Query 011324
Match_columns 488
No_of_seqs 336 out of 1993
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 00:05:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011324.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011324hhsearch_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 7E-49 1.5E-53 411.3 26.8 234 253-486 58-333 (415)
2 PRK05949 RNA polymerase sigma 100.0 4.9E-46 1.1E-50 380.8 27.3 234 253-486 16-249 (327)
3 TIGR02997 Sig70-cyanoRpoD RNA 100.0 4.7E-46 1E-50 375.4 26.8 232 255-486 1-232 (298)
4 PRK07406 RNA polymerase sigma 100.0 9.6E-46 2.1E-50 384.2 27.6 233 254-486 62-294 (373)
5 PRK07405 RNA polymerase sigma 100.0 1.1E-44 2.3E-49 369.3 27.3 234 253-486 6-239 (317)
6 COG0568 RpoD DNA-directed RNA 100.0 4.9E-42 1.1E-46 350.5 19.9 234 254-487 8-262 (342)
7 PRK05901 RNA polymerase sigma 100.0 4.5E-41 9.7E-46 360.1 23.0 220 253-485 209-429 (509)
8 PRK07921 RNA polymerase sigma 100.0 2.5E-40 5.3E-45 338.4 23.0 219 254-485 25-244 (324)
9 PRK09210 RNA polymerase sigma 100.0 4.8E-37 1E-41 318.8 21.7 197 250-486 91-288 (367)
10 PRK05658 RNA polymerase sigma 100.0 1.6E-34 3.4E-39 317.7 21.0 158 328-485 380-538 (619)
11 PRK07500 rpoH2 RNA polymerase 100.0 2.3E-32 5E-37 275.4 21.0 194 254-486 5-206 (289)
12 PRK06596 RNA polymerase factor 100.0 1.5E-31 3.2E-36 268.8 21.5 192 253-486 12-209 (284)
13 TIGR02392 rpoH_proteo alternat 100.0 3.1E-31 6.8E-36 264.1 20.4 190 256-486 2-197 (270)
14 PRK07122 RNA polymerase sigma 100.0 5.5E-31 1.2E-35 262.2 18.9 153 328-480 40-196 (264)
15 TIGR02393 RpoD_Cterm RNA polym 100.0 3.6E-31 7.7E-36 258.6 17.0 157 329-485 1-158 (238)
16 PRK05657 RNA polymerase sigma 100.0 9E-30 1.9E-34 260.7 21.8 193 253-485 51-244 (325)
17 PRK07408 RNA polymerase sigma 100.0 7.9E-30 1.7E-34 252.4 20.3 158 325-482 21-184 (256)
18 TIGR02850 spore_sigG RNA polym 100.0 7.4E-29 1.6E-33 244.7 21.5 177 264-481 10-188 (254)
19 PRK08215 sporulation sigma fac 100.0 7.7E-28 1.7E-32 237.8 20.8 177 264-481 13-191 (258)
20 TIGR02394 rpoS_proteo RNA poly 99.9 2.3E-26 5E-31 230.7 22.7 192 250-481 8-199 (285)
21 PRK05911 RNA polymerase sigma 99.9 1E-26 2.2E-31 230.6 19.8 155 325-482 19-183 (257)
22 TIGR02885 spore_sigF RNA polym 99.9 2.2E-26 4.8E-31 223.1 17.8 159 322-481 4-165 (231)
23 COG1191 FliA DNA-directed RNA 99.9 6.8E-26 1.5E-30 223.9 18.1 152 318-471 13-168 (247)
24 PRK06288 RNA polymerase sigma 99.9 3.7E-25 7.9E-30 220.0 19.4 180 264-485 6-194 (268)
25 TIGR02941 Sigma_B RNA polymera 99.9 1.4E-24 3.1E-29 213.8 21.5 144 327-470 28-173 (255)
26 TIGR02980 SigBFG RNA polymeras 99.9 9.1E-25 2E-29 211.1 18.9 153 327-479 2-158 (227)
27 PRK05572 sporulation sigma fac 99.9 1.6E-23 3.4E-28 206.5 22.3 178 262-480 6-185 (252)
28 PRK07670 RNA polymerase sigma 99.9 1.4E-23 3.1E-28 206.6 18.1 161 316-479 8-176 (251)
29 PRK08583 RNA polymerase sigma 99.9 7.2E-23 1.6E-27 202.0 21.1 143 327-469 28-172 (257)
30 PRK12427 flagellar biosynthesi 99.9 5.9E-23 1.3E-27 200.9 17.3 139 328-470 15-158 (231)
31 TIGR02479 FliA_WhiG RNA polyme 99.9 9.6E-23 2.1E-27 197.0 16.1 150 333-485 1-157 (224)
32 PRK06986 fliA flagellar biosyn 99.9 1.9E-21 4.2E-26 189.5 17.4 143 325-470 5-152 (236)
33 PRK05803 sporulation sigma fac 99.8 2.1E-20 4.6E-25 182.1 17.3 163 256-458 17-222 (233)
34 PRK08301 sporulation sigma fac 99.8 7.4E-18 1.6E-22 163.8 17.0 141 318-458 41-225 (234)
35 TIGR02846 spore_sigmaK RNA pol 99.8 9.1E-18 2E-22 163.2 16.7 140 319-458 38-221 (227)
36 TIGR02895 spore_sigI RNA polym 99.8 1E-17 2.2E-22 163.4 14.6 129 322-450 3-142 (218)
37 TIGR02835 spore_sigmaE RNA pol 99.7 4.7E-17 1E-21 158.9 17.4 135 324-458 47-225 (234)
38 PRK08295 RNA polymerase factor 99.7 2.3E-17 5.1E-22 156.2 14.8 146 313-459 8-198 (208)
39 TIGR02859 spore_sigH RNA polym 99.7 2.6E-17 5.7E-22 154.5 14.8 146 314-459 4-193 (198)
40 PRK05602 RNA polymerase sigma 99.7 7.3E-17 1.6E-21 150.9 13.5 145 314-459 5-172 (186)
41 PRK12513 RNA polymerase sigma 99.7 1.9E-16 4.1E-21 149.1 14.2 144 314-459 11-183 (194)
42 PRK06811 RNA polymerase factor 99.7 2.4E-16 5.1E-21 148.4 13.9 144 314-458 3-174 (189)
43 PRK09646 RNA polymerase sigma 99.7 2.3E-16 5E-21 149.1 13.3 144 315-459 16-186 (194)
44 TIGR02954 Sig70_famx3 RNA poly 99.7 4.5E-16 9.9E-21 143.3 13.4 144 314-459 1-163 (169)
45 TIGR02948 SigW_bacill RNA poly 99.7 3.9E-16 8.4E-21 145.1 12.7 142 316-459 5-180 (187)
46 PRK13919 putative RNA polymera 99.7 5E-16 1.1E-20 144.9 13.4 145 314-459 8-179 (186)
47 PRK09640 RNA polymerase sigma 99.7 6E-16 1.3E-20 145.4 13.9 145 312-458 6-177 (188)
48 PRK09648 RNA polymerase sigma 99.7 7.4E-16 1.6E-20 144.5 14.4 141 317-458 12-182 (189)
49 PRK12514 RNA polymerase sigma 99.7 6.2E-16 1.3E-20 143.6 13.0 145 314-459 4-173 (179)
50 PRK12537 RNA polymerase sigma 99.7 6.2E-16 1.3E-20 144.6 12.8 144 314-458 8-176 (182)
51 TIGR02952 Sig70_famx2 RNA poly 99.7 9.6E-16 2.1E-20 140.1 13.3 138 320-458 2-165 (170)
52 PRK12524 RNA polymerase sigma 99.7 8.8E-16 1.9E-20 145.3 13.4 146 313-459 10-180 (196)
53 PRK06759 RNA polymerase factor 99.7 1.2E-15 2.6E-20 137.8 13.2 130 328-459 4-150 (154)
54 PRK09641 RNA polymerase sigma 99.7 1.3E-15 2.7E-20 141.6 13.1 143 315-459 4-180 (187)
55 PRK09638 RNA polymerase sigma 99.6 1.9E-15 4.1E-20 139.6 13.5 144 314-459 3-170 (176)
56 PRK09643 RNA polymerase sigma 99.6 2.1E-15 4.7E-20 142.6 14.2 144 314-459 12-178 (192)
57 PRK09652 RNA polymerase sigma 99.6 1.5E-15 3.3E-20 139.3 12.0 136 322-459 3-172 (182)
58 PRK12534 RNA polymerase sigma 99.6 1.7E-15 3.8E-20 141.6 12.1 143 316-459 12-181 (187)
59 PRK12538 RNA polymerase sigma 99.6 2.3E-15 4.9E-20 147.7 13.4 145 314-459 48-215 (233)
60 PRK12526 RNA polymerase sigma 99.6 3E-15 6.6E-20 143.2 13.8 140 319-459 28-197 (206)
61 PRK12531 RNA polymerase sigma 99.6 2.1E-15 4.6E-20 142.5 12.6 142 317-459 15-185 (194)
62 TIGR02939 RpoE_Sigma70 RNA pol 99.6 3.1E-15 6.7E-20 139.4 13.5 144 314-459 5-182 (190)
63 PRK12519 RNA polymerase sigma 99.6 2.6E-15 5.7E-20 141.1 13.0 142 315-458 15-184 (194)
64 PRK11923 algU RNA polymerase s 99.6 4.7E-15 1E-19 139.3 13.7 143 315-459 6-182 (193)
65 PRK11922 RNA polymerase sigma 99.6 4.3E-15 9.2E-20 144.7 13.5 143 314-458 15-192 (231)
66 PRK12536 RNA polymerase sigma 99.6 8E-15 1.7E-19 137.0 13.8 142 316-459 8-173 (181)
67 PRK12539 RNA polymerase sigma 99.6 8.3E-15 1.8E-19 137.2 13.9 141 316-458 8-174 (184)
68 PRK12515 RNA polymerase sigma 99.6 9.6E-15 2.1E-19 137.2 13.4 145 313-459 6-175 (189)
69 PRK12542 RNA polymerase sigma 99.6 4.3E-15 9.3E-20 139.1 10.0 135 325-459 5-166 (185)
70 TIGR02999 Sig-70_X6 RNA polyme 99.6 1.3E-14 2.7E-19 134.9 11.9 141 316-458 4-177 (183)
71 TIGR03001 Sig-70_gmx1 RNA poly 99.6 2.2E-14 4.7E-19 141.9 13.6 145 312-458 22-204 (244)
72 TIGR02989 Sig-70_gvs1 RNA poly 99.6 2.3E-14 5E-19 129.8 12.6 130 328-459 1-155 (159)
73 PRK09649 RNA polymerase sigma 99.6 1.9E-14 4.1E-19 135.4 12.2 142 317-461 12-176 (185)
74 PRK11924 RNA polymerase sigma 99.6 2.9E-14 6.3E-19 130.5 13.1 139 319-459 3-169 (179)
75 PRK12512 RNA polymerase sigma 99.6 4.5E-14 9.7E-19 131.7 14.1 140 318-459 11-175 (184)
76 COG1595 RpoE DNA-directed RNA 99.6 5.6E-14 1.2E-18 131.6 13.8 134 324-459 11-171 (182)
77 TIGR02937 sigma70-ECF RNA poly 99.6 4E-14 8.7E-19 124.0 11.9 127 329-458 2-153 (158)
78 PRK12543 RNA polymerase sigma 99.5 4.8E-14 1E-18 131.5 12.4 133 325-459 3-161 (179)
79 PRK12522 RNA polymerase sigma 99.5 6E-14 1.3E-18 129.8 12.5 130 328-459 3-163 (173)
80 PRK12520 RNA polymerase sigma 99.5 4.6E-14 1E-18 132.8 11.7 129 329-459 3-175 (191)
81 TIGR02947 SigH_actino RNA poly 99.5 4.3E-14 9.4E-19 133.2 10.6 130 328-459 11-175 (193)
82 PRK09415 RNA polymerase factor 99.5 8.9E-14 1.9E-18 129.9 12.3 131 327-459 15-171 (179)
83 PRK12518 RNA polymerase sigma 99.5 1E-13 2.2E-18 127.9 12.6 136 321-459 3-164 (175)
84 PRK09645 RNA polymerase sigma 99.5 1.1E-13 2.3E-18 127.8 12.5 132 326-458 7-161 (173)
85 TIGR02985 Sig70_bacteroi1 RNA 99.5 7E-14 1.5E-18 125.6 10.8 129 328-458 1-156 (161)
86 PRK12516 RNA polymerase sigma 99.5 1.1E-13 2.4E-18 130.8 12.7 132 326-459 8-160 (187)
87 TIGR02984 Sig-70_plancto1 RNA 99.5 1.3E-13 2.8E-18 128.1 12.2 134 325-458 3-183 (189)
88 PRK08241 RNA polymerase factor 99.5 1.2E-13 2.6E-18 141.2 12.9 141 317-459 7-197 (339)
89 PRK12547 RNA polymerase sigma 99.5 2.8E-13 6E-18 124.7 12.9 130 327-458 5-155 (164)
90 PRK12529 RNA polymerase sigma 99.5 2E-13 4.3E-18 127.6 11.9 135 324-458 8-170 (178)
91 TIGR02983 SigE-fam_strep RNA p 99.5 2.9E-13 6.4E-18 123.4 12.4 132 326-459 4-154 (162)
92 PRK12541 RNA polymerase sigma 99.5 3.6E-13 7.9E-18 123.0 12.4 130 327-459 4-156 (161)
93 PRK12535 RNA polymerase sigma 99.5 3.9E-13 8.5E-18 128.1 12.8 139 317-458 13-176 (196)
94 PRK08311 putative RNA polymera 99.5 7.9E-13 1.7E-17 130.6 15.0 91 315-405 4-97 (237)
95 TIGR02960 SigX5 RNA polymerase 99.5 2.7E-13 5.9E-18 137.3 11.8 131 327-459 4-186 (324)
96 PRK12533 RNA polymerase sigma 99.5 4.9E-13 1.1E-17 129.9 13.0 134 323-459 13-178 (216)
97 PRK09644 RNA polymerase sigma 99.5 4.2E-13 9.1E-18 123.3 11.6 127 330-459 3-152 (165)
98 PRK12523 RNA polymerase sigma 99.5 2.2E-13 4.8E-18 126.1 9.6 133 324-459 5-163 (172)
99 PRK09639 RNA polymerase sigma 99.4 8.8E-13 1.9E-17 120.5 11.7 128 327-459 2-155 (166)
100 PRK12545 RNA polymerase sigma 99.4 8.2E-13 1.8E-17 126.0 11.8 126 332-459 12-183 (201)
101 PRK12528 RNA polymerase sigma 99.4 9.3E-13 2E-17 120.3 11.5 127 328-457 4-155 (161)
102 PRK09642 RNA polymerase sigma 99.4 4.7E-13 1E-17 122.0 9.5 122 335-459 2-150 (160)
103 PRK12540 RNA polymerase sigma 99.4 1.3E-12 2.8E-17 123.1 12.5 130 328-459 5-155 (182)
104 PRK09647 RNA polymerase sigma 99.4 1.3E-12 2.8E-17 125.5 12.4 129 328-459 28-182 (203)
105 PRK12532 RNA polymerase sigma 99.4 1.1E-12 2.3E-17 123.9 11.2 126 331-458 8-179 (195)
106 PRK12517 RNA polymerase sigma 99.4 2.5E-12 5.4E-17 121.6 12.8 134 324-459 19-172 (188)
107 PRK09637 RNA polymerase sigma 99.4 3.1E-12 6.7E-17 120.3 13.0 127 330-458 3-149 (181)
108 PRK12530 RNA polymerase sigma 99.4 1.7E-12 3.8E-17 122.5 11.3 126 331-458 10-177 (189)
109 TIGR02943 Sig70_famx1 RNA poly 99.4 1.9E-12 4.2E-17 122.2 11.6 127 331-459 5-175 (188)
110 PF04542 Sigma70_r2: Sigma-70 99.4 1E-12 2.2E-17 103.5 7.9 70 333-402 1-70 (71)
111 PRK12544 RNA polymerase sigma 99.4 2.4E-12 5.2E-17 123.9 12.0 129 329-459 19-192 (206)
112 TIGR02950 SigM_subfam RNA poly 99.4 1.8E-12 4E-17 116.8 10.4 122 334-458 1-148 (154)
113 PRK12546 RNA polymerase sigma 99.4 4.4E-12 9.5E-17 120.3 12.6 128 328-458 8-156 (188)
114 TIGR02959 SigZ RNA polymerase 99.4 4.4E-12 9.6E-17 117.7 11.2 123 335-459 2-144 (170)
115 PRK12511 RNA polymerase sigma 99.3 9.8E-12 2.1E-16 117.2 11.5 128 330-459 6-155 (182)
116 PRK09651 RNA polymerase sigma 99.3 2E-11 4.3E-16 113.4 12.8 129 327-458 9-162 (172)
117 PRK06704 RNA polymerase factor 99.3 2.3E-11 5E-16 119.6 11.6 134 320-459 9-160 (228)
118 PRK07037 extracytoplasmic-func 99.3 3E-11 6.6E-16 110.2 11.0 124 332-458 2-152 (163)
119 PRK12525 RNA polymerase sigma 99.3 5.3E-11 1.1E-15 110.0 12.3 128 327-457 8-160 (168)
120 PRK12527 RNA polymerase sigma 99.3 2.8E-11 6.1E-16 110.3 10.3 123 334-459 1-149 (159)
121 PRK09636 RNA polymerase sigma 99.2 1E-10 2.3E-15 117.8 12.5 128 328-459 4-159 (293)
122 TIGR02957 SigX4 RNA polymerase 99.1 3.8E-10 8.3E-15 113.4 12.1 124 332-459 1-152 (281)
123 PRK09191 two-component respons 99.1 3.2E-10 7E-15 109.8 10.6 129 329-459 2-132 (261)
124 PRK09635 sigI RNA polymerase s 99.1 2.8E-10 6.2E-15 115.4 10.6 128 328-459 5-162 (290)
125 PF04539 Sigma70_r3: Sigma-70 99.1 1.2E-10 2.6E-15 95.1 5.7 75 412-486 1-76 (78)
126 TIGR03209 P21_Cbot clostridium 99.1 9.3E-10 2E-14 98.7 10.3 113 330-449 1-141 (142)
127 PRK09047 RNA polymerase factor 99.0 1.2E-09 2.6E-14 99.1 8.9 107 350-459 2-150 (161)
128 PF07638 Sigma70_ECF: ECF sigm 98.8 1E-07 2.2E-12 90.3 12.8 141 317-457 5-177 (185)
129 PF00140 Sigma70_r1_2: Sigma-7 97.9 2.7E-06 5.8E-11 61.1 0.5 34 254-287 1-34 (37)
130 PRK05658 RNA polymerase sigma 97.1 0.012 2.7E-07 66.0 16.3 34 253-286 102-135 (619)
131 TIGR02393 RpoD_Cterm RNA polym 96.5 0.023 4.9E-07 55.9 10.7 33 288-320 89-121 (238)
132 PRK07670 RNA polymerase sigma 96.2 0.039 8.6E-07 54.6 10.9 30 429-458 215-244 (251)
133 PRK05911 RNA polymerase sigma 96.2 0.031 6.7E-07 55.9 9.8 30 429-458 219-248 (257)
134 PRK07408 RNA polymerase sigma 96.1 0.015 3.1E-07 58.1 7.3 34 287-320 114-147 (256)
135 COG1191 FliA DNA-directed RNA 96.1 0.17 3.8E-06 50.9 14.7 149 256-455 88-236 (247)
136 PRK06288 RNA polymerase sigma 96.0 0.072 1.6E-06 53.4 11.6 34 287-320 119-152 (268)
137 PF12645 HTH_16: Helix-turn-he 96.0 0.022 4.7E-07 46.0 6.3 56 319-374 3-65 (65)
138 PRK09210 RNA polymerase sigma 96.0 0.1 2.3E-06 55.0 13.2 128 288-456 218-350 (367)
139 PRK07122 RNA polymerase sigma 96.0 0.055 1.2E-06 54.4 10.5 34 288-321 129-162 (264)
140 PRK05949 RNA polymerase sigma 95.8 0.053 1.2E-06 56.4 10.0 34 287-320 179-212 (327)
141 PRK05901 RNA polymerase sigma 95.7 0.16 3.6E-06 56.0 13.8 34 287-320 359-392 (509)
142 PRK07500 rpoH2 RNA polymerase 95.7 0.13 2.9E-06 52.4 12.1 30 430-459 244-273 (289)
143 PRK07598 RNA polymerase sigma 95.6 0.13 2.9E-06 55.3 12.1 35 287-321 263-297 (415)
144 TIGR02885 spore_sigF RNA polym 95.4 0.043 9.3E-07 53.4 7.1 31 290-320 101-131 (231)
145 PRK07921 RNA polymerase sigma 95.4 0.16 3.5E-06 52.8 11.6 34 287-320 174-207 (324)
146 TIGR02997 Sig70-cyanoRpoD RNA 95.3 0.23 5.1E-06 50.6 12.2 34 287-320 162-195 (298)
147 TIGR02479 FliA_WhiG RNA polyme 94.9 0.25 5.5E-06 47.9 10.7 34 287-320 84-117 (224)
148 PRK07405 RNA polymerase sigma 94.8 0.15 3.3E-06 52.7 9.5 34 287-320 169-202 (317)
149 TIGR02941 Sigma_B RNA polymera 94.8 0.16 3.5E-06 50.3 9.3 29 429-457 219-247 (255)
150 PRK07406 RNA polymerase sigma 94.7 0.31 6.8E-06 51.8 11.7 34 287-320 224-257 (373)
151 PF04539 Sigma70_r3: Sigma-70 94.6 0.072 1.6E-06 43.2 5.2 37 286-322 4-40 (78)
152 TIGR02850 spore_sigG RNA polym 94.5 0.49 1.1E-05 47.0 12.0 35 288-322 122-156 (254)
153 PRK06986 fliA flagellar biosyn 93.8 0.53 1.1E-05 46.1 10.4 30 429-458 198-227 (236)
154 PRK05572 sporulation sigma fac 93.6 0.49 1.1E-05 46.9 9.8 29 430-458 217-245 (252)
155 PRK08215 sporulation sigma fac 93.3 0.76 1.7E-05 45.7 10.7 33 289-321 126-158 (258)
156 TIGR02980 SigBFG RNA polymeras 93.2 0.47 1E-05 46.0 8.8 29 430-458 193-221 (227)
157 PF08281 Sigma70_r4_2: Sigma-7 92.5 0.11 2.3E-06 39.3 2.6 31 427-457 22-52 (54)
158 PRK12427 flagellar biosynthesi 92.4 1 2.3E-05 44.3 10.2 33 288-320 103-135 (231)
159 PRK08583 RNA polymerase sigma 92.4 0.72 1.6E-05 45.7 9.0 30 429-458 219-248 (257)
160 PF01726 LexA_DNA_bind: LexA D 91.9 0.52 1.1E-05 37.9 6.0 43 412-454 6-49 (65)
161 PF04545 Sigma70_r4: Sigma-70, 91.8 0.45 9.8E-06 35.5 5.3 31 426-456 15-45 (50)
162 TIGR02394 rpoS_proteo RNA poly 91.7 0.37 8.1E-06 48.8 6.2 31 429-459 240-270 (285)
163 PHA02547 55 RNA polymerase sig 91.4 0.55 1.2E-05 44.8 6.5 66 336-401 45-113 (179)
164 PRK06596 RNA polymerase factor 89.5 7.6 0.00016 39.5 13.4 28 430-457 247-274 (284)
165 PF13404 HTH_AsnC-type: AsnC-t 87.8 1.8 3.9E-05 31.9 5.6 34 420-454 7-40 (42)
166 cd06171 Sigma70_r4 Sigma70, re 85.2 1.7 3.7E-05 31.0 4.4 28 430-457 25-52 (55)
167 PF06971 Put_DNA-bind_N: Putat 84.1 2.9 6.3E-05 32.2 5.3 48 405-452 2-49 (50)
168 COG4941 Predicted RNA polymera 82.9 4.5 9.8E-05 42.9 7.7 126 331-458 8-163 (415)
169 TIGR03879 near_KaiC_dom probab 82.9 2.3 4.9E-05 35.4 4.5 25 430-454 31-55 (73)
170 PRK06930 positive control sigm 82.5 1.3 2.8E-05 42.1 3.4 31 428-458 127-157 (170)
171 PRK05657 RNA polymerase sigma 79.7 1.8 3.9E-05 45.0 3.7 31 429-459 280-310 (325)
172 smart00421 HTH_LUXR helix_turn 79.6 1.6 3.5E-05 31.9 2.4 29 431-459 18-46 (58)
173 PRK00118 putative DNA-binding 79.4 2.1 4.5E-05 37.8 3.4 29 430-458 32-60 (104)
174 PF10668 Phage_terminase: Phag 79.2 4.1 9E-05 32.6 4.7 30 424-453 15-44 (60)
175 PF04967 HTH_10: HTH DNA bindi 79.1 1.7 3.7E-05 33.8 2.5 28 430-457 22-49 (53)
176 PF13412 HTH_24: Winged helix- 78.9 6.6 0.00014 28.8 5.5 27 427-454 14-40 (48)
177 PRK04217 hypothetical protein; 78.7 2.2 4.8E-05 38.0 3.4 30 430-459 57-86 (110)
178 COG0568 RpoD DNA-directed RNA 76.7 35 0.00075 36.3 12.0 33 287-319 190-222 (342)
179 cd06170 LuxR_C_like C-terminal 76.5 2.3 5.1E-05 31.3 2.5 28 431-458 15-42 (57)
180 PF08279 HTH_11: HTH domain; 74.2 7.9 0.00017 29.1 4.9 32 423-455 8-39 (55)
181 PHA02591 hypothetical protein; 74.0 3.9 8.4E-05 34.5 3.4 23 431-453 59-81 (83)
182 PF00325 Crp: Bacterial regula 73.8 4.6 0.0001 28.4 3.2 23 432-454 3-25 (32)
183 TIGR00721 tfx DNA-binding prot 73.3 2.6 5.6E-05 39.0 2.4 29 430-458 20-48 (137)
184 PF13542 HTH_Tnp_ISL3: Helix-t 73.2 8.7 0.00019 28.5 4.9 24 431-454 27-50 (52)
185 PF13936 HTH_38: Helix-turn-he 73.1 6.2 0.00013 29.1 4.0 27 428-454 17-43 (44)
186 PF00196 GerE: Bacterial regul 72.5 4.5 9.7E-05 31.1 3.3 32 428-459 15-46 (58)
187 PF02796 HTH_7: Helix-turn-hel 70.3 6.4 0.00014 29.0 3.5 23 431-453 21-43 (45)
188 PRK03975 tfx putative transcri 69.4 3.6 7.9E-05 38.2 2.5 27 430-456 20-46 (141)
189 PF06056 Terminase_5: Putative 68.1 13 0.00029 29.2 5.1 26 431-456 13-38 (58)
190 COG2197 CitB Response regulato 67.1 6.7 0.00015 38.1 4.0 39 423-461 155-193 (211)
191 PRK15411 rcsA colanic acid cap 65.9 6 0.00013 38.2 3.3 43 419-461 140-182 (207)
192 TIGR02392 rpoH_proteo alternat 65.9 11 0.00023 38.0 5.2 27 430-456 235-261 (270)
193 PF13384 HTH_23: Homeodomain-l 65.3 6.3 0.00014 29.0 2.7 25 431-455 17-41 (50)
194 PRK10840 transcriptional regul 65.2 8.3 0.00018 36.5 4.1 39 423-461 157-195 (216)
195 COG4367 Uncharacterized protei 64.9 18 0.00039 31.3 5.5 28 431-458 23-50 (97)
196 cd00092 HTH_CRP helix_turn_hel 64.9 22 0.00048 27.2 5.8 25 431-455 25-49 (67)
197 PF01325 Fe_dep_repress: Iron 64.0 23 0.00051 27.9 5.8 36 418-454 10-45 (60)
198 PF13744 HTH_37: Helix-turn-he 63.7 15 0.00032 30.3 4.8 34 430-463 30-63 (80)
199 TIGR03020 EpsA transcriptional 63.2 8.6 0.00019 38.8 4.0 31 429-459 203-233 (247)
200 PRK11179 DNA-binding transcrip 63.2 14 0.0003 34.0 5.1 38 417-455 10-47 (153)
201 PF12728 HTH_17: Helix-turn-he 62.8 9.5 0.00021 28.3 3.2 24 432-455 2-25 (51)
202 PRK13719 conjugal transfer tra 62.7 9 0.0002 38.1 3.9 43 419-461 146-188 (217)
203 PF04297 UPF0122: Putative hel 62.1 16 0.00036 32.1 5.0 35 424-458 26-60 (101)
204 PRK11475 DNA-binding transcrip 61.6 9.7 0.00021 37.0 3.9 40 422-461 140-179 (207)
205 PF09012 FeoC: FeoC like trans 61.3 15 0.00033 29.3 4.4 31 423-454 7-37 (69)
206 PF00356 LacI: Bacterial regul 60.8 9 0.00019 28.9 2.7 22 433-454 1-22 (46)
207 PRK11169 leucine-responsive tr 60.7 18 0.00039 33.7 5.4 41 414-455 12-52 (164)
208 PF01710 HTH_Tnp_IS630: Transp 60.3 26 0.00055 31.1 6.1 34 422-456 63-96 (119)
209 PF09339 HTH_IclR: IclR helix- 59.9 14 0.0003 27.8 3.7 27 428-454 15-41 (52)
210 PF14502 HTH_41: Helix-turn-he 58.9 14 0.0003 28.5 3.4 36 428-463 3-40 (48)
211 TIGR01764 excise DNA binding d 58.9 13 0.00028 26.5 3.3 24 432-455 2-25 (49)
212 PF13730 HTH_36: Helix-turn-he 58.6 12 0.00026 28.1 3.2 25 430-454 24-48 (55)
213 PRK15201 fimbriae regulatory p 58.3 11 0.00024 36.7 3.5 35 425-459 142-176 (198)
214 COG1522 Lrp Transcriptional re 58.2 21 0.00045 32.2 5.2 38 417-455 9-46 (154)
215 smart00550 Zalpha Z-DNA-bindin 58.2 32 0.00069 27.6 5.7 31 424-454 14-45 (68)
216 PF08220 HTH_DeoR: DeoR-like h 57.7 23 0.00049 27.4 4.6 28 426-454 10-37 (57)
217 PF04703 FaeA: FaeA-like prote 57.6 16 0.00034 29.4 3.8 26 429-454 13-38 (62)
218 PRK13870 transcriptional regul 57.1 12 0.00025 37.1 3.7 30 430-459 187-216 (234)
219 PRK10188 DNA-binding transcrip 56.4 11 0.00025 37.3 3.5 30 430-459 193-222 (240)
220 PRK09483 response regulator; P 56.3 11 0.00024 34.7 3.2 33 429-461 161-193 (217)
221 PF03444 HrcA_DNA-bdg: Winged 55.9 41 0.00089 28.4 6.1 41 415-455 7-47 (78)
222 TIGR03541 reg_near_HchA LuxR f 55.7 8.3 0.00018 37.9 2.4 30 430-459 185-214 (232)
223 COG2771 CsgD DNA-binding HTH d 55.7 17 0.00037 27.5 3.7 29 430-458 18-46 (65)
224 PRK00423 tfb transcription ini 55.6 1E+02 0.0022 31.9 10.4 28 428-455 273-300 (310)
225 COG0856 Orotate phosphoribosyl 55.0 15 0.00033 35.7 3.8 34 430-463 17-50 (203)
226 smart00345 HTH_GNTR helix_turn 54.2 17 0.00038 26.8 3.4 25 431-455 20-44 (60)
227 TIGR02844 spore_III_D sporulat 54.0 31 0.00067 29.1 5.2 28 424-453 14-41 (80)
228 PRK11511 DNA-binding transcrip 53.9 38 0.00082 30.2 6.1 38 417-454 11-48 (127)
229 PRK10430 DNA-binding transcrip 53.5 25 0.00055 33.9 5.3 32 428-459 175-206 (239)
230 PF01978 TrmB: Sugar-specific 53.2 29 0.00062 27.3 4.7 24 431-454 22-45 (68)
231 PRK10100 DNA-binding transcrip 53.0 14 0.0003 36.1 3.4 30 430-459 169-198 (216)
232 PRK12423 LexA repressor; Provi 52.5 40 0.00086 32.6 6.4 40 415-454 9-49 (202)
233 COG3413 Predicted DNA binding 52.2 9.6 0.00021 37.0 2.1 30 430-459 177-206 (215)
234 PRK10046 dpiA two-component re 51.9 24 0.00053 33.7 4.9 40 426-465 172-213 (225)
235 cd04762 HTH_MerR-trunc Helix-T 51.8 22 0.00049 25.0 3.6 24 433-456 2-25 (49)
236 PRK15369 two component system 50.9 19 0.0004 32.2 3.7 32 430-461 163-194 (211)
237 PHA02943 hypothetical protein; 50.0 52 0.0011 31.3 6.4 27 427-454 21-47 (165)
238 TIGR00498 lexA SOS regulatory 49.5 45 0.00097 31.7 6.2 39 416-454 10-49 (199)
239 PRK10403 transcriptional regul 49.2 23 0.0005 32.0 4.0 33 430-462 167-199 (215)
240 PF01381 HTH_3: Helix-turn-hel 49.0 35 0.00076 25.3 4.4 24 431-454 9-32 (55)
241 TIGR02337 HpaR homoprotocatech 48.3 87 0.0019 27.1 7.4 64 382-454 2-65 (118)
242 PRK10219 DNA-binding transcrip 48.2 54 0.0012 27.8 6.0 37 418-454 8-44 (107)
243 TIGR03070 couple_hipB transcri 48.1 45 0.00097 24.4 4.8 23 431-453 15-37 (58)
244 PRK14082 hypothetical protein; 48.1 70 0.0015 26.1 6.0 54 328-383 9-62 (65)
245 TIGR03826 YvyF flagellar opero 47.7 67 0.0015 29.8 6.8 34 428-461 43-76 (137)
246 PF00440 TetR_N: Bacterial reg 47.5 45 0.00097 24.4 4.7 32 420-451 5-36 (47)
247 PRK09935 transcriptional regul 47.4 25 0.00053 32.0 4.0 32 430-461 163-194 (210)
248 PRK15320 transcriptional activ 47.2 18 0.00038 36.0 3.0 35 423-457 171-205 (251)
249 cd00569 HTH_Hin_like Helix-tur 46.8 36 0.00079 21.3 3.7 21 431-451 21-41 (42)
250 PRK10651 transcriptional regul 46.8 20 0.00043 32.5 3.3 35 428-462 167-201 (216)
251 TIGR02531 yecD_yerC TrpR-relat 46.2 45 0.00098 28.5 5.0 23 431-453 50-72 (88)
252 smart00346 HTH_ICLR helix_turn 45.8 60 0.0013 26.4 5.7 25 431-455 20-44 (91)
253 smart00420 HTH_DEOR helix_turn 45.3 65 0.0014 23.0 5.3 25 431-455 14-38 (53)
254 PRK09390 fixJ response regulat 45.3 48 0.001 29.4 5.5 30 431-460 156-185 (202)
255 PF09862 DUF2089: Protein of u 45.0 13 0.00028 33.5 1.6 53 433-485 51-106 (113)
256 PRK10572 DNA-binding transcrip 44.9 2.5E+02 0.0054 27.9 11.0 38 417-454 185-222 (290)
257 PF12324 HTH_15: Helix-turn-he 44.5 42 0.00092 28.3 4.5 28 428-455 35-62 (77)
258 smart00419 HTH_CRP helix_turn_ 44.2 33 0.00071 24.4 3.5 25 431-455 8-32 (48)
259 PF08280 HTH_Mga: M protein tr 43.1 80 0.0017 24.5 5.7 27 430-456 18-44 (59)
260 PRK13239 alkylmercury lyase; P 42.7 53 0.0012 32.5 5.6 29 428-456 33-61 (206)
261 PF04760 IF2_N: Translation in 42.3 23 0.00049 26.9 2.4 37 432-468 4-42 (54)
262 PF02001 DUF134: Protein of un 41.9 27 0.00058 31.1 3.1 29 431-459 57-85 (106)
263 COG1318 Predicted transcriptio 41.7 46 0.001 32.2 4.8 24 431-454 61-84 (182)
264 smart00344 HTH_ASNC helix_turn 41.6 50 0.0011 28.0 4.7 25 431-455 17-41 (108)
265 PF13518 HTH_28: Helix-turn-he 41.2 50 0.0011 24.0 4.1 25 432-456 13-37 (52)
266 PHA01976 helix-turn-helix prot 41.0 69 0.0015 24.7 5.1 23 431-453 15-37 (67)
267 PRK00215 LexA repressor; Valid 40.9 75 0.0016 30.3 6.3 34 422-455 14-48 (205)
268 PF07374 DUF1492: Protein of u 40.5 1.4E+02 0.003 25.7 7.3 31 426-456 66-96 (100)
269 COG4566 TtrR Response regulato 40.4 60 0.0013 32.0 5.5 44 410-453 136-179 (202)
270 cd04761 HTH_MerR-SF Helix-Turn 40.1 36 0.00078 24.5 3.1 24 433-456 2-25 (49)
271 PF04218 CENP-B_N: CENP-B N-te 40.1 27 0.0006 26.8 2.6 24 430-453 21-44 (53)
272 PRK09685 DNA-binding transcrip 39.9 2.8E+02 0.0062 27.5 10.6 45 343-388 205-249 (302)
273 PRK09726 antitoxin HipB; Provi 39.9 67 0.0015 26.8 5.1 31 431-462 25-55 (88)
274 PRK11161 fumarate/nitrate redu 39.6 1.1E+02 0.0023 29.4 7.3 25 431-455 184-208 (235)
275 PF08784 RPA_C: Replication pr 39.4 41 0.00089 28.7 3.8 25 430-454 64-88 (102)
276 PF13551 HTH_29: Winged helix- 39.1 78 0.0017 26.5 5.5 25 431-455 80-111 (112)
277 PRK06424 transcription factor; 39.1 1E+02 0.0022 28.7 6.7 42 410-453 78-119 (144)
278 PRK10219 DNA-binding transcrip 39.1 1.3E+02 0.0029 25.4 7.0 40 349-388 18-57 (107)
279 PF00392 GntR: Bacterial regul 38.2 38 0.00083 26.4 3.2 25 430-454 23-47 (64)
280 PF13560 HTH_31: Helix-turn-he 37.7 66 0.0014 24.9 4.5 23 431-453 14-36 (64)
281 PF02082 Rrf2: Transcriptional 37.3 54 0.0012 26.9 4.1 24 432-455 26-49 (83)
282 COG2344 AT-rich DNA-binding pr 37.2 95 0.0021 30.7 6.3 51 404-454 5-55 (211)
283 PF10078 DUF2316: Uncharacteri 37.1 34 0.00074 29.6 2.9 25 431-455 23-47 (89)
284 PRK09958 DNA-binding transcrip 36.9 45 0.00098 30.3 4.0 34 428-461 155-188 (204)
285 smart00354 HTH_LACI helix_turn 36.7 35 0.00076 27.3 2.8 22 432-453 1-22 (70)
286 PF13443 HTH_26: Cro/C1-type H 36.5 28 0.00061 26.6 2.2 32 431-462 10-41 (63)
287 TIGR03697 NtcA_cyano global ni 36.5 1.8E+02 0.004 26.6 8.0 26 431-456 143-168 (193)
288 PF13545 HTH_Crp_2: Crp-like h 36.1 49 0.0011 26.1 3.6 24 432-455 29-52 (76)
289 PRK15044 transcriptional regul 35.8 2.1E+02 0.0046 29.8 9.0 60 257-325 172-231 (295)
290 PRK15418 transcriptional regul 35.4 29 0.00064 36.1 2.7 36 430-465 28-67 (318)
291 PF01726 LexA_DNA_bind: LexA D 35.4 1.2E+02 0.0027 24.3 5.8 19 297-315 20-38 (65)
292 PF05225 HTH_psq: helix-turn-h 35.4 1.2E+02 0.0026 22.5 5.3 36 416-454 4-39 (45)
293 PF12802 MarR_2: MarR family; 35.1 68 0.0015 24.2 4.1 23 432-454 22-44 (62)
294 PF13309 HTH_22: HTH domain 35.0 68 0.0015 25.6 4.2 20 433-452 44-63 (64)
295 cd07377 WHTH_GntR Winged helix 34.4 85 0.0018 23.5 4.6 24 432-455 26-49 (66)
296 PRK15044 transcriptional regul 34.3 1.5E+02 0.0032 31.0 7.6 38 417-454 194-231 (295)
297 PF00376 MerR: MerR family reg 34.2 42 0.00091 24.1 2.6 22 433-454 1-22 (38)
298 PF00165 HTH_AraC: Bacterial r 33.6 61 0.0013 23.1 3.4 28 428-455 5-32 (42)
299 COG3355 Predicted transcriptio 33.3 83 0.0018 28.9 4.9 27 427-454 39-65 (126)
300 PRK10072 putative transcriptio 33.2 76 0.0017 27.6 4.5 25 431-455 46-70 (96)
301 COG2390 DeoR Transcriptional r 32.4 75 0.0016 33.4 5.2 38 430-467 25-66 (321)
302 PRK10360 DNA-binding transcrip 31.8 53 0.0011 29.6 3.5 31 430-460 151-181 (196)
303 PRK04841 transcriptional regul 31.7 44 0.00094 38.7 3.6 33 428-460 850-882 (903)
304 PRK03902 manganese transport t 31.6 1.2E+02 0.0026 27.3 5.8 35 419-454 11-45 (142)
305 PRK14101 bifunctional glucokin 31.5 2.5E+02 0.0055 31.9 9.5 23 431-453 374-396 (638)
306 PF13411 MerR_1: MerR HTH fami 31.2 54 0.0012 25.4 3.1 24 433-456 2-25 (69)
307 PF05138 PaaA_PaaC: Phenylacet 30.9 2.5E+02 0.0054 28.6 8.5 114 265-398 5-119 (263)
308 PRK11511 DNA-binding transcrip 30.6 1.9E+02 0.0041 25.7 6.8 49 349-397 22-70 (127)
309 PF01371 Trp_repressor: Trp re 30.5 1.5E+02 0.0033 25.4 5.8 23 430-452 48-70 (87)
310 smart00342 HTH_ARAC helix_turn 30.2 2.5E+02 0.0054 21.4 7.8 36 416-454 38-74 (84)
311 PF08535 KorB: KorB domain; I 30.2 51 0.0011 27.8 2.9 27 431-457 3-29 (93)
312 TIGR02607 antidote_HigA addict 30.2 99 0.0021 24.5 4.5 31 431-462 18-48 (78)
313 TIGR00180 parB_part ParB-like 29.9 1.1E+02 0.0025 29.0 5.6 35 431-465 120-154 (187)
314 PF13022 HTH_Tnp_1_2: Helix-tu 29.7 62 0.0013 30.3 3.5 28 426-453 29-56 (142)
315 PRK08359 transcription factor; 29.7 1.4E+02 0.0031 28.8 6.1 40 410-451 79-118 (176)
316 PF15545 Toxin_67: Putative to 29.5 51 0.0011 27.2 2.6 30 380-409 6-35 (70)
317 COG2524 Predicted transcriptio 29.5 91 0.002 32.2 4.9 41 415-455 9-49 (294)
318 TIGR02297 HpaA 4-hydroxyphenyl 29.5 5.3E+02 0.011 25.3 10.5 35 420-454 191-225 (287)
319 TIGR02944 suf_reg_Xantho FeS a 29.3 1E+02 0.0022 27.3 4.8 28 428-455 22-49 (130)
320 TIGR01610 phage_O_Nterm phage 29.2 1.4E+02 0.0031 25.3 5.6 26 429-454 45-70 (95)
321 TIGR00373 conserved hypothetic 29.1 65 0.0014 30.2 3.7 25 431-455 28-52 (158)
322 PRK09975 DNA-binding transcrip 28.8 1.3E+02 0.0028 28.2 5.7 42 410-451 9-51 (213)
323 PF04157 EAP30: EAP30/Vps36 fa 28.8 5.6E+02 0.012 25.0 10.4 166 270-455 23-214 (223)
324 PRK09464 pdhR transcriptional 28.7 89 0.0019 30.7 4.8 26 430-455 33-58 (254)
325 PF13551 HTH_29: Winged helix- 28.6 59 0.0013 27.2 3.1 24 433-456 14-37 (112)
326 COG4977 Transcriptional regula 28.5 94 0.002 32.9 5.1 72 383-454 186-259 (328)
327 PRK05472 redox-sensing transcr 28.5 1.4E+02 0.0031 28.8 6.1 50 405-454 6-55 (213)
328 PRK11753 DNA-binding transcrip 28.4 2.9E+02 0.0063 25.7 8.1 25 431-455 168-192 (211)
329 PF10975 DUF2802: Protein of u 28.3 2.8E+02 0.0061 22.7 6.8 25 431-455 44-68 (70)
330 PF12840 HTH_20: Helix-turn-he 28.2 1.4E+02 0.003 23.0 4.8 26 429-454 22-47 (61)
331 TIGR01321 TrpR trp operon repr 27.9 1.2E+02 0.0027 26.4 4.8 24 430-453 54-77 (94)
332 smart00351 PAX Paired Box doma 27.7 1E+02 0.0022 27.6 4.5 28 431-458 33-60 (125)
333 COG1476 Predicted transcriptio 27.6 1.2E+02 0.0025 25.1 4.4 22 431-452 14-35 (68)
334 cd01104 HTH_MlrA-CarA Helix-Tu 27.5 71 0.0015 24.7 3.1 22 433-454 2-23 (68)
335 TIGR03830 CxxCG_CxxCG_HTH puta 27.5 1.8E+02 0.004 25.2 6.1 23 431-453 78-100 (127)
336 TIGR00270 conserved hypothetic 27.4 2.1E+02 0.0045 26.9 6.7 40 412-453 65-104 (154)
337 smart00088 PINT motif in prote 27.3 1.2E+02 0.0026 24.7 4.6 43 422-465 16-58 (88)
338 smart00753 PAM PCI/PINT associ 27.3 1.2E+02 0.0026 24.7 4.6 43 422-465 16-58 (88)
339 PRK09940 transcriptional regul 27.2 2.5E+02 0.0053 28.6 7.7 48 340-388 138-185 (253)
340 TIGR02147 Fsuc_second hypothet 26.7 7.1E+02 0.015 25.5 11.9 25 431-455 137-163 (271)
341 COG2207 AraC AraC-type DNA-bin 26.6 2.1E+02 0.0045 23.8 6.2 50 348-397 32-81 (127)
342 smart00418 HTH_ARSR helix_turn 26.5 95 0.0021 22.6 3.6 25 431-455 10-34 (66)
343 PRK09480 slmA division inhibit 26.4 5E+02 0.011 23.6 10.6 74 296-369 24-97 (194)
344 PF07022 Phage_CI_repr: Bacter 26.2 53 0.0011 26.1 2.2 30 424-454 6-36 (66)
345 PF08765 Mor: Mor transcriptio 26.2 1.7E+02 0.0036 25.5 5.5 26 431-456 72-97 (108)
346 smart00342 HTH_ARAC helix_turn 25.9 2E+02 0.0044 22.0 5.6 61 302-364 1-62 (84)
347 PRK06266 transcription initiat 25.7 1.2E+02 0.0027 29.0 5.0 25 431-455 36-60 (178)
348 PRK09764 DNA-binding transcrip 25.7 1.3E+02 0.0028 29.5 5.3 27 428-454 26-52 (240)
349 PRK09393 ftrA transcriptional 25.2 1.4E+02 0.0031 30.4 5.7 40 416-455 219-258 (322)
350 KOG1597 Transcription initiati 25.0 2E+02 0.0043 30.2 6.5 24 431-454 260-283 (308)
351 PRK09480 slmA division inhibit 24.9 1.6E+02 0.0034 27.0 5.4 40 412-451 10-50 (194)
352 PRK13503 transcriptional activ 24.9 2.6E+02 0.0056 27.4 7.3 38 349-386 184-221 (278)
353 PRK15121 right oriC-binding tr 24.9 1.6E+02 0.0035 29.6 6.0 40 415-454 5-44 (289)
354 PRK10371 DNA-binding transcrip 24.9 4.2E+02 0.009 27.0 9.0 59 339-398 195-253 (302)
355 smart00422 HTH_MERR helix_turn 24.8 85 0.0018 24.3 3.1 22 433-454 2-23 (70)
356 TIGR03613 RutR pyrimidine util 24.6 1.1E+02 0.0024 28.4 4.4 32 417-448 14-45 (202)
357 PRK11512 DNA-binding transcrip 24.5 4.6E+02 0.01 23.4 8.3 24 431-454 54-77 (144)
358 COG1725 Predicted transcriptio 24.5 2.1E+02 0.0046 26.2 6.0 26 428-453 32-57 (125)
359 TIGR02431 pcaR_pcaU beta-ketoa 24.5 1.6E+02 0.0034 29.0 5.6 27 428-454 21-47 (248)
360 PRK09391 fixK transcriptional 24.3 2.9E+02 0.0062 26.7 7.4 26 431-456 179-204 (230)
361 COG1342 Predicted DNA-binding 24.1 84 0.0018 27.7 3.1 29 431-459 49-77 (99)
362 TIGR00738 rrf2_super rrf2 fami 24.0 1.5E+02 0.0031 26.1 4.8 24 431-454 25-48 (132)
363 smart00530 HTH_XRE Helix-turn- 23.9 1.1E+02 0.0024 20.8 3.3 23 431-453 10-32 (56)
364 PF01022 HTH_5: Bacterial regu 23.6 2.1E+02 0.0046 20.9 4.9 24 431-454 15-38 (47)
365 cd04764 HTH_MlrA-like_sg1 Heli 23.4 83 0.0018 24.5 2.8 22 433-454 2-23 (67)
366 PRK10402 DNA-binding transcrip 23.3 2E+02 0.0044 27.6 6.0 24 432-455 170-193 (226)
367 PRK03573 transcriptional regul 23.2 4.6E+02 0.0099 23.3 8.0 24 431-454 46-69 (144)
368 PRK10681 DNA-binding transcrip 23.1 1.4E+02 0.0031 29.7 5.1 30 424-454 15-44 (252)
369 PF11268 DUF3071: Protein of u 23.1 87 0.0019 30.1 3.4 25 427-451 65-89 (170)
370 smart00389 HOX Homeodomain. DN 22.9 1.6E+02 0.0034 21.7 4.2 23 433-455 29-51 (56)
371 PF12844 HTH_19: Helix-turn-he 22.8 1.8E+02 0.0039 22.1 4.6 24 431-454 12-35 (64)
372 PRK13558 bacterio-opsin activa 22.7 53 0.0011 36.8 2.1 29 430-458 629-657 (665)
373 PRK13918 CRP/FNR family transc 22.6 91 0.002 29.0 3.4 25 431-455 149-173 (202)
374 PRK10411 DNA-binding transcrip 22.4 1.6E+02 0.0034 29.4 5.2 28 427-455 15-42 (240)
375 PRK13503 transcriptional activ 22.3 2E+02 0.0043 28.2 5.9 37 418-454 174-210 (278)
376 TIGR02325 C_P_lyase_phnF phosp 22.2 2.1E+02 0.0046 27.5 6.0 27 428-454 29-55 (238)
377 PRK10079 phosphonate metabolis 22.2 1.4E+02 0.003 29.2 4.7 27 428-454 32-58 (241)
378 PF00046 Homeobox: Homeobox do 21.9 1.1E+02 0.0024 22.9 3.1 21 433-453 29-49 (57)
379 TIGR00122 birA_repr_reg BirA b 21.9 2E+02 0.0042 22.6 4.7 25 431-455 13-37 (69)
380 PRK13509 transcriptional repre 21.8 1.6E+02 0.0035 29.4 5.1 27 427-454 16-42 (251)
381 PRK11050 manganese transport r 21.7 2.9E+02 0.0063 25.4 6.5 25 431-455 51-75 (152)
382 PRK15340 transcriptional regul 21.6 5.2E+02 0.011 25.8 8.5 31 424-454 118-148 (216)
383 cd00090 HTH_ARSR Arsenical Res 21.3 2.7E+02 0.0058 20.7 5.3 24 432-455 21-44 (78)
384 smart00531 TFIIE Transcription 21.2 1E+02 0.0022 28.3 3.4 27 431-457 15-41 (147)
385 PRK14999 histidine utilization 21.0 2.3E+02 0.0049 27.7 6.0 27 428-454 33-59 (241)
386 cd00131 PAX Paired Box domain 20.9 1.7E+02 0.0036 26.5 4.6 32 431-462 33-64 (128)
387 TIGR02702 SufR_cyano iron-sulf 20.8 1.9E+02 0.0042 27.7 5.3 25 431-455 15-39 (203)
388 PRK10434 srlR DNA-bindng trans 20.7 1.6E+02 0.0034 29.6 4.8 28 426-454 15-42 (256)
389 PRK10371 DNA-binding transcrip 20.7 2E+02 0.0044 29.2 5.8 38 417-454 193-230 (302)
390 PF02954 HTH_8: Bacterial regu 20.7 2.4E+02 0.0052 20.3 4.5 21 433-453 20-40 (42)
391 COG2345 Predicted transcriptio 20.6 1.6E+02 0.0036 29.4 4.8 30 424-454 19-48 (218)
392 PF05344 DUF746: Domain of Unk 20.6 1.5E+02 0.0032 24.3 3.7 36 423-458 5-40 (65)
393 COG1321 TroR Mn-dependent tran 20.6 2.1E+02 0.0045 26.9 5.3 38 417-455 11-48 (154)
394 PRK09706 transcriptional repre 20.4 2.1E+02 0.0046 25.6 5.2 23 431-453 18-40 (135)
395 PF04255 DUF433: Protein of un 20.4 1.5E+02 0.0033 22.8 3.6 25 431-455 31-56 (56)
396 COG3415 Transposase and inacti 20.4 2.2E+02 0.0048 26.4 5.4 32 430-461 20-51 (138)
397 PRK10163 DNA-binding transcrip 20.3 2E+02 0.0042 29.0 5.4 27 428-454 37-63 (271)
398 KOG0037 Ca2+-binding protein, 20.2 7.8E+02 0.017 24.8 9.3 97 260-377 101-203 (221)
399 PF01418 HTH_6: Helix-turn-hel 20.2 2.8E+02 0.0061 22.5 5.4 27 426-453 30-56 (77)
400 PRK10906 DNA-binding transcrip 20.1 1.6E+02 0.0034 29.5 4.7 27 426-453 15-41 (252)
401 cd01392 HTH_LacI Helix-turn-he 20.1 78 0.0017 23.1 1.9 18 436-453 2-19 (52)
No 1
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=100.00 E-value=7e-49 Score=411.27 Aligned_cols=234 Identities=38% Similarity=0.627 Sum_probs=223.2
Q ss_pred CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHH--------------------HHHHHHHHHhhhCCCCcHHHHHH--
Q 011324 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR--------------------LEKEKSKLQSQFGREPTLIEWAK-- 310 (488)
Q Consensus 253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~--------------------le~~~~~l~~~~Gr~Pt~~ewA~-- 310 (488)
.+|+++.||++|++.||||++||++|+++||.++. |++++..|++.+|++||..|||.
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 47899999999999999999999999999999999 89999999999999999999994
Q ss_pred --------------------HhcCCHHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhH
Q 011324 311 --------------------AIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSV 370 (488)
Q Consensus 311 --------------------a~gm~eeeLi~~l~~Gd~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAi 370 (488)
++||++++|+..++.|..|+++||.+|+++|+++|++|.++|++++||||||+||||+|+
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 455677778888889999999999999999999999999999999999999999999999
Q ss_pred HhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHH
Q 011324 371 EKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLER 450 (488)
Q Consensus 371 ekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~ 450 (488)
++|||++|++|+||++||||++|.+++++++++|++|.++.+.+++++++.+.|.+.+|+.|+.+|||+.|||++++|+.
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 HHHHhCCCccccccCCCCCCCccccccCCCCCCCCC
Q 011324 451 LIFITRMPLSMQQPVWADQDTTFQVMPLLLSHLPSD 486 (488)
Q Consensus 451 ~L~~ar~~lSLD~~i~~d~~~tl~e~i~D~s~~ped 486 (488)
++..++.++|||.+++++++..+.|++.++..+|++
T Consensus 298 ~l~~~~~~~SLd~~vg~~~d~~l~d~l~~~~~~pee 333 (415)
T PRK07598 298 VLLRVPRSVSLETKVGKDKDTELGDLLETDDISPEE 333 (415)
T ss_pred HHHHccCCcccccccCCCccccHHHhccCCCCCHHH
Confidence 999999999999999988888899999887777764
No 2
>PRK05949 RNA polymerase sigma factor; Validated
Probab=100.00 E-value=4.9e-46 Score=380.77 Aligned_cols=234 Identities=37% Similarity=0.625 Sum_probs=226.2
Q ss_pred CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHH
Q 011324 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 332 (488)
Q Consensus 253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~Arek 332 (488)
..|++..||++|+++|+||++||++|+++|+.++.+++.+..|+..+|++|+..+||.+++|++.+|+..++.|+.|++.
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 011324 333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 412 (488)
Q Consensus 333 LIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~e 412 (488)
||..|+++|+++|++|.+++.+++|||||||||||+++++|||++|++|+|||+||||++|.++|+++++.||+|.++..
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 HHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCCCccccccCCCCCCCCC
Q 011324 413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVMPLLLSHLPSD 486 (488)
Q Consensus 413 ~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~tl~e~i~D~s~~ped 486 (488)
.++++.++.+.+...+|+.|+.+|||+.+|+++++|..++..++.++|||.+++++++.++.++++|+..+|++
T Consensus 176 ~~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~l~d~~~~pe~ 249 (327)
T PRK05949 176 KLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEGPSPDQ 249 (327)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCccHHhhcCCCCCCHHH
Confidence 99999999999999999999999999999999999999999999999999999887778899999988777764
No 3
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=100.00 E-value=4.7e-46 Score=375.39 Aligned_cols=232 Identities=42% Similarity=0.697 Sum_probs=222.3
Q ss_pred cHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHHHH
Q 011324 255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLI 334 (488)
Q Consensus 255 d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~ArekLI 334 (488)
|++..||++++++|+||++||.+|++++++++.+++.+..|+++.|++|+..+||+++|+++.+|+.+++.|..|+++||
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 011324 335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL 414 (488)
Q Consensus 335 esnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~e~l 414 (488)
.+|+++|+++|++|.++|.+++|||||||+|||+|+++|||.+|++|+||++||||++|.+++.++.+.+|+|.++...+
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 HHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCCCccccccCCCCCCCCC
Q 011324 415 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVMPLLLSHLPSD 486 (488)
Q Consensus 415 ~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~tl~e~i~D~s~~ped 486 (488)
++++++...+...+|+.|+.+|||+.+|+++++|..++..+...+|||.+++++++.++.++++|...+|++
T Consensus 161 ~~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~~~~~pe~ 232 (298)
T TIGR02997 161 NKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDDGESPEE 232 (298)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCcchHHHhccCCCCCHHH
Confidence 999999999999999999999999999999999999999999999999999877667888888887666653
No 4
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=9.6e-46 Score=384.22 Aligned_cols=233 Identities=36% Similarity=0.691 Sum_probs=225.2
Q ss_pred CcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHHH
Q 011324 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL 333 (488)
Q Consensus 254 ~d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~ArekL 333 (488)
.|++..||++|+++|+||++||++|+++|++++.+++.+..|++..|++|+..+||.++|++..+|..++..|..|+++|
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 011324 334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTL 413 (488)
Q Consensus 334 IesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~e~ 413 (488)
|.+|+++|+++|++|.++|++++||+||||||||+|+++||+.+|++|+|||+||||++|.++|+++++.||+|.++.+.
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 HHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCCCccccccCCCCCCCCC
Q 011324 414 LSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVMPLLLSHLPSD 486 (488)
Q Consensus 414 l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~tl~e~i~D~s~~ped 486 (488)
+++++++...|.+.+|+.||.+|||+.||+++++|..++..+..++|||.+++++++.++.|+++|+..+|++
T Consensus 222 ~~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~~~l~d~l~d~~~~pee 294 (373)
T PRK07406 222 ISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADGETPED 294 (373)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCcccHHHhcCCCCCCHHH
Confidence 9999999999999999999999999999999999999999889999999999887777899999987666653
No 5
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=1.1e-44 Score=369.32 Aligned_cols=234 Identities=39% Similarity=0.620 Sum_probs=225.4
Q ss_pred CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHH
Q 011324 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 332 (488)
Q Consensus 253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~Arek 332 (488)
.+|++..||++|+++|+||++||++|+++|++++.+++++..|++++|++|+..+||.++++++.+|+..++.|+.|+++
T Consensus 6 ~~~~~~~yl~~i~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~~ 85 (317)
T PRK07405 6 STDLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRK 85 (317)
T ss_pred CCcHHHHHHHHccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHHH
Confidence 36789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHH
Q 011324 333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 412 (488)
Q Consensus 333 LIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~e 412 (488)
||..|+++|+++|++|.+++.+++||+||||+|||+++++|||++|++|+|||+||||++|.++|+++++.||+|.++..
T Consensus 86 L~~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir~p~~~~~ 165 (317)
T PRK07405 86 MVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITE 165 (317)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCccCChHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCCCccccccCCCCCCCCC
Q 011324 413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVMPLLLSHLPSD 486 (488)
Q Consensus 413 ~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~tl~e~i~D~s~~ped 486 (488)
.+++++++...+...+|+.||.+|||+.+|+++++|..++...+..+|||.+++++++.++.++++|...+|++
T Consensus 166 ~~~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~~~d~~~~pe~ 239 (317)
T PRK07405 166 KLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTGASPED 239 (317)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCccHHHhhcCCCCCHHH
Confidence 99999999999999999999999999999999999999999889999999999887777899999987766664
No 6
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=100.00 E-value=4.9e-42 Score=350.54 Aligned_cols=234 Identities=35% Similarity=0.601 Sum_probs=215.7
Q ss_pred CcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHh-hhCCCCcHH---------------HHHHHhcCCH-
Q 011324 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQS-QFGREPTLI---------------EWAKAIGLSC- 316 (488)
Q Consensus 254 ~d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~-~~Gr~Pt~~---------------ewA~a~gm~e- 316 (488)
.|.+..|+.+++..++++.++|..+.+.++....+......+.. ..|..|+.. +|+..+..++
T Consensus 8 ~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Ee 87 (342)
T COG0568 8 ADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEEE 87 (342)
T ss_pred hhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHHH
Confidence 57889999999999999999999999999888777677777777 677888876 6666665555
Q ss_pred HHHHHHhhhc--H-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHH
Q 011324 317 RDLKSELHSG--N-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 393 (488)
Q Consensus 317 eeLi~~l~~G--d-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI 393 (488)
..|..++..| + .|+.+||++|+|||++||++|.|+|+.+.||||||+||||+|++||||++|+||||||+||||++|
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 HHHHHHhcCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCCCcc
Q 011324 394 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 473 (488)
Q Consensus 394 ~~~IRk~sr~irlP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~tl 473 (488)
.++|.++.|+||+|.|+.+.++++.+..+.+.++++++|+.+|||+.||++.++|+.++.++..++|||.|+|++++..+
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 ccccCCCCC-CCCCC
Q 011324 474 QVMPLLLSH-LPSDI 487 (488)
Q Consensus 474 ~e~i~D~s~-~ped~ 487 (488)
+|+++|+.. +|+++
T Consensus 248 ~d~leD~~~~~p~~~ 262 (342)
T COG0568 248 GDFLEDDKSVSPEDA 262 (342)
T ss_pred HHHhhcCCcCCHHHH
Confidence 999999965 77754
No 7
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=100.00 E-value=4.5e-41 Score=360.10 Aligned_cols=220 Identities=35% Similarity=0.550 Sum_probs=197.6
Q ss_pred CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHH
Q 011324 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 332 (488)
Q Consensus 253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~Arek 332 (488)
..|+++.||++|+++|+||++||++|+++|+.+..++.. +. ...+|+. ....+|...+..|..|+++
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 478999999999999999999999999999986433321 11 1122432 2456788888999999999
Q ss_pred HHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHH
Q 011324 333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 412 (488)
Q Consensus 333 LIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~e 412 (488)
||.+|+|||++||++|.++|++++||||||+||||+|+++|||++|++|+|||+||||++|.++|+++.+.||+|.++.+
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 HHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCCCccccccCCCC-CCCC
Q 011324 413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVMPLLLS-HLPS 485 (488)
Q Consensus 413 ~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~tl~e~i~D~s-~~pe 485 (488)
.+++|.++.+.|.+.+|+.||.+|||+.|||++++|..++..++.++|||.+++++++..+.|+|+|.. ..|+
T Consensus 356 ~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~~p~ 429 (509)
T PRK05901 356 TINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSPV 429 (509)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCcccHHHhccCCCCCCHH
Confidence 999999999999999999999999999999999999999999999999999998887788999999874 3454
No 8
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=100.00 E-value=2.5e-40 Score=338.42 Aligned_cols=219 Identities=35% Similarity=0.557 Sum_probs=197.3
Q ss_pred CcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHHH
Q 011324 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL 333 (488)
Q Consensus 254 ~d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~ArekL 333 (488)
+|++..||++++++|+||++||.+|+++|+.+..++.. |+..+|+... ...+|...+..|..|+++|
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 1122332111 3467889999999999999
Q ss_pred HHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHH
Q 011324 334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTL 413 (488)
Q Consensus 334 IesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~e~ 413 (488)
|..|+++|+++|++|.++|.+++||+|||+||||+|+++|||++|++|+|||+||||++|.++|+++.+.|++|.++.+.
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 HHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCCCccccccCCCC-CCCC
Q 011324 414 LSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVMPLLLS-HLPS 485 (488)
Q Consensus 414 l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~tl~e~i~D~s-~~pe 485 (488)
++++.++...|...+|+.||.+|||+.||+++++|..++..+...+|||.+++++++.++.|+++|+. ..|+
T Consensus 172 ~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~pe 244 (324)
T PRK07921 172 VNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAE 244 (324)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCchHHHHhcCCCCCCHH
Confidence 99999999999999999999999999999999999999988889999999998777778999999854 3454
No 9
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=4.8e-37 Score=318.80 Aligned_cols=197 Identities=38% Similarity=0.687 Sum_probs=183.4
Q ss_pred CCCCCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHH
Q 011324 250 GFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSS 329 (488)
Q Consensus 250 ~~~~~d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~A 329 (488)
+....|+++.||++|+++|+||++||.+|+++++. ++..|
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 34457899999999999999999999999987764 12389
Q ss_pred HHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchh
Q 011324 330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 409 (488)
Q Consensus 330 rekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~ 409 (488)
++.||..|+++|+++|++|.++|.+++||+||||||||+|+++|||.+|++|+|||+||||++|.++|+++.+.+|+|.+
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 HHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCCCccccccCCCC-CCCCC
Q 011324 410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVMPLLLS-HLPSD 486 (488)
Q Consensus 410 v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~tl~e~i~D~s-~~ped 486 (488)
+.+.++++.++.+.|..++|+.||.+|||+.||+++++|+.++..++.++|||.+++++++..+.|+++|+. ..|++
T Consensus 211 ~~~~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~i~d~~~~~p~~ 288 (367)
T PRK09210 211 MVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPAD 288 (367)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCCCcchhhhhccCCCCCCHHH
Confidence 999999999999999999999999999999999999999999999999999999999877788999999875 45654
No 10
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=1.6e-34 Score=317.75 Aligned_cols=158 Identities=36% Similarity=0.711 Sum_probs=151.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc
Q 011324 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 407 (488)
Q Consensus 328 ~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP 407 (488)
.|+++||.+|+|||++||++|.++|++++||||||+||||+|+++|||.+|++|+|||+||||++|.++|+++.++||+|
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 hhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCCCccccccCCCCC-CCC
Q 011324 408 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVMPLLLSH-LPS 485 (488)
Q Consensus 408 ~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~tl~e~i~D~s~-~pe 485 (488)
.++.+.++++.++.+.+.+++|+.||.+|||+.||+++++|+.++..+..++|||.|++++++.++.|+++|... +|+
T Consensus 460 ~~~~~~~~k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~Sld~~i~~~~~~~l~d~i~d~~~~~p~ 538 (619)
T PRK05658 460 VHMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPI 538 (619)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCcCCCCCCCCCCCchhhhcCCCCCCChH
Confidence 999999999999999999999999999999999999999999999999999999999998888889999998743 454
No 11
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=100.00 E-value=2.3e-32 Score=275.40 Aligned_cols=194 Identities=22% Similarity=0.411 Sum_probs=164.7
Q ss_pred CcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHHH
Q 011324 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL 333 (488)
Q Consensus 254 ~d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~ArekL 333 (488)
.+..+.||+++.++|+||+++|.+|+++++. .++..|++.|
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 3567789999999999999999999987643 1234899999
Q ss_pred HHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHH-
Q 011324 334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT- 412 (488)
Q Consensus 334 IesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~e- 412 (488)
|..|+++|+++|++|.+++.+++||+||||+|||+++++||+.+|.+|+|||+||||++|.++|+++.+.+|+|.+...
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 9999999999999999999999999999999999999999999999999999999999999999999999999987554
Q ss_pred -HHHHHHHHHHHH---HHhcCCCCcHHHHHHHhCCCHHHHHHHHH-HhCCCccccccCCCCCCC--ccccccCCCCCCCC
Q 011324 413 -LLSKVLEAKRLY---IQEGNHSPDKEDLARRVGITVEKLERLIF-ITRMPLSMQQPVWADQDT--TFQVMPLLLSHLPS 485 (488)
Q Consensus 413 -~l~kI~ka~~~L---~~elgr~pS~eEIAe~LGIS~etVk~~L~-~ar~~lSLD~~i~~d~~~--tl~e~i~D~s~~pe 485 (488)
...++.+....+ ...+++.||.+|||+.||+++++|..+.. .....+|||.+++++++. ++.|+++|+..+|+
T Consensus 126 ~~~~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~i~d~~~~pe 205 (289)
T PRK07500 126 ALFFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDDSPLPD 205 (289)
T ss_pred HHHHHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCCCCCCcccHHHhccCCCCCch
Confidence 333444444433 34678899999999999999999988753 345789999998765543 68899999877776
Q ss_pred C
Q 011324 486 D 486 (488)
Q Consensus 486 d 486 (488)
+
T Consensus 206 ~ 206 (289)
T PRK07500 206 E 206 (289)
T ss_pred H
Confidence 4
No 12
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=99.98 E-value=1.5e-31 Score=268.81 Aligned_cols=192 Identities=27% Similarity=0.465 Sum_probs=161.8
Q ss_pred CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcH-HHHH
Q 011324 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGN-SSRE 331 (488)
Q Consensus 253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd-~Are 331 (488)
+.+.+..|+++++++|+||.++|.+|+.+.+. .|+ .|++
T Consensus 12 ~~~~~~~y~~~~~~~~~l~~~~e~~l~~~~~~----------------------------------------~Gd~~a~~ 51 (284)
T PRK06596 12 PEGNLDAYIQAVNKIPMLTAEEEYMLAKRLRE----------------------------------------HGDLEAAK 51 (284)
T ss_pred CccHHHHHHHHHhccCCCCHHHHHHHHHHHHH----------------------------------------cCCHHHHH
Confidence 46789999999999999999999999886432 234 8999
Q ss_pred HHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHH
Q 011324 332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY 411 (488)
Q Consensus 332 kLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~ 411 (488)
.||..|+++|+++|++|.+.+.+++||+|||++||++|+++|||++|++|+|||+|||+++|.++|+++.+.+++|.+..
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 99999999999999999999999999999999999999999999999999999999999999999999887889998654
Q ss_pred H--HHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHh-CCCccccccCCCCC--CCccccccCCCCCCCCC
Q 011324 412 T--LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT-RMPLSMQQPVWADQ--DTTFQVMPLLLSHLPSD 486 (488)
Q Consensus 412 e--~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~a-r~~lSLD~~i~~d~--~~tl~e~i~D~s~~ped 486 (488)
. ...++.+....+. .++.|+.+|||+.||+++++|..++... ...+|||.++++++ +.++.++++|+..+|++
T Consensus 132 ~~~~~~~~~~~~~~l~--~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~~~l~d~~~~p~~ 209 (284)
T PRK06596 132 QRKLFFNLRKAKKRLG--WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLEDKSSDPAD 209 (284)
T ss_pred HHHHHHHHHHHHHHhc--cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCCCCCcchHHHHcCCCCCCchH
Confidence 2 2233433333332 3479999999999999999999987643 46899999987553 34688999998767754
No 13
>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=3.1e-31 Score=264.12 Aligned_cols=190 Identities=26% Similarity=0.493 Sum_probs=156.8
Q ss_pred HHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHHHHH
Q 011324 256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 335 (488)
Q Consensus 256 ~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~ArekLIe 335 (488)
++..||++++++|+|++++|.+|+.++.. .++..|++.||.
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 011324 336 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY--TL 413 (488)
Q Consensus 336 snlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~--e~ 413 (488)
.|+++|+++|++|.+++.+++||+||||+||++|+++|||++|++|+|||+||||++|.++|+++.+.+++|.+.. ..
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 9999999999999999999999999999999999999999999999999999999999999999877889996543 33
Q ss_pred HHHHHHHHHHHHHhcCCCC-cHHHHHHHhCCCHHHHHHHHHHhC-CCccccccCCCCCC--CccccccCCCCCCCCC
Q 011324 414 LSKVLEAKRLYIQEGNHSP-DKEDLARRVGITVEKLERLIFITR-MPLSMQQPVWADQD--TTFQVMPLLLSHLPSD 486 (488)
Q Consensus 414 l~kI~ka~~~L~~elgr~p-S~eEIAe~LGIS~etVk~~L~~ar-~~lSLD~~i~~d~~--~tl~e~i~D~s~~ped 486 (488)
..++.+....+. ..+.| +.+|||+.||+++++|..++.... ..+|||.+++++++ .++.+++.|+..+|++
T Consensus 123 ~~~~~~~~~~~~--~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~l~d~~~~pe~ 197 (270)
T TIGR02392 123 FFNLRKMKKRLQ--GWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDDEDDGGAPIAYLVDKTSDPED 197 (270)
T ss_pred HHHHHHHHHHHh--cCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCCCCCccccHHHHhcCCCCChHH
Confidence 444444444332 22345 699999999999999999875443 47999999876544 3678888888766654
No 14
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=99.97 E-value=5.5e-31 Score=262.19 Aligned_cols=153 Identities=22% Similarity=0.346 Sum_probs=140.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc
Q 011324 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 407 (488)
Q Consensus 328 ~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP 407 (488)
.++++||..|++||+++|++|.++|++++||||||+|||++|+++|||++|++|+|||+||||++|.++|+++.+.|++|
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--hCCCccccccCCCCCC--CccccccCCC
Q 011324 408 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI--TRMPLSMQQPVWADQD--TTFQVMPLLL 480 (488)
Q Consensus 408 ~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~--ar~~lSLD~~i~~d~~--~tl~e~i~D~ 480 (488)
.++.+.+.+++++...|.+.+|+.||.+|||+.||+++++|..++.. ...++|||.+++++++ ..+.+.++|.
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 4578999999875433 3455655553
No 15
>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=3.6e-31 Score=258.63 Aligned_cols=157 Identities=39% Similarity=0.724 Sum_probs=148.2
Q ss_pred HHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccch
Q 011324 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE 408 (488)
Q Consensus 329 ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~ 408 (488)
|+++||..|+++|+++|++|.++|.+++||+|||+|||++|+++|||++|++|+|||+||||++|.++++++.+.+++|.
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 hHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCCCccccccCCCC-CCCC
Q 011324 409 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVMPLLLS-HLPS 485 (488)
Q Consensus 409 ~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~tl~e~i~D~s-~~pe 485 (488)
++.+.++++.++...+...+|+.||.+|||+.||+++++|..++......+|||.+++++++.++.|+++|+. ..|+
T Consensus 81 ~~~~~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~p~ 158 (238)
T TIGR02393 81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDTSIESPD 158 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCCCCCCcccHHHHhcCCCCCChH
Confidence 9999999999999999999999999999999999999999999988888999999998777678889998875 3454
No 16
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=99.97 E-value=9e-30 Score=260.70 Aligned_cols=193 Identities=35% Similarity=0.594 Sum_probs=176.4
Q ss_pred CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHH
Q 011324 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 332 (488)
Q Consensus 253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~Arek 332 (488)
..|.++.||.+|+..|+||+++|..|+.+++. ++..|++.
T Consensus 51 ~~~~~~~y~~~~~~~~~l~~~ee~~li~~~~~----------------------------------------Gd~~A~~~ 90 (325)
T PRK05657 51 VLDATQLYLNEIGYSPLLTAEEEVYFARRALR----------------------------------------GDFAARQR 90 (325)
T ss_pred cccHHHHHHHHHhcCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHH
Confidence 47799999999999999999999998886653 23489999
Q ss_pred HHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHH
Q 011324 333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 412 (488)
Q Consensus 333 LIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~e 412 (488)
||..|.++|+++|++|.+++.+++||+||||||||+++++||+.+|++|+||++||||..|.++++++.+.+++|.++..
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 99999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred HHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCCCccccccCCCC-CCCC
Q 011324 413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVMPLLLS-HLPS 485 (488)
Q Consensus 413 ~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~tl~e~i~D~s-~~pe 485 (488)
.++.+.++.+.|...+++.|+.+|||+.||+++++|+.++.......|||.++..+...++.|.++|.. ..|+
T Consensus 171 ~l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~~~~~~~~l~d~l~d~~~~~pe 244 (325)
T PRK05657 171 ELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGPE 244 (325)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCCCCCCCcchhhhccCCCCCCHH
Confidence 888888888889999999999999999999999999999988778899999988777778888888764 3443
No 17
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=99.97 E-value=7.9e-30 Score=252.41 Aligned_cols=158 Identities=27% Similarity=0.467 Sum_probs=143.2
Q ss_pred hcH-HHHHHHHHHHHHHHHHHHHHccCC-CCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcC
Q 011324 325 SGN-SSREKLINANLRLVVHVAKQYQGR-GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR 402 (488)
Q Consensus 325 ~Gd-~ArekLIesnlrLV~sIAkry~~~-g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr 402 (488)
.|+ .|+++||..|+++|+++|++|.+. +.+++||+|||+||||+|+++|||++|++|+|||+|||+|+|.+++|++.+
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 445 899999999999999999999876 667999999999999999999999999999999999999999999999999
Q ss_pred CcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHH--HhCCCccccccCCCCCC--CccccccC
Q 011324 403 TIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF--ITRMPLSMQQPVWADQD--TTFQVMPL 478 (488)
Q Consensus 403 ~irlP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~--~ar~~lSLD~~i~~d~~--~tl~e~i~ 478 (488)
.+++|+++.+.++++.++...|.+.+|+.|+.+|||+.||+++++|..++. .....+|||.+++++++ .++.+.++
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 36777777
Q ss_pred CCCC
Q 011324 479 LLSH 482 (488)
Q Consensus 479 D~s~ 482 (488)
|+..
T Consensus 181 d~~~ 184 (256)
T PRK07408 181 DPRY 184 (256)
T ss_pred Cccc
Confidence 7653
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=7.4e-29 Score=244.72 Aligned_cols=177 Identities=27% Similarity=0.430 Sum_probs=159.6
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHHHHHHHHHHHHH
Q 011324 264 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH 343 (488)
Q Consensus 264 i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~ArekLIesnlrLV~s 343 (488)
.+++|+||++||.+|+.+++. ++..|++.||..|.++|++
T Consensus 10 ~~~~~~l~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~~~~~~~v~~ 49 (254)
T TIGR02850 10 TSKLPVLKNQEMRELFIRMQS----------------------------------------GDTTAREKLINGNLRLVLS 49 (254)
T ss_pred ccCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHHHH
Confidence 467899999999888776543 2348999999999999999
Q ss_pred HHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHHHHHHHHHHHH
Q 011324 344 VAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRL 423 (488)
Q Consensus 344 IAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~e~l~kI~ka~~~ 423 (488)
+|++|.+++.+++||+||||+|||+++++||+.+|.+|+||+++||+|.|++++|++. .+++|.++.+.+.++.++...
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 HHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCC--CccccccCCCC
Q 011324 424 YIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD--TTFQVMPLLLS 481 (488)
Q Consensus 424 L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~--~tl~e~i~D~s 481 (488)
+..++|+.||.+|||+.||+++++|..++.....++|||.++.++++ .++.+.+.|+.
T Consensus 129 l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~~~d~~ 188 (254)
T TIGR02850 129 LISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDEK 188 (254)
T ss_pred HHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCCCCCcchhhhhcCCcc
Confidence 99999999999999999999999999999988889999999865443 35678887754
No 19
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=99.96 E-value=7.7e-28 Score=237.79 Aligned_cols=177 Identities=27% Similarity=0.448 Sum_probs=158.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHHHHHHHHHHHHH
Q 011324 264 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH 343 (488)
Q Consensus 264 i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~ArekLIesnlrLV~s 343 (488)
..++|+|+++|+..|+.+++. ++..|++.||..|.++|++
T Consensus 13 ~~~~~~l~~~~~~~l~~~~~~----------------------------------------gd~~a~~~l~~~~~~~v~~ 52 (258)
T PRK08215 13 TSKLPVLKNEEMRELFERMQN----------------------------------------GDKEAREKLINGNLRLVLS 52 (258)
T ss_pred CCCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHHHHHHHH
Confidence 356789999999888876543 2348999999999999999
Q ss_pred HHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHHHHHHHHHHHH
Q 011324 344 VAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRL 423 (488)
Q Consensus 344 IAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~e~l~kI~ka~~~ 423 (488)
+|++|.+++.+++||+|||++|||+++++||+.+|.+|+||+++||+|.|.+++|++. .+++|.++.....++.++...
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 HHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCCC--ccccccCCCC
Q 011324 424 YIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT--TFQVMPLLLS 481 (488)
Q Consensus 424 L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~--tl~e~i~D~s 481 (488)
+..++++.|+.+|||+.||+++++|...+.....++|||.+++++++. ++.|.++|+.
T Consensus 132 l~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~ 191 (258)
T PRK08215 132 LINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQISDEK 191 (258)
T ss_pred HHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCCCCcchhhhhhccCcc
Confidence 999999999999999999999999999998888889999998655432 4667777654
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=2.3e-26 Score=230.71 Aligned_cols=192 Identities=35% Similarity=0.557 Sum_probs=173.1
Q ss_pred CCCCCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHH
Q 011324 250 GFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSS 329 (488)
Q Consensus 250 ~~~~~d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~A 329 (488)
.....+.+++||.+|+.+|.||.++|.+|+..++. ++..|
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~----------------------------------------gd~~a 47 (285)
T TIGR02394 8 ETRVADVTQLYLREIGFKPLLTAEEEIAYARRALA----------------------------------------GDFEA 47 (285)
T ss_pred ccCcchHHHHHHHHHhccCCCCHHHHHHHHHHHHc----------------------------------------CCHHH
Confidence 34468899999999999999999999988887654 22489
Q ss_pred HHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchh
Q 011324 330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 409 (488)
Q Consensus 330 rekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~ 409 (488)
++.||..|.++|+++|++|.+++.+++||+||||||||+|+++||+.+|++|+||+.|||+.++.++++++.+.+++|.+
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 HHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCCCccccccCCCC
Q 011324 410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVMPLLLS 481 (488)
Q Consensus 410 v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~tl~e~i~D~s 481 (488)
+...++.+.+..+.+...+++.|+..|+|+.+|++++.|..++..+...+|||.++.+++..++.+.+.++.
T Consensus 128 ~~~~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~~ 199 (285)
T TIGR02394 128 VIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQ 199 (285)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCCCCCCCcchhhhhcCCC
Confidence 999999888887777788888999999999999999999999998888999999887666556667766553
No 21
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=99.95 E-value=1e-26 Score=230.57 Aligned_cols=155 Identities=22% Similarity=0.328 Sum_probs=137.6
Q ss_pred hcH-HHHHHHHHHHHHHHHHHHHHccC---CCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHh
Q 011324 325 SGN-SSREKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH 400 (488)
Q Consensus 325 ~Gd-~ArekLIesnlrLV~sIAkry~~---~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~ 400 (488)
.|+ .|++.||..|+++|+++|++|.+ .+++++||+|||+||||+|+++|||++|++|+|||+||||++|.+++|++
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 445 89999999999999999999852 35689999999999999999999999999999999999999999999998
Q ss_pred cCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhC--CCccccccCCC--C--CCCccc
Q 011324 401 SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR--MPLSMQQPVWA--D--QDTTFQ 474 (488)
Q Consensus 401 sr~irlP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar--~~lSLD~~i~~--d--~~~tl~ 474 (488)
. ++|+++.+.++++.++...|.+.+|+.|+.+|||+.||+++++|..++..++ ..+|||.++.. + ++.++.
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 46899988643 2 234678
Q ss_pred cccCCCCC
Q 011324 475 VMPLLLSH 482 (488)
Q Consensus 475 e~i~D~s~ 482 (488)
+.++|+..
T Consensus 176 ~~l~d~~~ 183 (257)
T PRK05911 176 ERIADERA 183 (257)
T ss_pred hhccCCCC
Confidence 88888654
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=2.2e-26 Score=223.12 Aligned_cols=159 Identities=26% Similarity=0.392 Sum_probs=145.1
Q ss_pred HhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHh
Q 011324 322 ELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH 400 (488)
Q Consensus 322 ~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~ 400 (488)
+++.|+ .|++.||..|.++|+++|++|.+++.+++||+||||+|||+++++||+.+|.+|.||+++||+|.|.+++|++
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 344555 8999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred cCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCC--CccccccC
Q 011324 401 SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD--TTFQVMPL 478 (488)
Q Consensus 401 sr~irlP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~--~tl~e~i~ 478 (488)
. .+++|+++.....++.++...+..++|+.||.+|||+.||+++++|..++..+....|||.+++++++ .++.|.+.
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 25667777
Q ss_pred CCC
Q 011324 479 LLS 481 (488)
Q Consensus 479 D~s 481 (488)
|+.
T Consensus 163 ~~~ 165 (231)
T TIGR02885 163 DKG 165 (231)
T ss_pred CCC
Confidence 763
No 23
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=99.94 E-value=6.8e-26 Score=223.90 Aligned_cols=152 Identities=28% Similarity=0.506 Sum_probs=139.4
Q ss_pred HHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCC-CHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHH
Q 011324 318 DLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGI-SLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK 395 (488)
Q Consensus 318 eLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~-d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~ 395 (488)
.++...+.|+ .++ .||+.|+|||.++|++|.+++. +.+||+|.|+|||++|+++|||++|.+|+|||..+|+++|++
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 3455566677 788 9999999999999999998887 999999999999999999999999999999999999999999
Q ss_pred HHHHhcCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhC--CCccccccCCCCCCC
Q 011324 396 AIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR--MPLSMQQPVWADQDT 471 (488)
Q Consensus 396 ~IRk~sr~irlP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar--~~lSLD~~i~~d~~~ 471 (488)
++|++. .+++|+.+.+..+++..+...|..++||.||.+|||+.|||+.++|...+.... ..+|+|..+..+++.
T Consensus 92 ~LR~~~-~v~vpR~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~d~ 168 (247)
T COG1191 92 YLRKND-SVKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDD 168 (247)
T ss_pred HHHhCC-CccCcHHHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhcccccc
Confidence 999999 999999999999999999999999999999999999999999999999988664 789999877654433
No 24
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=99.93 E-value=3.7e-25 Score=220.04 Aligned_cols=180 Identities=21% Similarity=0.303 Sum_probs=153.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHHHHHHHHHHHHH
Q 011324 264 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH 343 (488)
Q Consensus 264 i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~ArekLIesnlrLV~s 343 (488)
.+.+|+||.++|.+|+..++. .++..+++.|+..|.++|+.
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 378999999999999987653 12347999999999999999
Q ss_pred HHHHcc-C--CCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHHHHHHHHH
Q 011324 344 VAKQYQ-G--RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEA 420 (488)
Q Consensus 344 IAkry~-~--~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~e~l~kI~ka 420 (488)
+|++|. + .+.+++||+||||+|||+++++||+.+|++|+||+++||||.|.+++|+.. ++|+++.....++.++
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 6899999999999999
Q ss_pred HHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHh--CCCccccccCCCCC---CCccccccCCCC-CCCC
Q 011324 421 KRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQ---DTTFQVMPLLLS-HLPS 485 (488)
Q Consensus 421 ~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~a--r~~lSLD~~i~~d~---~~tl~e~i~D~s-~~pe 485 (488)
...|...+++.||.+|||+.+|++.+.|..++... ...+|||.++..++ ..++.+.++++. .+|+
T Consensus 124 ~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~l~~~~~~~~~~~pe 194 (268)
T PRK06288 124 IAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGDEVSLMDTLESPAALNPD 194 (268)
T ss_pred HHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhccCCCcccchhhhhccCCCCCCHH
Confidence 99999999999999999999999999999998754 45799999874222 245777776643 3443
No 25
>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=1.4e-24 Score=213.78 Aligned_cols=144 Identities=23% Similarity=0.364 Sum_probs=135.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc
Q 011324 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 406 (488)
Q Consensus 327 d~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irl 406 (488)
..|+++||..|.++|+++|++|.+++.+++||+||||+|||+++++||++.|.+|.||+++||+|.|.+++|++.+.+++
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 48999999999999999999999999999999999999999999999999999999999999999999999999989999
Q ss_pred chhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHh--CCCccccccCCCCCC
Q 011324 407 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQD 470 (488)
Q Consensus 407 P~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~a--r~~lSLD~~i~~d~~ 470 (488)
|.++.+...+++++...+...+|+.|+.+|||+.||++.+.+..++... ...+|||.+++.+++
T Consensus 108 ~~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~~~ 173 (255)
T TIGR02941 108 PRRIKELGPKIKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSD 173 (255)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCCCC
Confidence 9999999999999999999999999999999999999999999887654 467899999876544
No 26
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=99.93 E-value=9.1e-25 Score=211.07 Aligned_cols=153 Identities=25% Similarity=0.425 Sum_probs=139.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc
Q 011324 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 406 (488)
Q Consensus 327 d~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irl 406 (488)
..|++.||..|.++|+++|++|.+++.+++||+|||++|||+|+++||+.+|.+|+||+++||+|.|.++++++.+.+++
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 36899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCC--CccccccCCCCC--CCccccccCC
Q 011324 407 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRM--PLSMQQPVWADQ--DTTFQVMPLL 479 (488)
Q Consensus 407 P~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~--~lSLD~~i~~d~--~~tl~e~i~D 479 (488)
|.++...+.+++++...+.+.+++.|+.+|||+.||+++++|..++..... .+|||.++.+++ +.++.+.+.+
T Consensus 82 ~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~d~~~~ 158 (227)
T TIGR02980 82 PRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIEDDDGDPIALLDTLGD 158 (227)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCCCCCCCcccccccCC
Confidence 999999999999999999999999999999999999999999998886655 899999987332 2345555554
No 27
>PRK05572 sporulation sigma factor SigF; Validated
Probab=99.92 E-value=1.6e-23 Score=206.49 Aligned_cols=178 Identities=26% Similarity=0.382 Sum_probs=155.7
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHHHHHHHHHHH
Q 011324 262 WGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLV 341 (488)
Q Consensus 262 ~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~ArekLIesnlrLV 341 (488)
+.-+..|.||.+++.+|+..++. ++..|++.||..|.++|
T Consensus 6 ~~~~~~~~l~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~~~y~~~v 45 (252)
T PRK05572 6 KNKKKKPQLKDEENKELIKKSQD----------------------------------------GDQEARDTLVEKNLRLV 45 (252)
T ss_pred ccCcCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHH
Confidence 34467899999988877765432 23489999999999999
Q ss_pred HHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHHHHHHHHHH
Q 011324 342 VHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAK 421 (488)
Q Consensus 342 ~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~e~l~kI~ka~ 421 (488)
+++|++|.+++.+++||+||||+++|+++++|++.+|.+|.||+++||+|.|.+++|+.. .+++|..+.....+++++.
T Consensus 46 ~~~a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~~lr~~~-~~r~~~~~~~~~~~~~~~~ 124 (252)
T PRK05572 46 WSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANKIRKDK 124 (252)
T ss_pred HHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CCCCCHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999988889999999999999999999885 7899999999999999999
Q ss_pred HHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCC--CccccccCCC
Q 011324 422 RLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD--TTFQVMPLLL 480 (488)
Q Consensus 422 ~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~--~tl~e~i~D~ 480 (488)
..+..++++.|+..|||+.+|++++.|..++.......||+.++.+++. .++.|.+.++
T Consensus 125 ~~l~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~~ 185 (252)
T PRK05572 125 DELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGDPITLLDQIADQ 185 (252)
T ss_pred HHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCcccCCCCcchhhhhcCCC
Confidence 9998888999999999999999999999998888888999998865543 2345555554
No 28
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=99.91 E-value=1.4e-23 Score=206.61 Aligned_cols=161 Identities=22% Similarity=0.283 Sum_probs=139.7
Q ss_pred HHHHHHHh-hhcH-HHHHHHHHHHHHHHHHHHHHccC---CCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHH
Q 011324 316 CRDLKSEL-HSGN-SSREKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVR 390 (488)
Q Consensus 316 eeeLi~~l-~~Gd-~ArekLIesnlrLV~sIAkry~~---~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIR 390 (488)
+..|+.++ ..|+ .|++.||..|.++|+++|++|.+ ++.+.+||+||||+|||+++++||+.+|.+|+||+++||+
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 45666664 4445 89999999999999999999965 6889999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhcCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHH--HhCCCccccccCCCC
Q 011324 391 QTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF--ITRMPLSMQQPVWAD 468 (488)
Q Consensus 391 naI~~~IRk~sr~irlP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~--~ar~~lSLD~~i~~d 468 (488)
|.|++++|++. ++|..+.+.+.+++++...+.+.+|+.|+.+|||+.||+++++|+.++. .....+|||.++.++
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 345789999998655
Q ss_pred CCC-ccccccCC
Q 011324 469 QDT-TFQVMPLL 479 (488)
Q Consensus 469 ~~~-tl~e~i~D 479 (488)
++. .+.+.+.|
T Consensus 165 ~~~~~~~~~~~~ 176 (251)
T PRK07670 165 DDGENVSVTIRD 176 (251)
T ss_pred CCcchhhhhhcC
Confidence 432 33344433
No 29
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=99.91 E-value=7.2e-23 Score=201.96 Aligned_cols=143 Identities=24% Similarity=0.375 Sum_probs=133.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc
Q 011324 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 406 (488)
Q Consensus 327 d~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irl 406 (488)
..|++.||..|.++|+++|++|.+++.+++||+||||+|||+++++||+.+|.+|.||+++||+|.|.+++|++...+++
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 48999999999999999999999999999999999999999999999999888999999999999999999999999999
Q ss_pred chhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHh--CCCccccccCCCCC
Q 011324 407 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQ 469 (488)
Q Consensus 407 P~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~a--r~~lSLD~~i~~d~ 469 (488)
|+++.+..+++..+...+...+++.|+.+|+|+.+|++.+.|..++... ...+|+|.+++.++
T Consensus 108 ~r~~~~~~~~~~~~~~~~~~~~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~~ 172 (257)
T PRK08583 108 PRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADS 172 (257)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCCC
Confidence 9999999999999999998888999999999999999999998887654 46789999886544
No 30
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=99.90 E-value=5.9e-23 Score=200.86 Aligned_cols=139 Identities=22% Similarity=0.309 Sum_probs=124.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHccC---CCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCc
Q 011324 328 SSREKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 404 (488)
Q Consensus 328 ~ArekLIesnlrLV~sIAkry~~---~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~i 404 (488)
.....|+..|+++|.++|++|.+ .+.+.+||+|||+||||+|+++||+.+| +|+||++|||||+|.+++|+..
T Consensus 15 ~~~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~il~~lr~~~--- 90 (231)
T PRK12427 15 QEEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELRELD--- 90 (231)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHHHHhcC---
Confidence 34567899999999999999875 4679999999999999999999998665 8999999999999999999865
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH--hCCCccccccCCCCCC
Q 011324 405 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI--TRMPLSMQQPVWADQD 470 (488)
Q Consensus 405 rlP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~--ar~~lSLD~~i~~d~~ 470 (488)
+.|+.+....++++++...+.+.+|+.|+.+|||+.||+++++|..++.. +...+|||.+++++++
T Consensus 91 ~~~r~vr~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~ 158 (231)
T PRK12427 91 WRPRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALEAH 158 (231)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccCCCc
Confidence 57999999999999999999999999999999999999999999998764 4578999999876543
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=9.6e-23 Score=197.03 Aligned_cols=150 Identities=21% Similarity=0.327 Sum_probs=130.7
Q ss_pred HHHHHHHHHHHHHHHccC---CCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchh
Q 011324 333 LINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 409 (488)
Q Consensus 333 LIesnlrLV~sIAkry~~---~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~ 409 (488)
||..|.++|+++|++|.+ ++.+++||+||||+|||+++++||+.+|++|+||+++||+|.|++++|+.. ++|..
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 HHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHh--CCCccccccCCCC-CCCccccccCC-CCCCCC
Q 011324 410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWAD-QDTTFQVMPLL-LSHLPS 485 (488)
Q Consensus 410 v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~a--r~~lSLD~~i~~d-~~~tl~e~i~D-~s~~pe 485 (488)
+...++++.++...+...+|+.|+.+|||+.||++++.|..++..+ ...+|+|..+.++ +..++.+++++ ...+|+
T Consensus 78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (224)
T TIGR02479 78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLIDRIEDDKSEDPE 157 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcccCCCccchhhhhccccccCCHH
Confidence 9999999999999999999999999999999999999999998644 4568899876543 33466666663 333443
No 32
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=99.87 E-value=1.9e-21 Score=189.54 Aligned_cols=143 Identities=21% Similarity=0.389 Sum_probs=128.6
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHHcc---CCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhc
Q 011324 325 SGNSSREKLINANLRLVVHVAKQYQ---GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS 401 (488)
Q Consensus 325 ~Gd~ArekLIesnlrLV~sIAkry~---~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~s 401 (488)
.|.-+++.||..|.++|+.+|++|. +++.+++||+||||+|||+++++||+.+|.+|+||+++||+|.|.+++|++.
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 5667999999999999999999997 6789999999999999999999999999999999999999999999999976
Q ss_pred CCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHh--CCCccccccCCCCCC
Q 011324 402 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQD 470 (488)
Q Consensus 402 r~irlP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~a--r~~lSLD~~i~~d~~ 470 (488)
++|..+.....++.++...+.+.+++.|+.+|||+.||+++++|..++... ...+|++..++++++
T Consensus 85 ---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~~ 152 (236)
T PRK06986 85 ---WVPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGD 152 (236)
T ss_pred ---CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccccCCCc
Confidence 478888888888888888898899999999999999999999999988743 456789988766544
No 33
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=99.85 E-value=2.1e-20 Score=182.11 Aligned_cols=163 Identities=21% Similarity=0.342 Sum_probs=127.9
Q ss_pred HHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHHHHH
Q 011324 256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 335 (488)
Q Consensus 256 ~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~ArekLIe 335 (488)
.|..|+.+++..|+||+++|..|+..++. ++..|++.|+.
T Consensus 17 ~~~~~~~~~~~~~~~~~~~e~~l~~~~~~----------------------------------------gd~~a~~~l~~ 56 (233)
T PRK05803 17 FLVSYVKNNSFPQPLSEEEERKYLELMKE----------------------------------------GDEEARNILIE 56 (233)
T ss_pred HHHHHHHHhcccCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHH
Confidence 67889999999999999999887765443 23489999999
Q ss_pred HHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCc---cc------
Q 011324 336 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI---RL------ 406 (488)
Q Consensus 336 snlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~i---rl------ 406 (488)
.|.++|+++|.+|.+++.+++|++|||||+||+++++||+++|.+|.||+++|++|.|++++|+..+.. .+
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 -------------c------hhH-H--HHHHHHHHHHHHHH--------Hhc----CCCCcHHHHHHHhCCCHHHHHHHH
Q 011324 407 -------------P------ENI-Y--TLLSKVLEAKRLYI--------QEG----NHSPDKEDLARRVGITVEKLERLI 452 (488)
Q Consensus 407 -------------P------~~v-~--e~l~kI~ka~~~L~--------~el----gr~pS~eEIAe~LGIS~etVk~~L 452 (488)
+ ... . .....+.++...|+ ..+ ..+.|++|||+.||+|.++|+.++
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 0 000 0 11112333332221 112 357899999999999999999998
Q ss_pred HHhCCC
Q 011324 453 FITRMP 458 (488)
Q Consensus 453 ~~ar~~ 458 (488)
++|+..
T Consensus 217 ~rA~~k 222 (233)
T PRK05803 217 KRALKK 222 (233)
T ss_pred HHHHHH
Confidence 887654
No 34
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=99.77 E-value=7.4e-18 Score=163.83 Aligned_cols=141 Identities=25% Similarity=0.392 Sum_probs=108.9
Q ss_pred HHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHH
Q 011324 318 DLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKA 396 (488)
Q Consensus 318 eLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~ 396 (488)
.|+.+++.|+ .|++.|+..|.++|+.+|++|.+++.+++|++||+|+++|+++++|++..+++|.||++++++|.|+++
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 3444444555 899999999999999999999999999999999999999999999999888899999999999999999
Q ss_pred HHHhcCCcc---c--c--------------------h---hHH---HHHHHHHHHHHHHHH--------hc----CCCCc
Q 011324 397 IFQHSRTIR---L--P--------------------E---NIY---TLLSKVLEAKRLYIQ--------EG----NHSPD 433 (488)
Q Consensus 397 IRk~sr~ir---l--P--------------------~---~v~---e~l~kI~ka~~~L~~--------el----gr~pS 433 (488)
+|++.+... + + . ... .....+.+++..|+. .+ ..+.|
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 998654211 0 0 0 000 011123344433321 12 35889
Q ss_pred HHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324 434 KEDLARRVGITVEKLERLIFITRMP 458 (488)
Q Consensus 434 ~eEIAe~LGIS~etVk~~L~~ar~~ 458 (488)
++|||+.||+|+++|+..+++++..
T Consensus 201 ~~EIA~~lgis~~tVk~~~~rA~~~ 225 (234)
T PRK08301 201 QKEVADMLGISQSYISRLEKRIIKR 225 (234)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 9999999999999999999888654
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=99.77 E-value=9.1e-18 Score=163.19 Aligned_cols=140 Identities=24% Similarity=0.422 Sum_probs=107.1
Q ss_pred HHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHH
Q 011324 319 LKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI 397 (488)
Q Consensus 319 Li~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~I 397 (488)
|+.+++.|+ .|++.|+..|.++|+++|.+|.++..+++|++||+|+++|+++++|+++++.+|.||+++|++|.|++++
T Consensus 38 li~~~~~gd~~af~~l~~~y~~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~~d~~ 117 (227)
T TIGR02846 38 YLDRLKEGDEEARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEILMHL 117 (227)
T ss_pred HHHHHHcCCHHHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHHHHHH
Confidence 333334455 8999999999999999999999999999999999999999999999998888899999999999999999
Q ss_pred HHhcCCcc-c----------------------c-----hh---HHHHHHHHHHHHHHHH--------Hhc----CCCCcH
Q 011324 398 FQHSRTIR-L----------------------P-----EN---IYTLLSKVLEAKRLYI--------QEG----NHSPDK 434 (488)
Q Consensus 398 Rk~sr~ir-l----------------------P-----~~---v~e~l~kI~ka~~~L~--------~el----gr~pS~ 434 (488)
|+..+..+ . + .. ..+....+.+++..|. ..+ ..+.|+
T Consensus 118 Rk~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~il~l~y~~~~~e~~S~ 197 (227)
T TIGR02846 118 RALKKTKGEVSLQDPIGVDKEGNEISLIDILGSDGDSVIEQVELNLEIKKLYKKLSVLDGREREVIEMRYGLGDGRRKTQ 197 (227)
T ss_pred HHHhccccceeccccccCCcccCcccHHHHhcCCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHcCCCCCCcCH
Confidence 98754211 0 0 00 0011122333333322 122 257899
Q ss_pred HHHHHHhCCCHHHHHHHHHHhCCC
Q 011324 435 EDLARRVGITVEKLERLIFITRMP 458 (488)
Q Consensus 435 eEIAe~LGIS~etVk~~L~~ar~~ 458 (488)
+|||+.||+++++|+.++++++..
T Consensus 198 ~EIAe~lgis~~tV~~~~~rAl~~ 221 (227)
T TIGR02846 198 REIAKILGISRSYVSRIEKRALMK 221 (227)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHH
Confidence 999999999999999999887654
No 36
>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=99.76 E-value=1e-17 Score=163.43 Aligned_cols=129 Identities=19% Similarity=0.280 Sum_probs=111.1
Q ss_pred HhhhcHHHHHHHHHHHHHHHHHHHHHccCCC--CCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHH
Q 011324 322 ELHSGNSSREKLINANLRLVVHVAKQYQGRG--ISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQ 399 (488)
Q Consensus 322 ~l~~Gd~ArekLIesnlrLV~sIAkry~~~g--~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk 399 (488)
.++.|+..++.||..|.|+|.++|.+|.+++ .+.+|++|+|+||||+|+++||+++|.+|.|||.+||+++|++++|+
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 hc---CCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHH------hCCCHHHHHH
Q 011324 400 HS---RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARR------VGITVEKLER 450 (488)
Q Consensus 400 ~s---r~irlP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~------LGIS~etVk~ 450 (488)
.. ..+++|....+....+..+...+....++.++.+||+.. .||+.+.+-+
T Consensus 83 ~~k~~~~v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~~~~~L~~~gi~~~dLv~ 142 (218)
T TIGR02895 83 NQKYQNLLYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILEYKKLLKQFGIEFVELVK 142 (218)
T ss_pred cccccCeeeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcCCcHHHHhh
Confidence 87 456788766666667777777888888889999999853 4888776643
No 37
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=99.74 E-value=4.7e-17 Score=158.86 Aligned_cols=135 Identities=24% Similarity=0.379 Sum_probs=105.8
Q ss_pred hhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcC
Q 011324 324 HSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR 402 (488)
Q Consensus 324 ~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr 402 (488)
..|+ .|++.|+..|.+.|+.+|++|.+++.+++|++||+|+++|+++++|++..+++|.||++++++|.+++++|++.+
T Consensus 47 ~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~~d~~Rk~~r 126 (234)
T TIGR02835 47 TQGDESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEILMYLRRNNK 126 (234)
T ss_pred HcCCHHHHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence 3444 899999999999999999999999999999999999999999999998878889999999999999999998764
Q ss_pred Ccc-cc----------------------h-----hH---HHHHHHHHHHHHHHHH--------hc----CCCCcHHHHHH
Q 011324 403 TIR-LP----------------------E-----NI---YTLLSKVLEAKRLYIQ--------EG----NHSPDKEDLAR 439 (488)
Q Consensus 403 ~ir-lP----------------------~-----~v---~e~l~kI~ka~~~L~~--------el----gr~pS~eEIAe 439 (488)
... .+ . .. ......+.+++..|+. .+ ..+.|++|||+
T Consensus 127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~ 206 (234)
T TIGR02835 127 TRSEVSFDEPLNVDWDGNELLLSDVLGTDSDIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGTEKTQKEVAD 206 (234)
T ss_pred ccCcccccccccCCCCCCcchHHHhcCCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHH
Confidence 211 00 0 00 0011224444443321 12 25789999999
Q ss_pred HhCCCHHHHHHHHHHhCCC
Q 011324 440 RVGITVEKLERLIFITRMP 458 (488)
Q Consensus 440 ~LGIS~etVk~~L~~ar~~ 458 (488)
.||+|+++|+..+++++..
T Consensus 207 ~Lgis~~tV~~~l~ra~~~ 225 (234)
T TIGR02835 207 MLGISQSYISRLEKRILKR 225 (234)
T ss_pred HHCCCHHHHHHHHHHHHHH
Confidence 9999999999999887643
No 38
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=99.74 E-value=2.3e-17 Score=156.20 Aligned_cols=146 Identities=23% Similarity=0.284 Sum_probs=114.0
Q ss_pred cCCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHH
Q 011324 313 GLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ 391 (488)
Q Consensus 313 gm~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRn 391 (488)
.++++.|+..++.|+ .|++.|+..|.++|+.+|++|.+++.+++|++||+|++||+++.+||+.+|.+|.||++.+++|
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 8999999999999999999999999999999999999999999999998778999999999999
Q ss_pred HHHHHHHHhcCCccc--------------------------------chh-H--HHHH--------HHHHHHHHH-HHHh
Q 011324 392 TIRKAIFQHSRTIRL--------------------------------PEN-I--YTLL--------SKVLEAKRL-YIQE 427 (488)
Q Consensus 392 aI~~~IRk~sr~irl--------------------------------P~~-v--~e~l--------~kI~ka~~~-L~~e 427 (488)
.+.+++++..+..+. |.. + .+.. ..+....+. +..
T Consensus 88 ~~~d~~r~~~r~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~~r~vl~l- 166 (208)
T PRK08295 88 QIITAIKTANRQKHIPLNSYVSLDKPIYDEESDRTLLDVISEAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLEL- 166 (208)
T ss_pred HHHHHHHHhhhhccccccceeecCCcccCCccchhHHHHhcCcccCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHH-
Confidence 999999864332111 000 0 0011 111112122 222
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 428 GNHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 428 lgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
+..+.+++|||+.||+|+++|+..+++++..+
T Consensus 167 ~~e~~s~~EIA~~lgis~~tV~~~l~rar~~L 198 (208)
T PRK08295 167 YLDGKSYQEIAEELNRHVKSIDNALQRVKRKL 198 (208)
T ss_pred HHccCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 44578999999999999999999999887653
No 39
>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=99.74 E-value=2.6e-17 Score=154.50 Aligned_cols=146 Identities=23% Similarity=0.295 Sum_probs=113.3
Q ss_pred CCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011324 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (488)
Q Consensus 314 m~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRna 392 (488)
|++.+|+..++.|+ .|++.||..|.+.|+.+|+++.++..+++|++||+|+++|+++.+|++..+..|.||++.+|++.
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 56788899999988 89999999999999999999999999999999999999999999999987779999999999999
Q ss_pred HHHHHHHhcCCcc--------------------------------cchhH---HHHHHHHHHHHHH--------HHHhcC
Q 011324 393 IRKAIFQHSRTIR--------------------------------LPENI---YTLLSKVLEAKRL--------YIQEGN 429 (488)
Q Consensus 393 I~~~IRk~sr~ir--------------------------------lP~~v---~e~l~kI~ka~~~--------L~~elg 429 (488)
|++++++..+..+ -|... .+....+.+++.. +...+-
T Consensus 84 ~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~~~~~ 163 (198)
T TIGR02859 84 IITAIKTATRQKHIPLNSYVSLNKPIYDEESDRTLLDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVLQSYL 163 (198)
T ss_pred HHHHHHHHHHhcccchhhhcCcccccccccccchHHHHhhccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence 9888874311100 01100 0111122233332 222233
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
.+.|++|||+.||+|+++|+.++++++..+
T Consensus 164 ~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L 193 (198)
T TIGR02859 164 DGKSYQEIACDLNRHVKSIDNALQRVKRKL 193 (198)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 478999999999999999999999887653
No 40
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=99.72 E-value=7.3e-17 Score=150.93 Aligned_cols=145 Identities=17% Similarity=0.194 Sum_probs=114.6
Q ss_pred CCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011324 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (488)
Q Consensus 314 m~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRna 392 (488)
++++.|+..+..|+ .|++.|+..|.++|+.+|++|.+++.+++|++||+|++||+++.+|++. +.+|.+|++.+++|.
T Consensus 5 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n~ 83 (186)
T PRK05602 5 DPDEELLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLNL 83 (186)
T ss_pred ccHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHHH
Confidence 56778888888888 8999999999999999999999999999999999999999999999975 457999999999999
Q ss_pred HHHHHHHhcCCcc--c---------chh---HHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHH
Q 011324 393 IRKAIFQHSRTIR--L---------PEN---IYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLER 450 (488)
Q Consensus 393 I~~~IRk~sr~ir--l---------P~~---v~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~etVk~ 450 (488)
+.+++|++..... + |.. ..+....+.+++..|. ..+..+.+++|||+.||+|..+|+.
T Consensus 84 ~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~ 163 (186)
T PRK05602 84 CYDRLRRRREVPVEDAPDVPDPAPGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALES 163 (186)
T ss_pred HHHHHHhcCCCCcccccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHhcCCCHHHHHHHhCcCHHHHHH
Confidence 9999998764211 1 111 0011122333333322 2233478999999999999999999
Q ss_pred HHHHhCCCc
Q 011324 451 LIFITRMPL 459 (488)
Q Consensus 451 ~L~~ar~~l 459 (488)
.+++++..+
T Consensus 164 ~l~Rar~~L 172 (186)
T PRK05602 164 LLARGRRAL 172 (186)
T ss_pred HHHHHHHHH
Confidence 999987654
No 41
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=99.70 E-value=1.9e-16 Score=149.11 Aligned_cols=144 Identities=15% Similarity=0.196 Sum_probs=114.7
Q ss_pred CCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011324 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (488)
Q Consensus 314 m~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRna 392 (488)
++++.|+..+..|+ .|++.|+..|.+.|+++|+++.++..+++|++||+|+++|+++++|++. ..|.+|++++++|.
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 45788999999888 8999999999999999999999999999999999999999999999974 36999999999999
Q ss_pred HHHHHHHhcCCcccc-----------------hhH---HHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCC
Q 011324 393 IRKAIFQHSRTIRLP-----------------ENI---YTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGIT 444 (488)
Q Consensus 393 I~~~IRk~sr~irlP-----------------~~v---~e~l~kI~ka~~~L~~e--------lgr~pS~eEIAe~LGIS 444 (488)
+++++|+..+....+ ... .+....+.+++..|... +..+.|++|||+.||||
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 01122344444444322 22467999999999999
Q ss_pred HHHHHHHHHHhCCCc
Q 011324 445 VEKLERLIFITRMPL 459 (488)
Q Consensus 445 ~etVk~~L~~ar~~l 459 (488)
+++|+..+++|+..+
T Consensus 169 ~~tV~~~l~ra~~~L 183 (194)
T PRK12513 169 EETVKSRLRYALQKL 183 (194)
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999999887654
No 42
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=99.69 E-value=2.4e-16 Score=148.42 Aligned_cols=144 Identities=14% Similarity=0.220 Sum_probs=111.8
Q ss_pred CCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCC---CCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHH
Q 011324 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRG---ISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWV 389 (488)
Q Consensus 314 m~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g---~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wI 389 (488)
++++.|+..+..|+ .|++.|+..|.++|++++.++.+++ .+++|++||++++||+++++|++..+ .|.||++.++
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 57999999999999999999997544 7999999999
Q ss_pred HHHHHHHHHHhcCCcccc---h-------h-------------HHHHHHHHHHHHHHHH-HhcCCCCcHHHHHHHhCCCH
Q 011324 390 RQTIRKAIFQHSRTIRLP---E-------N-------------IYTLLSKVLEAKRLYI-QEGNHSPDKEDLARRVGITV 445 (488)
Q Consensus 390 RnaI~~~IRk~sr~irlP---~-------~-------------v~e~l~kI~ka~~~L~-~elgr~pS~eEIAe~LGIS~ 445 (488)
+|.+++++|++.+..... . . +...+.++....+.+. ..+..+.+++|||+.||+|.
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 0 0 1112222222222222 12234789999999999999
Q ss_pred HHHHHHHHHhCCC
Q 011324 446 EKLERLIFITRMP 458 (488)
Q Consensus 446 etVk~~L~~ar~~ 458 (488)
.+|+..+++++..
T Consensus 162 ~~V~~~l~Ra~~~ 174 (189)
T PRK06811 162 SAIDNRLSRGRKK 174 (189)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999988653
No 43
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=99.69 E-value=2.3e-16 Score=149.08 Aligned_cols=144 Identities=9% Similarity=0.069 Sum_probs=112.2
Q ss_pred CHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHH
Q 011324 315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 393 (488)
Q Consensus 315 ~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI 393 (488)
+...|+..+..|+ .+++.|+..|.++|+++|.+|.++..+++|++||+|+++|+++.+||+.+| .|.+|++.+++|.+
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 4567888888887 899999999999999999999999999999999999999999999998655 79999999999999
Q ss_pred HHHHHHhcCCccc---------c------hh---HHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHH
Q 011324 394 RKAIFQHSRTIRL---------P------EN---IYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEK 447 (488)
Q Consensus 394 ~~~IRk~sr~irl---------P------~~---v~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~et 447 (488)
++++|++.+..+. . .. ..+....+.+++..|. ..+..+.+++|||+.||+++++
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 0 00 0011122333333222 2233478999999999999999
Q ss_pred HHHHHHHhCCCc
Q 011324 448 LERLIFITRMPL 459 (488)
Q Consensus 448 Vk~~L~~ar~~l 459 (488)
|+..+++++..+
T Consensus 175 Vk~~l~ra~~~L 186 (194)
T PRK09646 175 VKTRMRDGLIRL 186 (194)
T ss_pred HHHHHHHHHHHH
Confidence 999999887543
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=99.68 E-value=4.5e-16 Score=143.25 Aligned_cols=144 Identities=15% Similarity=0.169 Sum_probs=113.8
Q ss_pred CCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011324 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (488)
Q Consensus 314 m~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRna 392 (488)
|++++|+..+..|+ .|++.|+..|.+.|++++.++.++..+++|++||+|+.+|+.+++|++. ..|.||++.+++|.
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 45678888888888 8999999999999999999999999999999999999999999999974 36999999999999
Q ss_pred HHHHHHHhcCCcccch-----------------hHHHHHHHHHHHHHHHH-HhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 393 IRKAIFQHSRTIRLPE-----------------NIYTLLSKVLEAKRLYI-QEGNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 393 I~~~IRk~sr~irlP~-----------------~v~e~l~kI~ka~~~L~-~elgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
+++++|+..+...++. .+...+.++....+++. ..+..+.+++|||+.||+|+++|+..+.+
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 9999998765332211 01122223322222222 22334789999999999999999999998
Q ss_pred hCCCc
Q 011324 455 TRMPL 459 (488)
Q Consensus 455 ar~~l 459 (488)
++..+
T Consensus 159 a~~~L 163 (169)
T TIGR02954 159 ALKKL 163 (169)
T ss_pred HHHHH
Confidence 87543
No 45
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=99.68 E-value=3.9e-16 Score=145.07 Aligned_cols=142 Identities=12% Similarity=0.178 Sum_probs=110.2
Q ss_pred HHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHH
Q 011324 316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR 394 (488)
Q Consensus 316 eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~ 394 (488)
++.|+..++.|+ .+++.|+..|.++|+.+|++|.+++.+++|++||+|+++|+++.+|++.. .|.+|++.+++|.+.
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 356777888888 89999999999999999999999999999999999999999999999865 599999999999999
Q ss_pred HHHHHhcCCcccc----------------------hhH-H--HHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHh
Q 011324 395 KAIFQHSRTIRLP----------------------ENI-Y--TLLSKVLEAKRLYI--------QEGNHSPDKEDLARRV 441 (488)
Q Consensus 395 ~~IRk~sr~irlP----------------------~~v-~--e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~L 441 (488)
+++|+..+..... ... . +....+.++...|+ ..+..+.+++|||+.|
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 9999865421100 000 0 01112333333322 1133478999999999
Q ss_pred CCCHHHHHHHHHHhCCCc
Q 011324 442 GITVEKLERLIFITRMPL 459 (488)
Q Consensus 442 GIS~etVk~~L~~ar~~l 459 (488)
|+++++|+..+++++..+
T Consensus 163 gis~~~v~~~l~Rar~~L 180 (187)
T TIGR02948 163 DLPVGTVKTRIHRGREAL 180 (187)
T ss_pred CCCHHHHHHHHHHHHHHH
Confidence 999999999999887543
No 46
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=99.67 E-value=5e-16 Score=144.87 Aligned_cols=145 Identities=14% Similarity=0.126 Sum_probs=112.7
Q ss_pred CCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011324 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (488)
Q Consensus 314 m~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRna 392 (488)
+++.+|+..+..|+ .|++.|+..|.+.|+.++++|.+++.+++|++||+|+++|+++++|++.. ..|.+|++++++|.
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 46778888888888 89999999999999999999999999999999999999999999998754 36999999999999
Q ss_pred HHHHHHHhcCCcc-c------------c-----hhHHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHH
Q 011324 393 IRKAIFQHSRTIR-L------------P-----ENIYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVE 446 (488)
Q Consensus 393 I~~~IRk~sr~ir-l------------P-----~~v~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~e 446 (488)
+++++|+..+... + + .........+.+++..|. ..+..+.+++|||+.||||++
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 000011112333333332 123347899999999999999
Q ss_pred HHHHHHHHhCCCc
Q 011324 447 KLERLIFITRMPL 459 (488)
Q Consensus 447 tVk~~L~~ar~~l 459 (488)
+|+..+++++..+
T Consensus 167 ~V~~~l~ra~~~L 179 (186)
T PRK13919 167 TLKTRARRALSRL 179 (186)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999887543
No 47
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=99.67 E-value=6e-16 Score=145.40 Aligned_cols=145 Identities=13% Similarity=0.087 Sum_probs=114.5
Q ss_pred hcCCHHHHHHHhhh---cH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHH
Q 011324 312 IGLSCRDLKSELHS---GN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYW 387 (488)
Q Consensus 312 ~gm~eeeLi~~l~~---Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~ 387 (488)
..++++.|+..++. |+ .|++.|+..|.+.|+.+|.+|.++..+++|++||+|++||+++++|++. ..|.+|+++
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 35778888888875 35 8999999999999999999999999999999999999999999999863 479999999
Q ss_pred HHHHHHHHHHHHhcCCcccch------------h---HHHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCC
Q 011324 388 WVRQTIRKAIFQHSRTIRLPE------------N---IYTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGIT 444 (488)
Q Consensus 388 wIRnaI~~~IRk~sr~irlP~------------~---v~e~l~kI~ka~~~L~~e--------lgr~pS~eEIAe~LGIS 444 (488)
+++|.+++++|+..+...... . ..+....+.++...|+.. +..+.+++|||+.||||
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 999999999997654222110 0 011223345555555432 22367999999999999
Q ss_pred HHHHHHHHHHhCCC
Q 011324 445 VEKLERLIFITRMP 458 (488)
Q Consensus 445 ~etVk~~L~~ar~~ 458 (488)
.++|+..+.+|+..
T Consensus 164 ~~tV~~~l~Ra~~~ 177 (188)
T PRK09640 164 LSATKMRYKRALDK 177 (188)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999988754
No 48
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=99.67 E-value=7.4e-16 Score=144.51 Aligned_cols=141 Identities=18% Similarity=0.213 Sum_probs=108.6
Q ss_pred HHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCC----CCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHH
Q 011324 317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGR----GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ 391 (488)
Q Consensus 317 eeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~----g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRn 391 (488)
..|+..+..|+ .|++.|+..|.+.|+++|.++.++ +.+++|++||+|++||+++.+|+.. +..|.+|++.+++|
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 45788888887 899999999999999999998764 4689999999999999999999864 45799999999999
Q ss_pred HHHHHHHHhcCCcccc--------------hh---HHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHH
Q 011324 392 TIRKAIFQHSRTIRLP--------------EN---IYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVE 446 (488)
Q Consensus 392 aI~~~IRk~sr~irlP--------------~~---v~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~e 446 (488)
.+++++|++.+....+ .. ..+....+.+++..|+ ..+..+.+++|||+.||+|++
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 00 0111122333333322 223347899999999999999
Q ss_pred HHHHHHHHhCCC
Q 011324 447 KLERLIFITRMP 458 (488)
Q Consensus 447 tVk~~L~~ar~~ 458 (488)
+|+..+++++..
T Consensus 171 tV~~~l~Ra~~~ 182 (189)
T PRK09648 171 AVRVAQHRALAR 182 (189)
T ss_pred HHHHHHHHHHHH
Confidence 999999988654
No 49
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=99.67 E-value=6.2e-16 Score=143.64 Aligned_cols=145 Identities=10% Similarity=0.060 Sum_probs=111.6
Q ss_pred CCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011324 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (488)
Q Consensus 314 m~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRna 392 (488)
++...|+..+..|+ .+++.|+..|.+.|+.+|.++.++..+++|++||+|+++|+++++|++.. ..|.||++.+++|.
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 34567777777787 89999999999999999999999999999999999999999999998653 46999999999999
Q ss_pred HHHHHHHhcCCcc-c------------chhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHH
Q 011324 393 IRKAIFQHSRTIR-L------------PENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKL 448 (488)
Q Consensus 393 I~~~IRk~sr~ir-l------------P~~v---~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~etV 448 (488)
|++++|++.+... + |... .+....+..++..|. ..+..+.|++|||+.||||+++|
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 1100 011112333333322 22334789999999999999999
Q ss_pred HHHHHHhCCCc
Q 011324 449 ERLIFITRMPL 459 (488)
Q Consensus 449 k~~L~~ar~~l 459 (488)
+..+++++..+
T Consensus 163 ~~~l~Rar~~L 173 (179)
T PRK12514 163 RTWLRRSLLKL 173 (179)
T ss_pred HHHHHHHHHHH
Confidence 99999987543
No 50
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=99.67 E-value=6.2e-16 Score=144.58 Aligned_cols=144 Identities=11% Similarity=0.163 Sum_probs=113.3
Q ss_pred CCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011324 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (488)
Q Consensus 314 m~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRna 392 (488)
++..+|+..+..|+ .|++.|+..|.+.|+.+++++.++..+++|++||+|+.+|+.+++|++.. ..|.+|++.+++|.
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 45667888888888 89999999999999999999999999999999999999999999998643 37999999999999
Q ss_pred HHHHHHHhcCCcccch-------------h---HHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHH
Q 011324 393 IRKAIFQHSRTIRLPE-------------N---IYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKL 448 (488)
Q Consensus 393 I~~~IRk~sr~irlP~-------------~---v~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~etV 448 (488)
+++++|++.+...... . ..+....+.++...|+ .....+.+++|||+.||||+++|
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 9999999865322110 0 0011222333333322 22334789999999999999999
Q ss_pred HHHHHHhCCC
Q 011324 449 ERLIFITRMP 458 (488)
Q Consensus 449 k~~L~~ar~~ 458 (488)
+..+++++..
T Consensus 167 ~~~l~ra~~~ 176 (182)
T PRK12537 167 KAWIKRSLKA 176 (182)
T ss_pred HHHHHHHHHH
Confidence 9999988754
No 51
>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=99.66 E-value=9.6e-16 Score=140.13 Aligned_cols=138 Identities=15% Similarity=0.149 Sum_probs=106.8
Q ss_pred HHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHH
Q 011324 320 KSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIF 398 (488)
Q Consensus 320 i~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IR 398 (488)
+.++.+|+ .|++.|+..|.+.+++++.++.++..+++|++||+|+++|+++++|+...+ .|.+|++.+++|.+++++|
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 899999999999999999999988899999999999999999999986544 8999999999999999999
Q ss_pred HhcCCcccc--------------hhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHH
Q 011324 399 QHSRTIRLP--------------ENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIF 453 (488)
Q Consensus 399 k~sr~irlP--------------~~v---~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~etVk~~L~ 453 (488)
++.+....+ ... .+....+.++...|+ ..+..+.+++|||+.||||+++|+..++
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 876433221 000 011122333333222 2233478999999999999999999999
Q ss_pred HhCCC
Q 011324 454 ITRMP 458 (488)
Q Consensus 454 ~ar~~ 458 (488)
+++..
T Consensus 161 ra~~~ 165 (170)
T TIGR02952 161 RAIKK 165 (170)
T ss_pred HHHHH
Confidence 88654
No 52
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=99.66 E-value=8.8e-16 Score=145.33 Aligned_cols=146 Identities=18% Similarity=0.172 Sum_probs=114.5
Q ss_pred cCCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHH
Q 011324 313 GLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ 391 (488)
Q Consensus 313 gm~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRn 391 (488)
.+++..|+.++..|+ .|++.|+..|.+.|+.+|.++.++..+++|++||+++++|+.+.+|++. ...|.||++.+++|
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----------c--hhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHH
Q 011324 392 TIRKAIFQHSRTI-RL----------P--ENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEK 447 (488)
Q Consensus 392 aI~~~IRk~sr~i-rl----------P--~~v---~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~et 447 (488)
.+++++|++.+.. .+ + ... .+....+.+++..|+ ..+..+.+++|||+.||+|..+
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 9999999865421 10 0 010 011122333333322 2233578999999999999999
Q ss_pred HHHHHHHhCCCc
Q 011324 448 LERLIFITRMPL 459 (488)
Q Consensus 448 Vk~~L~~ar~~l 459 (488)
|+..+++|+..+
T Consensus 169 V~~~l~Ra~~~L 180 (196)
T PRK12524 169 VESLTARGKRAL 180 (196)
T ss_pred HHHHHHHHHHHH
Confidence 999999988654
No 53
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=99.66 E-value=1.2e-15 Score=137.76 Aligned_cols=130 Identities=16% Similarity=0.181 Sum_probs=100.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC----
Q 011324 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT---- 403 (488)
Q Consensus 328 ~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~---- 403 (488)
.|++.|+..|.++|+.+++++ +...+++|++|||++++|+++++|++..| .|.+|++.+++|.+++++|++.+.
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 56679999999999999999999997666 799999999999999999987421
Q ss_pred --cccchh----------HHHHHHHHHHHHHHH-HHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 404 --IRLPEN----------IYTLLSKVLEAKRLY-IQEGNHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 404 --irlP~~----------v~e~l~kI~ka~~~L-~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
...|.. +...+.++....+.+ ...+..+.|++|||+.||+|+++|+.++.+++..+
T Consensus 82 ~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~ii~l~~~~~~s~~EIA~~l~is~~tV~~~~~ra~~~L 150 (154)
T PRK06759 82 VCVGEYEDHFHFEDVEMKVKDFMSVLDEKEKYIIFERFFVGKTMGEIALETEMTYYQVRWIYRQALEKM 150 (154)
T ss_pred cccCCCcccccHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 111211 122222332222222 23344578999999999999999999999886543
No 54
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=99.65 E-value=1.3e-15 Score=141.63 Aligned_cols=143 Identities=13% Similarity=0.192 Sum_probs=111.2
Q ss_pred CHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHH
Q 011324 315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 393 (488)
Q Consensus 315 ~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI 393 (488)
..+.|+..++.|+ .+++.|+..|.++|+++|+++.++..+++|++||+|++||+++.+|++.. +|.+|++.+++|.+
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 3567788888888 89999999999999999999999999999999999999999999999753 69999999999999
Q ss_pred HHHHHHhcCCccc----------------------chh---HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHH
Q 011324 394 RKAIFQHSRTIRL----------------------PEN---IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARR 440 (488)
Q Consensus 394 ~~~IRk~sr~irl----------------------P~~---v~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~ 440 (488)
++++|+..+.... |.. ..+....+.++...|+. .+..+.+++|||+.
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 000 00111223333333321 12347799999999
Q ss_pred hCCCHHHHHHHHHHhCCCc
Q 011324 441 VGITVEKLERLIFITRMPL 459 (488)
Q Consensus 441 LGIS~etVk~~L~~ar~~l 459 (488)
||||+++|+..+++++..+
T Consensus 162 lgis~~~v~~~l~Rar~~L 180 (187)
T PRK09641 162 LDLPVGTVKTRIHRGREAL 180 (187)
T ss_pred HCCCHHHHHHHHHHHHHHH
Confidence 9999999999999887543
No 55
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=99.65 E-value=1.9e-15 Score=139.63 Aligned_cols=144 Identities=13% Similarity=0.141 Sum_probs=113.4
Q ss_pred CCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011324 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (488)
Q Consensus 314 m~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRna 392 (488)
|++..++..+..|+ .|++.|+..|.+.|+.+|++|.++..+++|++||+|+++|+++++|++. .+|.+|++.+++|.
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 56777888888888 8999999999999999999999999999999999999999999999864 47999999999999
Q ss_pred HHHHHHHhcCCcccch------------h---HHHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHH
Q 011324 393 IRKAIFQHSRTIRLPE------------N---IYTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLE 449 (488)
Q Consensus 393 I~~~IRk~sr~irlP~------------~---v~e~l~kI~ka~~~L~~e--------lgr~pS~eEIAe~LGIS~etVk 449 (488)
+++++|+..+...... . .......+.+....|+.. +..+.+++|||+.||+++.+|+
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 9999998764322110 0 011222333444433322 2246799999999999999999
Q ss_pred HHHHHhCCCc
Q 011324 450 RLIFITRMPL 459 (488)
Q Consensus 450 ~~L~~ar~~l 459 (488)
..+.+++..+
T Consensus 161 ~~l~ra~~~l 170 (176)
T PRK09638 161 SRVHHGIKQL 170 (176)
T ss_pred HHHHHHHHHH
Confidence 9999887543
No 56
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=99.65 E-value=2.1e-15 Score=142.60 Aligned_cols=144 Identities=16% Similarity=0.120 Sum_probs=113.9
Q ss_pred CCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011324 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (488)
Q Consensus 314 m~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRna 392 (488)
+++..++..+..|+ .+++.|+..|.+.|++++.++.++..+++|++||+|+.+|+++++|+.. ..|.+|++.+++|.
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 46778888888888 8999999999999999999999999999999999999999999999964 36999999999999
Q ss_pred HHHHHHHhcCCcccc-----------hh---HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHH
Q 011324 393 IRKAIFQHSRTIRLP-----------EN---IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLER 450 (488)
Q Consensus 393 I~~~IRk~sr~irlP-----------~~---v~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~ 450 (488)
+++++|+..+....+ .. ..+....+.+++..|+. .+..+.+++|||+.||++..+|+.
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 999999875432211 00 01112233333333322 233478999999999999999999
Q ss_pred HHHHhCCCc
Q 011324 451 LIFITRMPL 459 (488)
Q Consensus 451 ~L~~ar~~l 459 (488)
.+++++..+
T Consensus 170 rl~rar~~L 178 (192)
T PRK09643 170 RCARGRARL 178 (192)
T ss_pred HHHHHHHHH
Confidence 999987654
No 57
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=99.64 E-value=1.5e-15 Score=139.26 Aligned_cols=136 Identities=20% Similarity=0.260 Sum_probs=104.4
Q ss_pred HhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHh
Q 011324 322 ELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH 400 (488)
Q Consensus 322 ~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~ 400 (488)
+++.|+ .|++.|+..|.++|+.++++|.+++.+.+|++||++++||+++.+|+ .+.+|.+|++.++++.+.+++|+.
T Consensus 3 ~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~r~~ 80 (182)
T PRK09652 3 RVQRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR--GGAAFYTWLYRIARNTAINYLRKQ 80 (182)
T ss_pred hhhcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHHHHHHHHcc
Confidence 345666 89999999999999999999999999999999999999999999999 356899999999999999999986
Q ss_pred cCCcccc----------------------hhHH---HHHHHHHHHHHHH-------H-HhcCCCCcHHHHHHHhCCCHHH
Q 011324 401 SRTIRLP----------------------ENIY---TLLSKVLEAKRLY-------I-QEGNHSPDKEDLARRVGITVEK 447 (488)
Q Consensus 401 sr~irlP----------------------~~v~---e~l~kI~ka~~~L-------~-~elgr~pS~eEIAe~LGIS~et 447 (488)
.+....+ .... .....+..+...| . ..+..+.+++|||+.||+|+.+
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~t 160 (182)
T PRK09652 81 GRRPPASDVDAEEAEDFDLADALRDISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGT 160 (182)
T ss_pred cCCCCccccccccccccccccccccccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHH
Confidence 5432211 0000 1122222222222 1 2233478999999999999999
Q ss_pred HHHHHHHhCCCc
Q 011324 448 LERLIFITRMPL 459 (488)
Q Consensus 448 Vk~~L~~ar~~l 459 (488)
|+..+++++..+
T Consensus 161 V~~~l~ra~~~L 172 (182)
T PRK09652 161 VRSRIFRAREAL 172 (182)
T ss_pred HHHHHHHHHHHH
Confidence 999998876543
No 58
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=99.63 E-value=1.7e-15 Score=141.55 Aligned_cols=143 Identities=13% Similarity=0.073 Sum_probs=110.9
Q ss_pred HHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHH
Q 011324 316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR 394 (488)
Q Consensus 316 eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~ 394 (488)
...++..+..|+ .+++.|+..|.++|+.+|++|.++..+++|++||+|+++|+++++|++.++ .|.||++.+++|.++
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 899999999999999999999999999999999999999999999997644 689999999999999
Q ss_pred HHHHHhcCCcc------c---------chh---HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHH
Q 011324 395 KAIFQHSRTIR------L---------PEN---IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKL 448 (488)
Q Consensus 395 ~~IRk~sr~ir------l---------P~~---v~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etV 448 (488)
+++|+..+... . |.. ..+....+..++..|+. .+..+.+++|||+.||+|+++|
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 11122334444433322 2334789999999999999999
Q ss_pred HHHHHHhCCCc
Q 011324 449 ERLIFITRMPL 459 (488)
Q Consensus 449 k~~L~~ar~~l 459 (488)
+..+++++..+
T Consensus 171 ~~~l~Rar~~L 181 (187)
T PRK12534 171 KSWIRRGLAKL 181 (187)
T ss_pred HHHHHHHHHHH
Confidence 99999987643
No 59
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=99.63 E-value=2.3e-15 Score=147.69 Aligned_cols=145 Identities=14% Similarity=0.174 Sum_probs=113.2
Q ss_pred CCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011324 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (488)
Q Consensus 314 m~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRna 392 (488)
.++..|+..+..|+ .+++.|+..|.+.|+.+++++.++..+++|++||+|+++|+.+++|++..+ .|.+|++.+++|.
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 45678888888888 899999999999999999999999999999999999999999999986444 7999999999999
Q ss_pred HHHHHHHhcCCcc---------cch--h-H--HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHH
Q 011324 393 IRKAIFQHSRTIR---------LPE--N-I--YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLER 450 (488)
Q Consensus 393 I~~~IRk~sr~ir---------lP~--~-v--~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~ 450 (488)
+++++|++.+... .+. . + .+....+.+++..|+. .+..+.+++|||+.||+|+++|+.
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 1111223333333322 233478999999999999999999
Q ss_pred HHHHhCCCc
Q 011324 451 LIFITRMPL 459 (488)
Q Consensus 451 ~L~~ar~~l 459 (488)
.+++++..+
T Consensus 207 ~l~RAr~kL 215 (233)
T PRK12538 207 LLKRGRQQL 215 (233)
T ss_pred HHHHHHHHH
Confidence 999987654
No 60
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=99.63 E-value=3e-15 Score=143.23 Aligned_cols=140 Identities=12% Similarity=0.125 Sum_probs=107.0
Q ss_pred HHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHH
Q 011324 319 LKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI 397 (488)
Q Consensus 319 Li~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~I 397 (488)
|+..+..|+ .+++.|+..|.+.|+.++.++.++..+++|++||+|+++|+++.+|++.++ .|.||++.+++|.+++++
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 445556566 899999999999999999999999899999999999999999999997655 599999999999999999
Q ss_pred HHhcCCccc-------c------------hhHHH--HHHHHHHHHHHH--------HHhcCCCCcHHHHHHHhCCCHHHH
Q 011324 398 FQHSRTIRL-------P------------ENIYT--LLSKVLEAKRLY--------IQEGNHSPDKEDLARRVGITVEKL 448 (488)
Q Consensus 398 Rk~sr~irl-------P------------~~v~e--~l~kI~ka~~~L--------~~elgr~pS~eEIAe~LGIS~etV 448 (488)
|++.+.... + ..... ....+.+++..| ...+..+.+++|||+.||+|+++|
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 011233333322 222334789999999999999999
Q ss_pred HHHHHHhCCCc
Q 011324 449 ERLIFITRMPL 459 (488)
Q Consensus 449 k~~L~~ar~~l 459 (488)
+..+++++..+
T Consensus 187 ~~~l~Ra~~~L 197 (206)
T PRK12526 187 KSRLRLALAKL 197 (206)
T ss_pred HHHHHHHHHHH
Confidence 99999887654
No 61
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=99.63 E-value=2.1e-15 Score=142.54 Aligned_cols=142 Identities=11% Similarity=0.091 Sum_probs=109.3
Q ss_pred HHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHH
Q 011324 317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK 395 (488)
Q Consensus 317 eeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~ 395 (488)
.+|+..+..|+ .+++.|+..|.+.|+.+|.++.++..+++|++||+|+.+|+.+.+|++.++ .|.+|++.+++|.+++
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 45777888888 899999999999999999999999899999999999999999999987544 7999999999999999
Q ss_pred HHHHhcCCc-cc------ch-----------hHH--HHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHH
Q 011324 396 AIFQHSRTI-RL------PE-----------NIY--TLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEK 447 (488)
Q Consensus 396 ~IRk~sr~i-rl------P~-----------~v~--e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~et 447 (488)
++|+..+.. .. +. ... .....+.+++..|+. .+-.+.+++|||+.||||+++
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 999865321 10 00 000 011223333333221 233478999999999999999
Q ss_pred HHHHHHHhCCCc
Q 011324 448 LERLIFITRMPL 459 (488)
Q Consensus 448 Vk~~L~~ar~~l 459 (488)
|+..+++++..+
T Consensus 174 Vk~rl~ra~~~L 185 (194)
T PRK12531 174 VKSRLRLAVEKL 185 (194)
T ss_pred HHHHHHHHHHHH
Confidence 999999887543
No 62
>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=99.63 E-value=3.1e-15 Score=139.38 Aligned_cols=144 Identities=19% Similarity=0.260 Sum_probs=111.6
Q ss_pred CCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011324 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (488)
Q Consensus 314 m~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRna 392 (488)
.++..|+..+..|+ .+++.|+..|.+.|+.+|+++.++..+++|++||+|+++|+++.+|++. ..|.+|++.+++|.
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 35667888888888 8999999999999999999999999999999999999999999999974 36999999999999
Q ss_pred HHHHHHHhcCCccc----------------------chhH---HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHH
Q 011324 393 IRKAIFQHSRTIRL----------------------PENI---YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLAR 439 (488)
Q Consensus 393 I~~~IRk~sr~irl----------------------P~~v---~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe 439 (488)
+++++++..+.... |... .+....+.++...|+. .+..+.+++|||+
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 1234679999999
Q ss_pred HhCCCHHHHHHHHHHhCCCc
Q 011324 440 RVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 440 ~LGIS~etVk~~L~~ar~~l 459 (488)
.|||++++|+..+++++..+
T Consensus 163 ~lgis~~tv~~~l~rar~~L 182 (190)
T TIGR02939 163 IMDCPVGTVRSRIFRAREAI 182 (190)
T ss_pred HHCcCHHHHHHHHHHHHHHH
Confidence 99999999999999987643
No 63
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=99.63 E-value=2.6e-15 Score=141.13 Aligned_cols=142 Identities=20% Similarity=0.218 Sum_probs=109.7
Q ss_pred CHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHH
Q 011324 315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 393 (488)
Q Consensus 315 ~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI 393 (488)
++.+|+..+..|+ .+++.|+..|.+.|+.+++++.++..+++|++||+|+++|+. ..|++.++ .|.||++.+++|.+
T Consensus 15 ~~~~l~~~~~~gd~~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn~~ 92 (194)
T PRK12519 15 SDAELFSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRSRA 92 (194)
T ss_pred cHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHHHH
Confidence 4577888888888 899999999999999999999999999999999999999976 67886554 79999999999999
Q ss_pred HHHHHHhcCCcccc----------------h-h--HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHH
Q 011324 394 RKAIFQHSRTIRLP----------------E-N--IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVE 446 (488)
Q Consensus 394 ~~~IRk~sr~irlP----------------~-~--v~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~e 446 (488)
++++|++.+..... . . ..+....+..++..|.. .+..+.+++|||+.||+|+.
T Consensus 93 ~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~~~g~s~~EIA~~lgis~~ 172 (194)
T PRK12519 93 IDRLRSRRSRQRLLERWQQELLGEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLG 172 (194)
T ss_pred HHHHHhcccccchhhhhhhhhcccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhhhcCCCHHHHHHHhCCCHH
Confidence 99999875421110 0 0 00111223333333322 12347899999999999999
Q ss_pred HHHHHHHHhCCC
Q 011324 447 KLERLIFITRMP 458 (488)
Q Consensus 447 tVk~~L~~ar~~ 458 (488)
+|+..+++++..
T Consensus 173 tV~~~l~Ra~~~ 184 (194)
T PRK12519 173 TVKARARQGLLK 184 (194)
T ss_pred HHHHHHHHHHHH
Confidence 999999988654
No 64
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=99.62 E-value=4.7e-15 Score=139.31 Aligned_cols=143 Identities=15% Similarity=0.215 Sum_probs=110.2
Q ss_pred CHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHH
Q 011324 315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 393 (488)
Q Consensus 315 ~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI 393 (488)
+++.|+..++.|+ .+++.|+..|.+.|+.+++++.++..+++|++||+|+++|+++.+|++.. .|.+|++.+++|.+
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 3567788888887 89999999999999999999999989999999999999999999999864 49999999999999
Q ss_pred HHHHHHhcCCcc---c-------------------chh---HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHH
Q 011324 394 RKAIFQHSRTIR---L-------------------PEN---IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARR 440 (488)
Q Consensus 394 ~~~IRk~sr~ir---l-------------------P~~---v~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~ 440 (488)
++++|++.+... . |.. ..+....+.++...|+. .+-.+.+++|||+.
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 0 000 00011123333332222 12346799999999
Q ss_pred hCCCHHHHHHHHHHhCCCc
Q 011324 441 VGITVEKLERLIFITRMPL 459 (488)
Q Consensus 441 LGIS~etVk~~L~~ar~~l 459 (488)
||+|+++|+..+.+++..|
T Consensus 164 lgis~~tv~~~l~Rar~~L 182 (193)
T PRK11923 164 MQCPVGTVRSRIFRAREAI 182 (193)
T ss_pred HCCCHHHHHHHHHHHHHHH
Confidence 9999999999999887543
No 65
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=99.62 E-value=4.3e-15 Score=144.72 Aligned_cols=143 Identities=15% Similarity=0.193 Sum_probs=113.2
Q ss_pred CCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011324 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (488)
Q Consensus 314 m~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRna 392 (488)
++++.|+..+..|+ .|++.|+..|.+.|+++|+++.+.+.+++|++||+|++||+++++|++. ..|.+|++.+++|.
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 45667888887777 8999999999999999999999999999999999999999999999975 47999999999999
Q ss_pred HHHHHHHhcCCcccch-----------------------h---HHHHHHHHHHHHHHHHHh--------cCCCCcHHHHH
Q 011324 393 IRKAIFQHSRTIRLPE-----------------------N---IYTLLSKVLEAKRLYIQE--------GNHSPDKEDLA 438 (488)
Q Consensus 393 I~~~IRk~sr~irlP~-----------------------~---v~e~l~kI~ka~~~L~~e--------lgr~pS~eEIA 438 (488)
+++++|+..+....+. . ..+....+.+++..|... +..+.+++|||
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 011122344444443322 22467999999
Q ss_pred HHhCCCHHHHHHHHHHhCCC
Q 011324 439 RRVGITVEKLERLIFITRMP 458 (488)
Q Consensus 439 e~LGIS~etVk~~L~~ar~~ 458 (488)
+.||+|.++|+..+++++..
T Consensus 173 e~lgis~~tVk~~l~Rar~k 192 (231)
T PRK11922 173 QALGLPEETVKTRLHRARRL 192 (231)
T ss_pred HHHCcCHHHHHHHHHHHHHH
Confidence 99999999999999988754
No 66
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=99.61 E-value=8e-15 Score=136.96 Aligned_cols=142 Identities=10% Similarity=0.046 Sum_probs=108.4
Q ss_pred HHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccC-CCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHH
Q 011324 316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQG-RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 393 (488)
Q Consensus 316 eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~-~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI 393 (488)
...++..+..|+ .|++.|+..|.+.|+.++.++.+ ...+++|++||+|++||+.++.|++. ..|.+|++.+++|.+
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 345777777777 89999999999999999988764 57899999999999999999999974 469999999999999
Q ss_pred HHHHHHhcCCcccc--------------hhHHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHH
Q 011324 394 RKAIFQHSRTIRLP--------------ENIYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERL 451 (488)
Q Consensus 394 ~~~IRk~sr~irlP--------------~~v~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~etVk~~ 451 (488)
++++|+..+..... ....+....+.+++..|+ ..+-.+.+++|||+.||||+++|+..
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 99999965421100 011112222334443332 12234789999999999999999999
Q ss_pred HHHhCCCc
Q 011324 452 IFITRMPL 459 (488)
Q Consensus 452 L~~ar~~l 459 (488)
+++++..+
T Consensus 166 l~rar~~L 173 (181)
T PRK12536 166 IHRGLKAL 173 (181)
T ss_pred HHHHHHHH
Confidence 99887543
No 67
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=99.61 E-value=8.3e-15 Score=137.22 Aligned_cols=141 Identities=11% Similarity=0.125 Sum_probs=108.7
Q ss_pred HHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHH----HccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHH
Q 011324 316 CRDLKSELHSGN-SSREKLINANLRLVVHVAK----QYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVR 390 (488)
Q Consensus 316 eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAk----ry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIR 390 (488)
...|+..+..|+ .|++.|+..|.+.|+.+|+ ++.++..+++|++||+|+.+|+.+..|++.. .|.+|++.+++
T Consensus 8 ~~~l~~~~~~gd~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~--~f~~wl~~i~~ 85 (184)
T PRK12539 8 LKALMLASLDGDAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTPWVYAIAR 85 (184)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCCC--ChHHHHHHHHH
Confidence 566777888887 8999999999999999986 4557889999999999999999999999753 69999999999
Q ss_pred HHHHHHHHHhcCCc-ccc---------h---hHHHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHH
Q 011324 391 QTIRKAIFQHSRTI-RLP---------E---NIYTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLE 449 (488)
Q Consensus 391 naI~~~IRk~sr~i-rlP---------~---~v~e~l~kI~ka~~~L~~e--------lgr~pS~eEIAe~LGIS~etVk 449 (488)
|.+++++|+..+.. ..+ . ...+....+..+...|+.. +..+.+++|||+.||+|+++|+
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 99999999865421 111 0 0112223344444333221 2247899999999999999999
Q ss_pred HHHHHhCCC
Q 011324 450 RLIFITRMP 458 (488)
Q Consensus 450 ~~L~~ar~~ 458 (488)
..+++++..
T Consensus 166 ~~l~ra~~~ 174 (184)
T PRK12539 166 VSVHRGLKA 174 (184)
T ss_pred HHHHHHHHH
Confidence 999988754
No 68
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=99.60 E-value=9.6e-15 Score=137.18 Aligned_cols=145 Identities=14% Similarity=0.134 Sum_probs=112.8
Q ss_pred cCCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHH
Q 011324 313 GLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ 391 (488)
Q Consensus 313 gm~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRn 391 (488)
.++++.|+..+..|+ .|++.|+..|.+.|+.+++++.++..+++|++||+|+.+|+++.+|++. ..|.+|++.+++|
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 8999999999999999999999999999999999999999999999963 4799999999999
Q ss_pred HHHHHHHHhcCCccc-------------chhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHH
Q 011324 392 TIRKAIFQHSRTIRL-------------PENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEK 447 (488)
Q Consensus 392 aI~~~IRk~sr~irl-------------P~~v---~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~et 447 (488)
.+.+++|+..+.... |... .+....+.++...|+ ..+..+.+++|||+.||+|+++
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 999999976532110 0000 001111222222221 2233478999999999999999
Q ss_pred HHHHHHHhCCCc
Q 011324 448 LERLIFITRMPL 459 (488)
Q Consensus 448 Vk~~L~~ar~~l 459 (488)
|+..+.+++..+
T Consensus 164 V~~~l~Rar~~L 175 (189)
T PRK12515 164 VKTRMFYARKKL 175 (189)
T ss_pred HHHHHHHHHHHH
Confidence 999999987654
No 69
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=99.59 E-value=4.3e-15 Score=139.08 Aligned_cols=135 Identities=16% Similarity=0.103 Sum_probs=104.8
Q ss_pred hcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC
Q 011324 325 SGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 403 (488)
Q Consensus 325 ~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~ 403 (488)
.|+ .+++.|+..|.+.|+.+|+++.++..+++|++||+|+.+|+++.+|+...+..|.||++.+++|.+++++|++.+.
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 8999999999999999999999999999999999999999999999865445799999999999999999987643
Q ss_pred cccc------------hhH------HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHhCC
Q 011324 404 IRLP------------ENI------YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRM 457 (488)
Q Consensus 404 irlP------------~~v------~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (488)
.... ... ......+.+++..|+. .+..+.+++|||+.||+|+++|+..+.+++.
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 0011223333333321 1334789999999999999999999999876
Q ss_pred Cc
Q 011324 458 PL 459 (488)
Q Consensus 458 ~l 459 (488)
.+
T Consensus 165 ~L 166 (185)
T PRK12542 165 RV 166 (185)
T ss_pred HH
Confidence 54
No 70
>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=99.58 E-value=1.3e-14 Score=134.91 Aligned_cols=141 Identities=17% Similarity=0.194 Sum_probs=106.5
Q ss_pred HHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCC-----CHhHHHHHHHHHHHH-hHHhhCCCCCCchhhHHHHH
Q 011324 316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGI-----SLHDLLQEGSMGLMK-SVEKFKPQAGCRFASYAYWW 388 (488)
Q Consensus 316 eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~-----d~EDLIQEG~IGL~r-AiekFDpskG~rFSTYA~~w 388 (488)
...|+..+..|+ .|++.|+..|.+.|+.+|++|.++.. +++|++||+|+.+|+ ...+|++. ..|.+|++.+
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 89999999999999999999998877 899999999999998 78889754 3699999999
Q ss_pred HHHHHHHHHHHhcCCcc------c------c---hhHHHH---HHH-------HHHHHHH-HHHhcCCCCcHHHHHHHhC
Q 011324 389 VRQTIRKAIFQHSRTIR------L------P---ENIYTL---LSK-------VLEAKRL-YIQEGNHSPDKEDLARRVG 442 (488)
Q Consensus 389 IRnaI~~~IRk~sr~ir------l------P---~~v~e~---l~k-------I~ka~~~-L~~elgr~pS~eEIAe~LG 442 (488)
++|.+++++|+..+..+ . + ....+. +.. +....+. +...+..+.|++|||+.||
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 99999999997542111 0 0 011111 111 2221122 2222334789999999999
Q ss_pred CCHHHHHHHHHHhCCC
Q 011324 443 ITVEKLERLIFITRMP 458 (488)
Q Consensus 443 IS~etVk~~L~~ar~~ 458 (488)
||+++|+..+++++..
T Consensus 162 is~~tVk~~l~Rar~~ 177 (183)
T TIGR02999 162 VSVRTVERDWRFARAW 177 (183)
T ss_pred CCHHHHHHHHHHHHHH
Confidence 9999999999998754
No 71
>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=99.57 E-value=2.2e-14 Score=141.90 Aligned_cols=145 Identities=12% Similarity=0.044 Sum_probs=113.1
Q ss_pred hcCCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHH-------hHHhhCCCCCCchhh
Q 011324 312 IGLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMK-------SVEKFKPQAGCRFAS 383 (488)
Q Consensus 312 ~gm~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~r-------AiekFDpskG~rFST 383 (488)
++.++..|+..++.|+ .|++.|+..|.+.|+.+++++.++..+++|++||.|+.+|. .+.+|++. ..|.|
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 3456788999999998 89999999999999999999999999999999999999994 78889863 36999
Q ss_pred HHHHHHHHHHHHHHHHhcCCccc---------------chhH-H------HHHHHHHHHHHHHHHh--------cCCCCc
Q 011324 384 YAYWWVRQTIRKAIFQHSRTIRL---------------PENI-Y------TLLSKVLEAKRLYIQE--------GNHSPD 433 (488)
Q Consensus 384 YA~~wIRnaI~~~IRk~sr~irl---------------P~~v-~------e~l~kI~ka~~~L~~e--------lgr~pS 433 (488)
|++.+++|.+++++|++.+...+ |... . +....+.+++..|+.. +-.+.|
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 0100 0 0112244444444322 224789
Q ss_pred HHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324 434 KEDLARRVGITVEKLERLIFITRMP 458 (488)
Q Consensus 434 ~eEIAe~LGIS~etVk~~L~~ar~~ 458 (488)
++|||+.||||+++|+..+++++..
T Consensus 180 ~~EIA~~Lgis~~TVk~rl~RAr~~ 204 (244)
T TIGR03001 180 MDRIGAMYQVHRSTVSRWVAQARER 204 (244)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 9999999999999999999988753
No 72
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=99.57 E-value=2.3e-14 Score=129.83 Aligned_cols=130 Identities=15% Similarity=0.142 Sum_probs=101.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc
Q 011324 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 407 (488)
Q Consensus 328 ~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP 407 (488)
++++.++..|.+.|+.+|+++.++..++||++||+++.+|+++++|++.. .|.+|++.+++|.+++++|++.+....-
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 5999999999999999999876542210
Q ss_pred -hh----------------HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 408 -EN----------------IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 408 -~~----------------v~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
.. ..+....+.+++..|+. ..-.+.+++|||+.||||.++|+..+++++..+
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 00 01111223333333321 133478999999999999999999999987654
No 73
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=99.57 E-value=1.9e-14 Score=135.43 Aligned_cols=142 Identities=19% Similarity=0.154 Sum_probs=109.4
Q ss_pred HHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHH
Q 011324 317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK 395 (488)
Q Consensus 317 eeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~ 395 (488)
..|+.++..|+ .|++.|+..|.+.|+.+++ +.++..+++|++||.|+.+|+.+++|++. ..|.+|++.+++|.+++
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 45777777887 8999999999999999995 67788899999999999999999999864 46999999999999999
Q ss_pred HHHHhcCCccc-----chh---------HHHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHHHHHH
Q 011324 396 AIFQHSRTIRL-----PEN---------IYTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLERLIF 453 (488)
Q Consensus 396 ~IRk~sr~irl-----P~~---------v~e~l~kI~ka~~~L~~e--------lgr~pS~eEIAe~LGIS~etVk~~L~ 453 (488)
++|+..+.... +.. ..+....+.+++..|+.. +..+.+++|||+.||+|+++|+..+.
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 99986432211 000 011222344444433222 33478999999999999999999999
Q ss_pred HhCCCccc
Q 011324 454 ITRMPLSM 461 (488)
Q Consensus 454 ~ar~~lSL 461 (488)
+++..+--
T Consensus 169 Rar~~Lr~ 176 (185)
T PRK09649 169 RARDALLA 176 (185)
T ss_pred HHHHHHHh
Confidence 99876543
No 74
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=99.57 E-value=2.9e-14 Score=130.47 Aligned_cols=139 Identities=14% Similarity=0.127 Sum_probs=106.7
Q ss_pred HHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHH
Q 011324 319 LKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI 397 (488)
Q Consensus 319 Li~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~I 397 (488)
|...+..|+ .|++.|+..|.+.|+.+|+++.++..+++|++||+|++||+++++|+ .+..|.+|++.++++.+.+++
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 455666777 89999999999999999999999999999999999999999999998 345899999999999999999
Q ss_pred HHhcCCcccch-------------h-------------HHHHHHHHHHHHHHHH-HhcCCCCcHHHHHHHhCCCHHHHHH
Q 011324 398 FQHSRTIRLPE-------------N-------------IYTLLSKVLEAKRLYI-QEGNHSPDKEDLARRVGITVEKLER 450 (488)
Q Consensus 398 Rk~sr~irlP~-------------~-------------v~e~l~kI~ka~~~L~-~elgr~pS~eEIAe~LGIS~etVk~ 450 (488)
++..+...... . +...+.++....+.+. ..+..+.+.+|||+.||+|..+|+.
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 97654322110 0 1112222222222221 2223478999999999999999999
Q ss_pred HHHHhCCCc
Q 011324 451 LIFITRMPL 459 (488)
Q Consensus 451 ~L~~ar~~l 459 (488)
.+++++..+
T Consensus 161 ~~~ra~~~l 169 (179)
T PRK11924 161 RLRRARQLL 169 (179)
T ss_pred HHHHHHHHH
Confidence 999886543
No 75
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=99.56 E-value=4.5e-14 Score=131.73 Aligned_cols=140 Identities=14% Similarity=0.167 Sum_probs=106.2
Q ss_pred HHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCC----CCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011324 318 DLKSELHSGN-SSREKLINANLRLVVHVAKQYQGR----GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (488)
Q Consensus 318 eLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~----g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRna 392 (488)
.|+..+..|+ .|++.|+..|.+.|+.+|++++++ ..+++|++||+|+.+|+..++|+.. ..|.+|++.+++|.
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 4566666666 999999999999999999998752 4689999999999999999999863 47999999999999
Q ss_pred HHHHHHHhcCCcccc---------h-h--HHHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHHHHH
Q 011324 393 IRKAIFQHSRTIRLP---------E-N--IYTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLERLI 452 (488)
Q Consensus 393 I~~~IRk~sr~irlP---------~-~--v~e~l~kI~ka~~~L~~e--------lgr~pS~eEIAe~LGIS~etVk~~L 452 (488)
+.+++|++.+....+ . . -......+.++...|+.. +-.+.+++|||+.||+|..+|+..+
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 011122333333333221 2247899999999999999999999
Q ss_pred HHhCCCc
Q 011324 453 FITRMPL 459 (488)
Q Consensus 453 ~~ar~~l 459 (488)
++++..+
T Consensus 169 ~ra~~~L 175 (184)
T PRK12512 169 HRGLAAL 175 (184)
T ss_pred HHHHHHH
Confidence 9887543
No 76
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=99.55 E-value=5.6e-14 Score=131.56 Aligned_cols=134 Identities=16% Similarity=0.202 Sum_probs=106.3
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC
Q 011324 324 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 403 (488)
Q Consensus 324 ~~Gd~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~ 403 (488)
.++..+++.++..|.+.++.+|+++.++..+++||+||+|+.+|+++..| .. +..|.||++.+++|.+++++|+..+.
T Consensus 11 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~-~~~~~~wl~~Ia~n~~iD~~R~~~r~ 88 (182)
T COG1595 11 RGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RG-RSSFKAWLYRIARNLAIDRLRKRKRR 88 (182)
T ss_pred hcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CC-CCchHHHHHHHHHHHHHHHHHHhccc
Confidence 34448999999999999999999999998899999999999999999999 33 45799999999999999999987654
Q ss_pred ccc-c-------------h-h----HHHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHHHHHHHhC
Q 011324 404 IRL-P-------------E-N----IYTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLERLIFITR 456 (488)
Q Consensus 404 irl-P-------------~-~----v~e~l~kI~ka~~~L~~e--------lgr~pS~eEIAe~LGIS~etVk~~L~~ar 456 (488)
... + . . ..+....+.++...|+.. ...+.|++|||+.|||++++|+..+++++
T Consensus 89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~~~gls~~EIA~~l~i~~~tVks~l~ra~ 168 (182)
T COG1595 89 RARVEEADLLPEEADPAPDLAELLLAEEELERLRRALARLPPRQREAFLLRYLEGLSYEEIAEILGISVGTVKSRLHRAR 168 (182)
T ss_pred ccccccccccccccCcccccchHHHHHHHHHHHHHHHHhCCHHHhHHhhhHhhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 321 0 1 1 122334455555544332 33478999999999999999999999987
Q ss_pred CCc
Q 011324 457 MPL 459 (488)
Q Consensus 457 ~~l 459 (488)
..+
T Consensus 169 ~~l 171 (182)
T COG1595 169 KKL 171 (182)
T ss_pred HHH
Confidence 653
No 77
>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=99.55 E-value=4e-14 Score=123.99 Aligned_cols=127 Identities=24% Similarity=0.393 Sum_probs=100.8
Q ss_pred HHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc--
Q 011324 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL-- 406 (488)
Q Consensus 329 ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irl-- 406 (488)
|++.|+..|.++|+++++++.+++.+.+|++|||+++++++++.|++. .+|.+|+++++++.+.++++++.+ .+.
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 689999999999999999999874 110
Q ss_pred ------------ch----------hHHHHHHHHHHHHHHHH-HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324 407 ------------PE----------NIYTLLSKVLEAKRLYI-QEGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (488)
Q Consensus 407 ------------P~----------~v~e~l~kI~ka~~~L~-~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (488)
|. .+...+..+....+.+. ..+..+.+..|||+.+|+|..+|+.++.+++..
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~ii~~~~~~g~s~~eIA~~l~~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 79 DLLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKK 153 (158)
T ss_pred hhhhhcccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 10 01222333333333332 222447899999999999999999999887543
No 78
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=99.54 E-value=4.8e-14 Score=131.54 Aligned_cols=133 Identities=16% Similarity=0.186 Sum_probs=102.7
Q ss_pred hcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC
Q 011324 325 SGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 403 (488)
Q Consensus 325 ~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~ 403 (488)
.|+ .|++.|+..|.+.|+.++++|.++..+++|++||+|+.+|+++.+|++.. .|.+|++.+++|.+.+++|+..+.
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 599999999999999999865421
Q ss_pred cc---------------cchhH--HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324 404 IR---------------LPENI--YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (488)
Q Consensus 404 ir---------------lP~~v--~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (488)
.+ .|..+ .+....+.++...|+ ..+..+.+++|||+.||||+++|+..+++++..
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 11111 111223333333332 123347899999999999999999999988765
Q ss_pred c
Q 011324 459 L 459 (488)
Q Consensus 459 l 459 (488)
+
T Consensus 161 L 161 (179)
T PRK12543 161 L 161 (179)
T ss_pred H
Confidence 4
No 79
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=99.54 E-value=6e-14 Score=129.82 Aligned_cols=130 Identities=10% Similarity=0.075 Sum_probs=101.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc-
Q 011324 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL- 406 (488)
Q Consensus 328 ~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irl- 406 (488)
..++.|+..|.++|+.+|++|.++..+++|++||+|+.||+++++|++.. +|.+|++.+++|.+++++|++.+....
T Consensus 3 ~~~~~l~~~y~~~i~~~~~~~~~~~~daeDvvQe~~i~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~Rk~~~~~~~~ 80 (173)
T PRK12522 3 EKVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVE--NYKKWITTICVRTFYDFYRKKKRWKDRI 80 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcCCcc--chHHHHHHHHHHHHHHHHHHhccccccc
Confidence 45899999999999999999999999999999999999999999999753 799999999999999999987543210
Q ss_pred --------------------chhH--HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHhC
Q 011324 407 --------------------PENI--YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITR 456 (488)
Q Consensus 407 --------------------P~~v--~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~~L~~ar 456 (488)
+... .+....+.+++..|+. .+..+.+++|||+.||+++++|+..+.+++
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 0000 0111223333333322 233478999999999999999999999887
Q ss_pred CCc
Q 011324 457 MPL 459 (488)
Q Consensus 457 ~~l 459 (488)
..+
T Consensus 161 ~~L 163 (173)
T PRK12522 161 KQM 163 (173)
T ss_pred HHH
Confidence 654
No 80
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=99.54 E-value=4.6e-14 Score=132.75 Aligned_cols=129 Identities=16% Similarity=0.176 Sum_probs=101.0
Q ss_pred HHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccch
Q 011324 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE 408 (488)
Q Consensus 329 ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~ 408 (488)
+++.|+..|.+.|+.+|+++.++..+++|++||.|+.+|+.+++|+.. .+|.||++.+++|.+++++|++.+......
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 689999999999999999999999999999999999999999999864 369999999999999999998765322110
Q ss_pred ------------------------------hH------HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCC
Q 011324 409 ------------------------------NI------YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGIT 444 (488)
Q Consensus 409 ------------------------------~v------~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS 444 (488)
.. .+....+..++..|+. .+..+.|++|||+.||+|
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 223467999999999999
Q ss_pred HHHHHHHHHHhCCCc
Q 011324 445 VEKLERLIFITRMPL 459 (488)
Q Consensus 445 ~etVk~~L~~ar~~l 459 (488)
+++|+..+++++..+
T Consensus 161 ~~tV~~~l~Rar~~L 175 (191)
T PRK12520 161 ATNAWVLLYRARMRL 175 (191)
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999999987654
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=99.53 E-value=4.3e-14 Score=133.15 Aligned_cols=130 Identities=16% Similarity=0.152 Sum_probs=102.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc
Q 011324 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 407 (488)
Q Consensus 328 ~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP 407 (488)
.+|+.|+..|.+.|+.+|+++.++..+++|++||.|+.+|+.+.+|++. ..|.+|++.+++|.+++++|++.+.....
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 46999999999999999999876432110
Q ss_pred --hhH------------------H-------HHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHHHHH
Q 011324 408 --ENI------------------Y-------TLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLERLI 452 (488)
Q Consensus 408 --~~v------------------~-------e~l~kI~ka~~~L~~e--------lgr~pS~eEIAe~LGIS~etVk~~L 452 (488)
... . .....+..++..|+.. +..+.+++|||+.||||+++|+..+
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 0113344445444333 2246799999999999999999999
Q ss_pred HHhCCCc
Q 011324 453 FITRMPL 459 (488)
Q Consensus 453 ~~ar~~l 459 (488)
++++..+
T Consensus 169 ~Rar~~L 175 (193)
T TIGR02947 169 HRGRKQL 175 (193)
T ss_pred HHHHHHH
Confidence 9987654
No 82
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=99.52 E-value=8.9e-14 Score=129.89 Aligned_cols=131 Identities=12% Similarity=0.081 Sum_probs=101.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc
Q 011324 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 406 (488)
Q Consensus 327 d~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irl 406 (488)
..|++.|+..|.+.|+++|+++.++..+++|++||+|+.+|+++.+|+.. ..|.+|++.+++|.+++++|+..+....
T Consensus 15 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~--~~~~awl~~ia~n~~~d~~Rk~~~~~~~ 92 (179)
T PRK09415 15 EDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGK--SSLKTWLYRIAINHCKDYLKSWHNKKVI 92 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--cccHHHHHHHHHHHHHHHHHhhcccccc
Confidence 38999999999999999999999999999999999999999999999864 3699999999999999999985322111
Q ss_pred ---------------chh---HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 407 ---------------PEN---IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 407 ---------------P~~---v~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
|.. ..+....+.++...|+. ....+.+++|||+.||||+++|+..+++++..+
T Consensus 93 ~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tv~~~l~Ra~~~L 171 (179)
T PRK09415 93 VTEDIFTYMESQKESVEEEVIQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELL 171 (179)
T ss_pred ccccccccccccccCcHHHHHHHHHHHHHHHHHHhCCHHHhhHhHhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 000 11112223333333322 122367999999999999999999999987654
No 83
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=99.52 E-value=1e-13 Score=127.93 Aligned_cols=136 Identities=18% Similarity=0.193 Sum_probs=102.7
Q ss_pred HHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHH
Q 011324 321 SELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQ 399 (488)
Q Consensus 321 ~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk 399 (488)
..++.|+ .+++.|+..|.+.|+.+++++.+ ..+++|++||+|+.+|+.++.|++. ..|.+|++.+++|.+++++|+
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 4455666 89999999999999999999875 4789999999999999999999974 469999999999999999997
Q ss_pred hcCCcc----cc-----------hhHH--HHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 400 HSRTIR----LP-----------ENIY--TLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 400 ~sr~ir----lP-----------~~v~--e~l~kI~ka~~~L~~e--------lgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
..+... .+ .... +....+.++...|+.. +..+.+++|||+.||+|+++|+..+++
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 0111233344444322 223679999999999999999999998
Q ss_pred hCCCc
Q 011324 455 TRMPL 459 (488)
Q Consensus 455 ar~~l 459 (488)
++..+
T Consensus 160 ar~~L 164 (175)
T PRK12518 160 ARRQL 164 (175)
T ss_pred HHHHH
Confidence 87654
No 84
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=99.52 E-value=1.1e-13 Score=127.76 Aligned_cols=132 Identities=11% Similarity=0.067 Sum_probs=101.3
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcc
Q 011324 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR 405 (488)
Q Consensus 326 Gd~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~ir 405 (488)
+..+++.|+..|.+.|+.+|.++.++..+++|++||.|+.+|+..++|++. ...|.+|++.+++|.+++++|++.+...
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 348999999999999999999999998999999999999999999999743 2479999999999999999997653211
Q ss_pred --------c-----chhHHH--HHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324 406 --------L-----PENIYT--LLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (488)
Q Consensus 406 --------l-----P~~v~e--~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (488)
. +..+.. ....+..++..|+ ..+..+.+++|||+.||+|+++|+..+++++..
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 1 011110 1112333333322 223347899999999999999999999988754
No 85
>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=99.52 E-value=7e-14 Score=125.59 Aligned_cols=129 Identities=19% Similarity=0.221 Sum_probs=99.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc-
Q 011324 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL- 406 (488)
Q Consensus 328 ~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irl- 406 (488)
.|++.|+..|.+.|+.+++++.++..+.+|++||+++++|+++.+|++. .+|.+|++.++++.+.+++++..+....
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 3789999999999999999999998999999999999999999999863 4799999999999999999977532110
Q ss_pred ---------------chh----------HHHHHHHHHHHHHHHH-HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324 407 ---------------PEN----------IYTLLSKVLEAKRLYI-QEGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (488)
Q Consensus 407 ---------------P~~----------v~e~l~kI~ka~~~L~-~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (488)
|.. +...+..+....+.+. ..+..+.+.+|||+.||+|..+|+..+++++..
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 000 1111222222222222 213347899999999999999999999988654
No 86
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=99.52 E-value=1.1e-13 Score=130.84 Aligned_cols=132 Identities=17% Similarity=0.151 Sum_probs=103.0
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcc
Q 011324 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR 405 (488)
Q Consensus 326 Gd~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~ir 405 (488)
++.+++.|+..|.+.|+.+|++++++..+++|++||.|+.+|+..++|+.. ..|.+|++.+++|.+++++|++.+...
T Consensus 8 ~~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~awL~~Ia~n~~~d~~R~~~~~~~ 85 (187)
T PRK12516 8 GTPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVG--TNMKAWLFTILRNEFYSQMRKRGREVQ 85 (187)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCc--ccHHHHHHHHHHHHHHHHHHhhcCCcc
Confidence 348999999999999999999999999999999999999999999999864 369999999999999999998765321
Q ss_pred cch-------------hHHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 406 LPE-------------NIYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 406 lP~-------------~v~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
... ........+..++..|+. ....+.+++|||+.||||+++|+..+.+++..|
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~i~~L~~~~g~s~~EIA~~Lgis~~tVk~~l~Rar~~L 160 (187)
T PRK12516 86 DTDGMFTEQLAVHPSQYGTLDLQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRL 160 (187)
T ss_pred ccccccccccCCCcchhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 100 001112233333333322 233478999999999999999999999887643
No 87
>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=99.51 E-value=1.3e-13 Score=128.13 Aligned_cols=134 Identities=16% Similarity=0.179 Sum_probs=100.3
Q ss_pred hcH-HHHHHHHHHHHHHHHHHHHHcc----CCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHH
Q 011324 325 SGN-SSREKLINANLRLVVHVAKQYQ----GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQ 399 (488)
Q Consensus 325 ~Gd-~ArekLIesnlrLV~sIAkry~----~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk 399 (488)
.|+ .|++.|+..|.+.|+.+|++|. ++..+++|++||+|+.+|+++.+|+...+..|.+|++.+++|.+.+++|+
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 445 8999999999999999999874 35678999999999999999999987656689999999999999999987
Q ss_pred hc----CCc----cc-----------------------chh---HHHHHHHHHHHHHHHH--------HhcCCCCcHHHH
Q 011324 400 HS----RTI----RL-----------------------PEN---IYTLLSKVLEAKRLYI--------QEGNHSPDKEDL 437 (488)
Q Consensus 400 ~s----r~i----rl-----------------------P~~---v~e~l~kI~ka~~~L~--------~elgr~pS~eEI 437 (488)
.. +.. .+ |.. ..+....+.+++..|. ..+..+.+++||
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 00 000 0111122333332221 223347899999
Q ss_pred HHHhCCCHHHHHHHHHHhCCC
Q 011324 438 ARRVGITVEKLERLIFITRMP 458 (488)
Q Consensus 438 Ae~LGIS~etVk~~L~~ar~~ 458 (488)
|+.||||+++|+..+++++..
T Consensus 163 A~~lgis~~~v~~~l~Ra~~~ 183 (189)
T TIGR02984 163 AERMDRSEGAVSMLWVRGLAR 183 (189)
T ss_pred HHHHCcCHHHHHHHHHHHHHH
Confidence 999999999999999988654
No 88
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=99.51 E-value=1.2e-13 Score=141.18 Aligned_cols=141 Identities=13% Similarity=0.153 Sum_probs=109.7
Q ss_pred HHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHH
Q 011324 317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK 395 (488)
Q Consensus 317 eeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~ 395 (488)
.+|+.++..|+ .+++.|+..|.+.|+.+|+++.++..+++|++||.|+.+|+.+++|++. ..|.+|++.+++|.+++
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 46999999999999999
Q ss_pred HHHHhcCCcc---c----------------------------------chhH---HHHH-HHHHHHHHHHHHh-------
Q 011324 396 AIFQHSRTIR---L----------------------------------PENI---YTLL-SKVLEAKRLYIQE------- 427 (488)
Q Consensus 396 ~IRk~sr~ir---l----------------------------------P~~v---~e~l-~kI~ka~~~L~~e------- 427 (488)
++|++.+... . |... .+.+ ..+.+++..|+..
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 0000 0101 1233344433322
Q ss_pred -cCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 428 -GNHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 428 -lgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
+..+.+++|||+.||+|+++|+..+++++..+
T Consensus 165 ~~~~g~s~~EIA~~lgis~~tVk~~l~RAr~~L 197 (339)
T PRK08241 165 RDVLGWSAAEVAELLDTSVAAVNSALQRARATL 197 (339)
T ss_pred HHhhCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 23467999999999999999999999887544
No 89
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=99.49 E-value=2.8e-13 Score=124.68 Aligned_cols=130 Identities=15% Similarity=0.110 Sum_probs=101.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc
Q 011324 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 406 (488)
Q Consensus 327 d~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irl 406 (488)
+..|..++..|.+.|+.+|+++.++..+++|++||+|+.+|+...+|+.. ..|.+|++.+++|.+++++|+..+....
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 3599999999999999999976543211
Q ss_pred c------------h-hHHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324 407 P------------E-NIYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (488)
Q Consensus 407 P------------~-~v~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (488)
. . ........+..++..|+ ..+-.+.+++|||+.||||+++|+..+++++..
T Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~~ 155 (164)
T PRK12547 83 SDGVFTARVAVHPAQYGSLDLQDFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNR 155 (164)
T ss_pred ccccccccCCCCchhhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 0 0 00011122333333332 222347899999999999999999999988754
No 90
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=99.49 E-value=2e-13 Score=127.61 Aligned_cols=135 Identities=13% Similarity=0.055 Sum_probs=100.5
Q ss_pred hhcH-HHHHHHHHHHHHHHHHHHHHccC--CCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHh
Q 011324 324 HSGN-SSREKLINANLRLVVHVAKQYQG--RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH 400 (488)
Q Consensus 324 ~~Gd-~ArekLIesnlrLV~sIAkry~~--~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~ 400 (488)
..|+ .+++.|+..|.+.|+.++.++.+ +..+++|++||.|+.+|+...+|+......|.||++.+++|.+++++|++
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 4455 89999999999999998766555 45789999999999999999999754345799999999999999999976
Q ss_pred cCCcc--------------cchh---HHHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 401 SRTIR--------------LPEN---IYTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 401 sr~ir--------------lP~~---v~e~l~kI~ka~~~L~~e--------lgr~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
.+... -|.. ..+....|.+++..|+.+ .-.+.+++|||+.||+|+++|+..++++
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 1111 112223344444444322 2236899999999999999999999887
Q ss_pred CCC
Q 011324 456 RMP 458 (488)
Q Consensus 456 r~~ 458 (488)
...
T Consensus 168 l~~ 170 (178)
T PRK12529 168 YVT 170 (178)
T ss_pred HHH
Confidence 543
No 91
>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=99.49 E-value=2.9e-13 Score=123.38 Aligned_cols=132 Identities=14% Similarity=0.117 Sum_probs=101.5
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcc
Q 011324 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR 405 (488)
Q Consensus 326 Gd~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~ir 405 (488)
+..+++.|+..|.+.|+.+|.++.++..+++|++||+|+.+|+.+++|+. ...|.+|++.+++|.+++++|+..+...
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 44899999999999999999999999999999999999999999999964 3479999999999999999998754110
Q ss_pred ----cc-------h-------hHHHHHHHHHHHHHHHH-HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 406 ----LP-------E-------NIYTLLSKVLEAKRLYI-QEGNHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 406 ----lP-------~-------~v~e~l~kI~ka~~~L~-~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
.+ . .+...+.++....+.+. ..+-.+.+++|||+.||+|+++|+..+.+++..+
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ra~~~L 154 (162)
T TIGR02983 82 PTRELPDAAAPDPAPDVALRAALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARL 154 (162)
T ss_pred cccccCcccCCccchhHHHHHHHHHHHHhCCHHHHHHhhhHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 00 0 01122222222222221 2223478999999999999999999999887643
No 92
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=99.48 E-value=3.6e-13 Score=123.03 Aligned_cols=130 Identities=12% Similarity=0.132 Sum_probs=100.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc
Q 011324 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 406 (488)
Q Consensus 327 d~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irl 406 (488)
..+++.++..|.+.|+.+|.++.++..+++|++||+|+.+|+.+++|++. .|.||++.+++|.+++++|+..+....
T Consensus 4 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDv~Qe~f~~~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~~~~ 80 (161)
T PRK12541 4 KQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE---EIRPWLFTIAYNAFIDWYRKEKKYKTT 80 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhHHHccCC---ChHHHHHHHHHHHHHHHHHhccccccc
Confidence 37999999999999999999999999999999999999999999999863 599999999999999999986542211
Q ss_pred c------------hh---HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 407 P------------EN---IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 407 P------------~~---v~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
. .. ..+....+..+...|+. ....+.+++|||+.||+|.++|+..+++++..+
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~Rar~~L 156 (161)
T PRK12541 81 TIEEFHLPNVPSTEHEYFIKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKET 156 (161)
T ss_pred chhhhhccCCCCcHHHHHHHhHHHHHHHHHHHCCHHHHHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 0 00 01111222223222222 123478999999999999999999999987543
No 93
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=99.47 E-value=3.9e-13 Score=128.12 Aligned_cols=139 Identities=15% Similarity=0.109 Sum_probs=106.2
Q ss_pred HHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHH
Q 011324 317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK 395 (488)
Q Consensus 317 eeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~ 395 (488)
.+|+..+..|+ .+++.|+..|.+.++.+++ +.++..+++|++||.|+.+|+..++|++. ..|.+|++.+++|.+++
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 45777777777 8999999999999999975 56888899999999999999999999863 36999999999999999
Q ss_pred HHHHhcCCccc--------------ch--hHHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHH
Q 011324 396 AIFQHSRTIRL--------------PE--NIYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERL 451 (488)
Q Consensus 396 ~IRk~sr~irl--------------P~--~v~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~~ 451 (488)
++|+..+..+. |. ...+....+.+++..|+. .+-.+.+++|||+.||+++++|+..
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 99986532210 00 011112234444433322 2223679999999999999999999
Q ss_pred HHHhCCC
Q 011324 452 IFITRMP 458 (488)
Q Consensus 452 L~~ar~~ 458 (488)
+++++..
T Consensus 170 l~Rar~~ 176 (196)
T PRK12535 170 VARARAD 176 (196)
T ss_pred HHHHHHH
Confidence 9988654
No 94
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=99.47 E-value=7.9e-13 Score=130.63 Aligned_cols=91 Identities=21% Similarity=0.337 Sum_probs=81.9
Q ss_pred CHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCC--CHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHH
Q 011324 315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGI--SLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ 391 (488)
Q Consensus 315 ~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~--d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRn 391 (488)
+.++|+..++.|+ .|++.|+..|.++|+++|.+|+++.. +.+|++|||++++|+++++|++.+|..|.+|++++|+|
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 3466778888887 89999999999999999999998875 58999999999999999999999888899999999999
Q ss_pred HHHHHHHHhcCCcc
Q 011324 392 TIRKAIFQHSRTIR 405 (488)
Q Consensus 392 aI~~~IRk~sr~ir 405 (488)
.+++++|++.+...
T Consensus 84 ~~iDylRk~~~~~~ 97 (237)
T PRK08311 84 RLIDYFRKESKHNL 97 (237)
T ss_pred HHHHHHHHhhcccc
Confidence 99999998876433
No 95
>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=99.47 E-value=2.7e-13 Score=137.29 Aligned_cols=131 Identities=15% Similarity=0.158 Sum_probs=101.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcc-
Q 011324 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR- 405 (488)
Q Consensus 327 d~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~ir- 405 (488)
..+++.|+..|.+.|+++|++++++..+++|++||.|+.+|+.+.+|+.. ..|.+|++.+++|.|++++|++.+...
T Consensus 4 ~~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~~~~~~ 81 (324)
T TIGR02960 4 GAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGR--SSVRTWLYRIATNACLDALEARQRRPRP 81 (324)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCcc--cchHHHHHHHHHHHHHHHHHhccCCcCc
Confidence 38999999999999999999999999999999999999999999999864 469999999999999999998654211
Q ss_pred -------------------------cc--------------hhH---HHHH-HHHHHHHHHHHH--------hcCCCCcH
Q 011324 406 -------------------------LP--------------ENI---YTLL-SKVLEAKRLYIQ--------EGNHSPDK 434 (488)
Q Consensus 406 -------------------------lP--------------~~v---~e~l-~kI~ka~~~L~~--------elgr~pS~ 434 (488)
++ ... .+.+ ..+.+++..|+. .+..+.++
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~ 161 (324)
T TIGR02960 82 VGLGAPSADGTAAASEAAEVTWLEPLPDLTLDLDDPAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRDVLGWRA 161 (324)
T ss_pred cccCCCCCcccccccccccccccCCCCccccccccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHHhCCCH
Confidence 00 000 0111 123333333322 22346799
Q ss_pred HHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 435 EDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 435 eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
+|||+.||+|+++|+..+++++..|
T Consensus 162 ~EIA~~lgis~~tV~~~l~Rar~~L 186 (324)
T TIGR02960 162 AETAELLGTSTASVNSALQRARATL 186 (324)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 9999999999999999999887543
No 96
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=99.47 E-value=4.9e-13 Score=129.93 Aligned_cols=134 Identities=14% Similarity=0.096 Sum_probs=103.8
Q ss_pred hhhcHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcC
Q 011324 323 LHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR 402 (488)
Q Consensus 323 l~~Gd~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr 402 (488)
+.....+++.|+..|.+.|+.+++++.++..+.+|++||+|+.+|+.+.+|++ + .|.+|++++++|.+++++|++++
T Consensus 13 ~~~~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~--~-~~~aWL~~IarN~~~d~~Rk~~~ 89 (216)
T PRK12533 13 AAARGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRG--D-NARPWLLAIVRHTWYSEWRRRAN 89 (216)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCc--c-chHhHHHHHHHHHHHHHHHhhcc
Confidence 34456899999999999999999999999999999999999999999999985 2 49999999999999999998753
Q ss_pred Cccc------c---------------hh---HHHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHHH
Q 011324 403 TIRL------P---------------EN---IYTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLER 450 (488)
Q Consensus 403 ~irl------P---------------~~---v~e~l~kI~ka~~~L~~e--------lgr~pS~eEIAe~LGIS~etVk~ 450 (488)
.... . .. ..+....+.+++..|... +-.+.+++|||+.||||+++|+.
T Consensus 90 ~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y~eg~s~~EIAe~LgiS~~tVk~ 169 (216)
T PRK12533 90 AHEVAAPDTLDDADSLDDWQPAGEDPLALLLRAEDVRLVNAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMS 169 (216)
T ss_pred cccccccccccccccccccccCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHhHhhhHHhcCCCHHHHHHHHCCCHHHHHH
Confidence 2110 0 00 011223344444433221 23478999999999999999999
Q ss_pred HHHHhCCCc
Q 011324 451 LIFITRMPL 459 (488)
Q Consensus 451 ~L~~ar~~l 459 (488)
.+++++..|
T Consensus 170 ~L~RAr~~L 178 (216)
T PRK12533 170 RLARARRRL 178 (216)
T ss_pred HHHHHHHHH
Confidence 999887654
No 97
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=99.46 E-value=4.2e-13 Score=123.29 Aligned_cols=127 Identities=14% Similarity=0.117 Sum_probs=98.4
Q ss_pred HHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc--
Q 011324 330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP-- 407 (488)
Q Consensus 330 rekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP-- 407 (488)
++.|+..|.+.|+.+|+++.++..+++|++||+|+.+|+++++|++. +|.+|++.+++|.+.+++|+..+.....
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 57899999999999999999999999999999999999999999862 5999999999999999999876532211
Q ss_pred ----------hhH---HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 408 ----------ENI---YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 408 ----------~~v---~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
... .+....+.++...|+. ....+.+++|||+.||+|+++|+..+++++..+
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Rar~~L 152 (165)
T PRK09644 80 EIEAIQAESTEEYVVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRL 152 (165)
T ss_pred HHhhhcccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 110 1111223333332221 223467999999999999999999999887643
No 98
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=99.46 E-value=2.2e-13 Score=126.11 Aligned_cols=133 Identities=11% Similarity=0.055 Sum_probs=100.4
Q ss_pred hhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcC
Q 011324 324 HSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR 402 (488)
Q Consensus 324 ~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr 402 (488)
+.|+ .++..|+..|.+.|+.+|.++.++..+++|++||+|+.+|+. ..|... ..|.+|++.+++|.+++++|++.+
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 4566 899999999999999999999999999999999999999987 446543 369999999999999999998653
Q ss_pred Ccc--------------cchh---HHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCC
Q 011324 403 TIR--------------LPEN---IYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRM 457 (488)
Q Consensus 403 ~ir--------------lP~~---v~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (488)
... -|.. ..+....+.+++..|+ ..+..+.+++|||+.||||+++|+..+++++.
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 0111 0111223333333332 22334789999999999999999999998865
Q ss_pred Cc
Q 011324 458 PL 459 (488)
Q Consensus 458 ~l 459 (488)
.+
T Consensus 162 ~~ 163 (172)
T PRK12523 162 QC 163 (172)
T ss_pred HH
Confidence 54
No 99
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=99.43 E-value=8.8e-13 Score=120.51 Aligned_cols=128 Identities=18% Similarity=0.116 Sum_probs=99.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc
Q 011324 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 406 (488)
Q Consensus 327 d~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irl 406 (488)
+.+++.|+..|.+.|+.+|+++.++..+++|++||+|+.+|++ .|+. +..|.+|++.+++|.+.+++|+..+....
T Consensus 2 ~~~f~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fi~~~~~--~~~~--~~~~~~wl~~i~rn~~~d~~rk~~~~~~~ 77 (166)
T PRK09639 2 DETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKG--IENEKGWLIKSARNVAYNYLRSEKRRRAR 77 (166)
T ss_pred chHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH--hccc--ccchHHHHHHHHHHHHHHHHHHhcccccc
Confidence 3689999999999999999999999999999999999999999 6764 34799999999999999999987643211
Q ss_pred ---------------chhH---HHHHHHHHHHHHH--------HHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 407 ---------------PENI---YTLLSKVLEAKRL--------YIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 407 ---------------P~~v---~e~l~kI~ka~~~--------L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
|... .+....+.++... +...+ .+.+++|||+.||+|+++|+..+.+++..+
T Consensus 78 ~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~-~g~s~~eIA~~lgis~~tV~~~i~ra~~~L 155 (166)
T PRK09639 78 ILGEFQWQEVDNEPSPEEIWIRKEEITKVQEVLAKMTERDRTVLLLRF-SGYSYKEIAEALGIKESSVGTTLARAKKKF 155 (166)
T ss_pred ccchhhhhhccCCCChHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 1000 1112223333322 22335 688999999999999999999999887543
No 100
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=99.43 E-value=8.2e-13 Score=126.00 Aligned_cols=126 Identities=13% Similarity=0.166 Sum_probs=96.4
Q ss_pred HHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc----
Q 011324 332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP---- 407 (488)
Q Consensus 332 kLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP---- 407 (488)
.++..|.+.|+.+|++++++..+++|++||.|+.+|+.+++|++. ..|.+|++.+++|.+++++|++.+...++
T Consensus 12 ~~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~~~ 89 (201)
T PRK12545 12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQ--SAHKTWVFGILRNKLIDTLRARQRTVNLSALDA 89 (201)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhcccc--chHHHHHHHHHHHHHHHHHHhhccccccccccc
Confidence 348899999999999999999999999999999999999999875 36999999999999999999876532211
Q ss_pred -------------------------------hhHH---HHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCH
Q 011324 408 -------------------------------ENIY---TLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITV 445 (488)
Q Consensus 408 -------------------------------~~v~---e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~ 445 (488)
.... +....+.+++..|+ ..+..+.+++|||+.||+|+
T Consensus 90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~v~~L~~~eg~s~~EIA~~lgis~ 169 (201)
T PRK12545 90 ELDGEALLDRELFKDNGHWAAHAKPRPWPKPETILQQQQFWTLFETCLDHLPEQIGRVFMMREFLDFEIDDICTELTLTA 169 (201)
T ss_pred ccchhhhhhhhhhcccccccccccCcCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCH
Confidence 0000 01112333333322 22334789999999999999
Q ss_pred HHHHHHHHHhCCCc
Q 011324 446 EKLERLIFITRMPL 459 (488)
Q Consensus 446 etVk~~L~~ar~~l 459 (488)
++|+..+.+++..+
T Consensus 170 ~tVk~~l~RAr~~L 183 (201)
T PRK12545 170 NHCSVLLYRARTRL 183 (201)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999887643
No 101
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=99.43 E-value=9.3e-13 Score=120.35 Aligned_cols=127 Identities=14% Similarity=0.122 Sum_probs=97.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCc---
Q 011324 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI--- 404 (488)
Q Consensus 328 ~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~i--- 404 (488)
.|++.|+..|.+.|+.+|.++.++..+++|++||.|+.+|+..+.|++ ..|.+|++++++|.+++++|+..+..
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 36999999999999999999854211
Q ss_pred ----ccc-----h--h---HHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCC
Q 011324 405 ----RLP-----E--N---IYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRM 457 (488)
Q Consensus 405 ----rlP-----~--~---v~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (488)
..+ . . ..+....+.+++..|+ .....+.+++|||+.||+|+++|+..+++++.
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 0 0 0111122333333322 22334789999999999999999999988754
No 102
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=99.43 E-value=4.7e-13 Score=122.02 Aligned_cols=122 Identities=11% Similarity=0.062 Sum_probs=93.0
Q ss_pred HHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcc-c-------
Q 011324 335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR-L------- 406 (488)
Q Consensus 335 esnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~ir-l------- 406 (488)
+.|.+.|+.+|.++.++..+++|++||+|+.+|+++++|++ . .|.+|++.+++|.+++++|++.+... .
T Consensus 2 ~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~-~--~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~~~~~~~ 78 (160)
T PRK09642 2 QTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQF-R--GLKTWMARIATNHAIDYKRKKARENEELSLCKETE 78 (160)
T ss_pred chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccccccc-c--hhHHHHHHHHHHHHHHHHHHhcccccccccchhhh
Confidence 57899999999999999999999999999999999999986 2 49999999999999999998654211 0
Q ss_pred --------chhH---HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 407 --------PENI---YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 407 --------P~~v---~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
|... .+....+.+++..|+. .+..+.+++|||+.||+|+++|+..+++++..+
T Consensus 79 ~~~~~~~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~L 150 (160)
T PRK09642 79 ENIKSSHNIEDLLLTKEQKLLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKWI 150 (160)
T ss_pred hhccCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 0000 0111123333333322 233478999999999999999999999987653
No 103
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=99.43 E-value=1.3e-12 Score=123.11 Aligned_cols=130 Identities=19% Similarity=0.216 Sum_probs=101.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc-
Q 011324 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL- 406 (488)
Q Consensus 328 ~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irl- 406 (488)
.++..++..|.+.|+++|.++.++..+++|++||.|+.+|+..++|++.. .|.+|++.+++|.+++++|++.+....
T Consensus 5 ~~~~~~~~~~~~~l~~~~~~~~~~~~~AEDivQevflkl~~~~~~~~~~~--~~~~WL~~Ia~n~~~d~~Rk~~~~~~~~ 82 (182)
T PRK12540 5 DSLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGS--NLPAWLFTILRNLFRSDYRKRRREVEDA 82 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCc--hHHHHHHHHHHHHHHHHHHhcccccccc
Confidence 57788999999999999999999999999999999999999999998653 699999999999999999986643210
Q ss_pred -----------chh-HHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 407 -----------PEN-IYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 407 -----------P~~-v~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
+.. .......+.+++..|+ ..+..+.+++|||+.||||+++|+..+++++..+
T Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RAr~~L 155 (182)
T PRK12540 83 DGSYAKTLKSQPGQNAHLEFEEFRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKL 155 (182)
T ss_pred cccccccccCCCchHHHHHHHHHHHHHHhCCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 100 0111122333333332 2233478999999999999999999999987654
No 104
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=99.42 E-value=1.3e-12 Score=125.50 Aligned_cols=129 Identities=21% Similarity=0.277 Sum_probs=100.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCc--c
Q 011324 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI--R 405 (488)
Q Consensus 328 ~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~i--r 405 (488)
.+++.|+..|.+.|+.+++++.++..+.+|++||+|+.+|+.+.+|++ + .|.+|++.+++|.+++++|+..+.. .
T Consensus 28 ~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~~~d~~Rk~~~~~~~~ 104 (203)
T PRK09647 28 PSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNLFLDMVRRRARIRMEA 104 (203)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHHHHHHHHhcccCcccc
Confidence 899999999999999999999999999999999999999999999985 3 6999999999999999999875321 0
Q ss_pred c-------------chhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 406 L-------------PENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 406 l-------------P~~v---~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
. |... .+....+..++..|. .....+.+++|||+.|||++++|+..+.+++..+
T Consensus 105 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~L~~~~r~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RArk~L 182 (203)
T PRK09647 105 LPEDYDRVPGDEPNPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQL 182 (203)
T ss_pred ccccccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 0 0000 011222333333222 1223478999999999999999999999987653
No 105
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=99.42 E-value=1.1e-12 Score=123.92 Aligned_cols=126 Identities=14% Similarity=0.197 Sum_probs=95.6
Q ss_pred HHHHHHHHHHHHHHHHHccCCCCC-HhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc---
Q 011324 331 EKLINANLRLVVHVAKQYQGRGIS-LHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL--- 406 (488)
Q Consensus 331 ekLIesnlrLV~sIAkry~~~g~d-~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irl--- 406 (488)
+..+..|.+.|+.+|+++.++..+ ++|++||+|+.+|+++++|+.. .+|.+|++.+++|.+++++|++.+....
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 456778999999999999998888 9999999999999999999864 4799999999999999999987643211
Q ss_pred -------------------------------chhH---HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCC
Q 011324 407 -------------------------------PENI---YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGIT 444 (488)
Q Consensus 407 -------------------------------P~~v---~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS 444 (488)
|... .+....+.++...|.. .+..+.+++|||+.||+|
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 0111123333333322 223468999999999999
Q ss_pred HHHHHHHHHHhCCC
Q 011324 445 VEKLERLIFITRMP 458 (488)
Q Consensus 445 ~etVk~~L~~ar~~ 458 (488)
+++|+..+++++..
T Consensus 166 ~~tVk~~l~Rar~~ 179 (195)
T PRK12532 166 TSNYHTIMHRARES 179 (195)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999988754
No 106
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=99.40 E-value=2.5e-12 Score=121.64 Aligned_cols=134 Identities=13% Similarity=0.031 Sum_probs=102.1
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC
Q 011324 324 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 403 (488)
Q Consensus 324 ~~Gd~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~ 403 (488)
..+..+++.++..|.+.|+.+|+++.++..+++|++||.|+.+|+.++.|++. ..|.+|++.+++|.+.+..++..+.
T Consensus 19 ~~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~--~~~~~wL~~Iarn~~~~~~r~~~~~ 96 (188)
T PRK12517 19 LSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDE--KAAKAWLITILRRENARRFERKQFD 96 (188)
T ss_pred hccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCc--cchHHHHHHHHHHHHHHHHHHhccC
Confidence 34558999999999999999999999999999999999999999999999864 3699999999999998887764432
Q ss_pred cc------cc------hhHHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 404 IR------LP------ENIYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 404 ir------lP------~~v~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
.. .+ .........+..++..|+. .+..+.+++|||+.|||++++|+..+++++..+
T Consensus 97 ~~~~~~~~~~~~~~~~~e~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~L 172 (188)
T PRK12517 97 LVDIEDDSIEDDASHSSEEEMEQEWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARNQL 172 (188)
T ss_pred ccCcccccccCccccChhHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 10 00 0001111223444443332 233478999999999999999999999887643
No 107
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=99.40 E-value=3.1e-12 Score=120.28 Aligned_cols=127 Identities=15% Similarity=0.195 Sum_probs=98.2
Q ss_pred HHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchh
Q 011324 330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 409 (488)
Q Consensus 330 rekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~ 409 (488)
++.|++.|.+.|+.+|.++.++..+++|++||.|+.+|+.+..|+. +..|.+|++.+++|.+++++|++.+...++..
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~aeDi~QEvflkl~~~~~~~~~--~~~~~~wL~~i~~n~~~d~~Rk~~~~~~~~~~ 80 (181)
T PRK09637 3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKD--GSSIKSWLYQIANNTIIDFYRKKNRSEELPDD 80 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHhHHHhcc--ccchHHHHHHHHHHHHHHHHHhccccCCcchh
Confidence 6789999999999999999999999999999999999999999985 34799999999999999999987654332210
Q ss_pred -------------------HHHHHHHHHHHHHHH-HHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324 410 -------------------IYTLLSKVLEAKRLY-IQEGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (488)
Q Consensus 410 -------------------v~e~l~kI~ka~~~L-~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (488)
+...+.++....+.+ ......+.+.+|||+.||+|+++|+..+.+++..
T Consensus 81 ~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~~~~EIA~~lgis~~tV~~~l~Rar~~ 149 (181)
T PRK09637 81 LLFEDEEREENAKKELAPCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVK 149 (181)
T ss_pred hhccCCChhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 111112222222221 1223347899999999999999999999888653
No 108
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=99.40 E-value=1.7e-12 Score=122.51 Aligned_cols=126 Identities=14% Similarity=0.150 Sum_probs=95.4
Q ss_pred HHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc---
Q 011324 331 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP--- 407 (488)
Q Consensus 331 ekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP--- 407 (488)
+.-|..|.+.|+.+|.++.++..+++|++||.|+.+|+.+.+|++. .+|.+|++++++|.+++++|++.+.....
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 4457788999999999999999999999999999999999999864 36999999999999999999876432110
Q ss_pred ----------------------h------h-H--HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHH
Q 011324 408 ----------------------E------N-I--YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKL 448 (488)
Q Consensus 408 ----------------------~------~-v--~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etV 448 (488)
. . + .+....+..++..|+. .+..+.+++|||+.||+|+++|
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 0 0001123333333322 2223789999999999999999
Q ss_pred HHHHHHhCCC
Q 011324 449 ERLIFITRMP 458 (488)
Q Consensus 449 k~~L~~ar~~ 458 (488)
+..+++++..
T Consensus 168 k~~l~RAr~~ 177 (189)
T PRK12530 168 HVLLYRARLQ 177 (189)
T ss_pred HHHHHHHHHH
Confidence 9999988754
No 109
>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=99.40 E-value=1.9e-12 Score=122.23 Aligned_cols=127 Identities=11% Similarity=0.164 Sum_probs=97.2
Q ss_pred HHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc---
Q 011324 331 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP--- 407 (488)
Q Consensus 331 ekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP--- 407 (488)
.+.+..|.+.|+.+|+++.++..+++|++||+|+.+|+..++|++. .+|.+|++.+++|.+++++|++.+....+
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 3577889999999999999999999999999999999999999864 47999999999999999999876432111
Q ss_pred ------------------------------hhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHH
Q 011324 408 ------------------------------ENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVE 446 (488)
Q Consensus 408 ------------------------------~~v---~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~e 446 (488)
... .+....+.+++..|+ ..+..+.+++|||+.||+|++
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 001122333333322 223347899999999999999
Q ss_pred HHHHHHHHhCCCc
Q 011324 447 KLERLIFITRMPL 459 (488)
Q Consensus 447 tVk~~L~~ar~~l 459 (488)
+|+..+.+++..+
T Consensus 163 tvk~rl~Rar~~L 175 (188)
T TIGR02943 163 NCHVLLYRARLSL 175 (188)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999987654
No 110
>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=99.39 E-value=1e-12 Score=103.51 Aligned_cols=70 Identities=23% Similarity=0.432 Sum_probs=67.3
Q ss_pred HHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcC
Q 011324 333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR 402 (488)
Q Consensus 333 LIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr 402 (488)
|++.|.++|++++++|.+++.+.+|++||++++||+++++||+++|..|.+|++.+++|.+.+++|++.+
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 7899999999999999999999999999999999999999999999899999999999999999998764
No 111
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=99.39 E-value=2.4e-12 Score=123.87 Aligned_cols=129 Identities=14% Similarity=0.212 Sum_probs=98.2
Q ss_pred HHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc-
Q 011324 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP- 407 (488)
Q Consensus 329 ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP- 407 (488)
.-..++..|.+.|+.+|+++.++..+++|++||+|+.+|+.+.+|+.. .+|.+|++++++|.+++++|+..+....+
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 011324 408 ---------------------------------ENIY---TLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGI 443 (488)
Q Consensus 408 ---------------------------------~~v~---e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGI 443 (488)
.... +....+.+++..|+ ..+..+.+++|||+.||+
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 01112222333222 122347799999999999
Q ss_pred CHHHHHHHHHHhCCCc
Q 011324 444 TVEKLERLIFITRMPL 459 (488)
Q Consensus 444 S~etVk~~L~~ar~~l 459 (488)
|+++|+..+++++..+
T Consensus 177 s~~tV~~~l~RAr~~L 192 (206)
T PRK12544 177 SVSNLNVLLYRARLRL 192 (206)
T ss_pred CHHHHHHHHHHHHHHH
Confidence 9999999999987653
No 112
>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=99.39 E-value=1.8e-12 Score=116.80 Aligned_cols=122 Identities=12% Similarity=0.129 Sum_probs=94.5
Q ss_pred HHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc-------
Q 011324 334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL------- 406 (488)
Q Consensus 334 IesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irl------- 406 (488)
+..|.+.|+.+++++.++..+++|++||+|+.+|+.+++|++ .+|.||++.++++.+.++++++.+....
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 357899999999999998899999999999999999999997 4799999999999999999976532211
Q ss_pred --------chhH---HHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324 407 --------PENI---YTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (488)
Q Consensus 407 --------P~~v---~e~l~kI~ka~~~L~~e--------lgr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (488)
|... .+....+.+++..|+.. ...+.+++|||+.||+|+++|+..+++++..
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 1100 11123344555544322 2246799999999999999999999988654
No 113
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=99.38 E-value=4.4e-12 Score=120.31 Aligned_cols=128 Identities=17% Similarity=0.190 Sum_probs=97.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc
Q 011324 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 407 (488)
Q Consensus 328 ~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP 407 (488)
++++.|+. |.+.|+++|+++.++..+++|++||.|+.+|+.+..|+.. ..|.+|++.+++|.+++++|+..+.....
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 7799999999999999999999999999999999999863 46999999999999999999876432110
Q ss_pred ------------hh-HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324 408 ------------EN-IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (488)
Q Consensus 408 ------------~~-v~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (488)
.. .......+..++..|+. .+..+.+.+|||+.||||+.+|+..+.+++..
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 12347899999999999999999999988754
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=99.36 E-value=4.4e-12 Score=117.67 Aligned_cols=123 Identities=19% Similarity=0.234 Sum_probs=94.5
Q ss_pred HHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhH----
Q 011324 335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI---- 410 (488)
Q Consensus 335 esnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v---- 410 (488)
..|.+.|+.+++++.++..+++|++||+|+.+|+++.+|+. +.+|.+|++.+++|.+++++|+..+...++...
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~l~~~~~~~~~--~~~f~~wl~~iarn~~~d~~Rk~~~~~~~~~~~~~~~ 79 (170)
T TIGR02959 2 DEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKD--GQKIQSWLYQIARNTIIDFYRSKSRSVELPESLLAAD 79 (170)
T ss_pred chHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCC--cccHHHHHHHHHHHHHHHHHHhccCccccchhhcccC
Confidence 46889999999999999999999999999999999999986 357999999999999999999987544322110
Q ss_pred --------HHHHHHHHHHHHHH--------HHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 411 --------YTLLSKVLEAKRLY--------IQEGNHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 411 --------~e~l~kI~ka~~~L--------~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
.+....+.+++..| ......+.+++|||+.||||+.+|+..+++++..+
T Consensus 80 ~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~~L 144 (170)
T TIGR02959 80 SAREETFVKELSQCIPPMIKELPDEYREAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQRGRKKL 144 (170)
T ss_pred CccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 11111222222222 12233478999999999999999999999887653
No 115
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=99.33 E-value=9.8e-12 Score=117.24 Aligned_cols=128 Identities=13% Similarity=0.114 Sum_probs=97.2
Q ss_pred HHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc---
Q 011324 330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL--- 406 (488)
Q Consensus 330 rekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irl--- 406 (488)
.+..+..+.+.|+.+|.++.++..+++|++||.|+.+|+.+..|+.. ..|.+|++.+++|.+++++|++.+....
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 44567889999999999999999999999999999999999999863 3699999999999999999986542110
Q ss_pred ---------ch--hHHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 407 ---------PE--NIYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 407 ---------P~--~v~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
+. ........+.+++..|+. .+-.+.+++|||+.||||+++|+..+++++..+
T Consensus 84 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~eg~s~~EIA~~lgis~~tV~~~l~Rar~~L 155 (182)
T PRK12511 84 LAVLADASLPAAQEHAVRLAQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAAL 155 (182)
T ss_pred hhhccccCCCcchHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHHHHH
Confidence 00 011112223333333322 133478999999999999999999999887643
No 116
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=99.32 E-value=2e-11 Score=113.41 Aligned_cols=129 Identities=11% Similarity=0.080 Sum_probs=97.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcc-
Q 011324 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR- 405 (488)
Q Consensus 327 d~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~ir- 405 (488)
..|++.++..|.+.++.++.++.++..+++|++||.|+.+|+. ..|++-. .|.+|++.+++|.+++++|++.+...
T Consensus 9 ~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~-~~~~~~~--~~~~wL~~iarn~~~d~~R~~~~~~~~ 85 (172)
T PRK09651 9 SLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRNALEKAY 85 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhh-ccccccc--CHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 3799999999999999999999999999999999999999998 3565432 58999999999999999997542110
Q ss_pred -------------cchhH---HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324 406 -------------LPENI---YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (488)
Q Consensus 406 -------------lP~~v---~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (488)
-|... .+....+.+++..|+. .+..+.+++|||+.||+++++|+..+++++..
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~ 162 (172)
T PRK09651 86 LEMLALMPEGGAPSPEERESQLETLQLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKATEH 162 (172)
T ss_pred hhHHhhccccCCCChHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhhhccCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 01111 1122233334433322 23347799999999999999999999988653
No 117
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=99.28 E-value=2.3e-11 Score=119.62 Aligned_cols=134 Identities=15% Similarity=0.075 Sum_probs=97.7
Q ss_pred HHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHH
Q 011324 320 KSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIF 398 (488)
Q Consensus 320 i~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IR 398 (488)
.+....|+ .+++.+++.| +.|+++|.++.++..+++||+||.|+.+|+. |+.. ..|.+|++.+++|.+++++|
T Consensus 9 ~~~~~~~~~~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~~---~~~~--~~~~~WL~~IarN~~id~~R 82 (228)
T PRK06704 9 LKNHIDMNHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQK---YSNK--DICMTLVYKIARNRWLDQIK 82 (228)
T ss_pred HhcccCCCHHHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH---cCcc--ccHHHHHHHHHHHHHHHHHh
Confidence 33444555 7888888877 7899999999999999999999999999985 5543 35999999999999999999
Q ss_pred HhcCCcccc--------hh-HHHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 399 QHSRTIRLP--------EN-IYTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 399 k~sr~irlP--------~~-v~e~l~kI~ka~~~L~~e--------lgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
++.+...+. .. ..+....+.++...|+.. ...+.|++|||+.||+|+++|+..+++++..+
T Consensus 83 k~k~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~R~v~lL~~~eg~S~~EIAe~LgiS~~tVksrL~Rark~L 160 (228)
T PRK06704 83 SKSVHEKIRDQITFEEPHEKIADLHEMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRL 160 (228)
T ss_pred ccccccccccccccCChHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHhhCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 876432211 00 111112233333333221 22367999999999999999999999998754
No 118
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=99.27 E-value=3e-11 Score=110.24 Aligned_cols=124 Identities=17% Similarity=0.200 Sum_probs=92.4
Q ss_pred HHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcc------
Q 011324 332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR------ 405 (488)
Q Consensus 332 kLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~ir------ 405 (488)
.++..|.+.|+++|.++.++..+++|++||+++++|+....|++. .|.+|++.+++|.+++++|++.+...
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 48899999999999999997653211
Q ss_pred ----cc------hh---HHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324 406 ----LP------EN---IYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (488)
Q Consensus 406 ----lP------~~---v~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (488)
.+ .. ..+....+..+...|+ ..+..+.+++|||+.||+|+++|+..+.+++..
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~EIA~~lgis~~tV~~~l~ra~~~ 152 (163)
T PRK07037 79 DGLDVPSPEASPEAALINRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALVH 152 (163)
T ss_pred cccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 11 00 0011222233332221 223347899999999999999999999887653
No 119
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=99.26 E-value=5.3e-11 Score=109.99 Aligned_cols=128 Identities=9% Similarity=0.055 Sum_probs=95.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCc--
Q 011324 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI-- 404 (488)
Q Consensus 327 d~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~i-- 404 (488)
+.++.+++..|.+.++++|.++.++..+++|++||.|+.+|+..+.++. ..|.+|++++++|.+++++|+.....
T Consensus 8 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~~---~~~~~wl~~Iarn~~~d~~Rr~~~~~~~ 84 (168)
T PRK12525 8 NTLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEGWRRQDLERAY 84 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCcccc---cCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3789999999999999999999999999999999999999986665542 36999999999999999998753210
Q ss_pred ------------ccchh---HHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCC
Q 011324 405 ------------RLPEN---IYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRM 457 (488)
Q Consensus 405 ------------rlP~~---v~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (488)
..|.. ..+....+.+++..|+ ..+..+.+++|||+.||+|+++|+..+.+++.
T Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~eg~s~~EIA~~l~is~~tV~~~l~ra~~ 160 (168)
T PRK12525 85 LQSLAEAPEAVQPSPEEQWMVIETLLAIDRLLDGLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAFK 160 (168)
T ss_pred HHHHhcccccccCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 01111 1111222333333322 22334789999999999999999999988754
No 120
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=99.26 E-value=2.8e-11 Score=110.35 Aligned_cols=123 Identities=11% Similarity=0.083 Sum_probs=91.8
Q ss_pred HHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc-------
Q 011324 334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL------- 406 (488)
Q Consensus 334 IesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irl------- 406 (488)
+..|.+.++.++.++.++..+++|++||.|+.+|+..+.|++ .+|.||++.+++|.+++++|++.+....
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 357889999999999999899999999999999999999875 3799999999999999999976421110
Q ss_pred --------chhH---HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 407 --------PENI---YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 407 --------P~~v---~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
|... .+....+..++..|+. ....+.+++|||+.||+|+++|+..+.+++..+
T Consensus 78 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~ra~~~L 149 (159)
T PRK12527 78 EERLHSPSPQTRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHC 149 (159)
T ss_pred cccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 1111 1112223333333322 233478999999999999999999999886543
No 121
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=99.21 E-value=1e-10 Score=117.82 Aligned_cols=128 Identities=12% Similarity=0.046 Sum_probs=94.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC--c-
Q 011324 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT--I- 404 (488)
Q Consensus 328 ~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~--i- 404 (488)
..+..|++.|.+.++.+|+++.++..++||++||.|+. |.....|+ ...|.+|++++++|.|++++|++.+. .
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 34678999999999999999999999999999999999 55567775 34799999999999999999976421 1
Q ss_pred ---cc----------chhH---HHHH-HHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 405 ---RL----------PENI---YTLL-SKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 405 ---rl----------P~~v---~e~l-~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
.+ |... .+.+ ..+..++..|+ .....+.+++|||+.||+|+++|+.++++++..+
T Consensus 80 ~~~~~~e~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~R~v~~L~~~~g~s~~EIA~~lg~s~~tVk~~l~RAr~~L 159 (293)
T PRK09636 80 VGPWLPEPVVEELDDPLEAVVAAEDLSLALMLALERLSPLERAAFLLHDVFGVPFDEIASTLGRSPAACRQLASRARKHV 159 (293)
T ss_pred cCCcCCcCCCCCCCChHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 11 1110 1111 11223333222 1222367999999999999999999999887543
No 122
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=99.13 E-value=3.8e-10 Score=113.41 Aligned_cols=124 Identities=17% Similarity=0.079 Sum_probs=89.7
Q ss_pred HHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCc------c
Q 011324 332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI------R 405 (488)
Q Consensus 332 kLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~i------r 405 (488)
+++..|.+.++.+|+++.++..++||++||+|+.+++. .|+. ...|.+|++++++|.|++++|+..+.. .
T Consensus 1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~--~~~~~awL~~Ia~n~~ld~lR~~~~~~~~~~~~~ 76 (281)
T TIGR02957 1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQ--IENPKAYLTKVVTRRCIDVLRSARARREVYVGPW 76 (281)
T ss_pred ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Cccc--ccCHHHHHHHHHHHHHHHHHHHhhhcccccCCCC
Confidence 37899999999999999999999999999999998775 5543 236999999999999999999764211 1
Q ss_pred cc----------hhHH---HHHH-HHHHHHHHH--------HHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 406 LP----------ENIY---TLLS-KVLEAKRLY--------IQEGNHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 406 lP----------~~v~---e~l~-kI~ka~~~L--------~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
+| .... +.+. .+..+...| ......+.+++|||+.||+|+.+|+.++++++..+
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 1111 111222222 11222367999999999999999999999887654
No 123
>PRK09191 two-component response regulator; Provisional
Probab=99.12 E-value=3.2e-10 Score=109.78 Aligned_cols=129 Identities=14% Similarity=0.086 Sum_probs=95.2
Q ss_pred HHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC-cccc
Q 011324 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT-IRLP 407 (488)
Q Consensus 329 ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~-irlP 407 (488)
++..|+..|.+.|+++|.++.++..+++|++||+|+.+|+...+|++. ..|.+|+++++++...+........ ....
T Consensus 2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~--~~~~~wl~~~~~~~~~~~~~~~~~~~~~~~ 79 (261)
T PRK09191 2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEA--SSPRVGLYRLFHRLWSSAGANDPEPGSPFE 79 (261)
T ss_pred chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCC--cchhhHHHHHHHHHhccccccCCCCCCCch
Confidence 578999999999999999999999999999999999999999999864 4699999999988764432221100 0011
Q ss_pred hhHHHHHHHHHHHHHH-HHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 408 ENIYTLLSKVLEAKRL-YIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 408 ~~v~e~l~kI~ka~~~-L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
..+...+.++....+. +....-.+.|++|||+.||+++++|+..+.+++..+
T Consensus 80 ~~l~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l 132 (261)
T PRK09191 80 ARAERRLAGLTPLPRQAFLLTALEGFSVEEAAEILGVDPAEAEALLDDARAEI 132 (261)
T ss_pred HHHHHHHHhCCHHHhHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 1234444444433333 222233478999999999999999999998876543
No 124
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=99.12 E-value=2.8e-10 Score=115.36 Aligned_cols=128 Identities=12% Similarity=-0.039 Sum_probs=94.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC--c-
Q 011324 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT--I- 404 (488)
Q Consensus 328 ~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~--i- 404 (488)
..+..+++.|.+.++.+|+++.++..++||++||.|+.+|++...+ ...|.+|++.+++|.|++++|+..+. .
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 5788999999999999999999999999999999999999987543 13599999999999999999975321 0
Q ss_pred -----ccc----------hhH---HHH-HHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCC
Q 011324 405 -----RLP----------ENI---YTL-LSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRM 457 (488)
Q Consensus 405 -----rlP----------~~v---~e~-l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (488)
..| ... .+. ...+..+...|. .....+.+++|||+.||+|+.+|+.++++++.
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 111 000 010 112222222221 11223679999999999999999999998876
Q ss_pred Cc
Q 011324 458 PL 459 (488)
Q Consensus 458 ~l 459 (488)
.+
T Consensus 161 ~L 162 (290)
T PRK09635 161 KI 162 (290)
T ss_pred HH
Confidence 54
No 125
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=99.10 E-value=1.2e-10 Score=95.08 Aligned_cols=75 Identities=29% Similarity=0.416 Sum_probs=64.2
Q ss_pred HHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCCCccccccCCC-CCCCCC
Q 011324 412 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVMPLLL-SHLPSD 486 (488)
Q Consensus 412 e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~tl~e~i~D~-s~~ped 486 (488)
+.+++|.++.+.|.+++||.||.+|||+.|||++++|+.++..++..+|||.+++.+++.++.++|.|+ ..+|++
T Consensus 1 E~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~~~~l~~~i~d~~~~~P~e 76 (78)
T PF04539_consen 1 EKLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDEDDSTLGDFIEDDDAPSPEE 76 (78)
T ss_dssp HHHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSSSEEGGGSSB-SSS--HHH
T ss_pred ChHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCCCCchhheecCCCCCChhh
Confidence 467899999999999999999999999999999999999999999999999999988889999999998 556654
No 126
>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=99.06 E-value=9.3e-10 Score=98.71 Aligned_cols=113 Identities=11% Similarity=0.056 Sum_probs=80.2
Q ss_pred HHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHh-----hCCCCCCchhhHHHHHHHHHHHHHHHHhcCCc
Q 011324 330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEK-----FKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 404 (488)
Q Consensus 330 rekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiek-----FDpskG~rFSTYA~~wIRnaI~~~IRk~sr~i 404 (488)
++.|+..|.++++.+|++|.. .+| +||.|+.+|+.+.+ |++ +..|.||++.+++|.+++++|++.+..
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 468999999999999999965 224 49999999999875 543 246999999999999999999765421
Q ss_pred cc------------c-hh--HHHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHH
Q 011324 405 RL------------P-EN--IYTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLE 449 (488)
Q Consensus 405 rl------------P-~~--v~e~l~kI~ka~~~L~~e--------lgr~pS~eEIAe~LGIS~etVk 449 (488)
.. + .. ..+....+.+++..|+.. ...+.|++|||+.||||+++|+
T Consensus 74 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~~~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 74 KIIYNSEITDIKLSLINVYSSNDLEFEFNDLISILPNKQKKIIYMKFFEDMKEIDIAKKLHISRQSVY 141 (142)
T ss_pred hhhhhhhhhccccchhHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHhhc
Confidence 11 0 00 001112233444433322 2246799999999999999986
No 127
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=99.01 E-value=1.2e-09 Score=99.15 Aligned_cols=107 Identities=12% Similarity=0.080 Sum_probs=75.1
Q ss_pred CCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc-----------------------
Q 011324 350 GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL----------------------- 406 (488)
Q Consensus 350 ~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irl----------------------- 406 (488)
++..+++|++||+|+.+|+.+..+ + +..|.+|++.+++|.|++++|++.+....
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 345679999999999999998863 3 45799999999999999999986532111
Q ss_pred --------chh---HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 407 --------PEN---IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 407 --------P~~---v~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
|.. ..+....+.+++..|+. .+..+.+++|||+.||||+++|+..+++++..+
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~L 150 (161)
T PRK09047 79 SADEGAESPADKLERAQVLQLIEEAIQKLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATHAL 150 (161)
T ss_pred cccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 000 00111223333333322 133478999999999999999999999887543
No 128
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=98.76 E-value=1e-07 Score=90.34 Aligned_cols=141 Identities=18% Similarity=0.185 Sum_probs=96.9
Q ss_pred HHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCC---CCCHhH--HHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHH
Q 011324 317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGR---GISLHD--LLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVR 390 (488)
Q Consensus 317 eeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~---g~d~ED--LIQEG~IGL~rAiekFDpskG~rFSTYA~~wIR 390 (488)
.+|+.+++.|| .|++.|+..|.+-+..+|+++.+. +.+.+| |++|.|+.+++.-...+.+.-..|-.|+...++
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 46888899999 899999999999999999876532 345555 477888877773332233333469999999999
Q ss_pred HHHHHHHHHhcCCcc------cc---------hhHHHHHHHHHHHHH-----------HHHHhcCCCCcHHHHHHHhCCC
Q 011324 391 QTIRKAIFQHSRTIR------LP---------ENIYTLLSKVLEAKR-----------LYIQEGNHSPDKEDLARRVGIT 444 (488)
Q Consensus 391 naI~~~IRk~sr~ir------lP---------~~v~e~l~kI~ka~~-----------~L~~elgr~pS~eEIAe~LGIS 444 (488)
+.+++++|++.+..| .+ ..-.+.+-.+.++.. .+......+.|.+|||+.||||
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 999999997654332 11 000111112222222 1222222378999999999999
Q ss_pred HHHHHHHHHHhCC
Q 011324 445 VEKLERLIFITRM 457 (488)
Q Consensus 445 ~etVk~~L~~ar~ 457 (488)
+.+|+..+..++.
T Consensus 165 ~~tV~r~l~~aR~ 177 (185)
T PF07638_consen 165 ERTVRRRLRRARA 177 (185)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999988764
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=97.92 E-value=2.7e-06 Score=61.14 Aligned_cols=34 Identities=41% Similarity=0.464 Sum_probs=30.1
Q ss_pred CcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHH
Q 011324 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR 287 (488)
Q Consensus 254 ~d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~ 287 (488)
+|+++.||++|+++|+||++||++|+++|+.+..
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=97.13 E-value=0.012 Score=65.96 Aligned_cols=34 Identities=32% Similarity=0.493 Sum_probs=31.7
Q ss_pred CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHH
Q 011324 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLI 286 (488)
Q Consensus 253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~ 286 (488)
.+||+++||+++|+.||||+|+|++++++|..+.
T Consensus 102 t~DPVRMYLREMG~V~LLTREgEIeIAKRIE~G~ 135 (619)
T PRK05658 102 TDDPVRMYLREMGTVELLTREGEIEIAKRIEAGE 135 (619)
T ss_pred CCChHHHHHHHhccCcCCCcHHHHHHHHHHHHHH
Confidence 5899999999999999999999999999998754
No 131
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=96.48 E-value=0.023 Score=55.89 Aligned_cols=33 Identities=33% Similarity=0.579 Sum_probs=27.8
Q ss_pred HHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011324 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 320 (488)
Q Consensus 288 le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi 320 (488)
+.++...+...+|++||.+|.|+.+|++.+.+.
T Consensus 89 ~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~ 121 (238)
T TIGR02393 89 LIKAERQLTQELGREPTDEELAERMGMPAEKVR 121 (238)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHH
Confidence 445667788889999999999999999987664
No 132
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=96.25 E-value=0.039 Score=54.64 Aligned_cols=30 Identities=0% Similarity=0.129 Sum_probs=26.4
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324 429 NHSPDKEDLARRVGITVEKLERLIFITRMP 458 (488)
Q Consensus 429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (488)
..+.|++|||+.||+|+++|+..+++++..
T Consensus 215 ~~~~s~~EIA~~lgis~~tV~~~~~ra~~~ 244 (251)
T PRK07670 215 KEELTLTEIGQVLNLSTSRISQIHSKALFK 244 (251)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 347899999999999999999999887654
No 133
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=96.17 E-value=0.031 Score=55.89 Aligned_cols=30 Identities=3% Similarity=0.149 Sum_probs=26.1
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324 429 NHSPDKEDLARRVGITVEKLERLIFITRMP 458 (488)
Q Consensus 429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (488)
..+.|++|||+.||+|.++|+.+++++...
T Consensus 219 ~e~~t~~EIA~~lgis~~~V~~~~~ral~k 248 (257)
T PRK05911 219 YEELVLKEIGKILGVSESRVSQIHSKALLK 248 (257)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 447899999999999999999998877543
No 134
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=96.14 E-value=0.015 Score=58.14 Aligned_cols=34 Identities=29% Similarity=0.510 Sum_probs=28.7
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011324 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 320 (488)
Q Consensus 287 ~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi 320 (488)
++.++...|...+|++|+..+.|+.+|++.+++.
T Consensus 114 ~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~ 147 (256)
T PRK07408 114 QAKKVRQELRQELGRQPTDQEIAQALDISLEEWQ 147 (256)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHH
Confidence 3455677888899999999999999999987664
No 135
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=96.11 E-value=0.17 Score=50.89 Aligned_cols=149 Identities=19% Similarity=0.192 Sum_probs=83.8
Q ss_pred HHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHHHHH
Q 011324 256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 335 (488)
Q Consensus 256 ~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~ArekLIe 335 (488)
.+..||++-. +.--+.--.+++. +++.+..+|+..+||+||..|.|...|++.+++...+..+.
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 5667888876 2112222233333 45567788999999999999999999999877764443332
Q ss_pred HHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHHHH
Q 011324 336 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLS 415 (488)
Q Consensus 336 snlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~e~l~ 415 (488)
-.....+-......+... +. ..-+..+..+-.+...+.+...+. .+|.. -
T Consensus 152 --~~~~~sld~~~~~~~d~~--------------~~---~~~~~~~~~~~~~~~~~~l~~ai~------~L~ER----E- 201 (247)
T COG1191 152 --GSQLLSLDEDVLKDDDDD--------------VD---DQIENPDDGVEKEELLEILKEAIE------PLPER----E- 201 (247)
T ss_pred --cccccchhhhhccccccc--------------hh---hccccchhHHHHHHHHHHHHHHHH------ccCHH----H-
Confidence 111111111111111100 11 111233445555555566665554 12211 0
Q ss_pred HHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 416 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 416 kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
+. -+...+..+.|..|||+.||||+.+|-.+...+
T Consensus 202 ---k~--Vl~l~y~eelt~kEI~~~LgISes~VSql~kka 236 (247)
T COG1191 202 ---KL--VLVLRYKEELTQKEIAEVLGISESRVSRLHKKA 236 (247)
T ss_pred ---HH--HHHHHHHhccCHHHHHHHhCccHHHHHHHHHHH
Confidence 11 122233447899999999999999998876654
No 136
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=96.02 E-value=0.072 Score=53.37 Aligned_cols=34 Identities=26% Similarity=0.526 Sum_probs=28.0
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011324 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 320 (488)
Q Consensus 287 ~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi 320 (488)
.+.+....|+..+|++|+..+.|...|++.+.+.
T Consensus 119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~ 152 (268)
T PRK06288 119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYN 152 (268)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHH
Confidence 4555667788889999999999999999876654
No 137
>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=96.01 E-value=0.022 Score=46.00 Aligned_cols=56 Identities=18% Similarity=0.301 Sum_probs=46.6
Q ss_pred HHHHhhhcH-HHHHHHHHHHHHHHHHHHHHcc----C--CCCCHhHHHHHHHHHHHHhHHhhC
Q 011324 319 LKSELHSGN-SSREKLINANLRLVVHVAKQYQ----G--RGISLHDLLQEGSMGLMKSVEKFK 374 (488)
Q Consensus 319 Li~~l~~Gd-~ArekLIesnlrLV~sIAkry~----~--~g~d~EDLIQEG~IGL~rAiekFD 374 (488)
++.++.+|| .|.+++++.|.+++.+.+.|-. + .+.--+|+-|+--..|++++-+|+
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 9999999999999999998722 2 244569999999999999999996
No 138
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=96.00 E-value=0.1 Score=55.01 Aligned_cols=128 Identities=20% Similarity=0.251 Sum_probs=70.9
Q ss_pred HHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHH-HHHHH
Q 011324 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQE-GSMGL 366 (488)
Q Consensus 288 le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQE-G~IGL 366 (488)
+.+...+|...+|++||..|.|+.+|++.+.+...+.. +.+ ...+++.+.+ +-..|
T Consensus 218 ~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~-------------------~~~----~~SLd~~~~~~~~~~l 274 (367)
T PRK09210 218 LIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKI-------------------AQE----PVSLETPIGEEDDSHL 274 (367)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHH-------------------hcC----CCCcCCCCCCCCcchh
Confidence 45567788889999999999999999998776432211 111 1111111111 00111
Q ss_pred HHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHHHHHHHHHHHHHHHhc----CCCCcHHHHHHHhC
Q 011324 367 MKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEG----NHSPDKEDLARRVG 442 (488)
Q Consensus 367 ~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~e~l~kI~ka~~~L~~el----gr~pS~eEIAe~LG 442 (488)
...+. |..............++..+.++|. .+|..-. .| +...+ +.+.|.+|||+.||
T Consensus 275 ~d~i~--d~~~~~p~~~~~~~~~~~~l~~~l~------~L~~rEr----~V------l~lrygl~~~~~~tl~EIa~~lg 336 (367)
T PRK09210 275 GDFIE--DQDATSPADHAAYELLKEQLEDVLD------TLTDREE----NV------LRLRFGLDDGRTRTLEEVGKVFG 336 (367)
T ss_pred hhhcc--CCCCCCHHHHHHHHHHHHHHHHHHH------hCCHHHH----HH------HHHHhccCCCCCccHHHHHHHHC
Confidence 11121 1111223344445555555555553 2332111 11 22222 35789999999999
Q ss_pred CCHHHHHHHHHHhC
Q 011324 443 ITVEKLERLIFITR 456 (488)
Q Consensus 443 IS~etVk~~L~~ar 456 (488)
+|.++|+.+...|.
T Consensus 337 vs~erVrQi~~~Al 350 (367)
T PRK09210 337 VTRERIRQIEAKAL 350 (367)
T ss_pred CCHHHHHHHHHHHH
Confidence 99999999977663
No 139
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=95.97 E-value=0.055 Score=54.42 Aligned_cols=34 Identities=26% Similarity=0.524 Sum_probs=28.2
Q ss_pred HHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHH
Q 011324 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 321 (488)
Q Consensus 288 le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~ 321 (488)
+.+...++...+|++||..|.|+.+|++.+++..
T Consensus 129 i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~ 162 (264)
T PRK07122 129 LGRATAELSQRLGRAPTASELAAELGMDREEVVE 162 (264)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 4456677888899999999999999999877643
No 140
>PRK05949 RNA polymerase sigma factor; Validated
Probab=95.82 E-value=0.053 Score=56.41 Aligned_cols=34 Identities=26% Similarity=0.472 Sum_probs=27.9
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011324 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 320 (488)
Q Consensus 287 ~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi 320 (488)
++.+.+..+...+|++|+..|.|+.+|++.+.+.
T Consensus 179 ~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~ 212 (327)
T PRK05949 179 KIKKTQRELSQKLGRSATPAEIAKELELEPSQIR 212 (327)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHH
Confidence 3455666777889999999999999999987664
No 141
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=95.75 E-value=0.16 Score=55.97 Aligned_cols=34 Identities=32% Similarity=0.567 Sum_probs=29.0
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011324 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 320 (488)
Q Consensus 287 ~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi 320 (488)
++.+++.+|...+|++||.+|.|+.+|++.+.+.
T Consensus 359 kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~ 392 (509)
T PRK05901 359 KLGRIERELLQELGREPTPEELAKEMGFTPEKVR 392 (509)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHH
Confidence 4556778888999999999999999999987664
No 142
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=95.69 E-value=0.13 Score=52.37 Aligned_cols=30 Identities=20% Similarity=0.279 Sum_probs=26.2
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
.+.|.+|||+.||||.++|+.+++.+...+
T Consensus 244 ~~~t~~EIa~~lgvs~~~V~q~~~~Al~kL 273 (289)
T PRK07500 244 DGATLEALGEELGISKERVRQIEARALEKL 273 (289)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 478999999999999999999998876543
No 143
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=95.57 E-value=0.13 Score=55.32 Aligned_cols=35 Identities=20% Similarity=0.485 Sum_probs=30.3
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHH
Q 011324 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 321 (488)
Q Consensus 287 ~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~ 321 (488)
++.+.+..|...+|+.|+..|.|+.+||+.+.+..
T Consensus 263 ~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~ 297 (415)
T PRK07598 263 KIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVRE 297 (415)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 56677888888999999999999999999887753
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=95.41 E-value=0.043 Score=53.42 Aligned_cols=31 Identities=39% Similarity=0.612 Sum_probs=25.8
Q ss_pred HHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011324 290 KEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 320 (488)
Q Consensus 290 ~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi 320 (488)
+....+...+|++||..+.|+.+|++.+++.
T Consensus 101 ~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~ 131 (231)
T TIGR02885 101 YMKEELSKELGREPTINELAEALGVSPEEIV 131 (231)
T ss_pred HHHHHHHHHHCcCCCHHHHHHHHCcCHHHHH
Confidence 3456677788999999999999999987664
No 145
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=95.38 E-value=0.16 Score=52.83 Aligned_cols=34 Identities=32% Similarity=0.460 Sum_probs=28.9
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011324 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 320 (488)
Q Consensus 287 ~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi 320 (488)
++.++..+|...+|++||..|.|+.+|++.+.+.
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 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=95.26 E-value=0.23 Score=50.64 Aligned_cols=34 Identities=26% Similarity=0.509 Sum_probs=28.0
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011324 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 320 (488)
Q Consensus 287 ~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi 320 (488)
++.+.+..+...+|++|+..+.|+.+|++.+.+.
T Consensus 162 ~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~ 195 (298)
T TIGR02997 162 KIKKVQRELSQKLGRTPSEAEIAEALELEPEQVR 195 (298)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHH
Confidence 4455666777889999999999999999987764
No 147
>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=94.85 E-value=0.25 Score=47.88 Aligned_cols=34 Identities=32% Similarity=0.651 Sum_probs=27.5
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011324 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 320 (488)
Q Consensus 287 ~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi 320 (488)
++.++..++...+|++|+.++.|+.+|++.+++.
T Consensus 84 ~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~ 117 (224)
T TIGR02479 84 KLERAIRELEARLGREPTEEEIAEELGMDLKEYR 117 (224)
T ss_pred HHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHH
Confidence 3455667788889999999999999999876653
No 148
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=94.82 E-value=0.15 Score=52.72 Aligned_cols=34 Identities=26% Similarity=0.522 Sum_probs=28.2
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011324 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 320 (488)
Q Consensus 287 ~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi 320 (488)
++.+.+..+...+|++|+..+.|+.+|++.+.+.
T Consensus 169 ~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~ 202 (317)
T PRK07405 169 KIKKAQRQLSQQLGRAATIGELAEELELTPKQVR 202 (317)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHH
Confidence 4556777788889999999999999999876653
No 149
>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=94.79 E-value=0.16 Score=50.28 Aligned_cols=29 Identities=17% Similarity=0.250 Sum_probs=25.5
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHHhCC
Q 011324 429 NHSPDKEDLARRVGITVEKLERLIFITRM 457 (488)
Q Consensus 429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (488)
..+.|++|||+.||+++++|+.++++++.
T Consensus 219 ~~g~s~~eIA~~lgis~~~V~~~~~ra~~ 247 (255)
T TIGR02941 219 EENLSQKETGERLGISQMHVSRLQRQAIS 247 (255)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 44789999999999999999999887754
No 150
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=94.73 E-value=0.31 Score=51.79 Aligned_cols=34 Identities=32% Similarity=0.584 Sum_probs=28.6
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011324 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 320 (488)
Q Consensus 287 ~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi 320 (488)
++.+....|...+|++||..|.|+.+|++.+.+.
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 4556677888899999999999999999987663
No 151
>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=94.61 E-value=0.072 Score=43.20 Aligned_cols=37 Identities=30% Similarity=0.593 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHH
Q 011324 286 IRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 322 (488)
Q Consensus 286 ~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~ 322 (488)
.++.+++.+|+..+||+||.+|.|+.+|++.+++...
T Consensus 4 ~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~ 40 (78)
T PF04539_consen 4 RKIERARRELEQELGREPTDEEIAEELGISVEEVREL 40 (78)
T ss_dssp HHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHH
Confidence 3567889999999999999999999999998777543
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=94.52 E-value=0.49 Score=47.03 Aligned_cols=35 Identities=26% Similarity=0.297 Sum_probs=28.1
Q ss_pred HHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHH
Q 011324 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 322 (488)
Q Consensus 288 le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~ 322 (488)
+.+...++...+|++|+.++.|+.+|++.+++...
T Consensus 122 ~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~ 156 (254)
T TIGR02850 122 ALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFA 156 (254)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHH
Confidence 33456677788999999999999999998877543
No 153
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=93.81 E-value=0.53 Score=46.09 Aligned_cols=30 Identities=3% Similarity=0.147 Sum_probs=26.3
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324 429 NHSPDKEDLARRVGITVEKLERLIFITRMP 458 (488)
Q Consensus 429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (488)
..+.|++|||+.||+|+++|+..+++++..
T Consensus 198 ~~g~s~~EIA~~lgis~~tV~~~~~ra~~~ 227 (236)
T PRK06986 198 QEELNLKEIGAVLGVSESRVSQIHSQAIKR 227 (236)
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 347899999999999999999999887654
No 154
>PRK05572 sporulation sigma factor SigF; Validated
Probab=93.56 E-value=0.49 Score=46.92 Aligned_cols=29 Identities=21% Similarity=0.308 Sum_probs=25.2
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFITRMP 458 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (488)
.+.|.+|||+.+|++..+|..+.+++...
T Consensus 217 ~~~s~~eIA~~lgis~~~V~~~~~ral~k 245 (252)
T PRK05572 217 KDKTQSEVAKRLGISQVQVSRLEKKILKQ 245 (252)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 47899999999999999999998876543
No 155
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=93.28 E-value=0.76 Score=45.72 Aligned_cols=33 Identities=24% Similarity=0.307 Sum_probs=26.9
Q ss_pred HHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHH
Q 011324 289 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 321 (488)
Q Consensus 289 e~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~ 321 (488)
.+...++...+|++|+..|.|..+|++.+++..
T Consensus 126 ~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~ 158 (258)
T PRK08215 126 LQVREKLINENSKEPTVEEIAKELEVPREEVVF 158 (258)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHH
Confidence 345567777889999999999999999887653
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=93.18 E-value=0.47 Score=45.95 Aligned_cols=29 Identities=21% Similarity=0.350 Sum_probs=25.6
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFITRMP 458 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (488)
.+.|++|||+.||++..+|+.+++++...
T Consensus 193 ~~~s~~eIA~~lgis~~~v~~~~~ra~~~ 221 (227)
T TIGR02980 193 EDKTQSEIAERLGISQMHVSRLLRRALKK 221 (227)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 47899999999999999999999887543
No 157
>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=92.53 E-value=0.11 Score=39.34 Aligned_cols=31 Identities=16% Similarity=0.171 Sum_probs=23.2
Q ss_pred hcCCCCcHHHHHHHhCCCHHHHHHHHHHhCC
Q 011324 427 EGNHSPDKEDLARRVGITVEKLERLIFITRM 457 (488)
Q Consensus 427 elgr~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (488)
.+..+.+.+|||+.+|+|+.+|+..+.+++.
T Consensus 22 ~~~~g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 22 RYFQGMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp HHTS---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred HHHHCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 3455789999999999999999999988753
No 158
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=92.43 E-value=1 Score=44.32 Aligned_cols=33 Identities=15% Similarity=0.402 Sum_probs=27.5
Q ss_pred HHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011324 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 320 (488)
Q Consensus 288 le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi 320 (488)
+.+....+...+|++|+..+.|+.+|++.+++.
T Consensus 103 i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~ 135 (231)
T PRK12427 103 TNDAIREIAKRLGHEPNFEEISAELNLTAEEYQ 135 (231)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHH
Confidence 345567788889999999999999999987764
No 159
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=92.36 E-value=0.72 Score=45.74 Aligned_cols=30 Identities=17% Similarity=0.194 Sum_probs=26.1
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324 429 NHSPDKEDLARRVGITVEKLERLIFITRMP 458 (488)
Q Consensus 429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (488)
..+.+++|||+.||||.++|+.++++++..
T Consensus 219 ~~g~s~~eIA~~l~is~~tV~~~~~ra~~k 248 (257)
T PRK08583 219 IENLSQKETGERLGISQMHVSRLQRQAIKK 248 (257)
T ss_pred hCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 347899999999999999999999877643
No 160
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=91.88 E-value=0.52 Score=37.95 Aligned_cols=43 Identities=26% Similarity=0.409 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCC-HHHHHHHHHH
Q 011324 412 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGIT-VEKLERLIFI 454 (488)
Q Consensus 412 e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS-~etVk~~L~~ 454 (488)
+.-.+|-..+..+..+.|..||+.|||+.+|+. ...|...|..
T Consensus 6 ~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~ 49 (65)
T PF01726_consen 6 ERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKA 49 (65)
T ss_dssp HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence 445566677777788888899999999999997 9999988864
No 161
>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=91.85 E-value=0.45 Score=35.53 Aligned_cols=31 Identities=19% Similarity=0.239 Sum_probs=25.6
Q ss_pred HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhC
Q 011324 426 QEGNHSPDKEDLARRVGITVEKLERLIFITR 456 (488)
Q Consensus 426 ~elgr~pS~eEIAe~LGIS~etVk~~L~~ar 456 (488)
..+..+.|.+|||+.||+|.++|+.+...+.
T Consensus 15 ~~y~~~~t~~eIa~~lg~s~~~V~~~~~~al 45 (50)
T PF04545_consen 15 LRYFEGLTLEEIAERLGISRSTVRRILKRAL 45 (50)
T ss_dssp HHHTST-SHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred HHhcCCCCHHHHHHHHCCcHHHHHHHHHHHH
Confidence 3446688999999999999999999988764
No 162
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=91.69 E-value=0.37 Score=48.75 Aligned_cols=31 Identities=23% Similarity=0.323 Sum_probs=27.3
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 429 NHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
..+.|++|||+.||+|+++|+.++++|+..+
T Consensus 240 ~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkL 270 (285)
T TIGR02394 240 YEPATLEEVAAEVGLTRERVRQIQVEALKKL 270 (285)
T ss_pred CCCccHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4578999999999999999999999887654
No 163
>PHA02547 55 RNA polymerase sigma factor; Provisional
Probab=91.39 E-value=0.55 Score=44.82 Aligned_cols=66 Identities=12% Similarity=0.151 Sum_probs=53.3
Q ss_pred HHHHHHHHHHHHccCCCCC---HhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhc
Q 011324 336 ANLRLVVHVAKQYQGRGIS---LHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS 401 (488)
Q Consensus 336 snlrLV~sIAkry~~~g~d---~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~s 401 (488)
+-+..+-.+.++|.-+|-. -+|+|.+|.-.+++.+..||+++...+-+|+..++-++..+.|.+..
T Consensus 45 ~imkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~kEk 113 (179)
T PHA02547 45 AIMKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIKKEK 113 (179)
T ss_pred HHHHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHHHHH
Confidence 3445555566665444544 59999999999999999999999999999999999999998887654
No 164
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=89.48 E-value=7.6 Score=39.53 Aligned_cols=28 Identities=14% Similarity=0.253 Sum_probs=24.6
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHhCC
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFITRM 457 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (488)
.+.|.+|||+.||+|.++|+.+...+..
T Consensus 247 ~~~Tl~EIA~~lgvS~~rVrqi~~~Al~ 274 (284)
T PRK06596 247 DKSTLQELAAEYGVSAERVRQIEKNAMK 274 (284)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4789999999999999999999887643
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=87.84 E-value=1.8 Score=31.89 Aligned_cols=34 Identities=21% Similarity=0.238 Sum_probs=23.4
Q ss_pred HHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 420 AKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 420 a~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
.+-.+.+..+ ..++.|||+.+|+|..+|..++++
T Consensus 7 ~Il~~Lq~d~-r~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 7 KILRLLQEDG-RRSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHH-T-TS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHcC-CccHHHHHHHHCcCHHHHHHHHHH
Confidence 3333334445 579999999999999999998764
No 166
>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=85.22 E-value=1.7 Score=31.03 Aligned_cols=28 Identities=14% Similarity=0.209 Sum_probs=24.7
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHhCC
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFITRM 457 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (488)
.+.+..+||+.+|++..+|...+..++.
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4789999999999999999999887654
No 167
>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=84.13 E-value=2.9 Score=32.21 Aligned_cols=48 Identities=21% Similarity=0.320 Sum_probs=35.5
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHH
Q 011324 405 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLI 452 (488)
Q Consensus 405 rlP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L 452 (488)
.+|....+.+...-+....|..++....+-.|||+.+|++..+|+.=+
T Consensus 2 ~Ip~~ti~RL~~Y~r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRKDl 49 (50)
T PF06971_consen 2 KIPKATIRRLPLYLRYLEQLKEEGVERVSSQELAEALGITPAQVRKDL 49 (50)
T ss_dssp S-SHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHcCCeeECHHHHHHHHCCCHHHhcccC
Confidence 467667777777777777888777778899999999999999998643
No 168
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=82.91 E-value=4.5 Score=42.85 Aligned_cols=126 Identities=10% Similarity=0.026 Sum_probs=80.6
Q ss_pred HHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhH
Q 011324 331 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI 410 (488)
Q Consensus 331 ekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v 410 (488)
+..+..-.+.+..-.-+|.++-.-.||.+||+|+..++.-.+=.+-+ .-..|++-.-||.-++.+|++.+.-..|.+.
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 33444444445544455666666789999999987665555444433 3789999999999999999987654444322
Q ss_pred HHHH---------------------HHH---------HHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324 411 YTLL---------------------SKV---------LEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (488)
Q Consensus 411 ~e~l---------------------~kI---------~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (488)
.... +-| ......|.-..--+.|..|||...=+++.++.+++-+++..
T Consensus 86 ~~~~e~~e~~~a~~~~d~~i~Dd~LRLiFvccHPal~~~~riALtLR~v~GLs~~eIArAFLv~e~am~QRivRAK~r 163 (415)
T COG4941 86 LLSDEDEEMEEAEALDDEHIRDDRLRLIFVCCHPALPPEQRIALTLRLVGGLSTAEIARAFLVPEAAMAQRIVRAKAR 163 (415)
T ss_pred cccccchhhhccccccccccchhhHHhhhhhcCCCCChhhHHHHHHHHHcCCcHHHHHHHHcCCcHHHHHHHHHHHHH
Confidence 1111 110 01111122222226799999999999999999998877654
No 169
>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=82.86 E-value=2.3 Score=35.36 Aligned_cols=25 Identities=12% Similarity=0.155 Sum_probs=22.7
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
.+.|+.|||+.||+|+.+|+..+..
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 3789999999999999999999873
No 170
>PRK06930 positive control sigma-like factor; Validated
Probab=82.54 E-value=1.3 Score=42.09 Aligned_cols=31 Identities=10% Similarity=0.082 Sum_probs=26.9
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324 428 GNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (488)
Q Consensus 428 lgr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (488)
+..+.++.|||+.||+++++|+..+.+++..
T Consensus 127 ~~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~k 157 (170)
T PRK06930 127 RGYGLSYSEIADYLNIKKSTVQSMIERAEKK 157 (170)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 3347899999999999999999999988654
No 171
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=79.72 E-value=1.8 Score=45.04 Aligned_cols=31 Identities=26% Similarity=0.399 Sum_probs=27.1
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 429 NHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
..+.|++|||+.||++.++|+.++++|+..+
T Consensus 280 ~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kL 310 (325)
T PRK05657 280 YEAATLEDVAREIGLTRERVRQIQVEALRRL 310 (325)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 3478999999999999999999999887554
No 172
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=79.58 E-value=1.6 Score=31.94 Aligned_cols=29 Identities=17% Similarity=0.276 Sum_probs=25.1
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 431 SPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
+.+..|||+.+|++..+|+..+.++...+
T Consensus 18 g~s~~eia~~l~is~~tv~~~~~~~~~kl 46 (58)
T smart00421 18 GLTNKEIAERLGISEKTVKTHLSNIMRKL 46 (58)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 57999999999999999999998775443
No 173
>PRK00118 putative DNA-binding protein; Validated
Probab=79.37 E-value=2.1 Score=37.81 Aligned_cols=29 Identities=10% Similarity=0.023 Sum_probs=25.7
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFITRMP 458 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (488)
.+.|+.|||+.+|+|..+|...+.+++..
T Consensus 32 eg~S~~EIAe~lGIS~~TV~r~L~RArkk 60 (104)
T PRK00118 32 DDYSLGEIAEEFNVSRQAVYDNIKRTEKL 60 (104)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 37899999999999999999999887643
No 174
>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=79.23 E-value=4.1 Score=32.61 Aligned_cols=30 Identities=17% Similarity=0.316 Sum_probs=24.1
Q ss_pred HHHhcCCCCcHHHHHHHhCCCHHHHHHHHH
Q 011324 424 YIQEGNHSPDKEDLARRVGITVEKLERLIF 453 (488)
Q Consensus 424 L~~elgr~pS~eEIAe~LGIS~etVk~~L~ 453 (488)
+..+.+...+..+||+.||++..+|+..-.
T Consensus 15 ~y~~~~g~i~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 15 IYKESNGKIKLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred HHHHhCCCccHHHHHHHHCCCHHHHHHHhh
Confidence 334444489999999999999999998754
No 175
>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=79.14 E-value=1.7 Score=33.83 Aligned_cols=28 Identities=18% Similarity=0.224 Sum_probs=24.7
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHhCC
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFITRM 457 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (488)
|..+..|||+.|||+..++...++++..
T Consensus 22 R~~tl~elA~~lgis~st~~~~LRrae~ 49 (53)
T PF04967_consen 22 RRITLEELAEELGISKSTVSEHLRRAER 49 (53)
T ss_pred CcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 5669999999999999999999987743
No 176
>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=78.95 E-value=6.6 Score=28.85 Aligned_cols=27 Identities=22% Similarity=0.399 Sum_probs=21.3
Q ss_pred hcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 427 EGNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 427 elgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
+.+ ..|..|||+.+|++..+|...++.
T Consensus 14 ~~~-~~t~~ela~~~~is~~tv~~~l~~ 40 (48)
T PF13412_consen 14 ENP-RITQKELAEKLGISRSTVNRYLKK 40 (48)
T ss_dssp HCT-TS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred HcC-CCCHHHHHHHhCCCHHHHHHHHHH
Confidence 344 589999999999999999998864
No 177
>PRK04217 hypothetical protein; Provisional
Probab=78.66 E-value=2.2 Score=38.00 Aligned_cols=30 Identities=17% Similarity=0.313 Sum_probs=26.2
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
.+.|++|||+.+||+..+|..++.+++..|
T Consensus 57 eGlS~~EIAk~LGIS~sTV~r~L~RArkkL 86 (110)
T PRK04217 57 EGLTQEEAGKRMGVSRGTVWRALTSARKKV 86 (110)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 367999999999999999999998876544
No 178
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=76.74 E-value=35 Score=36.27 Aligned_cols=33 Identities=36% Similarity=0.567 Sum_probs=27.2
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHH
Q 011324 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDL 319 (488)
Q Consensus 287 ~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeL 319 (488)
+|.+++.+|...+|++|+.++.|+.+|++..++
T Consensus 190 kl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V 222 (342)
T COG0568 190 KLRRVKRELLQELGREPTPEEIAEELGVSPDKV 222 (342)
T ss_pred HHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHH
Confidence 455677788888999999999999999986543
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=76.53 E-value=2.3 Score=31.25 Aligned_cols=28 Identities=11% Similarity=0.162 Sum_probs=24.7
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324 431 SPDKEDLARRVGITVEKLERLIFITRMP 458 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (488)
+.+.+|||+.+|++..+|+..+++++..
T Consensus 15 ~~s~~eia~~l~~s~~tv~~~~~~~~~~ 42 (57)
T cd06170 15 GKTNKEIADILGISEKTVKTHLRNIMRK 42 (57)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 5799999999999999999999876543
No 180
>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=74.19 E-value=7.9 Score=29.09 Aligned_cols=32 Identities=19% Similarity=0.305 Sum_probs=24.4
Q ss_pred HHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 423 LYIQEGNHSPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 423 ~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
.|....+ ..|.+|||+.||+|..+|...+...
T Consensus 8 ~L~~~~~-~it~~eLa~~l~vS~rTi~~~i~~L 39 (55)
T PF08279_consen 8 LLLESKE-PITAKELAEELGVSRRTIRRDIKEL 39 (55)
T ss_dssp HHHHTTT-SBEHHHHHHHCTS-HHHHHHHHHHH
T ss_pred HHHHcCC-CcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 3434444 4899999999999999999988754
No 181
>PHA02591 hypothetical protein; Provisional
Probab=74.04 E-value=3.9 Score=34.52 Aligned_cols=23 Identities=26% Similarity=0.401 Sum_probs=21.5
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHH
Q 011324 431 SPDKEDLARRVGITVEKLERLIF 453 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~ 453 (488)
+.|.++||+.||++..+|+..++
T Consensus 59 GlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 59 GFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHh
Confidence 68999999999999999999876
No 182
>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=73.77 E-value=4.6 Score=28.39 Aligned_cols=23 Identities=26% Similarity=0.466 Sum_probs=18.3
Q ss_pred CcHHHHHHHhCCCHHHHHHHHHH
Q 011324 432 PDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 432 pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
.|.+|||+.+|++.++|-.++..
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~ 25 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKK 25 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHH
T ss_pred cCHHHHHHHhCCcHHHHHHHHHH
Confidence 57899999999999999988764
No 183
>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=73.35 E-value=2.6 Score=39.01 Aligned_cols=29 Identities=7% Similarity=0.072 Sum_probs=25.1
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFITRMP 458 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (488)
.+.|.+|||+.||+|..+|+.+.++++..
T Consensus 20 ~GlTq~EIAe~LgiS~stV~~~e~ra~kk 48 (137)
T TIGR00721 20 KGLSQKEIAKELKTTRANVSAIEKRAMEN 48 (137)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHhHHHH
Confidence 47899999999999999999888776543
No 184
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=73.20 E-value=8.7 Score=28.50 Aligned_cols=24 Identities=25% Similarity=0.393 Sum_probs=21.7
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 431 SPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
..|..+||+.+|++..+|..++..
T Consensus 27 ~~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 27 SRSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHh
Confidence 469999999999999999999864
No 185
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=73.08 E-value=6.2 Score=29.12 Aligned_cols=27 Identities=15% Similarity=0.207 Sum_probs=18.6
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 428 GNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 428 lgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
+..+.|..|||+.||.+..+|...+++
T Consensus 17 ~~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 17 LEQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp HCS---HHHHHHHTT--HHHHHHHHHH
T ss_pred HHcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 334689999999999999999888764
No 186
>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=72.50 E-value=4.5 Score=31.05 Aligned_cols=32 Identities=13% Similarity=0.123 Sum_probs=25.1
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 428 GNHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 428 lgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
...+.+.+|||+.+|+++.+|+..+...+..+
T Consensus 15 l~~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 15 LAQGMSNKEIAEELGISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp HHTTS-HHHHHHHHTSHHHHHHHHHHHHHHHH
T ss_pred HHhcCCcchhHHhcCcchhhHHHHHHHHHHHh
Confidence 33478999999999999999999887665443
No 187
>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=70.32 E-value=6.4 Score=29.04 Aligned_cols=23 Identities=13% Similarity=0.315 Sum_probs=17.8
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHH
Q 011324 431 SPDKEDLARRVGITVEKLERLIF 453 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~ 453 (488)
+.++.+||+.+||+..+|..++.
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 47999999999999999988763
No 188
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=69.36 E-value=3.6 Score=38.21 Aligned_cols=27 Identities=11% Similarity=0.208 Sum_probs=23.6
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHhC
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFITR 456 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar 456 (488)
.+.|.+|||+.||+|..+|..+...++
T Consensus 20 ~GlTq~EIAe~LGiS~~tVs~ie~ra~ 46 (141)
T PRK03975 20 RGLTQQEIADILGTSRANVSSIEKRAR 46 (141)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 478999999999999999998876654
No 189
>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=68.10 E-value=13 Score=29.24 Aligned_cols=26 Identities=8% Similarity=0.049 Sum_probs=23.2
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHhC
Q 011324 431 SPDKEDLARRVGITVEKLERLIFITR 456 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar 456 (488)
+.++.|||+.||++..+|.....+..
T Consensus 13 G~~~~eIA~~Lg~~~~TV~~W~~r~~ 38 (58)
T PF06056_consen 13 GWSIKEIAEELGVPRSTVYSWKDRYK 38 (58)
T ss_pred CCCHHHHHHHHCCChHHHHHHHHhhC
Confidence 67999999999999999999987653
No 190
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=67.14 E-value=6.7 Score=38.11 Aligned_cols=39 Identities=5% Similarity=0.069 Sum_probs=30.0
Q ss_pred HHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccc
Q 011324 423 LYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSM 461 (488)
Q Consensus 423 ~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSL 461 (488)
++...+.++.+.+|||+.|++|++||+........++-+
T Consensus 155 eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~v 193 (211)
T COG2197 155 EVLRLLAEGLSNKEIAEELNLSEKTVKTHVSNILRKLGV 193 (211)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHhHHHHHHHHHHHHcCC
Confidence 344445568899999999999999999988766555443
No 191
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=65.90 E-value=6 Score=38.18 Aligned_cols=43 Identities=2% Similarity=-0.012 Sum_probs=31.6
Q ss_pred HHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccc
Q 011324 419 EAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSM 461 (488)
Q Consensus 419 ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSL 461 (488)
+...+.......+.|.+|||+.||+|+.+|+..+.....++-.
T Consensus 140 ~RE~eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~v 182 (207)
T PRK15411 140 RTESSMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKIKT 182 (207)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCC
Confidence 3344444445558899999999999999999998766554433
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=65.86 E-value=11 Score=38.01 Aligned_cols=27 Identities=15% Similarity=0.258 Sum_probs=23.8
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHhC
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFITR 456 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar 456 (488)
.+.|.+|||+.||||.++|+.+...+.
T Consensus 235 ~~~t~~eIA~~lgvS~~~V~q~~~~Al 261 (270)
T TIGR02392 235 DKLTLQELAAEYGVSAERIRQIEKNAM 261 (270)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 368999999999999999998887664
No 193
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=65.35 E-value=6.3 Score=29.03 Aligned_cols=25 Identities=20% Similarity=0.272 Sum_probs=18.9
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 431 SPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
+.|..+||+.+|++..+|..++++.
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 5799999999999999999998764
No 194
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=65.20 E-value=8.3 Score=36.45 Aligned_cols=39 Identities=8% Similarity=0.044 Sum_probs=29.9
Q ss_pred HHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccc
Q 011324 423 LYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSM 461 (488)
Q Consensus 423 ~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSL 461 (488)
+....+..+.|.+|||+.||||..+|+..+.....++-.
T Consensus 157 evl~~~~~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~v 195 (216)
T PRK10840 157 EVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGV 195 (216)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 333344457899999999999999999998766555543
No 195
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=64.95 E-value=18 Score=31.31 Aligned_cols=28 Identities=29% Similarity=0.458 Sum_probs=24.3
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324 431 SPDKEDLARRVGITVEKLERLIFITRMP 458 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (488)
..|++|||+.||+++..++.++.....+
T Consensus 23 ~LS~~~iA~~Ln~t~~~lekil~~tqr~ 50 (97)
T COG4367 23 PLSDEEIATALNWTEVKLEKILQVTQRP 50 (97)
T ss_pred cccHHHHHHHhCCCHHHHHHHHHHhhcc
Confidence 6799999999999999999999765443
No 196
>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=64.95 E-value=22 Score=27.16 Aligned_cols=25 Identities=20% Similarity=0.329 Sum_probs=22.2
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 431 SPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
..+..|||+.+|++..+|..++..-
T Consensus 25 ~~s~~ela~~~g~s~~tv~r~l~~L 49 (67)
T cd00092 25 PLTRQEIADYLGLTRETVSRTLKEL 49 (67)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 5799999999999999999988743
No 197
>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=63.97 E-value=23 Score=27.86 Aligned_cols=36 Identities=17% Similarity=0.246 Sum_probs=27.6
Q ss_pred HHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 418 LEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 418 ~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
-+++..+.. .+..++..+||+.||++..+|-..+++
T Consensus 10 L~~Iy~l~~-~~~~v~~~~iA~~L~vs~~tvt~ml~~ 45 (60)
T PF01325_consen 10 LKAIYELSE-EGGPVRTKDIAERLGVSPPTVTEMLKR 45 (60)
T ss_dssp HHHHHHHHH-CTSSBBHHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHc-CCCCccHHHHHHHHCCChHHHHHHHHH
Confidence 345556666 444889999999999999999998865
No 198
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=63.73 E-value=15 Score=30.35 Aligned_cols=34 Identities=24% Similarity=0.308 Sum_probs=23.1
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccc
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFITRMPLSMQQ 463 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~ 463 (488)
++.|..|+|+.||++..+|..+++--...+|+|.
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 4689999999999999999998864445567764
No 199
>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=63.22 E-value=8.6 Score=38.76 Aligned_cols=31 Identities=16% Similarity=0.191 Sum_probs=26.5
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 429 NHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
..+.|..|||+.||||+.+|+..+..+..++
T Consensus 203 a~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL 233 (247)
T TIGR03020 203 RDGKTNEEIAAILGISSLTVKNHLQHIFKKL 233 (247)
T ss_pred HCCCCHHHHHHHHCcCHHHHHHHHHHHHHHh
Confidence 3478999999999999999999998775543
No 200
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=63.16 E-value=14 Score=34.02 Aligned_cols=38 Identities=11% Similarity=0.086 Sum_probs=28.0
Q ss_pred HHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 417 VLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 417 I~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
+.+.+-.+.+..+ ..++.|||+.+|+|+.+|..++++-
T Consensus 10 ~D~~Il~~Lq~d~-R~s~~eiA~~lglS~~tV~~Ri~rL 47 (153)
T PRK11179 10 LDRGILEALMENA-RTPYAELAKQFGVSPGTIHVRVEKM 47 (153)
T ss_pred HHHHHHHHHHHcC-CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3333333344445 5799999999999999999998754
No 201
>PF12728 HTH_17: Helix-turn-helix domain
Probab=62.81 E-value=9.5 Score=28.30 Aligned_cols=24 Identities=21% Similarity=0.174 Sum_probs=21.1
Q ss_pred CcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 432 PDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 432 pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
.|.+|+|+.|||+..+|..++...
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcC
Confidence 478999999999999999988644
No 202
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=62.73 E-value=9 Score=38.11 Aligned_cols=43 Identities=14% Similarity=-0.029 Sum_probs=32.0
Q ss_pred HHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccc
Q 011324 419 EAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSM 461 (488)
Q Consensus 419 ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSL 461 (488)
....++...+.++.|.+|||+.|+|++.+|+..+.....++-+
T Consensus 146 ~RE~eVL~Lia~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLgv 188 (217)
T PRK13719 146 KYQNDVFILYSFGFSHEYIAQLLNITVGSSKNKISEILKFFGI 188 (217)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 3334444445568999999999999999999998776555444
No 203
>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=62.11 E-value=16 Score=32.13 Aligned_cols=35 Identities=11% Similarity=0.031 Sum_probs=25.3
Q ss_pred HHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324 424 YIQEGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (488)
Q Consensus 424 L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (488)
+..-+....|..|||+.+|||...|...++++...
T Consensus 26 l~lyy~eDlSlsEIAe~~~iSRqaV~d~ikr~~~~ 60 (101)
T PF04297_consen 26 LELYYEEDLSLSEIAEELGISRQAVYDSIKRAEKK 60 (101)
T ss_dssp HHHHCTS---HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred HHHHHccCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 34446668899999999999999999999887643
No 204
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=61.59 E-value=9.7 Score=37.02 Aligned_cols=40 Identities=10% Similarity=0.103 Sum_probs=30.1
Q ss_pred HHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccc
Q 011324 422 RLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSM 461 (488)
Q Consensus 422 ~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSL 461 (488)
.+......++.|.+|||+.||||+.+|+..+.....++-.
T Consensus 140 ~eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~I~~KLgv 179 (207)
T PRK11475 140 REILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKLGV 179 (207)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 3344444557899999999999999999988766554433
No 205
>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=61.30 E-value=15 Score=29.32 Aligned_cols=31 Identities=29% Similarity=0.430 Sum_probs=22.9
Q ss_pred HHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 423 LYIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 423 ~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
.+....+ ..|..|||..+|++++.|+.+|..
T Consensus 7 ~~l~~~~-~~S~~eLa~~~~~s~~~ve~mL~~ 37 (69)
T PF09012_consen 7 DYLRERG-RVSLAELAREFGISPEAVEAMLEQ 37 (69)
T ss_dssp HHHHHS--SEEHHHHHHHTT--HHHHHHHHHH
T ss_pred HHHHHcC-CcCHHHHHHHHCcCHHHHHHHHHH
Confidence 3333444 789999999999999999999875
No 206
>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=60.76 E-value=9 Score=28.86 Aligned_cols=22 Identities=23% Similarity=0.421 Sum_probs=19.9
Q ss_pred cHHHHHHHhCCCHHHHHHHHHH
Q 011324 433 DKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 433 S~eEIAe~LGIS~etVk~~L~~ 454 (488)
|+++||+.+|++..+|..+|+-
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~ 22 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNG 22 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTT
T ss_pred CHHHHHHHHCcCHHHHHHHHhC
Confidence 6789999999999999999874
No 207
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=60.68 E-value=18 Score=33.72 Aligned_cols=41 Identities=15% Similarity=0.143 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 414 LSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 414 l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
+..+...+-.+.++.+ ..+..|||+.+|+|..+|..++++-
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 3444444444444555 5799999999999999999998753
No 208
>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=60.28 E-value=26 Score=31.11 Aligned_cols=34 Identities=18% Similarity=0.306 Sum_probs=26.4
Q ss_pred HHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhC
Q 011324 422 RLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR 456 (488)
Q Consensus 422 ~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar 456 (488)
..+..... ..+..|||+.+||+..+|-..|+...
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 33444444 77999999999999999999987643
No 209
>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=59.85 E-value=14 Score=27.80 Aligned_cols=27 Identities=19% Similarity=0.347 Sum_probs=21.9
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 428 GNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 428 lgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
.+...+..|||+.+|++..++..++..
T Consensus 15 ~~~~~t~~eia~~~gl~~stv~r~L~t 41 (52)
T PF09339_consen 15 SGGPLTLSEIARALGLPKSTVHRLLQT 41 (52)
T ss_dssp TBSCEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 343569999999999999999999863
No 210
>PF14502 HTH_41: Helix-turn-helix domain
Probab=58.95 E-value=14 Score=28.49 Aligned_cols=36 Identities=8% Similarity=0.338 Sum_probs=28.6
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHHh--CCCccccc
Q 011324 428 GNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQ 463 (488)
Q Consensus 428 lgr~pS~eEIAe~LGIS~etVk~~L~~a--r~~lSLD~ 463 (488)
+.|-|++.|.++.++++.++|+.++..- ...+.|..
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 4568999999999999999999998754 34455543
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=58.88 E-value=13 Score=26.47 Aligned_cols=24 Identities=25% Similarity=0.336 Sum_probs=21.2
Q ss_pred CcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 432 PDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 432 pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
.|.+|+|+.||++..++..+++..
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g 25 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEG 25 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcC
Confidence 478999999999999999998754
No 212
>PF13730 HTH_36: Helix-turn-helix domain
Probab=58.63 E-value=12 Score=28.06 Aligned_cols=25 Identities=28% Similarity=0.460 Sum_probs=22.2
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
--||.+.||+.+|++..+|...+..
T Consensus 24 ~~pS~~~la~~~g~s~~Tv~~~i~~ 48 (55)
T PF13730_consen 24 CFPSQETLAKDLGVSRRTVQRAIKE 48 (55)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 4579999999999999999998764
No 213
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=58.27 E-value=11 Score=36.75 Aligned_cols=35 Identities=11% Similarity=-0.010 Sum_probs=27.7
Q ss_pred HHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 425 IQEGNHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 425 ~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
......+.+.+|||+.||+++.+|+..+......+
T Consensus 142 LrLLAqGkTnKEIAe~L~IS~rTVkth~srImkKL 176 (198)
T PRK15201 142 LKLIASGYHLSETAALLSLSEEQTKSLRRSIMRKL 176 (198)
T ss_pred HHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 33344578999999999999999999887665544
No 214
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=58.20 E-value=21 Score=32.17 Aligned_cols=38 Identities=24% Similarity=0.224 Sum_probs=28.1
Q ss_pred HHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 417 VLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 417 I~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
+...+-.+.+..+ ..++.|||+.+|+|..+|..++..-
T Consensus 9 ~D~~IL~~L~~d~-r~~~~eia~~lglS~~~v~~Ri~~L 46 (154)
T COG1522 9 IDRRILRLLQEDA-RISNAELAERVGLSPSTVLRRIKRL 46 (154)
T ss_pred HHHHHHHHHHHhC-CCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 3333344445555 3899999999999999999998753
No 215
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=58.17 E-value=32 Score=27.57 Aligned_cols=31 Identities=13% Similarity=0.517 Sum_probs=24.5
Q ss_pred HHHhcCC-CCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 424 YIQEGNH-SPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 424 L~~elgr-~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
+....+. +.+..|||+.|||+..+|...|..
T Consensus 14 ~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~ 45 (68)
T smart00550 14 FLENSGDETSTALQLAKNLGLPKKEVNRVLYS 45 (68)
T ss_pred HHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 3334442 489999999999999999999874
No 216
>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=57.66 E-value=23 Score=27.44 Aligned_cols=28 Identities=18% Similarity=0.259 Sum_probs=23.2
Q ss_pred HhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 426 QEGNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 426 ~elgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
.+.+ ..+.+|||+.+|+|..+|+.-+..
T Consensus 10 ~~~~-~~s~~ela~~~~VS~~TiRRDl~~ 37 (57)
T PF08220_consen 10 KEKG-KVSVKELAEEFGVSEMTIRRDLNK 37 (57)
T ss_pred HHcC-CEEHHHHHHHHCcCHHHHHHHHHH
Confidence 3344 789999999999999999887753
No 217
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=57.61 E-value=16 Score=29.41 Aligned_cols=26 Identities=12% Similarity=0.224 Sum_probs=21.3
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 429 NHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 429 gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
..+++..|||+.+||+..+++.+|..
T Consensus 13 ~~p~~T~eiA~~~gls~~~aR~yL~~ 38 (62)
T PF04703_consen 13 NGPLKTREIADALGLSIYQARYYLEK 38 (62)
T ss_dssp TS-EEHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 44789999999999999999999864
No 218
>PRK13870 transcriptional regulator TraR; Provisional
Probab=57.13 E-value=12 Score=37.14 Aligned_cols=30 Identities=10% Similarity=0.080 Sum_probs=26.3
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
.+.|..|||.+||||+.+|+..++.++.++
T Consensus 187 ~GKT~~EIa~ILgISe~TV~~Hl~na~~KL 216 (234)
T PRK13870 187 VGKTMEEIADVEGVKYNSVRVKLREAMKRF 216 (234)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHc
Confidence 467999999999999999999998876654
No 219
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=56.38 E-value=11 Score=37.31 Aligned_cols=30 Identities=7% Similarity=0.018 Sum_probs=26.3
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
.+.|..|||++||||+.+|+..+..++.++
T Consensus 193 ~G~t~~eIa~~l~is~~TV~~h~~~~~~KL 222 (240)
T PRK10188 193 EGKTSAEIAMILSISENTVNFHQKNMQKKF 222 (240)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 468999999999999999999998776654
No 220
>PRK09483 response regulator; Provisional
Probab=56.29 E-value=11 Score=34.73 Aligned_cols=33 Identities=3% Similarity=0.203 Sum_probs=28.2
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccc
Q 011324 429 NHSPDKEDLARRVGITVEKLERLIFITRMPLSM 461 (488)
Q Consensus 429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSL 461 (488)
..+.+.+|||+.|+++..+|+..++....++..
T Consensus 161 ~~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~v 193 (217)
T PRK09483 161 TKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNI 193 (217)
T ss_pred HCCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence 346899999999999999999999887766654
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=55.88 E-value=41 Score=28.42 Aligned_cols=41 Identities=12% Similarity=0.109 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 415 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 415 ~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
++|-+++-.+..+.++...-++||+.+|++..+|++.|..-
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 44455555555566778899999999999999999998743
No 222
>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=55.75 E-value=8.3 Score=37.92 Aligned_cols=30 Identities=23% Similarity=0.299 Sum_probs=26.3
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
.+.|..|||+.|||++.+|+..+..++..+
T Consensus 185 ~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl 214 (232)
T TIGR03541 185 LGRRQADIAAILGISERTVENHLRSARRKL 214 (232)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 468999999999999999999998876544
No 223
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=55.72 E-value=17 Score=27.50 Aligned_cols=29 Identities=17% Similarity=0.259 Sum_probs=24.4
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFITRMP 458 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (488)
.+.+..|||..+|++..+|...+......
T Consensus 18 ~G~s~~eia~~l~is~~tV~~h~~~i~~K 46 (65)
T COG2771 18 QGKSNKEIARILGISEETVKTHLRNIYRK 46 (65)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 35899999999999999999988765443
No 224
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=55.63 E-value=1e+02 Score=31.93 Aligned_cols=28 Identities=11% Similarity=0.043 Sum_probs=22.2
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 428 GNHSPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 428 lgr~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
.+...|.+|||...|++..+|++..+..
T Consensus 273 ~g~~~t~keIa~v~~Vs~~tI~~~ykel 300 (310)
T PRK00423 273 LGERRTQREVAEVAGVTEVTVRNRYKEL 300 (310)
T ss_pred hCCCCCHHHHHHHcCCCHHHHHHHHHHH
Confidence 3434599999999999999998876543
No 225
>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]
Probab=54.97 E-value=15 Score=35.67 Aligned_cols=34 Identities=12% Similarity=0.098 Sum_probs=27.8
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccc
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFITRMPLSMQQ 463 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~ 463 (488)
++.+..|||++|++|.+++..++.++....+--+
T Consensus 17 ~Glt~gEIAdELNvSreTa~WL~~r~~~~~~~~~ 50 (203)
T COG0856 17 KGLTTGEIADELNVSRETATWLLTRAFKKESVPA 50 (203)
T ss_pred CCCcHHHhhhhhhhhHHHHHHHHhhhhhccCCCC
Confidence 4789999999999999999999988665444433
No 226
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=54.17 E-value=17 Score=26.84 Aligned_cols=25 Identities=16% Similarity=0.352 Sum_probs=22.0
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 431 SPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
-||..|||+.+|++..+|...+..-
T Consensus 20 l~s~~~la~~~~vs~~tv~~~l~~L 44 (60)
T smart00345 20 LPSERELAAQLGVSRTTVREALSRL 44 (60)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 3599999999999999999988754
No 227
>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=54.04 E-value=31 Score=29.10 Aligned_cols=28 Identities=18% Similarity=0.355 Sum_probs=23.6
Q ss_pred HHHhcCCCCcHHHHHHHhCCCHHHHHHHHH
Q 011324 424 YIQEGNHSPDKEDLARRVGITVEKLERLIF 453 (488)
Q Consensus 424 L~~elgr~pS~eEIAe~LGIS~etVk~~L~ 453 (488)
+... + .+++.+||+.+|+|..+|...+.
T Consensus 14 ~l~~-~-~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 14 YIVE-T-KATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred HHHH-C-CCCHHHHHHHhCCCHHHHHHHhc
Confidence 3344 5 78999999999999999999875
No 228
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=53.92 E-value=38 Score=30.18 Aligned_cols=38 Identities=13% Similarity=0.095 Sum_probs=29.3
Q ss_pred HHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 417 VLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 417 I~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
+.++..-+...+...++.++||+.+|+++..+..+...
T Consensus 11 i~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 11 IHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 44455555566666789999999999999999887664
No 229
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=53.49 E-value=25 Score=33.89 Aligned_cols=32 Identities=13% Similarity=0.066 Sum_probs=27.2
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 428 GNHSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 428 lgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
+..+.+.+|||+.||++..+|+..+....+..
T Consensus 175 ~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~ 206 (239)
T PRK10430 175 QDYEFSTDELANAVNISRVSCRKYLIWLVNCH 206 (239)
T ss_pred CCCCcCHHHHHHHhCchHHHHHHHHHHHHhCC
Confidence 45678999999999999999999998765443
No 230
>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=53.17 E-value=29 Score=27.30 Aligned_cols=24 Identities=21% Similarity=0.350 Sum_probs=22.1
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 431 SPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
..|..|||+.+|++..+|...+..
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 231
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=52.95 E-value=14 Score=36.11 Aligned_cols=30 Identities=10% Similarity=0.186 Sum_probs=25.6
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
.+.|.+|||+.||+|+.+|+..+.....++
T Consensus 169 ~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl 198 (216)
T PRK10100 169 IGASNNEIARSLFISENTVKTHLYNLFKKI 198 (216)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 368999999999999999999988765443
No 232
>PRK12423 LexA repressor; Provisional
Probab=52.47 E-value=40 Score=32.57 Aligned_cols=40 Identities=15% Similarity=0.266 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHhcCCCCcHHHHHHHhCC-CHHHHHHHHHH
Q 011324 415 SKVLEAKRLYIQEGNHSPDKEDLARRVGI-TVEKLERLIFI 454 (488)
Q Consensus 415 ~kI~ka~~~L~~elgr~pS~eEIAe~LGI-S~etVk~~L~~ 454 (488)
+++-..+.....+.+..||..|||+.+|+ +...|+..+..
T Consensus 9 ~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~ 49 (202)
T PRK12423 9 AAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQA 49 (202)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence 34444445555566768999999999995 89999887654
No 233
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=52.18 E-value=9.6 Score=37.03 Aligned_cols=30 Identities=23% Similarity=0.307 Sum_probs=26.4
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
|..+.+|||+.|||+..++...|++|.+++
T Consensus 177 R~~~l~dLA~~lGISkst~~ehLRrAe~Kl 206 (215)
T COG3413 177 RRVSLKDLAKELGISKSTLSEHLRRAERKL 206 (215)
T ss_pred ccCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 566999999999999999999999886543
No 234
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=51.87 E-value=24 Score=33.72 Aligned_cols=40 Identities=13% Similarity=0.062 Sum_probs=28.9
Q ss_pred HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhC--CCccccccC
Q 011324 426 QEGNHSPDKEDLARRVGITVEKLERLIFITR--MPLSMQQPV 465 (488)
Q Consensus 426 ~elgr~pS~eEIAe~LGIS~etVk~~L~~ar--~~lSLD~~i 465 (488)
.++..+.|.+|||+.||||+.+|+..+.... ..++.+-..
T Consensus 172 ~~g~~g~s~~eIa~~l~iS~~Tv~~~~~~~~~~~~~~~~~~~ 213 (225)
T PRK10046 172 KEPGVQHTAETVAQALTISRTTARRYLEYCASRHLIIAEIVH 213 (225)
T ss_pred HcCCCCcCHHHHHHHhCccHHHHHHHHHHHHhCCeEEEEeec
Confidence 3333358999999999999999999987543 345554443
No 235
>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=51.80 E-value=22 Score=24.97 Aligned_cols=24 Identities=17% Similarity=0.307 Sum_probs=20.9
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHhC
Q 011324 433 DKEDLARRVGITVEKLERLIFITR 456 (488)
Q Consensus 433 S~eEIAe~LGIS~etVk~~L~~ar 456 (488)
+..|+|+.||++..+|........
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcCC
Confidence 678999999999999999887543
No 236
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=50.92 E-value=19 Score=32.25 Aligned_cols=32 Identities=16% Similarity=0.256 Sum_probs=27.2
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHhCCCccc
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFITRMPLSM 461 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~lSL 461 (488)
.+.+.+|||+.|+++..+|+..+..++..+-.
T Consensus 163 ~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~ 194 (211)
T PRK15369 163 EGYTNRDIAEQLSISIKTVETHRLNMMRKLDV 194 (211)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 35789999999999999999999887766544
No 237
>PHA02943 hypothetical protein; Provisional
Probab=49.96 E-value=52 Score=31.31 Aligned_cols=27 Identities=7% Similarity=0.277 Sum_probs=22.8
Q ss_pred hcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 427 EGNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 427 elgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
..| ..|..|||+.||+|-++++.++..
T Consensus 21 k~G-~~TtseIAkaLGlS~~qa~~~Lyv 47 (165)
T PHA02943 21 ADG-CKTTSRIANKLGVSHSMARNALYQ 47 (165)
T ss_pred hcC-CccHHHHHHHHCCCHHHHHHHHHH
Confidence 444 568999999999999999998864
No 238
>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=49.49 E-value=45 Score=31.71 Aligned_cols=39 Identities=26% Similarity=0.354 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHhcCCCCcHHHHHHHhCCC-HHHHHHHHHH
Q 011324 416 KVLEAKRLYIQEGNHSPDKEDLARRVGIT-VEKLERLIFI 454 (488)
Q Consensus 416 kI~ka~~~L~~elgr~pS~eEIAe~LGIS-~etVk~~L~~ 454 (488)
+|-..+.....+.+..|+..|||+.+|++ ..+|...+..
T Consensus 10 ~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~ 49 (199)
T TIGR00498 10 EVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKA 49 (199)
T ss_pred HHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHH
Confidence 34444444445566679999999999998 9999888764
No 239
>PRK10403 transcriptional regulator NarP; Provisional
Probab=49.23 E-value=23 Score=32.04 Aligned_cols=33 Identities=12% Similarity=0.129 Sum_probs=28.6
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHhCCCcccc
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFITRMPLSMQ 462 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD 462 (488)
.+.+.+|||+.+|++..+|+..+.+.+.++.+.
T Consensus 167 ~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~ 199 (215)
T PRK10403 167 QGLSNKQIASVLNISEQTVKVHIRNLLRKLNVR 199 (215)
T ss_pred CCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCCC
Confidence 468999999999999999999998887776554
No 240
>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=48.98 E-value=35 Score=25.26 Aligned_cols=24 Identities=21% Similarity=0.361 Sum_probs=19.5
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 431 SPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
+.|..|+|+.+|++..+|..+..-
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 589999999999999999988764
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=48.33 E-value=87 Score=27.12 Aligned_cols=64 Identities=17% Similarity=0.094 Sum_probs=39.1
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 382 ASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 382 STYA~~wIRnaI~~~IRk~sr~irlP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
..|...++.+.+.+.+...-....+.......+.. +. ..+ ..+..|||+.+|++..+|-.++..
T Consensus 2 ~~~~l~~~~~~~~~~~~~~l~~~~lt~~q~~iL~~-------l~-~~~-~~t~~ela~~~~~~~~tvs~~l~~ 65 (118)
T TIGR02337 2 LPLALLQAREAAMSFFRPILAQHGLTEQQWRILRI-------LA-EQG-SMEFTQLANQACILRPSLTGILAR 65 (118)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHH-------HH-HcC-CcCHHHHHHHhCCCchhHHHHHHH
Confidence 45666667777666665543322332222222222 22 233 679999999999999999888764
No 242
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=48.23 E-value=54 Score=27.85 Aligned_cols=37 Identities=11% Similarity=0.061 Sum_probs=27.7
Q ss_pred HHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 418 LEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 418 ~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
.++..-+...+...++.++||+.+|++...+..+...
T Consensus 8 ~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~ 44 (107)
T PRK10219 8 QTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRT 44 (107)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3344445555666789999999999999999887654
No 243
>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=48.08 E-value=45 Score=24.43 Aligned_cols=23 Identities=17% Similarity=0.215 Sum_probs=21.1
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHH
Q 011324 431 SPDKEDLARRVGITVEKLERLIF 453 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~ 453 (488)
+.|.+++|+.+|++..+|..+..
T Consensus 15 gltq~~lA~~~gvs~~~vs~~e~ 37 (58)
T TIGR03070 15 GLTQADLADLAGVGLRFIRDVEN 37 (58)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHC
Confidence 68999999999999999998875
No 244
>PRK14082 hypothetical protein; Provisional
Probab=48.08 E-value=70 Score=26.14 Aligned_cols=54 Identities=17% Similarity=0.074 Sum_probs=41.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhh
Q 011324 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAS 383 (488)
Q Consensus 328 ~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFST 383 (488)
...+.+|..+.+.+.+-... ....+.+||.||--|.+++-+..++...+--|--
T Consensus 9 ~e~e~ii~~FepkIkKsL~~--T~yqeREDLeQElk~Ki~eK~~~~~~~e~PGF~e 62 (65)
T PRK14082 9 EEIEHLIENFSPMIKKKLSN--TSYQEREDLEQELKIKIIEKADMLLCQEVPGFWE 62 (65)
T ss_pred HHHHHHHHHccHHHHHHHhc--CChhhHHHHHHHHHHHHHHHHHHhhcccCCcHHH
Confidence 56778898888887765543 3456889999999999999999998765544543
No 245
>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=47.68 E-value=67 Score=29.79 Aligned_cols=34 Identities=15% Similarity=0.288 Sum_probs=27.5
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccc
Q 011324 428 GNHSPDKEDLARRVGITVEKLERLIFITRMPLSM 461 (488)
Q Consensus 428 lgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSL 461 (488)
-++..|..||++.+|++++.|...++-.|-.++=
T Consensus 43 p~~~ati~eV~e~tgVs~~~I~~~IreGRL~~~~ 76 (137)
T TIGR03826 43 ENRQATVSEIVEETGVSEKLILKFIREGRLQLKH 76 (137)
T ss_pred CCCCCCHHHHHHHHCcCHHHHHHHHHcCCeeccC
Confidence 3445899999999999999999999877655443
No 246
>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=47.50 E-value=45 Score=24.43 Aligned_cols=32 Identities=28% Similarity=0.499 Sum_probs=25.3
Q ss_pred HHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHH
Q 011324 420 AKRLYIQEGNHSPDKEDLARRVGITVEKLERL 451 (488)
Q Consensus 420 a~~~L~~elgr~pS~eEIAe~LGIS~etVk~~ 451 (488)
+...+.+.+-...|..+||+.+|++...+...
T Consensus 5 a~~l~~~~G~~~~s~~~Ia~~~gvs~~~~y~~ 36 (47)
T PF00440_consen 5 ALELFAEKGYEAVSIRDIARRAGVSKGSFYRY 36 (47)
T ss_dssp HHHHHHHHHTTTSSHHHHHHHHTSCHHHHHHH
T ss_pred HHHHHHHhCHHhCCHHHHHHHHccchhhHHHH
Confidence 44455666667899999999999999988643
No 247
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=47.40 E-value=25 Score=31.97 Aligned_cols=32 Identities=6% Similarity=0.032 Sum_probs=28.3
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHhCCCccc
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFITRMPLSM 461 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~lSL 461 (488)
.+.+.+|||+.|+++..+|+..+.+.+..+..
T Consensus 163 ~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl~~ 194 (210)
T PRK09935 163 SGLSNKEIADQLLLSNKTVSAHKSNIYGKLGL 194 (210)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence 36899999999999999999999988877654
No 248
>PRK15320 transcriptional activator SprB; Provisional
Probab=47.24 E-value=18 Score=36.03 Aligned_cols=35 Identities=9% Similarity=0.029 Sum_probs=27.5
Q ss_pred HHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCC
Q 011324 423 LYIQEGNHSPDKEDLARRVGITVEKLERLIFITRM 457 (488)
Q Consensus 423 ~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (488)
++...+..+.+.+|||+.|+++.++|+..+.+...
T Consensus 171 EVL~LLAkG~SNKEIAekL~LS~KTVSTYKnRLLe 205 (251)
T PRK15320 171 ALLILLSSGHPAIELAKKFGLGTKTVSIYRKKVMY 205 (251)
T ss_pred HHHHHHHcCCCHHHHHHHhccchhhHHHHHHHHHH
Confidence 34444455789999999999999999998876543
No 249
>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=46.81 E-value=36 Score=21.28 Aligned_cols=21 Identities=29% Similarity=0.529 Sum_probs=18.2
Q ss_pred CCcHHHHHHHhCCCHHHHHHH
Q 011324 431 SPDKEDLARRVGITVEKLERL 451 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~ 451 (488)
+.+..+||+.+|++..+|..+
T Consensus 21 ~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 21 GESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCCHHHHHHHHCCCHHHHHHh
Confidence 459999999999999998764
No 250
>PRK10651 transcriptional regulator NarL; Provisional
Probab=46.78 E-value=20 Score=32.55 Aligned_cols=35 Identities=14% Similarity=0.129 Sum_probs=28.9
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCcccc
Q 011324 428 GNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQ 462 (488)
Q Consensus 428 lgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD 462 (488)
+..+.+.+|||+.|+++..+|+..+...+.++...
T Consensus 167 l~~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl~~~ 201 (216)
T PRK10651 167 IAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLK 201 (216)
T ss_pred HHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCCC
Confidence 33467999999999999999999998877766543
No 251
>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=46.17 E-value=45 Score=28.55 Aligned_cols=23 Identities=13% Similarity=0.245 Sum_probs=20.6
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHH
Q 011324 431 SPDKEDLARRVGITVEKLERLIF 453 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~ 453 (488)
+.|..|||+.+|++..+|..+.+
T Consensus 50 G~S~~eIA~~LgISrsTIyRi~R 72 (88)
T TIGR02531 50 GKTYSDIEAETGASTATISRVKR 72 (88)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHH
Confidence 57999999999999999998554
No 252
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=45.80 E-value=60 Score=26.39 Aligned_cols=25 Identities=24% Similarity=0.364 Sum_probs=22.7
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 431 SPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
..+..|||+.+|++..+|...+...
T Consensus 20 ~~t~~~ia~~l~i~~~tv~r~l~~L 44 (91)
T smart00346 20 GLTLAELAERLGLSKSTAHRLLNTL 44 (91)
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 6899999999999999999998753
No 253
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=45.32 E-value=65 Score=22.98 Aligned_cols=25 Identities=20% Similarity=0.234 Sum_probs=22.6
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 431 SPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
.++..+||+.+|++..+|...+..-
T Consensus 14 ~~s~~~l~~~l~~s~~tv~~~l~~L 38 (53)
T smart00420 14 KVSVEELAELLGVSEMTIRRDLNKL 38 (53)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 6899999999999999999988754
No 254
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=45.32 E-value=48 Score=29.39 Aligned_cols=30 Identities=13% Similarity=0.107 Sum_probs=25.8
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHhCCCcc
Q 011324 431 SPDKEDLARRVGITVEKLERLIFITRMPLS 460 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar~~lS 460 (488)
+.+.++||+.+|++..+|+..+.+++..+.
T Consensus 156 ~~~~~~ia~~l~~s~~tv~~~~~~~~~kl~ 185 (202)
T PRK09390 156 GLSNKVIARDLDISPRTVEVYRANVMTKMQ 185 (202)
T ss_pred cCchHHHHHHcCCCHHHHHHHHHHHHHHHc
Confidence 568999999999999999999887766653
No 255
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=45.04 E-value=13 Score=33.47 Aligned_cols=53 Identities=8% Similarity=-0.011 Sum_probs=35.7
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCC---CCCCccccccCCCCCCCC
Q 011324 433 DKEDLARRVGITVEKLERLIFITRMPLSMQQPVWA---DQDTTFQVMPLLLSHLPS 485 (488)
Q Consensus 433 S~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~---d~~~tl~e~i~D~s~~pe 485 (488)
+.+|+++.||||--+|+.+|...-..+.+...... .....+.+.+.+...+++
T Consensus 51 nlKe~e~~lgiSYPTvR~rLd~ii~~lg~~~~~~~~~~~~~~~IL~~L~~GeIs~e 106 (113)
T PF09862_consen 51 NLKEMEKELGISYPTVRNRLDKIIEKLGYEEDEEEEEEDERKEILDKLEKGEISVE 106 (113)
T ss_pred CHHHHHHHHCCCcHHHHHHHHHHHHHhCCCCCcccccchhHHHHHHHHHcCCCCHH
Confidence 89999999999999999999876666666211111 112355566666666554
No 256
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=44.92 E-value=2.5e+02 Score=27.88 Aligned_cols=38 Identities=24% Similarity=0.182 Sum_probs=28.6
Q ss_pred HHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 417 VLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 417 I~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
+.++...+........+++++|+.+|+|...+..+.+.
T Consensus 185 i~~~~~~i~~~~~~~isl~~lA~~~~lS~~~l~r~Fk~ 222 (290)
T PRK10572 185 VREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQ 222 (290)
T ss_pred HHHHHHHHHhcccCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 44444555556666889999999999999988877654
No 257
>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=44.48 E-value=42 Score=28.28 Aligned_cols=28 Identities=21% Similarity=0.258 Sum_probs=20.8
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 428 GNHSPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 428 lgr~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
.|+..|..++|..+|++.++|+.++...
T Consensus 35 ~G~PVt~~~LA~a~g~~~e~v~~~L~~~ 62 (77)
T PF12324_consen 35 KGQPVTVEQLAAALGWPVEEVRAALAAM 62 (77)
T ss_dssp TTS-B-HHHHHHHHT--HHHHHHHHHH-
T ss_pred cCCCcCHHHHHHHHCCCHHHHHHHHHhC
Confidence 3668899999999999999999999765
No 258
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=44.21 E-value=33 Score=24.38 Aligned_cols=25 Identities=20% Similarity=0.337 Sum_probs=21.9
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 431 SPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
.++..+||+.+|++..+|...+..-
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 259
>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=43.05 E-value=80 Score=24.49 Aligned_cols=27 Identities=15% Similarity=0.151 Sum_probs=22.6
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHhC
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFITR 456 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar 456 (488)
...+..|||+.||+|..+++..+..-.
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 260
>PRK13239 alkylmercury lyase; Provisional
Probab=42.70 E-value=53 Score=32.49 Aligned_cols=29 Identities=21% Similarity=0.237 Sum_probs=26.1
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHHhC
Q 011324 428 GNHSPDKEDLARRVGITVEKLERLIFITR 456 (488)
Q Consensus 428 lgr~pS~eEIAe~LGIS~etVk~~L~~ar 456 (488)
.|+.|+..+||+.+|+++++|+.+|+...
T Consensus 33 ~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 33 KGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 56799999999999999999999998653
No 261
>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=42.34 E-value=23 Score=26.94 Aligned_cols=37 Identities=14% Similarity=0.236 Sum_probs=24.8
Q ss_pred CcHHHHHHHhCCCHHHHHHHH-H-HhCCCccccccCCCC
Q 011324 432 PDKEDLARRVGITVEKLERLI-F-ITRMPLSMQQPVWAD 468 (488)
Q Consensus 432 pS~eEIAe~LGIS~etVk~~L-~-~ar~~lSLD~~i~~d 468 (488)
.++.|||+.||++..+|-..+ . ..-...+.++.+..+
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 467899999999999999888 4 333336666666544
No 262
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=41.88 E-value=27 Score=31.10 Aligned_cols=29 Identities=21% Similarity=0.432 Sum_probs=26.9
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 431 SPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
+.+.+|-|+.||||..++..++..||.++
T Consensus 57 gl~QeeaA~~MgVSR~T~~ril~~ARkKi 85 (106)
T PF02001_consen 57 GLSQEEAAERMGVSRPTFQRILESARKKI 85 (106)
T ss_pred CCCHHHHHHHcCCcHHHHHHHHHHHHHHH
Confidence 68999999999999999999999998765
No 263
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=41.68 E-value=46 Score=32.18 Aligned_cols=24 Identities=13% Similarity=0.124 Sum_probs=21.9
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 431 SPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
+.|+.|||+.||.++.+|++.+.-
T Consensus 61 g~Ti~EIAeelG~TeqTir~hlkg 84 (182)
T COG1318 61 GMTISEIAEELGRTEQTVRNHLKG 84 (182)
T ss_pred cCcHHHHHHHhCCCHHHHHHHHhc
Confidence 579999999999999999999864
No 264
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=41.60 E-value=50 Score=27.98 Aligned_cols=25 Identities=16% Similarity=0.259 Sum_probs=22.1
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 431 SPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
..+..|||+.+|++..+|...+..-
T Consensus 17 ~~~~~~la~~l~~s~~tv~~~l~~L 41 (108)
T smart00344 17 RISLAELAKKVGLSPSTVHNRVKRL 41 (108)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 5789999999999999999988653
No 265
>PF13518 HTH_28: Helix-turn-helix domain
Probab=41.17 E-value=50 Score=24.02 Aligned_cols=25 Identities=28% Similarity=0.353 Sum_probs=22.1
Q ss_pred CcHHHHHHHhCCCHHHHHHHHHHhC
Q 011324 432 PDKEDLARRVGITVEKLERLIFITR 456 (488)
Q Consensus 432 pS~eEIAe~LGIS~etVk~~L~~ar 456 (488)
.|..+||..+||+..+|..++....
T Consensus 13 ~s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 13 ESVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred CCHHHHHHHHCCCHhHHHHHHHHHH
Confidence 4999999999999999999987543
No 266
>PHA01976 helix-turn-helix protein
Probab=41.01 E-value=69 Score=24.74 Aligned_cols=23 Identities=17% Similarity=0.225 Sum_probs=20.2
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHH
Q 011324 431 SPDKEDLARRVGITVEKLERLIF 453 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~ 453 (488)
+.|.+|+|+.+|++..+|..+..
T Consensus 15 glt~~~lA~~~gvs~~~v~~~e~ 37 (67)
T PHA01976 15 AWSAPELSRRAGVRHSLIYDFEA 37 (67)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHc
Confidence 58999999999999999988765
No 267
>PRK00215 LexA repressor; Validated
Probab=40.87 E-value=75 Score=30.34 Aligned_cols=34 Identities=18% Similarity=0.318 Sum_probs=27.0
Q ss_pred HHHHHhcCCCCcHHHHHHHhCC-CHHHHHHHHHHh
Q 011324 422 RLYIQEGNHSPDKEDLARRVGI-TVEKLERLIFIT 455 (488)
Q Consensus 422 ~~L~~elgr~pS~eEIAe~LGI-S~etVk~~L~~a 455 (488)
.+.....+..++..|||+.+|+ +..+|..++..-
T Consensus 14 ~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L 48 (205)
T PRK00215 14 RDHIEETGYPPSRREIADALGLRSPSAVHEHLKAL 48 (205)
T ss_pred HHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHH
Confidence 3344455668999999999999 999999987643
No 268
>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=40.49 E-value=1.4e+02 Score=25.73 Aligned_cols=31 Identities=13% Similarity=0.007 Sum_probs=25.0
Q ss_pred HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhC
Q 011324 426 QEGNHSPDKEDLARRVGITVEKLERLIFITR 456 (488)
Q Consensus 426 ~elgr~pS~eEIAe~LGIS~etVk~~L~~ar 456 (488)
..+-...+..+||+.||+|..++-.+...|-
T Consensus 66 ~~Yi~~~~~~~I~~~l~~S~~t~yr~~~~Al 96 (100)
T PF07374_consen 66 MRYINKLTWEQIAEELNISRRTYYRIHKKAL 96 (100)
T ss_pred HHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3344567899999999999999988877663
No 269
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=40.45 E-value=60 Score=31.99 Aligned_cols=44 Identities=16% Similarity=0.102 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHH
Q 011324 410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF 453 (488)
Q Consensus 410 v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~ 453 (488)
+...+..+....++.....-++...++||..||||+.+|+....
T Consensus 136 ~~~~l~tLT~RERqVl~~vV~G~~NKqIA~dLgiS~rTVe~HRa 179 (202)
T COG4566 136 IRARLATLTPRERQVLDLVVRGLMNKQIAFDLGISERTVELHRA 179 (202)
T ss_pred HHHHHHhcCHHHHHHHHHHHcCcccHHHHHHcCCchhhHHHHHH
Confidence 34445555555555555555678999999999999999986643
No 270
>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=40.06 E-value=36 Score=24.50 Aligned_cols=24 Identities=21% Similarity=0.193 Sum_probs=20.5
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHhC
Q 011324 433 DKEDLARRVGITVEKLERLIFITR 456 (488)
Q Consensus 433 S~eEIAe~LGIS~etVk~~L~~ar 456 (488)
+..|+|+.+|++..+|+.......
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHHCCC
Confidence 678999999999999998876543
No 271
>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=40.06 E-value=27 Score=26.77 Aligned_cols=24 Identities=21% Similarity=0.461 Sum_probs=18.8
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHH
Q 011324 430 HSPDKEDLARRVGITVEKLERLIF 453 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~ 453 (488)
.+++..+||..+||+..+|..++.
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 367999999999999999999876
No 272
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=39.91 E-value=2.8e+02 Score=27.55 Aligned_cols=45 Identities=16% Similarity=0.063 Sum_probs=30.7
Q ss_pred HHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHH
Q 011324 343 HVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 388 (488)
Q Consensus 343 sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~w 388 (488)
.|...|....+..+++.+...|..-.-...|... |..|..|+...
T Consensus 205 ~I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk~~-G~T~~~yi~~~ 249 (302)
T PRK09685 205 LIDQSIQEEILRPEWIAGELGISVRSLYRLFAEQ-GLVVAQYIRNR 249 (302)
T ss_pred HHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHc-CCCHHHHHHHH
Confidence 3444454445899999999888876666777654 76677666553
No 273
>PRK09726 antitoxin HipB; Provisional
Probab=39.89 E-value=67 Score=26.76 Aligned_cols=31 Identities=13% Similarity=0.205 Sum_probs=24.2
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHhCCCcccc
Q 011324 431 SPDKEDLARRVGITVEKLERLIFITRMPLSMQ 462 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD 462 (488)
+.|.+|+|+.+|++..+|..+..- ....+++
T Consensus 25 gltq~elA~~~gvs~~tis~~e~g-~~~ps~~ 55 (88)
T PRK09726 25 GWTQSELAKKIGIKQATISNFENN-PDNTTLT 55 (88)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHCC-CCCCCHH
Confidence 689999999999999999988763 2333444
No 274
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=39.57 E-value=1.1e+02 Score=29.35 Aligned_cols=25 Identities=28% Similarity=0.441 Sum_probs=21.9
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 431 SPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
..|.++||+.||++.++|-.+++.-
T Consensus 184 ~lt~~~iA~~lG~sr~tvsR~l~~l 208 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETISRLLGRF 208 (235)
T ss_pred cccHHHHHHHhCCcHHHHHHHHHHH
Confidence 4689999999999999999988643
No 275
>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=39.40 E-value=41 Score=28.68 Aligned_cols=25 Identities=8% Similarity=0.360 Sum_probs=21.5
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
.+.++.+|++.||+++.+|+.++..
T Consensus 64 ~Gv~v~~I~~~l~~~~~~v~~al~~ 88 (102)
T PF08784_consen 64 EGVHVDEIAQQLGMSENEVRKALDF 88 (102)
T ss_dssp TTEEHHHHHHHSTS-HHHHHHHHHH
T ss_pred CcccHHHHHHHhCcCHHHHHHHHHH
Confidence 4689999999999999999999864
No 276
>PF13551 HTH_29: Winged helix-turn helix
Probab=39.14 E-value=78 Score=26.49 Aligned_cols=25 Identities=16% Similarity=0.236 Sum_probs=19.7
Q ss_pred CCcHHHHHHHh-------CCCHHHHHHHHHHh
Q 011324 431 SPDKEDLARRV-------GITVEKLERLIFIT 455 (488)
Q Consensus 431 ~pS~eEIAe~L-------GIS~etVk~~L~~a 455 (488)
..+..+|++.| .++..+|..+|+..
T Consensus 80 ~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~~~ 111 (112)
T PF13551_consen 80 RWTLEELAEWLIEEEFGIDVSPSTIRRILKRA 111 (112)
T ss_pred cccHHHHHHHHHHhccCccCCHHHHHHHHHHC
Confidence 46788888865 79999999998753
No 277
>PRK06424 transcription factor; Provisional
Probab=39.13 E-value=1e+02 Score=28.72 Aligned_cols=42 Identities=12% Similarity=0.000 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHH
Q 011324 410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF 453 (488)
Q Consensus 410 v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~ 453 (488)
..+....+...++.+.... +.|.+|+|+.+|++...|..+..
T Consensus 78 ~~~~~~~~g~~Ir~lRe~~--GLSQ~eLA~~iGvs~stIskiE~ 119 (144)
T PRK06424 78 DLDIVEDYAELVKNARERL--SMSQADLAAKIFERKNVIASIER 119 (144)
T ss_pred HHHHHHHHHHHHHHHHHHc--CCCHHHHHHHhCCCHHHHHHHHC
Confidence 3344455555555555554 58999999999999999998876
No 278
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=39.09 E-value=1.3e+02 Score=25.39 Aligned_cols=40 Identities=5% Similarity=0.047 Sum_probs=28.6
Q ss_pred cCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHH
Q 011324 349 QGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 388 (488)
Q Consensus 349 ~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~w 388 (488)
.....+.+||.+...+..-.--..|...-|..|..|+...
T Consensus 18 ~~~~~~~~~lA~~~~~S~~~l~r~f~~~~g~s~~~~i~~~ 57 (107)
T PRK10219 18 IDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQR 57 (107)
T ss_pred cCCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCHHHHHHHH
Confidence 3456889999998888776666666655677777776554
No 279
>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=38.16 E-value=38 Score=26.36 Aligned_cols=25 Identities=20% Similarity=0.389 Sum_probs=19.7
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
+-|+..+||+.+|++..+|+.++..
T Consensus 23 ~lps~~~la~~~~vsr~tvr~al~~ 47 (64)
T PF00392_consen 23 RLPSERELAERYGVSRTTVREALRR 47 (64)
T ss_dssp BE--HHHHHHHHTS-HHHHHHHHHH
T ss_pred EeCCHHHHHHHhccCCcHHHHHHHH
Confidence 3569999999999999999999875
No 280
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=37.69 E-value=66 Score=24.87 Aligned_cols=23 Identities=22% Similarity=0.395 Sum_probs=18.8
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHH
Q 011324 431 SPDKEDLARRVGITVEKLERLIF 453 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~ 453 (488)
+.|.+++|+.+|++..+|..+..
T Consensus 14 gls~~~lA~~~g~s~s~v~~iE~ 36 (64)
T PF13560_consen 14 GLSQAQLADRLGVSQSTVSRIER 36 (64)
T ss_dssp TS-HHHHHHHHTS-HHHHHHHHT
T ss_pred CCCHHHHHHHHCcCHHHHHHHHC
Confidence 58999999999999999998865
No 281
>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=37.31 E-value=54 Score=26.95 Aligned_cols=24 Identities=21% Similarity=0.416 Sum_probs=20.9
Q ss_pred CcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 432 PDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 432 pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
.+.+|||+.+|++...++.++..-
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 799999999999999999998753
No 282
>COG2344 AT-rich DNA-binding protein [General function prediction only]
Probab=37.24 E-value=95 Score=30.74 Aligned_cols=51 Identities=12% Similarity=0.177 Sum_probs=42.1
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 404 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 404 irlP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
..+|......+...-+....|....-...+-+|||+.+|++..+|+.=+.+
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 468888888887777777778777777789999999999999999876653
No 283
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=37.11 E-value=34 Score=29.56 Aligned_cols=25 Identities=24% Similarity=0.408 Sum_probs=22.7
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 431 SPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
+.|.++||..||+|.+.|+.+|..-
T Consensus 23 ~ls~~~ia~dL~~s~~~le~vL~l~ 47 (89)
T PF10078_consen 23 GLSLEQIAADLGTSPEHLEQVLNLK 47 (89)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHcCC
Confidence 6899999999999999999998743
No 284
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=36.86 E-value=45 Score=30.29 Aligned_cols=34 Identities=15% Similarity=0.054 Sum_probs=28.1
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccc
Q 011324 428 GNHSPDKEDLARRVGITVEKLERLIFITRMPLSM 461 (488)
Q Consensus 428 lgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSL 461 (488)
+..+.+.+|||+.++++..+|+..+.+.+.++..
T Consensus 155 l~~g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl~~ 188 (204)
T PRK09958 155 ILDGKDNNDIAEKMFISNKTVSTYKSRLMEKLEC 188 (204)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence 3346799999999999999999999887766643
No 285
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=36.69 E-value=35 Score=27.27 Aligned_cols=22 Identities=23% Similarity=0.436 Sum_probs=19.1
Q ss_pred CcHHHHHHHhCCCHHHHHHHHH
Q 011324 432 PDKEDLARRVGITVEKLERLIF 453 (488)
Q Consensus 432 pS~eEIAe~LGIS~etVk~~L~ 453 (488)
++..|||+.+|++..+|..+++
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln 22 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLN 22 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHC
Confidence 3678999999999999988875
No 286
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=36.49 E-value=28 Score=26.64 Aligned_cols=32 Identities=28% Similarity=0.385 Sum_probs=19.4
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHhCCCcccc
Q 011324 431 SPDKEDLARRVGITVEKLERLIFITRMPLSMQ 462 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD 462 (488)
+.|..++|+.+||+..++..++..-...++++
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 287
>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=36.46 E-value=1.8e+02 Score=26.58 Aligned_cols=26 Identities=23% Similarity=0.261 Sum_probs=22.6
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHhC
Q 011324 431 SPDKEDLARRVGITVEKLERLIFITR 456 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar 456 (488)
..|.+|||..+|++.++|-.+++.-+
T Consensus 143 ~~t~~~iA~~lG~tretvsR~l~~l~ 168 (193)
T TIGR03697 143 RLSHQAIAEAIGSTRVTITRLLGDLR 168 (193)
T ss_pred CCCHHHHHHHhCCcHHHHHHHHHHHH
Confidence 46999999999999999999887543
No 288
>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=36.11 E-value=49 Score=26.09 Aligned_cols=24 Identities=21% Similarity=0.400 Sum_probs=21.6
Q ss_pred CcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 432 PDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 432 pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
.|.++||+.+|++..+|...++.-
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 489999999999999999998753
No 289
>PRK15044 transcriptional regulator SirC; Provisional
Probab=35.78 E-value=2.1e+02 Score=29.85 Aligned_cols=60 Identities=22% Similarity=0.198 Sum_probs=43.5
Q ss_pred HHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhh
Q 011324 257 LRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS 325 (488)
Q Consensus 257 l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~ 325 (488)
+..|++..+..+.|..+...... +++..-+.+..+++++..+||+.+||+...|.+.++.
T Consensus 172 Ls~~l~~~~~~~~L~~~~~is~~---------~kV~~~I~~nl~~~~SLeeLA~~lgmS~~tL~R~Fk~ 231 (295)
T PRK15044 172 ISAFVRKPGGFDFLERAIKITTK---------EKVYNIIISDLTRKWSQAEVAGKLFMSVSSLKRKLAA 231 (295)
T ss_pred HHHHHhcccchhhHHHHhhhhHH---------HHHHHHHHhCcccCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 66677776666666555544333 3344455677889999999999999999999877764
No 290
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=35.44 E-value=29 Score=36.08 Aligned_cols=36 Identities=19% Similarity=0.346 Sum_probs=30.2
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHhCC----CccccccC
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFITRM----PLSMQQPV 465 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~----~lSLD~~i 465 (488)
.+.|..|||+.||+|.-+|..+|..||. .+.++.+.
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 4689999999999999999999999875 35666654
No 291
>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=35.42 E-value=1.2e+02 Score=24.26 Aligned_cols=19 Identities=42% Similarity=0.595 Sum_probs=14.1
Q ss_pred hhhCCCCcHHHHHHHhcCC
Q 011324 297 SQFGREPTLIEWAKAIGLS 315 (488)
Q Consensus 297 ~~~Gr~Pt~~ewA~a~gm~ 315 (488)
...|.+||..|.|+++|+.
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 292
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=35.41 E-value=1.2e+02 Score=22.54 Aligned_cols=36 Identities=14% Similarity=0.110 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 416 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 416 kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
.|..|+..+. .| ..++.+.|+..|||..++..++..
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 389999999999999999977653
No 293
>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=35.08 E-value=68 Score=24.19 Aligned_cols=23 Identities=26% Similarity=0.479 Sum_probs=20.2
Q ss_pred CcHHHHHHHhCCCHHHHHHHHHH
Q 011324 432 PDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 432 pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
.+..|||+.+|++..+|..++..
T Consensus 22 ~t~~~la~~l~~~~~~vs~~v~~ 44 (62)
T PF12802_consen 22 LTQSELAERLGISKSTVSRIVKR 44 (62)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHH
T ss_pred cCHHHHHHHHCcCHHHHHHHHHH
Confidence 79999999999999999988864
No 294
>PF13309 HTH_22: HTH domain
Probab=35.05 E-value=68 Score=25.58 Aligned_cols=20 Identities=25% Similarity=0.413 Sum_probs=18.1
Q ss_pred cHHHHHHHhCCCHHHHHHHH
Q 011324 433 DKEDLARRVGITVEKLERLI 452 (488)
Q Consensus 433 S~eEIAe~LGIS~etVk~~L 452 (488)
+.+.+|+.||||.-+|-..|
T Consensus 44 av~~vA~~L~iS~~TVY~YL 63 (64)
T PF13309_consen 44 AVEYVAEKLGISRATVYRYL 63 (64)
T ss_pred HHHHHHHHHCCCHHHHHHHc
Confidence 79999999999999997765
No 295
>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=34.38 E-value=85 Score=23.51 Aligned_cols=24 Identities=17% Similarity=0.385 Sum_probs=21.3
Q ss_pred CcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 432 PDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 432 pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
++..+||+.+|++..+|...+...
T Consensus 26 ~~~~~la~~~~is~~~v~~~l~~L 49 (66)
T cd07377 26 PSERELAEELGVSRTTVREALREL 49 (66)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Confidence 579999999999999999988754
No 296
>PRK15044 transcriptional regulator SirC; Provisional
Probab=34.31 E-value=1.5e+02 Score=30.98 Aligned_cols=38 Identities=13% Similarity=0.162 Sum_probs=30.4
Q ss_pred HHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 417 VLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 417 I~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
..++..-+...+.+.++.++||+.+|++..++..+++.
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 297
>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=34.16 E-value=42 Score=24.13 Aligned_cols=22 Identities=14% Similarity=0.156 Sum_probs=18.1
Q ss_pred cHHHHHHHhCCCHHHHHHHHHH
Q 011324 433 DKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 433 S~eEIAe~LGIS~etVk~~L~~ 454 (488)
|+.|+|+.+|++..+|+..-..
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~ 22 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYERE 22 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHT
T ss_pred CHHHHHHHHCCCHHHHHHHHHC
Confidence 4679999999999999988664
No 298
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=33.64 E-value=61 Score=23.06 Aligned_cols=28 Identities=21% Similarity=0.246 Sum_probs=20.1
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 428 GNHSPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 428 lgr~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
+....++++||+.+|++......+.+..
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 3446799999999999999998887654
No 299
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=33.34 E-value=83 Score=28.89 Aligned_cols=27 Identities=15% Similarity=0.117 Sum_probs=22.9
Q ss_pred hcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 427 EGNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 427 elgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
..+ ..|.+|||+.||++..+|...++.
T Consensus 39 ~~~-~~tvdelae~lnr~rStv~rsl~~ 65 (126)
T COG3355 39 ENG-PLTVDELAEILNRSRSTVYRSLQN 65 (126)
T ss_pred hcC-CcCHHHHHHHHCccHHHHHHHHHH
Confidence 344 779999999999999999888763
No 300
>PRK10072 putative transcriptional regulator; Provisional
Probab=33.20 E-value=76 Score=27.56 Aligned_cols=25 Identities=20% Similarity=0.276 Sum_probs=22.1
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 431 SPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
+.|..|+|+.+|++..+|..+..--
T Consensus 46 glTQ~elA~~lGvS~~TVs~WE~G~ 70 (96)
T PRK10072 46 GLKIDDFARVLGVSVAMVKEWESRR 70 (96)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHcCC
Confidence 5899999999999999999987643
No 301
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=32.45 E-value=75 Score=33.41 Aligned_cols=38 Identities=26% Similarity=0.462 Sum_probs=31.1
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHhCC----CccccccCCC
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFITRM----PLSMQQPVWA 467 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~----~lSLD~~i~~ 467 (488)
.+.|..|||+.||||.-+|..++..++. .++++.++..
T Consensus 25 ~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I~i~~~~~~ 66 (321)
T COG2390 25 EGLTQSEIAERLGISRATVSRLLAKAREEGIVKISINSPVEG 66 (321)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEEEeCCCCcc
Confidence 4689999999999999999999998875 3666655543
No 302
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=31.77 E-value=53 Score=29.63 Aligned_cols=31 Identities=10% Similarity=0.087 Sum_probs=26.0
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHhCCCcc
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFITRMPLS 460 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~lS 460 (488)
.+.+.++||+.||++..+|+..+...+.++.
T Consensus 151 ~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~ 181 (196)
T PRK10360 151 QGMAVKEIAAELGLSPKTVHVHRANLMEKLG 181 (196)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 3579999999999999999998887665543
No 303
>PRK04841 transcriptional regulator MalT; Provisional
Probab=31.70 E-value=44 Score=38.66 Aligned_cols=33 Identities=12% Similarity=0.072 Sum_probs=27.4
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCcc
Q 011324 428 GNHSPDKEDLARRVGITVEKLERLIFITRMPLS 460 (488)
Q Consensus 428 lgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lS 460 (488)
...+.|.+|||+.|+||+.||+..+.....++-
T Consensus 850 ~~~g~~~~~ia~~l~~s~~tv~~h~~~~~~kl~ 882 (903)
T PRK04841 850 IYSGYSNEQIAGELDVAATTIKTHIRNLYQKLG 882 (903)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 445789999999999999999999987655543
No 304
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=31.58 E-value=1.2e+02 Score=27.31 Aligned_cols=35 Identities=17% Similarity=0.264 Sum_probs=26.9
Q ss_pred HHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 419 EAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 419 ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
+++..+....+ .++..+||+.||++..+|...+..
T Consensus 11 ~~I~~l~~~~~-~~~~~ela~~l~vs~~svs~~l~~ 45 (142)
T PRK03902 11 EQIYLLIEEKG-YARVSDIAEALSVHPSSVTKMVQK 45 (142)
T ss_pred HHHHHHHhcCC-CcCHHHHHHHhCCChhHHHHHHHH
Confidence 34444444455 779999999999999999988864
No 305
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=31.45 E-value=2.5e+02 Score=31.87 Aligned_cols=23 Identities=17% Similarity=0.251 Sum_probs=19.5
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHH
Q 011324 431 SPDKEDLARRVGITVEKLERLIF 453 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~ 453 (488)
..|..|||+..|+|..+|-...+
T Consensus 374 ~~si~eLA~~~~vS~aTV~Rf~k 396 (638)
T PRK14101 374 NDPIVDIARKADVSQPTVIRFCR 396 (638)
T ss_pred hccHHHHHHHhCCCHHHHHHHHH
Confidence 45999999999999999976644
No 306
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=31.18 E-value=54 Score=25.43 Aligned_cols=24 Identities=13% Similarity=0.123 Sum_probs=20.9
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHhC
Q 011324 433 DKEDLARRVGITVEKLERLIFITR 456 (488)
Q Consensus 433 S~eEIAe~LGIS~etVk~~L~~ar 456 (488)
|..|+|+.+|++..+|+.......
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 678999999999999999987543
No 307
>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=30.86 E-value=2.5e+02 Score=28.58 Aligned_cols=114 Identities=18% Similarity=0.147 Sum_probs=69.5
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHH-HHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHHHHHHHHHHHHH
Q 011324 265 ETRKLLTADEEFELIAQIQDLIRLEKE-KSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH 343 (488)
Q Consensus 265 ~~~~lLT~eEE~eL~~~iq~l~~le~~-~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~ArekLIesnlrLV~s 343 (488)
....-++.+--..|++.|..+..=+-+ -..+.+-+|.-|+.++...-+.+ +.+. -.|-++.+.
T Consensus 5 e~~~~~~~~~~~~L~~~l~~laD~elil~~r~~ew~~~AP~LeediAl~~i--------------a~De--lGHAr~ly~ 68 (263)
T PF05138_consen 5 EDPDEMPEEYREALIRYLLRLADDELILGQRLSEWCGHAPSLEEDIALANI--------------AQDE--LGHARLLYR 68 (263)
T ss_dssp -TTSS--HHHHHHHHHHHHHHHHHHHHHHHHHHTGGGGSSSHHHHHHHHHH--------------HHHH--HHHHHHHHH
T ss_pred ccchhhhhhhHHHHHHHHHHHhChHHHhhhHHhHHHhhCCCHHHHHHHHHH--------------HHHH--HHHHHHHHH
Confidence 334456666667777777665533333 33445567888888766543222 2222 247788899
Q ss_pred HHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHH
Q 011324 344 VAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIF 398 (488)
Q Consensus 344 IAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IR 398 (488)
++..+-|.|.+.++|...=.-+=++.+.-|+ ..+..|+...+|+.+.+...
T Consensus 69 ll~el~g~G~~~d~la~~R~~~~~rn~~l~e----~p~~dwa~~v~r~~l~d~~~ 119 (263)
T PF05138_consen 69 LLEELEGEGRDEDDLAFLRDAREFRNLLLFE----QPNGDWADTVARQFLFDRAG 119 (263)
T ss_dssp HHHHCHCCCHHHHHHHHHHHTTCS-SSGGGG----S---SHHHHHHHHHHHHHHH
T ss_pred HHHHHhccCCChhHHHhhcccchhhhhhhhc----cCCCCHHHHHHHHHHHHHHH
Confidence 9999888887777776655555455555554 34678999999998887764
No 308
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=30.61 E-value=1.9e+02 Score=25.67 Aligned_cols=49 Identities=14% Similarity=0.173 Sum_probs=35.1
Q ss_pred cCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHH
Q 011324 349 QGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI 397 (488)
Q Consensus 349 ~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~I 397 (488)
.......+||..+..+.--.--..|...-|..|..|+..+-.......+
T Consensus 22 ~~~~~sl~~lA~~~g~S~~~l~r~Fk~~~G~s~~~~l~~~Rl~~A~~~L 70 (127)
T PRK11511 22 LESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKL 70 (127)
T ss_pred cCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3456899999999888877777778776788888887765444333333
No 309
>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=30.46 E-value=1.5e+02 Score=25.40 Aligned_cols=23 Identities=13% Similarity=0.429 Sum_probs=19.7
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHH
Q 011324 430 HSPDKEDLARRVGITVEKLERLI 452 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L 452 (488)
.+.|+.|||+.+|+|..+|-..-
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 46899999999999999986553
No 310
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=30.21 E-value=2.5e+02 Score=21.45 Aligned_cols=36 Identities=22% Similarity=0.298 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHhcCCCCcHHHHHHHhCC-CHHHHHHHHHH
Q 011324 416 KVLEAKRLYIQEGNHSPDKEDLARRVGI-TVEKLERLIFI 454 (488)
Q Consensus 416 kI~ka~~~L~~elgr~pS~eEIAe~LGI-S~etVk~~L~~ 454 (488)
++.++...+... ..+.++||..+|+ +........+.
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 344444444322 5799999999999 99888777654
No 311
>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=30.17 E-value=51 Score=27.78 Aligned_cols=27 Identities=15% Similarity=0.288 Sum_probs=19.6
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHhCC
Q 011324 431 SPDKEDLARRVGITVEKLERLIFITRM 457 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (488)
+.|..|||+.||.+...|..++....-
T Consensus 3 G~tq~eIA~~lGks~s~Vs~~l~Ll~l 29 (93)
T PF08535_consen 3 GWTQEEIAKRLGKSRSWVSNHLALLDL 29 (93)
T ss_dssp T--HHHHHHHTT--HHHHHHHHGGGS-
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHcC
Confidence 578999999999999999999886643
No 312
>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=30.17 E-value=99 Score=24.49 Aligned_cols=31 Identities=19% Similarity=0.355 Sum_probs=23.7
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHhCCCcccc
Q 011324 431 SPDKEDLARRVGITVEKLERLIFITRMPLSMQ 462 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD 462 (488)
+.|.+++|+.+|++..+|..++. ....++.+
T Consensus 18 ~~t~~~lA~~~gis~~tis~~~~-g~~~~~~~ 48 (78)
T TIGR02607 18 GLSIRALAKALGVSRSTLSRIVN-GRRGITAD 48 (78)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHc-CCCCCCHH
Confidence 57899999999999999998876 33334443
No 313
>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=29.92 E-value=1.1e+02 Score=28.98 Aligned_cols=35 Identities=26% Similarity=0.545 Sum_probs=27.7
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccC
Q 011324 431 SPDKEDLARRVGITVEKLERLIFITRMPLSMQQPV 465 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i 465 (488)
+.+.+|||+.+|++...|..++..+.-+-.+...+
T Consensus 120 g~s~~~iA~~lg~s~~~V~r~l~l~~lp~~v~~~~ 154 (187)
T TIGR00180 120 SMTQEDLAKKIGKSRAHITNLLRLLKLPSEIQSAI 154 (187)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHcCCHHHHHHH
Confidence 46899999999999999999999876444443333
No 314
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=29.66 E-value=62 Score=30.30 Aligned_cols=28 Identities=25% Similarity=0.333 Sum_probs=18.3
Q ss_pred HhcCCCCcHHHHHHHhCCCHHHHHHHHH
Q 011324 426 QEGNHSPDKEDLARRVGITVEKLERLIF 453 (488)
Q Consensus 426 ~elgr~pS~eEIAe~LGIS~etVk~~L~ 453 (488)
...+...|.+|||+.+||+..++-.+.+
T Consensus 29 ~~~~~r~T~~eiAee~Gis~~tLYrWr~ 56 (142)
T PF13022_consen 29 PENGERRTQAEIAEEVGISRSTLYRWRQ 56 (142)
T ss_dssp ------S-HHHHHHHHTS-HHHHHHHHH
T ss_pred hhccccchHHHHHHHhCCCHHHHHHHHh
Confidence 3344578999999999999999988764
No 315
>PRK08359 transcription factor; Validated
Probab=29.66 E-value=1.4e+02 Score=28.84 Aligned_cols=40 Identities=25% Similarity=0.355 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHH
Q 011324 410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERL 451 (488)
Q Consensus 410 v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~ 451 (488)
+.+.+..+.+.++++.... +.|.+|+|+.+|++...|..+
T Consensus 79 ~~elv~dy~~rIkeaRe~k--glSQeeLA~~lgvs~stI~~i 118 (176)
T PRK08359 79 TEDIVEDYAERVYEAIQKS--GLSYEELSHEVGLSVNDLRRI 118 (176)
T ss_pred HHHHHHHHHHHHHHHHHHc--CCCHHHHHHHhCCCHHHHHHH
Confidence 4455555555555555554 599999999999999999866
No 316
>PF15545 Toxin_67: Putative toxin 67
Probab=29.54 E-value=51 Score=27.16 Aligned_cols=30 Identities=23% Similarity=0.526 Sum_probs=25.4
Q ss_pred chhhHHHHHHHHHHHHHHHHhcCCcccchh
Q 011324 380 RFASYAYWWVRQTIRKAIFQHSRTIRLPEN 409 (488)
Q Consensus 380 rFSTYA~~wIRnaI~~~IRk~sr~irlP~~ 409 (488)
+-+.|+.-||+|.|...-+.....+|+|..
T Consensus 6 kq~~~vRGwiknEi~~i~~~~r~~iRlPpG 35 (70)
T PF15545_consen 6 KQPSWVRGWIKNEINRIKTGRRKSIRLPPG 35 (70)
T ss_pred cchHHHHHHHHHHHHHHHhCccceecCCCc
Confidence 468899999999999888877788999954
No 317
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=29.50 E-value=91 Score=32.23 Aligned_cols=41 Identities=10% Similarity=0.076 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 415 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 415 ~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
+.+-++.-.|..+.++...-+|||+.+|..+++|++.++.-
T Consensus 9 keIL~aLi~LY~~~~r~IKgeeIA~~l~rnpGTVRNqmq~L 49 (294)
T COG2524 9 KEILQALINLYRRKKRPIKGEEIAEVLNRNPGTVRNQMQSL 49 (294)
T ss_pred HHHHHHHHHHHHhcCCCcchHHHHHHHccCcchHHHHHHHH
Confidence 44455555666666778889999999999999999998754
No 318
>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=29.46 E-value=5.3e+02 Score=25.32 Aligned_cols=35 Identities=17% Similarity=0.156 Sum_probs=25.6
Q ss_pred HHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 420 AKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 420 a~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
+..-+.+.+....|.++||+.+|+|...+..+.+.
T Consensus 191 ~~~~I~~~~~~~~sl~~lA~~~~~S~~~l~r~Fk~ 225 (287)
T TIGR02297 191 FNFLIEENYKQHLRLPEYADRLGISESRLNDICRR 225 (287)
T ss_pred HHHHHHHhhccCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 33334445555789999999999999999777654
No 319
>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=29.31 E-value=1e+02 Score=27.27 Aligned_cols=28 Identities=7% Similarity=0.273 Sum_probs=23.7
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 428 GNHSPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 428 lgr~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
.+...+..|||+.+|++...|..++..-
T Consensus 22 ~~~~~s~~eia~~l~is~~~v~~~l~~L 49 (130)
T TIGR02944 22 DSQPYSAAEIAEQTGLNAPTVSKILKQL 49 (130)
T ss_pred CCCCccHHHHHHHHCcCHHHHHHHHHHH
Confidence 3446799999999999999999998753
No 320
>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=29.22 E-value=1.4e+02 Score=25.29 Aligned_cols=26 Identities=12% Similarity=0.104 Sum_probs=22.5
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 429 NHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 429 gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
...++..|||+.+|++..+|..++..
T Consensus 45 ~~~is~~eLa~~~g~sr~tVsr~L~~ 70 (95)
T TIGR01610 45 QDRVTATVIAELTGLSRTHVSDAIKS 70 (95)
T ss_pred CCccCHHHHHHHHCcCHHHHHHHHHH
Confidence 34679999999999999999998764
No 321
>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=29.08 E-value=65 Score=30.25 Aligned_cols=25 Identities=12% Similarity=0.417 Sum_probs=22.9
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 431 SPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
..|.+|||+.|||+...|+.++..-
T Consensus 28 ~~tdEeLa~~Lgi~~~~VRk~L~~L 52 (158)
T TIGR00373 28 EFTDEEISLELGIKLNEVRKALYAL 52 (158)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 6899999999999999999998754
No 322
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=28.81 E-value=1.3e+02 Score=28.22 Aligned_cols=42 Identities=10% Similarity=0.028 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHHHHHhc-CCCCcHHHHHHHhCCCHHHHHHH
Q 011324 410 IYTLLSKVLEAKRLYIQEG-NHSPDKEDLARRVGITVEKLERL 451 (488)
Q Consensus 410 v~e~l~kI~ka~~~L~~el-gr~pS~eEIAe~LGIS~etVk~~ 451 (488)
......+|-++..++..+. -...|.++||+..|++.+++...
T Consensus 9 ~~~~r~~Il~aa~~lf~~~G~~~~ti~~Ia~~agvsk~t~Y~~ 51 (213)
T PRK09975 9 ALKTRQELIETAIAQFALRGVSNTTLNDIADAANVTRGAIYWH 51 (213)
T ss_pred HHHHHHHHHHHHHHHHHHcCcccCCHHHHHHHcCCCHHHHHHH
Confidence 3444556666655555444 45789999999999999998653
No 323
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=28.76 E-value=5.6e+02 Score=25.03 Aligned_cols=166 Identities=17% Similarity=0.248 Sum_probs=78.8
Q ss_pred CCHHHHHHHHHHHHHHH-HHHHHHHHHHhhhCCCCc----HHHHHHHhcCCHHHHHH---HhhhcHHHHHHHHHHHHHHH
Q 011324 270 LTADEEFELIAQIQDLI-RLEKEKSKLQSQFGREPT----LIEWAKAIGLSCRDLKS---ELHSGNSSREKLINANLRLV 341 (488)
Q Consensus 270 LT~eEE~eL~~~iq~l~-~le~~~~~l~~~~Gr~Pt----~~ewA~a~gm~eeeLi~---~l~~Gd~ArekLIesnlrLV 341 (488)
+..+.-..|..+.+++. .++.....+....+..|. +.+.+..+|++.-.... .... .....+..--.-|
T Consensus 23 ~a~~dl~~L~~qa~~~~~~l~~fa~k~~~~i~~~~~~r~~f~~~~~~lGvdp~~s~~~~s~~l~---~~~~f~~ELa~qi 99 (223)
T PF04157_consen 23 LAFQDLEALMSQAKDFVELLENFARKHKSEIKSDPEFRSQFQSMCASLGVDPLASSKFWSESLK---GSGDFYYELAVQI 99 (223)
T ss_dssp CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCSHHHHHHHHHHHHHHT--CHCCTTCCCCCCS---CHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCCchHHHHHHHHHHHcCCCcccchhhhhhccc---cchhHHHHHHHHH
Confidence 55666677888887776 556667777777777775 45677777876421111 0001 2222222223334
Q ss_pred HHHHHHcc-CCC--CCHhHHHHHHHHH-----------HHHhHHhhCCCC-CCchhhHHHHHHHHHHHHHHHHhcCCc-c
Q 011324 342 VHVAKQYQ-GRG--ISLHDLLQEGSMG-----------LMKSVEKFKPQA-GCRFASYAYWWVRQTIRKAIFQHSRTI-R 405 (488)
Q Consensus 342 ~sIAkry~-~~g--~d~EDLIQEG~IG-----------L~rAiekFDpsk-G~rFSTYA~~wIRnaI~~~IRk~sr~i-r 405 (488)
..++.... .+| +.+.||+..-+-. +.+|++.|++-. |+++.+|- .....+ .
T Consensus 100 ~e~c~~~~~~~GGii~L~dl~~~~nr~R~g~~lISp~Di~~A~~~l~~lg~g~~l~~~~-------------sg~~vv~s 166 (223)
T PF04157_consen 100 AEVCLATRSKNGGIISLSDLYCRYNRARGGSELISPEDILRACKLLEVLGLGFRLRKFG-------------SGVKVVQS 166 (223)
T ss_dssp HHHHHHHCCTTTSEEEHHHHHHHHHHCTTTSST--HHHHHHHHHHHCCCTSSEEEEEET-------------TTEEEEEC
T ss_pred HHHHHHHHhcCCCEEEHHHHHHHHHHhcccCCCcCHHHHHHHHHHHHHcCCCeEEEEeC-------------CCcEEEEe
Confidence 44444432 233 3444444332220 223333333211 12211111 000011 1
Q ss_pred cc-hhHHHHHHHHHHHHHHHH-HhcCCCCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 406 LP-ENIYTLLSKVLEAKRLYI-QEGNHSPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 406 lP-~~v~e~l~kI~ka~~~L~-~elgr~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
.| ........+| -.+. ...+...|..+|++.+|++....+..|..+
T Consensus 167 ~~~~e~~~~~~~i----l~~~~~~~~g~vt~~~l~~~~~ws~~~a~~~L~~~ 214 (223)
T PF04157_consen 167 VPYSELSKDQSRI----LELAEEENGGGVTASELAEKLGWSVERAKEALEEL 214 (223)
T ss_dssp ST-CHH-HHHHHH----HHHH--TTTSEEEHHHHHHHHTB-HHHHHHHHHHH
T ss_pred CCchhhhHHHHHH----HHHHHhhcCCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 23 2222333333 2333 233447899999999999999999988754
No 324
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=28.67 E-value=89 Score=30.66 Aligned_cols=26 Identities=19% Similarity=0.309 Sum_probs=22.7
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
+-|+..|||+.+|+|...|++++..-
T Consensus 33 ~LpsE~eLa~~lgVSRtpVREAL~~L 58 (254)
T PRK09464 33 KLPPERELAKQFDVSRPSLREAIQRL 58 (254)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 35699999999999999999998753
No 325
>PF13551 HTH_29: Winged helix-turn helix
Probab=28.58 E-value=59 Score=27.23 Aligned_cols=24 Identities=29% Similarity=0.426 Sum_probs=21.8
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHhC
Q 011324 433 DKEDLARRVGITVEKLERLIFITR 456 (488)
Q Consensus 433 S~eEIAe~LGIS~etVk~~L~~ar 456 (488)
+..+||+.+|++..+|..+++...
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~ 37 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYR 37 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHH
Confidence 699999999999999999988654
No 326
>COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]
Probab=28.54 E-value=94 Score=32.86 Aligned_cols=72 Identities=26% Similarity=0.247 Sum_probs=46.3
Q ss_pred hHHHHHHHHHHHHHHHHhcCCcccchh--HHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 383 SYAYWWVRQTIRKAIFQHSRTIRLPEN--IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 383 TYA~~wIRnaI~~~IRk~sr~irlP~~--v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
..+....++-+...+|.-....++|.. ..-.-.+|.+++..+...+.+..+.+|||+.+|+|..++..+.+.
T Consensus 186 ~~a~~va~~lv~~~~R~~~~~Q~~~~~~~~~~~~~~l~~~i~~me~nle~plsl~~LA~~~~~S~R~leRlF~~ 259 (328)
T COG4977 186 ALANRVARQLVVDPIRSGGDRQRLPLLGRLGHRDPRLLRAIELMEANLEEPLSLEELADRAGLSRRQLERLFRA 259 (328)
T ss_pred HHHHHHHHHhhhccccCCCccccccccccCCCCCHHHHHHHHHHHHhhcCCcCHHHHHHHhCCCHHHHHHHHHH
Confidence 345555566666666553322223321 111234566666777777887889999999999999999887654
No 327
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=28.48 E-value=1.4e+02 Score=28.76 Aligned_cols=50 Identities=16% Similarity=0.269 Sum_probs=36.0
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 405 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 405 rlP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
.+|......+.+..+....|........+..|||+.+|++..+|+.=+..
T Consensus 6 ~~~~~~~~r~~~~~~il~~l~~~~~~~vs~~~L~~~~~v~~~tirrDl~~ 55 (213)
T PRK05472 6 KIPEATIKRLPLYYRYLKELKEEGVERVSSKELAEALGVDSAQIRKDLSY 55 (213)
T ss_pred cCCHHHHHHhHHHHHHHHHHHHcCCcEEeHHHHHHHhCcCHHHHHHHHHH
Confidence 46666666666666666666655534579999999999999999876543
No 328
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=28.43 E-value=2.9e+02 Score=25.68 Aligned_cols=25 Identities=20% Similarity=0.388 Sum_probs=22.0
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 431 SPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
..|.+|||..+|++.++|-.+++.-
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR~l~~l 192 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRVLKML 192 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 4689999999999999999988654
No 329
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=28.30 E-value=2.8e+02 Score=22.71 Aligned_cols=25 Identities=20% Similarity=0.357 Sum_probs=21.5
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 431 SPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
+.+.+||++..|+|..+++-++...
T Consensus 44 Ga~~~el~~~CgL~~aEAeLl~~Lh 68 (70)
T PF10975_consen 44 GASVEELMEECGLSRAEAELLLSLH 68 (70)
T ss_pred CCCHHHHHHHcCCCHHHHHHHHHHh
Confidence 5699999999999999998877643
No 330
>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=28.16 E-value=1.4e+02 Score=22.99 Aligned_cols=26 Identities=19% Similarity=0.222 Sum_probs=21.4
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 429 NHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 429 gr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
+.+.+..|||+.+|++..++..-+..
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 34789999999999999999887754
No 331
>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=27.92 E-value=1.2e+02 Score=26.44 Aligned_cols=24 Identities=13% Similarity=0.337 Sum_probs=20.1
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHH
Q 011324 430 HSPDKEDLARRVGITVEKLERLIF 453 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~ 453 (488)
.+.|..|||+.+||+..+|-..-+
T Consensus 54 ~~~tQrEIa~~lGiS~atIsR~sn 77 (94)
T TIGR01321 54 GNMSQREIASKLGVSIATITRGSN 77 (94)
T ss_pred CCCCHHHHHHHhCCChhhhhHHHh
Confidence 378999999999999999865533
No 332
>smart00351 PAX Paired Box domain.
Probab=27.68 E-value=1e+02 Score=27.64 Aligned_cols=28 Identities=7% Similarity=0.067 Sum_probs=24.5
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324 431 SPDKEDLARRVGITVEKLERLIFITRMP 458 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (488)
+.+..+||+.+||+..+|..++++.+..
T Consensus 33 G~s~~~iA~~~gvs~~tV~kwi~r~~~~ 60 (125)
T smart00351 33 GVRPCDISRQLCVSHGCVSKILGRYYET 60 (125)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHc
Confidence 5699999999999999999999876543
No 333
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=27.59 E-value=1.2e+02 Score=25.09 Aligned_cols=22 Identities=23% Similarity=0.407 Sum_probs=19.7
Q ss_pred CCcHHHHHHHhCCCHHHHHHHH
Q 011324 431 SPDKEDLARRVGITVEKLERLI 452 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L 452 (488)
+.|.+|+|+.+|++..++-.+-
T Consensus 14 ~ltQ~elA~~vgVsRQTi~~iE 35 (68)
T COG1476 14 GLTQEELAKLVGVSRQTIIAIE 35 (68)
T ss_pred CcCHHHHHHHcCcCHHHHHHHH
Confidence 5899999999999999998764
No 334
>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=27.55 E-value=71 Score=24.70 Aligned_cols=22 Identities=18% Similarity=0.161 Sum_probs=19.7
Q ss_pred cHHHHHHHhCCCHHHHHHHHHH
Q 011324 433 DKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 433 S~eEIAe~LGIS~etVk~~L~~ 454 (488)
+..|+|+.+||+..+++...+.
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh
Confidence 6789999999999999988764
No 335
>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=27.54 E-value=1.8e+02 Score=25.17 Aligned_cols=23 Identities=17% Similarity=0.151 Sum_probs=20.7
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHH
Q 011324 431 SPDKEDLARRVGITVEKLERLIF 453 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~ 453 (488)
+.|..++|+.+|++..+|..+..
T Consensus 78 gltq~~lA~~lg~~~~tis~~e~ 100 (127)
T TIGR03830 78 GLSQREAAELLGGGVNAFSRYER 100 (127)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHC
Confidence 58999999999999999988865
No 336
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=27.36 E-value=2.1e+02 Score=26.91 Aligned_cols=40 Identities=13% Similarity=0.067 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHH
Q 011324 412 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF 453 (488)
Q Consensus 412 e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~ 453 (488)
+.+..+.+.++.+.... +.|.+++|+.+|++...|..+-+
T Consensus 65 ~l~~~~g~~Ir~~Re~~--glSqeeLA~~lgvs~s~IsriE~ 104 (154)
T TIGR00270 65 ELVEDYGIIIRREREKR--GWSQEQLAKKIQEKESLIKKIEN 104 (154)
T ss_pred HHHHHHHHHHHHHHHHc--CCCHHHHHHHhCCCHHHHHHHHC
Confidence 33444444445444443 58999999999999999988754
No 337
>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=27.30 E-value=1.2e+02 Score=24.69 Aligned_cols=43 Identities=19% Similarity=0.203 Sum_probs=30.2
Q ss_pred HHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccC
Q 011324 422 RLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPV 465 (488)
Q Consensus 422 ~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i 465 (488)
..+...+. ..+..+||+.++++.+.|+..+..+-..-.++..+
T Consensus 16 ~~l~~~y~-~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~I 58 (88)
T smart00088 16 LQLSEPYS-SISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKI 58 (88)
T ss_pred HHHhHHhc-eeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEE
Confidence 44444454 78999999999999999998876553333344444
No 338
>smart00753 PAM PCI/PINT associated module.
Probab=27.30 E-value=1.2e+02 Score=24.69 Aligned_cols=43 Identities=19% Similarity=0.203 Sum_probs=30.2
Q ss_pred HHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccC
Q 011324 422 RLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPV 465 (488)
Q Consensus 422 ~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i 465 (488)
..+...+. ..+..+||+.++++.+.|+..+..+-..-.++..+
T Consensus 16 ~~l~~~y~-~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~I 58 (88)
T smart00753 16 LQLSEPYS-SISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKI 58 (88)
T ss_pred HHHhHHhc-eeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEE
Confidence 44444454 78999999999999999998876553333344444
No 339
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=27.23 E-value=2.5e+02 Score=28.60 Aligned_cols=48 Identities=13% Similarity=-0.000 Sum_probs=32.1
Q ss_pred HHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHH
Q 011324 340 LVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 388 (488)
Q Consensus 340 LV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~w 388 (488)
.|..++..........+||.++..+.--.=-..|... |..|..|+..|
T Consensus 138 kv~~~I~~~~~~~~tl~~LA~~~gmS~s~l~R~FK~~-G~T~~eyl~~~ 185 (253)
T PRK09940 138 KVRNIVNMKLAHPWKLKDICDCLYISESLLKKKLKQE-QTTFSQILLDA 185 (253)
T ss_pred HHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHHc-CCCHHHHHHHH
Confidence 3444444444556889999999888776666667654 77777776665
No 340
>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=26.67 E-value=7.1e+02 Score=25.54 Aligned_cols=25 Identities=28% Similarity=0.417 Sum_probs=21.6
Q ss_pred CCcHHHHHHHhC--CCHHHHHHHHHHh
Q 011324 431 SPDKEDLARRVG--ITVEKLERLIFIT 455 (488)
Q Consensus 431 ~pS~eEIAe~LG--IS~etVk~~L~~a 455 (488)
.+++++||+.++ ||.++|++.+..-
T Consensus 137 ~~~~~~ia~~l~p~is~~ev~~sL~~L 163 (271)
T TIGR02147 137 ADDPEELAKRCFPKISAEQVKESLDLL 163 (271)
T ss_pred CCCHHHHHHHhCCCCCHHHHHHHHHHH
Confidence 557889999999 9999999998753
No 341
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=26.62 E-value=2.1e+02 Score=23.81 Aligned_cols=50 Identities=18% Similarity=0.194 Sum_probs=32.5
Q ss_pred ccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHH
Q 011324 348 YQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI 397 (488)
Q Consensus 348 y~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~I 397 (488)
....+...+++.++..+.-..-...|....|..|..|+..+=.+.....+
T Consensus 32 ~~~~~~~l~~la~~~g~S~~~l~r~f~~~~g~s~~~~~~~~Rl~~A~~lL 81 (127)
T COG2207 32 NLAEPLTLEDLARRLGMSRRTLSRLFKKETGTSPSQYLRQLRLEEARRLL 81 (127)
T ss_pred HhcCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 33445788899888877777777777766777777666554444433333
No 342
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=26.49 E-value=95 Score=22.58 Aligned_cols=25 Identities=12% Similarity=0.074 Sum_probs=22.3
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 431 SPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
..+..+|++.+|++..+|..++...
T Consensus 10 ~~~~~~i~~~l~is~~~v~~~l~~L 34 (66)
T smart00418 10 ELCVCELAEILGLSQSTVSHHLKKL 34 (66)
T ss_pred CccHHHHHHHHCCCHHHHHHHHHHH
Confidence 6799999999999999999998753
No 343
>PRK09480 slmA division inhibitor protein; Provisional
Probab=26.41 E-value=5e+02 Score=23.63 Aligned_cols=74 Identities=18% Similarity=0.004 Sum_probs=50.1
Q ss_pred HhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHh
Q 011324 296 QSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKS 369 (488)
Q Consensus 296 ~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rA 369 (488)
.+.-|...|..+.|+.+|++...+..-..+-++-+..+++.+..-+............+..+.++..+-.++.-
T Consensus 24 ~~~~G~~~ti~~Ia~~agvs~gt~Y~~F~~K~~L~~~v~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~ 97 (194)
T PRK09480 24 ESPPGERITTAKLAARVGVSEAALYRHFPSKARMFEGLIEFIEESLFSRINQILKDEKDTLARARLILLLLLGF 97 (194)
T ss_pred HhcCCCccCHHHHHHHhCCCHhHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHH
Confidence 34446778999999999999999988888877777777776665555444443333345666666655555543
No 344
>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=26.19 E-value=53 Score=26.06 Aligned_cols=30 Identities=20% Similarity=0.212 Sum_probs=20.6
Q ss_pred HHHhcCCCCcHHHHHHHhCCCHHHHH-HHHHH
Q 011324 424 YIQEGNHSPDKEDLARRVGITVEKLE-RLIFI 454 (488)
Q Consensus 424 L~~elgr~pS~eEIAe~LGIS~etVk-~~L~~ 454 (488)
+.+.++ -.+..|+|+.|||+..+|. ....+
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 444455 5578899999999999999 66653
No 345
>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=26.17 E-value=1.7e+02 Score=25.50 Aligned_cols=26 Identities=27% Similarity=0.460 Sum_probs=20.2
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHhC
Q 011324 431 SPDKEDLARRVGITVEKLERLIFITR 456 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar 456 (488)
+.++.|||...|+|...|..++...+
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 56899999999999999999987643
No 346
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=25.91 E-value=2e+02 Score=21.97 Aligned_cols=61 Identities=16% Similarity=0.282 Sum_probs=33.5
Q ss_pred CCcHHHHHHHhcCCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHH
Q 011324 302 EPTLIEWAKAIGLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSM 364 (488)
Q Consensus 302 ~Pt~~ewA~a~gm~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~I 364 (488)
+++..++|+.+|++...|.+.+..-- ......+.. ..+..+...+.......+|+.++..+
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 36788999999999888876665322 111112111 11222222222335778888777544
No 347
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=25.69 E-value=1.2e+02 Score=29.02 Aligned_cols=25 Identities=16% Similarity=0.507 Sum_probs=22.8
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 431 SPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
..|.+|||+.|||+...|+.++..-
T Consensus 36 ~~tdeeLA~~Lgi~~~~VRk~L~~L 60 (178)
T PRK06266 36 EVTDEEIAEQTGIKLNTVRKILYKL 60 (178)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 6899999999999999999998753
No 348
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=25.66 E-value=1.3e+02 Score=29.48 Aligned_cols=27 Identities=15% Similarity=0.326 Sum_probs=23.5
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 428 GNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 428 lgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
+.+-||-.|||+.+|++..+|+.++..
T Consensus 26 G~~LPsE~eL~~~~~VSR~TvR~Al~~ 52 (240)
T PRK09764 26 GDALPTESALQTEFGVSRVTVRQALRQ 52 (240)
T ss_pred CCcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 345789999999999999999999863
No 349
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=25.20 E-value=1.4e+02 Score=30.40 Aligned_cols=40 Identities=10% Similarity=-0.005 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 416 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 416 kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
.+.++...+...+...++.++||+.+|++...+..+.+..
T Consensus 219 ~~~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~ 258 (322)
T PRK09393 219 RLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAA 258 (322)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4455555566666668899999999999999998887643
No 350
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=25.02 E-value=2e+02 Score=30.22 Aligned_cols=24 Identities=4% Similarity=0.097 Sum_probs=20.9
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 431 SPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
.-+.+||.+.+|+++.+|+.-.+.
T Consensus 260 kkt~keI~~vtgVaE~TIr~sYK~ 283 (308)
T KOG1597|consen 260 KKTQKEIGEVTGVAEVTIRNSYKD 283 (308)
T ss_pred cccHHHHHHHhhhhHHHHHHHHHH
Confidence 448999999999999999987664
No 351
>PRK09480 slmA division inhibitor protein; Provisional
Probab=24.94 E-value=1.6e+02 Score=27.01 Aligned_cols=40 Identities=23% Similarity=0.209 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHH-HHhcCCCCcHHHHHHHhCCCHHHHHHH
Q 011324 412 TLLSKVLEAKRLY-IQEGNHSPDKEDLARRVGITVEKLERL 451 (488)
Q Consensus 412 e~l~kI~ka~~~L-~~elgr~pS~eEIAe~LGIS~etVk~~ 451 (488)
....+|-++...+ ....|...|..+||+..|++.+++...
T Consensus 10 ~~r~~Il~aa~~l~~~~~G~~~ti~~Ia~~agvs~gt~Y~~ 50 (194)
T PRK09480 10 ERREQILQALAQMLESPPGERITTAKLAARVGVSEAALYRH 50 (194)
T ss_pred hHHHHHHHHHHHHHHhcCCCccCHHHHHHHhCCCHhHHHHH
Confidence 3344555554444 444347899999999999999988543
No 352
>PRK13503 transcriptional activator RhaS; Provisional
Probab=24.88 E-value=2.6e+02 Score=27.37 Aligned_cols=38 Identities=18% Similarity=0.185 Sum_probs=20.5
Q ss_pred cCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHH
Q 011324 349 QGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAY 386 (488)
Q Consensus 349 ~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~ 386 (488)
.......+|+....++.--.-.+.|...-|..|..|+.
T Consensus 184 ~~~~~tl~~lA~~~~lS~~~l~r~Fk~~~G~S~~~yi~ 221 (278)
T PRK13503 184 FAEEVNWEALADQFSLSLRTLHRQLKQQTGLTPQRYLN 221 (278)
T ss_pred hcCCCCHHHHHHHHCCCHHHHHHHHHHHhCcCHHHHHH
Confidence 34456677776666655554455554444544444443
No 353
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=24.86 E-value=1.6e+02 Score=29.57 Aligned_cols=40 Identities=10% Similarity=0.070 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 415 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 415 ~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
..+.+++.-+...+...++.++||+.+|+|...+..+.+.
T Consensus 5 ~~i~~~~~~i~~~~~~~~~l~~lA~~~~~S~~~l~r~F~~ 44 (289)
T PRK15121 5 GIIRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKD 44 (289)
T ss_pred HHHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 4455556666666676789999999999999988877653
No 354
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=24.86 E-value=4.2e+02 Score=26.99 Aligned_cols=59 Identities=10% Similarity=0.214 Sum_probs=38.2
Q ss_pred HHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHH
Q 011324 339 RLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIF 398 (488)
Q Consensus 339 rLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IR 398 (488)
+++..|...|. ...+.+||.....+..-.--..|...-|..|..|+...=.+...+.|.
T Consensus 195 ~~~~~i~~~~~-~~~tl~~lA~~~~~S~~~l~r~Fk~~~G~t~~~~l~~~Rl~~A~~lL~ 253 (302)
T PRK10371 195 QMLGFIAENYD-QALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRALLS 253 (302)
T ss_pred HHHHHHHHhhc-CCCCHHHHHHHHCcCHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHh
Confidence 33444445554 578999999998877766666666555777888877654444444443
No 355
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=24.78 E-value=85 Score=24.26 Aligned_cols=22 Identities=23% Similarity=0.310 Sum_probs=19.5
Q ss_pred cHHHHHHHhCCCHHHHHHHHHH
Q 011324 433 DKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 433 S~eEIAe~LGIS~etVk~~L~~ 454 (488)
+..|+|+.+|++..+++.....
T Consensus 2 s~~eva~~~gvs~~tlr~~~~~ 23 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYERI 23 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHHHC
Confidence 6789999999999999988763
No 356
>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=24.56 E-value=1.1e+02 Score=28.42 Aligned_cols=32 Identities=22% Similarity=0.313 Sum_probs=0.0
Q ss_pred HHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHH
Q 011324 417 VLEAKRLYIQEGNHSPDKEDLARRVGITVEKL 448 (488)
Q Consensus 417 I~ka~~~L~~elgr~pS~eEIAe~LGIS~etV 448 (488)
+..+...+.+.+....|..+||+..|++.+.+
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 357
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=24.53 E-value=4.6e+02 Score=23.44 Aligned_cols=24 Identities=13% Similarity=0.213 Sum_probs=21.7
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 431 SPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
..+..|||+.+|++..+|-.++..
T Consensus 54 ~~t~~eLa~~l~i~~~tvsr~l~~ 77 (144)
T PRK11512 54 CITPVELKKVLSVDLGALTRMLDR 77 (144)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
Confidence 579999999999999999888764
No 358
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=24.50 E-value=2.1e+02 Score=26.19 Aligned_cols=26 Identities=23% Similarity=0.520 Sum_probs=23.2
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHH
Q 011324 428 GNHSPDKEDLARRVGITVEKLERLIF 453 (488)
Q Consensus 428 lgr~pS~eEIAe~LGIS~etVk~~L~ 453 (488)
+.+-||..|+|..+|+.+.+|..+.+
T Consensus 32 GdkLPSvRelA~~~~VNpnTv~raY~ 57 (125)
T COG1725 32 GDKLPSVRELAKDLGVNPNTVQRAYQ 57 (125)
T ss_pred CCCCCcHHHHHHHhCCCHHHHHHHHH
Confidence 44689999999999999999998875
No 359
>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=24.49 E-value=1.6e+02 Score=29.05 Aligned_cols=27 Identities=19% Similarity=0.273 Sum_probs=23.5
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 428 GNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 428 lgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
.....+..|||+.+|++..++..++..
T Consensus 21 ~~~~~~l~eia~~lglpksT~~RlL~t 47 (248)
T TIGR02431 21 ERPRLTLTDVAEATGLTRAAARRFLLT 47 (248)
T ss_pred CCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 344689999999999999999999874
No 360
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=24.33 E-value=2.9e+02 Score=26.71 Aligned_cols=26 Identities=23% Similarity=0.433 Sum_probs=22.2
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHhC
Q 011324 431 SPDKEDLARRVGITVEKLERLIFITR 456 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar 456 (488)
..|.++||..+|++.++|-.+++.-+
T Consensus 179 ~lt~~~IA~~lGisretlsR~L~~L~ 204 (230)
T PRK09391 179 PMSRRDIADYLGLTIETVSRALSQLQ 204 (230)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45899999999999999999886543
No 361
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=24.07 E-value=84 Score=27.68 Aligned_cols=29 Identities=28% Similarity=0.385 Sum_probs=26.3
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324 431 SPDKEDLARRVGITVEKLERLIFITRMPL 459 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar~~l 459 (488)
+.+.+|-|..||||..++.+.+..||.++
T Consensus 49 ~l~QeeAA~rMgISr~Tfwr~l~sAR~Kv 77 (99)
T COG1342 49 GLTQEEAALRMGISRQTFWRLLTSARKKV 77 (99)
T ss_pred hccHHHHHHHhcccHHHHHHHHHHHHHHH
Confidence 68999999999999999999999888654
No 362
>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=24.03 E-value=1.5e+02 Score=26.08 Aligned_cols=24 Identities=25% Similarity=0.423 Sum_probs=22.0
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 431 SPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
.++.+|||+.+|++...|..++..
T Consensus 25 ~~s~~eia~~~~i~~~~v~~il~~ 48 (132)
T TIGR00738 25 PVSVKEIAERQGISRSYLEKILRT 48 (132)
T ss_pred cCcHHHHHHHHCcCHHHHHHHHHH
Confidence 679999999999999999999864
No 363
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=23.85 E-value=1.1e+02 Score=20.75 Aligned_cols=23 Identities=26% Similarity=0.473 Sum_probs=20.4
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHH
Q 011324 431 SPDKEDLARRVGITVEKLERLIF 453 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~ 453 (488)
..+..++|+.+|++..+|..+..
T Consensus 10 ~~s~~~la~~~~i~~~~i~~~~~ 32 (56)
T smart00530 10 GLTQEELAEKLGVSRSTLSRIEN 32 (56)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHC
Confidence 57999999999999999987764
No 364
>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=23.58 E-value=2.1e+02 Score=20.89 Aligned_cols=24 Identities=13% Similarity=0.225 Sum_probs=20.4
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 431 SPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
..+..|||+.+|++..+|..-+..
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 679999999999999999887764
No 365
>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=23.42 E-value=83 Score=24.50 Aligned_cols=22 Identities=9% Similarity=0.126 Sum_probs=19.3
Q ss_pred cHHHHHHHhCCCHHHHHHHHHH
Q 011324 433 DKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 433 S~eEIAe~LGIS~etVk~~L~~ 454 (488)
+..|+|+.+||+..+++..-..
T Consensus 2 ~i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 2 TIKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh
Confidence 6789999999999999988654
No 366
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=23.26 E-value=2e+02 Score=27.62 Aligned_cols=24 Identities=13% Similarity=0.164 Sum_probs=21.3
Q ss_pred CcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 432 PDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 432 pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
.+.+|||+.+|++.++|-..+..-
T Consensus 170 ~t~~~lA~~lG~sretvsR~L~~L 193 (226)
T PRK10402 170 EKHTQAAEYLGVSYRHLLYVLAQF 193 (226)
T ss_pred chHHHHHHHHCCcHHHHHHHHHHH
Confidence 488999999999999999988754
No 367
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=23.24 E-value=4.6e+02 Score=23.31 Aligned_cols=24 Identities=25% Similarity=0.311 Sum_probs=21.3
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 431 SPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
..+..|||+.+|++..+|..++..
T Consensus 46 ~~t~~eLa~~l~~~~~tvt~~v~~ 69 (144)
T PRK03573 46 EQSQIQLAKAIGIEQPSLVRTLDQ 69 (144)
T ss_pred CCCHHHHHHHhCCChhhHHHHHHH
Confidence 468999999999999999888764
No 368
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=23.12 E-value=1.4e+02 Score=29.71 Aligned_cols=30 Identities=13% Similarity=0.196 Sum_probs=24.6
Q ss_pred HHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 424 YIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 424 L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
+....+ ..+..|+|+.+|+|+.+|+.-|..
T Consensus 15 ~l~~~~-~v~v~eLa~~~~VS~~TIRRDL~~ 44 (252)
T PRK10681 15 ALKRSD-KLHLKDAAALLGVSEMTIRRDLNA 44 (252)
T ss_pred HHHHcC-CCcHHHHHHHhCCCHHHHHHHHHH
Confidence 344455 689999999999999999887764
No 369
>PF11268 DUF3071: Protein of unknown function (DUF3071); InterPro: IPR021421 Some members in this family of proteins are annotated as DNA-binding proteins however this cannot be confirmed. Currently no function is known.
Probab=23.09 E-value=87 Score=30.08 Aligned_cols=25 Identities=24% Similarity=0.481 Sum_probs=21.2
Q ss_pred hcCCCCcHHHHHHHhCCCHHHHHHH
Q 011324 427 EGNHSPDKEDLARRVGITVEKLERL 451 (488)
Q Consensus 427 elgr~pS~eEIAe~LGIS~etVk~~ 451 (488)
..+.+.|.+|||+..|++++.|+..
T Consensus 65 rIRaGas~eeVA~~~G~~~~rV~rf 89 (170)
T PF11268_consen 65 RIRAGASAEEVAEEAGVPVERVRRF 89 (170)
T ss_pred HHHCCCCHHHHHHHhCCCHHHhhhc
Confidence 3445789999999999999999864
No 370
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=22.94 E-value=1.6e+02 Score=21.66 Aligned_cols=23 Identities=17% Similarity=0.416 Sum_probs=19.4
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHh
Q 011324 433 DKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 433 S~eEIAe~LGIS~etVk~~L~~a 455 (488)
..++||..+|++...|.......
T Consensus 29 ~~~~la~~~~l~~~qV~~WF~nr 51 (56)
T smart00389 29 EREELAAKLGLSERQVKVWFQNR 51 (56)
T ss_pred HHHHHHHHHCcCHHHHHHhHHHH
Confidence 47889999999999999887543
No 371
>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=22.79 E-value=1.8e+02 Score=22.14 Aligned_cols=24 Identities=21% Similarity=0.354 Sum_probs=16.6
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 431 SPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
+.|..++|+.+|++...+..+..-
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 578888888888888888777653
No 372
>PRK13558 bacterio-opsin activator; Provisional
Probab=22.72 E-value=53 Score=36.77 Aligned_cols=29 Identities=17% Similarity=0.284 Sum_probs=25.6
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFITRMP 458 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (488)
|+.|.+|||+.|||+..++...|+++..+
T Consensus 629 r~~~~~e~a~~l~is~~t~~~~lr~a~~~ 657 (665)
T PRK13558 629 RRVEGEELAESMGISRSTFHQHLRAAERK 657 (665)
T ss_pred ccCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 45599999999999999999999988654
No 373
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=22.55 E-value=91 Score=28.99 Aligned_cols=25 Identities=24% Similarity=0.275 Sum_probs=22.0
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 431 SPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
..|.++||..+|++.++|-.++..-
T Consensus 149 ~~t~~~iA~~lG~tretvsR~l~~l 173 (202)
T PRK13918 149 YATHDELAAAVGSVRETVTKVIGEL 173 (202)
T ss_pred cCCHHHHHHHhCccHHHHHHHHHHH
Confidence 4589999999999999999988754
No 374
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=22.37 E-value=1.6e+02 Score=29.37 Aligned_cols=28 Identities=21% Similarity=0.240 Sum_probs=23.8
Q ss_pred hcCCCCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 427 EGNHSPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 427 elgr~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
+.+ ..+..|||+.||+|..+|+.-+...
T Consensus 15 ~~~-~~~~~eLa~~l~VS~~TiRRdL~~L 42 (240)
T PRK10411 15 NHT-SLTTEALAEQLNVSKETIRRDLNEL 42 (240)
T ss_pred HcC-CCcHHHHHHHHCcCHHHHHHHHHHH
Confidence 344 7899999999999999999888753
No 375
>PRK13503 transcriptional activator RhaS; Provisional
Probab=22.27 E-value=2e+02 Score=28.16 Aligned_cols=37 Identities=14% Similarity=0.073 Sum_probs=26.5
Q ss_pred HHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 418 LEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 418 ~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
.+...-+.+......|.++||+.+|++...+..+.+.
T Consensus 174 ~~~~~~I~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk~ 210 (278)
T PRK13503 174 NQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQ 210 (278)
T ss_pred HHHHHHHHHhhcCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3333444445555789999999999999998877653
No 376
>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=22.25 E-value=2.1e+02 Score=27.53 Aligned_cols=27 Identities=30% Similarity=0.480 Sum_probs=23.7
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 428 GNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 428 lgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
+.+-||-.|+|+.+|+|..+|++++..
T Consensus 29 G~~LPsE~eLa~~~~VSR~TvR~Al~~ 55 (238)
T TIGR02325 29 GDYLPAEMQLAERFGVNRHTVRRAIAA 55 (238)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 345789999999999999999999863
No 377
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=22.23 E-value=1.4e+02 Score=29.21 Aligned_cols=27 Identities=30% Similarity=0.394 Sum_probs=23.9
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 428 GNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 428 lgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
+.+-|+-.|||+.+|+|-.+|++++..
T Consensus 32 G~~LPsE~eLa~~~~VSR~TVR~Al~~ 58 (241)
T PRK10079 32 GDYLPAEQQLAARYEVNRHTLRRAIDQ 58 (241)
T ss_pred CCcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 446899999999999999999999863
No 378
>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=21.87 E-value=1.1e+02 Score=22.86 Aligned_cols=21 Identities=24% Similarity=0.571 Sum_probs=18.3
Q ss_pred cHHHHHHHhCCCHHHHHHHHH
Q 011324 433 DKEDLARRVGITVEKLERLIF 453 (488)
Q Consensus 433 S~eEIAe~LGIS~etVk~~L~ 453 (488)
..++||..|||+...|.....
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 478899999999999998764
No 379
>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=21.85 E-value=2e+02 Score=22.60 Aligned_cols=25 Identities=16% Similarity=0.232 Sum_probs=22.1
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 431 SPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
..+..|||+.+|++..+|...+...
T Consensus 13 ~~~~~eLa~~l~vS~~tv~~~l~~L 37 (69)
T TIGR00122 13 PFSGEKLGEALGMSRTAVNKHIQTL 37 (69)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 4579999999999999999988754
No 380
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=21.79 E-value=1.6e+02 Score=29.41 Aligned_cols=27 Identities=22% Similarity=0.156 Sum_probs=23.1
Q ss_pred hcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 427 EGNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 427 elgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
+.+ ..+.+|||+.+|+|..+|+.-|..
T Consensus 16 ~~~-~~~~~ela~~l~vS~~TirRdL~~ 42 (251)
T PRK13509 16 QLG-FVTVEKVIERLGISPATARRDINK 42 (251)
T ss_pred HcC-CcCHHHHHHHHCcCHHHHHHHHHH
Confidence 444 689999999999999999888764
No 381
>PRK11050 manganese transport regulator MntR; Provisional
Probab=21.71 E-value=2.9e+02 Score=25.44 Aligned_cols=25 Identities=16% Similarity=0.375 Sum_probs=22.3
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 431 SPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
..+..|||+.+|++...|..++...
T Consensus 51 ~~t~~eLA~~l~is~stVsr~l~~L 75 (152)
T PRK11050 51 EARQVDIAARLGVSQPTVAKMLKRL 75 (152)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 6799999999999999999988654
No 382
>PRK15340 transcriptional regulator InvF; Provisional
Probab=21.56 E-value=5.2e+02 Score=25.75 Aligned_cols=31 Identities=13% Similarity=0.210 Sum_probs=25.0
Q ss_pred HHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 424 YIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 424 L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
|........+.++||+.+|+++..+..+.+.
T Consensus 118 Ll~~~~~~~sleeLA~~~gvS~r~f~RlFk~ 148 (216)
T PRK15340 118 LLAQSTSGNTMRMLGEDYGVSYTHFRRLCSR 148 (216)
T ss_pred HHhCccCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 4455556789999999999999999888664
No 383
>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=21.28 E-value=2.7e+02 Score=20.67 Aligned_cols=24 Identities=21% Similarity=0.318 Sum_probs=21.6
Q ss_pred CcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 432 PDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 432 pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
.+..||++.+|++..++...+...
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~L 44 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKL 44 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHHH
Confidence 899999999999999999888753
No 384
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=21.21 E-value=1e+02 Score=28.35 Aligned_cols=27 Identities=26% Similarity=0.502 Sum_probs=23.9
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHhCC
Q 011324 431 SPDKEDLARRVGITVEKLERLIFITRM 457 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar~ 457 (488)
..+.++||+.|||....|+.++..-..
T Consensus 15 ~~~dedLa~~l~i~~n~vRkiL~~L~e 41 (147)
T smart00531 15 CVTEEDLAELLGIKQKQLRKILYLLYD 41 (147)
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHHHh
Confidence 689999999999999999999876543
No 385
>PRK14999 histidine utilization repressor; Provisional
Probab=21.02 E-value=2.3e+02 Score=27.71 Aligned_cols=27 Identities=15% Similarity=0.308 Sum_probs=23.6
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 428 GNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 428 lgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
+.+-|+-.|||+.+|++..+|++++..
T Consensus 33 G~~LPsE~eLa~~~gVSR~TVR~Al~~ 59 (241)
T PRK14999 33 HDRIPSEAELVAQYGFSRMTINRALRE 59 (241)
T ss_pred CCcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 345789999999999999999999863
No 386
>cd00131 PAX Paired Box domain
Probab=20.88 E-value=1.7e+02 Score=26.47 Aligned_cols=32 Identities=9% Similarity=0.101 Sum_probs=26.9
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHhCCCcccc
Q 011324 431 SPDKEDLARRVGITVEKLERLIFITRMPLSMQ 462 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD 462 (488)
+.+..+||+.+|++..+|..++++.+..-++.
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 57999999999999999999998876554443
No 387
>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=20.82 E-value=1.9e+02 Score=27.69 Aligned_cols=25 Identities=16% Similarity=0.171 Sum_probs=22.6
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 431 SPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
.+|..|||+.+||+..+|...+..-
T Consensus 15 ~~t~~eLA~~lgis~~tV~~~L~~L 39 (203)
T TIGR02702 15 QATAAALAEALAISPQAVRRHLKDL 39 (203)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 5899999999999999999998753
No 388
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=20.71 E-value=1.6e+02 Score=29.57 Aligned_cols=28 Identities=21% Similarity=0.267 Sum_probs=23.2
Q ss_pred HhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 426 QEGNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 426 ~elgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
.+.+ ..+..|||+.+|+|..+|+.-+..
T Consensus 15 ~~~~-~v~v~eLa~~l~VS~~TIRRDL~~ 42 (256)
T PRK10434 15 QKQG-KTSVEELAQYFDTTGTTIRKDLVI 42 (256)
T ss_pred HHcC-CEEHHHHHHHHCCCHHHHHHHHHH
Confidence 3444 689999999999999999887753
No 389
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=20.66 E-value=2e+02 Score=29.23 Aligned_cols=38 Identities=11% Similarity=0.075 Sum_probs=27.5
Q ss_pred HHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 417 VLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 417 I~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
+.+....+...+...++.++||+.+|+|...+..+.+.
T Consensus 193 i~~~~~~i~~~~~~~~tl~~lA~~~~~S~~~l~r~Fk~ 230 (302)
T PRK10371 193 VSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQR 230 (302)
T ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 33444444555555789999999999999988777664
No 390
>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=20.65 E-value=2.4e+02 Score=20.31 Aligned_cols=21 Identities=29% Similarity=0.330 Sum_probs=17.1
Q ss_pred cHHHHHHHhCCCHHHHHHHHH
Q 011324 433 DKEDLARRVGITVEKLERLIF 453 (488)
Q Consensus 433 S~eEIAe~LGIS~etVk~~L~ 453 (488)
...+.|+.|||+..++...+.
T Consensus 20 n~~~aA~~Lgisr~tL~~klk 40 (42)
T PF02954_consen 20 NVSKAARLLGISRRTLYRKLK 40 (42)
T ss_dssp -HHHHHHHHTS-HHHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 678999999999999988775
No 391
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=20.64 E-value=1.6e+02 Score=29.36 Aligned_cols=30 Identities=17% Similarity=0.299 Sum_probs=24.6
Q ss_pred HHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 424 YIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 424 L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
+..+.+ ..|..|||+.|||+...|+.-|..
T Consensus 19 lL~~~g-~~sa~elA~~Lgis~~avR~HL~~ 48 (218)
T COG2345 19 LLKKSG-PVSADELAEELGISPMAVRRHLDD 48 (218)
T ss_pred HHhccC-CccHHHHHHHhCCCHHHHHHHHHH
Confidence 344445 679999999999999999998864
No 392
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=20.59 E-value=1.5e+02 Score=24.32 Aligned_cols=36 Identities=17% Similarity=0.165 Sum_probs=29.0
Q ss_pred HHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324 423 LYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMP 458 (488)
Q Consensus 423 ~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~ 458 (488)
.+...++...+..+.|+.||++.+.|.+.....+.-
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 344556667899999999999999999988766553
No 393
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=20.56 E-value=2.1e+02 Score=26.85 Aligned_cols=38 Identities=16% Similarity=0.222 Sum_probs=28.5
Q ss_pred HHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324 417 VLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT 455 (488)
Q Consensus 417 I~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~a 455 (488)
.-+++..+....+ .+...+||+.||++..+|..+++.-
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 3345555555444 7899999999999999998887653
No 394
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=20.44 E-value=2.1e+02 Score=25.55 Aligned_cols=23 Identities=13% Similarity=0.150 Sum_probs=17.6
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHH
Q 011324 431 SPDKEDLARRVGITVEKLERLIF 453 (488)
Q Consensus 431 ~pS~eEIAe~LGIS~etVk~~L~ 453 (488)
+.|..++|+.+|++..+|..+..
T Consensus 18 gltq~~lA~~~gvs~~~is~~E~ 40 (135)
T PRK09706 18 KLSQRSLAKAVKVSHVSISQWER 40 (135)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHc
Confidence 47788888888888888877654
No 395
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=20.39 E-value=1.5e+02 Score=22.85 Aligned_cols=25 Identities=16% Similarity=0.291 Sum_probs=18.4
Q ss_pred CCcHHHHHHHhC-CCHHHHHHHHHHh
Q 011324 431 SPDKEDLARRVG-ITVEKLERLIFIT 455 (488)
Q Consensus 431 ~pS~eEIAe~LG-IS~etVk~~L~~a 455 (488)
+.+.+||++... ++.+.|+.++..+
T Consensus 31 G~s~eeI~~~yp~Lt~~~i~aAl~ya 56 (56)
T PF04255_consen 31 GESPEEIAEDYPSLTLEDIRAALAYA 56 (56)
T ss_dssp T--HHHHHHHSTT--HHHHHHHHHHH
T ss_pred CCCHHHHHHHCCCCCHHHHHHHHHhC
Confidence 689999999998 9999999988653
No 396
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=20.37 E-value=2.2e+02 Score=26.41 Aligned_cols=32 Identities=16% Similarity=0.154 Sum_probs=27.8
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHhCCCccc
Q 011324 430 HSPDKEDLARRVGITVEKLERLIFITRMPLSM 461 (488)
Q Consensus 430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~lSL 461 (488)
.+.|..|||+.+|++..+|...+.+.+..=++
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 47999999999999999999999988765444
No 397
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=20.28 E-value=2e+02 Score=28.98 Aligned_cols=27 Identities=15% Similarity=0.257 Sum_probs=23.5
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324 428 GNHSPDKEDLARRVGITVEKLERLIFI 454 (488)
Q Consensus 428 lgr~pS~eEIAe~LGIS~etVk~~L~~ 454 (488)
.+...+..|||+.+|++..++..++..
T Consensus 37 ~~~~~tl~eIa~~lglpkStv~RlL~t 63 (271)
T PRK10163 37 SGGSSSVSDISLNLDLPLSTTFRLLKV 63 (271)
T ss_pred CCCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 444679999999999999999999874
No 398
>KOG0037 consensus Ca2+-binding protein, EF-Hand protein superfamily [Signal transduction mechanisms]
Probab=20.18 E-value=7.8e+02 Score=24.79 Aligned_cols=97 Identities=13% Similarity=0.222 Sum_probs=57.4
Q ss_pred HHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhh-cHHHHHHHHHHHH
Q 011324 260 FLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS-GNSSREKLINANL 338 (488)
Q Consensus 260 YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~-Gd~ArekLIesnl 338 (488)
++-+......+..+|=.+|+..|+.+..+=+ ...+.=+ -.++..+|..++.. |- .-.-
T Consensus 101 ~mfd~~~~G~i~f~EF~~Lw~~i~~Wr~vF~-------~~D~D~S-------G~I~~sEL~~Al~~~Gy-------~Lsp 159 (221)
T KOG0037|consen 101 SMFDRDNSGTIGFKEFKALWKYINQWRNVFR-------TYDRDRS-------GTIDSSELRQALTQLGY-------RLSP 159 (221)
T ss_pred HHhcCCCCCccCHHHHHHHHHHHHHHHHHHH-------hcccCCC-------CcccHHHHHHHHHHcCc-------CCCH
Confidence 5556777788999999999999998654321 1122100 11455666544322 11 1111
Q ss_pred HHHHHHHHHcc---CCCCCHhHHHHHH--HHHHHHhHHhhCCCC
Q 011324 339 RLVVHVAKQYQ---GRGISLHDLLQEG--SMGLMKSVEKFKPQA 377 (488)
Q Consensus 339 rLV~sIAkry~---~~g~d~EDLIQEG--~IGL~rAiekFDpsk 377 (488)
.++-.|++||- +..+.++|.||-. ..+|.++..++|...
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 356788888888754
No 399
>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=20.17 E-value=2.8e+02 Score=22.47 Aligned_cols=27 Identities=19% Similarity=0.228 Sum_probs=19.3
Q ss_pred HhcCCCCcHHHHHHHhCCCHHHHHHHHH
Q 011324 426 QEGNHSPDKEDLARRVGITVEKLERLIF 453 (488)
Q Consensus 426 ~elgr~pS~eEIAe~LGIS~etVk~~L~ 453 (488)
.... ..|..|||+.+|++..+|-...+
T Consensus 30 ~~~~-~~si~elA~~~~vS~sti~Rf~k 56 (77)
T PF01418_consen 30 DEIA-FMSISELAEKAGVSPSTIVRFCK 56 (77)
T ss_dssp HHHC-T--HHHHHHHCTS-HHHHHHHHH
T ss_pred HHHH-HccHHHHHHHcCCCHHHHHHHHH
Confidence 3344 68999999999999999977655
No 400
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=20.09 E-value=1.6e+02 Score=29.54 Aligned_cols=27 Identities=11% Similarity=0.244 Sum_probs=22.5
Q ss_pred HhcCCCCcHHHHHHHhCCCHHHHHHHHH
Q 011324 426 QEGNHSPDKEDLARRVGITVEKLERLIF 453 (488)
Q Consensus 426 ~elgr~pS~eEIAe~LGIS~etVk~~L~ 453 (488)
.+.+ ..+..|||+.+|+|..+|+.-+.
T Consensus 15 ~~~~-~~~~~ela~~l~vS~~TiRRdL~ 41 (252)
T PRK10906 15 KQQG-YVSTEELVEHFSVSPQTIRRDLN 41 (252)
T ss_pred HHcC-CEeHHHHHHHhCCCHHHHHHHHH
Confidence 4444 68999999999999999988654
No 401
>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=20.08 E-value=78 Score=23.11 Aligned_cols=18 Identities=33% Similarity=0.685 Sum_probs=16.4
Q ss_pred HHHHHhCCCHHHHHHHHH
Q 011324 436 DLARRVGITVEKLERLIF 453 (488)
Q Consensus 436 EIAe~LGIS~etVk~~L~ 453 (488)
+||+.+|++..+|..+++
T Consensus 2 ~lA~~~gvs~~tvs~~l~ 19 (52)
T cd01392 2 DIARAAGVSVATVSRVLN 19 (52)
T ss_pred cHHHHHCcCHHHHHHHHc
Confidence 799999999999998876
Done!