pred hHHHHccCHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHHHHH
Confidence 44566677 899999999999999999999998999999999999999999999987544 8999999999999999999
Q ss_pred HhcCCcccc--------------hhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHH
Q 011577 399 QHSRTIRLP--------------ENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIF 453 (482)
Q Consensus 399 kq~r~irlP--------------~~v---~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~~L~ 453 (482)
++.+....+ ... .+....+.++...|. ..+..+.+++|||+.||||+++|+..++
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~eIA~~l~is~~tv~~~l~ 160 (170)
T TIGR02952 81 GSKRHPLFSLDVFKELLSNEPNPEEAILKEEANEKLLKALKILTPKQQHVIALRFGQNLPIAEVARILGKTEGAVKILQF 160 (170)
T ss_pred hcCCCCCCcHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 876433211 000 011122333333222 2234578999999999999999999999
Q ss_pred HcCCC
Q 011577 454 ITRMP 458 (482)
Q Consensus 454 ~ar~~ 458 (482)
+++..
T Consensus 161 ra~~~ 165 (170)
T TIGR02952 161 RAIKK 165 (170)
T ss_pred HHHHH
Confidence 88643
No 53
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=99.67 E-value=5.7e-16 Score=139.64 Aligned_cols=129 Identities=16% Similarity=0.151 Sum_probs=99.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC----
Q 011577 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT---- 403 (482)
Q Consensus 328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~---- 403 (482)
.||+.|+..|.++|+.+++++ +...+++|++|||++++|+++++|++..| .|.+|++.+++|.+++++|++.+.
T Consensus 4 ~af~~l~~~y~~~l~~~~~~~-~~~~~aeDi~Qe~~l~l~~~~~~~~~~~~-~f~~wl~~i~~n~~ld~~rk~~~~~~~~ 81 (154)
T PRK06759 4 ATFTEAVVLYEGLIVNQIKKL-GIYQDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYILERLKKEFAVQEKC 81 (154)
T ss_pred ccHHHHHHHHHHHHHHHHHHh-CCcccHHHHHHHHHHHHHHHHHHhCccCC-chHHHHHHHHHHHHHHHHHHHHhhcccc
Confidence 689999999999999999986 56689999999999999999999997666 799999999999999999987421
Q ss_pred --cccchh---HHHHHHHHHHHH-------HHH-HHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 404 --IRLPEN---IYTLLSKVLEAK-------RLY-IQEGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 404 --irlP~~---v~e~l~kI~ka~-------~eL-~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
...|.. ..+....+..+. +.+ ...+..+.|++|||+.||+|+++|+..+++++..
T Consensus 82 ~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~ii~l~~~~~~s~~EIA~~l~is~~tV~~~~~ra~~~ 149 (154)
T PRK06759 82 VCVGEYEDHFHFEDVEMKVKDFMSVLDEKEKYIIFERFFVGKTMGEIALETEMTYYQVRWIYRQALEK 149 (154)
T ss_pred cccCCCcccccHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 111211 111122233333 222 2334457899999999999999999999988653
No 54
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=99.66 E-value=9.7e-16 Score=144.69 Aligned_cols=144 Identities=16% Similarity=0.120 Sum_probs=113.6
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011577 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (482)
Q Consensus 314 mdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRna 392 (482)
+++++++..+..|+ .+++.|+..|.+.|++++.++.++..+++|++||+|+.+|+++++|+.. ..|.+|++.+++|.
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 56778888888888 8999999999999999999999999999999999999999999999975 36999999999999
Q ss_pred HHHHHHHhcCCcccc-----------hh---HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHH
Q 011577 393 IRKAIFQHSRTIRLP-----------EN---IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLER 450 (482)
Q Consensus 393 I~~~Lrkq~r~irlP-----------~~---v~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etVk~ 450 (482)
+++++|+..+....+ .. ..+....+..+...|+. .+..+.+++|||+.||++.++|+.
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 999999765432211 00 01112223333333221 233478999999999999999999
Q ss_pred HHHHcCCCc
Q 011577 451 LIFITRMPL 459 (482)
Q Consensus 451 ~L~~ar~~l 459 (482)
.+++++..+
T Consensus 170 rl~rar~~L 178 (192)
T PRK09643 170 RCARGRARL 178 (192)
T ss_pred HHHHHHHHH
Confidence 999987643
No 55
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=99.66 E-value=7.5e-16 Score=142.89 Aligned_cols=142 Identities=13% Similarity=0.176 Sum_probs=110.4
Q ss_pred CHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHH
Q 011577 315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 393 (482)
Q Consensus 315 dd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI 393 (482)
..+.|+..++.|+ .|++.|+..|.++|+++|+++.++..+++|++||+|++||+++++|++.. .|.+|++.+++|.+
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 3456788888888 89999999999999999999999999999999999999999999999753 79999999999999
Q ss_pred HHHHHHhcCCccc----------------------chhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHH
Q 011577 394 RKAIFQHSRTIRL----------------------PENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARR 440 (482)
Q Consensus 394 ~~~Lrkq~r~irl----------------------P~~v---~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~ 440 (482)
++++|+..+.... |... .+....+..+...|. ..+..+.+++|||+.
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 9999987542210 1000 011112333333222 122347799999999
Q ss_pred hCCCHHHHHHHHHHcCCC
Q 011577 441 VGITVEKLERLIFITRMP 458 (482)
Q Consensus 441 LGIS~etVk~~L~~ar~~ 458 (482)
||||+++|+..+++++..
T Consensus 162 lgis~~~v~~~l~Rar~~ 179 (187)
T PRK09641 162 LDLPVGTVKTRIHRGREA 179 (187)
T ss_pred HCCCHHHHHHHHHHHHHH
Confidence 999999999999988753
No 56
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=99.66 E-value=9.6e-16 Score=141.31 Aligned_cols=143 Identities=12% Similarity=0.133 Sum_probs=112.7
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011577 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (482)
Q Consensus 314 mdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRna 392 (482)
|++..|+..+..|+ .|++.|+..|.+.|+.+|++|.++..+++|++||+|+++|++++.|++. .+|.+|++.+++|.
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 55777888888888 8999999999999999999999999999999999999999999999874 47999999999999
Q ss_pred HHHHHHHhcCCcccch------------h---HHHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHH
Q 011577 393 IRKAIFQHSRTIRLPE------------N---IYTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLE 449 (482)
Q Consensus 393 I~~~Lrkq~r~irlP~------------~---v~e~l~kI~ka~~eL~~e--------~gr~pS~eEIAe~LGIS~etVk 449 (482)
+++++|+..+...... . .......+.+....|... +..+.+++|||+.||+++.+|+
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 9999998754322110 0 001222233333333222 2246799999999999999999
Q ss_pred HHHHHcCCC
Q 011577 450 RLIFITRMP 458 (482)
Q Consensus 450 ~~L~~ar~~ 458 (482)
..+++++..
T Consensus 161 ~~l~ra~~~ 169 (176)
T PRK09638 161 SRVHHGIKQ 169 (176)
T ss_pred HHHHHHHHH
Confidence 999988653
No 57
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=99.66 E-value=8e-16 Score=150.62 Aligned_cols=144 Identities=14% Similarity=0.158 Sum_probs=112.6
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011577 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (482)
Q Consensus 314 mdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRna 392 (482)
.++.+|+..++.|+ .|++.|+..|.+.|+.+++++.++..+++|++||+|+++|+.+++|++..+ .|.+|++.+++|.
T Consensus 48 ~~d~~Li~~~~~gd~~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN~ 126 (233)
T PRK12538 48 DEDEELLDRLATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSNR 126 (233)
T ss_pred ccHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHHH
Confidence 46778888888888 899999999999999999999999999999999999999999999986443 7999999999999
Q ss_pred HHHHHHHhcCCcc---------cch--h-H--HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHH
Q 011577 393 IRKAIFQHSRTIR---------LPE--N-I--YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLER 450 (482)
Q Consensus 393 I~~~Lrkq~r~ir---------lP~--~-v--~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~ 450 (482)
+++++|++.+... .+. . + .+....+..+...|. ..+..+.+++|||+.||+|+++|+.
T Consensus 127 ~id~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~L~~Lp~~~R~v~~L~~~eg~s~~EIA~~Lgis~~tVk~ 206 (233)
T PRK12538 127 CIDLRRKPRTENVDAVPEVADGKPDAVSVIERNELSDLLEAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVES 206 (233)
T ss_pred HHHHHHhhcccccccccccccCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHhcCCCHHHHHHHHCcCHHHHHH
Confidence 9999998643210 011 0 0 011122333333332 2233478999999999999999999
Q ss_pred HHHHcCCC
Q 011577 451 LIFITRMP 458 (482)
Q Consensus 451 ~L~~ar~~ 458 (482)
.+++++..
T Consensus 207 ~l~RAr~k 214 (233)
T PRK12538 207 LLKRGRQQ 214 (233)
T ss_pred HHHHHHHH
Confidence 99998754
No 58
>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=99.66 E-value=1.1e-15 Score=142.08 Aligned_cols=143 Identities=19% Similarity=0.256 Sum_probs=111.3
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011577 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (482)
Q Consensus 314 mdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRna 392 (482)
.++..|+..+..|+ .|++.|+..|.+.|+.+|+++.++..+++||+||+|+++|+++++|++. ..|.+|++.+++|.
T Consensus 5 ~~d~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~--~~~~~wl~~iarn~ 82 (190)
T TIGR02939 5 ELDLELVERVQRGEKQAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGD--SAFYTWLYRIAVNT 82 (190)
T ss_pred ccHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCC--CccHhHHHHHHHHH
Confidence 45677888888888 8999999999999999999999999999999999999999999999875 46999999999999
Q ss_pred HHHHHHHhcCCccc----------------------chhH---HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHH
Q 011577 393 IRKAIFQHSRTIRL----------------------PENI---YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLAR 439 (482)
Q Consensus 393 I~~~Lrkq~r~irl----------------------P~~v---~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe 439 (482)
+++++++..+.... |... .+....+..+...|.. .+..+.+++|||+
T Consensus 83 ~~~~~r~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~EIA~ 162 (190)
T TIGR02939 83 AKNHLVAQGRRPPTSDVEIEDAEHFEGADRLREIDTPERLLLSRELEQTVMRAVEALPEDLRTAITLRELEGLSYEDIAR 162 (190)
T ss_pred HHHHHHHhccCCCcccccccchhhhcccccccccCChHHHHHHHHHHHHHHHHHHcCCHHHhhhhhhhhhcCCCHHHHHH
Confidence 99999876542211 1000 0011123333333322 2234679999999
Q ss_pred HhCCCHHHHHHHHHHcCCC
Q 011577 440 RVGITVEKLERLIFITRMP 458 (482)
Q Consensus 440 ~LGIS~etVk~~L~~ar~~ 458 (482)
.||+++++|+..+++++..
T Consensus 163 ~lgis~~tv~~~l~rar~~ 181 (190)
T TIGR02939 163 IMDCPVGTVRSRIFRAREA 181 (190)
T ss_pred HHCcCHHHHHHHHHHHHHH
Confidence 9999999999999988754
No 59
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=99.66 E-value=6.8e-16 Score=144.04 Aligned_cols=142 Identities=13% Similarity=0.065 Sum_probs=110.2
Q ss_pred HHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHH
Q 011577 316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR 394 (482)
Q Consensus 316 d~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~ 394 (482)
...++..+..|+ .+++.|+..|.++|+.+|++|.++..+++|++||+|+++|+++++|++.++ .|.||++.+++|.++
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 455666666777 899999999999999999999999999999999999999999999998644 689999999999999
Q ss_pred HHHHHhcCCcc------c---------chh---HHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHH
Q 011577 395 KAIFQHSRTIR------L---------PEN---IYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKL 448 (482)
Q Consensus 395 ~~Lrkq~r~ir------l---------P~~---v~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etV 448 (482)
+++|+..+... . |.. ..+....+..++..|. ..+..+.+++|||+.||+|+++|
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 99998653210 0 000 0111223333433332 12334789999999999999999
Q ss_pred HHHHHHcCCC
Q 011577 449 ERLIFITRMP 458 (482)
Q Consensus 449 k~~L~~ar~~ 458 (482)
+..+++++..
T Consensus 171 ~~~l~Rar~~ 180 (187)
T PRK12534 171 KSWIRRGLAK 180 (187)
T ss_pred HHHHHHHHHH
Confidence 9999998754
No 60
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=99.65 E-value=1.3e-15 Score=145.50 Aligned_cols=140 Identities=12% Similarity=0.125 Sum_probs=106.8
Q ss_pred HHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHH
Q 011577 319 LKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI 397 (482)
Q Consensus 319 Li~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~L 397 (482)
|...+..|+ .|++.|+..|.+.|+.++.++.++..+++|++||+|+++|+++++|++.++ .|.||++++++|.+++++
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 445556666 899999999999999999999999999999999999999999999997654 599999999999999999
Q ss_pred HHhcCCccc-------c------------hhHHH--HHHHHHHHHHHH--------HHhcCCCCcHHHHHHHhCCCHHHH
Q 011577 398 FQHSRTIRL-------P------------ENIYT--LLSKVLEAKRLY--------IQEGNHSPDKEDLARRVGITVEKL 448 (482)
Q Consensus 398 rkq~r~irl-------P------------~~v~e--~l~kI~ka~~eL--------~~e~gr~pS~eEIAe~LGIS~etV 448 (482)
|+..+.... + ..... ....+.+++..| ...+..+.+++|||+.||+|+++|
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 986542110 0 00000 011233333222 222444789999999999999999
Q ss_pred HHHHHHcCCCc
Q 011577 449 ERLIFITRMPL 459 (482)
Q Consensus 449 k~~L~~ar~~l 459 (482)
+..+++++..+
T Consensus 187 ~~~l~Ra~~~L 197 (206)
T PRK12526 187 KSRLRLALAKL 197 (206)
T ss_pred HHHHHHHHHHH
Confidence 99999887543
No 61
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=99.65 E-value=9.2e-16 Score=144.74 Aligned_cols=141 Identities=10% Similarity=0.075 Sum_probs=108.6
Q ss_pred HHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHH
Q 011577 317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK 395 (482)
Q Consensus 317 ~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~ 395 (482)
.+|+..+..|+ .|++.|+..|.+.|+.+|.++.++..+++|++||+|+.+|+.+++|++..+ .|.+|++.+++|.+++
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 34777788888 899999999999999999999999999999999999999999999987543 7999999999999999
Q ss_pred HHHHhcCCcc-c------ch-----------hHH--HHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHH
Q 011577 396 AIFQHSRTIR-L------PE-----------NIY--TLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEK 447 (482)
Q Consensus 396 ~Lrkq~r~ir-l------P~-----------~v~--e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~et 447 (482)
++|+..+... . +. ... .....+.++...|.. .+-.+.+++|||+.||||+++
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 9998653211 0 00 000 011223333332221 233467999999999999999
Q ss_pred HHHHHHHcCCC
Q 011577 448 LERLIFITRMP 458 (482)
Q Consensus 448 Vk~~L~~ar~~ 458 (482)
|+..+++++..
T Consensus 174 Vk~rl~ra~~~ 184 (194)
T PRK12531 174 VKSRLRLAVEK 184 (194)
T ss_pred HHHHHHHHHHH
Confidence 99999988654
No 62
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=99.65 E-value=8.8e-16 Score=140.59 Aligned_cols=134 Identities=19% Similarity=0.242 Sum_probs=103.5
Q ss_pred HhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhc
Q 011577 323 LHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS 401 (482)
Q Consensus 323 l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~ 401 (482)
++.|+ .|++.|+..|.++|+.++++|.+++.+.+|++||++++||+++++|+ .+.+|.+|++.+++|.+.+++++..
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 45566 89999999999999999999999999999999999999999999999 3568999999999999999999865
Q ss_pred CCcccc----------------------hhHH---HHHHHHHHHHHHH--------HHhcCCCCcHHHHHHHhCCCHHHH
Q 011577 402 RTIRLP----------------------ENIY---TLLSKVLEAKRLY--------IQEGNHSPDKEDLARRVGITVEKL 448 (482)
Q Consensus 402 r~irlP----------------------~~v~---e~l~kI~ka~~eL--------~~e~gr~pS~eEIAe~LGIS~etV 448 (482)
+....+ .... .....+..+...| ...+..+.+++|||+.||+|+.+|
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 432211 0000 1122233222222 122334789999999999999999
Q ss_pred HHHHHHcCCC
Q 011577 449 ERLIFITRMP 458 (482)
Q Consensus 449 k~~L~~ar~~ 458 (482)
+..+++++..
T Consensus 162 ~~~l~ra~~~ 171 (182)
T PRK09652 162 RSRIFRAREA 171 (182)
T ss_pred HHHHHHHHHH
Confidence 9999988653
No 63
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=99.65 E-value=1.2e-15 Score=143.15 Aligned_cols=143 Identities=20% Similarity=0.203 Sum_probs=109.9
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011577 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (482)
Q Consensus 314 mdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRna 392 (482)
.++.+|+..++.|+ .|++.|+..|.+.|+.+++++.++..+++|++||+|+++|+. ..|++..+ .|.||++++++|.
T Consensus 14 ~~~~~l~~~~~~gd~~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn~ 91 (194)
T PRK12519 14 RSDAELFSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRSR 91 (194)
T ss_pred ccHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHHH
Confidence 35677888888888 899999999999999999999999999999999999999976 67887554 7999999999999
Q ss_pred HHHHHHHhcCCcccc----------------h-hH--HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCH
Q 011577 393 IRKAIFQHSRTIRLP----------------E-NI--YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITV 445 (482)
Q Consensus 393 I~~~Lrkq~r~irlP----------------~-~v--~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~ 445 (482)
+++++|++.+..... . .+ .+....+..+...|.. .+..+.+++|||+.||+|+
T Consensus 92 ~~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~~~g~s~~EIA~~lgis~ 171 (194)
T PRK12519 92 AIDRLRSRRSRQRLLERWQQELLGEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPL 171 (194)
T ss_pred HHHHHHhcccccchhhhhhhhhcccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhhhcCCCHHHHHHHhCCCH
Confidence 999999865421110 0 00 0111223333333322 2334779999999999999
Q ss_pred HHHHHHHHHcCCC
Q 011577 446 EKLERLIFITRMP 458 (482)
Q Consensus 446 etVk~~L~~ar~~ 458 (482)
.+|+..+++++..
T Consensus 172 ~tV~~~l~Ra~~~ 184 (194)
T PRK12519 172 GTVKARARQGLLK 184 (194)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999988653
No 64
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=99.64 E-value=2e-15 Score=141.64 Aligned_cols=142 Identities=15% Similarity=0.206 Sum_probs=109.9
Q ss_pred CHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHH
Q 011577 315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 393 (482)
Q Consensus 315 dd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI 393 (482)
+++.|+..++.|+ .|++.|+..|.+.|+.+++++.++..+++|++||+|+++|+++.+|++.. .|.+|++++++|.+
T Consensus 6 ~~~~ll~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~l~~~~~~~~~~~--~~~~wl~~ia~n~~ 83 (193)
T PRK11923 6 EDQQLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDS--AFYTWLYRIAINTA 83 (193)
T ss_pred cHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHhCcCCCC--ccHhHHHHHHHHHH
Confidence 4567888888888 89999999999999999999999999999999999999999999999864 59999999999999
Q ss_pred HHHHHHhcCCcc---c-------------------chhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHH
Q 011577 394 RKAIFQHSRTIR---L-------------------PENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARR 440 (482)
Q Consensus 394 ~~~Lrkq~r~ir---l-------------------P~~v---~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~ 440 (482)
++++|++.+... . |... .+....+.++...|. ..+-.+.+++|||+.
T Consensus 84 ~d~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~ 163 (193)
T PRK11923 84 KNHLVSRGRRPPDSDVSSEDAEFYDGDHALKDIESPERALLRDEIEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASV 163 (193)
T ss_pred HHHHHHhcCCCccccccccchhhhcccccccCcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHHhhHHhcCCCHHHHHHH
Confidence 999987654311 0 1000 001112223332222 113346799999999
Q ss_pred hCCCHHHHHHHHHHcCCC
Q 011577 441 VGITVEKLERLIFITRMP 458 (482)
Q Consensus 441 LGIS~etVk~~L~~ar~~ 458 (482)
||+++++|+..+++++..
T Consensus 164 lgis~~tv~~~l~Rar~~ 181 (193)
T PRK11923 164 MQCPVGTVRSRIFRAREA 181 (193)
T ss_pred HCCCHHHHHHHHHHHHHH
Confidence 999999999999988753
No 65
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=99.64 E-value=1.9e-15 Score=146.98 Aligned_cols=143 Identities=15% Similarity=0.193 Sum_probs=113.0
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011577 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (482)
Q Consensus 314 mdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRna 392 (482)
+++..|+..+..|+ .|++.|+..|.+.|+++++++.+++.+++||+||+|++||+++++|++. ..|.+|++++++|.
T Consensus 15 ~~~~~l~~~~~~gd~~a~~~l~~~y~~~l~~~a~~~~~~~~~AEDlvQE~fi~l~~~~~~~~~~--~~~~~wL~~iarn~ 92 (231)
T PRK11922 15 ASDRELVARVLAGDEAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGD--ASLSTWLSRIVLNE 92 (231)
T ss_pred ccHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHhcCCC--chhHHHHHHHHHHH
Confidence 45677888888777 8999999999999999999999999999999999999999999999985 47999999999999
Q ss_pred HHHHHHHhcCCcccch-----------------------h---HHHHHHHHHHHHHHHHHh--------cCCCCcHHHHH
Q 011577 393 IRKAIFQHSRTIRLPE-----------------------N---IYTLLSKVLEAKRLYIQE--------GNHSPDKEDLA 438 (482)
Q Consensus 393 I~~~Lrkq~r~irlP~-----------------------~---v~e~l~kI~ka~~eL~~e--------~gr~pS~eEIA 438 (482)
+++++|+..+...... . ..+....+.+++..|... +..+.+++|||
T Consensus 93 ~~d~~Rk~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA 172 (231)
T PRK11922 93 ALGRLRRRRRLVNLAEMVMASTIAGGERTPLADPAEDPERAAARREIRALLERAIDALPDAFRAVFVLRVVEELSVEETA 172 (231)
T ss_pred HHHHHHhhcccccchhcccccccccccccccCcccCChHHHHHHHHHHHHHHHHHHhCCHHHhhhheeehhcCCCHHHHH
Confidence 9999998764322110 0 001122244444433222 23467999999
Q ss_pred HHhCCCHHHHHHHHHHcCCC
Q 011577 439 RRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 439 e~LGIS~etVk~~L~~ar~~ 458 (482)
+.||+|.++|+..+++++..
T Consensus 173 e~lgis~~tVk~~l~Rar~k 192 (231)
T PRK11922 173 QALGLPEETVKTRLHRARRL 192 (231)
T ss_pred HHHCcCHHHHHHHHHHHHHH
Confidence 99999999999999988753
No 66
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=99.63 E-value=3.7e-15 Score=139.38 Aligned_cols=141 Identities=11% Similarity=0.104 Sum_probs=108.2
Q ss_pred HHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHH----HccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHH
Q 011577 316 CRDLKSELHSGN-SSREKLINANLRLVVHVAK----QYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVR 390 (482)
Q Consensus 316 d~eLi~~l~~Gd-~Are~LI~snlrLV~sIAk----rY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIR 390 (482)
+.+|+..+..|+ .||+.|+..|.+.|+.+|+ +|.++..+++|++||+|+.+|+.++.|++. ..|.+|++.+++
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 566777888888 8999999999999999986 455788999999999999999999999875 369999999999
Q ss_pred HHHHHHHHHhcCC-cccc---------h---hHHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHH
Q 011577 391 QTIRKAIFQHSRT-IRLP---------E---NIYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLE 449 (482)
Q Consensus 391 naI~~~Lrkq~r~-irlP---------~---~v~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etVk 449 (482)
|.+++++|+..+. ...+ . ...+....+..+...|.. .+..+.+++|||+.||+|+++|+
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 9999999986542 1111 0 011122233333333321 13347899999999999999999
Q ss_pred HHHHHcCCC
Q 011577 450 RLIFITRMP 458 (482)
Q Consensus 450 ~~L~~ar~~ 458 (482)
..+++++..
T Consensus 166 ~~l~ra~~~ 174 (184)
T PRK12539 166 VSVHRGLKA 174 (184)
T ss_pred HHHHHHHHH
Confidence 999988653
No 67
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=99.63 E-value=3.8e-15 Score=138.95 Aligned_cols=141 Identities=9% Similarity=0.037 Sum_probs=107.4
Q ss_pred HHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccC-CCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHH
Q 011577 316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQG-RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 393 (482)
Q Consensus 316 d~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~-~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI 393 (482)
...++..+..|+ .|++.|+..|.+.|+.++.++.+ ...+++|++||+|++||+.++.|++. ..|.+|++.+++|.+
T Consensus 8 ~~~~~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~--~~~~~wl~~iarN~~ 85 (181)
T PRK12536 8 LRALLLRGLAGDAAAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRAD--QPLTAWVHAIARYKL 85 (181)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCC--CchHHHHHHHHHHHH
Confidence 345667777777 89999999999999999988764 57899999999999999999999974 469999999999999
Q ss_pred HHHHHHhcCCcccc--------------hhHHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHH
Q 011577 394 RKAIFQHSRTIRLP--------------ENIYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERL 451 (482)
Q Consensus 394 ~~~Lrkq~r~irlP--------------~~v~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~~ 451 (482)
++++|+..+..... .........+.++...|. ..+-.+.+++|||+.||+|+++|+..
T Consensus 86 ~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tV~~~ 165 (181)
T PRK12536 86 MDFLRSRARREALHDPLDDESELFATSDDEAAEARRDLGKLLEQLPDRQRLPIVHVKLEGLSVAETAQLTGLSESAVKVG 165 (181)
T ss_pred HHHHHHHhccccccCCccchhhhcCCCCcchHHHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHH
Confidence 99999864422100 011112222333333321 22234789999999999999999999
Q ss_pred HHHcCCC
Q 011577 452 IFITRMP 458 (482)
Q Consensus 452 L~~ar~~ 458 (482)
+++++..
T Consensus 166 l~rar~~ 172 (181)
T PRK12536 166 IHRGLKA 172 (181)
T ss_pred HHHHHHH
Confidence 9988654
No 68
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=99.63 E-value=3.6e-15 Score=139.82 Aligned_cols=144 Identities=13% Similarity=0.126 Sum_probs=112.3
Q ss_pred cCCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHH
Q 011577 313 GLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ 391 (482)
Q Consensus 313 gmdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRn 391 (482)
.+++.+|+..+..|+ .|++.|+..|.+.|+.++.++.++..+++|++||+|+.+|+++++|++. ..|.+|++.+++|
T Consensus 6 ~~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~~~~~~~--~~~~~wl~~i~~n 83 (189)
T PRK12515 6 ATTDEMLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIARF 83 (189)
T ss_pred ccCHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CChHHHHHHHHHH
Confidence 356788888888888 8999999999999999999999999999999999999999999999964 4799999999999
Q ss_pred HHHHHHHHhcCCccc-------------chhHH---HHHHHHHHHHHHH--------HHhcCCCCcHHHHHHHhCCCHHH
Q 011577 392 TIRKAIFQHSRTIRL-------------PENIY---TLLSKVLEAKRLY--------IQEGNHSPDKEDLARRVGITVEK 447 (482)
Q Consensus 392 aI~~~Lrkq~r~irl-------------P~~v~---e~l~kI~ka~~eL--------~~e~gr~pS~eEIAe~LGIS~et 447 (482)
.+++++++..+.... |.... +....+.++...| ...+..+.+++|||+.||+|+++
T Consensus 84 ~~~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~t 163 (189)
T PRK12515 84 KALSALRRRKHEEIDDEAAAAIEDGADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPEST 163 (189)
T ss_pred HHHHHHHccCCCCCccccccccCCCCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHH
Confidence 999999976432110 01100 0111122222222 12233478999999999999999
Q ss_pred HHHHHHHcCCC
Q 011577 448 LERLIFITRMP 458 (482)
Q Consensus 448 Vk~~L~~ar~~ 458 (482)
|+..+++++..
T Consensus 164 V~~~l~Rar~~ 174 (189)
T PRK12515 164 VKTRMFYARKK 174 (189)
T ss_pred HHHHHHHHHHH
Confidence 99999998754
No 69
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=99.62 E-value=1.6e-15 Score=141.73 Aligned_cols=135 Identities=16% Similarity=0.095 Sum_probs=104.5
Q ss_pred hcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC
Q 011577 325 SGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 403 (482)
Q Consensus 325 ~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~ 403 (482)
+|+ .|++.|+..|.+.|+.+|.+++++..+++|++||+|+.+|+++++|+...+..|.||++.+++|.+++++|++.+.
T Consensus 5 ~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn~~~d~~Rk~~~~ 84 (185)
T PRK12542 5 NNDYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRKNKRH 84 (185)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 455 8999999999999999999999999999999999999999999999865445799999999999999999987543
Q ss_pred cccc------------hhH------HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577 404 IRLP------------ENI------YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRM 457 (482)
Q Consensus 404 irlP------------~~v------~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (482)
.... ... ......+.++...|. ..+..+.+++|||+.||+|+++|+..+++++.
T Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~ 164 (185)
T PRK12542 85 ETFLEEYERESIEAVDENIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARK 164 (185)
T ss_pred hhhhhhccccchhhhhccHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 2110 000 001122333333322 12334689999999999999999999998876
Q ss_pred Cc
Q 011577 458 PL 459 (482)
Q Consensus 458 ~l 459 (482)
.+
T Consensus 165 ~L 166 (185)
T PRK12542 165 RV 166 (185)
T ss_pred HH
Confidence 43
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=99.61 E-value=6.6e-15 Score=145.33 Aligned_cols=144 Identities=12% Similarity=0.046 Sum_probs=113.1
Q ss_pred hcCCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHH-------hHHhhCCCCCCchhh
Q 011577 312 IGLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMK-------SVEKFKPQAGCRFAS 383 (482)
Q Consensus 312 ~gmdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLir-------AiekFDp~kG~rFST 383 (482)
++.++..|+..+++|+ .||+.|+..|.+.|+.++.++.++..+++|++||+|+.+|. .+.+|++. ..|.|
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 4567788999999998 89999999999999999999999999999999999999994 78889864 47999
Q ss_pred HHHHHHHHHHHHHHHHhcCCccc---------------chhH-H------HHHHHHHHHHHHHHHh--------cCCCCc
Q 011577 384 YAYWWVRQTIRKAIFQHSRTIRL---------------PENI-Y------TLLSKVLEAKRLYIQE--------GNHSPD 433 (482)
Q Consensus 384 YA~~wIRnaI~~~Lrkq~r~irl---------------P~~v-~------e~l~kI~ka~~eL~~e--------~gr~pS 433 (482)
|++.+++|.+++++|++.+...+ |... . .....+.+++.+|... +..+.|
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 99999999999999976542211 1100 0 0112244444443322 234679
Q ss_pred HHHHHHHhCCCHHHHHHHHHHcCC
Q 011577 434 KEDLARRVGITVEKLERLIFITRM 457 (482)
Q Consensus 434 ~eEIAe~LGIS~etVk~~L~~ar~ 457 (482)
++|||+.|||++++|+..+++++.
T Consensus 180 ~~EIA~~Lgis~~TVk~rl~RAr~ 203 (244)
T TIGR03001 180 MDRIGAMYQVHRSTVSRWVAQARE 203 (244)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHH
Confidence 999999999999999999998865
No 71
>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=99.60 E-value=5.3e-15 Score=137.17 Aligned_cols=141 Identities=17% Similarity=0.194 Sum_probs=106.3
Q ss_pred HHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCC-----CHhHHHHHHHHHHHH-hHHhhCCCCCCchhhHHHHH
Q 011577 316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGI-----SLHDLLQEGSMGLMK-SVEKFKPQAGCRFASYAYWW 388 (482)
Q Consensus 316 d~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~-----d~EDLIQEG~IGLir-AiekFDp~kG~rFSTYA~~w 388 (482)
..+|+..++.|+ .|++.|+..|.+.|+.+|++|.++.. +++|++||+|+.+|+ ...+|++. ..|.+|++.+
T Consensus 4 ~~~li~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~--~~~~~wl~~i 81 (183)
T TIGR02999 4 VTELLQQWQNGDAAARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR--AHFFAAAAKA 81 (183)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCCch--HHHHHHHHHH
Confidence 356777888888 89999999999999999999998887 899999999999998 78889754 3699999999
Q ss_pred HHHHHHHHHHHhcCCcc------c------c---hhHHHH---HHH-------HHHHHHH-HHHhcCCCCcHHHHHHHhC
Q 011577 389 VRQTIRKAIFQHSRTIR------L------P---ENIYTL---LSK-------VLEAKRL-YIQEGNHSPDKEDLARRVG 442 (482)
Q Consensus 389 IRnaI~~~Lrkq~r~ir------l------P---~~v~e~---l~k-------I~ka~~e-L~~e~gr~pS~eEIAe~LG 442 (482)
++|.+++++|+..+..+ . + ...... +.. +....+. +...+..+.|++|||+.||
T Consensus 82 ~~n~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lg 161 (183)
T TIGR02999 82 MRRILVDHARRRRAQKRGGGAVRVPLDEVLPDAEADLDEELLDLDDALDKLAQVDPRQAEVVELRFFAGLTVEEIAELLG 161 (183)
T ss_pred HHHHHHHHHHHHHHHhccCCccccccccccCCCCccHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHcCCCHHHHHHHhC
Confidence 99999999987532111 0 0 011111 111 1111122 1222334789999999999
Q ss_pred CCHHHHHHHHHHcCCC
Q 011577 443 ITVEKLERLIFITRMP 458 (482)
Q Consensus 443 IS~etVk~~L~~ar~~ 458 (482)
||+++|+..+++++..
T Consensus 162 is~~tVk~~l~Rar~~ 177 (183)
T TIGR02999 162 VSVRTVERDWRFARAW 177 (183)
T ss_pred CCHHHHHHHHHHHHHH
Confidence 9999999999998753
No 72
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=99.59 E-value=8.2e-15 Score=137.62 Aligned_cols=141 Identities=19% Similarity=0.150 Sum_probs=108.7
Q ss_pred HHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHH
Q 011577 317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK 395 (482)
Q Consensus 317 ~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~ 395 (482)
..|+.++..|+ .|++.|+..|.+.|+.++. +.++..+++|++||+|+.+|+.+++|++. ..|.+|++.+++|.+++
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 45777778888 8999999999999999995 67888999999999999999999999864 47999999999999999
Q ss_pred HHHHhcCCccc-----chh---------HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHH
Q 011577 396 AIFQHSRTIRL-----PEN---------IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIF 453 (482)
Q Consensus 396 ~Lrkq~r~irl-----P~~---------v~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etVk~~L~ 453 (482)
++|+..+.... +.. ..+....+.+++..|.. .+..+.+++|||+.||+|+++|+..++
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 99976432211 100 01112233444433322 233467999999999999999999999
Q ss_pred HcCCCcc
Q 011577 454 ITRMPLS 460 (482)
Q Consensus 454 ~ar~~lS 460 (482)
+++..+-
T Consensus 169 Rar~~Lr 175 (185)
T PRK09649 169 RARDALL 175 (185)
T ss_pred HHHHHHH
Confidence 9986554
No 73
>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=99.59 E-value=1.1e-14 Score=131.67 Aligned_cols=130 Identities=15% Similarity=0.162 Sum_probs=101.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc-
Q 011577 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL- 406 (482)
Q Consensus 328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irl- 406 (482)
+|++.++..|.+.|+.+|+++.++..++||++||+++.+|+++++|++.. .|.+|++++++|.+++++|++.+....
T Consensus 1 ~~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~~~ 78 (159)
T TIGR02989 1 EAFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRDRLVF 78 (159)
T ss_pred CHHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhccccccc
Confidence 37899999999999999999999999999999999999999999999753 699999999999999999987654221
Q ss_pred chhH----------------HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCc
Q 011577 407 PENI----------------YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (482)
Q Consensus 407 P~~v----------------~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (482)
-... .+....+.+++..|.. ....+.+++|||+.||||.++|+..+++++..+
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~v~~l~~~~g~~~~eIA~~l~is~~tv~~~l~Rar~~L 155 (159)
T TIGR02989 79 DDELLEALAAEAEATEADRSEDELQALEGCLEKLPERQRELLQLRYQRGVSLTALAEQLGRTVNAVYKALSRLRVRL 155 (159)
T ss_pred CHHHHHHHHhhcccchHhhHHHHHHHHHHHHHHCCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 0000 0111223333333321 133478999999999999999999999887543
No 74
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=99.59 E-value=1.5e-14 Score=132.09 Aligned_cols=138 Identities=14% Similarity=0.128 Sum_probs=105.7
Q ss_pred HHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHH
Q 011577 319 LKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI 397 (482)
Q Consensus 319 Li~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~L 397 (482)
|...+..|+ .|++.|+..|.+.|+.+|+++.++..+++|++||+|++||+++++|+ .+..|.+|++.+++|.+.+++
T Consensus 3 ~~~~~~~~~~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~~~d~~ 80 (179)
T PRK11924 3 LMPVDATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNVCYDLL 80 (179)
T ss_pred HHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHHHHHHH
Confidence 455666677 89999999999999999999999999999999999999999999998 345899999999999999999
Q ss_pred HHhcCCcccc----------------hh----------HHHHHHHHHHHHHHH-HHhcCCCCcHHHHHHHhCCCHHHHHH
Q 011577 398 FQHSRTIRLP----------------EN----------IYTLLSKVLEAKRLY-IQEGNHSPDKEDLARRVGITVEKLER 450 (482)
Q Consensus 398 rkq~r~irlP----------------~~----------v~e~l~kI~ka~~eL-~~e~gr~pS~eEIAe~LGIS~etVk~ 450 (482)
++..+..... .. +...+.++....+.+ ...+..+.+++|||+.||+|..+|+.
T Consensus 81 r~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~~~~~~eIA~~lgis~~tv~~ 160 (179)
T PRK11924 81 RRRRREKAVLSDDALEPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKS 160 (179)
T ss_pred HhcccccccCcccccccccCCccCCHHHHHhhHHHHHHHHHHHHhCCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHH
Confidence 9765432211 00 111122222222221 12233477999999999999999999
Q ss_pred HHHHcCCC
Q 011577 451 LIFITRMP 458 (482)
Q Consensus 451 ~L~~ar~~ 458 (482)
.+++++..
T Consensus 161 ~~~ra~~~ 168 (179)
T PRK11924 161 RLRRARQL 168 (179)
T ss_pred HHHHHHHH
Confidence 99988653
No 75
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=99.58 E-value=2.2e-14 Score=133.51 Aligned_cols=139 Identities=12% Similarity=0.138 Sum_probs=105.6
Q ss_pred HHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccC----CCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011577 318 DLKSELHSGN-SSREKLINANLRLVVHVAKQYQG----RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (482)
Q Consensus 318 eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~----~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRna 392 (482)
.|+..+..|+ .|++.|+..|.+.|+.+|.++++ ...+++|++||+|+.+|...++|+.. ..|.+|++.+++|.
T Consensus 11 ~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~--~~~~~wl~~i~rn~ 88 (184)
T PRK12512 11 DLMRSANAGDAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWLFAIARNK 88 (184)
T ss_pred HHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCcc--ccHHHHHHHHHHHH
Confidence 3566666666 89999999999999999999875 34689999999999999999999863 47999999999999
Q ss_pred HHHHHHHhcCCcccc---------h-h--HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHH
Q 011577 393 IRKAIFQHSRTIRLP---------E-N--IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLI 452 (482)
Q Consensus 393 I~~~Lrkq~r~irlP---------~-~--v~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etVk~~L 452 (482)
+.+++|++.+....+ . . -......+.++...|.. .+-.+.+++|||+.||+|..+|+..+
T Consensus 89 ~~d~~Rr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l~is~~tV~~~l 168 (184)
T PRK12512 89 LIDALRRRGRRVFVDIDDFAETLPAEPATETLPAGDVGRHLETLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVRVAL 168 (184)
T ss_pred HHHHHHhhcccccCCchhccccccccchhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 999999876532211 0 0 01112233333333221 12347799999999999999999999
Q ss_pred HHcCCC
Q 011577 453 FITRMP 458 (482)
Q Consensus 453 ~~ar~~ 458 (482)
++++..
T Consensus 169 ~ra~~~ 174 (184)
T PRK12512 169 HRGLAA 174 (184)
T ss_pred HHHHHH
Confidence 988654
No 76
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=99.58 E-value=2.5e-14 Score=133.76 Aligned_cols=132 Identities=16% Similarity=0.186 Sum_probs=105.3
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCc
Q 011577 325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 404 (482)
Q Consensus 325 ~Gd~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~i 404 (482)
++..+++.++..|.+.++.++++++++..+++||+||+|+.+|+++..| .. +..|.||++++++|.+++++|+..+..
T Consensus 12 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~-~~~~~~wl~~Ia~n~~iD~~R~~~r~~ 89 (182)
T COG1595 12 GDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RG-RSSFKAWLYRIARNLAIDRLRKRKRRR 89 (182)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CC-CCchHHHHHHHHHHHHHHHHHHhcccc
Confidence 3448999999999999999999999998899999999999999999999 33 457999999999999999999876543
Q ss_pred cc-c-------------hhH-----HHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577 405 RL-P-------------ENI-----YTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLERLIFITRM 457 (482)
Q Consensus 405 rl-P-------------~~v-----~e~l~kI~ka~~eL~~e--------~gr~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (482)
.. + ... .+....+.++...|+.. ...+.|++|||+.|||++++|+..+++++.
T Consensus 90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~~~gls~~EIA~~l~i~~~tVks~l~ra~~ 169 (182)
T COG1595 90 ARVEEADLLPEEADPAPDLAELLLAEEELERLRRALARLPPRQREAFLLRYLEGLSYEEIAEILGISVGTVKSRLHRARK 169 (182)
T ss_pred cccccccccccccCcccccchHHHHHHHHHHHHHHHHhCCHHHhHHhhhHhhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 21 0 101 22333455555444332 334789999999999999999999999875
Q ss_pred C
Q 011577 458 P 458 (482)
Q Consensus 458 ~ 458 (482)
.
T Consensus 170 ~ 170 (182)
T COG1595 170 K 170 (182)
T ss_pred H
Confidence 4
No 77
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=99.57 E-value=2.1e-14 Score=132.58 Aligned_cols=129 Identities=10% Similarity=0.061 Sum_probs=100.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc-
Q 011577 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL- 406 (482)
Q Consensus 328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irl- 406 (482)
..+++|+..|.++|+.+|++|.++..+++|++||+|+.||+++++|++. .+|.+|++.+++|.+++++|++.+....
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 4689999999999999999999999999999999999999999999975 3799999999999999999986543210
Q ss_pred --------------------chhH--HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHcC
Q 011577 407 --------------------PENI--YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITR 456 (482)
Q Consensus 407 --------------------P~~v--~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etVk~~L~~ar 456 (482)
+... .+....+.+++..|.. .+..+.+++|||+.||+++++|+..+.+++
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 0110 0111223333333322 233477999999999999999999999887
Q ss_pred CC
Q 011577 457 MP 458 (482)
Q Consensus 457 ~~ 458 (482)
..
T Consensus 161 ~~ 162 (173)
T PRK12522 161 KQ 162 (173)
T ss_pred HH
Confidence 54
No 78
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=99.57 E-value=2e-14 Score=133.78 Aligned_cols=132 Identities=15% Similarity=0.182 Sum_probs=102.4
Q ss_pred hcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC
Q 011577 325 SGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 403 (482)
Q Consensus 325 ~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~ 403 (482)
.|+ .|++.|+..|.+.|+.++++|.++..+++|++||+|+.+|+++.+|++.. .|.+|++.+++|.+.+++++..+.
T Consensus 3 ~~d~~af~~l~~~~~~~l~~~~~~~~~~~~daeDl~Qevfl~l~~~~~~~~~~~--~f~~wl~~iarn~~~~~~r~~~~~ 80 (179)
T PRK12543 3 SGDQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNR--PFRFWLIGLVIKQIHSWRRKRWRR 80 (179)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--ChHHHHHHHHHHHHHHHHHhhccc
Confidence 345 89999999999999999999999999999999999999999999999864 699999999999999998765421
Q ss_pred cc---------------cchhHH--HHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 404 IR---------------LPENIY--TLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 404 ir---------------lP~~v~--e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
.+ .|..+. +....+.++...|+ ..+..+.+++|||+.||||+++|+..+++++..
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~i~~l~~~e~~s~~EIA~~lgis~~tV~~~l~ra~~~ 160 (179)
T PRK12543 81 FRIFEKAEEQRKPVSIDFSEDVLSKESNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKK 160 (179)
T ss_pred cccccccccccccccccChHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHccCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 11 111111 11223333333322 123347799999999999999999999988654
No 79
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=99.56 E-value=1.8e-14 Score=135.23 Aligned_cols=129 Identities=16% Similarity=0.176 Sum_probs=100.7
Q ss_pred HHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccch
Q 011577 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE 408 (482)
Q Consensus 329 Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~ 408 (482)
+|+.|+..|.+.|+.+|.+++++..+++|++||.|+.+|+.+++|++. .+|.||++.+++|.+++++|++.+......
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 789999999999999999999999999999999999999999999864 369999999999999999998765322110
Q ss_pred ------------------------------hH------HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCC
Q 011577 409 ------------------------------NI------YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGIT 444 (482)
Q Consensus 409 ------------------------------~v------~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS 444 (482)
.. .+....+..++..|.. .+..+.|++|||+.||+|
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 00 0111223333333322 233467999999999999
Q ss_pred HHHHHHHHHHcCCCc
Q 011577 445 VEKLERLIFITRMPL 459 (482)
Q Consensus 445 ~etVk~~L~~ar~~l 459 (482)
+++|+..+++++..+
T Consensus 161 ~~tV~~~l~Rar~~L 175 (191)
T PRK12520 161 ATNAWVLLYRARMRL 175 (191)
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999999987643
No 80
>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=99.56 E-value=3e-14 Score=124.62 Aligned_cols=126 Identities=25% Similarity=0.397 Sum_probs=100.1
Q ss_pred HHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcc---
Q 011577 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR--- 405 (482)
Q Consensus 329 Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~ir--- 405 (482)
|++.|+..|.++|+++++++.+++.+.+|++|||+++|+++++.|++. ..|.+|+++++++.+.++++++.+ .+
T Consensus 2 a~~~l~~~~~~~v~~~~~~~~~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~rk~~~-~~~~~ 78 (158)
T TIGR02937 2 AFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRR-LRREL 78 (158)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHHHHHHHHhcc-CCcch
Confidence 789999999999999999999999999999999999999999999997 689999999999999999998864 11
Q ss_pred -----------cch----------hHHHHHHHHHHHHHHHH-HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577 406 -----------LPE----------NIYTLLSKVLEAKRLYI-QEGNHSPDKEDLARRVGITVEKLERLIFITRM 457 (482)
Q Consensus 406 -----------lP~----------~v~e~l~kI~ka~~eL~-~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (482)
.|. .+...+..+....+.+. ..+..+.+..|||+.+|+|+.+|+..+.+++.
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~ii~~~~~~g~s~~eIA~~l~~s~~~v~~~~~~~~~ 152 (158)
T TIGR02937 79 DLLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARK 152 (158)
T ss_pred hhhhhcccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 011 01122222322233332 22234789999999999999999999988754
No 81
>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=99.55 E-value=1.8e-14 Score=135.47 Aligned_cols=129 Identities=16% Similarity=0.148 Sum_probs=102.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc
Q 011577 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 407 (482)
Q Consensus 328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP 407 (482)
.+|+.|+..|.+.|+.+|.+++++..+++|++||+|+.+|+.+.+|++. ..|.+|++.+++|.+++++|++.+.....
T Consensus 11 ~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~~~~~~~~~--~~~~~wL~~iarN~~~d~~Rk~~~~~~~~ 88 (193)
T TIGR02947 11 QRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPG--TNLKAWLYRILTNTYINSYRKAQRRPQQS 88 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcccCCC--CcchHHHHHHHHHHHHHHHHHhcCCcccc
Confidence 7999999999999999999999999999999999999999999999864 46999999999999999999875432110
Q ss_pred --hhH--------------------H-----HHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHHHHH
Q 011577 408 --ENI--------------------Y-----TLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLERLI 452 (482)
Q Consensus 408 --~~v--------------------~-----e~l~kI~ka~~eL~~e--------~gr~pS~eEIAe~LGIS~etVk~~L 452 (482)
... . .....+..++..|+.. +..+.+++|||+.||||+++|+..+
T Consensus 89 ~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~r~i~~L~~~~g~s~~EIA~~lgis~~tVk~~l 168 (193)
T TIGR02947 89 DDDDIEDWQLAKAASHTSNGLRSAELEALDGLPDQDIKDALQGLPEEFRQAVYLADVEGFAYKEIAEIMGTPIGTVMSRL 168 (193)
T ss_pred cchhhhhhhhccccccccccccchhHHHHhhhhHHHHHHHHHhCCHHHhhheeehhhcCCCHHHHHHHHCCCHHHHHHHH
Confidence 000 0 0112344444444332 2246799999999999999999999
Q ss_pred HHcCCC
Q 011577 453 FITRMP 458 (482)
Q Consensus 453 ~~ar~~ 458 (482)
++++..
T Consensus 169 ~Rar~~ 174 (193)
T TIGR02947 169 HRGRKQ 174 (193)
T ss_pred HHHHHH
Confidence 998764
No 82
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=99.55 E-value=3.9e-14 Score=130.48 Aligned_cols=132 Identities=11% Similarity=0.079 Sum_probs=101.1
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcc
Q 011577 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR 405 (482)
Q Consensus 326 Gd~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~ir 405 (482)
+..+++.|+..|.+.|+.+|.++.++..+++|++||.|+.+|+..++|++. ...|.+|++.+++|.+++++|++.+...
T Consensus 7 ~~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~~~~~~~~~-~~~~~~wL~~iarn~~~d~~Rk~~~~~~ 85 (173)
T PRK09645 7 EAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADT-GRSARAWLFTVARNLVIDERRSARARPV 85 (173)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcc-cccHHHHHHHHHHHHHHHHHHhhccccc
Confidence 348999999999999999999999999999999999999999999999743 2479999999999999999997653211
Q ss_pred --------c-----chhHHH--HHHHHHHHHHHH--------HHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 406 --------L-----PENIYT--LLSKVLEAKRLY--------IQEGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 406 --------l-----P~~v~e--~l~kI~ka~~eL--------~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
. +..+.. ....+..+...| ...+..+.+++|||+.||+|+++|+..+++++..
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 0 111110 111233333322 2223347899999999999999999999988653
No 83
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=99.55 E-value=4.1e-14 Score=131.95 Aligned_cols=129 Identities=12% Similarity=0.069 Sum_probs=100.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc-
Q 011577 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL- 406 (482)
Q Consensus 328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irl- 406 (482)
.|++.|+..|.+.|+.++.++.++..+++|++||+|+.+|+++++|++. ..|.+|++.+++|.+++++|+..+....
T Consensus 16 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~--~~~~awl~~ia~n~~~d~~Rk~~~~~~~~ 93 (179)
T PRK09415 16 DLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGK--SSLKTWLYRIAINHCKDYLKSWHNKKVIV 93 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--cccHHHHHHHHHHHHHHHHHhhccccccc
Confidence 7999999999999999999999999999999999999999999999874 3699999999999999999975332111
Q ss_pred --------------chh---HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 407 --------------PEN---IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 407 --------------P~~---v~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
|.. ..+....+.++...|.. .+..+.+++|||+.||||+++|+..+++++..
T Consensus 94 ~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tv~~~l~Ra~~~ 170 (179)
T PRK09415 94 TEDIFTYMESQKESVEEEVIQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKEL 170 (179)
T ss_pred cccccccccccccCcHHHHHHHHHHHHHHHHHHhCCHHHhhHhHhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 100 01112223333333221 22346799999999999999999999998754
No 84
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=99.55 E-value=5e-14 Score=129.80 Aligned_cols=135 Identities=18% Similarity=0.184 Sum_probs=101.9
Q ss_pred HHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHH
Q 011577 321 SELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQ 399 (482)
Q Consensus 321 ~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrk 399 (482)
..++.|+ .|++.|+..|.+.|+.+++++.+ ..+++|++||+|+.+|+.++.|++. ..|.+|++.+++|.+++++|+
T Consensus 3 ~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~ 79 (175)
T PRK12518 3 LRCQRGDRQSFRQLYRRYQQKVRSTLYQLCG-RELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATDARRQ 79 (175)
T ss_pred hHHHcCCHHHHHHHHHHHHHHHHHHHHHHcC-HhHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHHHHHH
Confidence 4456666 89999999999999999999875 4789999999999999999999974 479999999999999999997
Q ss_pred hcCCcc----cc-----------hhHH--HHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 400 HSRTIR----LP-----------ENIY--TLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 400 q~r~ir----lP-----------~~v~--e~l~kI~ka~~eL~~e--------~gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
..+... .+ .... +....+.++...|... +..+.+++|||+.||+|+++|+..+++
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~eIA~~lg~s~~tv~~~l~R 159 (175)
T PRK12518 80 FAQRPSRIQDDSLNDQPSRPSDTPDLMQLHYQDLVQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFY 159 (175)
T ss_pred hhccccchhcccccccccCCCCcHHHHHHHHHHHHHHHHHhCCHHHeeeeeehHhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 643211 00 0110 0111233333333322 224669999999999999999999998
Q ss_pred cCCC
Q 011577 455 TRMP 458 (482)
Q Consensus 455 ar~~ 458 (482)
++..
T Consensus 160 ar~~ 163 (175)
T PRK12518 160 ARRQ 163 (175)
T ss_pred HHHH
Confidence 8754
No 85
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=99.54 E-value=5.6e-14 Score=132.62 Aligned_cols=130 Identities=15% Similarity=0.114 Sum_probs=102.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc
Q 011577 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 406 (482)
Q Consensus 327 d~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irl 406 (482)
..+|+.|+..|.+.|+.+|.+++++..+++|++||.|+.+|+.+++|+.. ..|.+|++++++|.+++++|++.+....
T Consensus 9 ~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~awL~~Ia~n~~~d~~R~~~~~~~~ 86 (187)
T PRK12516 9 TPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVG--TNMKAWLFTILRNEFYSQMRKRGREVQD 86 (187)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCc--ccHHHHHHHHHHHHHHHHHHhhcCCccc
Confidence 48999999999999999999999999999999999999999999999864 3699999999999999999987653211
Q ss_pred c------------h-hHHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 407 P------------E-NIYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 407 P------------~-~v~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
. . ........+..++..|. .....+.+++|||+.||+|+++|+..+++++..
T Consensus 87 ~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~i~~L~~~~g~s~~EIA~~Lgis~~tVk~~l~Rar~~ 159 (187)
T PRK12516 87 TDGMFTEQLAVHPSQYGTLDLQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQR 159 (187)
T ss_pred cccccccccCCCcchhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 0 0 00111222333333332 223347899999999999999999999988754
No 86
>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=99.53 E-value=4.2e-14 Score=126.80 Aligned_cols=129 Identities=17% Similarity=0.177 Sum_probs=98.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc-
Q 011577 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL- 406 (482)
Q Consensus 328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irl- 406 (482)
+|++.|+..|.+.|+.+++++.++..+.+|++||+|+++|+.+.+|++. .+|.+|++.++++.+.+++++..+....
T Consensus 1 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~--~~~~~wl~~i~r~~~~d~~r~~~~~~~~~ 78 (161)
T TIGR02985 1 KAFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEV--ESFKAYLFTIVKNRSLNYLRHKQVEEKYQ 78 (161)
T ss_pred ChHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc--ccHHHHHHHHHHHHHHHHHHHHHhHhHHH
Confidence 3789999999999999999999999999999999999999999999874 4799999999999999999876532110
Q ss_pred ---------------chh---HHHHHHHHHHHH-------HHHH-HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 407 ---------------PEN---IYTLLSKVLEAK-------RLYI-QEGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 407 ---------------P~~---v~e~l~kI~ka~-------~eL~-~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
|.. ..+....+..+. +++. ..+..+.+.+|||+.||+|..+|+..+++++..
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~il~l~~~~~~~~~eIA~~lgis~~tv~~~~~ra~~~ 156 (161)
T TIGR02985 79 EEILEIEVDELSENDPEEELEAKELQLIIYKAIEKLPEQCRKIFILSRFEGKSYKEIAEELGISVKTVEYHISKALKE 156 (161)
T ss_pred HHHHhhcccccCCCCcHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 100 011111222222 2221 213347799999999999999999999988643
No 87
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=99.53 E-value=1.2e-13 Score=141.01 Aligned_cols=141 Identities=13% Similarity=0.155 Sum_probs=109.4
Q ss_pred HHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHH
Q 011577 317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK 395 (482)
Q Consensus 317 ~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~ 395 (482)
.+|+.+++.|+ .++++|+..|.+.|+.+|++++++..+++|++||.|+.+|+.+++|++. ..|.+|++.+++|.+++
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 46888888888 8999999999999999999999999999999999999999999999853 47999999999999999
Q ss_pred HHHHhcCCcc---c----------------------------------chhHH---HHH-HHHHHHHHHHHHh-------
Q 011577 396 AIFQHSRTIR---L----------------------------------PENIY---TLL-SKVLEAKRLYIQE------- 427 (482)
Q Consensus 396 ~Lrkq~r~ir---l----------------------------------P~~v~---e~l-~kI~ka~~eL~~e------- 427 (482)
++|++.+... . |.... +.+ ..+.+++..|...
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 9998653210 0 00000 001 1233333333222
Q ss_pred -cCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCc
Q 011577 428 -GNHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (482)
Q Consensus 428 -~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (482)
+..+.+++|||+.||+|+++|+..+++++..+
T Consensus 165 ~~~~g~s~~EIA~~lgis~~tVk~~l~RAr~~L 197 (339)
T PRK08241 165 RDVLGWSAAEVAELLDTSVAAVNSALQRARATL 197 (339)
T ss_pred HHhhCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 23467999999999999999999999887543
No 88
>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=99.53 E-value=5.8e-14 Score=130.27 Aligned_cols=134 Identities=15% Similarity=0.191 Sum_probs=100.2
Q ss_pred hcH-HHHHHHHHHHHHHHHHHHHHcc----CCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHH
Q 011577 325 SGN-SSREKLINANLRLVVHVAKQYQ----GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQ 399 (482)
Q Consensus 325 ~Gd-~Are~LI~snlrLV~sIAkrY~----~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrk 399 (482)
.|+ .|++.|+..|.+.|+.+|++|. ++..+++|++||+|+.+|+++.+|+...+..|.+|++.+++|.+++++++
T Consensus 3 ~~~~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r~ 82 (189)
T TIGR02984 3 GGDQEALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNVLADALRR 82 (189)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHHHHHHH
Confidence 455 8999999999999999999875 35678999999999999999999987656689999999999999999986
Q ss_pred hc----CCc----c-----------------------cchhH---HHHHHHHHHHHHHH--------HHhcCCCCcHHHH
Q 011577 400 HS----RTI----R-----------------------LPENI---YTLLSKVLEAKRLY--------IQEGNHSPDKEDL 437 (482)
Q Consensus 400 q~----r~i----r-----------------------lP~~v---~e~l~kI~ka~~eL--------~~e~gr~pS~eEI 437 (482)
.. +.. . -|... .+....+.++...| ...+..+.+++||
T Consensus 83 ~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vi~l~~~~g~s~~eI 162 (189)
T TIGR02984 83 HLGAQKRDIRREQSLDAGGRLDESSVRLAAQLAADGPSPSQVAARREAAVRLAQALAKLPEDYREVILLRHLEGLSFAEV 162 (189)
T ss_pred HHHHHhhhcccccCCCcccccCCcchhHHHHccCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCHHHH
Confidence 51 110 0 01000 11112233333222 1223357899999
Q ss_pred HHHhCCCHHHHHHHHHHcCCC
Q 011577 438 ARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 438 Ae~LGIS~etVk~~L~~ar~~ 458 (482)
|+.||||+++|+..+++++..
T Consensus 163 A~~lgis~~~v~~~l~Ra~~~ 183 (189)
T TIGR02984 163 AERMDRSEGAVSMLWVRGLAR 183 (189)
T ss_pred HHHHCcCHHHHHHHHHHHHHH
Confidence 999999999999999988643
No 89
>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=99.52 E-value=1.1e-13 Score=125.98 Aligned_cols=131 Identities=13% Similarity=0.115 Sum_probs=100.7
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcc
Q 011577 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR 405 (482)
Q Consensus 326 Gd~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~ir 405 (482)
+..+++.|+..|.+.|+.++.+++++..+++|++||+|+.+|+.+++|+. ...|.+|++.+++|.+++++|+..+...
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 34899999999999999999999999999999999999999999999964 3479999999999999999998654110
Q ss_pred ----cc-----h---------hHHHHHHHHHHHHHHHH-HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 406 ----LP-----E---------NIYTLLSKVLEAKRLYI-QEGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 406 ----lP-----~---------~v~e~l~kI~ka~~eL~-~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
.+ . .+...+.++....+.+. ..+-.+.+++|||+.||+|+++|+..+.+++..
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 01122222222222221 222346799999999999999999999988754
No 90
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=99.52 E-value=8.9e-14 Score=129.71 Aligned_cols=134 Identities=12% Similarity=0.041 Sum_probs=99.9
Q ss_pred hhcH-HHHHHHHHHHHHHHHHHHHHccC--CCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHh
Q 011577 324 HSGN-SSREKLINANLRLVVHVAKQYQG--RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH 400 (482)
Q Consensus 324 ~~Gd-~Are~LI~snlrLV~sIAkrY~~--~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq 400 (482)
..|+ .+|+.|+..|.+.|+.++.++.+ +..+++|++||.|+.+|+.+++|+......|.||++++++|.+++++|++
T Consensus 8 ~~~d~~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~~Rk~ 87 (178)
T PRK12529 8 LSADRDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSWRRRQ 87 (178)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHHHHHH
Confidence 3455 89999999999999998766555 46789999999999999999999754345799999999999999999976
Q ss_pred cCCcc--------------cchhH---HHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 401 SRTIR--------------LPENI---YTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 401 ~r~ir--------------lP~~v---~e~l~kI~ka~~eL~~e--------~gr~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
.+... -|... .+....+.+++..|+.+ .-.+.+++|||+.||+|+++|+..++++
T Consensus 88 ~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~rA 167 (178)
T PRK12529 88 SLELAWLEALATLPEPLHPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQA 167 (178)
T ss_pred HHHhhhhhHhhhccCcCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 42110 11111 11223344444443322 2236799999999999999999999987
Q ss_pred CC
Q 011577 456 RM 457 (482)
Q Consensus 456 r~ 457 (482)
..
T Consensus 168 l~ 169 (178)
T PRK12529 168 YV 169 (178)
T ss_pred HH
Confidence 54
No 91
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=99.51 E-value=1.5e-13 Score=126.28 Aligned_cols=130 Identities=15% Similarity=0.128 Sum_probs=100.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc
Q 011577 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 406 (482)
Q Consensus 327 d~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irl 406 (482)
+..|..|+..|.+.|+.+|+++.++..+++|++||+|+.+|+.+++|+.. ..|.+|++.+++|.+++++|+..+....
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 46899999999999999999999999999999999999999999999864 3699999999999999999976543211
Q ss_pred ------------ch-hHHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 407 ------------PE-NIYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 407 ------------P~-~v~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
+. ........+..++..|. ..+..+.+++|||+.|||++++|+..+++++..
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 00 00011122333333322 223347899999999999999999999988753
No 92
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=99.51 E-value=1.4e-13 Score=125.55 Aligned_cols=128 Identities=12% Similarity=0.135 Sum_probs=99.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc
Q 011577 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 407 (482)
Q Consensus 328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP 407 (482)
.|++.++..|.+.|+.++.++.++..+++|++||+|+.+|+.+++|++. .|.||++.+++|.+++++|+..+.....
T Consensus 5 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDv~Qe~f~~~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~~~~~ 81 (161)
T PRK12541 5 QSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE---EIRPWLFTIAYNAFIDWYRKEKKYKTTT 81 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhHHHccCC---ChHHHHHHHHHHHHHHHHHhcccccccc
Confidence 7999999999999999999999999999999999999999999999863 5999999999999999999865422110
Q ss_pred ------------hh---HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 408 ------------EN---IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 408 ------------~~---v~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
.. .......+..+...|.. ....+.+++|||+.||+|+++|+..+++++..
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~Rar~~ 155 (161)
T PRK12541 82 IEEFHLPNVPSTEHEYFIKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKE 155 (161)
T ss_pred hhhhhccCCCCcHHHHHHHhHHHHHHHHHHHCCHHHHHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 00 01111222223222221 12347799999999999999999999988754
No 93
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=99.51 E-value=1.5e-13 Score=130.82 Aligned_cols=138 Identities=15% Similarity=0.111 Sum_probs=105.2
Q ss_pred HHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHH
Q 011577 317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK 395 (482)
Q Consensus 317 ~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~ 395 (482)
.+|+..+..|+ .|++.|+..|.+.++.+++ +.++..+++|++||.|+.+|+.+++|++. ..|.+|++.+++|.+++
T Consensus 13 ~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~-~~~~~~~AEDivQevflkl~~~~~~~~~~--~~~~~WL~~Iarn~~id 89 (196)
T PRK12535 13 TDLALAAGRGDRAALTEFIRETQDDVWRLLA-HLGGHDIADDLTQETYLRVMSALPRFAAR--SSARTWLLSLARRVWVD 89 (196)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHHhhhcCCc--ccHHHHHHHHHHHHHHH
Confidence 44666777777 8999999999999999975 57888899999999999999999999864 37999999999999999
Q ss_pred HHHHhcCCccc--------------chh--HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHH
Q 011577 396 AIFQHSRTIRL--------------PEN--IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERL 451 (482)
Q Consensus 396 ~Lrkq~r~irl--------------P~~--v~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etVk~~ 451 (482)
++|+..+.... |.. ..+....+.+++..|.. .+..+.+++|||+.||+++++|+..
T Consensus 90 ~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIAe~lgis~~tV~~~ 169 (196)
T PRK12535 90 NIRHDMARPRKSATEYEDAAATTASNETTGSWSEWIDVRTLIDALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSR 169 (196)
T ss_pred HHHhhccCCCcccccccccccccCCcchhHHHHHHHHHHHHHHcCCHHHHHHhhhHHHhCCCHHHHHHHhCCCHHHHHHH
Confidence 99986432210 000 11112233334333322 2224679999999999999999999
Q ss_pred HHHcCC
Q 011577 452 IFITRM 457 (482)
Q Consensus 452 L~~ar~ 457 (482)
+++++.
T Consensus 170 l~Rar~ 175 (196)
T PRK12535 170 VARARA 175 (196)
T ss_pred HHHHHH
Confidence 998865
No 94
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=99.50 E-value=1.1e-13 Score=139.98 Aligned_cols=129 Identities=14% Similarity=0.149 Sum_probs=100.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcc--
Q 011577 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR-- 405 (482)
Q Consensus 328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~ir-- 405 (482)
.|++.|+..|.+.|+.+|++++++..+++|++||.|+.+|+.+++|+.. ..|.+|++++++|.|++++|++.+...
T Consensus 5 ~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~~~~~~~ 82 (324)
T TIGR02960 5 AAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGR--SSVRTWLYRIATNACLDALEARQRRPRPV 82 (324)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCcc--cchHHHHHHHHHHHHHHHHHhccCCcCcc
Confidence 8999999999999999999999999999999999999999999999864 469999999999999999997653211
Q ss_pred ------------------------cc--------------hhH---HHHH-HHHHHHHHHHHH--------hcCCCCcHH
Q 011577 406 ------------------------LP--------------ENI---YTLL-SKVLEAKRLYIQ--------EGNHSPDKE 435 (482)
Q Consensus 406 ------------------------lP--------------~~v---~e~l-~kI~ka~~eL~~--------e~gr~pS~e 435 (482)
++ ... .+.+ ..+..++..|.. .+..+.+++
T Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~ 162 (324)
T TIGR02960 83 GLGAPSADGTAAASEAAEVTWLEPLPDLTLDLDDPAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRDVLGWRAA 162 (324)
T ss_pred ccCCCCCcccccccccccccccCCCCccccccccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHHhCCCHH
Confidence 00 000 0001 113333333322 233467999
Q ss_pred HHHHHhCCCHHHHHHHHHHcCCC
Q 011577 436 DLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 436 EIAe~LGIS~etVk~~L~~ar~~ 458 (482)
|||+.||+|+++|+..+++++..
T Consensus 163 EIA~~lgis~~tV~~~l~Rar~~ 185 (324)
T TIGR02960 163 ETAELLGTSTASVNSALQRARAT 185 (324)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHH
Confidence 99999999999999999988754
No 95
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=99.50 E-value=2e-13 Score=132.38 Aligned_cols=132 Identities=14% Similarity=0.090 Sum_probs=102.4
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC
Q 011577 324 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 403 (482)
Q Consensus 324 ~~Gd~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~ 403 (482)
.....+|+.|+..|.+.|+.++.++.++..+++|++||+|+.+|+.+++|++. .|.+|++++++|.+++++|++.+.
T Consensus 14 ~~~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~~---~~~aWL~~IarN~~~d~~Rk~~~~ 90 (216)
T PRK12533 14 AARGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRGD---NARPWLLAIVRHTWYSEWRRRANA 90 (216)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCcc---chHhHHHHHHHHHHHHHHHhhccc
Confidence 34458999999999999999999999999999999999999999999999852 599999999999999999986532
Q ss_pred cc------cc---------------hh---HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHH
Q 011577 404 IR------LP---------------EN---IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERL 451 (482)
Q Consensus 404 ir------lP---------------~~---v~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etVk~~ 451 (482)
.. +. .. ..+....+.+++..|.. .+..+.+++|||+.||||+++|+..
T Consensus 91 ~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y~eg~s~~EIAe~LgiS~~tVk~~ 170 (216)
T PRK12533 91 HEVAAPDTLDDADSLDDWQPAGEDPLALLLRAEDVRLVNAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSR 170 (216)
T ss_pred ccccccccccccccccccccCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHhHhhhHHhcCCCHHHHHHHHCCCHHHHHHH
Confidence 11 00 00 00122234334333322 1334779999999999999999999
Q ss_pred HHHcCCC
Q 011577 452 IFITRMP 458 (482)
Q Consensus 452 L~~ar~~ 458 (482)
+++++..
T Consensus 171 L~RAr~~ 177 (216)
T PRK12533 171 LARARRR 177 (216)
T ss_pred HHHHHHH
Confidence 9988764
No 96
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=99.49 E-value=1.8e-13 Score=125.48 Aligned_cols=126 Identities=13% Similarity=0.107 Sum_probs=97.8
Q ss_pred HHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc--
Q 011577 330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP-- 407 (482)
Q Consensus 330 re~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP-- 407 (482)
|+.|+..|.+.|+.+|++|.++..+++|++||+|+.+|+++++|++. .|.+|++.+++|.+++++|+..+.....
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 5999999999999999999876532211
Q ss_pred ----------hhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 408 ----------ENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 408 ----------~~v---~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
... .+....+.++...|. .....+.+++|||+.||+++++|+..+++++..
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 110 111122333332221 123346799999999999999999999988754
No 97
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=99.49 E-value=1.3e-13 Score=127.50 Aligned_cols=132 Identities=10% Similarity=0.045 Sum_probs=99.8
Q ss_pred hhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcC
Q 011577 324 HSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR 402 (482)
Q Consensus 324 ~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r 402 (482)
+.|+ .|+..|+..|.+.|+.++.++.++..+++|++||+|+.+|+. ..|... ..|.+|++++++|.+++++|++.+
T Consensus 5 ~~~~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~~~d~~Rk~~~ 81 (172)
T PRK12523 5 QSPHSELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRRAAL 81 (172)
T ss_pred CCCCcHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHHHHHHHHHHHH
Confidence 4667 899999999999999999999999999999999999999987 446543 369999999999999999998643
Q ss_pred Ccc--------------cchhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577 403 TIR--------------LPENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRM 457 (482)
Q Consensus 403 ~ir--------------lP~~v---~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (482)
... -|... .+....+.+++..|. ..+..+.+++|||+.||||+++|+..+++++.
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~ 161 (172)
T PRK12523 82 EQAYLAELALVPEAEQPSPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGLR 161 (172)
T ss_pred HHHHHHHHhhcccccCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 110 11110 111222333333322 22334789999999999999999999998865
Q ss_pred C
Q 011577 458 P 458 (482)
Q Consensus 458 ~ 458 (482)
.
T Consensus 162 ~ 162 (172)
T PRK12523 162 Q 162 (172)
T ss_pred H
Confidence 4
No 98
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=99.49 E-value=4.9e-13 Score=131.90 Aligned_cols=91 Identities=21% Similarity=0.337 Sum_probs=82.0
Q ss_pred CHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCC--CHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHH
Q 011577 315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGI--SLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ 391 (482)
Q Consensus 315 dd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~--d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRn 391 (482)
+.++|+..++.|+ .|++.|+..|.++|+++|.+|+++.. +.+|++|||++++|+++++|++.+|..|.+|++++|+|
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 4566788888888 89999999999999999999998875 59999999999999999999999888899999999999
Q ss_pred HHHHHHHHhcCCcc
Q 011577 392 TIRKAIFQHSRTIR 405 (482)
Q Consensus 392 aI~~~Lrkq~r~ir 405 (482)
.+++++|++.+...
T Consensus 84 ~~iDylRk~~~~~~ 97 (237)
T PRK08311 84 RLIDYFRKESKHNL 97 (237)
T ss_pred HHHHHHHHhhcccc
Confidence 99999998776433
No 99
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=99.46 E-value=2e-13 Score=124.25 Aligned_cols=122 Identities=11% Similarity=0.073 Sum_probs=92.8
Q ss_pred HHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcc-c------
Q 011577 334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR-L------ 406 (482)
Q Consensus 334 I~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~ir-l------ 406 (482)
++.|.+.|+.+|.+++++..+++|++||+|+.+|+++++|++. .|.+|++.+++|.+++++|+..+... .
T Consensus 1 ~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~~~~~~ 77 (160)
T PRK09642 1 MQTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFR---GLKTWMARIATNHAIDYKRKKARENEELSLCKET 77 (160)
T ss_pred CchHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcccccccc---hhHHHHHHHHHHHHHHHHHHhcccccccccchhh
Confidence 3579999999999999999999999999999999999999863 49999999999999999998654211 0
Q ss_pred ---------chhHH---HHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 407 ---------PENIY---TLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 407 ---------P~~v~---e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
|.... +....+.++...|+. .+..+.+++|||+.||+|+++|+..+++++..
T Consensus 78 ~~~~~~~~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~ 149 (160)
T PRK09642 78 EENIKSSHNIEDLLLTKEQKLLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKW 149 (160)
T ss_pred hhhccCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 11000 111123333333222 23347899999999999999999999998754
No 100
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=99.46 E-value=3.9e-13 Score=128.04 Aligned_cols=124 Identities=13% Similarity=0.159 Sum_probs=95.6
Q ss_pred HHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc-----
Q 011577 333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP----- 407 (482)
Q Consensus 333 LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP----- 407 (482)
++..|.+.|+.+|++++++..+++|++||+|+.+|+.+++|++. ..|.+|++.+++|.+++++|++.+...++
T Consensus 13 ~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~~~~ 90 (201)
T PRK12545 13 YLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQ--SAHKTWVFGILRNKLIDTLRARQRTVNLSALDAE 90 (201)
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhcccc--chHHHHHHHHHHHHHHHHHHhhcccccccccccc
Confidence 48999999999999999999999999999999999999999875 36999999999999999999876432111
Q ss_pred ------------------------------hhHH---HHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHH
Q 011577 408 ------------------------------ENIY---TLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVE 446 (482)
Q Consensus 408 ------------------------------~~v~---e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~e 446 (482)
.... +....+.+++..|. ..+..+.+++|||+.||+|++
T Consensus 91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~v~~L~~~eg~s~~EIA~~lgis~~ 170 (201)
T PRK12545 91 LDGEALLDRELFKDNGHWAAHAKPRPWPKPETILQQQQFWTLFETCLDHLPEQIGRVFMMREFLDFEIDDICTELTLTAN 170 (201)
T ss_pred cchhhhhhhhhhcccccccccccCcCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHH
Confidence 0000 00112233333322 223347899999999999999
Q ss_pred HHHHHHHHcCCC
Q 011577 447 KLERLIFITRMP 458 (482)
Q Consensus 447 tVk~~L~~ar~~ 458 (482)
+|+..+++++..
T Consensus 171 tVk~~l~RAr~~ 182 (201)
T PRK12545 171 HCSVLLYRARTR 182 (201)
T ss_pred HHHHHHHHHHHH
Confidence 999999988754
No 101
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=99.46 E-value=5.1e-13 Score=121.89 Aligned_cols=126 Identities=18% Similarity=0.107 Sum_probs=98.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc-
Q 011577 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL- 406 (482)
Q Consensus 328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irl- 406 (482)
.+++.|+..|.+.|+.+|.++.++..+++|++||+|+.+|++ .|+. +..|.+|++.+++|.+.+++|+..+....
T Consensus 3 ~~f~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fi~~~~~--~~~~--~~~~~~wl~~i~rn~~~d~~rk~~~~~~~~ 78 (166)
T PRK09639 3 ETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKG--IENEKGWLIKSARNVAYNYLRSEKRRRARI 78 (166)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH--hccc--ccchHHHHHHHHHHHHHHHHHHhccccccc
Confidence 689999999999999999999999999999999999999999 6764 35799999999999999999987643211
Q ss_pred --------------chhH---HHHHHHHHHHHHH--------HHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 407 --------------PENI---YTLLSKVLEAKRL--------YIQEGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 407 --------------P~~v---~e~l~kI~ka~~e--------L~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
|... .+....+.++... +...+ .+.+++|||+.||+|+++|+..+++++..
T Consensus 79 ~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~-~g~s~~eIA~~lgis~~tV~~~i~ra~~~ 154 (166)
T PRK09639 79 LGEFQWQEVDNEPSPEEIWIRKEEITKVQEVLAKMTERDRTVLLLRF-SGYSYKEIAEALGIKESSVGTTLARAKKK 154 (166)
T ss_pred cchhhhhhccCCCChHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 1100 1111223333322 22335 67899999999999999999999988654
No 102
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=99.46 E-value=6.1e-13 Score=125.08 Aligned_cols=129 Identities=19% Similarity=0.205 Sum_probs=100.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc-
Q 011577 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL- 406 (482)
Q Consensus 328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irl- 406 (482)
.++..++..|.+.|+.+|.+++++..+++|++||.|+.+|+.+++|++. ..|.+|++++++|.++++++++.+....
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 5788999999999999999999999999999999999999999999865 3699999999999999999986543210
Q ss_pred -----------chh-HHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 407 -----------PEN-IYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 407 -----------P~~-v~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
+.. .......+..++..|. ..+..+.+++|||+.||+|+++|+..+++++..
T Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RAr~~ 154 (182)
T PRK12540 83 DGSYAKTLKSQPGQNAHLEFEEFRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSK 154 (182)
T ss_pred cccccccccCCCchHHHHHHHHHHHHHHhCCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 100 0111122333333332 223347899999999999999999999998764
No 103
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=99.45 E-value=5.6e-13 Score=127.76 Aligned_cols=131 Identities=20% Similarity=0.265 Sum_probs=101.1
Q ss_pred hcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC
Q 011577 325 SGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 403 (482)
Q Consensus 325 ~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~ 403 (482)
.|+ .++++|+..|.+.|+.++.++.++..+++||+||+|+.+|+.+.+|++ + .|.+|++.+++|.+++++|+..+.
T Consensus 24 ~~d~~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~~~d~~Rk~~~~ 100 (203)
T PRK09647 24 KATMPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNLFLDMVRRRARI 100 (203)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHHHHHHHHhcccC
Confidence 344 899999999999999999999999999999999999999999999985 3 699999999999999999987531
Q ss_pred c--cc-------------chhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577 404 I--RL-------------PENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRM 457 (482)
Q Consensus 404 i--rl-------------P~~v---~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (482)
. .. |... ......+..++..|. ..+..+.+++|||+.|||++++|+..+++++.
T Consensus 101 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~L~~~~r~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RArk 180 (203)
T PRK09647 101 RMEALPEDYDRVPGDEPNPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQ 180 (203)
T ss_pred ccccccccccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 1 00 1100 011222333333221 12234789999999999999999999999875
Q ss_pred C
Q 011577 458 P 458 (482)
Q Consensus 458 ~ 458 (482)
.
T Consensus 181 ~ 181 (203)
T PRK09647 181 Q 181 (203)
T ss_pred H
Confidence 4
No 104
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=99.45 E-value=9.4e-13 Score=120.11 Aligned_cols=127 Identities=14% Similarity=0.114 Sum_probs=97.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCc---
Q 011577 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI--- 404 (482)
Q Consensus 328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~i--- 404 (482)
.|++.|+..|.+.|+.++.++.++..+++|++||+|+.+|+..+.|++ ..|.+|++++++|.+++++|+..+..
T Consensus 4 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~---~~~~~wl~~i~~n~~~d~~R~~~~~~~~~ 80 (161)
T PRK12528 4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQI---IEPRAFLTTIAKRVLCNHYRRQDLERAYL 80 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhccccccc---cCHHHHHHHHHHHHHHHHHHHHHHHHhhH
Confidence 689999999999999999999999999999999999999999988864 36999999999999999999754211
Q ss_pred ----ccc-------hhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577 405 ----RLP-------ENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRM 457 (482)
Q Consensus 405 ----rlP-------~~v---~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (482)
..+ ... .+....+.++...|. ..+..+.+++|||+.||+|+++|+..+++++.
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~~g~s~~EIA~~l~is~~tV~~~l~ra~~ 155 (161)
T PRK12528 81 EALAQLPERVAPSEEERAIILETLVELDQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAM 155 (161)
T ss_pred HHhhccccccCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 011 000 111122333333222 22334789999999999999999999998754
No 105
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=99.44 E-value=5.8e-13 Score=125.50 Aligned_cols=125 Identities=14% Similarity=0.198 Sum_probs=95.2
Q ss_pred HHHHHHHHHHHHHHHHHccCCCCC-HhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc---
Q 011577 331 EKLINANLRLVVHVAKQYQGRGIS-LHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL--- 406 (482)
Q Consensus 331 e~LI~snlrLV~sIAkrY~~~g~d-~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irl--- 406 (482)
+..+..|.+.|+.+|+++.++..+ ++|++||+|+.+|+++++|++. ..|.+|++++++|.+++++|++.+....
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 457888999999999999999888 9999999999999999999864 4799999999999999999987542211
Q ss_pred -------------------------------chhH---HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCC
Q 011577 407 -------------------------------PENI---YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGIT 444 (482)
Q Consensus 407 -------------------------------P~~v---~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS 444 (482)
|... .+....+.++...|.. .+..+.+++|||+.||+|
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 0000 0111123333333221 223467999999999999
Q ss_pred HHHHHHHHHHcCC
Q 011577 445 VEKLERLIFITRM 457 (482)
Q Consensus 445 ~etVk~~L~~ar~ 457 (482)
+++|+..+++++.
T Consensus 166 ~~tVk~~l~Rar~ 178 (195)
T PRK12532 166 TSNYHTIMHRARE 178 (195)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999998865
No 106
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=99.43 E-value=1.4e-12 Score=122.51 Aligned_cols=126 Identities=14% Similarity=0.178 Sum_probs=97.7
Q ss_pred HHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchh
Q 011577 330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 409 (482)
Q Consensus 330 re~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~ 409 (482)
++.|++.|.+.|+.++.++.++..+++|++||.|+.+|+.+..|+.. ..|.+|++.+++|.+++++|++.+....+..
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~aeDi~QEvflkl~~~~~~~~~~--~~~~~wL~~i~~n~~~d~~Rk~~~~~~~~~~ 80 (181)
T PRK09637 3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDG--SSIKSWLYQIANNTIIDFYRKKNRSEELPDD 80 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHhHHHhccc--cchHHHHHHHHHHHHHHHHHhccccCCcchh
Confidence 67899999999999999999999999999999999999999999853 4799999999999999999987644332110
Q ss_pred -------------------HHHHHHHHHHHHHHH-HHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577 410 -------------------IYTLLSKVLEAKRLY-IQEGNHSPDKEDLARRVGITVEKLERLIFITRM 457 (482)
Q Consensus 410 -------------------v~e~l~kI~ka~~eL-~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (482)
+...+.++....+.+ ......+.+++|||+.||+|+++|+..+.+++.
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 111112222222221 122334789999999999999999999998864
No 107
>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=99.43 E-value=8.5e-13 Score=124.44 Aligned_cols=127 Identities=11% Similarity=0.164 Sum_probs=97.0
Q ss_pred HHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc---
Q 011577 331 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP--- 407 (482)
Q Consensus 331 e~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP--- 407 (482)
.+.+..|.+.|+.++++++++..+++|++||+|+.+|+..++|++. .+|.+|++.+++|.+++++|++.+....+
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 3578899999999999999999999999999999999999999864 47999999999999999999865432111
Q ss_pred ------------------------------hhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHH
Q 011577 408 ------------------------------ENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVE 446 (482)
Q Consensus 408 ------------------------------~~v---~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~e 446 (482)
... .+....+.+++..|. ..+..+.+++|||+.||+|++
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 000 001122333332221 223347899999999999999
Q ss_pred HHHHHHHHcCCCc
Q 011577 447 KLERLIFITRMPL 459 (482)
Q Consensus 447 tVk~~L~~ar~~l 459 (482)
+|+..+.+++..+
T Consensus 163 tvk~rl~Rar~~L 175 (188)
T TIGR02943 163 NCHVLLYRARLSL 175 (188)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999987643
No 108
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=99.43 E-value=9.4e-13 Score=126.46 Aligned_cols=128 Identities=13% Similarity=0.203 Sum_probs=97.7
Q ss_pred HHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc-
Q 011577 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP- 407 (482)
Q Consensus 329 Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP- 407 (482)
.-..++..|.+.|+.+|++++++..+++|++||+|+.+|+.+.+|+.. .+|.+|++++++|.+++++|+..+....+
T Consensus 19 ~~~~~~~~~~~~l~~~~~~~~~d~~~AEDivQEvfikl~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~~~~~~~~ 96 (206)
T PRK12544 19 QDPVFLEDLRKQMIKFATLQLSDLHLAEDAVQEALIGALKNADSFAGR--AAFKTWVFAILKNKIIDLLRQKKRHVSASS 96 (206)
T ss_pred hhHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhhcccccccc
Confidence 346788999999999999999999999999999999999999999864 46999999999999999999865432111
Q ss_pred ---------------------------------hhHH---HHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCC
Q 011577 408 ---------------------------------ENIY---TLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGI 443 (482)
Q Consensus 408 ---------------------------------~~v~---e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGI 443 (482)
.... +....+..++..|. ..+..+.+++|||+.||+
T Consensus 97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~L~~L~~~~r~v~~L~~~~g~s~~EIAe~lgi 176 (206)
T PRK12544 97 LLRDEEEEEDFEELFDESGHWQKDERPQAWGNPEESLEQEQFWRIFEACLDGLPAKYARVFMMREFIELETNEICHAVDL 176 (206)
T ss_pred cccccchhhHHHHhhcccccccccccccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCc
Confidence 0000 00112222232222 223346799999999999
Q ss_pred CHHHHHHHHHHcCCC
Q 011577 444 TVEKLERLIFITRMP 458 (482)
Q Consensus 444 S~etVk~~L~~ar~~ 458 (482)
|+++|+..+++++..
T Consensus 177 s~~tV~~~l~RAr~~ 191 (206)
T PRK12544 177 SVSNLNVLLYRARLR 191 (206)
T ss_pred CHHHHHHHHHHHHHH
Confidence 999999999998764
No 109
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=99.43 E-value=1.3e-12 Score=123.26 Aligned_cols=132 Identities=12% Similarity=0.026 Sum_probs=100.8
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCc
Q 011577 325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 404 (482)
Q Consensus 325 ~Gd~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~i 404 (482)
....+++.++..|.+.|+.+|.++.++..+++|++||+|+.+|+.++.|++. ..|.+|++.+++|.+.+.+++..+..
T Consensus 20 ~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~--~~~~~wL~~Iarn~~~~~~r~~~~~~ 97 (188)
T PRK12517 20 SKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDE--KAAKAWLITILRRENARRFERKQFDL 97 (188)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCc--cchHHHHHHHHHHHHHHHHHHhccCc
Confidence 3458999999999999999999999999999999999999999999999864 46999999999999988876643221
Q ss_pred c-c-----c-----h-hHHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 405 R-L-----P-----E-NIYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 405 r-l-----P-----~-~v~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
. . + . ........+..++..|+. .+..+.+++|||+.|||++++|+..+++++..
T Consensus 98 ~~~~~~~~~~~~~~~~e~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~ 171 (188)
T PRK12517 98 VDIEDDSIEDDASHSSEEEMEQEWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARNQ 171 (188)
T ss_pred cCcccccccCccccChhHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 1 0 0 0 001111223344433322 23346799999999999999999999988754
No 110
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=99.43 E-value=8.4e-13 Score=124.43 Aligned_cols=126 Identities=15% Similarity=0.178 Sum_probs=95.3
Q ss_pred HHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc---
Q 011577 331 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP--- 407 (482)
Q Consensus 331 e~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP--- 407 (482)
+.-|..|.+.|+.+|.+++++..+++|++||+|+.+|+.+++|++. .+|.+|++++++|.+++++|++.+.....
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 3457888999999999999999999999999999999999999865 36999999999999999999876432110
Q ss_pred ----------------------h------h-HH--HHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHH
Q 011577 408 ----------------------E------N-IY--TLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKL 448 (482)
Q Consensus 408 ----------------------~------~-v~--e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etV 448 (482)
. . +. +....+..++..|+. .+..+.+++|||+.||+|+++|
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 0 0 00 001112333333322 2223689999999999999999
Q ss_pred HHHHHHcCCC
Q 011577 449 ERLIFITRMP 458 (482)
Q Consensus 449 k~~L~~ar~~ 458 (482)
+..+++++..
T Consensus 168 k~~l~RAr~~ 177 (189)
T PRK12530 168 HVLLYRARLQ 177 (189)
T ss_pred HHHHHHHHHH
Confidence 9999988753
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=99.42 E-value=8.3e-13 Score=118.84 Aligned_cols=122 Identities=12% Similarity=0.129 Sum_probs=94.4
Q ss_pred HHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc-------
Q 011577 334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL------- 406 (482)
Q Consensus 334 I~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irl------- 406 (482)
+.+|.+.|+.++.++.++..+++|++||+|+.+|+.+++|++ .+|.||++.+++|.+.++++++.+....
T Consensus 1 y~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~~~d~~r~~~~~~~~~~~~~~~ 77 (154)
T TIGR02950 1 YREYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNAFIDWYRKDKKIQTIDDDAIGD 77 (154)
T ss_pred CchHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHHHHHHHHHhhhhccccHhhhhh
Confidence 357999999999999999999999999999999999999997 4799999999999999999976532211
Q ss_pred --------chhH---HHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 407 --------PENI---YTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 407 --------P~~v---~e~l~kI~ka~~eL~~e--------~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
|... .+....+.++...|... +..+.+++|||+.||+|+++|+..+++++..
T Consensus 78 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~ 148 (154)
T TIGR02950 78 LEQHPVESPEHHLLIKIEQEEITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARKE 148 (154)
T ss_pred ccccccCChhHHHHHHHHHHHHHHHHHhCCHhheeeeeehhhccCcHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 1110 11123344444444322 2246799999999999999999999988653
No 112
>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=99.41 E-value=7.7e-13 Score=104.03 Aligned_cols=70 Identities=23% Similarity=0.432 Sum_probs=67.3
Q ss_pred HHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcC
Q 011577 333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR 402 (482)
Q Consensus 333 LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r 402 (482)
|++.|.++|+.++.+|.+++.+.+|++||++++||+++++||+++|..|.+|++.+++|.++++++++.+
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 7899999999999999999999999999999999999999999999899999999999999999998765
No 113
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=99.41 E-value=2.1e-12 Score=122.23 Aligned_cols=128 Identities=17% Similarity=0.190 Sum_probs=97.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc
Q 011577 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 407 (482)
Q Consensus 328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP 407 (482)
++++.|+. |.+.|+.+|+++.++..+++|++||.|+.+|+.+..|+.. ..|.+|++.+++|.+++++|+..+.....
T Consensus 8 ~~~~~l~~-~~~~l~~~a~~~l~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n~~~d~~Rk~~r~~~~~ 84 (188)
T PRK12546 8 DPRDELVE-HLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSDRRKHKREVPDP 84 (188)
T ss_pred hHHHHHHH-HHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHHHHHHHHHHhcccccCc
Confidence 56777766 7799999999999999999999999999999999999864 46999999999999999999876432110
Q ss_pred ------------hh-HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 408 ------------EN-IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 408 ------------~~-v~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
.. .......+..++..|.. .+..+.+++|||+.||||+++|+..+++++..
T Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~v~~L~~~~g~s~~EIA~~LgiS~~tVk~~l~Rar~~ 156 (188)
T PRK12546 85 EGVHAASLAVKPAHDGRLAMSDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARAR 156 (188)
T ss_pred ccccccccccCCcchhHHHHHHHHHHHHhCCHHHhHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 00 00111223333333322 22347799999999999999999999988753
No 114
>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=99.40 E-value=1.9e-12 Score=119.99 Aligned_cols=122 Identities=17% Similarity=0.204 Sum_probs=94.0
Q ss_pred HHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhH----
Q 011577 335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI---- 410 (482)
Q Consensus 335 ~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v---- 410 (482)
..|.+.|+.+++++.++..+++|++||+|+.+|+++++|+.. .+|.+|++.+++|.+++++|+..+...++...
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~l~~~~~~~~~~--~~f~~wl~~iarn~~~d~~Rk~~~~~~~~~~~~~~~ 79 (170)
T TIGR02959 2 DEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDG--QKIQSWLYQIARNTIIDFYRSKSRSVELPESLLAAD 79 (170)
T ss_pred chHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhccCccccchhhcccC
Confidence 468899999999999999999999999999999999999863 58999999999999999999976544322110
Q ss_pred --------HHHHHHHHHHHHHH--------HHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 411 --------YTLLSKVLEAKRLY--------IQEGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 411 --------~e~l~kI~ka~~eL--------~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
.+....+.+++..| ...+..+.+++|||+.||+|+++|+..+++++..
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 01111222222222 1223347899999999999999999999988754
No 115
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=99.36 E-value=7.9e-12 Score=115.85 Aligned_cols=128 Identities=11% Similarity=0.079 Sum_probs=96.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcc-
Q 011577 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR- 405 (482)
Q Consensus 327 d~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~ir- 405 (482)
..|++.++..|.+.++.++.++.++..+++||+||.|+.+|+. ..|++- ..|.+|++.+++|.+++++|+..+...
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 3799999999999999999999999999999999999999998 356543 259999999999999999997542110
Q ss_pred -------------cchhH---HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577 406 -------------LPENI---YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRM 457 (482)
Q Consensus 406 -------------lP~~v---~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (482)
-|... .+....+..+...|.. .+..+.+++|||+.||+++++|+..+++++.
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 11111 1122223333333322 2334779999999999999999999998864
No 116
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=99.36 E-value=5e-12 Score=119.02 Aligned_cols=127 Identities=12% Similarity=0.095 Sum_probs=96.6
Q ss_pred HHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc---
Q 011577 330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL--- 406 (482)
Q Consensus 330 re~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irl--- 406 (482)
.+..+..+.+.|+.+|.++.++..+++|++||.|+.+|+.+..|+.. ..|.+|++.+++|.+++++|++.+....
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 34557889999999999999999999999999999999999999864 4799999999999999999986542110
Q ss_pred ---------ch--hHHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 407 ---------PE--NIYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 407 ---------P~--~v~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
+. ........+.+++..|. ..+-.+.+++|||+.||||+++|+..+++++..
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 01111222333333322 123347899999999999999999999988754
No 117
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=99.31 E-value=1.1e-11 Score=121.69 Aligned_cols=132 Identities=15% Similarity=0.080 Sum_probs=96.5
Q ss_pred HHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHh
Q 011577 322 ELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH 400 (482)
Q Consensus 322 ~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq 400 (482)
....|+ .+++.+++.| +.++.++.++.++..+++||+||.|+.+|+. |+.. ..|.+|++.+++|.+++++|++
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 334455 7888888887 7899999999999999999999999999986 5543 3599999999999999999987
Q ss_pred cCCcccc--------hh-HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCc
Q 011577 401 SRTIRLP--------EN-IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (482)
Q Consensus 401 ~r~irlP--------~~-v~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (482)
.+...+. .. ..+....+.++...|.. .+..+.|++|||+.||+|+++|+..++++++.+
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 5432211 00 11111222333333322 123367999999999999999999999997643
No 118
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=99.31 E-value=1.4e-11 Score=112.29 Aligned_cols=123 Identities=17% Similarity=0.209 Sum_probs=92.1
Q ss_pred HHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcc------
Q 011577 332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR------ 405 (482)
Q Consensus 332 ~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~ir------ 405 (482)
.++..|.+.|+.+|.++.++..+++|++||+|+++|+....|++. .|.+|++.+++|.+++++|++.+...
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 367889999999999999999999999999999999998877653 48999999999999999997653211
Q ss_pred ----cc------hhH---HHHHHHHHHHHHHH--------HHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577 406 ----LP------ENI---YTLLSKVLEAKRLY--------IQEGNHSPDKEDLARRVGITVEKLERLIFITRM 457 (482)
Q Consensus 406 ----lP------~~v---~e~l~kI~ka~~eL--------~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (482)
.+ ... .+....+..+...| ...+..+.+++|||+.||+|+++|+..+.+++.
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 01 110 01112223332222 122334789999999999999999999988764
No 119
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=99.30 E-value=1.3e-11 Score=112.40 Aligned_cols=122 Identities=11% Similarity=0.086 Sum_probs=91.5
Q ss_pred HHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcc--------
Q 011577 334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR-------- 405 (482)
Q Consensus 334 I~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~ir-------- 405 (482)
+..|.+.++.++.+++++..+++|++||+|+.+|+..+.|++ .+|.||++.+++|.+++++|++.+...
T Consensus 1 ~~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~---~~~~~wL~~ia~n~~~d~~R~~~~~~~~~~~~~~~ 77 (159)
T PRK12527 1 MENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQI---EHPRAFLYRTALNLVVDRHRRHRVRQAEPLEVLDE 77 (159)
T ss_pred ChhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhccccccc---cchHHHHHHHHHHHHHHHHHHHhcccccchhhhhc
Confidence 357889999999999999999999999999999999999875 379999999999999999997532111
Q ss_pred -------cchhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 406 -------LPENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 406 -------lP~~v---~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
-|... ......+..++..|. .....+.+++|||+.||+|+++|+..+.+++..
T Consensus 78 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~ra~~~ 148 (159)
T PRK12527 78 EERLHSPSPQTRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKH 148 (159)
T ss_pred cccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 01111 011222333333322 223347799999999999999999999988653
No 120
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=99.29 E-value=4e-11 Score=110.61 Aligned_cols=127 Identities=8% Similarity=0.045 Sum_probs=95.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCc---
Q 011577 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI--- 404 (482)
Q Consensus 328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~i--- 404 (482)
.++.+++..|.+.++.++.++.++..+++|++||.|+.+|+..+.++. ..|.+|++++++|.+++++|+.....
T Consensus 9 ~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~~---~~~~~wl~~Iarn~~~d~~Rr~~~~~~~~ 85 (168)
T PRK12525 9 TLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEGWRRQDLERAYL 85 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCcccc---cCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 789999999999999999999999999999999999999986665542 36999999999999999998753110
Q ss_pred -----------ccchh---HHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577 405 -----------RLPEN---IYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRM 457 (482)
Q Consensus 405 -----------rlP~~---v~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (482)
..|.. ..+....+.+++..|. ..+..+.+++|||+.||+|+++|+..+.+++.
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~eg~s~~EIA~~l~is~~tV~~~l~ra~~ 160 (168)
T PRK12525 86 QSLAEAPEAVQPSPEEQWMVIETLLAIDRLLDGLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAFK 160 (168)
T ss_pred HHHhcccccccCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 01111 1111222333333222 22334779999999999999999999998754
No 121
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=99.25 E-value=4.6e-11 Score=120.15 Aligned_cols=127 Identities=12% Similarity=0.041 Sum_probs=93.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC--c-
Q 011577 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT--I- 404 (482)
Q Consensus 328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~--i- 404 (482)
..+..|++.|.+.++.+|++++++..++||++||.|+. |.....|+ ...|.+|++++++|.|++++|+..+. .
T Consensus 4 ~~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~-~~~~~~~~---~~~~~~WL~~Ia~n~~~d~lR~~~~~~~~~ 79 (293)
T PRK09636 4 ADAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQ---IRDPRAWLTRVVTRLCLDRLRSARHRRETY 79 (293)
T ss_pred cHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHhccccc---ccCHHHHHHHHHHHHHHHHHHhhhcccccc
Confidence 35678999999999999999999999999999999999 55667775 24799999999999999999975421 0
Q ss_pred ---cc----------chhH---HHHH-HHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 405 ---RL----------PENI---YTLL-SKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 405 ---rl----------P~~v---~e~l-~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
.+ |... .+.+ ..+..+...|. .....+.+++|||+.||+|+++|+.++++++..
T Consensus 80 ~~~~~~e~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~R~v~~L~~~~g~s~~EIA~~lg~s~~tVk~~l~RAr~~ 158 (293)
T PRK09636 80 VGPWLPEPVVEELDDPLEAVVAAEDLSLALMLALERLSPLERAAFLLHDVFGVPFDEIASTLGRSPAACRQLASRARKH 158 (293)
T ss_pred cCCcCCcCCCCCCCChHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 01 1110 0111 11222232221 122346799999999999999999999988754
No 122
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=99.18 E-value=9.2e-11 Score=118.73 Aligned_cols=128 Identities=12% Similarity=-0.040 Sum_probs=94.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC-c--
Q 011577 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT-I-- 404 (482)
Q Consensus 328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~-i-- 404 (482)
..+..+++.|.+.++.+|++++++..++||++||.|+.+|++...+ ...|.+|++++++|.|++++|+..+. .
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 5788999999999999999999999999999999999999987553 13699999999999999999974321 0
Q ss_pred -----ccc----------hhH---HHH-HHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577 405 -----RLP----------ENI---YTL-LSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRM 457 (482)
Q Consensus 405 -----rlP----------~~v---~e~-l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (482)
..| ... .+. ...+..+...|. .....+.+++|||+.||+|+.+|+..+++++.
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 011 000 000 112222222221 11223679999999999999999999999876
Q ss_pred Cc
Q 011577 458 PL 459 (482)
Q Consensus 458 ~l 459 (482)
.+
T Consensus 161 ~L 162 (290)
T PRK09635 161 KI 162 (290)
T ss_pred HH
Confidence 54
No 123
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=99.17 E-value=1.9e-10 Score=115.40 Aligned_cols=124 Identities=17% Similarity=0.086 Sum_probs=89.7
Q ss_pred HHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCc------c
Q 011577 332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI------R 405 (482)
Q Consensus 332 ~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~i------r 405 (482)
+++..|.+.++.+|+++.++..++||++||+|+.+++. .|+.. ..|.+|++++++|.|++++|+..+.. .
T Consensus 1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~~--~~~~awL~~Ia~n~~ld~lR~~~~~~~~~~~~~ 76 (281)
T TIGR02957 1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQI--ENPKAYLTKVVTRRCIDVLRSARARREVYVGPW 76 (281)
T ss_pred ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Ccccc--cCHHHHHHHHHHHHHHHHHHHhhhcccccCCCC
Confidence 37899999999999999999999999999999998775 55432 36999999999999999999764211 1
Q ss_pred cc----------hhHH---HHHH-HHHHHHHHH--------HHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCc
Q 011577 406 LP----------ENIY---TLLS-KVLEAKRLY--------IQEGNHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (482)
Q Consensus 406 lP----------~~v~---e~l~-kI~ka~~eL--------~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (482)
+| .... +.+. .+..+...| ......+.+++|||+.||+|+++|+..+++++..+
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 11 1111 1110 111222221 11223467999999999999999999999887543
No 124
>PRK09191 two-component response regulator; Provisional
Probab=99.17 E-value=1.4e-10 Score=112.13 Aligned_cols=127 Identities=15% Similarity=0.086 Sum_probs=94.9
Q ss_pred HHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc-
Q 011577 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP- 407 (482)
Q Consensus 329 Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP- 407 (482)
++..|+..|.+.|+.+|.++.++..+++|++||+|+.+|+...+|++. ..|.+|+++++++.......... ....+
T Consensus 2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~--~~~~~wl~~~~~~~~~~~~~~~~-~~~~~~ 78 (261)
T PRK09191 2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEA--SSPRVGLYRLFHRLWSSAGANDP-EPGSPF 78 (261)
T ss_pred chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCC--cchhhHHHHHHHHHhccccccCC-CCCCCc
Confidence 588999999999999999999999999999999999999999999874 46999999999887644322211 11111
Q ss_pred -hhHHHHHHHHHHHHHH-HHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 408 -ENIYTLLSKVLEAKRL-YIQEGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 408 -~~v~e~l~kI~ka~~e-L~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
..+...+.++....++ +......+.|++|||+.||+++++|+..+++++..
T Consensus 79 ~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~l~~s~~tV~~~l~ra~~~ 131 (261)
T PRK09191 79 EARAERRLAGLTPLPRQAFLLTALEGFSVEEAAEILGVDPAEAEALLDDARAE 131 (261)
T ss_pred hHHHHHHHHhCCHHHhHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 1233444444333333 22223347899999999999999999999988653
No 125
>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=99.10 E-value=4.1e-10 Score=100.85 Aligned_cols=113 Identities=11% Similarity=0.060 Sum_probs=80.0
Q ss_pred HHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHh-----hCCCCCCchhhHHHHHHHHHHHHHHHHhcCCc
Q 011577 330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEK-----FKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 404 (482)
Q Consensus 330 re~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiek-----FDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~i 404 (482)
|+.|+..|.++++.+|++|.. .+| +||.|+.+|..+.+ |++ +..|.||++.+++|.+++++|++.+..
T Consensus 1 f~~~~~~y~~~l~~~~~~~~~----~~~-~qdvf~~~w~~~~~~~~~~~~~--~~~~~~wL~~iarN~~id~~Rk~~~~~ 73 (142)
T TIGR03209 1 FEEIYMNFKNTIDIFTRKYNL----YYD-YNDILYHLWIILKKIDLNKFNT--ENDLEKYISTSLKRYCLDICNKKNRDK 73 (142)
T ss_pred ChHHHHHHHHHHHHHHHHhcc----hhh-HHHHHHHHHHHHHHhhhhhcCc--hhHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 468999999999999999966 224 49999999999875 544 247999999999999999999765421
Q ss_pred cc------------c-hhH--HHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHH
Q 011577 405 RL------------P-ENI--YTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLE 449 (482)
Q Consensus 405 rl------------P-~~v--~e~l~kI~ka~~eL~~e--------~gr~pS~eEIAe~LGIS~etVk 449 (482)
.. + ... .+....+.+++..|+.. ...+.|++|||+.||||+++|+
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 0 000 01112233333333221 2346799999999999999996
No 126
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=99.07 E-value=4.8e-10 Score=101.60 Aligned_cols=106 Identities=11% Similarity=0.069 Sum_probs=74.5
Q ss_pred CCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc-----------------------
Q 011577 350 GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL----------------------- 406 (482)
Q Consensus 350 ~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irl----------------------- 406 (482)
++..+++|++||+|+.+|+.++.+ + +..|.+|++.+++|.|++++|++.+....
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 445679999999999999998863 3 45799999999999999999986532111
Q ss_pred --------chhH---HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 407 --------PENI---YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 407 --------P~~v---~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
|... ......+.+++..|+. .+..+.+++|||+.||+|+++|+..+++++..
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 0000 0011223333333221 23347799999999999999999999988654
No 127
>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=99.04 E-value=5.8e-10 Score=90.86 Aligned_cols=71 Identities=31% Similarity=0.474 Sum_probs=62.9
Q ss_pred HHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCCCcccccccCCCC
Q 011577 412 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDAAG 482 (482)
Q Consensus 412 e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~~l~d~i~D~~g 482 (482)
+.+++|.++.++|.+.+||.||.+|||+.|||++++|..++..++..+||+.+++.+++.++.++|+|+++
T Consensus 1 E~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~~~~l~~~i~d~~~ 71 (78)
T PF04539_consen 1 EKLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDEDDSTLGDFIEDDDA 71 (78)
T ss_dssp HHHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSSSEEGGGSSB-SSS
T ss_pred ChHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCCCCchhheecCCCC
Confidence 46789999999999999999999999999999999999999999999999999999888999999999853
No 128
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=98.78 E-value=6.4e-08 Score=91.55 Aligned_cols=141 Identities=18% Similarity=0.175 Sum_probs=96.1
Q ss_pred HHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCC---CCCHhH--HHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHH
Q 011577 317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGR---GISLHD--LLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVR 390 (482)
Q Consensus 317 ~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~---g~d~ED--LIQEG~IGLirAiekFDp~kG~rFSTYA~~wIR 390 (482)
.+|+..++.|| .|++.|+..|.+-+..+|+++... +.+.+| |++|+|+.+++.-...+.+.-..|-.|+...++
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 46888889999 899999999999999999877532 345554 577888877774332233333469999999999
Q ss_pred HHHHHHHHHhcCCcc------cc---------hhHHHHHHHHHHHHHH-----------HHHhcCCCCcHHHHHHHhCCC
Q 011577 391 QTIRKAIFQHSRTIR------LP---------ENIYTLLSKVLEAKRL-----------YIQEGNHSPDKEDLARRVGIT 444 (482)
Q Consensus 391 naI~~~Lrkq~r~ir------lP---------~~v~e~l~kI~ka~~e-----------L~~e~gr~pS~eEIAe~LGIS 444 (482)
+.+++++|++.+..+ .+ ..-...+-.+.++... +......+.|.+|||+.||||
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 999999996654322 11 0001111122222221 222222368999999999999
Q ss_pred HHHHHHHHHHcCC
Q 011577 445 VEKLERLIFITRM 457 (482)
Q Consensus 445 ~etVk~~L~~ar~ 457 (482)
+.+|+..+..++.
T Consensus 165 ~~tV~r~l~~aR~ 177 (185)
T PF07638_consen 165 ERTVRRRLRRARA 177 (185)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999998764
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=97.94 E-value=2.5e-06 Score=61.18 Aligned_cols=34 Identities=41% Similarity=0.464 Sum_probs=30.2
Q ss_pred CcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHH
Q 011577 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR 287 (482)
Q Consensus 254 ~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~ 287 (482)
+|+++.||++|+++|+||++||++|+++|+.+..
T Consensus 1 ~D~l~~Yl~ei~~~~LLt~eeE~~LA~~i~~g~~ 34 (37)
T PF00140_consen 1 SDSLRLYLKEIGRYPLLTAEEEIELARRIRKGDE 34 (37)
T ss_dssp HHHHHHHHHHHHHS-EETTHHHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhHH
Confidence 3789999999999999999999999999998654
No 130
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=97.27 E-value=0.0073 Score=67.65 Aligned_cols=35 Identities=31% Similarity=0.482 Sum_probs=32.4
Q ss_pred CCcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHH
Q 011577 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR 287 (482)
Q Consensus 253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~ 287 (482)
.+||+++||++|++.||||+|+|++++++|..+.+
T Consensus 102 t~DPVRMYLREMG~V~LLTREgEIeIAKRIE~G~~ 136 (619)
T PRK05658 102 TDDPVRMYLREMGTVELLTREGEIEIAKRIEAGEN 136 (619)
T ss_pred CCChHHHHHHHhccCcCCCcHHHHHHHHHHHHHHH
Confidence 47999999999999999999999999999998653
No 131
>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=96.23 E-value=0.015 Score=46.87 Aligned_cols=56 Identities=18% Similarity=0.301 Sum_probs=46.7
Q ss_pred HHHHHhhcH-HHHHHHHHHHHHHHHHHHHHcc----C--CCCCHhHHHHHHHHHHHHhHHhhC
Q 011577 319 LKSELHSGN-SSREKLINANLRLVVHVAKQYQ----G--RGISLHDLLQEGSMGLMKSVEKFK 374 (482)
Q Consensus 319 Li~~l~~Gd-~Are~LI~snlrLV~sIAkrY~----~--~g~d~EDLIQEG~IGLirAiekFD 374 (482)
++.++.+|| .|.+++++.|.+++.+.+.|-. + ++.--+|+-|+--..|+++|-+|+
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 556677777 8999999999999999998732 2 244569999999999999999996
No 132
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=96.15 E-value=0.049 Score=53.86 Aligned_cols=30 Identities=0% Similarity=0.129 Sum_probs=26.2
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 429 NHSPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
..+.|++|||+.||+|+++|+..+++++..
T Consensus 215 ~~~~s~~EIA~~lgis~~tV~~~~~ra~~~ 244 (251)
T PRK07670 215 KEELTLTEIGQVLNLSTSRISQIHSKALFK 244 (251)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 347899999999999999999999887653
No 133
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=96.09 E-value=0.015 Score=57.97 Aligned_cols=34 Identities=29% Similarity=0.510 Sum_probs=28.8
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011577 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 320 (482)
Q Consensus 287 ~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi 320 (482)
++.+...+|...+|++|+..+.|+.+|++.+++.
T Consensus 114 ~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~ 147 (256)
T PRK07408 114 QAKKVRQELRQELGRQPTDQEIAQALDISLEEWQ 147 (256)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHH
Confidence 3556778888999999999999999999987664
No 134
>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=96.08 E-value=0.053 Score=53.23 Aligned_cols=34 Identities=32% Similarity=0.589 Sum_probs=28.2
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011577 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 320 (482)
Q Consensus 287 ~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi 320 (482)
++.++...+...+|++||.++.|+.+|++.+++.
T Consensus 88 ~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~ 121 (238)
T TIGR02393 88 KLIKAERQLTQELGREPTDEELAERMGMPAEKVR 121 (238)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHH
Confidence 3445677888889999999999999999987664
No 135
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=96.03 E-value=0.21 Score=50.28 Aligned_cols=149 Identities=19% Similarity=0.184 Sum_probs=84.3
Q ss_pred HHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHHHHH
Q 011577 256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 335 (482)
Q Consensus 256 ~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~LI~ 335 (482)
.+..||++-. +.--+.--.++.+ ++..+..+|+..+|++||..|.|+..|++.++.......+.
T Consensus 88 ei~d~LR~~~--~v~vpR~~~~~~~------~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~-------- 151 (247)
T COG1191 88 EILDYLRKND--SVKVPRSLRELGR------RIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAIN-------- 151 (247)
T ss_pred HHHHHHHhCC--CccCcHHHHHHHH------HHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhc--------
Confidence 5666888766 2222223333443 45567888999999999999999999999887664433322
Q ss_pred HHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHHHH
Q 011577 336 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLS 415 (482)
Q Consensus 336 snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~e~l~ 415 (482)
-....++-......+.+. +. ..-+..+..+-.+...+.+..++. .+|..
T Consensus 152 --~~~~~sld~~~~~~~d~~--------------~~---~~~~~~~~~~~~~~~~~~l~~ai~------~L~ER------ 200 (247)
T COG1191 152 --GSQLLSLDEDVLKDDDDD--------------VD---DQIENPDDGVEKEELLEILKEAIE------PLPER------ 200 (247)
T ss_pred --cccccchhhhhccccccc--------------hh---hccccchhHHHHHHHHHHHHHHHH------ccCHH------
Confidence 111222221111111111 11 111234455555556566665554 12221
Q ss_pred HHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 416 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 416 kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
.+.+ +...+..+.|..|||+.||||+.+|-.+...+
T Consensus 201 --Ek~V--l~l~y~eelt~kEI~~~LgISes~VSql~kka 236 (247)
T COG1191 201 --EKLV--LVLRYKEELTQKEIAEVLGISESRVSRLHKKA 236 (247)
T ss_pred --HHHH--HHHHHHhccCHHHHHHHhCccHHHHHHHHHHH
Confidence 1111 12223346899999999999999998887655
No 136
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=95.98 E-value=0.046 Score=54.59 Aligned_cols=29 Identities=3% Similarity=0.161 Sum_probs=25.6
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577 429 NHSPDKEDLARRVGITVEKLERLIFITRM 457 (482)
Q Consensus 429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (482)
..+.|++|||+.||+|.++|+.+++++..
T Consensus 219 ~e~~t~~EIA~~lgis~~~V~~~~~ral~ 247 (257)
T PRK05911 219 YEELVLKEIGKILGVSESRVSQIHSKALL 247 (257)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 34789999999999999999999988754
No 137
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=95.86 E-value=0.097 Score=52.35 Aligned_cols=34 Identities=26% Similarity=0.526 Sum_probs=28.3
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011577 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 320 (482)
Q Consensus 287 ~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi 320 (482)
++.+....|+..+|++||..+.|+..|++.+.+.
T Consensus 119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~ 152 (268)
T PRK06288 119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYN 152 (268)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHH
Confidence 4556677888899999999999999999876654
No 138
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=95.73 E-value=0.068 Score=53.69 Aligned_cols=35 Identities=29% Similarity=0.554 Sum_probs=28.9
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHH
Q 011577 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 321 (482)
Q Consensus 287 ~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~ 321 (482)
++.+...+|...+|++||..+.|+.+|++.+++..
T Consensus 128 ~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~ 162 (264)
T PRK07122 128 RLGRATAELSQRLGRAPTASELAAELGMDREEVVE 162 (264)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 34456778888899999999999999999877654
No 139
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=95.62 E-value=0.15 Score=51.85 Aligned_cols=29 Identities=17% Similarity=0.243 Sum_probs=25.7
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 430 HSPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
.+.|++|||+.||||.++|+.+++++...
T Consensus 244 ~~~t~~EIa~~lgvs~~~V~q~~~~Al~k 272 (289)
T PRK07500 244 DGATLEALGEELGISKERVRQIEARALEK 272 (289)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 47899999999999999999999887543
No 140
>PRK05949 RNA polymerase sigma factor; Validated
Probab=95.59 E-value=0.071 Score=55.42 Aligned_cols=35 Identities=26% Similarity=0.461 Sum_probs=28.3
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHH
Q 011577 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 321 (482)
Q Consensus 287 ~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~ 321 (482)
++.+....+...+|++|+..+.|+.+|++.+.+..
T Consensus 179 ~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~ 213 (327)
T PRK05949 179 KIKKTQRELSQKLGRSATPAEIAKELELEPSQIRE 213 (327)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHH
Confidence 34556667778899999999999999999876643
No 141
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=95.58 E-value=0.19 Score=52.90 Aligned_cols=133 Identities=18% Similarity=0.267 Sum_probs=72.0
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHH-HHHH
Q 011577 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQE-GSMG 365 (482)
Q Consensus 287 ~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQE-G~IG 365 (482)
++.++..+|...+|++||..+.|+.+|++.+++....... .+ ...+++.+.+ +-..
T Consensus 217 ~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~-------------------~~----~~SLd~~~~~~~~~~ 273 (367)
T PRK09210 217 KLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIA-------------------QE----PVSLETPIGEEDDSH 273 (367)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHh-------------------cC----CCCcCCCCCCCCcch
Confidence 3456677888899999999999999999987665332111 11 0111111110 0011
Q ss_pred HHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCH
Q 011577 366 LMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITV 445 (482)
Q Consensus 366 LirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~ 445 (482)
|...+. |..............++..+.++|. .+|..-...+. . .+....+.+.|++|||+.||||.
T Consensus 274 l~d~i~--d~~~~~p~~~~~~~~~~~~l~~~l~------~L~~rEr~Vl~----l--rygl~~~~~~tl~EIa~~lgvs~ 339 (367)
T PRK09210 274 LGDFIE--DQDATSPADHAAYELLKEQLEDVLD------TLTDREENVLR----L--RFGLDDGRTRTLEEVGKVFGVTR 339 (367)
T ss_pred hhhhcc--CCCCCCHHHHHHHHHHHHHHHHHHH------hCCHHHHHHHH----H--HhccCCCCCccHHHHHHHHCCCH
Confidence 111121 1111223444455555555555553 23322111111 0 01112235789999999999999
Q ss_pred HHHHHHHHHcC
Q 011577 446 EKLERLIFITR 456 (482)
Q Consensus 446 etVk~~L~~ar 456 (482)
++|+.+...|.
T Consensus 340 erVrQi~~~Al 350 (367)
T PRK09210 340 ERIRQIEAKAL 350 (367)
T ss_pred HHHHHHHHHHH
Confidence 99999977663
No 142
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=95.26 E-value=0.33 Score=53.61 Aligned_cols=35 Identities=31% Similarity=0.553 Sum_probs=29.5
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHH
Q 011577 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 321 (482)
Q Consensus 287 ~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~ 321 (482)
++.+++.+|...+|++||.++.|+.+|++.+.+..
T Consensus 359 kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~ 393 (509)
T PRK05901 359 KLGRIERELLQELGREPTPEELAKEMGFTPEKVRE 393 (509)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 45567888889999999999999999999876643
No 143
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=95.18 E-value=0.2 Score=53.99 Aligned_cols=36 Identities=19% Similarity=0.454 Sum_probs=30.8
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHH
Q 011577 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 322 (482)
Q Consensus 287 ~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~ 322 (482)
++.+.+..|...+|+.|+..|.|+.+|++.+.+...
T Consensus 263 ~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~ 298 (415)
T PRK07598 263 KIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREV 298 (415)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 566778888889999999999999999998877643
No 144
>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=94.95 E-value=0.11 Score=50.53 Aligned_cols=32 Identities=38% Similarity=0.597 Sum_probs=26.2
Q ss_pred HHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011577 289 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 320 (482)
Q Consensus 289 e~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi 320 (482)
.+....+...+|++||..+.|+..|++.+++.
T Consensus 100 ~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~ 131 (231)
T TIGR02885 100 RYMKEELSKELGREPTINELAEALGVSPEEIV 131 (231)
T ss_pred HHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHH
Confidence 34556777888999999999999999987664
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=94.83 E-value=0.28 Score=47.54 Aligned_cols=34 Identities=32% Similarity=0.651 Sum_probs=27.6
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011577 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 320 (482)
Q Consensus 287 ~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi 320 (482)
++.++..++...+|++|+.++.|+.+|++.+++.
T Consensus 84 ~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~ 117 (224)
T TIGR02479 84 KLERAIRELEARLGREPTEEEIAEELGMDLKEYR 117 (224)
T ss_pred HHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHH
Confidence 3455667788889999999999999999876554
No 146
>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=94.73 E-value=0.42 Score=48.72 Aligned_cols=34 Identities=26% Similarity=0.509 Sum_probs=27.9
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011577 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 320 (482)
Q Consensus 287 ~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi 320 (482)
++.+.+..+...+|++|+..+.|+.+|++.+++.
T Consensus 162 ~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~ 195 (298)
T TIGR02997 162 KIKKVQRELSQKLGRTPSEAEIAEALELEPEQVR 195 (298)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHH
Confidence 4455667777889999999999999999987664
No 147
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=94.62 E-value=0.64 Score=48.39 Aligned_cols=34 Identities=32% Similarity=0.460 Sum_probs=28.8
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011577 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 320 (482)
Q Consensus 287 ~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi 320 (482)
++.++..+|...+|++||..|.|+.+|++.+++.
T Consensus 174 ~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~ 207 (324)
T PRK07921 174 KLARIKRELHQQLGREATDEELAEESGIPEEKIA 207 (324)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHH
Confidence 4556778888899999999999999999987664
No 148
>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=94.43 E-value=0.095 Score=51.84 Aligned_cols=29 Identities=17% Similarity=0.250 Sum_probs=25.4
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577 429 NHSPDKEDLARRVGITVEKLERLIFITRM 457 (482)
Q Consensus 429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (482)
..+.|++|||+.||+++++|+.++++++.
T Consensus 219 ~~g~s~~eIA~~lgis~~~V~~~~~ra~~ 247 (255)
T TIGR02941 219 EENLSQKETGERLGISQMHVSRLQRQAIS 247 (255)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 34789999999999999999999987754
No 149
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=94.42 E-value=0.21 Score=51.65 Aligned_cols=34 Identities=26% Similarity=0.522 Sum_probs=28.1
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011577 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 320 (482)
Q Consensus 287 ~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi 320 (482)
++.+.+..+...+|++|+..+.|+..|++.+.+.
T Consensus 169 ~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~ 202 (317)
T PRK07405 169 KIKKAQRQLSQQLGRAATIGELAEELELTPKQVR 202 (317)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHH
Confidence 4556777888889999999999999999876554
No 150
>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=94.33 E-value=0.096 Score=42.41 Aligned_cols=38 Identities=32% Similarity=0.613 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHH
Q 011577 286 IRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL 323 (482)
Q Consensus 286 ~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l 323 (482)
.++.++..+|+..+||+||.+|.|+.+|++.+++...+
T Consensus 4 ~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l 41 (78)
T PF04539_consen 4 RKIERARRELEQELGREPTDEEIAEELGISVEEVRELL 41 (78)
T ss_dssp HHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHH
Confidence 35778899999999999999999999999988775443
No 151
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=94.08 E-value=0.46 Score=46.41 Aligned_cols=30 Identities=3% Similarity=0.147 Sum_probs=26.1
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 429 NHSPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
..+.|++|||+.||+|+++|+..+++++..
T Consensus 198 ~~g~s~~EIA~~lgis~~tV~~~~~ra~~~ 227 (236)
T PRK06986 198 QEELNLKEIGAVLGVSESRVSQIHSQAIKR 227 (236)
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 347899999999999999999999887643
No 152
>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=93.97 E-value=0.34 Score=48.03 Aligned_cols=35 Identities=26% Similarity=0.297 Sum_probs=28.3
Q ss_pred HHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHH
Q 011577 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 322 (482)
Q Consensus 288 le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~ 322 (482)
+.+...++...+|++|+.++.|+.+|++.+++...
T Consensus 122 ~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~ 156 (254)
T TIGR02850 122 ALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFA 156 (254)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHH
Confidence 33456677888999999999999999998777544
No 153
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=93.76 E-value=1.3 Score=46.74 Aligned_cols=33 Identities=24% Similarity=0.326 Sum_probs=29.6
Q ss_pred CCcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHH
Q 011577 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDL 285 (482)
Q Consensus 253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l 285 (482)
....+..|+..+...++||++||.+|+..++.+
T Consensus 65 ~~~~~~~~~~~~~~~~~l~~~Ee~~la~~~~~g 97 (342)
T COG0568 65 PAGRLSFYIRAIEAAPLLTPEEEKALARRLKRG 97 (342)
T ss_pred hhhhHHHHHHHHhhhcccChHHHHHHHHHHHcC
Confidence 345788899999999999999999999999887
No 154
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=93.72 E-value=0.71 Score=49.08 Aligned_cols=34 Identities=32% Similarity=0.584 Sum_probs=28.6
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011577 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 320 (482)
Q Consensus 287 ~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi 320 (482)
++.+....|...+|++||..+.|+.+|++.+++.
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 4556777888899999999999999999987663
No 155
>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=92.86 E-value=0.15 Score=38.51 Aligned_cols=30 Identities=17% Similarity=0.172 Sum_probs=22.8
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577 428 GNHSPDKEDLARRVGITVEKLERLIFITRM 457 (482)
Q Consensus 428 ~gr~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (482)
+..+.+++|||+.+|+|+++|+..+++++.
T Consensus 23 ~~~g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 23 YFQGMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp HTS---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred HHHCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 445789999999999999999999998753
No 156
>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=92.83 E-value=0.17 Score=48.92 Aligned_cols=28 Identities=21% Similarity=0.369 Sum_probs=25.1
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577 430 HSPDKEDLARRVGITVEKLERLIFITRM 457 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (482)
.+.+++|||+.||++..+|+..++++..
T Consensus 193 ~~~s~~eIA~~lgis~~~v~~~~~ra~~ 220 (227)
T TIGR02980 193 EDKTQSEIAERLGISQMHVSRLLRRALK 220 (227)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4689999999999999999999988754
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=92.57 E-value=0.25 Score=49.90 Aligned_cols=31 Identities=23% Similarity=0.323 Sum_probs=27.2
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHHcCCCc
Q 011577 429 NHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (482)
Q Consensus 429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (482)
..+.|++|||+.||+|+++|+.++++|+..+
T Consensus 240 ~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkL 270 (285)
T TIGR02394 240 YEPATLEEVAAEVGLTRERVRQIQVEALKKL 270 (285)
T ss_pred CCCccHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4578999999999999999999999887543
No 158
>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=92.23 E-value=0.36 Score=35.98 Aligned_cols=30 Identities=20% Similarity=0.265 Sum_probs=25.1
Q ss_pred hcCCCCcHHHHHHHhCCCHHHHHHHHHHcC
Q 011577 427 EGNHSPDKEDLARRVGITVEKLERLIFITR 456 (482)
Q Consensus 427 e~gr~pS~eEIAe~LGIS~etVk~~L~~ar 456 (482)
.+..+.|++|||+.||+|.++|+.+...+.
T Consensus 16 ~y~~~~t~~eIa~~lg~s~~~V~~~~~~al 45 (50)
T PF04545_consen 16 RYFEGLTLEEIAERLGISRSTVRRILKRAL 45 (50)
T ss_dssp HHTST-SHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred HhcCCCCHHHHHHHHCCcHHHHHHHHHHHH
Confidence 345678999999999999999999988763
No 159
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=92.12 E-value=2.2 Score=42.41 Aligned_cols=33 Identities=24% Similarity=0.307 Sum_probs=27.0
Q ss_pred HHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHH
Q 011577 289 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 321 (482)
Q Consensus 289 e~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~ 321 (482)
.+...++...+|++|+..+.|+.+|++.+++..
T Consensus 126 ~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~ 158 (258)
T PRK08215 126 LQVREKLINENSKEPTVEEIAKELEVPREEVVF 158 (258)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHH
Confidence 345667778899999999999999999887653
No 160
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=91.87 E-value=0.41 Score=47.41 Aligned_cols=29 Identities=17% Similarity=0.208 Sum_probs=25.6
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577 429 NHSPDKEDLARRVGITVEKLERLIFITRM 457 (482)
Q Consensus 429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (482)
..+.+++|||+.|||++++|+.++++++.
T Consensus 219 ~~g~s~~eIA~~l~is~~tV~~~~~ra~~ 247 (257)
T PRK08583 219 IENLSQKETGERLGISQMHVSRLQRQAIK 247 (257)
T ss_pred hCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 34789999999999999999999987754
No 161
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=91.63 E-value=1.5 Score=43.15 Aligned_cols=34 Identities=15% Similarity=0.392 Sum_probs=28.0
Q ss_pred HHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHH
Q 011577 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 321 (482)
Q Consensus 288 le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~ 321 (482)
+.+....+...+|++|+..+.|+.+|++.+++..
T Consensus 103 i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~ 136 (231)
T PRK12427 103 TNDAIREIAKRLGHEPNFEEISAELNLTAEEYQE 136 (231)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHH
Confidence 4455677888899999999999999999877643
No 162
>PRK05572 sporulation sigma factor SigF; Validated
Probab=91.61 E-value=1.6 Score=43.24 Aligned_cols=28 Identities=21% Similarity=0.322 Sum_probs=24.8
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577 430 HSPDKEDLARRVGITVEKLERLIFITRM 457 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (482)
.+.|++|||+.+|++..+|..+.+++..
T Consensus 217 ~~~s~~eIA~~lgis~~~V~~~~~ral~ 244 (252)
T PRK05572 217 KDKTQSEVAKRLGISQVQVSRLEKKILK 244 (252)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4689999999999999999999887753
No 163
>PHA02547 55 RNA polymerase sigma factor; Provisional
Probab=91.33 E-value=0.57 Score=44.65 Aligned_cols=67 Identities=12% Similarity=0.134 Sum_probs=54.3
Q ss_pred HHHHHHHHHHHHHccCCCCC---HhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhc
Q 011577 335 NANLRLVVHVAKQYQGRGIS---LHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS 401 (482)
Q Consensus 335 ~snlrLV~sIAkrY~~~g~d---~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~ 401 (482)
..-+..+-.+.++|.-+|-. -+|.|.+|.-..++.+..||+++...+-+|...++-+++.+.|.+..
T Consensus 44 ~~imkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~kEk 113 (179)
T PHA02547 44 LAIMKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIKKEK 113 (179)
T ss_pred HHHHHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHHHHH
Confidence 34455555666666555554 59999999999999999999999999999999999999998887654
No 164
>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=90.30 E-value=0.92 Score=36.48 Aligned_cols=42 Identities=26% Similarity=0.419 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCC-HHHHHHHHHH
Q 011577 413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGIT-VEKLERLIFI 454 (482)
Q Consensus 413 ~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS-~etVk~~L~~ 454 (482)
.-.+|-..+..+..+.|..||+.|||+.+|++ ..+|...|..
T Consensus 7 rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~ 49 (65)
T PF01726_consen 7 RQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKA 49 (65)
T ss_dssp HHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence 34456666677778888899999999999997 9999988874
No 165
>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=88.99 E-value=1.4 Score=32.44 Aligned_cols=35 Identities=20% Similarity=0.235 Sum_probs=24.0
Q ss_pred HHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 419 EAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 419 ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
..+-.+.+..+ ..++.|||+.+|+|..+|..++++
T Consensus 6 ~~Il~~Lq~d~-r~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 6 RKILRLLQEDG-RRSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHH-T-TS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHcC-CccHHHHHHHHCcCHHHHHHHHHH
Confidence 33333344445 579999999999999999998864
No 166
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=86.85 E-value=14 Score=37.43 Aligned_cols=27 Identities=15% Similarity=0.279 Sum_probs=24.3
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHcC
Q 011577 430 HSPDKEDLARRVGITVEKLERLIFITR 456 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar 456 (482)
.+.|++|||+.||||.++|+.+.+.+.
T Consensus 247 ~~~Tl~EIA~~lgvS~~rVrqi~~~Al 273 (284)
T PRK06596 247 DKSTLQELAAEYGVSAERVRQIEKNAM 273 (284)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 468999999999999999999988764
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=86.00 E-value=1.4 Score=36.62 Aligned_cols=25 Identities=12% Similarity=0.155 Sum_probs=22.8
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 430 HSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
.+.|++|||+.||+|+.+|+..+..
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 3789999999999999999999874
No 168
>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=85.77 E-value=1.5 Score=31.29 Aligned_cols=28 Identities=14% Similarity=0.209 Sum_probs=24.6
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577 430 HSPDKEDLARRVGITVEKLERLIFITRM 457 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (482)
.+.+..+||+.+|++..+|...++.++.
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4679999999999999999999887643
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=84.44 E-value=2 Score=34.39 Aligned_cols=31 Identities=16% Similarity=0.280 Sum_probs=24.7
Q ss_pred HHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 424 YIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 424 L~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
+..+.+...+..+||+.||++..+|+..-..
T Consensus 15 ~y~~~~g~i~lkdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 15 IYKESNGKIKLKDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred HHHHhCCCccHHHHHHHHCCCHHHHHHHhhh
Confidence 3344444899999999999999999987553
No 170
>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=84.00 E-value=3 Score=32.05 Aligned_cols=47 Identities=21% Similarity=0.307 Sum_probs=34.6
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHH
Q 011577 405 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERL 451 (482)
Q Consensus 405 rlP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~ 451 (482)
.+|......+...-+....|..++....+-.|||+.+|++..+|+.=
T Consensus 2 ~Ip~~ti~RL~~Y~r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRKD 48 (50)
T PF06971_consen 2 KIPKATIRRLPLYLRYLEQLKEEGVERVSSQELAEALGITPAQVRKD 48 (50)
T ss_dssp S-SHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHcCCeeECHHHHHHHHCCCHHHhccc
Confidence 46666667777777777778777777789999999999999999864
No 171
>PRK06930 positive control sigma-like factor; Validated
Probab=83.97 E-value=1 Score=42.74 Aligned_cols=30 Identities=10% Similarity=0.095 Sum_probs=26.3
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 429 NHSPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
..+.+++|||+.||+++++|+..+.+++..
T Consensus 128 ~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~k 157 (170)
T PRK06930 128 GYGLSYSEIADYLNIKKSTVQSMIERAEKK 157 (170)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 347899999999999999999999988653
No 172
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=83.41 E-value=4.2 Score=43.00 Aligned_cols=125 Identities=10% Similarity=0.033 Sum_probs=82.0
Q ss_pred HHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhH
Q 011577 331 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI 410 (482)
Q Consensus 331 e~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v 410 (482)
+..+..-.+.+....-+|.++-...||.+||+|+..++.-.+=.+-+ .-..|++-.-||.-+|.+|+..+.-..|.+.
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 44455555555555566777777899999999987666555444433 3689999999999999999887654444322
Q ss_pred HHHH--HHHH----------------------------HHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577 411 YTLL--SKVL----------------------------EAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRM 457 (482)
Q Consensus 411 ~e~l--~kI~----------------------------ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (482)
.... .++. .....|....-.+.|..|||...=+++.++.+.+-+++.
T Consensus 86 ~~~~e~~e~~~a~~~~d~~i~Dd~LRLiFvccHPal~~~~riALtLR~v~GLs~~eIArAFLv~e~am~QRivRAK~ 162 (415)
T COG4941 86 LLSDEDEEMEEAEALDDEHIRDDRLRLIFVCCHPALPPEQRIALTLRLVGGLSTAEIARAFLVPEAAMAQRIVRAKA 162 (415)
T ss_pred cccccchhhhccccccccccchhhHHhhhhhcCCCCChhhHHHHHHHHHcCCcHHHHHHHHcCCcHHHHHHHHHHHH
Confidence 1111 0000 001112222222579999999999999999999888764
No 173
>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=82.10 E-value=4.8 Score=29.53 Aligned_cols=29 Identities=21% Similarity=0.421 Sum_probs=22.3
Q ss_pred HHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 425 IQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 425 ~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
..+.+ ..|..|||+.+|++..+|...++.
T Consensus 12 l~~~~-~~t~~ela~~~~is~~tv~~~l~~ 40 (48)
T PF13412_consen 12 LRENP-RITQKELAEKLGISRSTVNRYLKK 40 (48)
T ss_dssp HHHCT-TS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHcC-CCCHHHHHHHhCCCHHHHHHHHHH
Confidence 33444 589999999999999999998874
No 174
>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=81.50 E-value=1.2 Score=34.55 Aligned_cols=28 Identities=18% Similarity=0.224 Sum_probs=24.8
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577 430 HSPDKEDLARRVGITVEKLERLIFITRM 457 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (482)
|..+..|||+.|||+..++...|+++..
T Consensus 22 R~~tl~elA~~lgis~st~~~~LRrae~ 49 (53)
T PF04967_consen 22 RRITLEELAEELGISKSTVSEHLRRAER 49 (53)
T ss_pred CcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 5669999999999999999999988743
No 175
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=81.15 E-value=1.5 Score=45.59 Aligned_cols=30 Identities=23% Similarity=0.368 Sum_probs=26.6
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 429 NHSPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
..+.|++|||+.||++.++|+.++++++..
T Consensus 280 ~e~~s~~EIA~~Lgis~~tV~~~~~rAl~k 309 (325)
T PRK05657 280 YEAATLEDVAREIGLTRERVRQIQVEALRR 309 (325)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 347899999999999999999999988654
No 176
>PRK00118 putative DNA-binding protein; Validated
Probab=80.58 E-value=2.6 Score=37.19 Aligned_cols=28 Identities=11% Similarity=0.051 Sum_probs=25.3
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577 430 HSPDKEDLARRVGITVEKLERLIFITRM 457 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (482)
.+.|+.|||+.+|+|..+|...+.+++.
T Consensus 32 eg~S~~EIAe~lGIS~~TV~r~L~RArk 59 (104)
T PRK00118 32 DDYSLGEIAEEFNVSRQAVYDNIKRTEK 59 (104)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3689999999999999999999998764
No 177
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=80.50 E-value=2.3 Score=31.06 Aligned_cols=29 Identities=17% Similarity=0.276 Sum_probs=25.0
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHcCCCc
Q 011577 431 SPDKEDLARRVGITVEKLERLIFITRMPL 459 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (482)
+.+..|||+.+|++..+|+..+.++...+
T Consensus 18 g~s~~eia~~l~is~~tv~~~~~~~~~kl 46 (58)
T smart00421 18 GLTNKEIAERLGISEKTVKTHLSNIMRKL 46 (58)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 56999999999999999999998775443
No 178
>PRK04217 hypothetical protein; Provisional
Probab=79.96 E-value=1.8 Score=38.45 Aligned_cols=28 Identities=18% Similarity=0.309 Sum_probs=25.3
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 431 SPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
+.|++|||+.|||+..+|...+++++..
T Consensus 58 GlS~~EIAk~LGIS~sTV~r~L~RArkk 85 (110)
T PRK04217 58 GLTQEEAGKRMGVSRGTVWRALTSARKK 85 (110)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 6799999999999999999999987654
No 179
>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=77.55 E-value=2.8 Score=30.79 Aligned_cols=27 Identities=11% Similarity=0.175 Sum_probs=24.2
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577 431 SPDKEDLARRVGITVEKLERLIFITRM 457 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (482)
+.+.+|||+.+|++..+|+..+++++.
T Consensus 15 ~~s~~eia~~l~~s~~tv~~~~~~~~~ 41 (57)
T cd06170 15 GKTNKEIADILGISEKTVKTHLRNIMR 41 (57)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 579999999999999999999987654
No 180
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=76.48 E-value=4.4 Score=29.85 Aligned_cols=26 Identities=15% Similarity=0.271 Sum_probs=18.3
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 429 NHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 429 gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
..+.|..|||+.||++..+|...+++
T Consensus 18 ~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 18 EQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp CS---HHHHHHHTT--HHHHHHHHHH
T ss_pred HcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 34689999999999999999988764
No 181
>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=76.01 E-value=6.8 Score=29.39 Aligned_cols=33 Identities=18% Similarity=0.323 Sum_probs=24.8
Q ss_pred HHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 422 RLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 422 ~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
..|....+ ..|.+|||+.||+|..+|..-+...
T Consensus 7 ~~L~~~~~-~it~~eLa~~l~vS~rTi~~~i~~L 39 (55)
T PF08279_consen 7 KLLLESKE-PITAKELAEELGVSRRTIRRDIKEL 39 (55)
T ss_dssp HHHHHTTT-SBEHHHHHHHCTS-HHHHHHHHHHH
T ss_pred HHHHHcCC-CcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 33434444 4899999999999999999988754
No 182
>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=75.62 E-value=7.1 Score=30.76 Aligned_cols=26 Identities=8% Similarity=0.049 Sum_probs=23.3
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHcC
Q 011577 431 SPDKEDLARRVGITVEKLERLIFITR 456 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar 456 (482)
+.++.|||+.||++..+|.....+..
T Consensus 13 G~~~~eIA~~Lg~~~~TV~~W~~r~~ 38 (58)
T PF06056_consen 13 GWSIKEIAEELGVPRSTVYSWKDRYK 38 (58)
T ss_pred CCCHHHHHHHHCCChHHHHHHHHhhC
Confidence 56999999999999999999987654
No 183
>PHA02591 hypothetical protein; Provisional
Probab=74.44 E-value=6.6 Score=33.12 Aligned_cols=23 Identities=26% Similarity=0.401 Sum_probs=21.3
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHH
Q 011577 431 SPDKEDLARRVGITVEKLERLIF 453 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~ 453 (482)
+.|.++||+.||++..+|+..++
T Consensus 59 GlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 59 GFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHh
Confidence 57999999999999999999875
No 184
>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=73.91 E-value=4.7 Score=30.87 Aligned_cols=29 Identities=10% Similarity=0.143 Sum_probs=23.7
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 430 HSPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
.+.+.+|||+.||+++.+|+..+......
T Consensus 17 ~G~~~~eIA~~l~is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 17 QGMSNKEIAEELGISEKTVKSHRRRIMKK 45 (58)
T ss_dssp TTS-HHHHHHHHTSHHHHHHHHHHHHHHH
T ss_pred hcCCcchhHHhcCcchhhHHHHHHHHHHH
Confidence 46799999999999999999988766543
No 185
>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=73.07 E-value=5 Score=28.18 Aligned_cols=24 Identities=25% Similarity=0.429 Sum_probs=18.7
Q ss_pred CcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 432 PDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 432 pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
.|.+|||+.+|++.++|-.++...
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l 26 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKL 26 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHH
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHH
Confidence 478999999999999999888643
No 186
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=72.96 E-value=8.7 Score=28.47 Aligned_cols=24 Identities=25% Similarity=0.393 Sum_probs=21.6
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 431 SPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
..|..+||+.+|++..+|..++..
T Consensus 27 ~~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 27 SRSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHh
Confidence 359999999999999999999864
No 187
>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=72.88 E-value=2.6 Score=38.95 Aligned_cols=29 Identities=7% Similarity=0.072 Sum_probs=25.0
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 430 HSPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
.+.|++|||+.||+|..+|+.++++++..
T Consensus 20 ~GlTq~EIAe~LgiS~stV~~~e~ra~kk 48 (137)
T TIGR00721 20 KGLSQKEIAKELKTTRANVSAIEKRAMEN 48 (137)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHhHHHH
Confidence 47899999999999999999988876543
No 188
>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=71.16 E-value=5.8 Score=29.20 Aligned_cols=23 Identities=13% Similarity=0.315 Sum_probs=17.8
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHH
Q 011577 431 SPDKEDLARRVGITVEKLERLIF 453 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~ 453 (482)
+.++.+||+.+||+..+|..++.
T Consensus 21 G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 21 GMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp T--HHHHHHHTTS-HHHHHHHHC
T ss_pred CCCHHHHHHHHCcCHHHHHHHHh
Confidence 46999999999999999988763
No 189
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=70.07 E-value=3.3 Score=38.42 Aligned_cols=28 Identities=11% Similarity=0.177 Sum_probs=24.1
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577 430 HSPDKEDLARRVGITVEKLERLIFITRM 457 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (482)
.+.|++|||+.||+|..+|+.+.+.++.
T Consensus 20 ~GlTq~EIAe~LGiS~~tVs~ie~ra~k 47 (141)
T PRK03975 20 RGLTQQEIADILGTSRANVSSIEKRARE 47 (141)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4789999999999999999998876543
No 190
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=68.48 E-value=17 Score=27.74 Aligned_cols=25 Identities=20% Similarity=0.329 Sum_probs=22.4
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 431 SPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
.++..|||+.+|++..+|...+...
T Consensus 25 ~~s~~ela~~~g~s~~tv~r~l~~L 49 (67)
T cd00092 25 PLTRQEIADYLGLTRETVSRTLKEL 49 (67)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 5699999999999999999998754
No 191
>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=68.29 E-value=18 Score=28.52 Aligned_cols=37 Identities=16% Similarity=0.228 Sum_probs=28.3
Q ss_pred HHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 418 LEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 418 ~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
-+++..+.. .+..++..+||+.||++..+|-.++++-
T Consensus 10 L~~Iy~l~~-~~~~v~~~~iA~~L~vs~~tvt~ml~~L 46 (60)
T PF01325_consen 10 LKAIYELSE-EGGPVRTKDIAERLGVSPPTVTEMLKRL 46 (60)
T ss_dssp HHHHHHHHH-CTSSBBHHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHc-CCCCccHHHHHHHHCCChHHHHHHHHHH
Confidence 345566666 4448899999999999999999998753
No 192
>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=67.89 E-value=9.3 Score=38.34 Aligned_cols=27 Identities=15% Similarity=0.258 Sum_probs=23.8
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHcC
Q 011577 430 HSPDKEDLARRVGITVEKLERLIFITR 456 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar 456 (482)
.+.|++|||+.||||.++|+.+...+.
T Consensus 235 ~~~t~~eIA~~lgvS~~~V~q~~~~Al 261 (270)
T TIGR02392 235 DKLTLQELAAEYGVSAERIRQIEKNAM 261 (270)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 367999999999999999998887664
No 193
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=67.69 E-value=10 Score=34.88 Aligned_cols=39 Identities=10% Similarity=0.107 Sum_probs=28.9
Q ss_pred HHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcC
Q 011577 417 VLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR 456 (482)
Q Consensus 417 I~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar 456 (482)
+...+-.+.+..+ ..++.|||+.+|+|+.+|..++++-.
T Consensus 10 ~D~~Il~~Lq~d~-R~s~~eiA~~lglS~~tV~~Ri~rL~ 48 (153)
T PRK11179 10 LDRGILEALMENA-RTPYAELAKQFGVSPGTIHVRVEKMK 48 (153)
T ss_pred HHHHHHHHHHHcC-CCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3344444444445 57999999999999999999988653
No 194
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=67.36 E-value=5.5 Score=29.29 Aligned_cols=25 Identities=20% Similarity=0.272 Sum_probs=18.9
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 431 SPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
+.|..+||+.+|++..+|...+++.
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT--
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHc
Confidence 4699999999999999999998764
No 195
>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=66.80 E-value=11 Score=33.05 Aligned_cols=34 Identities=12% Similarity=0.038 Sum_probs=24.8
Q ss_pred HHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577 424 YIQEGNHSPDKEDLARRVGITVEKLERLIFITRM 457 (482)
Q Consensus 424 L~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (482)
+..-+..+.|..|||+.+|||...|...++++..
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 3344666889999999999999999999988754
No 196
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=66.67 E-value=10 Score=31.18 Aligned_cols=34 Identities=24% Similarity=0.308 Sum_probs=23.2
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcc
Q 011577 430 HSPDKEDLARRVGITVEKLERLIFITRMPLSMQQ 463 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~ 463 (482)
++.|..|+|+.||++..+|..+++--...+|+|.
T Consensus 30 ~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~ 63 (80)
T PF13744_consen 30 RGLTQAELAERLGISQPRVSRLENGKIDDFSLDT 63 (80)
T ss_dssp CT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHH
T ss_pred cCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHH
Confidence 4689999999999999999998864455677765
No 197
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=65.40 E-value=7.4 Score=37.74 Aligned_cols=35 Identities=6% Similarity=0.073 Sum_probs=27.5
Q ss_pred hcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccC
Q 011577 427 EGNHSPDKEDLARRVGITVEKLERLIFITRMPLSM 461 (482)
Q Consensus 427 e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSL 461 (482)
.+.++.+.+|||+.|++|++||+.........+-+
T Consensus 159 lla~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~v 193 (211)
T COG2197 159 LLAEGLSNKEIAEELNLSEKTVKTHVSNILRKLGV 193 (211)
T ss_pred HHHCCCCHHHHHHHHCCCHhHHHHHHHHHHHHcCC
Confidence 34457899999999999999999988765544433
No 198
>PF12728 HTH_17: Helix-turn-helix domain
Probab=65.06 E-value=8.1 Score=28.62 Aligned_cols=24 Identities=21% Similarity=0.174 Sum_probs=21.3
Q ss_pred CcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 432 PDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 432 pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
.|.+|+|+.|||+..+|..+++..
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcC
Confidence 478999999999999999998754
No 199
>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=65.02 E-value=12 Score=29.84 Aligned_cols=33 Identities=30% Similarity=0.438 Sum_probs=23.9
Q ss_pred HHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 422 RLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 422 ~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
+.+....+ ..|..|||..+|++++.|+.+|..-
T Consensus 6 ~~~l~~~~-~~S~~eLa~~~~~s~~~ve~mL~~l 38 (69)
T PF09012_consen 6 RDYLRERG-RVSLAELAREFGISPEAVEAMLEQL 38 (69)
T ss_dssp HHHHHHS--SEEHHHHHHHTT--HHHHHHHHHHH
T ss_pred HHHHHHcC-CcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 33444444 7899999999999999999998743
No 200
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=64.98 E-value=18 Score=31.30 Aligned_cols=27 Identities=26% Similarity=0.382 Sum_probs=23.7
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577 431 SPDKEDLARRVGITVEKLERLIFITRM 457 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (482)
..|++|||+.||+++..++.+++....
T Consensus 23 ~LS~~~iA~~Ln~t~~~lekil~~tqr 49 (97)
T COG4367 23 PLSDEEIATALNWTEVKLEKILQVTQR 49 (97)
T ss_pred cccHHHHHHHhCCCHHHHHHHHHHhhc
Confidence 569999999999999999999976543
No 201
>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=64.76 E-value=6.9 Score=29.43 Aligned_cols=23 Identities=22% Similarity=0.404 Sum_probs=20.5
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHc
Q 011577 433 DKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 433 S~eEIAe~LGIS~etVk~~L~~a 455 (482)
|+++||+.+|++..+|..+|+-.
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 67899999999999999998743
No 202
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=64.64 E-value=14 Score=34.42 Aligned_cols=41 Identities=15% Similarity=0.143 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 414 LSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 414 l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
+..+...+-.+.++.+ ..++.|||+.+|+|..+|..++++-
T Consensus 12 lD~~D~~IL~~Lq~d~-R~s~~eiA~~lglS~~tv~~Ri~rL 52 (164)
T PRK11169 12 LDRIDRNILNELQKDG-RISNVELSKRVGLSPTPCLERVRRL 52 (164)
T ss_pred HHHHHHHHHHHhccCC-CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4445544444455555 5799999999999999999998854
No 203
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=64.11 E-value=8.7 Score=36.23 Aligned_cols=34 Identities=9% Similarity=0.074 Sum_probs=27.2
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccC
Q 011577 428 GNHSPDKEDLARRVGITVEKLERLIFITRMPLSM 461 (482)
Q Consensus 428 ~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSL 461 (482)
...+.|.+|||+.||+|..+|+..+......+-+
T Consensus 162 ~~~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~v 195 (216)
T PRK10840 162 FAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGV 195 (216)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 3457899999999999999999998766544433
No 204
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=63.77 E-value=10 Score=36.46 Aligned_cols=38 Identities=3% Similarity=-0.026 Sum_probs=28.4
Q ss_pred HHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCcc
Q 011577 423 LYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLS 460 (482)
Q Consensus 423 eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lS 460 (482)
+.......+.|.+|||+.||+++.+|+..+......+-
T Consensus 144 eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~ 181 (207)
T PRK15411 144 SMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKIK 181 (207)
T ss_pred HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 33333444679999999999999999999876654433
No 205
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=63.55 E-value=23 Score=28.39 Aligned_cols=34 Identities=12% Similarity=0.410 Sum_probs=26.0
Q ss_pred HHHHHhcCC-CCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 422 RLYIQEGNH-SPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 422 ~eL~~e~gr-~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
-.+....+. ..+..|||+.||++..+|...|..-
T Consensus 12 L~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L 46 (68)
T smart00550 12 LEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSL 46 (68)
T ss_pred HHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 333444442 4899999999999999999998743
No 206
>PRK14082 hypothetical protein; Provisional
Probab=62.90 E-value=27 Score=28.48 Aligned_cols=55 Identities=16% Similarity=0.103 Sum_probs=42.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhH
Q 011577 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASY 384 (482)
Q Consensus 328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTY 384 (482)
...+.+|..+.+.|.+-... ......+||-||--|.+++-++.++...+.-|--|
T Consensus 9 ~e~e~ii~~FepkIkKsL~~--T~yqeREDLeQElk~Ki~eK~~~~~~~e~PGF~ef 63 (65)
T PRK14082 9 EEIEHLIENFSPMIKKKLSN--TSYQEREDLEQELKIKIIEKADMLLCQEVPGFWEF 63 (65)
T ss_pred HHHHHHHHHccHHHHHHHhc--CChhhHHHHHHHHHHHHHHHHHHhhcccCCcHHHh
Confidence 56788999999888765543 24467899999999999999999987765555443
No 207
>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=62.41 E-value=8.7 Score=38.65 Aligned_cols=30 Identities=17% Similarity=0.194 Sum_probs=25.9
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHcCCCc
Q 011577 430 HSPDKEDLARRVGITVEKLERLIFITRMPL 459 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (482)
.+.|.+|||+.||||+.+|+..+..+...+
T Consensus 204 ~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL 233 (247)
T TIGR03020 204 DGKTNEEIAAILGISSLTVKNHLQHIFKKL 233 (247)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHh
Confidence 467999999999999999999998775443
No 208
>PF13730 HTH_36: Helix-turn-helix domain
Probab=62.30 E-value=10 Score=28.44 Aligned_cols=26 Identities=27% Similarity=0.447 Sum_probs=22.8
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 429 NHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 429 gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
+--||++.||+.+|++..+|...+..
T Consensus 23 ~~~pS~~~la~~~g~s~~Tv~~~i~~ 48 (55)
T PF13730_consen 23 GCFPSQETLAKDLGVSRRTVQRAIKE 48 (55)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 34679999999999999999998864
No 209
>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=61.96 E-value=18 Score=27.97 Aligned_cols=28 Identities=18% Similarity=0.259 Sum_probs=23.4
Q ss_pred HhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 426 QEGNHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 426 ~e~gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
.+.+ ..+.+|||+.+|+|..+|+.-+..
T Consensus 10 ~~~~-~~s~~ela~~~~VS~~TiRRDl~~ 37 (57)
T PF08220_consen 10 KEKG-KVSVKELAEEFGVSEMTIRRDLNK 37 (57)
T ss_pred HHcC-CEEHHHHHHHHCcCHHHHHHHHHH
Confidence 3444 789999999999999999887763
No 210
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=61.65 E-value=17 Score=32.73 Aligned_cols=39 Identities=23% Similarity=0.229 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 416 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 416 kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
.+...+-.+.+..++ .++.|||+.+|+|..+|..++..-
T Consensus 8 ~~D~~IL~~L~~d~r-~~~~eia~~lglS~~~v~~Ri~~L 46 (154)
T COG1522 8 DIDRRILRLLQEDAR-ISNAELAERVGLSPSTVLRRIKRL 46 (154)
T ss_pred HHHHHHHHHHHHhCC-CCHHHHHHHHCCCHHHHHHHHHHH
Confidence 333344444455553 899999999999999999998754
No 211
>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=61.44 E-value=12 Score=26.52 Aligned_cols=25 Identities=24% Similarity=0.328 Sum_probs=21.7
Q ss_pred CcHHHHHHHhCCCHHHHHHHHHHcC
Q 011577 432 PDKEDLARRVGITVEKLERLIFITR 456 (482)
Q Consensus 432 pS~eEIAe~LGIS~etVk~~L~~ar 456 (482)
.|.+|+|+.||++..++...++...
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g~ 26 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEGE 26 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcCC
Confidence 4789999999999999999987543
No 212
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=61.21 E-value=32 Score=30.39 Aligned_cols=34 Identities=18% Similarity=0.306 Sum_probs=27.0
Q ss_pred HHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcC
Q 011577 422 RLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR 456 (482)
Q Consensus 422 ~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar 456 (482)
..+..... +.+..|||+.+||+..+|-..|++..
T Consensus 63 ~~~v~~~p-d~tl~Ela~~l~Vs~~ti~~~Lkrlg 96 (119)
T PF01710_consen 63 KALVEENP-DATLRELAERLGVSPSTIWRALKRLG 96 (119)
T ss_pred HHHHHHCC-CcCHHHHHHHcCCCHHHHHHHHHHcC
Confidence 34444444 77999999999999999999998654
No 213
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=61.08 E-value=9.8 Score=37.80 Aligned_cols=39 Identities=15% Similarity=-0.039 Sum_probs=29.5
Q ss_pred HHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccC
Q 011577 423 LYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSM 461 (482)
Q Consensus 423 eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSL 461 (482)
+....+.++.+.+|||+.|++++.+|+..+......+-+
T Consensus 150 eVL~Lia~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLgv 188 (217)
T PRK13719 150 DVFILYSFGFSHEYIAQLLNITVGSSKNKISEILKFFGI 188 (217)
T ss_pred HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 333344457899999999999999999998766554443
No 214
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=60.62 E-value=10 Score=36.84 Aligned_cols=35 Identities=9% Similarity=0.065 Sum_probs=27.4
Q ss_pred hcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccC
Q 011577 427 EGNHSPDKEDLARRVGITVEKLERLIFITRMPLSM 461 (482)
Q Consensus 427 e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSL 461 (482)
...++.+.+|||+.||||+.||+..+.....++-.
T Consensus 145 ll~~G~snkeIA~~L~iS~~TV~~h~~~I~~KLgv 179 (207)
T PRK11475 145 FMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKLGV 179 (207)
T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 33447899999999999999999988766544433
No 215
>PRK13870 transcriptional regulator TraR; Provisional
Probab=60.24 E-value=9.3 Score=37.79 Aligned_cols=30 Identities=10% Similarity=0.080 Sum_probs=26.1
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHcCCCc
Q 011577 430 HSPDKEDLARRVGITVEKLERLIFITRMPL 459 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (482)
.+.|..|||.+||||+.+|+..++.++.++
T Consensus 187 ~GKT~~EIa~ILgISe~TV~~Hl~na~~KL 216 (234)
T PRK13870 187 VGKTMEEIADVEGVKYNSVRVKLREAMKRF 216 (234)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHc
Confidence 356999999999999999999998876553
No 216
>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=59.30 E-value=20 Score=28.12 Aligned_cols=24 Identities=21% Similarity=0.350 Sum_probs=22.1
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 431 SPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
..|..|||+.+|++..+|...+..
T Consensus 22 ~~t~~eIa~~l~i~~~~v~~~L~~ 45 (68)
T PF01978_consen 22 PATAEEIAEELGISRSTVYRALKS 45 (68)
T ss_dssp HEEHHHHHHHHTSSHHHHHHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 679999999999999999999874
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=58.73 E-value=15 Score=27.49 Aligned_cols=28 Identities=21% Similarity=0.378 Sum_probs=22.4
Q ss_pred hcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 427 EGNHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 427 e~gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
..+...+..|||+.+|++..++..++..
T Consensus 14 ~~~~~~t~~eia~~~gl~~stv~r~L~t 41 (52)
T PF09339_consen 14 ESGGPLTLSEIARALGLPKSTVHRLLQT 41 (52)
T ss_dssp CTBSCEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred cCCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3443569999999999999999999873
No 218
>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=57.73 E-value=25 Score=29.60 Aligned_cols=30 Identities=17% Similarity=0.278 Sum_probs=24.5
Q ss_pred HHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 423 LYIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 423 eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
++... + .+++.+||+.+|+|..+|...+..
T Consensus 13 e~l~~-~-~~ti~dvA~~~gvS~~TVsr~L~~ 42 (80)
T TIGR02844 13 KYIVE-T-KATVRETAKVFGVSKSTVHKDVTE 42 (80)
T ss_pred HHHHH-C-CCCHHHHHHHhCCCHHHHHHHhcC
Confidence 33444 5 789999999999999999998753
No 219
>PF14502 HTH_41: Helix-turn-helix domain
Probab=57.50 E-value=15 Score=28.22 Aligned_cols=36 Identities=8% Similarity=0.338 Sum_probs=28.7
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHHcC--CCccCcc
Q 011577 428 GNHSPDKEDLARRVGITVEKLERLIFITR--MPLSMQQ 463 (482)
Q Consensus 428 ~gr~pS~eEIAe~LGIS~etVk~~L~~ar--~~lSLD~ 463 (482)
+.|-|++.|+++.++++.++|..++..-. ..+.|+.
T Consensus 3 GdRi~tI~e~~~~~~vs~GtiQ~Alk~Le~~gaI~Le~ 40 (48)
T PF14502_consen 3 GDRIPTISEYSEKFGVSRGTIQNALKFLEENGAIKLES 40 (48)
T ss_pred CcccCCHHHHHHHhCcchhHHHHHHHHHHHCCcEEeee
Confidence 45678999999999999999999988543 4555543
No 220
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=57.30 E-value=10 Score=37.54 Aligned_cols=30 Identities=7% Similarity=0.018 Sum_probs=26.0
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHcCCCc
Q 011577 430 HSPDKEDLARRVGITVEKLERLIFITRMPL 459 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (482)
.+.|..|||++||||+.+|+..+..++..+
T Consensus 193 ~G~t~~eIa~~l~is~~TV~~h~~~~~~KL 222 (240)
T PRK10188 193 EGKTSAEIAMILSISENTVNFHQKNMQKKF 222 (240)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 367999999999999999999998776554
No 221
>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=57.06 E-value=38 Score=28.54 Aligned_cols=41 Identities=12% Similarity=0.109 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 415 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 415 ~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
.+|-+++-++..+.++.+.-++||+.+|++..+|++.|..-
T Consensus 7 ~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~L 47 (78)
T PF03444_consen 7 REILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADL 47 (78)
T ss_pred HHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHH
Confidence 34445555555666778899999999999999999998754
No 222
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=56.80 E-value=15 Score=27.18 Aligned_cols=25 Identities=16% Similarity=0.352 Sum_probs=22.2
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 431 SPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
-|+..|||+.+|++..+|...+..-
T Consensus 20 l~s~~~la~~~~vs~~tv~~~l~~L 44 (60)
T smart00345 20 LPSERELAAQLGVSRTTVREALSRL 44 (60)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 3499999999999999999998754
No 223
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=56.79 E-value=13 Score=36.16 Aligned_cols=32 Identities=13% Similarity=-0.027 Sum_probs=26.0
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCc
Q 011577 428 GNHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (482)
Q Consensus 428 ~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (482)
...+.+.+|||+.||+++.+|+..+......+
T Consensus 145 LAqGkTnKEIAe~L~IS~rTVkth~srImkKL 176 (198)
T PRK15201 145 IASGYHLSETAALLSLSEEQTKSLRRSIMRKL 176 (198)
T ss_pred HHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 33467999999999999999999887665443
No 224
>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=56.76 E-value=11 Score=37.12 Aligned_cols=30 Identities=23% Similarity=0.299 Sum_probs=26.1
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHcCCCc
Q 011577 430 HSPDKEDLARRVGITVEKLERLIFITRMPL 459 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (482)
.+.|..|||+.||+++.+|+..+..++..+
T Consensus 185 ~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl 214 (232)
T TIGR03541 185 LGRRQADIAAILGISERTVENHLRSARRKL 214 (232)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 467999999999999999999999876543
No 225
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=56.44 E-value=24 Score=26.58 Aligned_cols=27 Identities=19% Similarity=0.271 Sum_probs=23.5
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577 431 SPDKEDLARRVGITVEKLERLIFITRM 457 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (482)
+.+..|||..+|+++.+|...+.....
T Consensus 19 G~s~~eia~~l~is~~tV~~h~~~i~~ 45 (65)
T COG2771 19 GKSNKEIARILGISEETVKTHLRNIYR 45 (65)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 479999999999999999998876543
No 226
>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=55.83 E-value=18 Score=25.45 Aligned_cols=24 Identities=17% Similarity=0.307 Sum_probs=21.1
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHcC
Q 011577 433 DKEDLARRVGITVEKLERLIFITR 456 (482)
Q Consensus 433 S~eEIAe~LGIS~etVk~~L~~ar 456 (482)
+..|+|+.||++..+|........
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcCC
Confidence 678999999999999999987543
No 227
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=55.43 E-value=22 Score=34.25 Aligned_cols=33 Identities=12% Similarity=0.068 Sum_probs=27.4
Q ss_pred hcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCc
Q 011577 427 EGNHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (482)
Q Consensus 427 e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (482)
.+..+.+.+|||+.||+++.+|+..+.+..+..
T Consensus 174 ~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~ 206 (239)
T PRK10430 174 HQDYEFSTDELANAVNISRVSCRKYLIWLVNCH 206 (239)
T ss_pred CCCCCcCHHHHHHHhCchHHHHHHHHHHHHhCC
Confidence 345678999999999999999999998764443
No 228
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=55.07 E-value=21 Score=34.05 Aligned_cols=41 Identities=12% Similarity=0.085 Sum_probs=29.3
Q ss_pred HHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcC--CCccCccc
Q 011577 424 YIQEGNHSPDKEDLARRVGITVEKLERLIFITR--MPLSMQQP 464 (482)
Q Consensus 424 L~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar--~~lSLD~~ 464 (482)
+..++..+.|.+|||+.|||++.+|+..+.... ..++.+-.
T Consensus 170 ~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~~~~~~~~~~~~~~~ 212 (225)
T PRK10046 170 LFKEPGVQHTAETVAQALTISRTTARRYLEYCASRHLIIAEIV 212 (225)
T ss_pred HHHcCCCCcCHHHHHHHhCccHHHHHHHHHHHHhCCeEEEEee
Confidence 333443357999999999999999999987543 34454443
No 229
>PRK09483 response regulator; Provisional
Probab=54.99 E-value=16 Score=33.59 Aligned_cols=32 Identities=3% Similarity=0.204 Sum_probs=27.3
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHcCCCccC
Q 011577 430 HSPDKEDLARRVGITVEKLERLIFITRMPLSM 461 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~lSL 461 (482)
.+.+.+|||+.|++++.+|+..++.....+.+
T Consensus 162 ~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~v 193 (217)
T PRK09483 162 KGQKVNEISEQLNLSPKTVNSYRYRMFSKLNI 193 (217)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence 46799999999999999999999877666554
No 230
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=54.25 E-value=15 Score=32.74 Aligned_cols=32 Identities=16% Similarity=0.256 Sum_probs=27.0
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHcCCCccC
Q 011577 430 HSPDKEDLARRVGITVEKLERLIFITRMPLSM 461 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~lSL 461 (482)
.+.+.+|||+.|+++..+|+..+...+..+-.
T Consensus 163 ~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~ 194 (211)
T PRK15369 163 EGYTNRDIAEQLSISIKTVETHRLNMMRKLDV 194 (211)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 35689999999999999999999887766544
No 231
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=53.55 E-value=21 Score=28.69 Aligned_cols=27 Identities=11% Similarity=0.199 Sum_probs=21.7
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 429 NHSPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 429 gr~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
...++-.|||+.+|++..+++..|..-
T Consensus 13 ~~p~~T~eiA~~~gls~~~aR~yL~~L 39 (62)
T PF04703_consen 13 NGPLKTREIADALGLSIYQARYYLEKL 39 (62)
T ss_dssp TS-EEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 447899999999999999999998743
No 232
>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=53.02 E-value=50 Score=30.59 Aligned_cols=35 Identities=14% Similarity=0.255 Sum_probs=28.3
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCc
Q 011577 428 GNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQ 462 (482)
Q Consensus 428 ~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD 462 (482)
-++..|..||++.+||++..|...++-.|-.++=.
T Consensus 43 p~~~ati~eV~e~tgVs~~~I~~~IreGRL~~~~~ 77 (137)
T TIGR03826 43 ENRQATVSEIVEETGVSEKLILKFIREGRLQLKHF 77 (137)
T ss_pred CCCCCCHHHHHHHHCcCHHHHHHHHHcCCeeccCC
Confidence 33457999999999999999999999777555443
No 233
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=52.89 E-value=11 Score=36.56 Aligned_cols=30 Identities=20% Similarity=0.253 Sum_probs=26.2
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 429 NHSPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
-|..+.+|||+.|||+..++...|++|.+.
T Consensus 176 PR~~~l~dLA~~lGISkst~~ehLRrAe~K 205 (215)
T COG3413 176 PRRVSLKDLAKELGISKSTLSEHLRRAERK 205 (215)
T ss_pred CccCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 356799999999999999999999988543
No 234
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=52.60 E-value=41 Score=29.89 Aligned_cols=40 Identities=13% Similarity=0.091 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 416 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 416 kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
.+.++..-+.......++.++||+.+|+++..+..+....
T Consensus 10 ~i~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 10 TIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3444555555666667899999999999999998877643
No 235
>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=52.27 E-value=25 Score=25.98 Aligned_cols=24 Identities=21% Similarity=0.361 Sum_probs=19.6
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 431 SPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
+.|..|+|+.+|++..+|..+..-
T Consensus 9 gls~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 9 GLSQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp TS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred CCCHHHHHHHhCCCcchhHHHhcC
Confidence 579999999999999999998764
No 236
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=52.18 E-value=25 Score=33.88 Aligned_cols=24 Identities=13% Similarity=0.124 Sum_probs=21.9
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 431 SPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
+.|+.|||+.||.++.+|++.+.-
T Consensus 61 g~Ti~EIAeelG~TeqTir~hlkg 84 (182)
T COG1318 61 GMTISEIAEELGRTEQTVRNHLKG 84 (182)
T ss_pred cCcHHHHHHHhCCCHHHHHHHHhc
Confidence 579999999999999999999873
No 237
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=52.14 E-value=1.2e+02 Score=31.28 Aligned_cols=28 Identities=11% Similarity=0.043 Sum_probs=22.4
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 428 GNHSPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 428 ~gr~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
.+...|.+|||+..|++..+|++..+..
T Consensus 273 ~g~~~t~keIa~v~~Vs~~tI~~~ykel 300 (310)
T PRK00423 273 LGERRTQREVAEVAGVTEVTVRNRYKEL 300 (310)
T ss_pred hCCCCCHHHHHHHcCCCHHHHHHHHHHH
Confidence 3434599999999999999998876643
No 238
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=52.02 E-value=22 Score=34.67 Aligned_cols=29 Identities=10% Similarity=0.218 Sum_probs=25.0
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHcCCCc
Q 011577 431 SPDKEDLARRVGITVEKLERLIFITRMPL 459 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (482)
+.+.+|||+.||+++.+|+..+......+
T Consensus 170 G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl 198 (216)
T PRK10100 170 GASNNEIARSLFISENTVKTHLYNLFKKI 198 (216)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 57999999999999999999988765443
No 239
>PRK10403 transcriptional regulator NarP; Provisional
Probab=51.89 E-value=19 Score=32.51 Aligned_cols=34 Identities=12% Similarity=0.128 Sum_probs=28.8
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcc
Q 011577 430 HSPDKEDLARRVGITVEKLERLIFITRMPLSMQQ 463 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~ 463 (482)
.+.+.+|||+.+|+++.+|+..+.+.+..+.+..
T Consensus 167 ~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~~ 200 (215)
T PRK10403 167 QGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRS 200 (215)
T ss_pred CCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCCCC
Confidence 3589999999999999999999998877665543
No 240
>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=51.37 E-value=35 Score=24.95 Aligned_cols=33 Identities=27% Similarity=0.484 Sum_probs=25.7
Q ss_pred HHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHH
Q 011577 419 EAKRLYIQEGNHSPDKEDLARRVGITVEKLERL 451 (482)
Q Consensus 419 ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~ 451 (482)
.+...+...+-...|..+||+.+|++...+...
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 344555666677899999999999999887643
No 241
>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=50.98 E-value=74 Score=27.51 Aligned_cols=65 Identities=17% Similarity=0.086 Sum_probs=39.6
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 382 ASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 382 STYA~~wIRnaI~~~Lrkq~r~irlP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
..|...++.+.+.+.+...-....+....+..+.. +. ..+ ..+..|||+.+|++..+|-.++..-
T Consensus 2 ~~~~l~~~~~~~~~~~~~~l~~~~lt~~q~~iL~~-------l~-~~~-~~t~~ela~~~~~~~~tvs~~l~~L 66 (118)
T TIGR02337 2 LPLALLQAREAAMSFFRPILAQHGLTEQQWRILRI-------LA-EQG-SMEFTQLANQACILRPSLTGILARL 66 (118)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHH-------HH-HcC-CcCHHHHHHHhCCCchhHHHHHHHH
Confidence 45666666666666665443323333222222222 22 233 6799999999999999998887754
No 242
>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=50.90 E-value=17 Score=31.06 Aligned_cols=27 Identities=7% Similarity=0.329 Sum_probs=22.4
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 429 NHSPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 429 gr~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
..+.++.+|++.||+++.+|+.++..-
T Consensus 63 ~~Gv~v~~I~~~l~~~~~~v~~al~~L 89 (102)
T PF08784_consen 63 EEGVHVDEIAQQLGMSENEVRKALDFL 89 (102)
T ss_dssp TTTEEHHHHHHHSTS-HHHHHHHHHHH
T ss_pred CCcccHHHHHHHhCcCHHHHHHHHHHH
Confidence 346899999999999999999998743
No 243
>PRK12423 LexA repressor; Provisional
Probab=50.69 E-value=44 Score=32.19 Aligned_cols=39 Identities=15% Similarity=0.248 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHhcCCCCcHHHHHHHhC-CCHHHHHHHHHH
Q 011577 416 KVLEAKRLYIQEGNHSPDKEDLARRVG-ITVEKLERLIFI 454 (482)
Q Consensus 416 kI~ka~~eL~~e~gr~pS~eEIAe~LG-IS~etVk~~L~~ 454 (482)
++-..+.....+.+-.||..|||+.+| .+...|+..+..
T Consensus 10 ~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~ 49 (202)
T PRK12423 10 AILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQA 49 (202)
T ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence 333444455556676799999999999 589999887763
No 244
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=50.17 E-value=50 Score=23.57 Aligned_cols=25 Identities=20% Similarity=0.234 Sum_probs=22.7
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 431 SPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
.++..+||+.+|++..+|...+...
T Consensus 14 ~~s~~~l~~~l~~s~~tv~~~l~~L 38 (53)
T smart00420 14 KVSVEELAELLGVSEMTIRRDLNKL 38 (53)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 5899999999999999999998754
No 245
>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=50.16 E-value=40 Score=24.67 Aligned_cols=23 Identities=17% Similarity=0.215 Sum_probs=21.2
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHH
Q 011577 431 SPDKEDLARRVGITVEKLERLIF 453 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~ 453 (482)
+.+.+++|+.+|++..+|..+..
T Consensus 15 gltq~~lA~~~gvs~~~vs~~e~ 37 (58)
T TIGR03070 15 GLTQADLADLAGVGLRFIRDVEN 37 (58)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHC
Confidence 57999999999999999999875
No 246
>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=50.03 E-value=36 Score=29.11 Aligned_cols=23 Identities=13% Similarity=0.245 Sum_probs=20.6
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHH
Q 011577 431 SPDKEDLARRVGITVEKLERLIF 453 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~ 453 (482)
+.|..|||+.+|++..+|..+.+
T Consensus 50 G~S~~eIA~~LgISrsTIyRi~R 72 (88)
T TIGR02531 50 GKTYSDIEAETGASTATISRVKR 72 (88)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHH
Confidence 56999999999999999999654
No 247
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=49.99 E-value=21 Score=32.33 Aligned_cols=32 Identities=6% Similarity=0.032 Sum_probs=28.2
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHcCCCccC
Q 011577 430 HSPDKEDLARRVGITVEKLERLIFITRMPLSM 461 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~lSL 461 (482)
.+.+.+|||+.|+++..+|+..+.+.+..+-+
T Consensus 163 ~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl~~ 194 (210)
T PRK09935 163 SGLSNKEIADQLLLSNKTVSAHKSNIYGKLGL 194 (210)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence 35899999999999999999999988877654
No 248
>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]
Probab=48.66 E-value=22 Score=34.57 Aligned_cols=35 Identities=14% Similarity=0.168 Sum_probs=28.5
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCccc
Q 011577 430 HSPDKEDLARRVGITVEKLERLIFITRMPLSMQQP 464 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~ 464 (482)
++.+..|||++|++|.+++.-++.++....+--.|
T Consensus 17 ~Glt~gEIAdELNvSreTa~WL~~r~~~~~~~~~p 51 (203)
T COG0856 17 KGLTTGEIADELNVSRETATWLLTRAFKKESVPAP 51 (203)
T ss_pred CCCcHHHhhhhhhhhHHHHHHHHhhhhhccCCCCC
Confidence 36799999999999999999999887655554443
No 249
>PHA02943 hypothetical protein; Provisional
Probab=48.50 E-value=57 Score=31.04 Aligned_cols=27 Identities=7% Similarity=0.277 Sum_probs=22.9
Q ss_pred hcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 427 EGNHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 427 e~gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
..| ..|..|||+.||+|-+.|+-.|..
T Consensus 21 k~G-~~TtseIAkaLGlS~~qa~~~Lyv 47 (165)
T PHA02943 21 ADG-CKTTSRIANKLGVSHSMARNALYQ 47 (165)
T ss_pred hcC-CccHHHHHHHHCCCHHHHHHHHHH
Confidence 444 568999999999999999998874
No 250
>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=48.35 E-value=33 Score=21.46 Aligned_cols=21 Identities=29% Similarity=0.529 Sum_probs=18.2
Q ss_pred CCcHHHHHHHhCCCHHHHHHH
Q 011577 431 SPDKEDLARRVGITVEKLERL 451 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~ 451 (482)
..+..+||+.+|++..+|...
T Consensus 21 ~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 21 GESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCCHHHHHHHHCCCHHHHHHh
Confidence 459999999999999998764
No 251
>PRK10651 transcriptional regulator NarL; Provisional
Probab=48.27 E-value=23 Score=32.12 Aligned_cols=33 Identities=15% Similarity=0.185 Sum_probs=27.9
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCc
Q 011577 430 HSPDKEDLARRVGITVEKLERLIFITRMPLSMQ 462 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD 462 (482)
.+.+.+|||+.|+++..+|+..+...+..+.+.
T Consensus 169 ~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl~~~ 201 (216)
T PRK10651 169 QGLPNKMIARRLDITESTVKVHVKHMLKKMKLK 201 (216)
T ss_pred cCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCCC
Confidence 457999999999999999999998877666543
No 252
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=47.37 E-value=57 Score=27.65 Aligned_cols=37 Identities=11% Similarity=0.061 Sum_probs=27.5
Q ss_pred HHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 418 LEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 418 ~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
.++...+...+...++.++||+.+|++...+..+...
T Consensus 8 ~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~ 44 (107)
T PRK10219 8 QTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRT 44 (107)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3344445556666789999999999999998877664
No 253
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=47.23 E-value=28 Score=24.73 Aligned_cols=25 Identities=20% Similarity=0.337 Sum_probs=22.0
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 431 SPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
.++..|||+.+|++..+|...+..-
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L 32 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRL 32 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHH
Confidence 4689999999999999999988754
No 254
>PF13518 HTH_28: Helix-turn-helix domain
Probab=47.08 E-value=36 Score=24.80 Aligned_cols=25 Identities=28% Similarity=0.353 Sum_probs=22.2
Q ss_pred CcHHHHHHHhCCCHHHHHHHHHHcC
Q 011577 432 PDKEDLARRVGITVEKLERLIFITR 456 (482)
Q Consensus 432 pS~eEIAe~LGIS~etVk~~L~~ar 456 (482)
.|+.+||..+||+..+|...+....
T Consensus 13 ~s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 13 ESVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred CCHHHHHHHHCCCHhHHHHHHHHHH
Confidence 3999999999999999999987653
No 255
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=47.05 E-value=37 Score=28.77 Aligned_cols=25 Identities=16% Similarity=0.259 Sum_probs=22.3
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 431 SPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
..+..|||+.+|++..+|...+..-
T Consensus 17 ~~~~~~la~~l~~s~~tv~~~l~~L 41 (108)
T smart00344 17 RISLAELAKKVGLSPSTVHNRVKRL 41 (108)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4789999999999999999988754
No 256
>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=46.70 E-value=19 Score=27.65 Aligned_cols=24 Identities=21% Similarity=0.461 Sum_probs=18.7
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHH
Q 011577 430 HSPDKEDLARRVGITVEKLERLIF 453 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~ 453 (482)
.+++..+||..+||+..+|..++.
T Consensus 21 ~g~s~~~ia~~fgv~~sTv~~I~K 44 (53)
T PF04218_consen 21 EGESKRDIAREFGVSRSTVSTILK 44 (53)
T ss_dssp CTT-HHHHHHHHT--CCHHHHHHH
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHH
Confidence 456999999999999999999876
No 257
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=46.54 E-value=58 Score=26.43 Aligned_cols=25 Identities=24% Similarity=0.364 Sum_probs=22.8
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 431 SPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
..+..|||+.+|++..+|...+...
T Consensus 20 ~~t~~~ia~~l~i~~~tv~r~l~~L 44 (91)
T smart00346 20 GLTLAELAERLGLSKSTAHRLLNTL 44 (91)
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 6899999999999999999998754
No 258
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=46.36 E-value=45 Score=31.62 Aligned_cols=37 Identities=22% Similarity=0.284 Sum_probs=28.1
Q ss_pred HHHHHHHHhcCCCCcHHHHHHHhCCC-HHHHHHHHHHc
Q 011577 419 EAKRLYIQEGNHSPDKEDLARRVGIT-VEKLERLIFIT 455 (482)
Q Consensus 419 ka~~eL~~e~gr~pS~eEIAe~LGIS-~etVk~~L~~a 455 (482)
..+.+...+.+..|+..|||+.+|++ ..+|...+..-
T Consensus 13 ~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L 50 (199)
T TIGR00498 13 DLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKAL 50 (199)
T ss_pred HHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHH
Confidence 33344445556679999999999998 99999888743
No 259
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=46.25 E-value=68 Score=28.33 Aligned_cols=30 Identities=13% Similarity=0.107 Sum_probs=25.6
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHcCCCcc
Q 011577 431 SPDKEDLARRVGITVEKLERLIFITRMPLS 460 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar~~lS 460 (482)
+.+.++||+.+|++..+|+..+.+.+..+.
T Consensus 156 ~~~~~~ia~~l~~s~~tv~~~~~~~~~kl~ 185 (202)
T PRK09390 156 GLSNKVIARDLDISPRTVEVYRANVMTKMQ 185 (202)
T ss_pred cCchHHHHHHcCCCHHHHHHHHHHHHHHHc
Confidence 468999999999999999999887766553
No 260
>PRK15320 transcriptional activator SprB; Provisional
Probab=46.23 E-value=18 Score=35.89 Aligned_cols=34 Identities=9% Similarity=0.042 Sum_probs=26.6
Q ss_pred HHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577 424 YIQEGNHSPDKEDLARRVGITVEKLERLIFITRM 457 (482)
Q Consensus 424 L~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (482)
+...+..+.+.+|||+.|+++.++|+..+.+...
T Consensus 172 VL~LLAkG~SNKEIAekL~LS~KTVSTYKnRLLe 205 (251)
T PRK15320 172 LLILLSSGHPAIELAKKFGLGTKTVSIYRKKVMY 205 (251)
T ss_pred HHHHHHcCCCHHHHHHHhccchhhHHHHHHHHHH
Confidence 3333445679999999999999999998876543
No 261
>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=45.40 E-value=68 Score=24.82 Aligned_cols=27 Identities=15% Similarity=0.151 Sum_probs=22.6
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHcC
Q 011577 430 HSPDKEDLARRVGITVEKLERLIFITR 456 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar 456 (482)
+..++.|||+.||+|..+++..+..-.
T Consensus 18 ~~~~~~ela~~l~~S~rti~~~i~~L~ 44 (59)
T PF08280_consen 18 KWITLKELAKKLNISERTIKNDINELN 44 (59)
T ss_dssp TSBBHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence 378999999999999999999887543
No 262
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=44.82 E-value=2.6e+02 Score=27.70 Aligned_cols=39 Identities=23% Similarity=0.177 Sum_probs=28.9
Q ss_pred HHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 417 VLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 417 I~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
+.++...+........+++++|+.+|+|...+..+.+..
T Consensus 185 i~~~~~~i~~~~~~~isl~~lA~~~~lS~~~l~r~Fk~~ 223 (290)
T PRK10572 185 VREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQ 223 (290)
T ss_pred HHHHHHHHHhcccCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 444445555666668899999999999998888776643
No 263
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=44.54 E-value=2.4e+02 Score=28.03 Aligned_cols=49 Identities=16% Similarity=0.112 Sum_probs=33.6
Q ss_pred HHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHH
Q 011577 339 RLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 388 (482)
Q Consensus 339 rLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~w 388 (482)
+.+-.|...|....+..++|.+...|..-.-...|... |..|..|+...
T Consensus 201 ~~~~~I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk~~-G~T~~~yi~~~ 249 (302)
T PRK09685 201 KVVALIDQSIQEEILRPEWIAGELGISVRSLYRLFAEQ-GLVVAQYIRNR 249 (302)
T ss_pred HHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHc-CCCHHHHHHHH
Confidence 33344445555556899999999888877777777654 77777776653
No 264
>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=44.03 E-value=21 Score=27.07 Aligned_cols=37 Identities=11% Similarity=0.181 Sum_probs=25.3
Q ss_pred CcHHHHHHHhCCCHHHHHHHH-HHcCC-CccCcccCCCC
Q 011577 432 PDKEDLARRVGITVEKLERLI-FITRM-PLSMQQPVWAD 468 (482)
Q Consensus 432 pS~eEIAe~LGIS~etVk~~L-~~ar~-~lSLD~~i~~d 468 (482)
.++.|||+.||++...|-..+ ....- ..+..+.+..+
T Consensus 4 i~V~elAk~l~v~~~~ii~~l~~~~Gi~~~~~~~~ld~e 42 (54)
T PF04760_consen 4 IRVSELAKELGVPSKEIIKKLFKELGIMVKSINSSLDEE 42 (54)
T ss_dssp E-TTHHHHHHSSSHHHHHHHH-HHHTS---SSSS-EETT
T ss_pred eEHHHHHHHHCcCHHHHHHHHHHhCCcCcCCCCCcCCHH
Confidence 467899999999999999998 41333 36777666544
No 265
>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=43.75 E-value=31 Score=24.82 Aligned_cols=24 Identities=21% Similarity=0.193 Sum_probs=20.7
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHcC
Q 011577 433 DKEDLARRVGITVEKLERLIFITR 456 (482)
Q Consensus 433 S~eEIAe~LGIS~etVk~~L~~ar 456 (482)
+..|+|+.+|++..+|+.......
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHHCCC
Confidence 678999999999999998876543
No 266
>PRK06424 transcription factor; Provisional
Probab=43.52 E-value=81 Score=29.34 Aligned_cols=43 Identities=12% Similarity=0.007 Sum_probs=31.8
Q ss_pred hHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHH
Q 011577 409 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF 453 (482)
Q Consensus 409 ~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~ 453 (482)
...+....+...++.+.... +.|.+|+|+.+|++...|..+.+
T Consensus 77 ~~~~~~~~~g~~Ir~lRe~~--GLSQ~eLA~~iGvs~stIskiE~ 119 (144)
T PRK06424 77 EDLDIVEDYAELVKNARERL--SMSQADLAAKIFERKNVIASIER 119 (144)
T ss_pred HHHHHHHHHHHHHHHHHHHc--CCCHHHHHHHhCCCHHHHHHHHC
Confidence 33444555555556555554 48999999999999999999876
No 267
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=43.26 E-value=39 Score=35.45 Aligned_cols=37 Identities=27% Similarity=0.470 Sum_probs=30.5
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHcCC----CccCcccCC
Q 011577 430 HSPDKEDLARRVGITVEKLERLIFITRM----PLSMQQPVW 466 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~----~lSLD~~i~ 466 (482)
.+.|..|||+.||||.-+|..++..++. .++++.++.
T Consensus 25 ~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I~i~~~~~ 65 (321)
T COG2390 25 EGLTQSEIAERLGISRATVSRLLAKAREEGIVKISINSPVE 65 (321)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEEEeCCCCc
Confidence 3579999999999999999999998875 466665543
No 268
>PHA01976 helix-turn-helix protein
Probab=43.05 E-value=62 Score=24.95 Aligned_cols=23 Identities=17% Similarity=0.225 Sum_probs=20.2
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHH
Q 011577 431 SPDKEDLARRVGITVEKLERLIF 453 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~ 453 (482)
..|.+|+|+.+|++..+|..+..
T Consensus 15 glt~~~lA~~~gvs~~~v~~~e~ 37 (67)
T PHA01976 15 AWSAPELSRRAGVRHSLIYDFEA 37 (67)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHc
Confidence 57999999999999999988765
No 269
>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=42.73 E-value=30 Score=26.94 Aligned_cols=26 Identities=19% Similarity=0.358 Sum_probs=20.1
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 430 HSPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
+-|+..+||+.+|++..+|+.++...
T Consensus 23 ~lps~~~la~~~~vsr~tvr~al~~L 48 (64)
T PF00392_consen 23 RLPSERELAERYGVSRTTVREALRRL 48 (64)
T ss_dssp BE--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred EeCCHHHHHHHhccCCcHHHHHHHHH
Confidence 34699999999999999999998753
No 270
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=42.62 E-value=29 Score=26.47 Aligned_cols=32 Identities=28% Similarity=0.385 Sum_probs=19.4
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHcCCCccCc
Q 011577 431 SPDKEDLARRVGITVEKLERLIFITRMPLSMQ 462 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD 462 (482)
+.+..+||+.+|++..++..+++.-...++++
T Consensus 10 ~it~~~La~~~gis~~tl~~~~~~~~~~~~~~ 41 (63)
T PF13443_consen 10 GITQKDLARKTGISRSTLSRILNGKPSNPSLD 41 (63)
T ss_dssp T--HHHHHHHHT--HHHHHHHHTTT-----HH
T ss_pred CCCHHHHHHHHCcCHHHHHHHHhcccccccHH
Confidence 46999999999999999999987433455554
No 271
>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=42.04 E-value=24 Score=25.37 Aligned_cols=23 Identities=13% Similarity=0.134 Sum_probs=18.6
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHc
Q 011577 433 DKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 433 S~eEIAe~LGIS~etVk~~L~~a 455 (482)
|+.|+|+.+||+..+++-.-...
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~G 23 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYEREG 23 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHTT
T ss_pred CHHHHHHHHCCCHHHHHHHHHCC
Confidence 56899999999999999887643
No 272
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=41.62 E-value=32 Score=30.54 Aligned_cols=29 Identities=21% Similarity=0.432 Sum_probs=26.6
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHcCCCc
Q 011577 431 SPDKEDLARRVGITVEKLERLIFITRMPL 459 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (482)
+.+.+|-|+.||||-.++..++..|+..+
T Consensus 57 gl~QeeaA~~MgVSR~T~~ril~~ARkKi 85 (106)
T PF02001_consen 57 GLSQEEAAERMGVSRPTFQRILESARKKI 85 (106)
T ss_pred CCCHHHHHHHcCCcHHHHHHHHHHHHHHH
Confidence 68999999999999999999999988754
No 273
>PRK09726 antitoxin HipB; Provisional
Probab=41.35 E-value=62 Score=26.93 Aligned_cols=23 Identities=17% Similarity=0.342 Sum_probs=20.9
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHH
Q 011577 431 SPDKEDLARRVGITVEKLERLIF 453 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~ 453 (482)
+.|.+|+|+.+|++..+|..+.+
T Consensus 25 gltq~elA~~~gvs~~tis~~e~ 47 (88)
T PRK09726 25 GWTQSELAKKIGIKQATISNFEN 47 (88)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHC
Confidence 58999999999999999998876
No 274
>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=41.12 E-value=1.1e+02 Score=22.84 Aligned_cols=24 Identities=17% Similarity=0.385 Sum_probs=21.5
Q ss_pred CcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 432 PDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 432 pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
++..+||+.+|++..+|...+...
T Consensus 26 ~~~~~la~~~~is~~~v~~~l~~L 49 (66)
T cd07377 26 PSERELAEELGVSRTTVREALREL 49 (66)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Confidence 579999999999999999988754
No 275
>PF07374 DUF1492: Protein of unknown function (DUF1492); InterPro: IPR010861 This entry is represented by Streptococcus phage 7201, Orf19. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several hypothetical, highly conserved Streptococcal and related phage proteins. The function of this family is unknown.
Probab=40.95 E-value=1e+02 Score=26.50 Aligned_cols=30 Identities=13% Similarity=0.018 Sum_probs=24.5
Q ss_pred hcCCCCcHHHHHHHhCCCHHHHHHHHHHcC
Q 011577 427 EGNHSPDKEDLARRVGITVEKLERLIFITR 456 (482)
Q Consensus 427 e~gr~pS~eEIAe~LGIS~etVk~~L~~ar 456 (482)
.+-...+..+||+.||++..++-.....|.
T Consensus 67 ~Yi~~~~~~~I~~~l~~S~~t~yr~~~~Al 96 (100)
T PF07374_consen 67 RYINKLTWEQIAEELNISRRTYYRIHKKAL 96 (100)
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 344467899999999999999988877663
No 276
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=40.90 E-value=35 Score=35.46 Aligned_cols=36 Identities=19% Similarity=0.346 Sum_probs=30.3
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHcCC----CccCcccC
Q 011577 430 HSPDKEDLARRVGITVEKLERLIFITRM----PLSMQQPV 465 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~----~lSLD~~i 465 (482)
.+.|..|||+.||+|--+|-.+|..||. .+.++.|.
T Consensus 28 ~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~I~I~~~~ 67 (318)
T PRK15418 28 DGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQINSRF 67 (318)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEEEEEeCCC
Confidence 3579999999999999999999999875 35666664
No 277
>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=40.51 E-value=47 Score=27.27 Aligned_cols=24 Identities=21% Similarity=0.416 Sum_probs=21.0
Q ss_pred CcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 432 PDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 432 pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
.+.+|||+.+|++...|+.+++.-
T Consensus 26 ~s~~eiA~~~~i~~~~l~kil~~L 49 (83)
T PF02082_consen 26 VSSKEIAERLGISPSYLRKILQKL 49 (83)
T ss_dssp BEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHH
Confidence 799999999999999999998744
No 278
>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=40.36 E-value=2.1e+02 Score=29.27 Aligned_cols=25 Identities=28% Similarity=0.417 Sum_probs=21.6
Q ss_pred CCcHHHHHHHhC--CCHHHHHHHHHHc
Q 011577 431 SPDKEDLARRVG--ITVEKLERLIFIT 455 (482)
Q Consensus 431 ~pS~eEIAe~LG--IS~etVk~~L~~a 455 (482)
..+.++||+.++ ||.++|++.|..-
T Consensus 137 ~~~~~~ia~~l~p~is~~ev~~sL~~L 163 (271)
T TIGR02147 137 ADDPEELAKRCFPKISAEQVKESLDLL 163 (271)
T ss_pred CCCHHHHHHHhCCCCCHHHHHHHHHHH
Confidence 557889999999 9999999998743
No 279
>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=40.13 E-value=63 Score=27.21 Aligned_cols=27 Identities=22% Similarity=0.281 Sum_probs=20.5
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 429 NHSPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 429 gr~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
|+.+|..+||..+|++.++|+.+|...
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 668899999999999999999999865
No 280
>PRK13239 alkylmercury lyase; Provisional
Probab=39.96 E-value=62 Score=31.96 Aligned_cols=29 Identities=21% Similarity=0.237 Sum_probs=26.1
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHHcC
Q 011577 428 GNHSPDKEDLARRVGITVEKLERLIFITR 456 (482)
Q Consensus 428 ~gr~pS~eEIAe~LGIS~etVk~~L~~ar 456 (482)
.|+.++..+||+.+|+++++|+.+|+...
T Consensus 33 ~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 33 KGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 56799999999999999999999998653
No 281
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=39.74 E-value=29 Score=27.66 Aligned_cols=22 Identities=23% Similarity=0.436 Sum_probs=19.4
Q ss_pred CcHHHHHHHhCCCHHHHHHHHH
Q 011577 432 PDKEDLARRVGITVEKLERLIF 453 (482)
Q Consensus 432 pS~eEIAe~LGIS~etVk~~L~ 453 (482)
++..|||+.+|++..+|..+++
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln 22 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLN 22 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHC
Confidence 3678999999999999998876
No 282
>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=39.72 E-value=94 Score=23.05 Aligned_cols=36 Identities=14% Similarity=0.110 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 416 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 416 kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
.+..|+..+. .| ..++.+.|+..|||..++...++.
T Consensus 4 ~l~~Ai~~v~--~g-~~S~r~AA~~ygVp~sTL~~r~~g 39 (45)
T PF05225_consen 4 DLQKAIEAVK--NG-KMSIRKAAKKYGVPRSTLRRRLRG 39 (45)
T ss_dssp HHHHHHHHHH--TT-SS-HHHHHHHHT--HHHHHHHHHH
T ss_pred HHHHHHHHHH--hC-CCCHHHHHHHHCcCHHHHHHHHcC
Confidence 3445555544 34 389999999999999999977663
No 283
>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=39.64 E-value=40 Score=26.57 Aligned_cols=24 Identities=21% Similarity=0.400 Sum_probs=21.7
Q ss_pred CcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 432 PDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 432 pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
++.++||+.+|++..+|...++.-
T Consensus 29 lt~~~iA~~~g~sr~tv~r~l~~l 52 (76)
T PF13545_consen 29 LTQEEIADMLGVSRETVSRILKRL 52 (76)
T ss_dssp SSHHHHHHHHTSCHHHHHHHHHHH
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Confidence 489999999999999999998754
No 284
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=39.16 E-value=1.1e+02 Score=29.21 Aligned_cols=26 Identities=27% Similarity=0.443 Sum_probs=22.3
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHcC
Q 011577 431 SPDKEDLARRVGITVEKLERLIFITR 456 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar 456 (482)
..|.++||+.||++..+|-.+++.-+
T Consensus 184 ~lt~~~iA~~lG~sr~tvsR~l~~l~ 209 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETISRLLGRFQ 209 (235)
T ss_pred cccHHHHHHHhCCcHHHHHHHHHHHH
Confidence 35899999999999999999887543
No 285
>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=39.10 E-value=56 Score=24.61 Aligned_cols=24 Identities=25% Similarity=0.441 Sum_probs=20.7
Q ss_pred CcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 432 PDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 432 pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
.+..|||+.+|++..+|..++...
T Consensus 22 ~t~~~la~~l~~~~~~vs~~v~~L 45 (62)
T PF12802_consen 22 LTQSELAERLGISKSTVSRIVKRL 45 (62)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHH
Confidence 799999999999999999988753
No 286
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=39.04 E-value=1.6e+02 Score=33.32 Aligned_cols=23 Identities=17% Similarity=0.251 Sum_probs=19.7
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHH
Q 011577 431 SPDKEDLARRVGITVEKLERLIF 453 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~ 453 (482)
..|..|||+..|+|..+|-...+
T Consensus 374 ~~si~eLA~~~~vS~aTV~Rf~k 396 (638)
T PRK14101 374 NDPIVDIARKADVSQPTVIRFCR 396 (638)
T ss_pred hccHHHHHHHhCCCHHHHHHHHH
Confidence 34999999999999999977655
No 287
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=38.96 E-value=39 Score=30.66 Aligned_cols=32 Identities=16% Similarity=0.135 Sum_probs=27.2
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHcCCCccC
Q 011577 430 HSPDKEDLARRVGITVEKLERLIFITRMPLSM 461 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~lSL 461 (482)
.+.+.+|||+.++++..+|+..+.+.+..+..
T Consensus 157 ~g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl~~ 188 (204)
T PRK09958 157 DGKDNNDIAEKMFISNKTVSTYKSRLMEKLEC 188 (204)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence 45699999999999999999999887766543
No 288
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=38.49 E-value=59 Score=25.12 Aligned_cols=24 Identities=21% Similarity=0.317 Sum_probs=19.4
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 431 SPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
+.|.+++|+.+|++..+|..+.+-
T Consensus 14 gls~~~lA~~~g~s~s~v~~iE~G 37 (64)
T PF13560_consen 14 GLSQAQLADRLGVSQSTVSRIERG 37 (64)
T ss_dssp TS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred CCCHHHHHHHHCcCHHHHHHHHCC
Confidence 579999999999999999998763
No 289
>COG2344 AT-rich DNA-binding protein [General function prediction only]
Probab=38.22 E-value=77 Score=31.30 Aligned_cols=51 Identities=12% Similarity=0.177 Sum_probs=41.8
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 404 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 404 irlP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
..+|......+...-+....|....-...+-+|||+.+|++..+|+.=+.+
T Consensus 5 ~~IP~AT~kRL~~YyR~le~l~a~~v~rvsS~els~~~~vdsatIRrDfSY 55 (211)
T COG2344 5 KKIPKATAKRLPLYYRVLERLHASGVERVSSKELSEALGVDSATIRRDFSY 55 (211)
T ss_pred ccCCHHHHHHhHHHHHHHHHHHHcCCceecHHHHHHHhCCCHHHHhhhhHH
Confidence 468888887777777777777777776789999999999999999886653
No 290
>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=38.10 E-value=79 Score=27.08 Aligned_cols=23 Identities=13% Similarity=0.429 Sum_probs=19.3
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHH
Q 011577 430 HSPDKEDLARRVGITVEKLERLI 452 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L 452 (482)
.+.++.|||+.+|+|..+|-..-
T Consensus 48 ~g~syreIa~~tgvS~aTItRvs 70 (87)
T PF01371_consen 48 EGKSYREIAEETGVSIATITRVS 70 (87)
T ss_dssp TTSSHHHHHHHHTSTHHHHHHHH
T ss_pred CCCCHHHHHHHhCCCHHHHHHHH
Confidence 36799999999999998886553
No 291
>PF05138 PaaA_PaaC: Phenylacetic acid catabolic protein; InterPro: IPR007814 This family includes proteins such as PaaA and PaaC that are part of a catabolic pathway of phenylacetic acid []. These proteins may form part of a dioxygenase complex.; PDB: 3PWQ_K 3PVT_B 1OTK_B 3PW1_B 3PW8_B 3PVR_B 3PVY_B 3Q1G_A 3PF7_B 3PM5_C ....
Probab=37.85 E-value=1.8e+02 Score=29.58 Aligned_cols=115 Identities=18% Similarity=0.152 Sum_probs=72.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHH-HHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHHHHHHHHHHHH
Q 011577 264 PETRKLLTADEEFELIAQIQDLIRLEKE-KSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVV 342 (482)
Q Consensus 264 i~~~~lLT~eEE~eL~~~Iq~l~~le~~-~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~LI~snlrLV~ 342 (482)
+....-++.+--..|++.|..+..=+-+ -.++.+.+|.-|++++...-++ -|.++| .|-++.+
T Consensus 4 ~e~~~~~~~~~~~~L~~~l~~laD~elil~~r~~ew~~~AP~LeediAl~~--------------ia~Del--GHAr~ly 67 (263)
T PF05138_consen 4 IEDPDEMPEEYREALIRYLLRLADDELILGQRLSEWCGHAPSLEEDIALAN--------------IAQDEL--GHARLLY 67 (263)
T ss_dssp B-TTSS--HHHHHHHHHHHHHHHHHHHHHHHHHHTGGGGSSSHHHHHHHHH--------------HHHHHH--HHHHHHH
T ss_pred cccchhhhhhhHHHHHHHHHHHhChHHHhhhHHhHHHhhCCCHHHHHHHHH--------------HHHHHH--HHHHHHH
Confidence 3444556677777788877665543322 4456667899998876654322 233332 5678889
Q ss_pred HHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHH
Q 011577 343 HVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIF 398 (482)
Q Consensus 343 sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lr 398 (482)
.++..+-|.|.+.++|...=.-+=++.+.-|+. .+..|+...+++.+.+...
T Consensus 68 ~ll~el~g~G~~~d~la~~R~~~~~rn~~l~e~----p~~dwa~~v~r~~l~d~~~ 119 (263)
T PF05138_consen 68 RLLEELEGEGRDEDDLAFLRDAREFRNLLLFEQ----PNGDWADTVARQFLFDRAG 119 (263)
T ss_dssp HHHHHCHCCCHHHHHHHHHHHTTCS-SSGGGGS-------SHHHHHHHHHHHHHHH
T ss_pred HHHHHHhccCCChhHHHhhcccchhhhhhhhcc----CCCCHHHHHHHHHHHHHHH
Confidence 999998888878888766555555555555543 4678999999988887654
No 292
>PF13551 HTH_29: Winged helix-turn helix
Probab=37.74 E-value=86 Score=26.17 Aligned_cols=25 Identities=16% Similarity=0.236 Sum_probs=20.0
Q ss_pred CCcHHHHHHHh-------CCCHHHHHHHHHHc
Q 011577 431 SPDKEDLARRV-------GITVEKLERLIFIT 455 (482)
Q Consensus 431 ~pS~eEIAe~L-------GIS~etVk~~L~~a 455 (482)
..+.++|++.| .++..+|..+|+..
T Consensus 80 ~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~~~ 111 (112)
T PF13551_consen 80 RWTLEELAEWLIEEEFGIDVSPSTIRRILKRA 111 (112)
T ss_pred cccHHHHHHHHHHhccCccCCHHHHHHHHHHC
Confidence 45788888865 78999999998764
No 293
>PRK00215 LexA repressor; Validated
Probab=37.60 E-value=90 Score=29.73 Aligned_cols=34 Identities=18% Similarity=0.318 Sum_probs=27.1
Q ss_pred HHHHHhcCCCCcHHHHHHHhCC-CHHHHHHHHHHc
Q 011577 422 RLYIQEGNHSPDKEDLARRVGI-TVEKLERLIFIT 455 (482)
Q Consensus 422 ~eL~~e~gr~pS~eEIAe~LGI-S~etVk~~L~~a 455 (482)
.++....+..++..|||+.+|+ +..+|..++...
T Consensus 14 ~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L 48 (205)
T PRK00215 14 RDHIEETGYPPSRREIADALGLRSPSAVHEHLKAL 48 (205)
T ss_pred HHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHH
Confidence 3334455668899999999999 999999987744
No 294
>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=37.58 E-value=1.1e+02 Score=24.50 Aligned_cols=19 Identities=42% Similarity=0.595 Sum_probs=14.0
Q ss_pred hhhCCCCcHHHHHHHhcCC
Q 011577 297 SQFGREPTLIEWAKAIGLS 315 (482)
Q Consensus 297 ~~~g~~pt~~ewA~a~gmd 315 (482)
...|.+||..|.|++.|+.
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 4579999999999999986
No 295
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=35.97 E-value=36 Score=29.34 Aligned_cols=25 Identities=24% Similarity=0.408 Sum_probs=22.8
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 431 SPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
+.|.++||..||++++.|..+|..-
T Consensus 23 ~ls~~~ia~dL~~s~~~le~vL~l~ 47 (89)
T PF10078_consen 23 GLSLEQIAADLGTSPEHLEQVLNLK 47 (89)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHcCC
Confidence 6899999999999999999998754
No 296
>PF13309 HTH_22: HTH domain
Probab=35.69 E-value=64 Score=25.68 Aligned_cols=20 Identities=25% Similarity=0.413 Sum_probs=18.1
Q ss_pred cHHHHHHHhCCCHHHHHHHH
Q 011577 433 DKEDLARRVGITVEKLERLI 452 (482)
Q Consensus 433 S~eEIAe~LGIS~etVk~~L 452 (482)
+.+.+|+.||||.-+|-..|
T Consensus 44 av~~vA~~L~iS~~TVY~YL 63 (64)
T PF13309_consen 44 AVEYVAEKLGISRATVYRYL 63 (64)
T ss_pred HHHHHHHHHCCCHHHHHHHc
Confidence 89999999999999997765
No 297
>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=35.45 E-value=2e+02 Score=26.24 Aligned_cols=26 Identities=23% Similarity=0.261 Sum_probs=22.7
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHcC
Q 011577 431 SPDKEDLARRVGITVEKLERLIFITR 456 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar 456 (482)
..|.+|||..+|++.++|-.+++.-+
T Consensus 143 ~~t~~~iA~~lG~tretvsR~l~~l~ 168 (193)
T TIGR03697 143 RLSHQAIAEAIGSTRVTITRLLGDLR 168 (193)
T ss_pred CCCHHHHHHHhCCcHHHHHHHHHHHH
Confidence 45999999999999999999987543
No 298
>PRK10072 putative transcriptional regulator; Provisional
Probab=35.44 E-value=67 Score=27.85 Aligned_cols=25 Identities=20% Similarity=0.276 Sum_probs=22.2
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 431 SPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
+.|..|+|+.+|++..+|.....--
T Consensus 46 glTQ~elA~~lGvS~~TVs~WE~G~ 70 (96)
T PRK10072 46 GLKIDDFARVLGVSVAMVKEWESRR 70 (96)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHcCC
Confidence 5899999999999999999997643
No 299
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=34.53 E-value=45 Score=25.83 Aligned_cols=24 Identities=13% Similarity=0.123 Sum_probs=21.1
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHcC
Q 011577 433 DKEDLARRVGITVEKLERLIFITR 456 (482)
Q Consensus 433 S~eEIAe~LGIS~etVk~~L~~ar 456 (482)
+..|+|+.+||+..+|+.......
T Consensus 2 ti~eva~~~gvs~~tlr~y~~~gl 25 (69)
T PF13411_consen 2 TIKEVAKLLGVSPSTLRYYEREGL 25 (69)
T ss_dssp EHHHHHHHTTTTHHHHHHHHHTTS
T ss_pred cHHHHHHHHCcCHHHHHHHHHhcC
Confidence 678999999999999999987553
No 300
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=34.47 E-value=1.9e+02 Score=24.38 Aligned_cols=42 Identities=5% Similarity=0.012 Sum_probs=29.1
Q ss_pred cCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHH
Q 011577 349 QGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVR 390 (482)
Q Consensus 349 ~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIR 390 (482)
.....+.+||.+...+..-.--..|...-|..|..|+...-.
T Consensus 18 ~~~~~~~~~lA~~~~~S~~~l~r~f~~~~g~s~~~~i~~~Rl 59 (107)
T PRK10219 18 IDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRL 59 (107)
T ss_pred cCCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCHHHHHHHHHH
Confidence 345588999998888877666666665567677777655433
No 301
>PRK15044 transcriptional regulator SirC; Provisional
Probab=34.23 E-value=2.4e+02 Score=29.39 Aligned_cols=60 Identities=22% Similarity=0.198 Sum_probs=43.7
Q ss_pred HHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhh
Q 011577 257 LRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS 325 (482)
Q Consensus 257 l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~ 325 (482)
+..|++..+..+.|..+..... ++++..-+.+..+++++.++||+.+|++...|.+..+.
T Consensus 172 Ls~~l~~~~~~~~L~~~~~is~---------~~kV~~~I~~nl~~~~SLeeLA~~lgmS~~tL~R~Fk~ 231 (295)
T PRK15044 172 ISAFVRKPGGFDFLERAIKITT---------KEKVYNIIISDLTRKWSQAEVAGKLFMSVSSLKRKLAA 231 (295)
T ss_pred HHHHHhcccchhhHHHHhhhhH---------HHHHHHHHHhCcccCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 6677787776666655544333 33444556677889999999999999999999887764
No 302
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=34.21 E-value=60 Score=23.06 Aligned_cols=28 Identities=21% Similarity=0.246 Sum_probs=20.2
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 428 GNHSPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 428 ~gr~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
+....++++||+.+|++......+.+..
T Consensus 5 ~~~~~~l~~iA~~~g~S~~~f~r~Fk~~ 32 (42)
T PF00165_consen 5 LQQKLTLEDIAEQAGFSPSYFSRLFKKE 32 (42)
T ss_dssp T-SS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred ccCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 3456799999999999999998887654
No 303
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=33.98 E-value=1.7e+02 Score=27.01 Aligned_cols=26 Identities=23% Similarity=0.262 Sum_probs=22.5
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHcC
Q 011577 431 SPDKEDLARRVGITVEKLERLIFITR 456 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar 456 (482)
..|.++||..+|++.++|-.++..-+
T Consensus 149 ~~t~~~iA~~lG~tretvsR~l~~l~ 174 (202)
T PRK13918 149 YATHDELAAAVGSVRETVTKVIGELS 174 (202)
T ss_pred cCCHHHHHHHhCccHHHHHHHHHHHH
Confidence 34899999999999999999887543
No 304
>PRK15044 transcriptional regulator SirC; Provisional
Probab=33.87 E-value=1.5e+02 Score=30.83 Aligned_cols=38 Identities=13% Similarity=0.162 Sum_probs=30.5
Q ss_pred HHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 417 VLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 417 I~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
..++..-+.....+.++.++||+.+|++..+++...+.
T Consensus 194 ~~kV~~~I~~nl~~~~SLeeLA~~lgmS~~tL~R~Fk~ 231 (295)
T PRK15044 194 KEKVYNIIISDLTRKWSQAEVAGKLFMSVSSLKRKLAA 231 (295)
T ss_pred HHHHHHHHHhCcccCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 44455556666777899999999999999999988764
No 305
>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=33.82 E-value=84 Score=27.40 Aligned_cols=24 Identities=13% Similarity=0.337 Sum_probs=20.2
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHH
Q 011577 430 HSPDKEDLARRVGITVEKLERLIF 453 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~ 453 (482)
.+.|+.|||+.+||+..+|-..-+
T Consensus 54 ~~~tQrEIa~~lGiS~atIsR~sn 77 (94)
T TIGR01321 54 GNMSQREIASKLGVSIATITRGSN 77 (94)
T ss_pred CCCCHHHHHHHhCCChhhhhHHHh
Confidence 368999999999999998876543
No 306
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=33.60 E-value=1.2e+02 Score=30.02 Aligned_cols=42 Identities=14% Similarity=0.090 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHH
Q 011577 412 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF 453 (482)
Q Consensus 412 e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~ 453 (482)
..+..+-...++.....-++...++||..||||+.+|+....
T Consensus 138 ~~l~tLT~RERqVl~~vV~G~~NKqIA~dLgiS~rTVe~HRa 179 (202)
T COG4566 138 ARLATLTPRERQVLDLVVRGLMNKQIAFDLGISERTVELHRA 179 (202)
T ss_pred HHHHhcCHHHHHHHHHHHcCcccHHHHHHcCCchhhHHHHHH
Confidence 334444444444444444577899999999999999987543
No 307
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=33.21 E-value=50 Score=30.83 Aligned_cols=30 Identities=23% Similarity=0.338 Sum_probs=19.1
Q ss_pred HHHhcCCCCcHHHHHHHhCCCHHHHHHHHH
Q 011577 424 YIQEGNHSPDKEDLARRVGITVEKLERLIF 453 (482)
Q Consensus 424 L~~e~gr~pS~eEIAe~LGIS~etVk~~L~ 453 (482)
+....+...|.+|||+.+||+..++-...+
T Consensus 27 ~~~~~~~r~T~~eiAee~Gis~~tLYrWr~ 56 (142)
T PF13022_consen 27 LMPENGERRTQAEIAEEVGISRSTLYRWRQ 56 (142)
T ss_dssp HS------S-HHHHHHHHTS-HHHHHHHHH
T ss_pred HhhhccccchHHHHHHHhCCCHHHHHHHHh
Confidence 333444578999999999999999988775
No 308
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=33.17 E-value=1.1e+02 Score=27.53 Aligned_cols=36 Identities=17% Similarity=0.244 Sum_probs=27.4
Q ss_pred HHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 419 EAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 419 ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
+++..+....+ .++..+||+.||++..+|...+..-
T Consensus 11 ~~I~~l~~~~~-~~~~~ela~~l~vs~~svs~~l~~L 46 (142)
T PRK03902 11 EQIYLLIEEKG-YARVSDIAEALSVHPSSVTKMVQKL 46 (142)
T ss_pred HHHHHHHhcCC-CcCHHHHHHHhCCChhHHHHHHHHH
Confidence 34444544455 6799999999999999999988643
No 309
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=32.75 E-value=55 Score=29.47 Aligned_cols=30 Identities=10% Similarity=0.077 Sum_probs=25.5
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHcCCCcc
Q 011577 431 SPDKEDLARRVGITVEKLERLIFITRMPLS 460 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar~~lS 460 (482)
+.+.++||+.|+++..+|+..+.+.+..+.
T Consensus 152 g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~ 181 (196)
T PRK10360 152 GMAVKEIAAELGLSPKTVHVHRANLMEKLG 181 (196)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 579999999999999999998887665543
No 310
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=32.47 E-value=87 Score=28.68 Aligned_cols=24 Identities=13% Similarity=0.070 Sum_probs=21.7
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 431 SPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
..|.+|||+.||++..+|...++.
T Consensus 42 ~~tvdelae~lnr~rStv~rsl~~ 65 (126)
T COG3355 42 PLTVDELAEILNRSRSTVYRSLQN 65 (126)
T ss_pred CcCHHHHHHHHCccHHHHHHHHHH
Confidence 679999999999999999888773
No 311
>TIGR00180 parB_part ParB-like partition proteins. This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.
Probab=32.01 E-value=98 Score=29.36 Aligned_cols=33 Identities=27% Similarity=0.544 Sum_probs=26.8
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcc
Q 011577 431 SPDKEDLARRVGITVEKLERLIFITRMPLSMQQ 463 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~ 463 (482)
+.+.+|||+.+|++...|..++..+.-+-.+..
T Consensus 120 g~s~~~iA~~lg~s~~~V~r~l~l~~lp~~v~~ 152 (187)
T TIGR00180 120 SMTQEDLAKKIGKSRAHITNLLRLLKLPSEIQS 152 (187)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHcCCHHHHH
Confidence 468999999999999999999998764444433
No 312
>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=31.83 E-value=54 Score=30.69 Aligned_cols=25 Identities=12% Similarity=0.417 Sum_probs=23.0
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 431 SPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
..|.+|||+.|||+...|+.++..-
T Consensus 28 ~~tdEeLa~~Lgi~~~~VRk~L~~L 52 (158)
T TIGR00373 28 EFTDEEISLELGIKLNEVRKALYAL 52 (158)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 6899999999999999999998754
No 313
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=31.63 E-value=82 Score=32.48 Aligned_cols=41 Identities=10% Similarity=0.076 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 415 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 415 ~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
+.+-.+.-.|..+.++...-+|||+.+|..+++|++.++.-
T Consensus 9 keIL~aLi~LY~~~~r~IKgeeIA~~l~rnpGTVRNqmq~L 49 (294)
T COG2524 9 KEILQALINLYRRKKRPIKGEEIAEVLNRNPGTVRNQMQSL 49 (294)
T ss_pred HHHHHHHHHHHHhcCCCcchHHHHHHHccCcchHHHHHHHH
Confidence 34445555666666667888999999999999999998854
No 314
>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=31.46 E-value=90 Score=27.57 Aligned_cols=28 Identities=7% Similarity=0.273 Sum_probs=23.8
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 428 GNHSPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 428 ~gr~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
.+...+..|||+.+|++...|..++..-
T Consensus 22 ~~~~~s~~eia~~l~is~~~v~~~l~~L 49 (130)
T TIGR02944 22 DSQPYSAAEIAEQTGLNAPTVSKILKQL 49 (130)
T ss_pred CCCCccHHHHHHHHCcCHHHHHHHHHHH
Confidence 3446799999999999999999998754
No 315
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=31.25 E-value=1.4e+02 Score=28.84 Aligned_cols=50 Identities=16% Similarity=0.269 Sum_probs=36.7
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 405 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 405 rlP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
.+|......+.+..+....|........+..|||+.+|++..+|+.=+..
T Consensus 6 ~~~~~~~~r~~~~~~il~~l~~~~~~~vs~~~L~~~~~v~~~tirrDl~~ 55 (213)
T PRK05472 6 KIPEATIKRLPLYYRYLKELKEEGVERVSSKELAEALGVDSAQIRKDLSY 55 (213)
T ss_pred cCCHHHHHHhHHHHHHHHHHHHcCCcEEeHHHHHHHhCcCHHHHHHHHHH
Confidence 46766666666666666666655534579999999999999999876553
No 316
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=31.24 E-value=1.2e+02 Score=26.44 Aligned_cols=26 Identities=27% Similarity=0.460 Sum_probs=20.2
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHcC
Q 011577 431 SPDKEDLARRVGITVEKLERLIFITR 456 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar 456 (482)
+.++.|||...|+|+..|..++...+
T Consensus 72 G~n~~eLA~kyglS~r~I~~Ii~~~~ 97 (108)
T PF08765_consen 72 GMNVRELARKYGLSERQIYRIIKRVR 97 (108)
T ss_dssp SS-HHHHHHHHT--HHHHHHHHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 56899999999999999999988653
No 317
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=31.23 E-value=1.3e+02 Score=25.60 Aligned_cols=26 Identities=12% Similarity=0.104 Sum_probs=22.5
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 429 NHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 429 gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
...++..|||+.+|++..+|..++..
T Consensus 45 ~~~is~~eLa~~~g~sr~tVsr~L~~ 70 (95)
T TIGR01610 45 QDRVTATVIAELTGLSRTHVSDAIKS 70 (95)
T ss_pred CCccCHHHHHHHHCcCHHHHHHHHHH
Confidence 34679999999999999999998764
No 318
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=31.01 E-value=64 Score=29.02 Aligned_cols=38 Identities=13% Similarity=0.290 Sum_probs=30.1
Q ss_pred HHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccC
Q 011577 421 KRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSM 461 (482)
Q Consensus 421 ~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSL 461 (482)
+..+....| +++|+++.||||--||+.+|...-..+.+
T Consensus 42 i~~Fi~~rG---nlKe~e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 42 IKLFIKNRG---NLKEMEKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred HHHHHHhcC---CHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence 344555566 89999999999999999999876655555
No 319
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=31.01 E-value=81 Score=30.91 Aligned_cols=26 Identities=19% Similarity=0.309 Sum_probs=22.8
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 430 HSPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
+-|+..|||+.+|+|-..|++++..-
T Consensus 33 ~LpsE~eLa~~lgVSRtpVREAL~~L 58 (254)
T PRK09464 33 KLPPERELAKQFDVSRPSLREAIQRL 58 (254)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 34699999999999999999998853
No 320
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=30.93 E-value=1.1e+02 Score=28.65 Aligned_cols=41 Identities=12% Similarity=0.105 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHHHHHHh-cCCCCcHHHHHHHhCCCHHHHHH
Q 011577 410 IYTLLSKVLEAKRLYIQE-GNHSPDKEDLARRVGITVEKLER 450 (482)
Q Consensus 410 v~e~l~kI~ka~~eL~~e-~gr~pS~eEIAe~LGIS~etVk~ 450 (482)
......+|-++..++..+ +-...|.++||+..|++.+++-.
T Consensus 9 ~~~~r~~Il~aa~~lf~~~G~~~~ti~~Ia~~agvsk~t~Y~ 50 (213)
T PRK09975 9 ALKTRQELIETAIAQFALRGVSNTTLNDIADAANVTRGAIYW 50 (213)
T ss_pred HHHHHHHHHHHHHHHHHHcCcccCCHHHHHHHcCCCHHHHHH
Confidence 334445566666665544 44678999999999999999854
No 321
>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=30.73 E-value=58 Score=25.16 Aligned_cols=23 Identities=17% Similarity=0.127 Sum_probs=20.2
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHc
Q 011577 433 DKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 433 S~eEIAe~LGIS~etVk~~L~~a 455 (482)
+..|+|+.+||+..+++...+..
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~~ 24 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERRY 24 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHhC
Confidence 67899999999999999987643
No 322
>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=30.72 E-value=96 Score=24.52 Aligned_cols=31 Identities=19% Similarity=0.355 Sum_probs=23.5
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHcCCCccCc
Q 011577 431 SPDKEDLARRVGITVEKLERLIFITRMPLSMQ 462 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD 462 (482)
+.+.+++|+.+|++..+|..++. ....++.+
T Consensus 18 ~~t~~~lA~~~gis~~tis~~~~-g~~~~~~~ 48 (78)
T TIGR02607 18 GLSIRALAKALGVSRSTLSRIVN-GRRGITAD 48 (78)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHc-CCCCCCHH
Confidence 57899999999999999999876 33334443
No 323
>smart00753 PAM PCI/PINT associated module.
Probab=30.39 E-value=93 Score=25.27 Aligned_cols=44 Identities=18% Similarity=0.183 Sum_probs=30.6
Q ss_pred HHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccC
Q 011577 421 KRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPV 465 (482)
Q Consensus 421 ~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i 465 (482)
...+...+. ..+.++||+.++++.+.|+..+..+-..-.|+..|
T Consensus 15 l~~l~~~y~-~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~I 58 (88)
T smart00753 15 LLQLSEPYS-SISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKI 58 (88)
T ss_pred HHHHhHHhc-eeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEE
Confidence 344554454 78999999999999999998877554333333333
No 324
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=30.39 E-value=93 Score=25.27 Aligned_cols=44 Identities=18% Similarity=0.183 Sum_probs=30.6
Q ss_pred HHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccC
Q 011577 421 KRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPV 465 (482)
Q Consensus 421 ~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i 465 (482)
...+...+. ..+.++||+.++++.+.|+..+..+-..-.|+..|
T Consensus 15 l~~l~~~y~-~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~I 58 (88)
T smart00088 15 LLQLSEPYS-SISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKI 58 (88)
T ss_pred HHHHhHHhc-eeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEE
Confidence 344554454 78999999999999999998877554333333333
No 325
>PRK08359 transcription factor; Validated
Probab=30.26 E-value=1.4e+02 Score=28.90 Aligned_cols=41 Identities=24% Similarity=0.340 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHH
Q 011577 410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLI 452 (482)
Q Consensus 410 v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L 452 (482)
+.+.+..+.+.++++.... +.|.+|+|+.+|++...|..+-
T Consensus 79 ~~elv~dy~~rIkeaRe~k--glSQeeLA~~lgvs~stI~~iE 119 (176)
T PRK08359 79 TEDIVEDYAERVYEAIQKS--GLSYEELSHEVGLSVNDLRRIA 119 (176)
T ss_pred HHHHHHHHHHHHHHHHHHc--CCCHHHHHHHhCCCHHHHHHHH
Confidence 3455555555556655554 5899999999999999998663
No 326
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=29.80 E-value=2.8e+02 Score=25.77 Aligned_cols=26 Identities=19% Similarity=0.378 Sum_probs=22.4
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHcC
Q 011577 431 SPDKEDLARRVGITVEKLERLIFITR 456 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar 456 (482)
..+.+|||..+|++..+|..+++.-+
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR~l~~l~ 193 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRVLKMLE 193 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 46889999999999999999987543
No 327
>PRK04841 transcriptional regulator MalT; Provisional
Probab=29.74 E-value=53 Score=37.88 Aligned_cols=32 Identities=13% Similarity=0.121 Sum_probs=26.4
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHHcCCCcc
Q 011577 429 NHSPDKEDLARRVGITVEKLERLIFITRMPLS 460 (482)
Q Consensus 429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lS 460 (482)
..+.|.+|||+.|+||+.||+..++....++-
T Consensus 851 ~~g~~~~~ia~~l~~s~~tv~~h~~~~~~kl~ 882 (903)
T PRK04841 851 YSGYSNEQIAGELDVAATTIKTHIRNLYQKLG 882 (903)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 34679999999999999999999987654433
No 328
>smart00351 PAX Paired Box domain.
Probab=29.59 E-value=85 Score=28.05 Aligned_cols=31 Identities=10% Similarity=0.064 Sum_probs=25.7
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHcCCCccC
Q 011577 431 SPDKEDLARRVGITVEKLERLIFITRMPLSM 461 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar~~lSL 461 (482)
+.+..+||+.+||+..+|..++++.+..=++
T Consensus 33 G~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~ 63 (125)
T smart00351 33 GVRPCDISRQLCVSHGCVSKILGRYYETGSI 63 (125)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHcCCc
Confidence 4699999999999999999999877544333
No 329
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=29.47 E-value=1.6e+02 Score=22.58 Aligned_cols=61 Identities=16% Similarity=0.282 Sum_probs=33.9
Q ss_pred CCcHHHHHHHhcCCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHH
Q 011577 302 EPTLIEWAKAIGLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSM 364 (482)
Q Consensus 302 ~pt~~ewA~a~gmdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~I 364 (482)
+++..++|+..|++...|.+.+..-- ......+.. ..+..+...+.......+|+.++..+
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~~~~s~~~~~~~--~r~~~a~~~l~~~~~~~~~ia~~~g~ 62 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKETGTTPKQYLRD--RRLERARRLLRDTDLSVTEIALRVGF 62 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHhCcCHHHHHHH--HHHHHHHHHHHcCCCCHHHHHHHhCC
Confidence 36788999999999888877665322 112222111 11222222222335788888877555
No 330
>PF13551 HTH_29: Winged helix-turn helix
Probab=29.42 E-value=61 Score=27.10 Aligned_cols=24 Identities=29% Similarity=0.426 Sum_probs=21.9
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHcC
Q 011577 433 DKEDLARRVGITVEKLERLIFITR 456 (482)
Q Consensus 433 S~eEIAe~LGIS~etVk~~L~~ar 456 (482)
+..+||+.+|++..+|...++...
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~ 37 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYR 37 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHH
Confidence 699999999999999999998654
No 331
>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=29.42 E-value=54 Score=27.61 Aligned_cols=28 Identities=18% Similarity=0.368 Sum_probs=19.7
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 431 SPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
+.|..|||+.||.+...|...+....-+
T Consensus 3 G~tq~eIA~~lGks~s~Vs~~l~Ll~lP 30 (93)
T PF08535_consen 3 GWTQEEIAKRLGKSRSWVSNHLALLDLP 30 (93)
T ss_dssp T--HHHHHHHTT--HHHHHHHHGGGS--
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHcCC
Confidence 4689999999999999999998876433
No 332
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=29.11 E-value=81 Score=22.94 Aligned_cols=25 Identities=12% Similarity=0.074 Sum_probs=22.4
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 431 SPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
..+..+|++.+|++..+|...++..
T Consensus 10 ~~~~~~i~~~l~is~~~v~~~l~~L 34 (66)
T smart00418 10 ELCVCELAEILGLSQSTVSHHLKKL 34 (66)
T ss_pred CccHHHHHHHHCCCHHHHHHHHHHH
Confidence 5699999999999999999998754
No 333
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=28.95 E-value=1.9e+02 Score=23.96 Aligned_cols=51 Identities=18% Similarity=0.169 Sum_probs=34.9
Q ss_pred ccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHH
Q 011577 348 YQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIF 398 (482)
Q Consensus 348 Y~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lr 398 (482)
....+...+++.++..+.-..-...|....|..|..|+..+-.+.....|.
T Consensus 32 ~~~~~~~l~~la~~~g~S~~~l~r~f~~~~g~s~~~~~~~~Rl~~A~~lL~ 82 (127)
T COG2207 32 NLAEPLTLEDLARRLGMSRRTLSRLFKKETGTSPSQYLRQLRLEEARRLLR 82 (127)
T ss_pred HhcCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 344558889999888887777777787777777776666555444444443
No 334
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=28.84 E-value=1.9e+02 Score=27.11 Aligned_cols=41 Identities=12% Similarity=0.043 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHH
Q 011577 411 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF 453 (482)
Q Consensus 411 ~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~ 453 (482)
.+.+..+...++.+.... +.|.+++|+.+|++...|..+.+
T Consensus 64 ~~l~~~~g~~Ir~~Re~~--glSqeeLA~~lgvs~s~IsriE~ 104 (154)
T TIGR00270 64 EELVEDYGIIIRREREKR--GWSQEQLAKKIQEKESLIKKIEN 104 (154)
T ss_pred HHHHHHHHHHHHHHHHHc--CCCHHHHHHHhCCCHHHHHHHHC
Confidence 344444444455554443 58999999999999999988764
No 335
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=28.81 E-value=2.3e+02 Score=25.10 Aligned_cols=49 Identities=14% Similarity=0.162 Sum_probs=36.8
Q ss_pred CCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHH
Q 011577 350 GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIF 398 (482)
Q Consensus 350 ~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lr 398 (482)
....+.+||..+..+.--.--..|...-|..|..|+..+-.......|.
T Consensus 23 ~~~~sl~~lA~~~g~S~~~l~r~Fk~~~G~s~~~~l~~~Rl~~A~~~L~ 71 (127)
T PRK11511 23 ESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLK 71 (127)
T ss_pred CCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4568999999998888877778887777888888887665554444444
No 336
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=28.79 E-value=1.6e+02 Score=22.52 Aligned_cols=26 Identities=19% Similarity=0.222 Sum_probs=21.4
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 429 NHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 429 gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
....+..|||+.+|++..++..-+..
T Consensus 22 ~~~~t~~ela~~l~~~~~t~s~hL~~ 47 (61)
T PF12840_consen 22 NGPMTVSELAEELGISQSTVSYHLKK 47 (61)
T ss_dssp CSTBEHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 34789999999999999999887764
No 337
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=28.65 E-value=2.2e+02 Score=20.49 Aligned_cols=22 Identities=27% Similarity=0.283 Sum_probs=17.6
Q ss_pred cHHHHHHHhCCCHHHHHHHHHH
Q 011577 433 DKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 433 S~eEIAe~LGIS~etVk~~L~~ 454 (482)
+..+.|+.|||+..++...+..
T Consensus 20 n~~~aA~~Lgisr~tL~~klkk 41 (42)
T PF02954_consen 20 NVSKAARLLGISRRTLYRKLKK 41 (42)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHHHh
Confidence 7889999999999999887753
No 338
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=28.27 E-value=1.8e+02 Score=25.19 Aligned_cols=24 Identities=17% Similarity=0.083 Sum_probs=21.2
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 431 SPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
+.|..++|+.+|++..+|....+-
T Consensus 78 gltq~~lA~~lg~~~~tis~~e~g 101 (127)
T TIGR03830 78 GLSQREAAELLGGGVNAFSRYERG 101 (127)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHCC
Confidence 579999999999999999888653
No 339
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=28.08 E-value=3e+02 Score=24.60 Aligned_cols=25 Identities=12% Similarity=0.187 Sum_probs=22.3
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 431 SPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
..+..|||+.+|++..+|-.++..-
T Consensus 54 ~~t~~eLa~~l~i~~~tvsr~l~~L 78 (144)
T PRK11512 54 CITPVELKKVLSVDLGALTRMLDRL 78 (144)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 5799999999999999999888754
No 340
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=28.04 E-value=1e+02 Score=29.59 Aligned_cols=25 Identities=16% Similarity=0.507 Sum_probs=22.9
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 431 SPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
..|.+|||+.|||+...|+.+|..-
T Consensus 36 ~~tdeeLA~~Lgi~~~~VRk~L~~L 60 (178)
T PRK06266 36 EVTDEEIAEQTGIKLNTVRKILYKL 60 (178)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 6899999999999999999998754
No 341
>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=27.56 E-value=5.9e+02 Score=24.92 Aligned_cols=33 Identities=18% Similarity=0.181 Sum_probs=24.7
Q ss_pred HHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 422 RLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 422 ~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
..+...+....|.++||+.+|+|...+..+.+.
T Consensus 193 ~~I~~~~~~~~sl~~lA~~~~~S~~~l~r~Fk~ 225 (287)
T TIGR02297 193 FLIEENYKQHLRLPEYADRLGISESRLNDICRR 225 (287)
T ss_pred HHHHHhhccCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 334445555779999999999999998776654
No 342
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=27.38 E-value=3.5e+02 Score=24.02 Aligned_cols=25 Identities=24% Similarity=0.282 Sum_probs=21.9
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 431 SPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
..+..|||+.+|++..+|..++..-
T Consensus 46 ~~t~~eLa~~l~~~~~tvt~~v~~L 70 (144)
T PRK03573 46 EQSQIQLAKAIGIEQPSLVRTLDQL 70 (144)
T ss_pred CCCHHHHHHHhCCChhhHHHHHHHH
Confidence 4689999999999999999888754
No 343
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=26.96 E-value=73 Score=24.58 Aligned_cols=22 Identities=23% Similarity=0.310 Sum_probs=19.6
Q ss_pred cHHHHHHHhCCCHHHHHHHHHH
Q 011577 433 DKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 433 S~eEIAe~LGIS~etVk~~L~~ 454 (482)
+..|+|+.+|++..+++.....
T Consensus 2 s~~eva~~~gvs~~tlr~~~~~ 23 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYERI 23 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHHHC
Confidence 6789999999999999988763
No 344
>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=26.84 E-value=94 Score=28.82 Aligned_cols=32 Identities=22% Similarity=0.313 Sum_probs=0.0
Q ss_pred HHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHH
Q 011577 417 VLEAKRLYIQEGNHSPDKEDLARRVGITVEKL 448 (482)
Q Consensus 417 I~ka~~eL~~e~gr~pS~eEIAe~LGIS~etV 448 (482)
+..+...+...+....|..+||+..|++.+.+
T Consensus 14 l~aA~~lf~e~G~~~~s~~~IA~~agvs~~~l 45 (202)
T TIGR03613 14 LSAALDTFSRFGFHGTSLEQIAELAGVSKTNL 45 (202)
T ss_pred HHHHHHHHHHhCcccCCHHHHHHHhCCCHHHH
No 345
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=26.66 E-value=1.6e+02 Score=28.40 Aligned_cols=27 Identities=30% Similarity=0.480 Sum_probs=23.8
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 428 GNHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 428 ~gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
+.+-||-.|||+.+|+|-.+|++++..
T Consensus 29 G~~LPsE~eLa~~~~VSR~TvR~Al~~ 55 (238)
T TIGR02325 29 GDYLPAEMQLAERFGVNRHTVRRAIAA 55 (238)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 345789999999999999999999873
No 346
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=26.66 E-value=1.2e+02 Score=30.22 Aligned_cols=28 Identities=21% Similarity=0.240 Sum_probs=23.8
Q ss_pred hcCCCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 427 EGNHSPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 427 e~gr~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
+.+ ..+.+|||+.||+|+.+|+.-+...
T Consensus 15 ~~~-~~~~~eLa~~l~VS~~TiRRdL~~L 42 (240)
T PRK10411 15 NHT-SLTTEALAEQLNVSKETIRRDLNEL 42 (240)
T ss_pred HcC-CCcHHHHHHHHCcCHHHHHHHHHHH
Confidence 444 7899999999999999999988743
No 347
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=26.41 E-value=1.2e+02 Score=24.87 Aligned_cols=23 Identities=22% Similarity=0.342 Sum_probs=20.1
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHH
Q 011577 431 SPDKEDLARRVGITVEKLERLIF 453 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~ 453 (482)
..|.+|+|+.+|++..++-.+-.
T Consensus 14 ~ltQ~elA~~vgVsRQTi~~iEk 36 (68)
T COG1476 14 GLTQEELAKLVGVSRQTIIAIEK 36 (68)
T ss_pred CcCHHHHHHHcCcCHHHHHHHHc
Confidence 58999999999999999987644
No 348
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=26.28 E-value=1.9e+02 Score=21.49 Aligned_cols=24 Identities=21% Similarity=0.318 Sum_probs=21.8
Q ss_pred CcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 432 PDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 432 pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
.+..|||+.+|++..++...+...
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~L 44 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKL 44 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHHH
Confidence 899999999999999999988754
No 349
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=25.88 E-value=1.2e+02 Score=30.24 Aligned_cols=31 Identities=13% Similarity=0.173 Sum_probs=24.9
Q ss_pred HHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 423 LYIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 423 eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
++....+ ..+..|||+.+|+|+.||+.=|..
T Consensus 14 ~~l~~~~-~v~v~eLa~~~~VS~~TIRRDL~~ 44 (252)
T PRK10681 14 QALKRSD-KLHLKDAAALLGVSEMTIRRDLNA 44 (252)
T ss_pred HHHHHcC-CCcHHHHHHHhCCCHHHHHHHHHH
Confidence 3444555 689999999999999999887764
No 350
>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=25.75 E-value=71 Score=24.85 Aligned_cols=22 Identities=9% Similarity=0.126 Sum_probs=19.5
Q ss_pred cHHHHHHHhCCCHHHHHHHHHH
Q 011577 433 DKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 433 S~eEIAe~LGIS~etVk~~L~~ 454 (482)
+..|+|+.+||+..+++.....
T Consensus 2 ~i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 2 TIKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh
Confidence 6789999999999999988654
No 351
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=25.53 E-value=99 Score=20.98 Aligned_cols=23 Identities=26% Similarity=0.473 Sum_probs=20.5
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHH
Q 011577 431 SPDKEDLARRVGITVEKLERLIF 453 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~ 453 (482)
..+..++|+.+|++..+|..+..
T Consensus 10 ~~s~~~la~~~~i~~~~i~~~~~ 32 (56)
T smart00530 10 GLTQEELAEKLGVSRSTLSRIEN 32 (56)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHC
Confidence 57999999999999999988765
No 352
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=25.42 E-value=3.1e+02 Score=20.89 Aligned_cols=36 Identities=22% Similarity=0.298 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHhcCCCCcHHHHHHHhCC-CHHHHHHHHHH
Q 011577 416 KVLEAKRLYIQEGNHSPDKEDLARRVGI-TVEKLERLIFI 454 (482)
Q Consensus 416 kI~ka~~eL~~e~gr~pS~eEIAe~LGI-S~etVk~~L~~ 454 (482)
++.++...+... ..+++|||..+|+ +........+.
T Consensus 38 r~~~a~~~l~~~---~~~~~~ia~~~g~~s~~~f~r~Fk~ 74 (84)
T smart00342 38 RLERARRLLRDT---DLSVTEIALRVGFSSQSYFSRAFKK 74 (84)
T ss_pred HHHHHHHHHHcC---CCCHHHHHHHhCCCChHHHHHHHHH
Confidence 344454444322 5799999999999 98888777654
No 353
>PRK09480 slmA division inhibitor protein; Provisional
Probab=25.22 E-value=1.6e+02 Score=26.90 Aligned_cols=38 Identities=24% Similarity=0.237 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHH-HHhcCCCCcHHHHHHHhCCCHHHHHH
Q 011577 413 LLSKVLEAKRLY-IQEGNHSPDKEDLARRVGITVEKLER 450 (482)
Q Consensus 413 ~l~kI~ka~~eL-~~e~gr~pS~eEIAe~LGIS~etVk~ 450 (482)
.-.+|-++..++ ..+.|...|.++||+..||+.+++-.
T Consensus 11 ~r~~Il~aa~~l~~~~~G~~~ti~~Ia~~agvs~gt~Y~ 49 (194)
T PRK09480 11 RREQILQALAQMLESPPGERITTAKLAARVGVSEAALYR 49 (194)
T ss_pred HHHHHHHHHHHHHHhcCCCccCHHHHHHHhCCCHhHHHH
Confidence 334555555555 44434799999999999999988743
No 354
>PRK14999 histidine utilization repressor; Provisional
Probab=25.17 E-value=1.7e+02 Score=28.57 Aligned_cols=27 Identities=15% Similarity=0.308 Sum_probs=23.7
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 428 GNHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 428 ~gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
+.+-|+..|||+.+|++-.+|++++..
T Consensus 33 G~~LPsE~eLa~~~gVSR~TVR~Al~~ 59 (241)
T PRK14999 33 HDRIPSEAELVAQYGFSRMTINRALRE 59 (241)
T ss_pred CCcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 345789999999999999999999873
No 355
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=25.13 E-value=1.5e+02 Score=27.75 Aligned_cols=38 Identities=16% Similarity=0.222 Sum_probs=28.7
Q ss_pred HHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 417 VLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 417 I~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
.-+++..+....+ .+...+||+.||++..+|.+++++-
T Consensus 11 YL~~Iy~l~~~~~-~~~~~diA~~L~Vsp~sVt~ml~rL 48 (154)
T COG1321 11 YLETIYELLEEKG-FARTKDIAERLKVSPPSVTEMLKRL 48 (154)
T ss_pred HHHHHHHHHhccC-cccHHHHHHHhCCCcHHHHHHHHHH
Confidence 3344555555444 6899999999999999998888754
No 356
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=25.13 E-value=55 Score=25.90 Aligned_cols=30 Identities=20% Similarity=0.212 Sum_probs=20.3
Q ss_pred HHHhcCCCCcHHHHHHHhCCCHHHHH-HHHHH
Q 011577 424 YIQEGNHSPDKEDLARRVGITVEKLE-RLIFI 454 (482)
Q Consensus 424 L~~e~gr~pS~eEIAe~LGIS~etVk-~~L~~ 454 (482)
+...++ ..+..|+|+.|||+..++. ....+
T Consensus 6 l~~~~g-~~~~~~lA~~lgis~st~s~~~~~r 36 (66)
T PF07022_consen 6 LKEALG-VKSDKELAERLGISKSTLSNNWKKR 36 (66)
T ss_dssp HHHHHT--SSCHHHHCCTT--HHHHH-HHHHS
T ss_pred HHHHhC-CCCHHHHHHHhCcCHHHhhHHHHhC
Confidence 334445 4577899999999999999 66654
No 357
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=25.12 E-value=1.4e+02 Score=26.22 Aligned_cols=25 Identities=24% Similarity=0.389 Sum_probs=22.4
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 431 SPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
.++.+|||+.+|++...|..++..-
T Consensus 25 ~~s~~eia~~~~i~~~~v~~il~~L 49 (132)
T TIGR00738 25 PVSVKEIAERQGISRSYLEKILRTL 49 (132)
T ss_pred cCcHHHHHHHHCcCHHHHHHHHHHH
Confidence 6799999999999999999998743
No 358
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=24.97 E-value=1.6e+02 Score=27.37 Aligned_cols=32 Identities=16% Similarity=0.154 Sum_probs=27.8
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHcCCCccC
Q 011577 430 HSPDKEDLARRVGITVEKLERLIFITRMPLSM 461 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~lSL 461 (482)
.+.|..|||+++|++..+|...+++.+..-++
T Consensus 20 ~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~~ 51 (138)
T COG3415 20 EGLSCREAAKRFGVSISTVYRWVRRYRETGLD 51 (138)
T ss_pred cCccHHHHHHHhCccHHHHHHHHHHhcccccc
Confidence 37899999999999999999999988765444
No 359
>COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]
Probab=24.54 E-value=1.2e+02 Score=31.97 Aligned_cols=72 Identities=26% Similarity=0.256 Sum_probs=45.1
Q ss_pred HHHHHHHHHHHHHHHHhcCCcccch--hHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 384 YAYWWVRQTIRKAIFQHSRTIRLPE--NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 384 YA~~wIRnaI~~~Lrkq~r~irlP~--~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
.+....+.-+.+.+|.-...-++|. ..-..-.+|.+++..+.....+..+.+|||+.+|+|..++..+.+..
T Consensus 187 ~a~~va~~lv~~~~R~~~~~Q~~~~~~~~~~~~~~l~~~i~~me~nle~plsl~~LA~~~~~S~R~leRlF~~~ 260 (328)
T COG4977 187 LANRVARQLVVDPIRSGGDRQRLPLLGRLGHRDPRLLRAIELMEANLEEPLSLEELADRAGLSRRQLERLFRAE 260 (328)
T ss_pred HHHHHHHHhhhccccCCCccccccccccCCCCCHHHHHHHHHHHHhhcCCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 3445555555555554222222221 11223345666667777778878899999999999999998876543
No 360
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=24.51 E-value=4.6e+02 Score=26.63 Aligned_cols=60 Identities=10% Similarity=0.216 Sum_probs=40.7
Q ss_pred HHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHH
Q 011577 339 RLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQ 399 (482)
Q Consensus 339 rLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrk 399 (482)
+++..|..+|. ...+.+||.....+..-.--..|...-|..|..|+...-.+.....|..
T Consensus 195 ~~~~~i~~~~~-~~~tl~~lA~~~~~S~~~l~r~Fk~~~G~t~~~~l~~~Rl~~A~~lL~~ 254 (302)
T PRK10371 195 QMLGFIAENYD-QALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRALLSD 254 (302)
T ss_pred HHHHHHHHhhc-CCCCHHHHHHHHCcCHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHhc
Confidence 34444555554 5799999999988877766666765567788888876655555555543
No 361
>PRK11050 manganese transport regulator MntR; Provisional
Probab=24.49 E-value=2.4e+02 Score=25.93 Aligned_cols=26 Identities=15% Similarity=0.353 Sum_probs=22.9
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHcC
Q 011577 431 SPDKEDLARRVGITVEKLERLIFITR 456 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar 456 (482)
..+..|||+.+|++..+|...+....
T Consensus 51 ~~t~~eLA~~l~is~stVsr~l~~Le 76 (152)
T PRK11050 51 EARQVDIAARLGVSQPTVAKMLKRLA 76 (152)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 67999999999999999999987543
No 362
>PRK13502 transcriptional activator RhaR; Provisional
Probab=24.47 E-value=5.6e+02 Score=25.13 Aligned_cols=29 Identities=10% Similarity=0.159 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHH
Q 011577 415 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVE 446 (482)
Q Consensus 415 ~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~e 446 (482)
.+|.+|...|... ..++.|||..+|.+-.
T Consensus 228 ~Rl~~A~~lL~~t---~~sI~eIA~~~GF~d~ 256 (282)
T PRK13502 228 VRICHAQYLLQHS---PLMISEISMQCGFEDS 256 (282)
T ss_pred HHHHHHHHHHHcC---CCCHHHHHHHcCCCCH
Confidence 4466666555422 5699999999987643
No 363
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=24.29 E-value=1.4e+02 Score=22.66 Aligned_cols=24 Identities=21% Similarity=0.354 Sum_probs=16.5
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 431 SPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
..|..++|+.+|++...+..+..-
T Consensus 12 ~lt~~~~a~~~~i~~~~i~~~e~g 35 (64)
T PF12844_consen 12 GLTQKDLAEKLGISRSTISKIENG 35 (64)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHTT
T ss_pred CCCHHHHHHHHCcCHHHHHHHHCC
Confidence 468888888888888888777653
No 364
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=24.27 E-value=1.5e+02 Score=30.15 Aligned_cols=40 Identities=10% Similarity=-0.005 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 416 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 416 kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
.+.++...+...+...++.++||+.+|++...+..+.+..
T Consensus 219 ~~~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~ 258 (322)
T PRK09393 219 RLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAA 258 (322)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4445555566666668899999999999999998887653
No 365
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=24.20 E-value=80 Score=27.76 Aligned_cols=28 Identities=29% Similarity=0.378 Sum_probs=25.6
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 431 SPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
+.+.+|-|..||||-.++-+.+..|+..
T Consensus 49 ~l~QeeAA~rMgISr~Tfwr~l~sAR~K 76 (99)
T COG1342 49 GLTQEEAALRMGISRQTFWRLLTSARKK 76 (99)
T ss_pred hccHHHHHHHhcccHHHHHHHHHHHHHH
Confidence 6799999999999999999999988764
No 366
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=24.20 E-value=1.4e+02 Score=29.88 Aligned_cols=28 Identities=21% Similarity=0.149 Sum_probs=23.5
Q ss_pred HhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 426 QEGNHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 426 ~e~gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
.+.+ ..+.+|||+.+|+|..+|+.-|..
T Consensus 15 ~~~~-~~~~~ela~~l~vS~~TirRdL~~ 42 (251)
T PRK13509 15 AQLG-FVTVEKVIERLGISPATARRDINK 42 (251)
T ss_pred HHcC-CcCHHHHHHHHCcCHHHHHHHHHH
Confidence 3444 689999999999999999888774
No 367
>KOG0037 consensus Ca2+-binding protein, EF-Hand protein superfamily [Signal transduction mechanisms]
Probab=24.18 E-value=6.8e+02 Score=25.16 Aligned_cols=97 Identities=13% Similarity=0.220 Sum_probs=58.3
Q ss_pred HHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhh-cHHHHHHHHHHHH
Q 011577 260 FLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS-GNSSREKLINANL 338 (482)
Q Consensus 260 YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~-Gd~Are~LI~snl 338 (482)
+|-+......+..+|=.+|++.|+.+..+-+- ..+.= .-.++..||..++.. |- .-.-
T Consensus 101 ~mfd~~~~G~i~f~EF~~Lw~~i~~Wr~vF~~-------~D~D~-------SG~I~~sEL~~Al~~~Gy-------~Lsp 159 (221)
T KOG0037|consen 101 SMFDRDNSGTIGFKEFKALWKYINQWRNVFRT-------YDRDR-------SGTIDSSELRQALTQLGY-------RLSP 159 (221)
T ss_pred HHhcCCCCCccCHHHHHHHHHHHHHHHHHHHh-------cccCC-------CCcccHHHHHHHHHHcCc-------CCCH
Confidence 55677778889999999999999986543221 11110 012455666544421 11 1111
Q ss_pred HHHHHHHHHcc---CCCCCHhHHHHHH--HHHHHHhHHhhCCCC
Q 011577 339 RLVVHVAKQYQ---GRGISLHDLLQEG--SMGLMKSVEKFKPQA 377 (482)
Q Consensus 339 rLV~sIAkrY~---~~g~d~EDLIQEG--~IGLirAiekFDp~k 377 (482)
.++-.|++||. +..+.++|.||.. ..+|.++..++|...
T Consensus 160 q~~~~lv~kyd~~~~g~i~FD~FI~ccv~L~~lt~~Fr~~D~~q 203 (221)
T KOG0037|consen 160 QFYNLLVRKYDRFGGGRIDFDDFIQCCVVLQRLTEAFRRRDTAQ 203 (221)
T ss_pred HHHHHHHHHhccccCCceeHHHHHHHHHHHHHHHHHHHHhcccc
Confidence 22233445554 4458899999864 457788888888754
No 368
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=24.02 E-value=1.3e+02 Score=30.19 Aligned_cols=29 Identities=21% Similarity=0.290 Sum_probs=23.6
Q ss_pred HHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 425 IQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 425 ~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
..+.+ ..+..|||+.+|+|+.+|+.-+..
T Consensus 14 L~~~~-~v~v~eLa~~l~VS~~TIRRDL~~ 42 (256)
T PRK10434 14 LQKQG-KTSVEELAQYFDTTGTTIRKDLVI 42 (256)
T ss_pred HHHcC-CEEHHHHHHHHCCCHHHHHHHHHH
Confidence 33444 689999999999999999887763
No 369
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=23.83 E-value=1.2e+02 Score=29.53 Aligned_cols=27 Identities=30% Similarity=0.394 Sum_probs=24.0
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 428 GNHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 428 ~gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
+.+-|+-.|||+.+|+|-.||++++..
T Consensus 32 G~~LPsE~eLa~~~~VSR~TVR~Al~~ 58 (241)
T PRK10079 32 GDYLPAEQQLAARYEVNRHTLRRAIDQ 58 (241)
T ss_pred CCcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 446889999999999999999999873
No 370
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=23.77 E-value=3.1e+02 Score=26.43 Aligned_cols=26 Identities=23% Similarity=0.433 Sum_probs=22.4
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHcC
Q 011577 431 SPDKEDLARRVGITVEKLERLIFITR 456 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar 456 (482)
.++.++||..+|++.++|-.+++.-+
T Consensus 179 ~lt~~~IA~~lGisretlsR~L~~L~ 204 (230)
T PRK09391 179 PMSRRDIADYLGLTIETVSRALSQLQ 204 (230)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 35899999999999999999887543
No 371
>PHA00675 hypothetical protein
Probab=23.76 E-value=1.7e+02 Score=24.72 Aligned_cols=23 Identities=9% Similarity=0.030 Sum_probs=20.7
Q ss_pred CcHHHHHHHhCCCHHHHHHHHHH
Q 011577 432 PDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 432 pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
.++.+||..+|++..+|..+.+.
T Consensus 40 ~s~~~IA~~fGVsrstV~~I~~g 62 (78)
T PHA00675 40 MSYAVLAEKFEQSKGAIAKICRY 62 (78)
T ss_pred ccHHHHHHHhCCCHHHHHHHHcc
Confidence 49999999999999999998763
No 372
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=23.72 E-value=1.8e+02 Score=28.04 Aligned_cols=27 Identities=19% Similarity=0.439 Sum_probs=23.8
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 428 GNHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 428 ~gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
+.+-||-.|||+.+|+|-.+|++++..
T Consensus 21 G~~LPsE~eLa~~~gVSR~TVR~Al~~ 47 (233)
T TIGR02404 21 GDYLPSEHELMDQYGASRETVRKALNL 47 (233)
T ss_pred CCCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 445789999999999999999999873
No 373
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=23.57 E-value=1.6e+02 Score=28.24 Aligned_cols=27 Identities=15% Similarity=0.151 Sum_probs=23.6
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 428 GNHSPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 428 ~gr~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
.+ .+|..|||+.+||+..+|...+..-
T Consensus 13 ~~-~~t~~eLA~~lgis~~tV~~~L~~L 39 (203)
T TIGR02702 13 QG-QATAAALAEALAISPQAVRRHLKDL 39 (203)
T ss_pred cC-CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 44 5899999999999999999998754
No 374
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=23.51 E-value=4.8e+02 Score=22.43 Aligned_cols=67 Identities=16% Similarity=0.155 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHHHHHhcCCcccchhHHH-HHHHHHHH-HHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 385 AYWWVRQTIRKAIFQHSRTIRLPENIYT-LLSKVLEA-KRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 385 A~~wIRnaI~~~Lrkq~r~irlP~~v~e-~l~kI~ka-~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
+.-.|++.+.+++.+... .. |..++. .+..+.+. +.......+ -...+.|+.|||+..++...++..
T Consensus 24 l~~~~~~~l~~~~~~l~~-~~-~~~~~~~~l~~~Er~~i~~aL~~~~--gn~s~AAr~LGIsRsTL~rKLkr~ 92 (95)
T PRK00430 24 LRDSVKQALKNYFAQLNG-QD-VNDLYELVLAEVEAPLLDMVMQYTR--GNQTRAALMLGINRGTLRKKLKKY 92 (95)
T ss_pred HHHHHHHHHHHHHHHhcC-CC-chhHHHHHHHHHHHHHHHHHHHHcC--CCHHHHHHHhCCCHHHHHHHHHHh
Confidence 344667777777765542 22 223332 23333322 222222222 368899999999999998888753
No 375
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=23.47 E-value=2.2e+02 Score=20.72 Aligned_cols=24 Identities=13% Similarity=0.225 Sum_probs=20.5
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 431 SPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
..+..|||+.+|++..+|..-+..
T Consensus 15 ~~~~~el~~~l~~s~~~vs~hL~~ 38 (47)
T PF01022_consen 15 PLTVSELAEELGLSQSTVSHHLKK 38 (47)
T ss_dssp SEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCchhhHHHhccccchHHHHHHHH
Confidence 679999999999999999888764
No 376
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=23.43 E-value=1.9e+02 Score=27.89 Aligned_cols=27 Identities=19% Similarity=0.361 Sum_probs=23.6
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 428 GNHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 428 ~gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
+.+-||..|||+.+|++-.+|++++..
T Consensus 22 g~~LPsE~eLa~~~~VSR~TVR~Al~~ 48 (230)
T TIGR02018 22 GHRIPSEHELVAQYGCSRMTVNRALRE 48 (230)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 345789999999999999999999873
No 377
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=23.25 E-value=2.2e+02 Score=23.10 Aligned_cols=24 Identities=17% Similarity=0.231 Sum_probs=18.6
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 431 SPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
..|..|||+.+|++..+|-...+.
T Consensus 34 ~~si~elA~~~~vS~sti~Rf~kk 57 (77)
T PF01418_consen 34 FMSISELAEKAGVSPSTIVRFCKK 57 (77)
T ss_dssp T--HHHHHHHCTS-HHHHHHHHHH
T ss_pred HccHHHHHHHcCCCHHHHHHHHHH
Confidence 679999999999999999887654
No 378
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=23.09 E-value=93 Score=28.59 Aligned_cols=27 Identities=26% Similarity=0.502 Sum_probs=24.0
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577 431 SPDKEDLARRVGITVEKLERLIFITRM 457 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (482)
..+.++||+.|||....|+.+|..-..
T Consensus 15 ~~~dedLa~~l~i~~n~vRkiL~~L~e 41 (147)
T smart00531 15 CVTEEDLAELLGIKQKQLRKILYLLYD 41 (147)
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHHHh
Confidence 689999999999999999999986543
No 379
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=23.04 E-value=2.3e+02 Score=29.75 Aligned_cols=24 Identities=4% Similarity=0.097 Sum_probs=21.0
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 431 SPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
..+.+||.+.+|+++.+++.....
T Consensus 260 kkt~keI~~vtgVaE~TIr~sYK~ 283 (308)
T KOG1597|consen 260 KKTQKEIGEVTGVAEVTIRNSYKD 283 (308)
T ss_pred cccHHHHHHHhhhhHHHHHHHHHH
Confidence 459999999999999999987663
No 380
>PRK13558 bacterio-opsin activator; Provisional
Probab=23.02 E-value=50 Score=36.87 Aligned_cols=28 Identities=18% Similarity=0.302 Sum_probs=25.1
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577 430 HSPDKEDLARRVGITVEKLERLIFITRM 457 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (482)
|+.|.+|||+.|||+..++...|+++..
T Consensus 629 r~~~~~e~a~~l~is~~t~~~~lr~a~~ 656 (665)
T PRK13558 629 RRVEGEELAESMGISRSTFHQHLRAAER 656 (665)
T ss_pred ccCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4559999999999999999999998854
No 381
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=22.99 E-value=1.8e+02 Score=22.79 Aligned_cols=25 Identities=16% Similarity=0.232 Sum_probs=22.1
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 431 SPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
..+..|||+.+|++..+|...+...
T Consensus 13 ~~~~~eLa~~l~vS~~tv~~~l~~L 37 (69)
T TIGR00122 13 PFSGEKLGEALGMSRTAVNKHIQTL 37 (69)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 4579999999999999999998765
No 382
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=22.89 E-value=2.1e+02 Score=27.99 Aligned_cols=27 Identities=15% Similarity=0.326 Sum_probs=23.6
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 428 GNHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 428 ~gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
+.+-|+..|||+.+|++-.+|+.++..
T Consensus 26 G~~LPsE~eL~~~~~VSR~TvR~Al~~ 52 (240)
T PRK09764 26 GDALPTESALQTEFGVSRVTVRQALRQ 52 (240)
T ss_pred CCcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 345789999999999999999999873
No 383
>cd00131 PAX Paired Box domain
Probab=22.80 E-value=1.3e+02 Score=27.07 Aligned_cols=32 Identities=9% Similarity=0.101 Sum_probs=26.9
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHcCCCccCc
Q 011577 431 SPDKEDLARRVGITVEKLERLIFITRMPLSMQ 462 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD 462 (482)
+.+..+||+.+|++..+|..++++.+..-++.
T Consensus 33 G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~ 64 (128)
T cd00131 33 GIRPCDISRQLRVSHGCVSKILNRYYETGSIR 64 (128)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcC
Confidence 57999999999999999999999876554443
No 384
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=22.48 E-value=3.6e+02 Score=27.39 Aligned_cols=57 Identities=14% Similarity=0.025 Sum_probs=36.4
Q ss_pred HHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHH
Q 011577 340 LVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI 397 (482)
Q Consensus 340 LV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~L 397 (482)
.|..++........+.+||.++..+.--.=-+.|... |..|..|+..|--+...+.+
T Consensus 138 kv~~~I~~~~~~~~tl~~LA~~~gmS~s~l~R~FK~~-G~T~~eyl~~~Rl~~A~~LL 194 (253)
T PRK09940 138 KVRNIVNMKLAHPWKLKDICDCLYISESLLKKKLKQE-QTTFSQILLDARMQHAKNLI 194 (253)
T ss_pred HHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHHc-CCCHHHHHHHHHHHHHHHHH
Confidence 3444444444556889999999888776666667655 77777777665444433433
No 385
>PF06970 RepA_N: Replication initiator protein A (RepA) N-terminus; InterPro: IPR010724 This entry represents the N terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids []. Most proteins in this entry are bacterial, but archaeal and eukaryotic members are also included.
Probab=22.43 E-value=94 Score=25.79 Aligned_cols=21 Identities=10% Similarity=0.044 Sum_probs=19.5
Q ss_pred cHHHHHHHhCCCHHHHHHHHH
Q 011577 433 DKEDLARRVGITVEKLERLIF 453 (482)
Q Consensus 433 S~eEIAe~LGIS~etVk~~L~ 453 (482)
+.+||++.||++..+|..++.
T Consensus 54 s~eel~~~L~~s~~tv~~~~k 74 (76)
T PF06970_consen 54 SIEELMELLNCSKSTVIKAKK 74 (76)
T ss_pred eHHHHHHHHCCCHHHHHHHHH
Confidence 999999999999999998865
No 386
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=22.41 E-value=1.8e+02 Score=28.54 Aligned_cols=27 Identities=19% Similarity=0.273 Sum_probs=23.6
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 428 GNHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 428 ~gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
.....+..|||+.+|++..++..++..
T Consensus 21 ~~~~~~l~eia~~lglpksT~~RlL~t 47 (248)
T TIGR02431 21 ERPRLTLTDVAEATGLTRAAARRFLLT 47 (248)
T ss_pred CCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 344679999999999999999999874
No 387
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=22.39 E-value=3.6e+02 Score=25.57 Aligned_cols=24 Identities=25% Similarity=0.560 Sum_probs=21.8
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 431 SPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
+.|+.+||+.|||+..+|..++..
T Consensus 172 g~s~~~iak~lgis~~Tv~r~~k~ 195 (200)
T PRK13413 172 GTSKSEIARKLGVSRTTLARFLKT 195 (200)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHh
Confidence 579999999999999999998864
No 388
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=22.36 E-value=1.4e+02 Score=29.69 Aligned_cols=31 Identities=16% Similarity=0.260 Sum_probs=25.1
Q ss_pred HHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 423 LYIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 423 eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
.+..+.+ ..|..|||++|||+.-.|+.-|..
T Consensus 18 ~lL~~~g-~~sa~elA~~Lgis~~avR~HL~~ 48 (218)
T COG2345 18 ELLKKSG-PVSADELAEELGISPMAVRRHLDD 48 (218)
T ss_pred HHHhccC-CccHHHHHHHhCCCHHHHHHHHHH
Confidence 3344445 679999999999999999998874
No 389
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=22.20 E-value=1.4e+02 Score=29.93 Aligned_cols=28 Identities=11% Similarity=0.272 Sum_probs=22.9
Q ss_pred HHhcCCCCcHHHHHHHhCCCHHHHHHHHH
Q 011577 425 IQEGNHSPDKEDLARRVGITVEKLERLIF 453 (482)
Q Consensus 425 ~~e~gr~pS~eEIAe~LGIS~etVk~~L~ 453 (482)
..+.+ ..+..|||+.+|+|+.+|+.-|.
T Consensus 14 l~~~~-~~~~~ela~~l~vS~~TiRRdL~ 41 (252)
T PRK10906 14 VKQQG-YVSTEELVEHFSVSPQTIRRDLN 41 (252)
T ss_pred HHHcC-CEeHHHHHHHhCCCHHHHHHHHH
Confidence 34444 68999999999999999988554
No 390
>PRK13503 transcriptional activator RhaS; Provisional
Probab=22.17 E-value=2e+02 Score=28.10 Aligned_cols=38 Identities=13% Similarity=0.087 Sum_probs=27.0
Q ss_pred HHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 417 VLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 417 I~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
+.+...-+........|.++||+.+|++...+..+.+.
T Consensus 173 i~~~~~~I~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk~ 210 (278)
T PRK13503 173 LNQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQ 210 (278)
T ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 33344444455556789999999999999988877654
No 391
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=22.14 E-value=1.1e+02 Score=27.98 Aligned_cols=27 Identities=22% Similarity=0.468 Sum_probs=23.7
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 428 GNHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 428 ~gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
+.+-||..|+|..+|+.+.||..+.+.
T Consensus 32 GdkLPSvRelA~~~~VNpnTv~raY~e 58 (125)
T COG1725 32 GDKLPSVRELAKDLGVNPNTVQRAYQE 58 (125)
T ss_pred CCCCCcHHHHHHHhCCCHHHHHHHHHH
Confidence 456899999999999999999998763
No 392
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=22.13 E-value=1.9e+02 Score=28.35 Aligned_cols=27 Identities=19% Similarity=0.430 Sum_probs=23.9
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 428 GNHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 428 ~gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
+.+-|+-.|+|+.+|+|--||++++..
T Consensus 28 G~~LPsE~eLa~~f~VSR~TvRkAL~~ 54 (236)
T COG2188 28 GDKLPSERELAEQFGVSRMTVRKALDE 54 (236)
T ss_pred CCCCCCHHHHHHHHCCcHHHHHHHHHH
Confidence 446789999999999999999999873
No 393
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=22.12 E-value=2e+02 Score=28.89 Aligned_cols=40 Identities=10% Similarity=0.070 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 415 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 415 ~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
..+.++..-+...+...++.++||+.+|+|...+..+.+.
T Consensus 5 ~~i~~~~~~i~~~~~~~~~l~~lA~~~~~S~~~l~r~F~~ 44 (289)
T PRK15121 5 GIIRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKD 44 (289)
T ss_pred HHHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 4455555556666676789999999999999888877653
No 394
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=22.09 E-value=67 Score=23.42 Aligned_cols=18 Identities=33% Similarity=0.685 Sum_probs=16.6
Q ss_pred HHHHHhCCCHHHHHHHHH
Q 011577 436 DLARRVGITVEKLERLIF 453 (482)
Q Consensus 436 EIAe~LGIS~etVk~~L~ 453 (482)
+||+.+|++..+|..+++
T Consensus 2 ~lA~~~gvs~~tvs~~l~ 19 (52)
T cd01392 2 DIARAAGVSVATVSRVLN 19 (52)
T ss_pred cHHHHHCcCHHHHHHHHc
Confidence 799999999999999886
No 395
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=22.06 E-value=1.3e+02 Score=24.63 Aligned_cols=36 Identities=17% Similarity=0.165 Sum_probs=29.0
Q ss_pred HHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577 423 LYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (482)
Q Consensus 423 eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (482)
.+...++...+..+.|+.||++++.|.+.+...+.-
T Consensus 5 ~fIrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~w 40 (65)
T PF05344_consen 5 AFIRLLSQQISVAQAADRLGTDPGTVRRWVRMFRQW 40 (65)
T ss_pred HHHHHhcccccHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 344556667899999999999999999998766653
No 396
>PRK01381 Trp operon repressor; Provisional
Probab=21.93 E-value=1.1e+02 Score=26.95 Aligned_cols=21 Identities=10% Similarity=0.381 Sum_probs=18.0
Q ss_pred CCcHHHHHHHhCCCHHHHHHH
Q 011577 431 SPDKEDLARRVGITVEKLERL 451 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~ 451 (482)
+.|+.|||+.||++..+|-..
T Consensus 55 ~~sQREIa~~lGvSiaTITRg 75 (99)
T PRK01381 55 ELSQREIKQELGVGIATITRG 75 (99)
T ss_pred CcCHHHHHHHhCCceeeehhh
Confidence 579999999999998887554
No 397
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=21.88 E-value=1.1e+02 Score=26.17 Aligned_cols=25 Identities=20% Similarity=0.569 Sum_probs=19.1
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 431 SPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
..+.++||+.+|++...|+.++..-
T Consensus 27 ~l~de~la~~~~l~~~~vRkiL~~L 51 (105)
T PF02002_consen 27 ELTDEDLAKKLGLKPKEVRKILYKL 51 (105)
T ss_dssp -B-HHHHHHTT-S-HHHHHHHHHHH
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 5799999999999999999998743
No 398
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=21.84 E-value=1.3e+02 Score=28.49 Aligned_cols=38 Identities=24% Similarity=0.229 Sum_probs=27.1
Q ss_pred HHHHHHHHHHH-HHHhcCCCCcHHHHHHHhCCCHHHHHH
Q 011577 413 LLSKVLEAKRL-YIQEGNHSPDKEDLARRVGITVEKLER 450 (482)
Q Consensus 413 ~l~kI~ka~~e-L~~e~gr~pS~eEIAe~LGIS~etVk~ 450 (482)
...+|-++... +...+....|..+||+..||+.+.+..
T Consensus 19 ~r~~IL~AA~~lf~e~Gy~~~s~~dIA~~aGvs~gtiY~ 57 (212)
T PRK15008 19 KKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLY 57 (212)
T ss_pred HHHHHHHHHHHHHHHhCcccCCHHHHHHHhCcCHHHHHH
Confidence 34445444444 445555678999999999999998854
No 399
>PRK09480 slmA division inhibitor protein; Provisional
Probab=21.83 E-value=6e+02 Score=23.00 Aligned_cols=75 Identities=17% Similarity=0.005 Sum_probs=49.4
Q ss_pred HhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhH
Q 011577 296 QSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSV 370 (482)
Q Consensus 296 ~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAi 370 (482)
...-|...|..+.|+.+|++...|-.-..+-++-+..++..+..-+............+..+.++..+-.++.-+
T Consensus 24 ~~~~G~~~ti~~Ia~~agvs~gt~Y~~F~~K~~L~~~v~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~ 98 (194)
T PRK09480 24 ESPPGERITTAKLAARVGVSEAALYRHFPSKARMFEGLIEFIEESLFSRINQILKDEKDTLARARLILLLLLGFA 98 (194)
T ss_pred HhcCCCccCHHHHHHHhCCCHhHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHH
Confidence 344467889999999999999888877777666666677666555544444433333456666666555555433
No 400
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=21.81 E-value=1.8e+02 Score=25.90 Aligned_cols=23 Identities=13% Similarity=0.150 Sum_probs=14.3
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHH
Q 011577 431 SPDKEDLARRVGITVEKLERLIF 453 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~ 453 (482)
+.|..++|+.+||+..+|..+.+
T Consensus 18 gltq~~lA~~~gvs~~~is~~E~ 40 (135)
T PRK09706 18 KLSQRSLAKAVKVSHVSISQWER 40 (135)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHc
Confidence 35666666666666666666543
No 401
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=21.59 E-value=2.2e+02 Score=27.76 Aligned_cols=26 Identities=15% Similarity=0.387 Sum_probs=23.3
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHH
Q 011577 428 GNHSPDKEDLARRVGITVEKLERLIF 453 (482)
Q Consensus 428 ~gr~pS~eEIAe~LGIS~etVk~~L~ 453 (482)
+.+-|+-.|||+.+|++-.||+.++.
T Consensus 30 g~kLPsE~eLa~~~~VSR~TvR~Al~ 55 (241)
T PRK11402 30 GQQIPTENELCTQYNVSRITIRKAIS 55 (241)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHH
Confidence 34578999999999999999999987
No 402
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=21.56 E-value=1.5e+02 Score=29.81 Aligned_cols=29 Identities=14% Similarity=0.239 Sum_probs=24.4
Q ss_pred hcCCCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 427 EGNHSPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 427 e~gr~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
..+...+..|||+.+|++..+|..+++.-
T Consensus 36 ~~~~~~tl~eIa~~lglpkStv~RlL~tL 64 (271)
T PRK10163 36 KSGGSSSVSDISLNLDLPLSTTFRLLKVL 64 (271)
T ss_pred hCCCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 34446799999999999999999998743
No 403
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=21.51 E-value=8.9e+02 Score=24.85 Aligned_cols=122 Identities=11% Similarity=0.065 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHH--HHhHHhhCCCCCCchhhHHH-HHHHHHHHHHHHHhcCCcccc
Q 011577 331 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGL--MKSVEKFKPQAGCRFASYAY-WWVRQTIRKAIFQHSRTIRLP 407 (482)
Q Consensus 331 e~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGL--irAiekFDp~kG~rFSTYA~-~wIRnaI~~~Lrkq~r~irlP 407 (482)
..+|..|++.+-..+-.+...-....||+.-..-|+ ++.+-..-......+..-+. ..+--.+...+.+........
T Consensus 56 r~~i~~~~~~l~~~~~~~~~~~~~~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ll~~lL~~l~~~~~~~~~~ 135 (274)
T PRK09978 56 RDTLSLFLPMLKEEALNLHAHKKVSSLLVHHCSRDIPVFQEVAQLSQNKNLRYAEMLRKRALIFALLSVFLEDEHFIPLL 135 (274)
T ss_pred HHHHHHHHHHhHHHHhcccccccCccHHHHHhccCcchHHHHHHHHHHhccchHHHHHHHHHHHHHHHHHHhcccccccc
Q ss_pred hhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHH
Q 011577 408 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF 453 (482)
Q Consensus 408 ~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~ 453 (482)
...... ..+.++...+...+....+.++||+.+|++...+....+
T Consensus 136 ~~~~~~-~~~~~v~~yI~~~~~~~lsl~~lA~~~g~S~~~L~R~Fk 180 (274)
T PRK09978 136 LNVLQP-NMRTRVCTVINNNIAHEWTLARIASELLMSPSLLKKKLR 180 (274)
T ss_pred ccccCH-HHHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHH
No 404
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=21.43 E-value=1.1e+02 Score=23.92 Aligned_cols=22 Identities=18% Similarity=0.028 Sum_probs=19.2
Q ss_pred cHHHHHHHhCCCHHHHHHHHHH
Q 011577 433 DKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 433 S~eEIAe~LGIS~etVk~~L~~ 454 (482)
+..|+|+.+||+..+++.....
T Consensus 2 ~i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 2 TIGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh
Confidence 6789999999999999988654
No 405
>TIGR03384 betaine_BetI transcriptional repressor BetI. BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (pfam00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet regulon genes in response to oxygen, as BetA is an oxygen-dependent enzyme.
Probab=21.39 E-value=1.3e+02 Score=27.23 Aligned_cols=33 Identities=15% Similarity=0.228 Sum_probs=24.7
Q ss_pred HHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHH
Q 011577 419 EAKRLYIQEGNHSPDKEDLARRVGITVEKLERL 451 (482)
Q Consensus 419 ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~ 451 (482)
.+...+...+....|..+||+..|++.+.+...
T Consensus 16 aA~~lf~~~G~~~~s~~~IA~~agvsk~~ly~~ 48 (189)
T TIGR03384 16 ATIESIGERGSLDVTIAQIARRAGVSSGIISHY 48 (189)
T ss_pred HHHHHHHhcCcccCCHHHHHHHhCCCHHHHHHH
Confidence 344445555667889999999999999988543
No 406
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=21.14 E-value=2.3e+02 Score=27.12 Aligned_cols=25 Identities=12% Similarity=0.126 Sum_probs=21.8
Q ss_pred CcHHHHHHHhCCCHHHHHHHHHHcC
Q 011577 432 PDKEDLARRVGITVEKLERLIFITR 456 (482)
Q Consensus 432 pS~eEIAe~LGIS~etVk~~L~~ar 456 (482)
.+.+|||+.+|++.++|-..+..-.
T Consensus 170 ~t~~~lA~~lG~sretvsR~L~~L~ 194 (226)
T PRK10402 170 EKHTQAAEYLGVSYRHLLYVLAQFI 194 (226)
T ss_pred chHHHHHHHHCCcHHHHHHHHHHHH
Confidence 4889999999999999999887543
No 407
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=21.06 E-value=1.5e+02 Score=27.84 Aligned_cols=21 Identities=14% Similarity=0.173 Sum_probs=10.6
Q ss_pred CcHHHHHHHhCCCHHHHHHHH
Q 011577 432 PDKEDLARRVGITVEKLERLI 452 (482)
Q Consensus 432 pS~eEIAe~LGIS~etVk~~L 452 (482)
.|.+|+|+.+|++..+|.++.
T Consensus 21 lt~~elA~~~gis~~~is~~E 41 (185)
T PRK09943 21 LSQRRAAELSGLTHSAISTIE 41 (185)
T ss_pred CCHHHHHHHHCCCHHHHHHHH
Confidence 455555555555555554443
No 408
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=21.03 E-value=1.8e+02 Score=21.28 Aligned_cols=23 Identities=17% Similarity=0.416 Sum_probs=19.5
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHc
Q 011577 433 DKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 433 S~eEIAe~LGIS~etVk~~L~~a 455 (482)
...+||..+|++...|.......
T Consensus 29 ~~~~la~~~~l~~~qV~~WF~nr 51 (56)
T smart00389 29 EREELAAKLGLSERQVKVWFQNR 51 (56)
T ss_pred HHHHHHHHHCcCHHHHHHhHHHH
Confidence 57899999999999999877643
No 409
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=20.99 E-value=1.9e+02 Score=22.67 Aligned_cols=26 Identities=23% Similarity=0.213 Sum_probs=22.1
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHcC
Q 011577 431 SPDKEDLARRVGITVEKLERLIFITR 456 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar 456 (482)
+.++.+||..+||+..++...+...+
T Consensus 23 g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 23 GESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp HCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCceEeeecccccccccccHHHHHHh
Confidence 45999999999999999999988664
No 410
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=20.78 E-value=2.8e+02 Score=25.17 Aligned_cols=27 Identities=15% Similarity=0.186 Sum_probs=23.5
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577 431 SPDKEDLARRVGITVEKLERLIFITRM 457 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (482)
+.|..+||+.||+|...|...+.--+.
T Consensus 22 G~Sq~~iA~LLGltqaAVS~Yls~krg 48 (119)
T COG2522 22 GLSQYRIAKLLGLTQAAVSQYLSGKRG 48 (119)
T ss_pred CCcHHHHHHHhCCCHHHHHHHHccCCc
Confidence 579999999999999999999875444
No 411
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=20.69 E-value=2.3e+02 Score=30.87 Aligned_cols=24 Identities=17% Similarity=0.299 Sum_probs=21.3
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHH
Q 011577 430 HSPDKEDLARRVGITVEKLERLIF 453 (482)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~ 453 (482)
+..+.++||+.+|+.+.||-.+..
T Consensus 317 kPLtlkdiA~~lglheSTVSRav~ 340 (429)
T TIGR02395 317 KPLTLREVAEELGLHESTISRAIN 340 (429)
T ss_pred cCCcHHHHHHHhCCCccchhhhhc
Confidence 466999999999999999988865
No 412
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=20.66 E-value=1.2e+02 Score=22.56 Aligned_cols=21 Identities=24% Similarity=0.571 Sum_probs=18.3
Q ss_pred cHHHHHHHhCCCHHHHHHHHH
Q 011577 433 DKEDLARRVGITVEKLERLIF 453 (482)
Q Consensus 433 S~eEIAe~LGIS~etVk~~L~ 453 (482)
..++||..|||+...|.....
T Consensus 29 ~~~~la~~l~l~~~~V~~WF~ 49 (57)
T PF00046_consen 29 EREELAKELGLTERQVKNWFQ 49 (57)
T ss_dssp HHHHHHHHHTSSHHHHHHHHH
T ss_pred ccccccccccccccccccCHH
Confidence 568999999999999988765
No 413
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and 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 []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=20.56 E-value=3.3e+02 Score=21.39 Aligned_cols=27 Identities=11% Similarity=0.347 Sum_probs=20.4
Q ss_pred HhcCCCCcHHHHHHHhCCCHHHHHHHHH
Q 011577 426 QEGNHSPDKEDLARRVGITVEKLERLIF 453 (482)
Q Consensus 426 ~e~gr~pS~eEIAe~LGIS~etVk~~L~ 453 (482)
...| ..|..+|...+|++...|+..+-
T Consensus 23 l~~G-~ltl~~i~~~t~l~~~~Vk~~L~ 49 (62)
T PF08221_consen 23 LSRG-RLTLREIVRRTGLSPKQVKKALV 49 (62)
T ss_dssp HHC--SEEHHHHHHHHT--HHHHHHHHH
T ss_pred HHcC-CcCHHHHHHHhCCCHHHHHHHHH
Confidence 3455 56899999999999999999875
No 414
>PRK13503 transcriptional activator RhaS; Provisional
Probab=20.55 E-value=3.8e+02 Score=26.15 Aligned_cols=37 Identities=19% Similarity=0.214 Sum_probs=19.7
Q ss_pred CCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHH
Q 011577 350 GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAY 386 (482)
Q Consensus 350 ~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~ 386 (482)
....+.+|+....++.--.-.+.|...-|..|.-|+.
T Consensus 185 ~~~~tl~~lA~~~~lS~~~l~r~Fk~~~G~S~~~yi~ 221 (278)
T PRK13503 185 AEEVNWEALADQFSLSLRTLHRQLKQQTGLTPQRYLN 221 (278)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHhCcCHHHHHH
Confidence 4456666666666555544444554444544444443
No 415
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=20.51 E-value=1.3e+02 Score=20.44 Aligned_cols=23 Identities=22% Similarity=0.456 Sum_probs=20.6
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHH
Q 011577 431 SPDKEDLARRVGITVEKLERLIF 453 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~ 453 (482)
..+..++|..+|++...|..++.
T Consensus 12 ~~s~~~~a~~~~~~~~~v~~~~~ 34 (58)
T cd00093 12 GLTQEELAEKLGVSRSTISRIEN 34 (58)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHc
Confidence 57999999999999999988766
No 416
>PHA00542 putative Cro-like protein
Probab=20.34 E-value=1.1e+02 Score=25.27 Aligned_cols=25 Identities=12% Similarity=0.110 Sum_probs=22.4
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 431 SPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
+.|..|+|+.+||+..+|..+..-.
T Consensus 31 glTq~elA~~lgIs~~tIsr~e~g~ 55 (82)
T PHA00542 31 GWSQEQIADATDVSQPTICRIYSGR 55 (82)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHcCC
Confidence 5799999999999999999998643
No 417
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=20.34 E-value=1.4e+02 Score=28.64 Aligned_cols=27 Identities=15% Similarity=0.095 Sum_probs=22.4
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 429 NHSPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 429 gr~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
|...+..|||+.+|+|-..|++++.+-
T Consensus 28 G~~L~e~eLae~lgVSRtpVREAL~~L 54 (224)
T PRK11534 28 DEKLRMSLLTSRYALGVGPLREALSQL 54 (224)
T ss_pred CCcCCHHHHHHHHCCChHHHHHHHHHH
Confidence 334567899999999999999998853
No 418
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=20.34 E-value=9.7e+02 Score=24.79 Aligned_cols=24 Identities=13% Similarity=0.174 Sum_probs=21.2
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 431 SPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
..|..|||+.+|+++.++++..+.
T Consensus 251 ~~tq~eva~v~~vtevTIrnryke 274 (285)
T COG1405 251 RRTQKEVAKVAGVTEVTIRNRYKE 274 (285)
T ss_pred chHHHHHHHHhCCeeeHHHHHHHH
Confidence 449999999999999999998753
No 419
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=20.31 E-value=1.6e+02 Score=26.58 Aligned_cols=27 Identities=7% Similarity=0.193 Sum_probs=23.1
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 429 NHSPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 429 gr~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
+..++..|||+.+|+|..-|++++..-
T Consensus 23 g~~~s~~~ia~~~~is~~~vrk~l~~L 49 (141)
T PRK11014 23 GRMTSISEVTEVYGVSRNHMVKIINQL 49 (141)
T ss_pred CCccCHHHHHHHHCcCHHHHHHHHHHH
Confidence 335789999999999999999998754
No 420
>PF15545 Toxin_67: Putative toxin 67
Probab=20.19 E-value=99 Score=25.47 Aligned_cols=30 Identities=23% Similarity=0.526 Sum_probs=25.0
Q ss_pred chhhHHHHHHHHHHHHHHHHhcCCcccchh
Q 011577 380 RFASYAYWWVRQTIRKAIFQHSRTIRLPEN 409 (482)
Q Consensus 380 rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~ 409 (482)
+-+.|+.-||+|.|...-+.....+|+|..
T Consensus 6 kq~~~vRGwiknEi~~i~~~~r~~iRlPpG 35 (70)
T PF15545_consen 6 KQPSWVRGWIKNEINRIKTGRRKSIRLPPG 35 (70)
T ss_pred cchHHHHHHHHHHHHHHHhCccceecCCCc
Confidence 467899999999998877777778999954
No 421
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=20.18 E-value=1.8e+02 Score=27.65 Aligned_cols=25 Identities=28% Similarity=0.445 Sum_probs=22.3
Q ss_pred CCcHHHHHHHh--CCCHHHHHHHHHHc
Q 011577 431 SPDKEDLARRV--GITVEKLERLIFIT 455 (482)
Q Consensus 431 ~pS~eEIAe~L--GIS~etVk~~L~~a 455 (482)
.+++.+||+.+ +||.++|++.|..-
T Consensus 39 ~~d~~~iak~l~p~is~~ev~~sL~~L 65 (171)
T PF14394_consen 39 APDPEWIAKRLRPKISAEEVRDSLEFL 65 (171)
T ss_pred CCCHHHHHHHhcCCCCHHHHHHHHHHH
Confidence 56999999999 99999999998754
No 422
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=20.14 E-value=1.7e+02 Score=23.84 Aligned_cols=32 Identities=13% Similarity=0.183 Sum_probs=25.3
Q ss_pred HHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577 423 LYIQEGNHSPDKEDLARRVGITVEKLERLIFIT 455 (482)
Q Consensus 423 eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~a 455 (482)
.+...+. ..+.++||+.++++.++|+.++..+
T Consensus 53 ~l~~~y~-~i~~~~ia~~l~~~~~~vE~~l~~~ 84 (105)
T PF01399_consen 53 QLSKPYS-SISISEIAKALQLSEEEVESILIDL 84 (105)
T ss_dssp HHHHC-S-EEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred HHHHHhc-ccchHHHHHHhccchHHHHHHHHHH
Confidence 3444343 7899999999999999999998755
No 423
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=20.12 E-value=1.8e+02 Score=21.89 Aligned_cols=28 Identities=25% Similarity=0.252 Sum_probs=24.0
Q ss_pred hcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577 427 EGNHSPDKEDLARRVGITVEKLERLIFI 454 (482)
Q Consensus 427 e~gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (482)
.++.+++.+.||...||+..+|..+.+.
T Consensus 15 ~LR~~~~~~~La~~FgIs~stvsri~~~ 42 (53)
T PF13613_consen 15 YLRLNLTFQDLAYRFGISQSTVSRIFHE 42 (53)
T ss_pred HHHcCCcHhHHhhheeecHHHHHHHHHH
Confidence 3455789999999999999999998764
Done!