Query 014764
Match_columns 419
No_of_seqs 226 out of 1811
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 08:17:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014764.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014764hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK07598 RNA polymerase sigma 100.0 1.6E-40 3.5E-45 341.6 23.7 212 191-402 60-314 (415)
2 PRK07406 RNA polymerase sigma 100.0 2.9E-39 6.2E-44 329.3 24.1 224 191-418 63-287 (373)
3 TIGR02997 Sig70-cyanoRpoD RNA 100.0 7.5E-39 1.6E-43 316.6 24.1 210 192-401 2-212 (298)
4 PRK05949 RNA polymerase sigma 100.0 1.6E-38 3.5E-43 319.0 24.4 224 191-418 18-242 (327)
5 PRK07405 RNA polymerase sigma 100.0 1.6E-37 3.4E-42 310.5 24.1 224 191-418 8-232 (317)
6 PRK05901 RNA polymerase sigma 100.0 1.4E-35 3.1E-40 311.6 21.0 212 190-418 210-422 (509)
7 PRK07921 RNA polymerase sigma 100.0 1.1E-34 2.3E-39 291.1 21.4 211 191-418 26-237 (324)
8 COG0568 RpoD DNA-directed RNA 100.0 8.4E-34 1.8E-38 284.6 18.5 226 190-419 8-254 (342)
9 PRK09210 RNA polymerase sigma 100.0 9.3E-33 2E-37 281.1 20.6 186 189-418 94-280 (367)
10 PRK05658 RNA polymerase sigma 100.0 2.1E-30 4.6E-35 279.4 20.7 186 192-418 345-531 (619)
11 PRK07500 rpoH2 RNA polymerase 100.0 5.5E-29 1.2E-33 245.9 21.3 186 191-418 6-199 (289)
12 PRK06596 RNA polymerase factor 100.0 1.7E-28 3.7E-33 241.8 21.0 189 184-418 10-202 (284)
13 TIGR02392 rpoH_proteo alternat 100.0 6.9E-28 1.5E-32 235.3 20.5 169 192-401 2-175 (270)
14 PRK05657 RNA polymerase sigma 100.0 8.1E-28 1.8E-32 241.4 21.1 187 188-418 50-237 (325)
15 TIGR02850 spore_sigG RNA polym 100.0 2.7E-27 5.8E-32 228.9 20.3 175 201-418 11-186 (254)
16 PRK07122 RNA polymerase sigma 100.0 2E-27 4.3E-32 232.0 18.2 138 264-401 40-180 (264)
17 PRK07408 RNA polymerase sigma 99.9 1.1E-26 2.4E-31 225.4 20.0 153 264-418 25-181 (256)
18 TIGR02393 RpoD_Cterm RNA polym 99.9 3.5E-27 7.5E-32 225.9 15.7 150 265-418 1-151 (238)
19 PRK08215 sporulation sigma fac 99.9 4.2E-26 9E-31 220.9 19.9 175 201-418 14-189 (258)
20 TIGR02394 rpoS_proteo RNA poly 99.9 4.3E-25 9.2E-30 217.1 20.8 173 188-400 10-183 (285)
21 COG1191 FliA DNA-directed RNA 99.9 1.3E-24 2.8E-29 210.7 18.2 156 204-401 4-163 (247)
22 PRK05911 RNA polymerase sigma 99.9 4.7E-24 1E-28 207.3 19.3 152 264-418 23-180 (257)
23 TIGR02885 spore_sigF RNA polym 99.9 3E-24 6.5E-29 204.0 17.5 152 264-418 11-163 (231)
24 TIGR02941 Sigma_B RNA polymera 99.9 2E-23 4.3E-28 201.5 20.2 160 204-403 8-171 (255)
25 PRK06288 RNA polymerase sigma 99.9 2.9E-23 6.3E-28 202.3 19.2 173 201-417 7-186 (268)
26 PRK05572 sporulation sigma fac 99.9 5.3E-23 1.2E-27 198.6 20.3 164 197-401 5-169 (252)
27 TIGR02980 SigBFG RNA polymeras 99.9 3.4E-23 7.4E-28 196.1 17.5 139 263-401 2-143 (227)
28 PRK08583 RNA polymerase sigma 99.9 3.7E-22 8.1E-27 192.9 19.8 160 204-403 8-171 (257)
29 PRK07670 RNA polymerase sigma 99.9 1.3E-21 2.8E-26 188.9 18.7 135 264-401 22-162 (251)
30 PRK05803 sporulation sigma fac 99.9 4.4E-21 9.6E-26 183.1 15.9 163 192-394 17-223 (233)
31 TIGR02479 FliA_WhiG RNA polyme 99.8 1.5E-20 3.3E-25 178.1 15.4 129 269-400 1-135 (224)
32 PRK12427 flagellar biosynthesi 99.8 2.6E-20 5.6E-25 178.6 16.9 135 264-402 15-155 (231)
33 TIGR02846 spore_sigmaK RNA pol 99.8 2.8E-19 6.1E-24 170.2 15.9 163 192-394 15-222 (227)
34 PRK06986 fliA flagellar biosyn 99.8 3.4E-19 7.3E-24 170.3 16.1 137 261-400 5-147 (236)
35 PRK08301 sporulation sigma fac 99.8 3.1E-19 6.8E-24 170.0 14.9 160 195-394 22-226 (234)
36 PRK09646 RNA polymerase sigma 99.8 1.4E-18 3.1E-23 160.8 12.0 153 201-394 7-186 (194)
37 TIGR02835 spore_sigmaE RNA pol 99.8 3.2E-18 6.9E-23 163.7 14.6 160 195-394 22-226 (234)
38 PRK09648 RNA polymerase sigma 99.8 8E-18 1.7E-22 154.6 14.0 148 206-394 6-183 (189)
39 PRK05602 RNA polymerase sigma 99.7 1.3E-17 2.8E-22 152.9 13.1 130 264-394 20-172 (186)
40 PRK12513 RNA polymerase sigma 99.7 2.2E-17 4.7E-22 152.3 13.7 129 264-394 26-183 (194)
41 PRK11922 RNA polymerase sigma 99.7 3E-17 6.4E-22 156.6 14.0 152 201-394 7-193 (231)
42 PRK08295 RNA polymerase factor 99.7 2E-17 4.4E-22 153.5 12.3 131 264-394 24-198 (208)
43 TIGR02859 spore_sigH RNA polym 99.7 4.3E-17 9.4E-22 149.9 13.7 131 264-394 19-193 (198)
44 PRK12531 RNA polymerase sigma 99.7 3.3E-17 7.2E-22 151.7 12.2 130 264-394 27-185 (194)
45 PRK12514 RNA polymerase sigma 99.7 3.5E-17 7.6E-22 148.9 12.1 130 264-394 19-173 (179)
46 PRK12524 RNA polymerase sigma 99.7 2.8E-17 6.1E-22 152.4 11.4 130 264-394 26-180 (196)
47 PRK13919 putative RNA polymera 99.7 3.3E-17 7.1E-22 149.7 11.6 130 264-394 23-179 (186)
48 PRK12534 RNA polymerase sigma 99.7 3.2E-17 6.9E-22 150.2 11.5 130 264-394 25-181 (187)
49 PRK06759 RNA polymerase factor 99.7 3.6E-17 7.8E-22 144.7 11.5 129 264-394 4-150 (154)
50 PRK06811 RNA polymerase factor 99.7 4.4E-17 9.6E-22 150.3 12.2 130 264-394 18-175 (189)
51 PRK11923 algU RNA polymerase s 99.7 6.6E-17 1.4E-21 148.8 13.2 147 206-394 2-182 (193)
52 PRK12537 RNA polymerase sigma 99.7 4.9E-17 1.1E-21 148.9 12.2 130 264-394 23-177 (182)
53 PRK09640 RNA polymerase sigma 99.7 9.1E-17 2E-21 147.9 14.0 143 250-394 8-178 (188)
54 TIGR02952 Sig70_famx2 RNA poly 99.7 5.3E-17 1.1E-21 145.4 11.6 130 264-394 11-166 (170)
55 TIGR02948 SigW_bacill RNA poly 99.7 6.8E-17 1.5E-21 147.1 12.3 129 264-394 18-180 (187)
56 PRK12519 RNA polymerase sigma 99.7 9.5E-17 2.1E-21 147.8 12.5 129 264-394 29-185 (194)
57 PRK12538 RNA polymerase sigma 99.7 8.4E-17 1.8E-21 154.6 12.5 130 264-394 63-215 (233)
58 TIGR02954 Sig70_famx3 RNA poly 99.7 1.1E-16 2.4E-21 144.4 12.4 129 264-394 16-163 (169)
59 PRK12536 RNA polymerase sigma 99.7 2.5E-16 5.4E-21 144.1 14.1 129 264-394 21-173 (181)
60 PRK09643 RNA polymerase sigma 99.7 1.4E-16 3E-21 147.6 12.4 129 264-394 27-178 (192)
61 PRK09649 RNA polymerase sigma 99.7 1.6E-16 3.5E-21 146.4 12.7 130 264-396 24-176 (185)
62 PRK12526 RNA polymerase sigma 99.7 2E-16 4.4E-21 148.3 12.8 130 264-394 38-197 (206)
63 TIGR02939 RpoE_Sigma70 RNA pol 99.7 3.1E-16 6.8E-21 143.1 13.5 129 264-394 20-182 (190)
64 PRK09638 RNA polymerase sigma 99.7 2.4E-16 5.2E-21 142.6 12.7 129 264-394 18-170 (176)
65 TIGR02895 spore_sigI RNA polym 99.7 3.8E-16 8.3E-21 149.3 14.4 121 265-385 10-142 (218)
66 PRK12542 RNA polymerase sigma 99.7 7.8E-17 1.7E-21 147.8 8.8 131 264-394 9-166 (185)
67 PRK09641 RNA polymerase sigma 99.7 4.2E-16 9.1E-21 141.9 13.0 129 264-394 18-180 (187)
68 PRK12539 RNA polymerase sigma 99.7 5.5E-16 1.2E-20 142.2 13.5 129 264-394 21-175 (184)
69 COG1595 RpoE DNA-directed RNA 99.7 7.3E-16 1.6E-20 141.4 12.7 133 260-394 11-171 (182)
70 TIGR02999 Sig-70_X6 RNA polyme 99.7 5.3E-16 1.1E-20 141.2 11.5 129 264-394 17-178 (183)
71 PRK12512 RNA polymerase sigma 99.7 1.3E-15 2.8E-20 139.2 13.6 129 264-394 22-175 (184)
72 PRK09652 RNA polymerase sigma 99.7 5.2E-16 1.1E-20 139.5 10.7 129 264-394 10-172 (182)
73 TIGR02989 Sig-70_gvs1 RNA poly 99.6 8.3E-16 1.8E-20 136.5 11.1 128 265-394 2-155 (159)
74 PRK12515 RNA polymerase sigma 99.6 1E-15 2.2E-20 140.9 12.0 129 264-394 22-175 (189)
75 PRK12520 RNA polymerase sigma 99.6 5.7E-16 1.2E-20 142.8 10.4 128 265-394 3-175 (191)
76 PRK09415 RNA polymerase factor 99.6 1E-15 2.2E-20 140.0 11.7 130 263-394 15-171 (179)
77 TIGR03001 Sig-70_gmx1 RNA poly 99.6 1.1E-15 2.5E-20 147.9 12.2 129 264-394 39-205 (244)
78 PRK12522 RNA polymerase sigma 99.6 1.4E-15 3.1E-20 137.8 11.5 129 264-394 3-163 (173)
79 TIGR02947 SigH_actino RNA poly 99.6 1.4E-15 3E-20 140.4 11.5 130 263-394 10-175 (193)
80 PRK09645 RNA polymerase sigma 99.6 1.3E-15 2.7E-20 137.8 10.8 131 263-394 8-162 (173)
81 PRK12516 RNA polymerase sigma 99.6 1.6E-15 3.5E-20 140.4 11.6 129 264-394 10-160 (187)
82 PRK12518 RNA polymerase sigma 99.6 2.6E-15 5.6E-20 135.8 12.0 128 264-394 11-164 (175)
83 PRK11924 RNA polymerase sigma 99.6 3.7E-15 7.9E-20 133.6 12.8 129 264-394 13-169 (179)
84 PRK12543 RNA polymerase sigma 99.6 1.8E-15 3.9E-20 138.2 11.0 130 263-394 6-161 (179)
85 PRK08241 RNA polymerase factor 99.6 3.2E-15 6.9E-20 149.6 13.4 130 264-395 19-198 (339)
86 PRK12547 RNA polymerase sigma 99.6 2.5E-15 5.5E-20 135.4 11.1 131 262-394 4-156 (164)
87 PRK12535 RNA polymerase sigma 99.6 4.5E-15 9.7E-20 138.6 13.0 128 264-394 25-177 (196)
88 TIGR02985 Sig70_bacteroi1 RNA 99.6 2.6E-15 5.7E-20 132.1 9.1 128 265-394 2-157 (161)
89 PRK12541 RNA polymerase sigma 99.6 6E-15 1.3E-19 132.1 11.3 129 263-394 4-156 (161)
90 PRK12529 RNA polymerase sigma 99.6 4E-15 8.6E-20 136.2 9.5 131 263-393 12-170 (178)
91 PRK09644 RNA polymerase sigma 99.6 6.5E-15 1.4E-19 132.5 10.6 126 266-394 3-152 (165)
92 TIGR02983 SigE-fam_strep RNA p 99.6 8.5E-15 1.8E-19 130.8 11.2 130 263-394 5-154 (162)
93 TIGR02937 sigma70-ECF RNA poly 99.6 1E-14 2.2E-19 125.3 10.3 126 265-393 2-153 (158)
94 PRK12540 RNA polymerase sigma 99.6 1.1E-14 2.3E-19 134.4 11.1 129 264-394 5-155 (182)
95 TIGR02960 SigX5 RNA polymerase 99.6 1.1E-14 2.4E-19 144.4 11.6 129 264-394 5-186 (324)
96 PRK12523 RNA polymerase sigma 99.6 6.5E-15 1.4E-19 133.6 8.8 128 264-394 10-163 (172)
97 PRK12533 RNA polymerase sigma 99.6 1.6E-14 3.5E-19 137.4 11.6 129 263-394 17-178 (216)
98 PRK09642 RNA polymerase sigma 99.6 7.2E-15 1.6E-19 131.2 8.5 121 271-394 2-150 (160)
99 TIGR02984 Sig-70_plancto1 RNA 99.6 1.7E-14 3.6E-19 131.4 10.9 132 263-394 6-184 (189)
100 PRK12528 RNA polymerase sigma 99.6 1.8E-14 3.8E-19 129.0 10.2 127 264-393 4-156 (161)
101 PRK09639 RNA polymerase sigma 99.5 2.1E-14 4.6E-19 128.5 10.0 127 264-394 3-155 (166)
102 PRK09637 RNA polymerase sigma 99.5 3.7E-14 8E-19 130.6 11.4 127 266-394 3-150 (181)
103 TIGR02950 SigM_subfam RNA poly 99.5 2.7E-14 5.8E-19 126.1 9.7 122 270-394 1-149 (154)
104 PRK12517 RNA polymerase sigma 99.5 3.8E-14 8.3E-19 131.2 11.1 132 261-394 20-172 (188)
105 PRK12532 RNA polymerase sigma 99.5 3.7E-14 7.9E-19 131.1 10.5 126 267-394 8-180 (195)
106 PRK12545 RNA polymerase sigma 99.5 3.1E-14 6.7E-19 133.0 9.9 125 268-394 12-183 (201)
107 PRK09647 RNA polymerase sigma 99.5 4.9E-14 1.1E-18 132.5 11.0 128 264-394 28-182 (203)
108 PRK12530 RNA polymerase sigma 99.5 5.2E-14 1.1E-18 130.2 10.1 125 268-394 11-178 (189)
109 PRK08311 putative RNA polymera 99.5 3.8E-13 8.2E-18 130.2 16.4 78 264-341 18-97 (237)
110 PRK12544 RNA polymerase sigma 99.5 5.6E-14 1.2E-18 132.4 10.2 126 267-394 21-192 (206)
111 PRK12546 RNA polymerase sigma 99.5 1.2E-13 2.6E-18 128.3 12.1 128 264-394 8-157 (188)
112 TIGR02943 Sig70_famx1 RNA poly 99.5 6.2E-14 1.3E-18 129.7 9.7 126 267-394 5-175 (188)
113 PRK09651 RNA polymerase sigma 99.5 1.2E-13 2.6E-18 125.6 11.2 128 263-393 9-162 (172)
114 TIGR02959 SigZ RNA polymerase 99.5 8.2E-14 1.8E-18 126.6 9.4 122 271-394 2-144 (170)
115 PRK12511 RNA polymerase sigma 99.5 1.3E-13 2.9E-18 127.2 10.1 127 266-394 6-155 (182)
116 PRK06704 RNA polymerase factor 99.5 1.8E-13 3.9E-18 131.7 10.7 127 262-394 16-160 (228)
117 PRK07037 extracytoplasmic-func 99.4 7E-13 1.5E-17 118.6 9.7 124 268-394 2-153 (163)
118 PRK12525 RNA polymerase sigma 99.4 7.6E-13 1.7E-17 119.7 9.8 127 264-393 9-161 (168)
119 PRK12527 RNA polymerase sigma 99.4 5.8E-13 1.3E-17 119.0 8.9 121 271-394 2-149 (159)
120 PF04542 Sigma70_r2: Sigma-70 99.4 1E-12 2.2E-17 101.5 7.8 70 269-338 1-70 (71)
121 PRK09636 RNA polymerase sigma 99.4 1.6E-12 3.4E-17 128.3 10.0 127 264-394 4-159 (293)
122 PRK09635 sigI RNA polymerase s 99.3 3.7E-12 8.1E-17 126.4 9.9 128 264-395 5-163 (290)
123 TIGR02957 SigX4 RNA polymerase 99.3 4.8E-12 1E-16 124.5 9.3 123 268-394 1-152 (281)
124 PRK09191 two-component respons 99.3 6.5E-12 1.4E-16 119.1 9.4 122 265-394 2-132 (261)
125 TIGR03209 P21_Cbot clostridium 99.2 2E-11 4.4E-16 107.2 7.9 112 266-384 1-141 (142)
126 PRK09047 RNA polymerase factor 99.2 3.3E-11 7.2E-16 107.2 7.5 106 286-394 2-150 (161)
127 PF07638 Sigma70_ECF: ECF sigm 98.9 3.2E-08 6.9E-13 91.8 13.0 130 264-393 17-178 (185)
128 PF04539 Sigma70_r3: Sigma-70 98.6 7.8E-08 1.7E-12 76.8 6.9 67 348-418 1-68 (78)
129 PRK09210 RNA polymerase sigma 97.7 0.00061 1.3E-08 70.2 13.7 134 226-394 220-353 (367)
130 PRK07921 RNA polymerase sigma 97.7 0.00051 1.1E-08 69.7 12.5 134 226-394 177-310 (324)
131 PRK05901 RNA polymerase sigma 97.6 0.0011 2.3E-08 71.3 14.2 133 226-393 362-494 (509)
132 TIGR02393 RpoD_Cterm RNA polym 97.6 0.0013 2.8E-08 63.3 13.0 132 227-394 92-224 (238)
133 PRK05911 RNA polymerase sigma 97.4 0.0021 4.6E-08 62.8 13.0 60 190-259 88-147 (257)
134 PRK07406 RNA polymerase sigma 97.4 0.003 6.6E-08 65.5 13.9 132 227-394 228-359 (373)
135 PRK07598 RNA polymerase sigma 97.3 0.0021 4.5E-08 67.5 12.1 135 224-394 264-398 (415)
136 PRK05949 RNA polymerase sigma 97.3 0.0029 6.4E-08 64.3 12.9 135 224-394 180-314 (327)
137 PRK07408 RNA polymerase sigma 97.3 0.00073 1.6E-08 66.0 7.9 63 189-258 87-149 (256)
138 COG1191 FliA DNA-directed RNA 97.3 0.0056 1.2E-07 60.2 14.0 152 191-392 87-238 (247)
139 PF00140 Sigma70_r1_2: Sigma-7 97.3 9.1E-05 2E-09 52.1 1.1 33 191-223 2-34 (37)
140 PRK07500 rpoH2 RNA polymerase 97.3 0.004 8.7E-08 62.1 12.9 30 365-394 244-273 (289)
141 PRK07122 RNA polymerase sigma 97.1 0.0021 4.6E-08 63.2 9.0 63 189-258 101-163 (264)
142 PRK07405 RNA polymerase sigma 97.1 0.0024 5.1E-08 64.6 9.2 135 224-394 170-304 (317)
143 TIGR02997 Sig70-cyanoRpoD RNA 97.1 0.0031 6.6E-08 63.0 9.7 133 226-394 165-297 (298)
144 PRK05658 RNA polymerase sigma 96.9 0.0098 2.1E-07 65.3 13.0 132 226-393 471-603 (619)
145 PRK06288 RNA polymerase sigma 96.9 0.027 5.9E-07 55.2 14.8 34 225-258 121-154 (268)
146 PRK07670 RNA polymerase sigma 96.9 0.0074 1.6E-07 58.5 10.3 34 227-260 114-147 (251)
147 PRK12427 flagellar biosynthesi 96.8 0.0047 1E-07 59.6 8.0 60 189-258 78-137 (231)
148 TIGR02850 spore_sigG RNA polym 96.8 0.014 3E-07 56.7 11.4 63 189-259 95-157 (254)
149 COG0568 RpoD DNA-directed RNA 96.8 0.019 4.2E-07 58.9 12.8 144 210-395 183-328 (342)
150 PF04539 Sigma70_r3: Sigma-70 96.7 0.0034 7.4E-08 49.9 5.7 34 226-259 8-41 (78)
151 TIGR02479 FliA_WhiG RNA polyme 96.6 0.02 4.4E-07 54.3 10.9 33 226-258 87-119 (224)
152 TIGR02885 spore_sigF RNA polym 96.4 0.036 7.7E-07 52.8 11.0 42 211-258 92-133 (231)
153 TIGR02941 Sigma_B RNA polymera 96.1 0.0094 2E-07 57.8 5.4 32 227-258 121-152 (255)
154 PF12645 HTH_16: Helix-turn-he 96.1 0.024 5.2E-07 44.7 6.6 47 264-310 13-65 (65)
155 TIGR02980 SigBFG RNA polymeras 96.0 0.01 2.3E-07 56.2 5.1 31 227-257 95-125 (227)
156 PRK06596 RNA polymerase factor 96.0 0.12 2.6E-06 51.4 12.7 29 365-393 247-275 (284)
157 PRK06986 fliA flagellar biosyn 96.0 0.056 1.2E-06 51.8 10.1 30 365-394 199-228 (236)
158 PRK05657 RNA polymerase sigma 95.8 0.026 5.7E-07 57.3 7.2 31 364-394 280-310 (325)
159 PRK08215 sporulation sigma fac 95.6 0.047 1E-06 53.1 8.3 32 227-258 128-159 (258)
160 PF08281 Sigma70_r4_2: Sigma-7 95.4 0.0057 1.2E-07 45.4 0.6 30 364-393 24-53 (54)
161 TIGR02394 rpoS_proteo RNA poly 95.3 0.05 1.1E-06 53.9 7.3 31 364-394 240-270 (285)
162 TIGR02392 rpoH_proteo alternat 95.2 0.32 6.9E-06 47.9 12.7 30 364-393 234-263 (270)
163 PRK05572 sporulation sigma fac 95.1 0.33 7.1E-06 47.1 12.2 30 365-394 217-246 (252)
164 PF04545 Sigma70_r4: Sigma-70, 93.8 0.12 2.6E-06 37.8 4.5 30 364-393 18-47 (50)
165 PF01726 LexA_DNA_bind: LexA D 90.5 0.8 1.7E-05 36.1 5.8 44 348-391 6-51 (65)
166 PHA02547 55 RNA polymerase sig 90.4 0.9 2E-05 42.5 6.8 64 274-337 47-113 (179)
167 PRK08583 RNA polymerase sigma 89.0 0.25 5.4E-06 48.0 2.2 31 364-394 219-249 (257)
168 PRK06930 positive control sigm 89.0 0.25 5.4E-06 45.9 2.1 30 365-394 129-158 (170)
169 PF04967 HTH_10: HTH DNA bindi 88.9 0.42 9E-06 36.4 2.8 30 364-393 21-50 (53)
170 TIGR03879 near_KaiC_dom probab 87.7 0.93 2E-05 36.8 4.4 26 364-389 30-55 (73)
171 COG4941 Predicted RNA polymera 87.0 3.4 7.4E-05 42.8 8.9 127 267-395 8-165 (415)
172 cd06171 Sigma70_r4 Sigma70, re 86.4 0.52 1.1E-05 33.1 2.0 29 365-393 25-53 (55)
173 smart00421 HTH_LUXR helix_turn 85.5 0.91 2E-05 32.5 3.0 31 365-395 17-47 (58)
174 PF01325 Fe_dep_repress: Iron 85.4 3.1 6.7E-05 32.1 6.0 42 350-391 6-47 (60)
175 PF13404 HTH_AsnC-type: AsnC-t 84.8 2.7 5.9E-05 30.2 5.1 26 365-390 16-41 (42)
176 PF08279 HTH_11: HTH domain; 84.4 2.9 6.3E-05 30.8 5.3 37 356-392 5-41 (55)
177 cd06170 LuxR_C_like C-terminal 82.6 1.2 2.6E-05 32.1 2.6 30 365-394 14-43 (57)
178 PF06971 Put_DNA-bind_N: Putat 82.5 4 8.7E-05 30.7 5.3 46 341-386 2-48 (50)
179 PRK04217 hypothetical protein; 82.3 1.1 2.3E-05 39.1 2.6 30 365-394 57-86 (110)
180 PF13412 HTH_24: Winged helix- 81.5 3.9 8.5E-05 29.4 5.0 27 364-390 15-41 (48)
181 PRK00118 putative DNA-binding 81.4 1.1 2.4E-05 38.7 2.3 29 365-393 32-60 (104)
182 PF10668 Phage_terminase: Phag 80.6 3.2 7E-05 32.5 4.4 27 361-387 17-43 (60)
183 PRK13719 conjugal transfer tra 80.4 2.4 5.3E-05 41.1 4.5 35 363-397 155-189 (217)
184 PF00196 GerE: Bacterial regul 79.9 1.2 2.6E-05 33.5 1.8 33 364-396 16-48 (58)
185 PF00325 Crp: Bacterial regula 79.3 2.6 5.6E-05 29.0 3.1 24 367-390 3-26 (32)
186 PF13936 HTH_38: Helix-turn-he 77.2 3 6.6E-05 30.0 3.2 26 364-389 18-43 (44)
187 PHA02591 hypothetical protein; 77.1 2.7 5.9E-05 34.7 3.1 34 353-388 48-81 (83)
188 PRK14082 hypothetical protein; 76.7 9 0.00019 30.5 5.8 55 264-320 9-63 (65)
189 TIGR00721 tfx DNA-binding prot 76.5 2.1 4.5E-05 38.7 2.6 31 364-394 19-49 (137)
190 PF09339 HTH_IclR: IclR helix- 76.4 4.7 0.0001 29.7 4.1 32 359-390 11-42 (52)
191 COG3413 Predicted DNA binding 76.0 3.3 7.2E-05 39.3 4.0 33 362-394 174-206 (215)
192 PF02796 HTH_7: Helix-turn-hel 74.4 7.2 0.00016 28.1 4.5 21 367-387 22-42 (45)
193 PRK03975 tfx putative transcri 73.9 4 8.7E-05 37.1 3.8 29 364-392 19-47 (141)
194 COG1522 Lrp Transcriptional re 73.2 6.5 0.00014 34.7 4.9 32 359-391 16-47 (154)
195 PF13384 HTH_23: Homeodomain-l 72.7 3.3 7.1E-05 29.9 2.4 25 366-390 17-41 (50)
196 PF04297 UPF0122: Putative hel 71.7 2.9 6.2E-05 36.0 2.2 31 364-394 31-61 (101)
197 PF12324 HTH_15: Helix-turn-he 70.7 9.5 0.00021 31.4 4.9 33 359-391 31-63 (77)
198 PF14502 HTH_41: Helix-turn-he 70.1 5.6 0.00012 29.9 3.1 34 364-397 4-39 (48)
199 PF13744 HTH_37: Helix-turn-he 70.0 9.6 0.00021 30.7 4.8 35 364-398 29-63 (80)
200 PF13730 HTH_36: Helix-turn-he 70.0 5.6 0.00012 29.2 3.2 27 364-390 23-49 (55)
201 PF00356 LacI: Bacterial regul 69.8 5.2 0.00011 29.4 2.9 23 368-390 1-23 (46)
202 smart00550 Zalpha Z-DNA-bindin 69.5 12 0.00026 29.4 5.1 32 360-391 15-47 (68)
203 PRK10840 transcriptional regul 69.2 7.1 0.00015 36.1 4.4 33 364-396 163-195 (216)
204 COG2197 CitB Response regulato 69.1 6.6 0.00014 37.3 4.3 34 364-397 161-194 (211)
205 PF12728 HTH_17: Helix-turn-he 68.4 5.5 0.00012 28.9 2.8 23 368-390 3-25 (51)
206 PRK13870 transcriptional regul 68.3 4.3 9.4E-05 39.3 2.9 31 364-394 186-216 (234)
207 PRK15411 rcsA colanic acid cap 68.3 6.8 0.00015 36.9 4.2 33 364-396 150-182 (207)
208 smart00345 HTH_GNTR helix_turn 66.7 7.5 0.00016 28.2 3.3 26 366-391 20-45 (60)
209 PF13542 HTH_Tnp_ISL3: Helix-t 66.1 12 0.00026 27.1 4.2 23 367-389 28-50 (52)
210 PF09862 DUF2089: Protein of u 66.0 2.8 6E-05 36.8 0.9 29 368-396 51-79 (113)
211 smart00346 HTH_ICLR helix_turn 65.7 19 0.00041 28.7 5.8 35 356-390 10-44 (91)
212 PRK10188 DNA-binding transcrip 65.3 5.4 0.00012 38.8 2.9 31 365-395 193-223 (240)
213 TIGR03541 reg_near_HchA LuxR f 65.1 5.3 0.00011 38.4 2.8 31 365-395 185-215 (232)
214 TIGR03020 EpsA transcriptional 64.9 5.3 0.00012 39.3 2.8 32 365-396 204-235 (247)
215 PRK11475 DNA-binding transcrip 64.8 9.3 0.0002 36.3 4.3 34 364-397 147-180 (207)
216 TIGR01764 excise DNA binding d 64.7 8.2 0.00018 26.9 3.1 23 368-390 3-25 (49)
217 PF08280 HTH_Mga: M protein tr 64.4 13 0.00027 28.3 4.2 30 364-393 17-46 (59)
218 PF02001 DUF134: Protein of un 64.0 5.9 0.00013 34.4 2.6 30 365-394 56-85 (106)
219 PF03444 HrcA_DNA-bdg: Winged 63.8 20 0.00043 29.6 5.4 42 350-391 6-48 (78)
220 COG4367 Uncharacterized protei 63.4 18 0.00039 30.6 5.2 39 354-392 9-49 (97)
221 PRK12469 RNA polymerase factor 61.9 1E+02 0.0022 33.5 12.0 24 365-388 368-391 (481)
222 COG4566 TtrR Response regulato 61.5 5.9 0.00013 38.0 2.3 26 365-390 156-181 (202)
223 TIGR03826 YvyF flagellar opero 61.5 34 0.00073 31.0 7.0 54 342-395 21-75 (137)
224 PF04967 HTH_10: HTH DNA bindi 61.1 38 0.00083 25.7 6.2 48 206-263 1-48 (53)
225 PF06056 Terminase_5: Putative 60.8 11 0.00024 29.0 3.4 27 365-391 12-38 (58)
226 PRK09483 response regulator; P 60.7 13 0.00028 33.4 4.4 33 364-396 161-193 (217)
227 cd00092 HTH_CRP helix_turn_hel 60.2 28 0.00061 26.0 5.5 26 366-391 25-50 (67)
228 PRK11179 DNA-binding transcrip 60.2 19 0.0004 32.4 5.2 27 365-391 22-48 (153)
229 TIGR02337 HpaR homoprotocatech 60.1 43 0.00092 28.4 7.2 66 318-391 2-67 (118)
230 PRK15201 fimbriae regulatory p 59.8 12 0.00026 35.7 3.9 33 364-396 146-178 (198)
231 PF08220 HTH_DeoR: DeoR-like h 59.8 21 0.00046 26.9 4.7 27 364-390 12-38 (57)
232 PRK05932 RNA polymerase factor 59.1 97 0.0021 33.3 11.2 23 366-388 343-365 (455)
233 COG2771 CsgD DNA-binding HTH d 59.0 9.7 0.00021 28.2 2.7 31 365-395 18-48 (65)
234 PRK13239 alkylmercury lyase; P 59.0 20 0.00044 34.6 5.5 29 363-391 33-61 (206)
235 PRK10403 transcriptional regul 58.9 15 0.00033 32.4 4.5 33 365-397 167-199 (215)
236 cd04762 HTH_MerR-trunc Helix-T 58.4 12 0.00026 25.8 3.0 23 368-390 2-24 (49)
237 COG1318 Predicted transcriptio 58.1 18 0.00038 34.2 4.7 26 366-391 61-86 (182)
238 COG1405 SUA7 Transcription ini 58.0 1.3E+02 0.0027 30.5 11.2 27 364-390 249-275 (285)
239 PRK10100 DNA-binding transcrip 57.4 13 0.00028 35.6 3.9 32 365-396 169-200 (216)
240 PF08784 RPA_C: Replication pr 57.1 20 0.00043 29.9 4.6 41 350-390 49-89 (102)
241 PRK15369 two component system 57.0 16 0.00034 32.0 4.1 33 365-397 163-195 (211)
242 smart00344 HTH_ASNC helix_turn 56.9 23 0.00049 29.4 4.9 25 366-390 17-41 (108)
243 smart00419 HTH_CRP helix_turn_ 56.5 16 0.00034 25.5 3.3 25 367-391 9-33 (48)
244 PRK15320 transcriptional activ 56.4 15 0.00032 35.7 4.0 32 363-394 176-207 (251)
245 PF09012 FeoC: FeoC like trans 56.3 17 0.00037 28.3 3.8 27 364-390 12-38 (69)
246 PF00392 GntR: Bacterial regul 55.6 14 0.00029 28.2 3.1 26 365-390 23-48 (64)
247 smart00420 HTH_DEOR helix_turn 55.0 34 0.00075 23.9 5.0 27 365-391 13-39 (53)
248 PF05225 HTH_psq: helix-turn-h 54.8 37 0.0008 24.7 5.1 37 351-389 3-39 (45)
249 PRK11169 leucine-responsive tr 54.7 28 0.0006 31.7 5.5 26 366-391 28-53 (164)
250 PRK09935 transcriptional regul 54.4 19 0.00041 32.0 4.3 33 365-397 163-195 (210)
251 TIGR01610 phage_O_Nterm phage 54.1 35 0.00076 28.4 5.6 27 364-390 45-71 (95)
252 PF04218 CENP-B_N: CENP-B N-te 53.1 13 0.00029 27.9 2.6 26 364-389 20-45 (53)
253 TIGR02844 spore_III_D sporulat 52.5 40 0.00086 27.8 5.5 25 365-389 18-42 (80)
254 KOG1597 Transcription initiati 52.4 1.8E+02 0.0038 29.9 11.0 126 233-390 159-284 (308)
255 PF01978 TrmB: Sugar-specific 52.1 17 0.00037 27.9 3.1 26 365-390 21-46 (68)
256 PRK00423 tfb transcription ini 51.6 1.8E+02 0.0039 29.4 11.3 26 368-393 278-303 (310)
257 PRK15418 transcriptional regul 50.8 13 0.00028 37.8 2.9 37 364-400 27-67 (318)
258 PRK10046 dpiA two-component re 50.8 16 0.00035 34.1 3.4 33 366-398 177-211 (225)
259 PRK12423 LexA repressor; Provi 50.5 44 0.00096 31.5 6.3 32 360-391 19-51 (202)
260 PF00376 MerR: MerR family reg 50.0 14 0.00031 25.9 2.2 23 368-390 1-23 (38)
261 PF12802 MarR_2: MarR family; 49.9 38 0.00083 25.0 4.7 26 366-391 21-46 (62)
262 PRK10430 DNA-binding transcrip 49.6 20 0.00043 33.8 3.8 34 363-396 175-208 (239)
263 COG3413 Predicted DNA binding 49.3 63 0.0014 30.6 7.2 58 205-275 155-212 (215)
264 TIGR00498 lexA SOS regulatory 48.8 39 0.00086 31.4 5.6 40 351-390 9-50 (199)
265 cd04761 HTH_MerR-SF Helix-Turn 48.0 20 0.00044 25.2 2.8 23 368-390 2-24 (49)
266 COG1342 Predicted DNA-binding 47.9 14 0.00031 31.6 2.2 30 365-394 48-77 (99)
267 PF01371 Trp_repressor: Trp re 47.5 44 0.00095 28.0 5.0 41 343-386 29-69 (87)
268 cd07377 WHTH_GntR Winged helix 47.4 45 0.00097 24.5 4.7 25 367-391 26-50 (66)
269 PRK03902 manganese transport t 47.1 52 0.0011 29.0 5.9 40 352-391 8-47 (142)
270 PF04703 FaeA: FaeA-like prote 47.1 30 0.00066 27.1 3.8 27 364-390 13-39 (62)
271 smart00354 HTH_LACI helix_turn 46.9 19 0.0004 28.2 2.6 22 367-388 1-22 (70)
272 PRK11511 DNA-binding transcrip 46.7 53 0.0011 28.5 5.8 39 352-390 10-49 (127)
273 PRK09390 fixJ response regulat 46.3 34 0.00074 29.7 4.5 31 366-396 156-186 (202)
274 COG1725 Predicted transcriptio 46.1 61 0.0013 29.0 6.0 28 363-390 32-59 (125)
275 PRK09480 slmA division inhibit 45.9 1.9E+02 0.0041 25.8 9.5 72 233-304 25-96 (194)
276 PF13551 HTH_29: Winged helix- 45.5 66 0.0014 26.3 6.0 42 349-390 62-111 (112)
277 PRK10651 transcriptional regul 45.4 32 0.0007 30.4 4.3 33 365-397 169-201 (216)
278 PF13518 HTH_28: Helix-turn-he 45.0 28 0.0006 24.8 3.2 25 367-391 13-37 (52)
279 PF01381 HTH_3: Helix-turn-hel 44.7 27 0.00058 25.3 3.1 25 365-389 8-32 (55)
280 TIGR00373 conserved hypothetic 44.3 38 0.00082 31.1 4.6 26 366-391 28-53 (158)
281 PF13443 HTH_26: Cro/C1-type H 43.8 17 0.00037 27.2 1.9 32 365-396 9-40 (63)
282 cd00569 HTH_Hin_like Helix-tur 43.2 22 0.00049 21.8 2.2 21 366-386 21-41 (42)
283 COG3355 Predicted transcriptio 42.5 46 0.001 29.8 4.7 27 364-390 40-66 (126)
284 PHA02943 hypothetical protein; 42.3 71 0.0015 29.8 6.0 25 366-390 24-48 (165)
285 PF11251 DUF3050: Protein of u 41.9 1.1E+02 0.0023 30.3 7.5 101 191-325 80-185 (232)
286 COG0856 Orotate phosphoribosyl 41.8 48 0.001 31.6 4.9 33 364-396 16-48 (203)
287 PRK13558 bacterio-opsin activa 41.7 19 0.00041 39.4 2.6 30 364-393 628-657 (665)
288 PF01710 HTH_Tnp_IS630: Transp 41.6 54 0.0012 28.4 5.0 28 364-391 69-96 (119)
289 PF13545 HTH_Crp_2: Crp-like h 41.5 33 0.00071 26.5 3.3 24 368-391 30-53 (76)
290 PRK06266 transcription initiat 41.4 49 0.0011 31.0 5.0 26 366-391 36-61 (178)
291 PRK11512 DNA-binding transcrip 41.2 1.5E+02 0.0033 25.9 7.9 27 365-391 53-79 (144)
292 PF01022 HTH_5: Bacterial regu 41.1 36 0.00077 24.5 3.2 26 365-390 14-39 (47)
293 smart00418 HTH_ARSR helix_turn 41.0 40 0.00087 24.1 3.6 28 364-391 8-35 (66)
294 TIGR02531 yecD_yerC TrpR-relat 40.7 63 0.0014 27.0 5.0 23 365-387 49-71 (88)
295 PF13411 MerR_1: MerR HTH fami 40.7 31 0.00067 26.2 3.0 24 368-391 2-25 (69)
296 COG2390 DeoR Transcriptional r 40.6 24 0.00051 36.3 3.0 37 364-400 24-64 (321)
297 PRK10219 DNA-binding transcrip 40.6 77 0.0017 26.3 5.6 38 353-390 7-45 (107)
298 PF12840 HTH_20: Helix-turn-he 39.8 77 0.0017 23.8 5.0 27 364-390 22-48 (61)
299 TIGR02431 pcaR_pcaU beta-ketoa 39.8 70 0.0015 30.8 6.0 29 362-390 20-48 (248)
300 PRK05472 redox-sensing transcr 39.3 56 0.0012 30.9 5.2 49 341-389 6-55 (213)
301 PRK03573 transcriptional regul 39.3 1.4E+02 0.0031 26.0 7.4 28 364-391 44-71 (144)
302 PRK14101 bifunctional glucokin 39.1 2.8E+02 0.006 30.8 11.2 22 368-389 376-397 (638)
303 PRK09726 antitoxin HipB; Provi 38.6 56 0.0012 26.6 4.4 24 365-388 24-47 (88)
304 PRK04841 transcriptional regul 38.6 25 0.00055 39.6 3.1 33 365-397 852-884 (903)
305 PF13936 HTH_38: Helix-turn-he 38.5 47 0.001 23.8 3.5 42 203-261 2-43 (44)
306 PRK09802 DNA-binding transcrip 38.5 66 0.0014 31.8 5.7 38 352-390 18-55 (269)
307 PRK09958 DNA-binding transcrip 38.4 47 0.001 29.5 4.3 33 365-397 157-189 (204)
308 COG1321 TroR Mn-dependent tran 38.4 72 0.0016 29.2 5.5 41 351-391 9-49 (154)
309 TIGR03070 couple_hipB transcri 38.1 42 0.0009 24.0 3.2 25 365-389 14-38 (58)
310 PF08535 KorB: KorB domain; I 38.0 33 0.00071 28.3 2.9 26 366-391 3-28 (93)
311 PF13551 HTH_29: Winged helix- 37.8 36 0.00077 27.9 3.2 24 368-391 14-37 (112)
312 PF02082 Rrf2: Transcriptional 37.6 41 0.00089 27.0 3.4 26 366-391 25-50 (83)
313 PF00382 TFIIB: Transcription 37.4 52 0.0011 25.5 3.8 20 364-383 52-71 (71)
314 PF07374 DUF1492: Protein of u 37.4 40 0.00086 28.4 3.4 27 366-392 71-97 (100)
315 smart00342 HTH_ARAC helix_turn 36.9 85 0.0018 23.6 5.0 58 238-298 1-60 (84)
316 PRK10163 DNA-binding transcrip 36.8 70 0.0015 31.5 5.5 34 357-390 31-64 (271)
317 PRK00215 LexA repressor; Valid 36.8 95 0.0021 28.9 6.2 31 361-391 18-49 (205)
318 PRK09480 slmA division inhibit 36.3 83 0.0018 28.2 5.6 40 347-386 9-50 (194)
319 PRK11161 fumarate/nitrate redu 36.1 2.2E+02 0.0047 26.6 8.6 25 367-391 185-209 (235)
320 PRK10434 srlR DNA-bindng trans 35.8 70 0.0015 31.3 5.3 33 357-390 11-43 (256)
321 PHA01976 helix-turn-helix prot 35.7 41 0.0009 25.4 3.0 26 364-389 13-38 (67)
322 PF04963 Sigma54_CBD: Sigma-54 35.5 99 0.0021 29.1 6.1 24 368-391 121-144 (194)
323 PF02796 HTH_7: Helix-turn-hel 35.1 57 0.0012 23.3 3.5 41 203-260 3-43 (45)
324 cd01104 HTH_MlrA-CarA Helix-Tu 35.1 45 0.00097 25.2 3.1 22 368-389 2-23 (68)
325 COG2524 Predicted transcriptio 34.8 67 0.0014 32.5 4.9 40 351-390 9-49 (294)
326 PRK10079 phosphonate metabolis 34.8 64 0.0014 30.9 4.8 27 363-389 32-58 (241)
327 PF13309 HTH_22: HTH domain 34.2 94 0.002 24.2 4.8 20 368-387 44-63 (64)
328 PF13730 HTH_36: Helix-turn-he 34.0 1.5E+02 0.0032 21.5 5.6 25 235-259 22-46 (55)
329 TIGR00122 birA_repr_reg BirA b 34.0 58 0.0013 25.0 3.6 26 366-391 13-38 (69)
330 cd00090 HTH_ARSR Arsenical Res 33.9 98 0.0021 22.6 4.8 24 367-390 21-44 (78)
331 TIGR01636 phage_rinA phage tra 33.9 46 0.00099 29.5 3.4 25 367-391 101-125 (134)
332 PF06970 RepA_N: Replication i 33.8 43 0.00094 27.2 2.9 21 368-388 54-74 (76)
333 COG2902 NAD-specific glutamate 33.2 1.1E+03 0.023 29.6 16.8 30 368-397 1468-1497(1592)
334 PF14493 HTH_40: Helix-turn-he 33.1 70 0.0015 26.2 4.2 28 364-391 11-38 (91)
335 TIGR01321 TrpR trp operon repr 32.8 37 0.00079 29.0 2.4 23 365-387 54-76 (94)
336 smart00422 HTH_MERR helix_turn 32.7 49 0.0011 25.0 3.0 21 368-388 2-22 (70)
337 PRK10360 DNA-binding transcrip 32.0 71 0.0015 28.1 4.3 33 365-397 151-183 (196)
338 smart00531 TFIIE Transcription 31.9 66 0.0014 28.9 4.1 27 366-392 15-41 (147)
339 PF02954 HTH_8: Bacterial regu 31.8 60 0.0013 22.9 3.1 22 368-389 20-41 (42)
340 cd04764 HTH_MlrA-like_sg1 Heli 31.7 55 0.0012 24.9 3.1 22 368-389 2-23 (67)
341 PF13560 HTH_31: Helix-turn-he 31.6 45 0.00098 25.2 2.6 26 365-390 13-38 (64)
342 COG1476 Predicted transcriptio 31.6 96 0.0021 24.9 4.5 24 365-388 13-36 (68)
343 PRK04217 hypothetical protein; 31.5 2.1E+02 0.0046 24.9 7.0 29 240-268 60-88 (110)
344 COG2344 AT-rich DNA-binding pr 31.4 1E+02 0.0023 29.8 5.4 49 340-388 5-54 (211)
345 PRK10411 DNA-binding transcrip 31.4 97 0.0021 30.1 5.5 27 364-390 16-42 (240)
346 PF11740 KfrA_N: Plasmid repli 31.1 1.4E+02 0.0029 25.3 5.8 41 351-391 4-45 (120)
347 PRK10512 selenocysteinyl-tRNA- 30.9 7.9E+02 0.017 27.4 14.8 134 237-390 376-530 (614)
348 TIGR03697 NtcA_cyano global ni 30.9 49 0.0011 29.7 3.1 26 366-391 143-168 (193)
349 cd06445 ATase The DNA repair p 30.8 86 0.0019 25.2 4.2 30 362-391 13-44 (79)
350 PRK11569 transcriptional repre 30.8 99 0.0021 30.4 5.5 33 358-390 35-67 (274)
351 PF00165 HTH_AraC: Bacterial r 30.4 73 0.0016 22.1 3.3 27 364-390 6-32 (42)
352 PF14394 DUF4423: Domain of un 30.4 95 0.0021 28.8 5.0 27 365-391 38-66 (171)
353 PF10078 DUF2316: Uncharacteri 30.3 1.1E+02 0.0023 25.9 4.7 25 365-389 22-46 (89)
354 PRK11014 transcriptional repre 30.0 61 0.0013 28.7 3.5 28 364-391 23-50 (141)
355 TIGR02607 antidote_HigA addict 29.9 58 0.0013 25.2 3.0 24 365-388 17-40 (78)
356 TIGR02404 trehalos_R_Bsub treh 29.6 76 0.0016 30.1 4.3 26 364-389 22-47 (233)
357 TIGR02612 mob_myst_A mobile my 29.5 2E+02 0.0042 26.4 6.8 25 365-389 37-61 (150)
358 TIGR02702 SufR_cyano iron-sulf 28.9 1E+02 0.0022 28.9 5.0 25 366-390 15-39 (203)
359 TIGR02325 C_P_lyase_phnF phosp 28.9 63 0.0014 30.5 3.6 26 364-389 30-55 (238)
360 PHA00675 hypothetical protein 28.9 1.2E+02 0.0027 25.0 4.7 22 368-389 41-62 (78)
361 PF05138 PaaA_PaaC: Phenylacet 28.8 1.3E+02 0.0028 30.0 5.9 86 228-333 33-118 (263)
362 PRK14999 histidine utilization 28.7 86 0.0019 30.0 4.5 26 364-389 34-59 (241)
363 PF01418 HTH_6: Helix-turn-hel 28.5 1.4E+02 0.0031 23.7 5.1 26 364-389 32-57 (77)
364 PRK09975 DNA-binding transcrip 28.4 1.1E+02 0.0024 27.9 5.1 40 347-386 10-51 (213)
365 cd01392 HTH_LacI Helix-turn-he 28.4 42 0.00091 24.0 1.8 19 371-389 2-20 (52)
366 PRK00430 fis global DNA-bindin 28.4 3.6E+02 0.0078 22.7 8.2 23 368-390 70-92 (95)
367 PF01035 DNA_binding_1: 6-O-me 28.2 74 0.0016 26.1 3.4 38 352-390 6-45 (85)
368 PF07022 Phage_CI_repr: Bacter 28.2 1.3E+02 0.0027 23.3 4.6 43 228-271 3-46 (66)
369 COG2188 PhnF Transcriptional r 28.1 77 0.0017 30.5 4.1 26 364-389 29-54 (236)
370 smart00530 HTH_XRE Helix-turn- 27.8 82 0.0018 20.9 3.2 24 365-388 9-32 (56)
371 PRK04984 fatty acid metabolism 27.7 61 0.0013 30.7 3.3 26 365-390 30-55 (239)
372 PRK13509 transcriptional repre 27.7 1.3E+02 0.0028 29.3 5.7 27 364-390 17-43 (251)
373 PRK11534 DNA-binding transcrip 27.7 92 0.002 29.2 4.5 27 364-390 28-54 (224)
374 PRK09834 DNA-binding transcrip 27.6 1.5E+02 0.0033 28.8 6.2 29 362-390 22-50 (263)
375 COG2522 Predicted transcriptio 27.5 1.5E+02 0.0033 26.3 5.5 25 365-389 21-45 (119)
376 PRK13918 CRP/FNR family transc 27.4 61 0.0013 29.5 3.1 25 367-391 150-174 (202)
377 TIGR02018 his_ut_repres histid 27.4 99 0.0022 29.2 4.7 26 364-389 23-48 (230)
378 COG1476 Predicted transcriptio 27.2 1.1E+02 0.0024 24.6 4.1 50 239-298 15-64 (68)
379 PF04760 IF2_N: Translation in 27.1 44 0.00096 24.7 1.8 21 367-387 4-24 (54)
380 COG1497 Predicted transcriptio 27.0 91 0.002 31.1 4.3 28 363-390 22-49 (260)
381 cd04763 HTH_MlrA-like Helix-Tu 26.9 73 0.0016 24.3 3.1 22 368-389 2-23 (68)
382 PF01726 LexA_DNA_bind: LexA D 26.8 1.3E+02 0.0028 23.5 4.5 26 232-257 19-45 (65)
383 TIGR00738 rrf2_super rrf2 fami 26.4 1.6E+02 0.0034 25.3 5.4 26 366-391 25-50 (132)
384 PF00440 TetR_N: Bacterial reg 26.3 1.7E+02 0.0038 20.7 4.8 23 364-386 14-36 (47)
385 PRK11511 DNA-binding transcrip 26.1 3.4E+02 0.0073 23.5 7.5 34 229-262 16-49 (127)
386 TIGR02944 suf_reg_Xantho FeS a 25.9 81 0.0018 27.2 3.5 28 364-391 23-50 (130)
387 PRK09464 pdhR transcriptional 25.6 70 0.0015 30.7 3.3 26 365-390 33-58 (254)
388 COG1414 IclR Transcriptional r 25.5 1.4E+02 0.0031 29.0 5.5 27 364-390 17-43 (246)
389 PHA00542 putative Cro-like pro 25.3 80 0.0017 25.6 3.1 26 365-390 30-55 (82)
390 PF12793 SgrR_N: Sugar transpo 25.0 1.2E+02 0.0027 26.3 4.5 26 366-391 19-44 (115)
391 PRK00901 methylated-DNA--prote 25.0 1.4E+02 0.0031 27.4 5.1 67 328-397 51-121 (155)
392 PF12324 HTH_15: Helix-turn-he 24.8 80 0.0017 26.0 3.0 27 235-261 35-61 (77)
393 COG2345 Predicted transcriptio 24.7 1.3E+02 0.0029 29.3 5.0 27 364-390 23-49 (218)
394 PRK11414 colanic acid/biofilm 24.6 1E+02 0.0022 29.0 4.2 27 364-390 32-58 (221)
395 PF12844 HTH_19: Helix-turn-he 24.5 1.6E+02 0.0035 21.8 4.6 25 365-389 11-35 (64)
396 PF04297 UPF0122: Putative hel 24.5 4E+02 0.0086 23.0 7.3 42 238-280 33-74 (101)
397 PRK03837 transcriptional regul 24.5 76 0.0016 30.0 3.3 26 365-390 36-61 (241)
398 smart00342 HTH_ARAC helix_turn 24.4 3E+02 0.0065 20.4 7.5 38 351-390 37-75 (84)
399 PRK09685 DNA-binding transcrip 24.4 6.5E+02 0.014 24.3 10.5 44 280-324 206-249 (302)
400 PRK11050 manganese transport r 24.3 2E+02 0.0043 25.9 5.8 28 364-391 49-76 (152)
401 PF08765 Mor: Mor transcriptio 24.2 1.8E+02 0.0038 24.8 5.2 26 366-391 72-97 (108)
402 PRK09764 DNA-binding transcrip 24.2 85 0.0018 30.0 3.6 27 364-390 27-53 (240)
403 TIGR03338 phnR_burk phosphonat 24.2 1E+02 0.0022 28.5 4.1 27 364-390 32-58 (212)
404 PF01399 PCI: PCI domain; Int 24.1 2E+02 0.0044 22.9 5.4 34 357-390 51-84 (105)
405 PF01047 MarR: MarR family; I 24.1 1.6E+02 0.0034 21.5 4.4 25 366-390 17-41 (59)
406 TIGR00180 parB_part ParB-like 24.1 1.8E+02 0.0038 27.0 5.6 26 366-391 120-145 (187)
407 smart00351 PAX Paired Box doma 24.0 73 0.0016 27.9 2.9 27 366-392 33-59 (125)
408 PRK15090 DNA-binding transcrip 24.0 1.5E+02 0.0032 28.8 5.2 26 365-390 27-52 (257)
409 TIGR03337 phnR transcriptional 23.9 86 0.0019 29.4 3.6 27 364-390 23-49 (231)
410 TIGR02787 codY_Gpos GTP-sensin 23.9 1.5E+02 0.0033 29.6 5.2 39 352-390 184-222 (251)
411 PRK06424 transcription factor; 23.8 1.8E+02 0.004 26.4 5.4 26 364-389 95-120 (144)
412 PRK13239 alkylmercury lyase; P 23.8 80 0.0017 30.5 3.3 27 235-261 33-59 (206)
413 PRK11402 DNA-binding transcrip 23.7 84 0.0018 30.0 3.5 26 364-389 31-56 (241)
414 PRK10225 DNA-binding transcrip 23.7 1.4E+02 0.0029 28.8 4.9 26 365-390 32-57 (257)
415 COG1675 TFA1 Transcription ini 23.7 1.2E+02 0.0027 28.6 4.5 32 359-391 26-57 (176)
416 PF09824 ArsR: ArsR transcript 23.5 35 0.00075 31.8 0.7 30 95-126 34-64 (160)
417 PF04218 CENP-B_N: CENP-B N-te 23.4 98 0.0021 23.1 3.1 42 204-262 5-46 (53)
418 COG2739 Uncharacterized protei 23.3 91 0.002 27.1 3.2 28 365-392 32-59 (105)
419 PRK15044 transcriptional regul 23.2 3.7E+02 0.008 27.5 8.0 60 193-261 172-231 (295)
420 PRK10681 DNA-binding transcrip 23.1 1.4E+02 0.0031 29.1 5.0 27 364-390 19-45 (252)
421 PRK10906 DNA-binding transcrip 22.9 1.3E+02 0.0029 29.4 4.8 26 364-389 17-42 (252)
422 PF13613 HTH_Tnp_4: Helix-turn 22.8 1.4E+02 0.003 22.0 3.8 32 360-391 13-44 (53)
423 PF13309 HTH_22: HTH domain 22.8 3.4E+02 0.0073 21.0 6.1 58 188-257 2-61 (64)
424 PRK10072 putative transcriptio 22.8 91 0.002 26.5 3.1 26 365-390 45-70 (96)
425 TIGR02812 fadR_gamma fatty aci 22.6 85 0.0019 29.7 3.3 26 365-390 29-54 (235)
426 PRK10402 DNA-binding transcrip 22.6 2.8E+02 0.0061 26.0 6.8 25 367-391 170-194 (226)
427 PF13463 HTH_27: Winged helix 22.5 1.7E+02 0.0036 21.8 4.3 29 363-391 15-43 (68)
428 PRK09954 putative kinase; Prov 22.5 1.6E+02 0.0035 29.8 5.4 26 366-391 17-42 (362)
429 PRK10421 DNA-binding transcrip 22.4 87 0.0019 30.1 3.3 26 365-390 25-50 (253)
430 PRK11753 DNA-binding transcrip 22.3 81 0.0018 28.8 3.0 31 367-397 169-201 (211)
431 PRK09639 RNA polymerase sigma 22.2 3.5E+02 0.0077 23.6 7.0 34 238-271 127-160 (166)
432 PF00046 Homeobox: Homeobox do 22.1 84 0.0018 22.9 2.5 21 368-388 29-49 (57)
433 PRK09652 RNA polymerase sigma 22.0 3.8E+02 0.0082 23.4 7.2 31 240-270 146-176 (182)
434 PRK10572 DNA-binding transcrip 21.9 7.2E+02 0.016 24.0 10.5 38 352-389 184-222 (290)
435 PRK09990 DNA-binding transcrip 21.8 91 0.002 29.8 3.3 26 365-390 30-55 (251)
436 PF05043 Mga: Mga helix-turn-h 21.7 58 0.0012 26.1 1.6 31 364-394 28-58 (87)
437 TIGR03076 near_not_gcvH Chlamy 21.5 4.2E+02 0.0092 29.5 8.3 128 261-388 159-295 (686)
438 PRK01381 Trp operon repressor; 21.5 89 0.0019 26.9 2.8 22 365-386 54-75 (99)
439 PF13556 HTH_30: PucR C-termin 21.4 77 0.0017 23.9 2.2 32 366-397 12-43 (59)
440 TIGR02147 Fsuc_second hypothet 21.3 1.8E+02 0.0038 29.2 5.3 25 366-390 137-163 (271)
441 COG1510 Predicted transcriptio 21.3 1.6E+02 0.0035 27.9 4.6 26 365-390 40-65 (177)
442 PF03428 RP-C: Replication pro 21.3 4E+02 0.0086 25.1 7.3 23 368-390 72-95 (177)
443 COG0350 Ada Methylated DNA-pro 21.2 1.9E+02 0.0042 26.8 5.2 50 348-400 88-139 (168)
444 smart00753 PAM PCI/PINT associ 21.2 2.6E+02 0.0056 22.1 5.4 35 356-390 14-48 (88)
445 smart00088 PINT motif in prote 21.2 2.6E+02 0.0056 22.1 5.4 35 356-390 14-48 (88)
446 PRK11924 RNA polymerase sigma 21.2 3.7E+02 0.008 23.4 6.9 33 239-271 142-174 (179)
447 cd00093 HTH_XRE Helix-turn-hel 21.2 1.2E+02 0.0026 20.2 3.1 25 365-389 11-35 (58)
448 PF02885 Glycos_trans_3N: Glyc 21.1 2.5E+02 0.0054 21.6 5.1 31 193-223 2-32 (66)
449 PRK03887 methylated-DNA--prote 20.9 2.3E+02 0.005 26.8 5.6 29 362-390 106-134 (175)
450 PF01498 HTH_Tnp_Tc3_2: Transp 20.9 1.1E+02 0.0024 23.5 3.1 28 364-391 11-43 (72)
451 COG2186 FadR Transcriptional r 20.8 1E+02 0.0022 30.0 3.4 27 364-390 32-58 (241)
452 TIGR03613 RutR pyrimidine util 20.8 6.2E+02 0.013 22.7 9.8 74 232-306 21-95 (202)
453 PRK09647 RNA polymerase sigma 20.8 3.5E+02 0.0076 25.3 7.0 36 240-275 156-191 (203)
454 PRK12527 RNA polymerase sigma 20.6 4.1E+02 0.009 23.1 7.1 33 240-272 123-155 (159)
455 PF01371 Trp_repressor: Trp re 20.5 3.3E+02 0.0072 22.8 5.9 43 205-257 26-68 (87)
456 PRK12519 RNA polymerase sigma 20.5 3.2E+02 0.0069 24.7 6.5 36 238-273 157-192 (194)
457 PRK10219 DNA-binding transcrip 20.5 1.8E+02 0.0039 24.0 4.5 33 229-261 12-44 (107)
458 PRK15481 transcriptional regul 20.5 1.4E+02 0.003 30.9 4.6 27 364-390 27-53 (431)
459 PRK09391 fixK transcriptional 20.2 3.4E+02 0.0073 25.6 6.8 25 367-391 180-204 (230)
460 PF02002 TFIIE_alpha: TFIIE al 20.1 1.5E+02 0.0031 24.8 3.8 26 366-391 27-52 (105)
461 COG1349 GlpR Transcriptional r 20.1 1.3E+02 0.0029 29.4 4.0 26 364-389 17-42 (253)
No 1
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=100.00 E-value=1.6e-40 Score=341.55 Aligned_cols=212 Identities=38% Similarity=0.656 Sum_probs=199.2
Q ss_pred hhHHHHHHhhcCCCCCCHHHHHHHHHHHHccCc--------------------chhHHHHHHHhhCCCCchHHHHHHhcC
Q 014764 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS--------------------LDDHKLRLKERLGCEPSMEQLAASLRI 250 (419)
Q Consensus 191 ~~l~~yl~~i~~~~lLt~~eE~eL~rkik~Gd~--------------------l~~~~~~l~~~lg~~p~~~e~A~~~~~ 250 (419)
|.++.||++|++.|+||++||++|+++|+.+.. |+..+.+|++.+|++||.+|||.++|+
T Consensus 60 d~v~~yl~~igr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~~~~~ 139 (415)
T PRK07598 60 DLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKTADI 139 (415)
T ss_pred ChHHHHHHhcccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHHHhCC
Confidence 789999999999999999999999999999988 888899999999999999999966554
Q ss_pred ----------------------ChHHHHHHHhHHHHHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhh
Q 014764 251 ----------------------SRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEK 308 (419)
Q Consensus 251 ----------------------s~~eLr~~l~~~~~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIer 308 (419)
+.++|...+..|..|+++||..|+++|+++|++|.+++.+++||+|||++|||+|+++
T Consensus 140 ~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~ravek 219 (415)
T PRK07598 140 SLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEK 219 (415)
T ss_pred cHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHH
Confidence 5555555567788999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccchHHHHHHHHHHHHHHH-hcCCCccHHHHHHHcCCCHHHHHHHH
Q 014764 309 FDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNAT 387 (419)
Q Consensus 309 FDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~l~e~~~~I~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~~l 387 (419)
|||.+|++|+||++||||+.|.+++.++.+.+++|.++.+.+++++++...|. .+||.|+..|||+.|||++++|+.++
T Consensus 220 FDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~l 299 (415)
T PRK07598 220 FDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVL 299 (415)
T ss_pred cCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999984 78999999999999999999999999
Q ss_pred HHhCcccccccccCC
Q 014764 388 EAIGKVFSLDREAFP 402 (419)
Q Consensus 388 ~rark~lSLD~~~~~ 402 (419)
..+..++|||.+++.
T Consensus 300 ~~~~~~~SLd~~vg~ 314 (415)
T PRK07598 300 LRVPRSVSLETKVGK 314 (415)
T ss_pred HHccCCcccccccCC
Confidence 999999999998853
No 2
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=2.9e-39 Score=329.31 Aligned_cols=224 Identities=36% Similarity=0.565 Sum_probs=211.6
Q ss_pred hhHHHHHHhhcCCCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHH
Q 014764 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (419)
Q Consensus 191 ~~l~~yl~~i~~~~lLt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LI 270 (419)
+.+..||++|.++|+||++||.+|+++++.|..++..+..|...+|++|+.++||.+.+++..+|+..+..|..|++.||
T Consensus 63 d~l~~Yl~~i~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Li 142 (373)
T PRK07406 63 DSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEKMV 142 (373)
T ss_pred CHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHHHHH
Confidence 67889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccchHHHH
Q 014764 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL 350 (419)
Q Consensus 271 e~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~l~e~~ 350 (419)
..|+++|+++|++|.+++.+++||+|||+||||+++++||+.+|++|+||++||||+.|.++|+++.+.+++|.++.+..
T Consensus 143 ~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~~~~~ 222 (373)
T PRK07406 143 QSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETI 222 (373)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHH-hcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCCCCCCCCcccccCCC
Q 014764 351 GLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSVIHC 418 (419)
Q Consensus 351 ~~I~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~~l~rark~lSLD~~~~~~~d~~~~~tl~d~IaD 418 (419)
.++.++...|. .+|+.||.+|||+.||+++++|..++..+...+|||.+++. +++.+++|+|+|
T Consensus 223 ~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~----~~~~~l~d~l~d 287 (373)
T PRK07406 223 SRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGK----EEDSRLGDFIEA 287 (373)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCC----CCcccHHHhcCC
Confidence 99999999995 68999999999999999999999998888889999998742 223367777764
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=7.5e-39 Score=316.64 Aligned_cols=210 Identities=39% Similarity=0.662 Sum_probs=202.6
Q ss_pred hHHHHHHhhcCCCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHH
Q 014764 192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM 271 (419)
Q Consensus 192 ~l~~yl~~i~~~~lLt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe 271 (419)
.+..||+++.++|+||++||.+|+++++.|..+++.+..|.+.+|++|+..+||.+++++..+|...+..|..|++.||.
T Consensus 2 ~~~~yl~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Lv~ 81 (298)
T TIGR02997 2 LVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMIK 81 (298)
T ss_pred cHHHHHHHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHHHH
Confidence 46789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccchHHHHH
Q 014764 272 SNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG 351 (419)
Q Consensus 272 ~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~l~e~~~ 351 (419)
.|+++|+++|++|.+++.+++||+||||+|||+|+++|||.+|++|+||++|||++.|.+++.++.+.+++|.++...+.
T Consensus 82 ~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~I~r~i~~~~r~vr~p~~~~~~~~ 161 (298)
T TIGR02997 82 ANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLN 161 (298)
T ss_pred HhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHHHHHHHHhcCCCeeCcHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHH-hcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccC
Q 014764 352 LIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAF 401 (419)
Q Consensus 352 ~I~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~~l~rark~lSLD~~~~ 401 (419)
.++++...+. .+|+.||.+|||+.||++.++|..++..+...+|||.++.
T Consensus 162 ~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~ 212 (298)
T TIGR02997 162 KIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVG 212 (298)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcC
Confidence 9999998884 6899999999999999999999999998889999998873
No 4
>PRK05949 RNA polymerase sigma factor; Validated
Probab=100.00 E-value=1.6e-38 Score=318.98 Aligned_cols=224 Identities=32% Similarity=0.585 Sum_probs=211.0
Q ss_pred hhHHHHHHhhcCCCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHH
Q 014764 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (419)
Q Consensus 191 ~~l~~yl~~i~~~~lLt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LI 270 (419)
|.+..|+++|.++|+||++||.+|+++++.|..+++.+..|...+|++|+..+||.+++++..+|...+..|..||+.||
T Consensus 18 d~~~~yl~~i~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~~Li 97 (327)
T PRK05949 18 DMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQKMI 97 (327)
T ss_pred CHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHHHHH
Confidence 68889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccchHHHH
Q 014764 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL 350 (419)
Q Consensus 271 e~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~l~e~~ 350 (419)
..|+++|+++|++|.+++.+++||+||||+|||+++++||+++|++|+||++||||+.|.+++.++.+.+++|.++.+.+
T Consensus 98 ~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~~~~~~~ 177 (327)
T PRK05949 98 EANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEKL 177 (327)
T ss_pred HHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHH-HhcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCCCCCCCCcccccCCC
Q 014764 351 GLIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSVIHC 418 (419)
Q Consensus 351 ~~I~~a~~~L-~e~gRepS~eEIAe~LGIS~etVr~~l~rark~lSLD~~~~~~~d~~~~~tl~d~IaD 418 (419)
..++++...+ ..+|++|+.+|||+.+|+++++|..++..+...+|||.++..+ ...++.|.++|
T Consensus 178 ~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~----~~~~l~~~l~d 242 (327)
T PRK05949 178 NKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDN----QDTELSELLED 242 (327)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCC----CCccHHhhcCC
Confidence 9999999998 4689999999999999999999999999999999999987422 22356666654
No 5
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=1.6e-37 Score=310.47 Aligned_cols=224 Identities=36% Similarity=0.607 Sum_probs=210.2
Q ss_pred hhHHHHHHhhcCCCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHH
Q 014764 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (419)
Q Consensus 191 ~~l~~yl~~i~~~~lLt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LI 270 (419)
+.+..||++|.++|+||++||.+|+++++.|..++..+..|.+.+|++|+..+||.++++++.+|...+..|..||+.||
T Consensus 8 ~~~~~yl~~i~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~~L~ 87 (317)
T PRK07405 8 DLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRKMV 87 (317)
T ss_pred cHHHHHHHHccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHHHHH
Confidence 67889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccchHHHH
Q 014764 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL 350 (419)
Q Consensus 271 e~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~l~e~~ 350 (419)
..|+++|+++|++|.+++.+++||+||||+|||+++++|||.+|++|+||++||||+.|.+++.++.+.+++|.++...+
T Consensus 88 ~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir~p~~~~~~~ 167 (317)
T PRK07405 88 EANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKL 167 (317)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCccCChHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHH-hcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCCCCCCCCcccccCCC
Q 014764 351 GLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSVIHC 418 (419)
Q Consensus 351 ~~I~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~~l~rark~lSLD~~~~~~~d~~~~~tl~d~IaD 418 (419)
..++++...+. .+|+.||.+|||+.+|++.+.|..++......+|||.++.. +++.++.++++|
T Consensus 168 ~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~----~~~~~l~~~~~d 232 (317)
T PRK07405 168 NKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGD----NQDTELGELLED 232 (317)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCC----CCCccHHHhhcC
Confidence 99999999984 68999999999999999999999999988899999987732 222356666554
No 6
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=100.00 E-value=1.4e-35 Score=311.60 Aligned_cols=212 Identities=33% Similarity=0.548 Sum_probs=187.2
Q ss_pred hhhHHHHHHhhcCCCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHH
Q 014764 190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKL 269 (419)
Q Consensus 190 ~~~l~~yl~~i~~~~lLt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~L 269 (419)
.+.+..||+.|.++|+||++||.+|+++++.|+.+++.. . ...+|+. ....+|+..+..|..|++.|
T Consensus 210 ~d~l~~YL~~i~~~~lLt~eEE~~La~~i~~g~~~~~~~---~-------~~~~~~~---~~~~~l~~~~~~g~~Ar~~L 276 (509)
T PRK05901 210 ADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEELL---A-------EGEKLDP---ELRRDLQWIGRDGKRAKNHL 276 (509)
T ss_pred ccHHHHHHHHhccCCCCCHHHHHHHHHHHHhCCchhhhh---h-------hcccchh---hhhhhhhhhccchHHHHHHH
Confidence 368999999999999999999999999999998744321 1 1122332 24567888888999999999
Q ss_pred HHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccchHHH
Q 014764 270 VMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHER 349 (419)
Q Consensus 270 Ie~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~l~e~ 349 (419)
|..|++||+++|++|.++|++++||||||+|||++|+++|||++|++|+||++||||+.|.++|+++.+.+++|.++.+.
T Consensus 277 I~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP~~~~e~ 356 (509)
T PRK05901 277 LEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVET 356 (509)
T ss_pred HHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecCHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHH-hcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCCCCCCCCcccccCCC
Q 014764 350 LGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSVIHC 418 (419)
Q Consensus 350 ~~~I~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~~l~rark~lSLD~~~~~~~d~~~~~tl~d~IaD 418 (419)
+++|.++...|. .+|+.||.+|||+.||++++.|..++......+|||.+++.+ +..+++|+|+|
T Consensus 357 i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d----~~~~l~d~l~D 422 (509)
T PRK05901 357 INKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKE----GDSQFGDFIED 422 (509)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccC----CcccHHHhccC
Confidence 999999999995 689999999999999999999999998888999999988422 22367777765
No 7
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=100.00 E-value=1.1e-34 Score=291.09 Aligned_cols=211 Identities=33% Similarity=0.552 Sum_probs=185.3
Q ss_pred hhHHHHHHhhcCCCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHH
Q 014764 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (419)
Q Consensus 191 ~~l~~yl~~i~~~~lLt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LI 270 (419)
+.+..||++|.++|+||++||.+|+++++.|..++.. +|..++++.. ...+|+..+..|..|++.||
T Consensus 26 ~~~~~Yl~~i~~~~lLt~eeE~~La~~~~~g~~~~~~----------~~~~~~~~~~---~~~~l~~~~~~~~~A~~~Lv 92 (324)
T PRK07921 26 DLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHL----------LETRKRLSEA---RKRDLAAVVRDGEAARRHLL 92 (324)
T ss_pred ChHHHHHHHhcccCCCCHHHHHHHHHHHHhhhhhhhh----------hccccccchh---HHHHHHHHHhcCHHHHHHHH
Confidence 5788999999999999999999999999998764433 1222222211 34578888889999999999
Q ss_pred HHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccchHHHH
Q 014764 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL 350 (419)
Q Consensus 271 e~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~l~e~~ 350 (419)
..|+++|+++|++|.+++.+++||+|||+||||+|+++|||++|++|+|||+||||+.|.++|+++.+.+++|.++.+..
T Consensus 93 ~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~~~~~~~ 172 (324)
T PRK07921 93 EANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQV 172 (324)
T ss_pred HHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHH-hcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCCCCCCCCcccccCCC
Q 014764 351 GLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSVIHC 418 (419)
Q Consensus 351 ~~I~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~~l~rark~lSLD~~~~~~~d~~~~~tl~d~IaD 418 (419)
.++.++...|. .+|+.||.+|||+.||++.++|..++..+...+|||.++.. +++.++.|+|+|
T Consensus 173 ~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~----~~~~~l~d~l~d 237 (324)
T PRK07921 173 NKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGS----DEEAPLGDFIED 237 (324)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCC----CCCchHHHHhcC
Confidence 99999999995 68999999999999999999999998888889999998732 222367777765
No 8
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=100.00 E-value=8.4e-34 Score=284.55 Aligned_cols=226 Identities=35% Similarity=0.520 Sum_probs=196.0
Q ss_pred hhhHHHHHHhhcCCCCCCHHHHHHHHHHHHccCcchhHHHHHHH-hhCCCCchH---------------HHHHHhcCCh-
Q 014764 190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKE-RLGCEPSME---------------QLAASLRISR- 252 (419)
Q Consensus 190 ~~~l~~yl~~i~~~~lLt~~eE~eL~rkik~Gd~l~~~~~~l~~-~lg~~p~~~---------------e~A~~~~~s~- 252 (419)
.+.+..|+..+...++++.+++..+...+.....+......|.. .++..|+.. +++..+....
T Consensus 8 ~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Ee 87 (342)
T COG0568 8 ADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEEE 87 (342)
T ss_pred hhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHHH
Confidence 47889999999999999999999999999877766666667776 678888875 3333333332
Q ss_pred HHHHHHHhHH---HHHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhH
Q 014764 253 PELQSILMEC---SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGV 329 (419)
Q Consensus 253 ~eLr~~l~~~---~~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I 329 (419)
.+|...+..| ..|..+||+.|+++|++||++|.++|..+.||+|||+|||++|+++|||.+|++|+||++||||+.|
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 3344555555 3499999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhcccccCccchHHHHHHHHHHHHHHH-hcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCCCCCC
Q 014764 330 SRALVENSRTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLP 408 (419)
Q Consensus 330 ~~~Lrd~~r~irip~~l~e~~~~I~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~~l~rark~lSLD~~~~~~~d~~~ 408 (419)
.++|.++.+.+++|.|+.+..+++.+....|. ..+++|+++|||+.||++.++|+.++.++..++|||.+++.+ +
T Consensus 168 ~raI~~q~rtIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd~~ig~d----e 243 (342)
T COG0568 168 TRAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDD----E 243 (342)
T ss_pred HHHHHHhcchhhHhHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccCCcCCCC----c
Confidence 99999999999999999999999999999995 569999999999999999999999999999999999998532 2
Q ss_pred CCcccccCCCC
Q 014764 409 GETHHSVIHCG 419 (419)
Q Consensus 409 ~~tl~d~IaDg 419 (419)
+..+.|+|+|+
T Consensus 244 d~~l~d~leD~ 254 (342)
T COG0568 244 DSELGDFLEDD 254 (342)
T ss_pred ccHHHHHhhcC
Confidence 33788888874
No 9
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=9.3e-33 Score=281.10 Aligned_cols=186 Identities=36% Similarity=0.580 Sum_probs=173.3
Q ss_pred hhhhHHHHHHhhcCCCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHH
Q 014764 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREK 268 (419)
Q Consensus 189 ~~~~l~~yl~~i~~~~lLt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~ 268 (419)
..+.++.||++|.+.|+|+++++.+|+++++.||. .|++.
T Consensus 94 ~~d~~~~yl~~i~~~~~l~~~ee~~L~~~~~~Gd~----------------------------------------~A~~~ 133 (367)
T PRK09210 94 INDPVRMYLKEIGRVPLLTAEEEIELAKRIEEGDE----------------------------------------EAKQR 133 (367)
T ss_pred cCcHHHHHHHHhhccCCCCHHHHHHHHHHHHhhHH----------------------------------------HHHHH
Confidence 34789999999999999999999999999999987 89999
Q ss_pred HHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccchHH
Q 014764 269 LVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHE 348 (419)
Q Consensus 269 LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~l~e 348 (419)
||..|+++|+++|++|.+++.+++||+||||||||+|+++|||.+|++|+||++|||++.|.++|+++.+.+++|.++.+
T Consensus 134 Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~~~~~ 213 (367)
T PRK09210 134 LAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 213 (367)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHH-hcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCCCCCCCCcccccCCC
Q 014764 349 RLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSVIHC 418 (419)
Q Consensus 349 ~~~~I~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~~l~rark~lSLD~~~~~~~d~~~~~tl~d~IaD 418 (419)
.++++.++...|. .+||.||.+|||+.||+++++|++++..+..++|||.++.. +++.++.|+|+|
T Consensus 214 ~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~----~~~~~l~d~i~d 280 (367)
T PRK09210 214 TINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGE----EDDSHLGDFIED 280 (367)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCC----CCcchhhhhccC
Confidence 9999999999994 78999999999999999999999999988889999998742 223467777765
No 10
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=99.97 E-value=2.1e-30 Score=279.44 Aligned_cols=186 Identities=31% Similarity=0.579 Sum_probs=169.0
Q ss_pred hHHHHHHhhcCCCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHH
Q 014764 192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM 271 (419)
Q Consensus 192 ~l~~yl~~i~~~~lLt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe 271 (419)
.+..||..+...+.|++++..+++++++.|+. ....|+++||.
T Consensus 345 ~lq~~L~~ie~~~~Ls~eElk~l~~~i~~g~~-------------------------------------~~~~a~~~Li~ 387 (619)
T PRK05658 345 KLQQELEAIEEETGLTIEELKEINRQISKGEA-------------------------------------KARRAKKEMVE 387 (619)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHHHHhccch-------------------------------------hhhHHHHHHHH
Confidence 55678888888888999999899999998875 12268999999
Q ss_pred HhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccchHHHHH
Q 014764 272 SNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG 351 (419)
Q Consensus 272 ~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~l~e~~~ 351 (419)
.|++||+++|++|.++|.+++||+|||+|||++|+++|||.+|++|+|||+|||++.|.++|+++.+.+++|.++.+..+
T Consensus 388 ~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA~~wIr~aI~~~i~~~~r~irip~~~~~~~~ 467 (619)
T PRK05658 388 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 467 (619)
T ss_pred HHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCchHHHhHHHHHHHHHHHHHHcCCceecCHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHH-HhcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCCCCCCCCcccccCCC
Q 014764 352 LIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSVIHC 418 (419)
Q Consensus 352 ~I~~a~~~L-~e~gRepS~eEIAe~LGIS~etVr~~l~rark~lSLD~~~~~~~d~~~~~tl~d~IaD 418 (419)
++.++...+ ..+|++||.+|||+.||+|+++|+.++..+..++|||.+++++ ++.+++|+|+|
T Consensus 468 k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~Sld~~i~~~----~~~~l~d~i~d 531 (619)
T PRK05658 468 KLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDD----EDSHLGDFIED 531 (619)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCcCCCCCCCC----CCCchhhhcCC
Confidence 999999998 4789999999999999999999999999998999999987432 23478888876
No 11
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=99.97 E-value=5.5e-29 Score=245.90 Aligned_cols=186 Identities=22% Similarity=0.317 Sum_probs=157.0
Q ss_pred hhHHHHHHhhcCCCCCCHHHHHHHHHHH-HccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHH
Q 014764 191 NRLKGYVKGVVSEELLTHAEVVRLSKKI-KTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKL 269 (419)
Q Consensus 191 ~~l~~yl~~i~~~~lLt~~eE~eL~rki-k~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~L 269 (419)
+.+..||+++...|+||++++.+|++++ ..||. .|++.|
T Consensus 6 ~~~~~y~~~~~~~~~l~~~~e~~L~~~~~~~gd~----------------------------------------~A~~~L 45 (289)
T PRK07500 6 SADRSMIRSAMKAPYLEREEEHALAYRWKDHRDE----------------------------------------DALHRI 45 (289)
T ss_pred hHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCCCH----------------------------------------HHHHHH
Confidence 5677899999999999999999999997 47887 899999
Q ss_pred HHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccchHH-
Q 014764 270 VMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHE- 348 (419)
Q Consensus 270 Ie~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~l~e- 348 (419)
|..|.++|+++|++|.+++.+++||+||||+|||+++++||+.+|.+|+||++|||++.|.++|++..+.+++|.+...
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 9999999999999999999999999999999999999999999999999999999999999999998888899987654
Q ss_pred -HHHHHHHHHHHHH----hcCCCccHHHHHHHcCCCHHHHHHHHHH-hCcccccccccCCCCCCCCCCcccccCCC
Q 014764 349 -RLGLIRNAKLRLE----EKGVTPSVDRIAEYLNMSQKKVRNATEA-IGKVFSLDREAFPSLNGLPGETHHSVIHC 418 (419)
Q Consensus 349 -~~~~I~~a~~~L~----e~gRepS~eEIAe~LGIS~etVr~~l~r-ark~lSLD~~~~~~~d~~~~~tl~d~IaD 418 (419)
...++.+....+. .+++.||.+|||+.||+++++|..++.. ....+|||.+..++ ++...++.|.|+|
T Consensus 126 ~~~~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~--~~~~~~l~d~i~d 199 (289)
T PRK07500 126 ALFFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEE--DEGRSERMDFLVD 199 (289)
T ss_pred HHHHHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCCC--CCCcccHHHhccC
Confidence 2234444444442 4689999999999999999999887644 34789999887432 2222356676655
No 12
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=99.96 E-value=1.7e-28 Score=241.79 Aligned_cols=189 Identities=28% Similarity=0.433 Sum_probs=158.8
Q ss_pred cchhHhhhhHHHHHHhhcCCCCCCHHHHHHHHHHH-HccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHH
Q 014764 184 ISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKI-KTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMEC 262 (419)
Q Consensus 184 ~~~e~~~~~l~~yl~~i~~~~lLt~~eE~eL~rki-k~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~ 262 (419)
.+|+ +.+..|++++.+.|+++++++.+|+.++ +.||.
T Consensus 10 ~~~~---~~~~~y~~~~~~~~~l~~~~e~~l~~~~~~~Gd~--------------------------------------- 47 (284)
T PRK06596 10 LSPE---GNLDAYIQAVNKIPMLTAEEEYMLAKRLREHGDL--------------------------------------- 47 (284)
T ss_pred CCCc---cHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCCH---------------------------------------
Confidence 4565 5788999999999999999999999994 68887
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccC
Q 014764 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (419)
Q Consensus 263 ~~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~iri 342 (419)
.|++.||..|+++|+++|++|.+++.+.+||+|||++||++|+++|||++|++|+||++|||++.|.+++++..+.+++
T Consensus 48 -~a~~~Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~~~l~~~~~~vr~ 126 (284)
T PRK06596 48 -EAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKV 126 (284)
T ss_pred -HHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHcCCeeec
Confidence 8999999999999999999999999999999999999999999999999999999999999999999999998767888
Q ss_pred ccchHH--HHHHHHHHHHHHHhcCCCccHHHHHHHcCCCHHHHHHHHHHhC-cccccccccCCCCCCCCCCcccccCCC
Q 014764 343 PNHLHE--RLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG-KVFSLDREAFPSLNGLPGETHHSVIHC 418 (419)
Q Consensus 343 p~~l~e--~~~~I~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~~l~rar-k~lSLD~~~~~~~d~~~~~tl~d~IaD 418 (419)
|.+... ....+..+...+. .++.|+.+|||+.||+++++|.+++.... ..+|||.++.++ ++.+.++.|.|+|
T Consensus 127 p~~~~~~~~~~~~~~~~~~l~-~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~--~~~~~~l~~~l~d 202 (284)
T PRK06596 127 ATTKAQRKLFFNLRKAKKRLG-WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDD--DEESGAPQDYLED 202 (284)
T ss_pred cchHHHHHHHHHHHHHHHHhc-cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCC--CCCcchHHHHcCC
Confidence 876542 2344555555553 45889999999999999999999876543 688999987432 1223456666655
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=99.96 E-value=6.9e-28 Score=235.34 Aligned_cols=169 Identities=30% Similarity=0.502 Sum_probs=146.0
Q ss_pred hHHHHHHhhcCCCCCCHHHHHHHHHH-HHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHH
Q 014764 192 RLKGYVKGVVSEELLTHAEVVRLSKK-IKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (419)
Q Consensus 192 ~l~~yl~~i~~~~lLt~~eE~eL~rk-ik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LI 270 (419)
.+..||+++..+|+|+++++.+|+.+ .+.||. .|++.||
T Consensus 2 ~~~~yl~~~~~~~~l~~~~e~~l~~~~~~~gd~----------------------------------------~a~~~Lv 41 (270)
T TIGR02392 2 SLDAYIRAVNRIPMLTPEEEYQLAKRLREHGDL----------------------------------------DAAKKLV 41 (270)
T ss_pred hHHHHHHHHhcCCCCCHHHHHHHHHHHHHCCCH----------------------------------------HHHHHHH
Confidence 46789999999999999999999998 568887 8999999
Q ss_pred HHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccchH--H
Q 014764 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLH--E 348 (419)
Q Consensus 271 e~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~l~--e 348 (419)
+.|+++|+++|++|.+++.+++||+|||++||++|+++|||++|++|+|||.|||++.|.+++++..+.+++|.... +
T Consensus 42 ~~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA~~~Ir~~i~~~l~~~~~~ir~p~~~~~~~ 121 (270)
T TIGR02392 42 LSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRK 121 (270)
T ss_pred HHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhhHHHHHHHHHHHHHHcCCceecCchHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999998876678886543 3
Q ss_pred HHHHHHHHHHHHHhcCCCc-cHHHHHHHcCCCHHHHHHHHHHhC-cccccccccC
Q 014764 349 RLGLIRNAKLRLEEKGVTP-SVDRIAEYLNMSQKKVRNATEAIG-KVFSLDREAF 401 (419)
Q Consensus 349 ~~~~I~~a~~~L~e~gRep-S~eEIAe~LGIS~etVr~~l~rar-k~lSLD~~~~ 401 (419)
....+..+...+. ..+.| +.+|||+.||+++++|.+++.... ..+|||.++.
T Consensus 122 ~~~~~~~~~~~~~-~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~ 175 (270)
T TIGR02392 122 LFFNLRKMKKRLQ-GWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASID 175 (270)
T ss_pred HHHHHHHHHHHHh-cCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCC
Confidence 3445555555553 12455 699999999999999999876544 4789999874
No 14
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=99.96 E-value=8.1e-28 Score=241.40 Aligned_cols=187 Identities=34% Similarity=0.558 Sum_probs=168.8
Q ss_pred HhhhhHHHHHHhhcCCCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHH
Q 014764 188 LIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLARE 267 (419)
Q Consensus 188 ~~~~~l~~yl~~i~~~~lLt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e 267 (419)
.+.+.+++|+++|...|+||++++..|+++++.||. .||+
T Consensus 50 ~~~~~~~~y~~~~~~~~~l~~~ee~~li~~~~~Gd~----------------------------------------~A~~ 89 (325)
T PRK05657 50 RVLDATQLYLNEIGYSPLLTAEEEVYFARRALRGDF----------------------------------------AARQ 89 (325)
T ss_pred ccccHHHHHHHHHhcCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHH
Confidence 344789999999999999999999999999999998 8999
Q ss_pred HHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccchH
Q 014764 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLH 347 (419)
Q Consensus 268 ~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~l~ 347 (419)
.||.+|.++|+++|++|++++.+++||+||||+|+|+++++||+.+|++|+||++||||..|.++++++.+.+++|.++.
T Consensus 90 ~Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~~i~~~~r~ir~p~~~~ 169 (325)
T PRK05657 90 RMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVV 169 (325)
T ss_pred HHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHcCCccccCHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999988
Q ss_pred HHHHHHHHHHHHHH-hcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCCCCCCCCcccccCCC
Q 014764 348 ERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSVIHC 418 (419)
Q Consensus 348 e~~~~I~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~~l~rark~lSLD~~~~~~~d~~~~~tl~d~IaD 418 (419)
..++.+.++...|. ..++.|+.+|||+.||++++.|+.++......+|||++.. .++..++.|.|+|
T Consensus 170 ~~l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~~----~~~~~~l~d~l~d 237 (325)
T PRK05657 170 KELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLG----GDPEKSLLDILAD 237 (325)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCCC----CCCCcchhhhccC
Confidence 88887888888885 5789999999999999999999999987777889998762 3333455555543
No 15
>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=99.95 E-value=2.7e-27 Score=228.93 Aligned_cols=175 Identities=31% Similarity=0.374 Sum_probs=156.7
Q ss_pred cCCCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHHHhHHHHHHH
Q 014764 201 VSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSI 280 (419)
Q Consensus 201 ~~~~lLt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~yl~LV~sI 280 (419)
.++|+|+++++.+|+.+++.||. .|++.|+..|.++|+++
T Consensus 11 ~~~~~l~~~~~~~li~~~~~gd~----------------------------------------~a~~~L~~~~~~~v~~~ 50 (254)
T TIGR02850 11 SKLPVLKNQEMRELFIRMQSGDT----------------------------------------TAREKLINGNLRLVLSV 50 (254)
T ss_pred cCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhHHHHHHH
Confidence 47799999999999999999987 89999999999999999
Q ss_pred HHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccchHHHHHHHHHHHHHH
Q 014764 281 AQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRL 360 (419)
Q Consensus 281 Akry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~l~e~~~~I~~a~~~L 360 (419)
|++|.+++.+++||+||||+|||+++++||+.+|.+|+||+++||+|.|.+++++.. .+++|.+..+...++.++...+
T Consensus 51 a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~~lr~~~-~ir~p~~~~~~~~~~~~~~~~l 129 (254)
T TIGR02850 51 IQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRDKL 129 (254)
T ss_pred HHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CccCchHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999889999999999999999999865 7899999999999999998888
Q ss_pred H-hcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCCCCCCCCcccccCCC
Q 014764 361 E-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSVIHC 418 (419)
Q Consensus 361 ~-e~gRepS~eEIAe~LGIS~etVr~~l~rark~lSLD~~~~~~~d~~~~~tl~d~IaD 418 (419)
. ++|+.||.+|||+.||+++++|..++......+|||+++..++ ....++.|.++|
T Consensus 130 ~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~~--~~~~~~~~~~~d 186 (254)
T TIGR02850 130 ISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDG--GDPIYVMDQISD 186 (254)
T ss_pred HHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCCC--CCcchhhhhcCC
Confidence 4 6899999999999999999999999998888899998774322 222345565554
No 16
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=99.95 E-value=2e-27 Score=231.95 Aligned_cols=138 Identities=26% Similarity=0.371 Sum_probs=130.9
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCc
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip 343 (419)
.++++||..|++||.++|++|.+++.+.+||+|||+|||++|+++|||++|++|+||++|||++.|.+++++..+.+++|
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 cchHHHHHHHHHHHHHHH-hcCCCccHHHHHHHcCCCHHHHHHHHHH--hCcccccccccC
Q 014764 344 NHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEA--IGKVFSLDREAF 401 (419)
Q Consensus 344 ~~l~e~~~~I~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~~l~r--ark~lSLD~~~~ 401 (419)
.++.+...++.++...|. .+|+.||.+|||+.||+++++|.+++.. ..+.+|||.+..
T Consensus 120 r~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~ 180 (264)
T PRK07122 120 RRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGG 180 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCccccccc
Confidence 999999999999999995 6899999999999999999999998865 347899999874
No 17
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=99.95 E-value=1.1e-26 Score=225.43 Aligned_cols=153 Identities=29% Similarity=0.400 Sum_probs=134.9
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCC-CCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccC
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNM-GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~-g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~iri 342 (419)
.|+++||..|+++|+++|++|.+. +.+++||+|||+||||+|+++|||++|++|+||+++||+|.|.+++++..+.+++
T Consensus 25 ~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~~~vr~ 104 (256)
T PRK07408 25 ALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTVRI 104 (256)
T ss_pred HHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHHcCCeeee
Confidence 799999999999999999999865 6679999999999999999999999999999999999999999999999999999
Q ss_pred ccchHHHHHHHHHHHHHHH-hcCCCccHHHHHHHcCCCHHHHHHHHHH--hCcccccccccCCCCCCCCCCcccccCCC
Q 014764 343 PNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEA--IGKVFSLDREAFPSLNGLPGETHHSVIHC 418 (419)
Q Consensus 343 p~~l~e~~~~I~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~~l~r--ark~lSLD~~~~~~~d~~~~~tl~d~IaD 418 (419)
|.++.+..+++.++...|. .+|+.||.+|||+.||+++++|..++.. ....+|||.++..+++ ...++.+.++|
T Consensus 105 pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~~~~--~~~~l~d~~~d 181 (256)
T PRK07408 105 PRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQDED--GSTSLGDLLPD 181 (256)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCCCCC--CccccccccCC
Confidence 9999999999999999995 6899999999999999999999998753 3468899998743222 22355555544
No 18
>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=99.95 E-value=3.5e-27 Score=225.94 Aligned_cols=150 Identities=39% Similarity=0.650 Sum_probs=136.4
Q ss_pred HHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCcc
Q 014764 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPN 344 (419)
Q Consensus 265 A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~ 344 (419)
|+++||..|+++|+++|++|.+++.+.+||+|||++||++|+++|||.+|++|+||++|||++.|.++++++.+.+++|.
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 chHHHHHHHHHHHHHHH-hcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCCCCCCCCcccccCCC
Q 014764 345 HLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSVIHC 418 (419)
Q Consensus 345 ~l~e~~~~I~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~~l~rark~lSLD~~~~~~~d~~~~~tl~d~IaD 418 (419)
++.+..+++.++...|. ..|+.||.+|||+.||++.++|.+++......+|||+++..+ +..++.|.|+|
T Consensus 81 ~~~~~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~----~~~~l~d~l~d 151 (238)
T TIGR02393 81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEE----EDSFLGDFIED 151 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCCCCC----CcccHHHHhcC
Confidence 99999999999999995 689999999999999999999999988887899999987432 22255555543
No 19
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=99.94 E-value=4.2e-26 Score=220.93 Aligned_cols=175 Identities=31% Similarity=0.407 Sum_probs=155.2
Q ss_pred cCCCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHHHhHHHHHHH
Q 014764 201 VSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSI 280 (419)
Q Consensus 201 ~~~~lLt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~yl~LV~sI 280 (419)
..+|+|+++++..|+.+++.||. .|++.||..|.++|+++
T Consensus 14 ~~~~~l~~~~~~~l~~~~~~gd~----------------------------------------~a~~~l~~~~~~~v~~~ 53 (258)
T PRK08215 14 SKLPVLKNEEMRELFERMQNGDK----------------------------------------EAREKLINGNLRLVLSV 53 (258)
T ss_pred CCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHH
Confidence 45689999999999999999987 89999999999999999
Q ss_pred HHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccchHHHHHHHHHHHHHH
Q 014764 281 AQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRL 360 (419)
Q Consensus 281 Akry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~l~e~~~~I~~a~~~L 360 (419)
|++|.+++.+++||+||||+|||+++++||+.+|.+|+||+++||+|.|.+++++.. .+++|.+......++.++...+
T Consensus 54 a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~~~lr~~~-~vrip~~~~~~~~~~~~~~~~l 132 (258)
T PRK08215 54 IQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVREKL 132 (258)
T ss_pred HHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-ceEecHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999885 7799999999888898888888
Q ss_pred H-hcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCCCCCCCCcccccCCC
Q 014764 361 E-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSVIHC 418 (419)
Q Consensus 361 ~-e~gRepS~eEIAe~LGIS~etVr~~l~rark~lSLD~~~~~~~d~~~~~tl~d~IaD 418 (419)
. ..++.|+..|||+.||+++++|...+......+|||++..++ +....++.|.++|
T Consensus 133 ~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~--~~~~~~~~~~~~~ 189 (258)
T PRK08215 133 INENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHD--GGDPIYVMDQISD 189 (258)
T ss_pred HHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCC--CCcchhhhhhccC
Confidence 4 689999999999999999999999988877888999887532 2222345555543
No 20
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=99.93 E-value=4.3e-25 Score=217.10 Aligned_cols=173 Identities=36% Similarity=0.595 Sum_probs=162.2
Q ss_pred HhhhhHHHHHHhhcCCCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHH
Q 014764 188 LIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLARE 267 (419)
Q Consensus 188 ~~~~~l~~yl~~i~~~~lLt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e 267 (419)
...+.+++||++|..+|.|+.+++.+|+.++++|+. .|++
T Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~gd~----------------------------------------~a~~ 49 (285)
T TIGR02394 10 RVADVTQLYLREIGFKPLLTAEEEIAYARRALAGDF----------------------------------------EARK 49 (285)
T ss_pred CcchHHHHHHHHHhccCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHH
Confidence 456899999999999999999999999999999998 8999
Q ss_pred HHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccchH
Q 014764 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLH 347 (419)
Q Consensus 268 ~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~l~ 347 (419)
.||.+|.++|+++|.+|.+++.+++||+||||+|||+++++||+.+|++|+||+.|+++..+.+++++..+.+++|..+.
T Consensus 50 ~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ain~~i~~~~~~~~~p~~~~ 129 (285)
T TIGR02394 50 VMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHVI 129 (285)
T ss_pred HHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHHHHHHHHcCCceeCcHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHH-hcCCCccHHHHHHHcCCCHHHHHHHHHHhCccccccccc
Q 014764 348 ERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREA 400 (419)
Q Consensus 348 e~~~~I~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~~l~rark~lSLD~~~ 400 (419)
...+.+.+....+. ..++.++..|+|+.||+++..|..++..+.+.+|||.+.
T Consensus 130 ~~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~ 183 (285)
T TIGR02394 130 KELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPL 183 (285)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCC
Confidence 88888887777664 468999999999999999999999998888889999765
No 21
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=99.93 E-value=1.3e-24 Score=210.70 Aligned_cols=156 Identities=35% Similarity=0.507 Sum_probs=144.7
Q ss_pred CCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHHHhHHHHHHHHHH
Q 014764 204 ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQR 283 (419)
Q Consensus 204 ~lLt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~yl~LV~sIAkr 283 (419)
+.++..+...++...+.|+. .++ .||++|+|||.++|++
T Consensus 4 ~~~~~~e~~~~~~~~~~g~~----------------------------------------~~~-~Li~~ylpLV~~ia~k 42 (247)
T COG1191 4 QPLSKEEEEKLLEYYAEGDE----------------------------------------EAR-RLIERYLPLVKSIARK 42 (247)
T ss_pred cccchHHHHHHHHHHHhcCH----------------------------------------HHH-HHHHHHHHHHHHHHHH
Confidence 45667777788888888887 788 9999999999999999
Q ss_pred ccCCCC-ChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccchHHHHHHHHHHHHHHH-
Q 014764 284 YDNMGA-DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE- 361 (419)
Q Consensus 284 y~~~g~-d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~l~e~~~~I~~a~~~L~- 361 (419)
|.+++. +.|||+|.|+|||++|+++|||++|.+|+|||.++|++.|++++|+.. .+++|+.+++..+++..+...|.
T Consensus 43 ~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d~LR~~~-~v~vpR~~~~~~~~i~~~~~~l~~ 121 (247)
T COG1191 43 FENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILDYLRKND-SVKVPRSLRELGRRIEEAIDELEQ 121 (247)
T ss_pred HHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHHHHHhCC-CccCcHHHHHHHHHHHHHHHHHHH
Confidence 998776 999999999999999999999999999999999999999999999998 89999999999999999999995
Q ss_pred hcCCCccHHHHHHHcCCCHHHHHHHHHHhC--cccccccccC
Q 014764 362 EKGVTPSVDRIAEYLNMSQKKVRNATEAIG--KVFSLDREAF 401 (419)
Q Consensus 362 e~gRepS~eEIAe~LGIS~etVr~~l~rar--k~lSLD~~~~ 401 (419)
++||+||..|||+.|||+.+.|...+.... ..+|+|+...
T Consensus 122 el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~ 163 (247)
T COG1191 122 ELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVL 163 (247)
T ss_pred HhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhc
Confidence 789999999999999999999999998875 7889997664
No 22
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=99.92 E-value=4.7e-24 Score=207.29 Aligned_cols=152 Identities=24% Similarity=0.352 Sum_probs=131.3
Q ss_pred HHHHHHHHHhHHHHHHHHHHccC---CCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccc
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~---~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~i 340 (419)
.|++.||..|+|+|+.+|++|.. .+.+.+||+|||+||||+|+++|||++|++|+||+.+||++.|.+++|+..
T Consensus 23 ~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~--- 99 (257)
T PRK05911 23 EYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQD--- 99 (257)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcC---
Confidence 79999999999999999999852 356899999999999999999999999999999999999999999999875
Q ss_pred cCccchHHHHHHHHHHHHHHH-hcCCCccHHHHHHHcCCCHHHHHHHHHHhC--cccccccccCCCCCCCCCCcccccCC
Q 014764 341 RLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIG--KVFSLDREAFPSLNGLPGETHHSVIH 417 (419)
Q Consensus 341 rip~~l~e~~~~I~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~~l~rar--k~lSLD~~~~~~~d~~~~~tl~d~Ia 417 (419)
++|+++.+..+++..+...|. .+|+.|+.+|||+.||+++++|..++..+. ..+|||++.....+++.+.++.|.++
T Consensus 100 ~~pr~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~Sld~~~~~~~~~~~~~~l~~~l~ 179 (257)
T PRK05911 100 WVPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPCQSDDEAGLALEERIA 179 (257)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHHhhccceeeccccCCCCCCCccccchhhhcc
Confidence 489999999999999999985 689999999999999999999999987664 46899987643233333445666665
Q ss_pred C
Q 014764 418 C 418 (419)
Q Consensus 418 D 418 (419)
|
T Consensus 180 d 180 (257)
T PRK05911 180 D 180 (257)
T ss_pred C
Confidence 4
No 23
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=99.92 E-value=3e-24 Score=204.03 Aligned_cols=152 Identities=33% Similarity=0.377 Sum_probs=135.4
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCc
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip 343 (419)
.|++.|+..|.++|+++|.+|.+++.+++||+||||+|||+++++||+.+|.+|.||+++||+|.|.+++++.. .+++|
T Consensus 11 ~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~lr~~~-~i~~p 89 (231)
T TIGR02885 11 EARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDDG-IIKVS 89 (231)
T ss_pred HHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-CeECC
Confidence 79999999999999999999999999999999999999999999999998889999999999999999999886 78999
Q ss_pred cchHHHHHHHHHHHHHHH-hcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCCCCCCCCcccccCCC
Q 014764 344 NHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSVIHC 418 (419)
Q Consensus 344 ~~l~e~~~~I~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~~l~rark~lSLD~~~~~~~d~~~~~tl~d~IaD 418 (419)
+++.....++.++...|. ++|+.||.+|||+.||++.++|..++..+....|||.++..+ +....+++|.++|
T Consensus 90 ~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~--~~~~~~~~d~~~~ 163 (231)
T TIGR02885 90 RSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQD--DGDPIYLLDQIAD 163 (231)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCC--CCCcchhhhhcCC
Confidence 999999999999999885 679999999999999999999999988888889999877432 1122345555543
No 24
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=99.91 E-value=2e-23 Score=201.55 Aligned_cols=160 Identities=28% Similarity=0.334 Sum_probs=147.4
Q ss_pred CCCCHHHHHHHHHHHHc-cCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHHHhHHHHHHHHH
Q 014764 204 ELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQ 282 (419)
Q Consensus 204 ~lLt~~eE~eL~rkik~-Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~yl~LV~sIAk 282 (419)
|.|++.++.+|+.+++. ||. .||++||..|.++|+.+|+
T Consensus 8 ~~l~~~~~~~li~~~~~~gd~----------------------------------------~a~~~l~~~y~~~v~~~a~ 47 (255)
T TIGR02941 8 TNLTKEDVIQWIAEFQQNQNG----------------------------------------EAQEKLVDHYQNLVYSIAY 47 (255)
T ss_pred CCCCHHHHHHHHHHHHHCCCH----------------------------------------HHHHHHHHHhHHHHHHHHH
Confidence 66999999999999988 576 8999999999999999999
Q ss_pred HccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccchHHHHHHHHHHHHHHH-
Q 014764 283 RYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE- 361 (419)
Q Consensus 283 ry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~l~e~~~~I~~a~~~L~- 361 (419)
+|.+++.+++||+||||++||+++++|++..|.+|.||+++||+|.|.+++++..+.+++|..+.+...++..+...+.
T Consensus 48 ~~~~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~iri~~~~~~~~~~~~~~~~~l~~ 127 (255)
T TIGR02941 48 KYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAIDELTD 127 (255)
T ss_pred HHhcCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999998889999999999999999999998888999999999999999999995
Q ss_pred hcCCCccHHHHHHHcCCCHHHHHHHHHHhC--cccccccccCCC
Q 014764 362 EKGVTPSVDRIAEYLNMSQKKVRNATEAIG--KVFSLDREAFPS 403 (419)
Q Consensus 362 e~gRepS~eEIAe~LGIS~etVr~~l~rar--k~lSLD~~~~~~ 403 (419)
.+|+.|+.+|||+.||++.+.+..++.... ..+|||.++..+
T Consensus 128 ~~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~ 171 (255)
T TIGR02941 128 HLQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEAD 171 (255)
T ss_pred HhCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCC
Confidence 579999999999999999999999877653 578999887543
No 25
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=99.91 E-value=2.9e-23 Score=202.30 Aligned_cols=173 Identities=25% Similarity=0.317 Sum_probs=147.7
Q ss_pred cCCCCCCHHHHHHHHHHHHc-cCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHHHhHHHHHH
Q 014764 201 VSEELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMS 279 (419)
Q Consensus 201 ~~~~lLt~~eE~eL~rkik~-Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~yl~LV~s 279 (419)
+.+|+||++++.+|+++++. ||. .|++.|+..|.++|+.
T Consensus 7 ~~~~~~~~~~e~~l~~~~~~~~d~----------------------------------------~a~~~l~~~y~~lv~~ 46 (268)
T PRK06288 7 GKIPKYAQQDETELWREYKKTGDP----------------------------------------KIREYLILKYSPLVKY 46 (268)
T ss_pred CCCccccchHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHH
Confidence 57899999999999999764 565 7999999999999999
Q ss_pred HHHHcc-C--CCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccchHHHHHHHHHH
Q 014764 280 IAQRYD-N--MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNA 356 (419)
Q Consensus 280 IAkry~-~--~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~l~e~~~~I~~a 356 (419)
+|++|. + .+.+++||+||||+|||+++++||+.+|.+|+||+++||+|.|.+++|+.. ++|.++......+.++
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 567899999999999999999999998889999999999999999998653 6899998888899999
Q ss_pred HHHHH-hcCCCccHHHHHHHcCCCHHHHHHHHHHh--CcccccccccCCCCCCCCCCcccccCC
Q 014764 357 KLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAI--GKVFSLDREAFPSLNGLPGETHHSVIH 417 (419)
Q Consensus 357 ~~~L~-e~gRepS~eEIAe~LGIS~etVr~~l~ra--rk~lSLD~~~~~~~d~~~~~tl~d~Ia 417 (419)
...|. .+++.||.+|||+.||++.+.|.+++... ...+|||+....+ ++.+..++.+.++
T Consensus 124 ~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~~~-~~~~~~~l~~~~~ 186 (268)
T PRK06288 124 IAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGG-DEGDEVSLMDTLE 186 (268)
T ss_pred HHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhccC-CCcccchhhhhcc
Confidence 99995 68999999999999999999999998765 3678999876422 2223345555554
No 26
>PRK05572 sporulation sigma factor SigF; Validated
Probab=99.91 E-value=5.3e-23 Score=198.63 Aligned_cols=164 Identities=36% Similarity=0.456 Sum_probs=150.7
Q ss_pred HHhhcCCCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHHHhHHH
Q 014764 197 VKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRL 276 (419)
Q Consensus 197 l~~i~~~~lLt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~yl~L 276 (419)
++.-...|.|+++++.+|+.+++.|+. .|++.||..|.++
T Consensus 5 ~~~~~~~~~l~~~~~~~li~~~~~gd~----------------------------------------~a~~~L~~~y~~~ 44 (252)
T PRK05572 5 VKNKKKKPQLKDEENKELIKKSQDGDQ----------------------------------------EARDTLVEKNLRL 44 (252)
T ss_pred hccCcCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhHHH
Confidence 344567899999999999999999987 8999999999999
Q ss_pred HHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccchHHHHHHHHHH
Q 014764 277 VMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNA 356 (419)
Q Consensus 277 V~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~l~e~~~~I~~a 356 (419)
|+++|.+|.+++.+++||+||||+++|+++++|++.++.+|.||+++||+|.|.+++++.. .+++|..+.....++.++
T Consensus 45 v~~~a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~~lr~~~-~~r~~~~~~~~~~~~~~~ 123 (252)
T PRK05572 45 VWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANKIRKD 123 (252)
T ss_pred HHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CCCCCHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999988889999999999999999999875 779999999999999999
Q ss_pred HHHHH-hcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccC
Q 014764 357 KLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAF 401 (419)
Q Consensus 357 ~~~L~-e~gRepS~eEIAe~LGIS~etVr~~l~rark~lSLD~~~~ 401 (419)
...+. +.++.|+..|||+.||++++.|..++.......||+.++.
T Consensus 124 ~~~l~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~ 169 (252)
T PRK05572 124 KDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVH 169 (252)
T ss_pred HHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCcc
Confidence 98884 5799999999999999999999998887778889998764
No 27
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=99.91 E-value=3.4e-23 Score=196.08 Aligned_cols=139 Identities=39% Similarity=0.485 Sum_probs=130.2
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccC
Q 014764 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (419)
Q Consensus 263 ~~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~iri 342 (419)
..|++.|+..|.++|+++|++|.+++.++|||+|||++|||+++++||+.+|.+|+||+++||+|.|.++++++.+.+++
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 36999999999999999999999999999999999999999999999999999999999999999999999999888999
Q ss_pred ccchHHHHHHHHHHHHHHH-hcCCCccHHHHHHHcCCCHHHHHHHHHHhCc--ccccccccC
Q 014764 343 PNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGK--VFSLDREAF 401 (419)
Q Consensus 343 p~~l~e~~~~I~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~~l~rark--~lSLD~~~~ 401 (419)
|.++.+...++.++...+. ..++.|+.+|+|+.||+++++|.+++..... .+|||+++.
T Consensus 82 ~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~ 143 (227)
T TIGR02980 82 PRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIE 143 (227)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCC
Confidence 9999999999999999984 6799999999999999999999998887664 889998774
No 28
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=99.89 E-value=3.7e-22 Score=192.91 Aligned_cols=160 Identities=28% Similarity=0.336 Sum_probs=146.1
Q ss_pred CCCCHHHHHHHHHHHHc-cCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHHHhHHHHHHHHH
Q 014764 204 ELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQ 282 (419)
Q Consensus 204 ~lLt~~eE~eL~rkik~-Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~yl~LV~sIAk 282 (419)
|.|+++++.+|+.+++. ||. .|++.||..|.++|+++|+
T Consensus 8 ~~l~~~e~~~li~~~~~~gd~----------------------------------------~a~~~l~~~~~~~v~~~a~ 47 (257)
T PRK08583 8 TKLTKEEVNKWIAEYQENQDE----------------------------------------EAQEKLVKHYKNLVESLAY 47 (257)
T ss_pred CcCChHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHHHH
Confidence 67999999999999885 787 8999999999999999999
Q ss_pred HccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccchHHHHHHHHHHHHHHH-
Q 014764 283 RYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE- 361 (419)
Q Consensus 283 ry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~l~e~~~~I~~a~~~L~- 361 (419)
+|.+++.+++||+||||++||+++++||+..|.+|.||+++||+|.|.+++++....+++|.++.+..+++..+...+.
T Consensus 48 ~~~~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~~~i~r~~~~~~~~~~~~~~~~~~ 127 (257)
T PRK08583 48 KYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELTT 127 (257)
T ss_pred HHhcCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHHHHHHHhcCCCcCCCHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999988889999999999999999999998889999999999999999988885
Q ss_pred hcCCCccHHHHHHHcCCCHHHHHHHHHHh--CcccccccccCCC
Q 014764 362 EKGVTPSVDRIAEYLNMSQKKVRNATEAI--GKVFSLDREAFPS 403 (419)
Q Consensus 362 e~gRepS~eEIAe~LGIS~etVr~~l~ra--rk~lSLD~~~~~~ 403 (419)
..++.|+.+|+|+.+|++.+.|..++... ...+|+|.++.++
T Consensus 128 ~~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~ 171 (257)
T PRK08583 128 ELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEAD 171 (257)
T ss_pred HhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCC
Confidence 57899999999999999999998887654 3578999887543
No 29
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=99.88 E-value=1.3e-21 Score=188.89 Aligned_cols=135 Identities=25% Similarity=0.366 Sum_probs=123.3
Q ss_pred HHHHHHHHHhHHHHHHHHHHccC---CCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccc
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~---~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~i 340 (419)
.||+.||+.|.++|+++|.+|.+ ++.+++||+||||+|||+++++||+.+|.+|+||+++||+|.|.+++|++.
T Consensus 22 ~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~d~lR~~~--- 98 (251)
T PRK07670 22 DAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKED--- 98 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC---
Confidence 89999999999999999999965 678999999999999999999999999889999999999999999999865
Q ss_pred cCccchHHHHHHHHHHHHHHH-hcCCCccHHHHHHHcCCCHHHHHHHHHHh--CcccccccccC
Q 014764 341 RLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAI--GKVFSLDREAF 401 (419)
Q Consensus 341 rip~~l~e~~~~I~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~~l~ra--rk~lSLD~~~~ 401 (419)
++|....+....++.+...+. ..|+.|+..|||+.||+++++|+.++... ...+|||++..
T Consensus 99 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~ 162 (251)
T PRK07670 99 WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTH 162 (251)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCcccc
Confidence 588888888888988888885 67999999999999999999999998643 47889998764
No 30
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=99.86 E-value=4.4e-21 Score=183.11 Aligned_cols=163 Identities=28% Similarity=0.375 Sum_probs=136.1
Q ss_pred hHHHHHHhhcCCCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHH
Q 014764 192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM 271 (419)
Q Consensus 192 ~l~~yl~~i~~~~lLt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe 271 (419)
++..|+.++...|+|++.++..|+..++.|+. .|++.|+.
T Consensus 17 ~~~~~~~~~~~~~~~~~~~e~~l~~~~~~gd~----------------------------------------~a~~~l~~ 56 (233)
T PRK05803 17 FLVSYVKNNSFPQPLSEEEERKYLELMKEGDE----------------------------------------EARNILIE 56 (233)
T ss_pred HHHHHHHHhcccCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHH
Confidence 68899999999999999999999999999987 89999999
Q ss_pred HhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhccccc-C--------
Q 014764 272 SNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR-L-------- 342 (419)
Q Consensus 272 ~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~ir-i-------- 342 (419)
.|.++|+++|.+|.+++.+++|++||+|+++|+++.+|+++++.+|.||+++|++|.+++++|+..+..+ .
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 9999999999999999999999999999999999999999888899999999999999999987653211 0
Q ss_pred -------------cc---ch------HHHHHHHHHHHHHHHh---------c----CCCccHHHHHHHcCCCHHHHHHHH
Q 014764 343 -------------PN---HL------HERLGLIRNAKLRLEE---------K----GVTPSVDRIAEYLNMSQKKVRNAT 387 (419)
Q Consensus 343 -------------p~---~l------~e~~~~I~~a~~~L~e---------~----gRepS~eEIAe~LGIS~etVr~~l 387 (419)
+. .. .+....+..++..|++ . ..+.|++|||+.||+|.++|++++
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 00 00 0112346666666643 1 245699999999999999999999
Q ss_pred HHhCccc
Q 014764 388 EAIGKVF 394 (419)
Q Consensus 388 ~rark~l 394 (419)
.++.+.+
T Consensus 217 ~rA~~kL 223 (233)
T PRK05803 217 KRALKKL 223 (233)
T ss_pred HHHHHHH
Confidence 8887644
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=99.85 E-value=1.5e-20 Score=178.07 Aligned_cols=129 Identities=33% Similarity=0.477 Sum_probs=117.1
Q ss_pred HHHHhHHHHHHHHHHccC---CCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccc
Q 014764 269 LVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH 345 (419)
Q Consensus 269 LIe~yl~LV~sIAkry~~---~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~ 345 (419)
|+..|.++|+++|.+|.+ ++.+++||+||||+|||+++++||+.+|.+|+||+++||+|.+.+++|+.. ++|..
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 688999999999999985 789999999999999999999999999999999999999999999998764 58888
Q ss_pred hHHHHHHHHHHHHHHH-hcCCCccHHHHHHHcCCCHHHHHHHHHHhC--ccccccccc
Q 014764 346 LHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIG--KVFSLDREA 400 (419)
Q Consensus 346 l~e~~~~I~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~~l~rar--k~lSLD~~~ 400 (419)
.....+++.++...|. .+|+.|+.+|||+.||++++.|..++..+. ..+|+|+..
T Consensus 78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~ 135 (224)
T TIGR02479 78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELL 135 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcc
Confidence 8889999999999995 679999999999999999999999987554 567888755
No 32
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=99.85 E-value=2.6e-20 Score=178.61 Aligned_cols=135 Identities=20% Similarity=0.272 Sum_probs=118.8
Q ss_pred HHHHHHHHHhHHHHHHHHHHccC---CCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccc
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~---~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~i 340 (419)
.-...|+..|+|+|..+|++|.. .+.+.+||+|||++|||+|+++||+..+ +|+||+++||+|.|.+++++..
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 34567899999999999999874 4679999999999999999999997666 8999999999999999999754
Q ss_pred cCccchHHHHHHHHHHHHHHH-hcCCCccHHHHHHHcCCCHHHHHHHHHH--hCcccccccccCC
Q 014764 341 RLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEA--IGKVFSLDREAFP 402 (419)
Q Consensus 341 rip~~l~e~~~~I~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~~l~r--ark~lSLD~~~~~ 402 (419)
+.|+.+....+++.++...|. .+|+.|+.+|||+.||++.++|.+++.. +...+|||++..+
T Consensus 91 ~~~r~vr~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~ 155 (231)
T PRK12427 91 WRPRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLAL 155 (231)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccC
Confidence 468888888899999999995 6799999999999999999999998764 3468899998743
No 33
>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=99.82 E-value=2.8e-19 Score=170.25 Aligned_cols=163 Identities=26% Similarity=0.372 Sum_probs=131.3
Q ss_pred hHHHHHHhhc-CCCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHH
Q 014764 192 RLKGYVKGVV-SEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (419)
Q Consensus 192 ~l~~yl~~i~-~~~lLt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LI 270 (419)
++-+|+-.-+ ..+.|++.++.+|+.+++.|+. .|++.|+
T Consensus 15 ~~~~~~~~~~~~~~~~~~~~~~~li~~~~~gd~----------------------------------------~af~~l~ 54 (227)
T TIGR02846 15 FLVGYVTNNGSFPQPLSEEEEKKYLDRLKEGDE----------------------------------------EARNVLI 54 (227)
T ss_pred HHHHHHHHHHhCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHH
Confidence 4556766554 4456999999999999999997 8999999
Q ss_pred HHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhccccc-C-------
Q 014764 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR-L------- 342 (419)
Q Consensus 271 e~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~ir-i------- 342 (419)
+.|.++|+++|.+|.++..++||++||+|+++|+++++|+++.+.+|.||++++++|.|++++|+..+... .
T Consensus 55 ~~y~~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~~d~~Rk~~r~~~~~~~~~~~~ 134 (227)
T TIGR02846 55 ERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEILMHLRALKKTKGEVSLQDPIG 134 (227)
T ss_pred HHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHHHHHHHHHhccccceecccccc
Confidence 99999999999999999999999999999999999999999887789999999999999999987654211 0
Q ss_pred --------------cc---c------hHHHHHHHHHHHHHHHhc---------C----CCccHHHHHHHcCCCHHHHHHH
Q 014764 343 --------------PN---H------LHERLGLIRNAKLRLEEK---------G----VTPSVDRIAEYLNMSQKKVRNA 386 (419)
Q Consensus 343 --------------p~---~------l~e~~~~I~~a~~~L~e~---------g----RepS~eEIAe~LGIS~etVr~~ 386 (419)
+. . ..+....+..++..|++. . .+.|++|||++||+|+++|+.+
T Consensus 135 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~ 214 (227)
T TIGR02846 135 VDKEGNEISLIDILGSDGDSVIEQVELNLEIKKLYKKLSVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRI 214 (227)
T ss_pred CCcccCcccHHHHhcCCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHH
Confidence 00 0 011123466666666431 1 4569999999999999999999
Q ss_pred HHHhCccc
Q 014764 387 TEAIGKVF 394 (419)
Q Consensus 387 l~rark~l 394 (419)
+.++++.+
T Consensus 215 ~~rAl~~L 222 (227)
T TIGR02846 215 EKRALMKL 222 (227)
T ss_pred HHHHHHHH
Confidence 99887543
No 34
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=99.81 E-value=3.4e-19 Score=170.28 Aligned_cols=137 Identities=28% Similarity=0.415 Sum_probs=120.7
Q ss_pred HHHHHHHHHHHHhHHHHHHHHHHcc---CCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhc
Q 014764 261 ECSLAREKLVMSNVRLVMSIAQRYD---NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENS 337 (419)
Q Consensus 261 ~~~~A~e~LIe~yl~LV~sIAkry~---~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~ 337 (419)
+|.-++++|+..|.++|+++|++|. +++.+++||+||||++||+++++||+..|.+|+||+++||+|.|.+++|++.
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 4556899999999999999999997 6789999999999999999999999998889999999999999999999875
Q ss_pred ccccCccchHHHHHHHHHHHHHHH-hcCCCccHHHHHHHcCCCHHHHHHHHHHh--Cccccccccc
Q 014764 338 RTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAI--GKVFSLDREA 400 (419)
Q Consensus 338 r~irip~~l~e~~~~I~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~~l~ra--rk~lSLD~~~ 400 (419)
++|..+......+.++...+. ..+++|+.+|||+.||++++.|..++... ...+|+|+..
T Consensus 85 ---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~ 147 (236)
T PRK06986 85 ---WVPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELR 147 (236)
T ss_pred ---CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccc
Confidence 367777777777888877774 57999999999999999999999988764 3567888765
No 35
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=99.81 E-value=3.1e-19 Score=169.96 Aligned_cols=160 Identities=26% Similarity=0.428 Sum_probs=129.6
Q ss_pred HHHHhhcCC-CCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHHHh
Q 014764 195 GYVKGVVSE-ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSN 273 (419)
Q Consensus 195 ~yl~~i~~~-~lLt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~y 273 (419)
-|+++.... +.+++..+.+|+.+++.||. .||+.|+..|
T Consensus 22 ~~~~~~~~~~~~~~~~~~~~L~~~~~~gd~----------------------------------------~af~~l~~~y 61 (234)
T PRK08301 22 YYIGGSEALPPPLSKEEEEYLLNKLPKGDE----------------------------------------AVRSLLIERN 61 (234)
T ss_pred HHhccccccCCcCCHHHHHHHHHHHHccCH----------------------------------------HHHHHHHHHh
Confidence 466666544 44888888899999999997 8999999999
Q ss_pred HHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhccccc---C--c-----
Q 014764 274 VRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR---L--P----- 343 (419)
Q Consensus 274 l~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~ir---i--p----- 343 (419)
.++|+.+|.+|.+++.+++|++||+|+++|+++++|++..+++|.||++++++|.|++++|++.+... . +
T Consensus 62 ~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~~d~lRk~~~~~~~~~~~~~~~~~~ 141 (234)
T PRK08301 62 LRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLRRNNKVKAEVSFDEPLNIDW 141 (234)
T ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHHHHHHhcccccccccccccccc
Confidence 99999999999999999999999999999999999998877789999999999999999997654211 0 0
Q ss_pred ------------c--ch------H-HHHHHHHHHHHHHHhc-------------CCCccHHHHHHHcCCCHHHHHHHHHH
Q 014764 344 ------------N--HL------H-ERLGLIRNAKLRLEEK-------------GVTPSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 344 ------------~--~l------~-e~~~~I~~a~~~L~e~-------------gRepS~eEIAe~LGIS~etVr~~l~r 389 (419)
. .. . .....+..++..|++. ..+.|++|||+.||+|+++|++.+.+
T Consensus 142 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~r 221 (234)
T PRK08301 142 DGNELLLSDVLGTDNDIIYKDIEDEVDRKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKR 221 (234)
T ss_pred CCCcccHHHhccCcccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 0 00 0 0123467777777431 25679999999999999999999999
Q ss_pred hCccc
Q 014764 390 IGKVF 394 (419)
Q Consensus 390 ark~l 394 (419)
+++.+
T Consensus 222 A~~~L 226 (234)
T PRK08301 222 IIKRL 226 (234)
T ss_pred HHHHH
Confidence 87654
No 36
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=99.78 E-value=1.4e-18 Score=160.82 Aligned_cols=153 Identities=11% Similarity=0.078 Sum_probs=123.6
Q ss_pred cCCCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHHHhHHHHHHH
Q 014764 201 VSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSI 280 (419)
Q Consensus 201 ~~~~lLt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~yl~LV~sI 280 (419)
...|+..+.++..|+..+..|+. .||+.|+++|.++|+.+
T Consensus 7 ~~~~~~~~~~~~~li~~~~~g~~----------------------------------------~a~~~l~~~y~~~l~~~ 46 (194)
T PRK09646 7 MTGPPAESPDLDALLRRVARGDQ----------------------------------------DAFAELYDRTSSRVYGL 46 (194)
T ss_pred ccCCCCCcccHHHHHHHHHccCH----------------------------------------HHHHHHHHHHHHHHHHH
Confidence 34566667777788888998887 89999999999999999
Q ss_pred HHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccC---------cc---ch--
Q 014764 281 AQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL---------PN---HL-- 346 (419)
Q Consensus 281 Akry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~iri---------p~---~l-- 346 (419)
|.+|+++..++||++||+|+++|+++++|++.+| .|.+|++.+++|.+++++|.+.+..+. .. ..
T Consensus 47 ~~~~~~~~~dAeDivQe~fi~l~~~~~~~~~~~~-~~~~wl~~ia~n~~~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~ 125 (194)
T PRK09646 47 VRRVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SALAWLLTLAHRRAVDRVRSEQAASQREVRYGARNVDPAFDQVAE 125 (194)
T ss_pred HHHHhCCHHHHHHHHHHHHHHHHHhhhhcCcccc-cHHHHHHHHHHHHHHHHHHhhccccccccccccccccccccchHH
Confidence 9999999999999999999999999999998766 799999999999999999976532111 00 00
Q ss_pred ----HHHHHHHHHHHHHHHhcC---------CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 347 ----HERLGLIRNAKLRLEEKG---------VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 347 ----~e~~~~I~~a~~~L~e~g---------RepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
.+....+..++..|++.. .+.+++|||+.||+|.++|++.+.++++.+
T Consensus 126 ~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~EIA~~Lgis~~tVk~~l~ra~~~L 186 (194)
T PRK09646 126 EVEARLERERVRDCLDALTDTQRESVTLAYYGGLTYREVAERLAVPLGTVKTRMRDGLIRL 186 (194)
T ss_pred HHHHHhHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCChHhHHHHHHHHHHHH
Confidence 112234666777775433 345999999999999999999999998654
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=99.78 E-value=3.2e-18 Score=163.70 Aligned_cols=160 Identities=29% Similarity=0.422 Sum_probs=128.3
Q ss_pred HHHHhhc-CCCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHHHh
Q 014764 195 GYVKGVV-SEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSN 273 (419)
Q Consensus 195 ~yl~~i~-~~~lLt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~y 273 (419)
.|+.+-. ..+.|++.++.+|+..++.|+. .||+.|+..|
T Consensus 22 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~d~----------------------------------------~a~~~l~~~y 61 (234)
T TIGR02835 22 YYIGGSEALPPPLTGEEEEALLQKLTQGDE----------------------------------------SAKSTLIERN 61 (234)
T ss_pred HHhcccccCCCcCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHh
Confidence 3444433 3456888888899999999987 8999999999
Q ss_pred HHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhccccc-Cc---------
Q 014764 274 VRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR-LP--------- 343 (419)
Q Consensus 274 l~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~ir-ip--------- 343 (419)
.+.|+++|.+|.+++.++||++||+|+++|+++++|++..+++|.||++++++|.+.+++|+..+... .+
T Consensus 62 ~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~~d~~Rk~~r~~~~~~~~~~~~~~~ 141 (234)
T TIGR02835 62 LRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEILMYLRRNNKTRSEVSFDEPLNVDW 141 (234)
T ss_pred HHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHhccccCcccccccccCCC
Confidence 99999999999999999999999999999999999998877789999999999999999998654211 00
Q ss_pred -------------c-----ch---HHHHHHHHHHHHHHHh---------c----CCCccHHHHHHHcCCCHHHHHHHHHH
Q 014764 344 -------------N-----HL---HERLGLIRNAKLRLEE---------K----GVTPSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 344 -------------~-----~l---~e~~~~I~~a~~~L~e---------~----gRepS~eEIAe~LGIS~etVr~~l~r 389 (419)
. .. ......+..++..|++ . +.+.|++|||+.||+|+++|+.++.+
T Consensus 142 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~r 221 (234)
T TIGR02835 142 DGNELLLSDVLGTDSDIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKR 221 (234)
T ss_pred CCCcchHHHhcCCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 0 00 0112346777777743 1 15679999999999999999999988
Q ss_pred hCccc
Q 014764 390 IGKVF 394 (419)
Q Consensus 390 ark~l 394 (419)
+++.+
T Consensus 222 a~~~L 226 (234)
T TIGR02835 222 ILKRL 226 (234)
T ss_pred HHHHH
Confidence 86543
No 38
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=99.76 E-value=8e-18 Score=154.61 Aligned_cols=148 Identities=18% Similarity=0.128 Sum_probs=118.8
Q ss_pred CCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHHHhHHHHHHHHHHcc
Q 014764 206 LTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYD 285 (419)
Q Consensus 206 Lt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~yl~LV~sIAkry~ 285 (419)
+|+.+...|+..++.|+. .||+.|+..|.+.|+.+|.++.
T Consensus 6 ~~~~~~~~l~~~~~~gd~----------------------------------------~a~~~l~~~~~~~l~~~~~~~~ 45 (189)
T PRK09648 6 DTGEELDALVAEAVAGDR----------------------------------------RALREVLEIIRPLVVRYCRARL 45 (189)
T ss_pred CCchHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHHHHHHh
Confidence 477777889999999887 8999999999999999999987
Q ss_pred CC----CCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccC-----cc------c-----
Q 014764 286 NM----GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL-----PN------H----- 345 (419)
Q Consensus 286 ~~----g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~iri-----p~------~----- 345 (419)
++ ..+++|++||+|+++|+++.+|+... .+|.+|++.+++|.+++++++..+.... +. .
T Consensus 46 ~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~~-~~~~~wl~~i~~n~~~d~~r~~~r~~~~~~~~~~~~~~~~~~~~~~~ 124 (189)
T PRK09648 46 GGVERPGLSADDVAQEVCLAVITALPRYRDQG-RPFLAFVYGIAAHKVADAHRAAGRDKAVPTEEVPERPSDDAGPEERA 124 (189)
T ss_pred cccccCCCCHHHHHHHHHHHHHHHHHHHhccC-CcHHHHHHHHHHHHHHHHHHHhCCCccccccccccccccCCCHHHHH
Confidence 64 36899999999999999999998643 4899999999999999999987653211 10 0
Q ss_pred -hHHHHHHHHHHHHHHHhcCC---------CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 346 -LHERLGLIRNAKLRLEEKGV---------TPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 346 -l~e~~~~I~~a~~~L~e~gR---------epS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
..+....+..++..|++..| +.+++|||+.||+|.++|+..+.++++.+
T Consensus 125 ~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~L 183 (189)
T PRK09648 125 LRSESSNRMRELLDTLPEKQREILILRVVVGLSAEETAEAVGSTPGAVRVAQHRALARL 183 (189)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 11122346677777755443 34999999999999999999999987653
No 39
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=99.75 E-value=1.3e-17 Score=152.86 Aligned_cols=130 Identities=14% Similarity=0.131 Sum_probs=106.2
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhccccc--
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR-- 341 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~ir-- 341 (419)
.||+.|+..|.++|+.+|.++.++..+++|++||+|+++|+++.+|++.. ..|.+|++.+++|.+.+++|++.....
T Consensus 20 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~~-~~f~~wl~~ia~n~~~d~~R~~~~~~~~~ 98 (186)
T PRK05602 20 AAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPGE-ARFDTWLHRVVLNLCYDRLRRRREVPVED 98 (186)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCCC-CcHHHHHHHHHHHHHHHHHHhcCCCCccc
Confidence 89999999999999999999999999999999999999999999999763 489999999999999999987653211
Q ss_pred Ccc---------c---hHHHHHHHHHHHHHHHhcCC---------CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 342 LPN---------H---LHERLGLIRNAKLRLEEKGV---------TPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 342 ip~---------~---l~e~~~~I~~a~~~L~e~gR---------epS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
.+. . ..+....+..++..|++..+ +.+++|||+.||+|.++|+..++++++.+
T Consensus 99 ~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~L 172 (186)
T PRK05602 99 APDVPDPAPGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLARGRRAL 172 (186)
T ss_pred ccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHhcCCCHHHHHHHhCcCHHHHHHHHHHHHHHH
Confidence 110 0 11223446677777754333 44999999999999999999999998765
No 40
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=99.74 E-value=2.2e-17 Score=152.30 Aligned_cols=129 Identities=14% Similarity=0.119 Sum_probs=106.1
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCc
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip 343 (419)
.|++.|+..|.+.|+++|.++.++..+++|++||+|+++|+++.+|++.. .|.+|++++++|.+++++|+..+....+
T Consensus 26 ~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~~~~~~~~~--~f~~wl~~i~~n~~~~~~R~~~~~~~~~ 103 (194)
T PRK12513 26 AAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRA--RFRTWLYQIARNLLIDHWRRHGARQAPS 103 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCCC--chHHHHHHHHHHHHHHHHHHhccccccc
Confidence 89999999999999999999999989999999999999999999998653 7999999999999999999876432211
Q ss_pred c------------c--------hHHHHHHHHHHHHHHHhcCC---------CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 344 N------------H--------LHERLGLIRNAKLRLEEKGV---------TPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 344 ~------------~--------l~e~~~~I~~a~~~L~e~gR---------epS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
. . ..+....+..++..|++..+ +.|++|||+.||+|+++|++.+.++++.+
T Consensus 104 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~L 183 (194)
T PRK12513 104 LDADEQLHALADDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYALQKL 183 (194)
T ss_pred cccchhhhhcCCCCCCHHHHHHHHHHHHHHHHHHHhCCHhHhhheeeehccCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 0 0 01122456777777754433 34999999999999999999999998654
No 41
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=99.73 E-value=3e-17 Score=156.59 Aligned_cols=152 Identities=19% Similarity=0.205 Sum_probs=126.1
Q ss_pred cCCCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHHHhHHHHHHH
Q 014764 201 VSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSI 280 (419)
Q Consensus 201 ~~~~lLt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~yl~LV~sI 280 (419)
...|+|++..+.+|+.+++.|+. .|++.|+..|.+.|+++
T Consensus 7 ~~~~~~~~~~~~~l~~~~~~gd~----------------------------------------~a~~~l~~~y~~~l~~~ 46 (231)
T PRK11922 7 SRPPPLSAASDRELVARVLAGDE----------------------------------------AAFEALMRRHNRRLYRT 46 (231)
T ss_pred CCCCCcCcccHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHH
Confidence 45688999999999999999997 89999999999999999
Q ss_pred HHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCcc----------------
Q 014764 281 AQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPN---------------- 344 (419)
Q Consensus 281 Akry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~---------------- 344 (419)
+.++.++..++||++||+|+++|+.+++|++.. .|.+|++++++|.+++++|+..+....+.
T Consensus 47 a~~~~~~~~~AEDlvQE~fi~l~~~~~~~~~~~--~~~~wL~~iarn~~~d~~Rk~~r~~~~~~~~~~~~~~~~~~~~~~ 124 (231)
T PRK11922 47 ARAILRNDAEAEDVVQEAYLRAFRALGTFRGDA--SLSTWLSRIVLNEALGRLRRRRRLVNLAEMVMASTIAGGERTPLA 124 (231)
T ss_pred HHHHhCChhhHHHHHHHHHHHHHHHHHhcCCCc--hhHHHHHHHHHHHHHHHHHhhcccccchhcccccccccccccccC
Confidence 999999999999999999999999999998763 79999999999999999997664322110
Q ss_pred -------c---hHHHHHHHHHHHHHHHhcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 345 -------H---LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 345 -------~---l~e~~~~I~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
. ..+....+..++..|++..++ .+++|||+.||+|.++|++++.++++.+
T Consensus 125 ~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIAe~lgis~~tVk~~l~Rar~kL 193 (231)
T PRK11922 125 DPAEDPERAAARREIRALLERAIDALPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRLHRARRLL 193 (231)
T ss_pred cccCChHHHHHHHHHHHHHHHHHHhCCHHHhhhheeehhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 0 011223477777777554433 3999999999999999999999998655
No 42
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=99.73 E-value=2e-17 Score=153.47 Aligned_cols=131 Identities=28% Similarity=0.335 Sum_probs=102.2
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCc
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip 343 (419)
.|++.|++.|.++|+.+|.+|.++..++||++||+|+++|+++.+|++.++.+|.||++.+++|.+.++++...+..+.+
T Consensus 24 ~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~~n~~~d~~r~~~r~~~~~ 103 (208)
T PRK08295 24 EALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQIITAIKTANRQKHIP 103 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHhhhhcccc
Confidence 89999999999999999999999999999999999999999999999887669999999999999999987543321110
Q ss_pred -----------------------------cch------HHHHHHHH-HHHHHHHhc--------CCCccHHHHHHHcCCC
Q 014764 344 -----------------------------NHL------HERLGLIR-NAKLRLEEK--------GVTPSVDRIAEYLNMS 379 (419)
Q Consensus 344 -----------------------------~~l------~e~~~~I~-~a~~~L~e~--------gRepS~eEIAe~LGIS 379 (419)
... .+....+. .+...|++. ..+.+++|||+.||+|
T Consensus 104 ~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~~r~vl~l~~e~~s~~EIA~~lgis 183 (208)
T PRK08295 104 LNSYVSLDKPIYDEESDRTLLDVISEAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLELYLDGKSYQEIAEELNRH 183 (208)
T ss_pred ccceeecCCcccCCccchhHHHHhcCcccCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCHHHHHHHHCCC
Confidence 000 00111222 233344322 2445999999999999
Q ss_pred HHHHHHHHHHhCccc
Q 014764 380 QKKVRNATEAIGKVF 394 (419)
Q Consensus 380 ~etVr~~l~rark~l 394 (419)
.++|+.++.++++.+
T Consensus 184 ~~tV~~~l~rar~~L 198 (208)
T PRK08295 184 VKSIDNALQRVKRKL 198 (208)
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999999998654
No 43
>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=99.73 E-value=4.3e-17 Score=149.90 Aligned_cols=131 Identities=26% Similarity=0.335 Sum_probs=102.9
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccC-
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL- 342 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~iri- 342 (419)
.||+.|+..|.+.|+.+|.++.++..+++|++||+|+++|+++.+|++..+..|.||++.+|++.+.++++...+..+.
T Consensus 19 ~a~~~l~~~~~~~l~~~a~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~~~f~~wl~~~~~~~~~~~~r~~~~~~~~~ 98 (198)
T TIGR02859 19 HALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELCVTRQIITAIKTATRQKHIP 98 (198)
T ss_pred HHHHHHHHHHHHHHHHHHHHHccccCcHHHHHHHHHHHHHHHHHHhCcccCCChHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence 8999999999999999999999999999999999999999999999987766999999999999888888743211100
Q ss_pred -------------------------------ccch---HHHHHHHHHHHHHH-Hhc--------CCCccHHHHHHHcCCC
Q 014764 343 -------------------------------PNHL---HERLGLIRNAKLRL-EEK--------GVTPSVDRIAEYLNMS 379 (419)
Q Consensus 343 -------------------------------p~~l---~e~~~~I~~a~~~L-~e~--------gRepS~eEIAe~LGIS 379 (419)
|... .+....+..++..| ++. ..+.|++|||+.||+|
T Consensus 99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~~~~~~~~s~~eIA~~l~~s 178 (198)
T TIGR02859 99 LNSYVSLNKPIYDEESDRTLLDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVLQSYLDGKSYQEIACDLNRH 178 (198)
T ss_pred hhhhcCcccccccccccchHHHHhhccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHcCCCHHHHHHHHCCC
Confidence 0000 11123355566664 222 2344999999999999
Q ss_pred HHHHHHHHHHhCccc
Q 014764 380 QKKVRNATEAIGKVF 394 (419)
Q Consensus 380 ~etVr~~l~rark~l 394 (419)
+++|+.++.++++.+
T Consensus 179 ~~tV~~~l~r~r~~L 193 (198)
T TIGR02859 179 VKSIDNALQRVKRKL 193 (198)
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999999998654
No 44
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=99.72 E-value=3.3e-17 Score=151.68 Aligned_cols=130 Identities=15% Similarity=0.107 Sum_probs=104.5
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhccccc-C
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR-L 342 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~ir-i 342 (419)
.+|+.|+..|.+.|+.+|.++.++..+++|++||+|+.+|+.+.+|++..+ .|.+|++++++|.+++++|+..+... .
T Consensus 27 ~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l~l~~~~~~~~~~~~-~~~~wL~~iarn~~ld~~Rk~~~~~~~~ 105 (194)
T PRK12531 27 QAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYTIIRNLCFDLLRKQKGKDLHI 105 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-hHHHHHHHHHHHHHHHHHHHhccccccc
Confidence 899999999999999999999998889999999999999999999987554 79999999999999999998653211 0
Q ss_pred ------cc---------c-hH---HHHHHHHHHHHHHHhcC---------CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 343 ------PN---------H-LH---ERLGLIRNAKLRLEEKG---------VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 343 ------p~---------~-l~---e~~~~I~~a~~~L~e~g---------RepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
+. . .. .....+..++..|++.. .+.+++|||+.||+|.++|+.+++++++.+
T Consensus 106 ~~~~~~~~~~~~~~~~~~~~~e~~~~~~~l~~~l~~Lp~~~r~v~~l~~~eg~s~~EIA~~lgis~~tVk~rl~ra~~~L 185 (194)
T PRK12531 106 HADDIWPSDYYPPDLVDHYSPEQDMLKEQVMKFLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLRLAVEKL 185 (194)
T ss_pred chhhcccccccccccccccCHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHHHHH
Confidence 00 0 00 11234566666665433 344999999999999999999999998654
No 45
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=99.72 E-value=3.5e-17 Score=148.90 Aligned_cols=130 Identities=14% Similarity=0.058 Sum_probs=104.6
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccc-cC
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL-RL 342 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~i-ri 342 (419)
.|+..|+..|.+.|+.+|.++.++..+++|++||+|+++|+++++|++..+ .|.||++.+++|.+++++|+..+.. ..
T Consensus 19 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~~~-~~~~wl~~ia~n~~~d~~R~~~~~~~~~ 97 (179)
T PRK12514 19 DAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGL-SPMTWLITIARNHAIDRLRARKAVAVDI 97 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCcccc-cHHHHHHHHHHHHHHHHHHhcCCccccc
Confidence 899999999999999999999999999999999999999999999986544 7999999999999999998765321 00
Q ss_pred ------------ccc---hHHHHHHHHHHHHHHHhcC---------CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 343 ------------PNH---LHERLGLIRNAKLRLEEKG---------VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 343 ------------p~~---l~e~~~~I~~a~~~L~e~g---------RepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
|.. ..+....+..++..|++.. .+.|++|||+.||+|+++|+..+.++++.+
T Consensus 98 ~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~~L 173 (179)
T PRK12514 98 DEAHDLADPSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRRSLLKL 173 (179)
T ss_pred ccchhccccCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCChHHHHHHHHHHHHHH
Confidence 000 0111234666666665333 344999999999999999999999997654
No 46
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=99.72 E-value=2.8e-17 Score=152.40 Aligned_cols=130 Identities=20% Similarity=0.244 Sum_probs=105.5
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccc-cC
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL-RL 342 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~i-ri 342 (419)
.||+.|+.+|.+.|+.+|.++.++..+++|++||+|+++|+.+.+|++..+ .|.||++++++|.+++++|++.+.. ..
T Consensus 26 ~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~~-~~~~wl~~ia~n~~~d~~Rk~~~~~~~~ 104 (196)
T PRK12524 26 AAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGEA-RVSTWLYRVVCNLCTDRLRRRRRASVDL 104 (196)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhccccccc-hHHHHHHHHHHHHHHHHHHhhcCCCCCc
Confidence 899999999999999999999999999999999999999999999985443 7999999999999999999754321 10
Q ss_pred ---c------c---c---hHHHHHHHHHHHHHHHhcC---------CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 343 ---P------N---H---LHERLGLIRNAKLRLEEKG---------VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 343 ---p------~---~---l~e~~~~I~~a~~~L~e~g---------RepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
+ . . ..+....+..++..|++.. .+.+++|||+.||+|..+|+++++++++.+
T Consensus 105 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~L~~~~g~s~~eIA~~lgis~~tV~~~l~Ra~~~L 180 (196)
T PRK12524 105 DDAPEPADAAPGAEEALIEGDRMRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVESLTARGKRAL 180 (196)
T ss_pred cccccccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 0 0 0 1112244666777775432 455999999999999999999999998765
No 47
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=99.72 E-value=3.3e-17 Score=149.74 Aligned_cols=130 Identities=15% Similarity=0.163 Sum_probs=105.2
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhccccc-C
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR-L 342 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~ir-i 342 (419)
.|++.|+..|.+.|+.++.++.+++.+++|++||+|+++|+++++|++..+ .|.+|++++++|.+++++|+..+... +
T Consensus 23 ~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~~-~~~~wl~~ia~n~~~d~~rk~~~~~~~~ 101 (186)
T PRK13919 23 EALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRG-SARAWLLALAHHAAVDHVRRRAARPQPL 101 (186)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCcccc-chHHHHHHHHHHHHHHHHHhhhcccccc
Confidence 899999999999999999999988899999999999999999999987654 79999999999999999987653211 1
Q ss_pred ------c------cc-----hHHHHHHHHHHHHHHHhcC---------CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 343 ------P------NH-----LHERLGLIRNAKLRLEEKG---------VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 343 ------p------~~-----l~e~~~~I~~a~~~L~e~g---------RepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
+ .. .......+..++..|++.. .+.+++|||+.||+|+++|+..++++++.+
T Consensus 102 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~~V~~~l~ra~~~L 179 (186)
T PRK13919 102 EPDEREPEAFDLPGPGLDEEGHLDRTRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALSRL 179 (186)
T ss_pred cccccccccccCCCccccHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 0 00 0111234677777775433 334999999999999999999999998654
No 48
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=99.72 E-value=3.2e-17 Score=150.15 Aligned_cols=130 Identities=15% Similarity=0.063 Sum_probs=105.8
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhccccc--
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR-- 341 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~ir-- 341 (419)
.+|+.|+..|.++|+++|.++.++..++||++||+|+++|+.+++|++.++ .|.||++++++|.+++++|+..+...
T Consensus 25 ~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~~n~~~d~~R~~~~~~~~~ 103 (187)
T PRK12534 25 HAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIARNKAIDHLRANAPQRRNV 103 (187)
T ss_pred HHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHHHHHHhcccccccc
Confidence 899999999999999999999999999999999999999999999998655 69999999999999999987653211
Q ss_pred ----Cc---------cc---hHHHHHHHHHHHHHHHhcC---------CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 342 ----LP---------NH---LHERLGLIRNAKLRLEEKG---------VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 342 ----ip---------~~---l~e~~~~I~~a~~~L~e~g---------RepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
.+ .. ..+....+..++..|++.. .+.+++|||+.||+|+++|+.++.++++.+
T Consensus 104 ~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~~v~~~l~Rar~~L 181 (187)
T PRK12534 104 ALDDAGELRAADASPLERTERASTRRRIDHCLAELEPPRSELIRTAFFEGITYEELAARTDTPIGTVKSWIRRGLAKL 181 (187)
T ss_pred cccchhhhccccCChhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCChhHHHHHHHHHHHHH
Confidence 00 00 1122345666777774322 445999999999999999999999998654
No 49
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=99.72 E-value=3.6e-17 Score=144.73 Aligned_cols=129 Identities=19% Similarity=0.202 Sum_probs=104.3
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccc---
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL--- 340 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~i--- 340 (419)
.||+.|++.|.++|+.++.++ ++..++||++||+|+++|+++++|++..+ .|.+|++.+++|.++++++++.+..
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 689999999999999999987 45679999999999999999999998666 7999999999999999999874211
Q ss_pred ---cCccc---hHHHHHHHHHHHHHHHhcC---------CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 341 ---RLPNH---LHERLGLIRNAKLRLEEKG---------VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 341 ---rip~~---l~e~~~~I~~a~~~L~e~g---------RepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
..|.. ..+....+..++..|++.. .+.|++|||+.||+|+++|+..+.++++.+
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 11221 2223455677777775432 445999999999999999999999987654
No 50
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=99.72 E-value=4.4e-17 Score=150.26 Aligned_cols=130 Identities=18% Similarity=0.183 Sum_probs=103.9
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCC---CCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccc
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNM---GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~---g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~i 340 (419)
.||+.|++.|.+.|+.++.++.++ ..++||++||+|+++|+++++|++..+ .|.||++.+++|.+.+++|+..+..
T Consensus 18 ~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~-~~~~wl~~iarn~~~d~~rk~~~~~ 96 (189)
T PRK06811 18 KALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKG-SFKKWIAAISKYKAIDYKRKLTKNN 96 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccc-cHHHHHHHHHHHHHHHHHHHhcccc
Confidence 899999999999999999999875 357999999999999999999987655 8999999999999999998766432
Q ss_pred cCc---c-------c------hHHHHHHHHHHHHHHHhcC---------CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 341 RLP---N-------H------LHERLGLIRNAKLRLEEKG---------VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 341 rip---~-------~------l~e~~~~I~~a~~~L~e~g---------RepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
... . . ..+....+..++..|++.. .+.+++|||+.||+|..+|++.+.++++.+
T Consensus 97 ~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIAe~lgis~~~V~~~l~Ra~~~L 175 (189)
T PRK06811 97 EIDSIDEFILISEESIENEIILKENKEEILKLINDLEKLDREIFIRRYLLGEKIEEIAKKLGLTRSAIDNRLSRGRKKL 175 (189)
T ss_pred ccccchhhhhcccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHccCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 211 0 0 1112234666666664432 345999999999999999999999997654
No 51
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=99.72 E-value=6.6e-17 Score=148.79 Aligned_cols=147 Identities=20% Similarity=0.235 Sum_probs=118.0
Q ss_pred CCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHHHhHHHHHHHHHHcc
Q 014764 206 LTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYD 285 (419)
Q Consensus 206 Lt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~yl~LV~sIAkry~ 285 (419)
||+..+..|+..++.||. .|++.|+..|.+.|+.+++++.
T Consensus 2 ~~~~~~~~ll~~~~~gd~----------------------------------------~a~~~l~~~y~~~l~~~~~~~~ 41 (193)
T PRK11923 2 LTQEEDQQLVERVQRGDK----------------------------------------RAFDLLVLKYQHKILGLIVRFV 41 (193)
T ss_pred CccccHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHHHHHHh
Confidence 566666778888888887 8999999999999999999999
Q ss_pred CCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhccccc-----Cc------------cc---
Q 014764 286 NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR-----LP------------NH--- 345 (419)
Q Consensus 286 ~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~ir-----ip------------~~--- 345 (419)
++..+++|++||+|+++|+++.+|++.. .|.+|++++++|.++++++++.+... +. ..
T Consensus 42 ~~~~daeDlvQe~~i~l~~~~~~~~~~~--~~~~wl~~ia~n~~~d~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 119 (193)
T PRK11923 42 HDTAEAQDVAQEAFIKAYRALGNFRGDS--AFYTWLYRIAINTAKNHLVSRGRRPPDSDVSSEDAEFYDGDHALKDIESP 119 (193)
T ss_pred CCHhhHHHHHHHHHHHHHHhHhCcCCCC--ccHhHHHHHHHHHHHHHHHHhcCCCccccccccchhhhcccccccCcCCH
Confidence 9989999999999999999999999864 69999999999999999987554321 00 00
Q ss_pred -----hHHHHHHHHHHHHHHHhcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 346 -----LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 346 -----l~e~~~~I~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
..+....+..++..|++..+. .+++|||+.||+|+++|+.++.++++.+
T Consensus 120 e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Rar~~L 182 (193)
T PRK11923 120 ERALLRDEIEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIFRAREAI 182 (193)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHHHhHHHhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 001123456666666543443 3999999999999999999999998654
No 52
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=99.72 E-value=4.9e-17 Score=148.93 Aligned_cols=130 Identities=22% Similarity=0.235 Sum_probs=105.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCc
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip 343 (419)
.||+.|+..|.+.|+.++.+++++..+++|++||+|+.+|+.+++|++..+ .|.+|++++++|.+++++++..+.....
T Consensus 23 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wL~~iarn~~~d~~r~~~~~~~~~ 101 (182)
T PRK12537 23 RALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARG-SARGWIYSVTRHLALNVLRDTRREVVLD 101 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHHHHHHhccccCccc
Confidence 899999999999999999999999999999999999999999999986544 7999999999999999999876432211
Q ss_pred c----------c------hHHHHHHHHHHHHHHHhcC---------CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 344 N----------H------LHERLGLIRNAKLRLEEKG---------VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 344 ~----------~------l~e~~~~I~~a~~~L~e~g---------RepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
. . ..+....+..++..|++.. .+.+++|||+.||+|+++|+..+.++++.+
T Consensus 102 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~~~s~~eIA~~lgis~~tV~~~l~ra~~~L 177 (182)
T PRK12537 102 DDAEETAQTLHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWIKRSLKAL 177 (182)
T ss_pred cchhhhcccccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCChhhHHHHHHHHHHHH
Confidence 0 0 0111234666666665433 344999999999999999999999987654
No 53
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=99.72 E-value=9.1e-17 Score=147.89 Aligned_cols=143 Identities=17% Similarity=0.218 Sum_probs=114.9
Q ss_pred CChHHHHHHHhH----HHHHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHH
Q 014764 250 ISRPELQSILME----CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWI 325 (419)
Q Consensus 250 ~s~~eLr~~l~~----~~~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~I 325 (419)
+++++|...+.. +..||+.|+..|.+.|+++|.+|.++..+++|++||+|+++|+++++|++. ..|.||+++++
T Consensus 8 ~~~~~li~~~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~~~~~~~~~--~~~~~wl~~ia 85 (188)
T PRK09640 8 LNDEELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGK--SKFKTWLYSIT 85 (188)
T ss_pred CCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHHHhcCC--CcchHHHHHHH
Confidence 455666666653 568999999999999999999999999999999999999999999999864 37999999999
Q ss_pred HhhHHHHHHHhcccccCc---------c---c---hHHHHHHHHHHHHHHHhcCCCc---------cHHHHHHHcCCCHH
Q 014764 326 RQGVSRALVENSRTLRLP---------N---H---LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQK 381 (419)
Q Consensus 326 rn~I~~~Lrd~~r~irip---------~---~---l~e~~~~I~~a~~~L~e~gRep---------S~eEIAe~LGIS~e 381 (419)
+|.+++++|+..+..... . . ..+....+..++..|++..+.+ +++|||+.||+|.+
T Consensus 86 ~n~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~lgis~~ 165 (188)
T PRK09640 86 YNECITQYRKERRKRRLMDALSLDPLEEASEEKAPKPEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMGLS 165 (188)
T ss_pred HHHHHHHHHHhcccccCcchhhhcccccccccccccHHHHHHHHHHHHhcChhheeeeeeHHhcCCCHHHHHHHHCCCHH
Confidence 999999998754322111 0 0 1122355778888886555544 99999999999999
Q ss_pred HHHHHHHHhCccc
Q 014764 382 KVRNATEAIGKVF 394 (419)
Q Consensus 382 tVr~~l~rark~l 394 (419)
+|+..+.++++.+
T Consensus 166 tV~~~l~Ra~~~L 178 (188)
T PRK09640 166 ATKMRYKRALDKL 178 (188)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999997654
No 54
>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=99.71 E-value=5.3e-17 Score=145.44 Aligned_cols=130 Identities=15% Similarity=0.077 Sum_probs=105.3
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCc
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip 343 (419)
.||+.|+..|.+.++.++.++.++..++||++||+|+++|+.+++|+...+ .|.+|++++++|.+++++|.+.+....+
T Consensus 11 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~~R~~~~~~~~~ 89 (170)
T TIGR02952 11 DAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVNDYFRGSKRHPLFS 89 (170)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHHHHHhcCCCCCCc
Confidence 899999999999999999999988899999999999999999999987555 8999999999999999999765432211
Q ss_pred c-----------ch------HHHHHHHHHHHHHHHhcC---------CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 344 N-----------HL------HERLGLIRNAKLRLEEKG---------VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 344 ~-----------~l------~e~~~~I~~a~~~L~e~g---------RepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
. .. .+....+..++..|++.. .+.+++|||+.||+|+++|+..+.++++.+
T Consensus 90 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~eIA~~l~is~~tv~~~l~ra~~~L 166 (170)
T TIGR02952 90 LDVFKELLSNEPNPEEAILKEEANEKLLKALKILTPKQQHVIALRFGQNLPIAEVARILGKTEGAVKILQFRAIKKL 166 (170)
T ss_pred HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 0 00 112244666666665433 345999999999999999999999987643
No 55
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=99.71 E-value=6.8e-17 Score=147.11 Aligned_cols=129 Identities=19% Similarity=0.160 Sum_probs=103.9
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCc
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip 343 (419)
.||++|+..|.+.|+.+|.+|.++..+++|++||+|+++|+++.+|++.. .|.||++++++|.+.+++|+..+.....
T Consensus 18 ~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~~~~rk~~~~~~~~ 95 (187)
T TIGR02948 18 NAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQR--KFSTWLYRIATNLTIDRLRKRKPDFYLD 95 (187)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHHHHHHHhhccccccc
Confidence 89999999999999999999999999999999999999999999999865 6999999999999999998755321100
Q ss_pred c-------------------ch------HHHHHHHHHHHHHHHhcCC---------CccHHHHHHHcCCCHHHHHHHHHH
Q 014764 344 N-------------------HL------HERLGLIRNAKLRLEEKGV---------TPSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 344 ~-------------------~l------~e~~~~I~~a~~~L~e~gR---------epS~eEIAe~LGIS~etVr~~l~r 389 (419)
. .. .+....+..++..|++..+ +.+++|||+.||+|.++|+.++.+
T Consensus 96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~~v~~~l~R 175 (187)
T TIGR02948 96 DEVQGTDGLTMESQLAADEAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKYMEDLSLKEISEILDLPVGTVKTRIHR 175 (187)
T ss_pred ccccCccccccccccccCcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 0 00 0112335666666654333 349999999999999999999999
Q ss_pred hCccc
Q 014764 390 IGKVF 394 (419)
Q Consensus 390 ark~l 394 (419)
+++.+
T Consensus 176 ar~~L 180 (187)
T TIGR02948 176 GREAL 180 (187)
T ss_pred HHHHH
Confidence 97654
No 56
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=99.71 E-value=9.5e-17 Score=147.84 Aligned_cols=129 Identities=22% Similarity=0.220 Sum_probs=102.8
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCc
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip 343 (419)
.|++.|+..|.+.|+.++.++.++..+++|++||+|+++|+. ..|++..+ .|.||++++++|.+++++|++.+.....
T Consensus 29 ~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn~~~d~~Rk~~~~~~~~ 106 (194)
T PRK12519 29 AALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRSRAIDRLRSRRSRQRLL 106 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHHHHHHHHHhcccccchh
Confidence 899999999999999999999998899999999999999976 67887655 7999999999999999998765421110
Q ss_pred ------------c-c------hHHHHHHHHHHHHHHHhcC---------CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 344 ------------N-H------LHERLGLIRNAKLRLEEKG---------VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 344 ------------~-~------l~e~~~~I~~a~~~L~e~g---------RepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
. . ..+....+..++..|++.. .+.++.|||+.||+|+.+|+..+.++++.+
T Consensus 107 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~L 185 (194)
T PRK12519 107 ERWQQELLGEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGLLKL 185 (194)
T ss_pred hhhhhhhcccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhhhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 0 0 0111234666777775433 344999999999999999999999987654
No 57
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=99.70 E-value=8.4e-17 Score=154.55 Aligned_cols=130 Identities=21% Similarity=0.208 Sum_probs=105.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhccccc--
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR-- 341 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~ir-- 341 (419)
.||+.|+..|.+.|+.++.+++++..++||++||+|+++|+.+++|++..+ .|.+|++.+++|.+++++|+..+...
T Consensus 63 ~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN~~id~~Rk~~~~~~~~ 141 (233)
T PRK12538 63 AAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSNRCIDLRRKPRTENVDA 141 (233)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHHHHHHHHHhhccccccc
Confidence 899999999999999999999999999999999999999999999986554 79999999999999999987542110
Q ss_pred C-------ccc-----hHHHHHHHHHHHHHHHhcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 342 L-------PNH-----LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 342 i-------p~~-----l~e~~~~I~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
. +.. ..+....+..++..|++..|. .+++|||+.||+|+++|+.+++++++.+
T Consensus 142 ~~~~~~~~~~~~~~~~~~e~~~~l~~~L~~Lp~~~R~v~~L~~~eg~s~~EIA~~Lgis~~tVk~~l~RAr~kL 215 (233)
T PRK12538 142 VPEVADGKPDAVSVIERNELSDLLEAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESLLKRGRQQL 215 (233)
T ss_pred ccccccCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 0 110 011223467777777554444 4999999999999999999999998654
No 58
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=99.70 E-value=1.1e-16 Score=144.35 Aligned_cols=129 Identities=17% Similarity=0.138 Sum_probs=105.3
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCc
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip 343 (419)
.|++.|+..|.+.|++++.++.++..+++|++||+|+.+|+.+.+|++.. +|.+|++.+++|.+++++|+..+....+
T Consensus 16 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~~~~~~ 93 (169)
T TIGR02954 16 PAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPK--YFNTWLTRILINECIDLLKKKKKVIPFD 93 (169)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCcc--ccHHHHHHHHHHHHHHHHHhcCCcCccc
Confidence 89999999999999999999999999999999999999999999998753 7999999999999999999766432211
Q ss_pred cc----------hHHHHHHHHHHHHHHHhcC---------CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 344 NH----------LHERLGLIRNAKLRLEEKG---------VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 344 ~~----------l~e~~~~I~~a~~~L~e~g---------RepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
.. ..+....+..++..|++.. .+.+++|||+.||+|+++|+..+.++++.+
T Consensus 94 ~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eiA~~lgis~~tv~~~l~Ra~~~L 163 (169)
T TIGR02954 94 PNTSIEKGECETHADSRLDLYKAIDTLNDKYQTAIILRYYHDLTIKEIAEVMNKPEGTVKTYLHRALKKL 163 (169)
T ss_pred cccccccchhhhchHHHHHHHHHHHhCCHHHhHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 10 0111224666666665433 334999999999999999999999997654
No 59
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=99.70 E-value=2.5e-16 Score=144.13 Aligned_cols=129 Identities=16% Similarity=0.134 Sum_probs=104.1
Q ss_pred HHHHHHHHHhHHHHHHHHHHcc-CCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccC
Q 014764 264 LAREKLVMSNVRLVMSIAQRYD-NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~-~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~iri 342 (419)
.||+.|+..|.+.|+.++.++. .+..++||++||+|++||+.++.|++.. .|.+|++.+++|.+++++|+..+....
T Consensus 21 ~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~~--~~~~wl~~iarN~~~d~~Rk~~~~~~~ 98 (181)
T PRK12536 21 AAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRADQ--PLTAWVHAIARYKLMDFLRSRARREAL 98 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHHHHHHHHHhccccc
Confidence 8999999999999999998866 4578999999999999999999999753 799999999999999999986542211
Q ss_pred c--------------cchHHHHHHHHHHHHHHHhcCC---------CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 343 P--------------NHLHERLGLIRNAKLRLEEKGV---------TPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 343 p--------------~~l~e~~~~I~~a~~~L~e~gR---------epS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
. ....+....+..++..|+...+ +.+++|||+.||+|+++|+..+.++++.+
T Consensus 99 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tV~~~l~rar~~L 173 (181)
T PRK12536 99 HDPLDDESELFATSDDEAAEARRDLGKLLEQLPDRQRLPIVHVKLEGLSVAETAQLTGLSESAVKVGIHRGLKAL 173 (181)
T ss_pred cCCccchhhhcCCCCcchHHHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 0 0112233456777777754333 34999999999999999999999998654
No 60
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=99.70 E-value=1.4e-16 Score=147.63 Aligned_cols=129 Identities=18% Similarity=0.192 Sum_probs=106.4
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCc
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip 343 (419)
.+|+.|++.|.+.|++++.++.++..++||++||+|+.+|+.+++|++.. .|.+|++++++|.+++++|+..+....+
T Consensus 27 ~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~~--~f~~wL~~i~rn~~~d~~Rk~~~~~~~~ 104 (192)
T PRK09643 27 YAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDA--AVSSWLHRIVVNACLDRLRRAKARPTVP 104 (192)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCCC--ccHHHHHHHHHHHHHHHHHccccCCCCC
Confidence 89999999999999999999999999999999999999999999999654 6999999999999999999765432111
Q ss_pred -----------cc---hHHHHHHHHHHHHHHHhcC---------CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 344 -----------NH---LHERLGLIRNAKLRLEEKG---------VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 344 -----------~~---l~e~~~~I~~a~~~L~e~g---------RepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
.. ..+....+..++..|++.. .+.+++|||+.||+|..+|+..+.++++.+
T Consensus 105 ~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~i~~l~~~~g~s~~EIA~~lg~s~~tV~~rl~rar~~L 178 (192)
T PRK09643 105 LDDVYPVAQLERDPTARVETALAVQRALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKSRCARGRARL 178 (192)
T ss_pred ccccccccCCcccHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 01 1122345777777775433 344999999999999999999999998765
No 61
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=99.70 E-value=1.6e-16 Score=146.42 Aligned_cols=130 Identities=15% Similarity=0.120 Sum_probs=105.1
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCc
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip 343 (419)
.||+.|+..|.+.++.++. +.++..++||++||+|+.+|+.+++|++.. .|.+|++++++|.+++++|+..+.....
T Consensus 24 ~af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~flkl~~~~~~~~~~~--~~~~Wl~~Iarn~~~d~~Rk~~~~~~~~ 100 (185)
T PRK09649 24 RALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSARS--SARTWLLAIARHVVADHIRHVRSRPRTT 100 (185)
T ss_pred HHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHhccccCccc--hHHHHHHHHHHHHHHHHHHHhccccccc
Confidence 8999999999999999995 677788999999999999999999998643 7999999999999999999754322110
Q ss_pred -----cc---------hHHHHHHHHHHHHHHHhcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014764 344 -----NH---------LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVFSL 396 (419)
Q Consensus 344 -----~~---------l~e~~~~I~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~~l~rark~lSL 396 (419)
.. ..+....+..++..|++..|.+ |++|||+.||+|+++|+..+.++++.+--
T Consensus 101 ~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 101 RGARPEHLIDGDRHARGFEDLVEVTTMIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred cccchhhccChhhhhhhHHHHHHHHHHHHhCCHHHhHHhhhHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 10 0122345777777776544443 99999999999999999999999877654
No 62
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=99.69 E-value=2e-16 Score=148.26 Aligned_cols=130 Identities=18% Similarity=0.149 Sum_probs=105.0
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccC-
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL- 342 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~iri- 342 (419)
.|++.|+..|.+.|+.++.++.++..+++|++||+|+.+|+++.+|++.++ .|.||++++++|.+++++|+..+....
T Consensus 38 ~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wl~~I~rn~~~d~~Rk~~~~~~~~ 116 (206)
T PRK12526 38 QAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYTVMRNAAFDMLRKIKAKKEQN 116 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCccc-chhHHHHHHHHHHHHHHHHHhccccccc
Confidence 899999999999999999999999899999999999999999999997665 699999999999999999876532210
Q ss_pred ------c--c-------c---hHH--HHHHHHHHHHHHHhcC---------CCccHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014764 343 ------P--N-------H---LHE--RLGLIRNAKLRLEEKG---------VTPSVDRIAEYLNMSQKKVRNATEAIGKV 393 (419)
Q Consensus 343 ------p--~-------~---l~e--~~~~I~~a~~~L~e~g---------RepS~eEIAe~LGIS~etVr~~l~rark~ 393 (419)
+ . . ... ....+..++..|++.. .+.|++|||+.||+|+++|+..++++++.
T Consensus 117 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~ 196 (206)
T PRK12526 117 LGDDIWPIEQALAESQSESEEFSDHLMDKQILSYIEKLPEAQQTVVKGVYFQELSQEQLAQQLNVPLGTVKSRLRLALAK 196 (206)
T ss_pred cccccchhhhhcccccCchHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 0 0 0 000 1134666666665433 34499999999999999999999999865
Q ss_pred c
Q 014764 394 F 394 (419)
Q Consensus 394 l 394 (419)
+
T Consensus 197 L 197 (206)
T PRK12526 197 L 197 (206)
T ss_pred H
Confidence 4
No 63
>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=99.69 E-value=3.1e-16 Score=143.08 Aligned_cols=129 Identities=19% Similarity=0.201 Sum_probs=103.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCc
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip 343 (419)
.||+.|+..|.+.|+.+|.++.++..+++|++||+|+++|+.+.+|++.. .|.+|++.+++|.+++++++..+.....
T Consensus 20 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~~--~~~~wl~~iarn~~~~~~r~~~r~~~~~ 97 (190)
T TIGR02939 20 QAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGDS--AFYTWLYRIAVNTAKNHLVAQGRRPPTS 97 (190)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCCC--ccHhHHHHHHHHHHHHHHHHhccCCCcc
Confidence 89999999999999999999999999999999999999999999998653 7999999999999999998655322110
Q ss_pred ----------------------cc---hHHHHHHHHHHHHHHHhcCCC---------ccHHHHHHHcCCCHHHHHHHHHH
Q 014764 344 ----------------------NH---LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 344 ----------------------~~---l~e~~~~I~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~~l~r 389 (419)
.. ..+....+..++..|++..+. .+++|||+.||+|+.+|+..+.+
T Consensus 98 ~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~EIA~~lgis~~tv~~~l~r 177 (190)
T TIGR02939 98 DVEIEDAEHFEGADRLREIDTPERLLLSRELEQTVMRAVEALPEDLRTAITLRELEGLSYEDIARIMDCPVGTVRSRIFR 177 (190)
T ss_pred cccccchhhhcccccccccCChHHHHHHHHHHHHHHHHHHcCCHHHhhhhhhhhhcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 00 011123466666666543333 39999999999999999999999
Q ss_pred hCccc
Q 014764 390 IGKVF 394 (419)
Q Consensus 390 ark~l 394 (419)
+++.+
T Consensus 178 ar~~L 182 (190)
T TIGR02939 178 AREAI 182 (190)
T ss_pred HHHHH
Confidence 98654
No 64
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=99.69 E-value=2.4e-16 Score=142.61 Aligned_cols=129 Identities=16% Similarity=0.112 Sum_probs=104.9
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCc
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip 343 (419)
.|++.|+..|.+.|+.+|.++.++..+++|++||+|+++|++++.|++. .+|.+|++.+++|.+++++++..+.....
T Consensus 18 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~r~~~~~~~~~ 95 (176)
T PRK09638 18 AALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGR--SKFSTWLISIASRLYKDHLRKQKREKLRL 95 (176)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHHhccccchh
Confidence 8999999999999999999999999999999999999999999999864 38999999999999999999765422111
Q ss_pred c------------c---hHHHHHHHHHHHHHHHhcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 344 N------------H---LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 344 ~------------~---l~e~~~~I~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
. . .......+..++..|++..+. .+++|||+.||+|+.+|+..+.++++.+
T Consensus 96 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l~is~~~V~~~l~ra~~~l 170 (176)
T PRK09638 96 QRAKEETLRKEKWEAAIKGAEWSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHHGIKQL 170 (176)
T ss_pred hhcccccCCccchHHHHHhhhHHHHHHHHHcCCHHHhheeeehhhcCCCHHHHHHHHCCChhHHHHHHHHHHHHH
Confidence 0 0 111234466677777543333 3999999999999999999999987654
No 65
>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=99.69 E-value=3.8e-16 Score=149.33 Aligned_cols=121 Identities=19% Similarity=0.206 Sum_probs=100.5
Q ss_pred HHHHHHHHhHHHHHHHHHHccCCC--CChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcc---c
Q 014764 265 AREKLVMSNVRLVMSIAQRYDNMG--ADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSR---T 339 (419)
Q Consensus 265 A~e~LIe~yl~LV~sIAkry~~~g--~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r---~ 339 (419)
.+++||..|.|+|.++|.+|+++. .+.||++|+|++|||+|+++||+++|.+|.||+.++|++.+.+++|+..+ .
T Consensus 10 ~~e~LI~~Y~plI~~~a~~~~~~~~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~sya~~~Ir~~i~dylRk~~k~~~~ 89 (218)
T TIGR02895 10 EREELIRQYKPFIAKIVSSVCGRYIDTKSDDELSIGLIAFNEAIESYDSNKGKSFLSFAKLIIKRRLIDYIRKNQKYQNL 89 (218)
T ss_pred HHHHHHHHhHHHHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHhcccccCe
Confidence 499999999999999999998664 58999999999999999999999999999999999999999999999873 4
Q ss_pred ccCccchHHHHHHHHHHHHHHH-hcCCCccHHHHHHH------cCCCHHHHHH
Q 014764 340 LRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEY------LNMSQKKVRN 385 (419)
Q Consensus 340 irip~~l~e~~~~I~~a~~~L~-e~gRepS~eEIAe~------LGIS~etVr~ 385 (419)
+++|+...+....+..+...+. ..++.++.+||+.. .||+.+.+-+
T Consensus 90 v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~~~~~L~~~gi~~~dLv~ 142 (218)
T TIGR02895 90 LYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILEYKKLLKQFGIEFVELVK 142 (218)
T ss_pred eeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcCCcHHHHhh
Confidence 4677655555556666666664 46788888888864 3777766544
No 66
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=99.68 E-value=7.8e-17 Score=147.76 Aligned_cols=131 Identities=18% Similarity=0.160 Sum_probs=106.6
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccC-
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL- 342 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~iri- 342 (419)
.||+.|+..|.+.|+.+|.+++++..++||++||+|+.+|+.+.+|++..+..|.||++.+++|.+++++|+..+....
T Consensus 9 ~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn~~~d~~Rk~~~~~~~~ 88 (185)
T PRK12542 9 EKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRKNKRHETFL 88 (185)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHhhhhhhhh
Confidence 7999999999999999999999999999999999999999999999865444899999999999999999987543211
Q ss_pred ---c--------cch------HHHHHHHHHHHHHHHhcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 343 ---P--------NHL------HERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 343 ---p--------~~l------~e~~~~I~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
+ ... .+....+..++..|++..|. .+++|||+.||+|+++|+..+.++++.+
T Consensus 89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~L 166 (185)
T PRK12542 89 EEYERESIEAVDENIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARKRV 166 (185)
T ss_pred hhccccchhhhhccHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 0 000 11123466777777654444 3999999999999999999999998655
No 67
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=99.68 E-value=4.2e-16 Score=141.89 Aligned_cols=129 Identities=21% Similarity=0.189 Sum_probs=103.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccC-
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL- 342 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~iri- 342 (419)
.|++.|+..|.++|+.+|.++.++..+++|++||+|++||+++.+|++.. .|.+|++++++|.+++++|+..+....
T Consensus 18 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn~~~d~~R~~~~~~~~~ 95 (187)
T PRK09641 18 NAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATNLTIDRLRKRKPDYYLD 95 (187)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHHHHHHHHHhcCcccccc
Confidence 89999999999999999999999989999999999999999999998753 799999999999999999976542211
Q ss_pred ---------------ccc---------hHHHHHHHHHHHHHHHhcC---------CCccHHHHHHHcCCCHHHHHHHHHH
Q 014764 343 ---------------PNH---------LHERLGLIRNAKLRLEEKG---------VTPSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 343 ---------------p~~---------l~e~~~~I~~a~~~L~e~g---------RepS~eEIAe~LGIS~etVr~~l~r 389 (419)
+.. ..+....+..++..|+... .+.+++|||+.||+|.++|++.+.+
T Consensus 96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~~~~~s~~eIA~~lgis~~~v~~~l~R 175 (187)
T PRK09641 96 AEVAGTEGLTMYSQLAADDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVKTRIHR 175 (187)
T ss_pred ccccCCcchhhhcccccCcCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHhhCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 000 0111133566666664322 3449999999999999999999999
Q ss_pred hCccc
Q 014764 390 IGKVF 394 (419)
Q Consensus 390 ark~l 394 (419)
+++.+
T Consensus 176 ar~~L 180 (187)
T PRK09641 176 GREAL 180 (187)
T ss_pred HHHHH
Confidence 97654
No 68
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=99.68 E-value=5.5e-16 Score=142.24 Aligned_cols=129 Identities=21% Similarity=0.185 Sum_probs=103.6
Q ss_pred HHHHHHHHHhHHHHHHHHH----HccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhccc
Q 014764 264 LAREKLVMSNVRLVMSIAQ----RYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRT 339 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAk----ry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~ 339 (419)
.||+.|+.+|.+.|+.+++ ++.++..+++|++||+|+.+|+.+..|++.. .|.+|++.+++|.+++++|+..+.
T Consensus 21 ~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~--~f~~wl~~i~~n~~~d~~R~~~~~ 98 (184)
T PRK12539 21 AAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTPWVYAIARYKLIDHLRRTRAS 98 (184)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCCC--ChHHHHHHHHHHHHHHHHHHHhcc
Confidence 8999999999999999976 4557888999999999999999999998754 699999999999999999976532
Q ss_pred c-cCc---------c---chHHHHHHHHHHHHHHHhcCC---------CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 340 L-RLP---------N---HLHERLGLIRNAKLRLEEKGV---------TPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 340 i-rip---------~---~l~e~~~~I~~a~~~L~e~gR---------epS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
. ..+ . ...+....+..++..|++..+ +.+++|||+.||+|.++|+..+.++++.+
T Consensus 99 ~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ra~~~L 175 (184)
T PRK12539 99 LADVPIDDADELVAHDDHAAVESTLDLGRLLARLPEKMRLAIQAVKLEGLSVAEAATRSGMSESAVKVSVHRGLKAL 175 (184)
T ss_pred ccccChhhhccccCCcHHhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCcHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 1 111 0 012233457777777754333 44999999999999999999999997654
No 69
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=99.66 E-value=7.3e-16 Score=141.36 Aligned_cols=133 Identities=24% Similarity=0.240 Sum_probs=110.1
Q ss_pred hHHHHHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhccc
Q 014764 260 MECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRT 339 (419)
Q Consensus 260 ~~~~~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~ 339 (419)
.....+++.++..|.+.++.++.+++++..++|||+||+|+.+|+++..| ...+ .|.||++++++|.+++++|+..+.
T Consensus 11 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~~~-~~~~wl~~Ia~n~~iD~~R~~~r~ 88 (182)
T COG1595 11 RGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RGRS-SFKAWLYRIARNLAIDRLRKRKRR 88 (182)
T ss_pred hcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CCCC-chHHHHHHHHHHHHHHHHHHhccc
Confidence 34457999999999999999999999988899999999999999999999 4444 899999999999999999977653
Q ss_pred ccC-c-------------cch-----HHHHHHHHHHHHHHHhcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 340 LRL-P-------------NHL-----HERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 340 iri-p-------------~~l-----~e~~~~I~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~~l~rar 391 (419)
... . ... .+....+..++..|+...|. .|++|||+.||||+++|++.+++++
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 0 001 23445688888888765544 3999999999999999999999998
Q ss_pred ccc
Q 014764 392 KVF 394 (419)
Q Consensus 392 k~l 394 (419)
+.+
T Consensus 169 ~~l 171 (182)
T COG1595 169 KKL 171 (182)
T ss_pred HHH
Confidence 654
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=99.66 E-value=5.3e-16 Score=141.23 Aligned_cols=129 Identities=19% Similarity=0.169 Sum_probs=99.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCC-----ChhhHhhHHHHHHHH-hHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhc
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGA-----DMADLVQGGLIGLLR-GIEKFDSSKGFKISTYVYWWIRQGVSRALVENS 337 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~-----d~EDLVQEG~IgLlr-AIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~ 337 (419)
.||+.|+..|.+.|+.+|.++.++.. +++|++||+|+.+|+ ...+|++. + .|.+|++.+++|.+++++|+..
T Consensus 17 ~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~-~-~~~~wl~~i~~n~~~d~~R~~~ 94 (183)
T TIGR02999 17 AARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR-A-HFFAAAAKAMRRILVDHARRRR 94 (183)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCCch-H-HHHHHHHHHHHHHHHHHHHHHH
Confidence 89999999999999999999998877 899999999999998 78888754 3 7999999999999999998754
Q ss_pred ccccC------------cc---chHHHHHHHHHHHHH---HHhcC---------CCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 338 RTLRL------------PN---HLHERLGLIRNAKLR---LEEKG---------VTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 338 r~iri------------p~---~l~e~~~~I~~a~~~---L~e~g---------RepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
+..+. +. ...+....+..+... |++.. .+.|++|||+.||+|+++|+..+.++
T Consensus 95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tVk~~l~Ra 174 (183)
T TIGR02999 95 AQKRGGGAVRVPLDEVLPDAEADLDEELLDLDDALDKLAQVDPRQAEVVELRFFAGLTVEEIAELLGVSVRTVERDWRFA 174 (183)
T ss_pred HHhccCCccccccccccCCCCccHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 32110 00 111222233344333 54433 34499999999999999999999999
Q ss_pred Cccc
Q 014764 391 GKVF 394 (419)
Q Consensus 391 rk~l 394 (419)
++.+
T Consensus 175 r~~L 178 (183)
T TIGR02999 175 RAWL 178 (183)
T ss_pred HHHH
Confidence 7654
No 71
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=99.66 E-value=1.3e-15 Score=139.18 Aligned_cols=129 Identities=19% Similarity=0.165 Sum_probs=103.6
Q ss_pred HHHHHHHHHhHHHHHHHHHHccC----CCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhccc
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDN----MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRT 339 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~----~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~ 339 (419)
.|++.|+..|.+.|+.+|.++++ +..+++|++||+|+.+|+..++|+... .|.+|++.+++|.+.++++++.+.
T Consensus 22 ~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~~--~~~~wl~~i~rn~~~d~~Rr~~~~ 99 (184)
T PRK12512 22 AAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPGA--PFAPWLFAIARNKLIDALRRRGRR 99 (184)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCccc--cHHHHHHHHHHHHHHHHHHhhccc
Confidence 89999999999999999998875 346899999999999999999998643 799999999999999999876543
Q ss_pred ccC---------ccc---hHHHHHHHHHHHHHHHhcCC---------CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 340 LRL---------PNH---LHERLGLIRNAKLRLEEKGV---------TPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 340 iri---------p~~---l~e~~~~I~~a~~~L~e~gR---------epS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
... +.. .......+..++..|++..+ +.+++|||+.||+|..+|+..+.++++.+
T Consensus 100 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l~is~~tV~~~l~ra~~~L 175 (184)
T PRK12512 100 VFVDIDDFAETLPAEPATETLPAGDVGRHLETLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVRVALHRGLAAL 175 (184)
T ss_pred ccCCchhccccccccchhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 221 111 11223456777777754433 34999999999999999999999998654
No 72
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=99.66 E-value=5.2e-16 Score=139.49 Aligned_cols=129 Identities=24% Similarity=0.192 Sum_probs=102.8
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCc
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip 343 (419)
.|++.|+..|.++|+.++.+|.+++.+++|++||+|++||+++.+|+ . +.+|.+|++.++++.+.+++++..+....+
T Consensus 10 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~-~-~~~~~~~l~~~~~~~~~~~~r~~~~~~~~~ 87 (182)
T PRK09652 10 AAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR-G-GAAFYTWLYRIARNTAINYLRKQGRRPPAS 87 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcC-C-CcchHHHHHHHHHHHHHHHHHcccCCCCcc
Confidence 89999999999999999999999889999999999999999999998 3 348999999999999999998765432211
Q ss_pred -------c---------c---h------HHHHHHHHHHHHHHHhcC---------CCccHHHHHHHcCCCHHHHHHHHHH
Q 014764 344 -------N---------H---L------HERLGLIRNAKLRLEEKG---------VTPSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 344 -------~---------~---l------~e~~~~I~~a~~~L~e~g---------RepS~eEIAe~LGIS~etVr~~l~r 389 (419)
. . . .+....+..++..|++.. .+.+++|||+.||+|+.+|+..+.+
T Consensus 88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~tV~~~l~r 167 (182)
T PRK09652 88 DVDAEEAEDFDLADALRDISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFR 167 (182)
T ss_pred ccccccccccccccccccccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 0 0 0 012234555555553322 3449999999999999999999999
Q ss_pred hCccc
Q 014764 390 IGKVF 394 (419)
Q Consensus 390 ark~l 394 (419)
+++.+
T Consensus 168 a~~~L 172 (182)
T PRK09652 168 AREAL 172 (182)
T ss_pred HHHHH
Confidence 87654
No 73
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=99.65 E-value=8.3e-16 Score=136.48 Aligned_cols=128 Identities=16% Similarity=0.163 Sum_probs=104.1
Q ss_pred HHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCc-
Q 014764 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP- 343 (419)
Q Consensus 265 A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip- 343 (419)
||+.++..|.+.|+.+|.++.++..++||++||+|+.+|+++++|++.. .|.+|++++++|.++++++++.+.....
T Consensus 2 ~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~~~~ 79 (159)
T TIGR02989 2 AFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRDRLVFD 79 (159)
T ss_pred HHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhcccccccC
Confidence 7899999999999999999999999999999999999999999999764 6999999999999999999876432210
Q ss_pred cc----------------hHHHHHHHHHHHHHHHhcC---------CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 344 NH----------------LHERLGLIRNAKLRLEEKG---------VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 344 ~~----------------l~e~~~~I~~a~~~L~e~g---------RepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
.. ..+....+..++..|++.. .+.+++|||+.||||.++|+..++++++.+
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~v~~l~~~~g~~~~eIA~~l~is~~tv~~~l~Rar~~L 155 (159)
T TIGR02989 80 DELLEALAAEAEATEADRSEDELQALEGCLEKLPERQRELLQLRYQRGVSLTALAEQLGRTVNAVYKALSRLRVRL 155 (159)
T ss_pred HHHHHHHHhhcccchHhhHHHHHHHHHHHHHHCCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 00 1112234566666665433 344999999999999999999999998654
No 74
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=99.65 E-value=1e-15 Score=140.89 Aligned_cols=129 Identities=16% Similarity=0.138 Sum_probs=103.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccC-
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL- 342 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~iri- 342 (419)
.||+.|+..|.+.|+.++.++.++..++||++||+|+.+|+.+.+|++. ..|.+|++.+++|.+.++++...+....
T Consensus 22 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~r~~~~~~~~~ 99 (189)
T PRK12515 22 TAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIARFKALSALRRRKHEEIDD 99 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CChHHHHHHHHHHHHHHHHHccCCCCCcc
Confidence 8999999999999999999999998999999999999999999999964 3799999999999999999865432110
Q ss_pred ------cc------ch---HHHHHHHHHHHHHHHhcC---------CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 343 ------PN------HL---HERLGLIRNAKLRLEEKG---------VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 343 ------p~------~l---~e~~~~I~~a~~~L~e~g---------RepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
+. .. .+....+..++..|++.. .+.+++|||+.||+|+++|+.++.++++.+
T Consensus 100 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~tV~~~l~Rar~~L 175 (189)
T PRK12515 100 EAAAAIEDGADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYARKKL 175 (189)
T ss_pred ccccccCCCCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 00 00 011233566666665433 345999999999999999999999998655
No 75
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=99.65 E-value=5.7e-16 Score=142.76 Aligned_cols=128 Identities=15% Similarity=0.135 Sum_probs=104.6
Q ss_pred HHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCcc
Q 014764 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPN 344 (419)
Q Consensus 265 A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~ 344 (419)
+|+.|+..|.+.|+.+|.+++++..++||++||+|+.+|+.+++|++.. +|.||++++++|.+++++|+..+......
T Consensus 3 ~~~~l~~~~~~~l~~~a~~~~~~~~~AeDivQevfl~~~~~~~~~~~~~--~~~~WL~~ia~n~~~d~~Rk~~r~~~~~~ 80 (191)
T PRK12520 3 IAPAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQS--SLKTYLVGILKHKIIDAIRSGRREVRLSL 80 (191)
T ss_pred chHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhcccc--cHHHHHHHHHHHHHHHHHHhhcCcCcccc
Confidence 7899999999999999999999999999999999999999999998553 79999999999999999998664322110
Q ss_pred ------------------------------ch------HHHHHHHHHHHHHHHhcCCC---------ccHHHHHHHcCCC
Q 014764 345 ------------------------------HL------HERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMS 379 (419)
Q Consensus 345 ------------------------------~l------~e~~~~I~~a~~~L~e~gRe---------pS~eEIAe~LGIS 379 (419)
.. .+....+..++..|++..|. .|++|||+.||+|
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 11123466777777554443 3999999999999
Q ss_pred HHHHHHHHHHhCccc
Q 014764 380 QKKVRNATEAIGKVF 394 (419)
Q Consensus 380 ~etVr~~l~rark~l 394 (419)
+++|+..+.++++.+
T Consensus 161 ~~tV~~~l~Rar~~L 175 (191)
T PRK12520 161 ATNAWVLLYRARMRL 175 (191)
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999999998765
No 76
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=99.65 E-value=1e-15 Score=140.01 Aligned_cols=130 Identities=12% Similarity=0.132 Sum_probs=105.6
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccC
Q 014764 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (419)
Q Consensus 263 ~~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~iri 342 (419)
..||+.|+..|.+.|++++.+++++..+++|++||+|+.+|+++.+|++.. .|.+|++++++|.+++++|+..+....
T Consensus 15 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~~--~~~awl~~ia~n~~~d~~Rk~~~~~~~ 92 (179)
T PRK09415 15 EDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKS--SLKTWLYRIAINHCKDYLKSWHNKKVI 92 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCCc--ccHHHHHHHHHHHHHHHHHhhcccccc
Confidence 479999999999999999999999999999999999999999999998643 799999999999999999875332111
Q ss_pred c---------------cc---hHHHHHHHHHHHHHHHhcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 343 P---------------NH---LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 343 p---------------~~---l~e~~~~I~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
+ .. ..+....+..++..|++..|++ |++|||+.||||.++|+.++.++++.+
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 0 00 1122345666777776545444 999999999999999999999998654
No 77
>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=99.64 E-value=1.1e-15 Score=147.92 Aligned_cols=129 Identities=15% Similarity=0.058 Sum_probs=103.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHH-------hHhhcCCCCCCchhhHHHHHHHhhHHHHHHHh
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLR-------GIEKFDSSKGFKISTYVYWWIRQGVSRALVEN 336 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlr-------AIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~ 336 (419)
.||+.|+..|.+.|+.++.+++++..++||++||+|+.+|. .+.+|++.. .|.||++++++|.++++++++
T Consensus 39 ~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~~--~~~tWL~~Ia~N~~id~lRk~ 116 (244)
T TIGR03001 39 AALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGRG--PLLSWVRIVATRIALELQAQE 116 (244)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccchhhhhhccCCCC--chHhHHHHHHHHHHHHHHHHh
Confidence 89999999999999999999999999999999999999994 788898643 799999999999999999976
Q ss_pred cccccCc---------------cch-H------HHHHHHHHHHHHHHhcCCC---------ccHHHHHHHcCCCHHHHHH
Q 014764 337 SRTLRLP---------------NHL-H------ERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRN 385 (419)
Q Consensus 337 ~r~irip---------------~~l-~------e~~~~I~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~ 385 (419)
.+...+. ... . +....+..++..|++..|+ .|++|||+.||||+++|+.
T Consensus 117 ~r~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~e~~~~l~~aL~~Lp~~~R~v~~L~~~eg~S~~EIA~~Lgis~~TVk~ 196 (244)
T TIGR03001 117 RRHSPVEEPTELAALPAPGSDPELDLLRERYRQDFRQALREALAALSERERHLLRLHFVDGLSMDRIGAMYQVHRSTVSR 196 (244)
T ss_pred cccCccccccccccccCCCCCHHHHHHHHhhHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHH
Confidence 5422110 000 0 1223467777777654433 4999999999999999999
Q ss_pred HHHHhCccc
Q 014764 386 ATEAIGKVF 394 (419)
Q Consensus 386 ~l~rark~l 394 (419)
.+.++++.+
T Consensus 197 rl~RAr~~L 205 (244)
T TIGR03001 197 WVAQARERL 205 (244)
T ss_pred HHHHHHHHH
Confidence 999987644
No 78
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=99.64 E-value=1.4e-15 Score=137.83 Aligned_cols=129 Identities=15% Similarity=0.109 Sum_probs=104.5
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccC-
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL- 342 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~iri- 342 (419)
..|++|+..|.++|+.+|.+|+++..++||++||+|+.+|+.+++|++.. +|.+|++.+++|.+.+++|++.+....
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 46999999999999999999999999999999999999999999998754 799999999999999999876543110
Q ss_pred --------------------ccc--hHHHHHHHHHHHHHHHhcC---------CCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 343 --------------------PNH--LHERLGLIRNAKLRLEEKG---------VTPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 343 --------------------p~~--l~e~~~~I~~a~~~L~e~g---------RepS~eEIAe~LGIS~etVr~~l~rar 391 (419)
+.. ..+....+..++..|+... .+.+++|||+.||+|+++|+..+.+++
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~~~s~~EIA~~lgis~~tV~~~l~Ra~ 160 (173)
T PRK12522 81 LDLFHKEDGGEIEFADDVNISEEFIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAK 160 (173)
T ss_pred ccccchhhhhhhccccCCCChHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 000 0112234666677775433 344999999999999999999999998
Q ss_pred ccc
Q 014764 392 KVF 394 (419)
Q Consensus 392 k~l 394 (419)
+.+
T Consensus 161 ~~L 163 (173)
T PRK12522 161 KQM 163 (173)
T ss_pred HHH
Confidence 655
No 79
>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=99.64 E-value=1.4e-15 Score=140.37 Aligned_cols=130 Identities=16% Similarity=0.143 Sum_probs=105.9
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccC
Q 014764 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (419)
Q Consensus 263 ~~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~iri 342 (419)
..+|+.|+..|.+.|+.+|.+++++..++||++||+|+.+|+.+.+|++.. .|.+|++++++|.+++++|+..+....
T Consensus 10 ~~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~~~~~~~~~~--~~~~wL~~iarN~~~d~~Rk~~~~~~~ 87 (193)
T TIGR02947 10 AQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPGT--NLKAWLYRILTNTYINSYRKAQRRPQQ 87 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcccCCCC--cchHHHHHHHHHHHHHHHHHhcCCccc
Confidence 378999999999999999999999999999999999999999999998643 799999999999999999876543211
Q ss_pred c--cc------------------hH-------HHHHHHHHHHHHHHhcCCCc---------cHHHHHHHcCCCHHHHHHH
Q 014764 343 P--NH------------------LH-------ERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNA 386 (419)
Q Consensus 343 p--~~------------------l~-------e~~~~I~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~~ 386 (419)
. .. .. +....+..++..|++..|.+ +++|||+.||+|+++|+..
T Consensus 88 ~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~r~i~~L~~~~g~s~~EIA~~lgis~~tVk~~ 167 (193)
T TIGR02947 88 SDDDDIEDWQLAKAASHTSNGLRSAELEALDGLPDQDIKDALQGLPEEFRQAVYLADVEGFAYKEIAEIMGTPIGTVMSR 167 (193)
T ss_pred ccchhhhhhhhccccccccccccchhHHHHhhhhHHHHHHHHHhCCHHHhhheeehhhcCCCHHHHHHHHCCCHHHHHHH
Confidence 0 00 00 11245677777776544443 9999999999999999999
Q ss_pred HHHhCccc
Q 014764 387 TEAIGKVF 394 (419)
Q Consensus 387 l~rark~l 394 (419)
+.++++.+
T Consensus 168 l~Rar~~L 175 (193)
T TIGR02947 168 LHRGRKQL 175 (193)
T ss_pred HHHHHHHH
Confidence 99998654
No 80
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=99.63 E-value=1.3e-15 Score=137.77 Aligned_cols=131 Identities=15% Similarity=0.095 Sum_probs=104.7
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhccccc-
Q 014764 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR- 341 (419)
Q Consensus 263 ~~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~ir- 341 (419)
..+|+.|+..|.+.|+++|.+++++..++||++||+|+.+|+..++|++..+ .|.+|++++++|.+++++|+..+...
T Consensus 8 ~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~~~~~~~~~~~-~~~~wL~~iarn~~~d~~Rk~~~~~~~ 86 (173)
T PRK09645 8 AALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTGR-SARAWLFTVARNLVIDERRSARARPVE 86 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-cHHHHHHHHHHHHHHHHHHhhcccccc
Confidence 3799999999999999999999998899999999999999999999975433 79999999999999999997553211
Q ss_pred -------Ccc-----chH--HHHHHHHHHHHHHHhcCC---------CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 342 -------LPN-----HLH--ERLGLIRNAKLRLEEKGV---------TPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 342 -------ip~-----~l~--e~~~~I~~a~~~L~e~gR---------epS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
.+. ... .....+..++..|++..| +.+++|||+.||+|+++|+..+.++++.+
T Consensus 87 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~L 162 (173)
T PRK09645 87 GGDDVLGVPEQSAPDEVDRALDRLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRAL 162 (173)
T ss_pred cccccccCCCCCCchHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 010 011 112346677777754333 44999999999999999999999997654
No 81
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=99.63 E-value=1.6e-15 Score=140.45 Aligned_cols=129 Identities=11% Similarity=0.127 Sum_probs=105.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCc
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip 343 (419)
.+|..|+..|.+.++.+|.+++++..++||++||+|+.+|+.+++|+... .|.+|++++++|.+++++|++.+.....
T Consensus 10 ~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~~--~~~awL~~Ia~n~~~d~~R~~~~~~~~~ 87 (187)
T PRK12516 10 PPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGT--NMKAWLFTILRNEFYSQMRKRGREVQDT 87 (187)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCcc--cHHHHHHHHHHHHHHHHHHhhcCCcccc
Confidence 79999999999999999999999999999999999999999999998653 6999999999999999999866422110
Q ss_pred c------------c-hHHHHHHHHHHHHHHHhcCC---------CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 344 N------------H-LHERLGLIRNAKLRLEEKGV---------TPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 344 ~------------~-l~e~~~~I~~a~~~L~e~gR---------epS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
. . .......+..++..|++..| +.+++|||+.||+|+++|+..+.++++.+
T Consensus 88 ~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~i~~L~~~~g~s~~EIA~~Lgis~~tVk~~l~Rar~~L 160 (187)
T PRK12516 88 DGMFTEQLAVHPSQYGTLDLQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRL 160 (187)
T ss_pred ccccccccCCCcchhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 0 0 11123456777777754333 44999999999999999999999998654
No 82
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=99.63 E-value=2.6e-15 Score=135.75 Aligned_cols=128 Identities=17% Similarity=0.129 Sum_probs=100.9
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhccccc--
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR-- 341 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~ir-- 341 (419)
.|++.|+..|.+.|+.++.++.+ ..+++|++||+|+.+|+.++.|++.. .|.+|++++++|.+++++|+..+...
T Consensus 11 ~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~ia~n~~~d~~R~~~~~~~~~ 87 (175)
T PRK12518 11 QSFRQLYRRYQQKVRSTLYQLCG-RELLDDLVQEVFLRVWKGLPKLRNPA--YFSTWLYRITWNVATDARRQFAQRPSRI 87 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcC-HhHHHHHHHHHHHHHHHhHHhhCCcc--cHHHHHHHHHHHHHHHHHHHhhccccch
Confidence 89999999999999999999874 47899999999999999999999753 79999999999999999987543211
Q ss_pred --Cc--------c--c-h--HHHHHHHHHHHHHHHhcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 342 --LP--------N--H-L--HERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 342 --ip--------~--~-l--~e~~~~I~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
.+ . . . .+....+..++..|++..+. .+++|||+.||+|.++|+..+.++++.+
T Consensus 88 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L 164 (175)
T PRK12518 88 QDDSLNDQPSRPSDTPDLMQLHYQDLVQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYARRQL 164 (175)
T ss_pred hcccccccccCCCCcHHHHHHHHHHHHHHHHHhCCHHHeeeeeehHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 00 0 0 0 01112355666667544333 3999999999999999999999998654
No 83
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=99.63 E-value=3.7e-15 Score=133.63 Aligned_cols=129 Identities=19% Similarity=0.125 Sum_probs=103.4
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCc
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip 343 (419)
.|++.|++.|.+.|++++.++.++..+++|++||+|++||+++.+|+ .. ..|.+|++.++++.+.++++...+.....
T Consensus 13 ~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~-~~-~~~~~~l~~i~~~~~~d~~r~~~~~~~~~ 90 (179)
T PRK11924 13 EAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN-GK-GSARTWLLTIARNVCYDLLRRRRREKAVL 90 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC-Cc-chHHHHHHHHHHHHHHHHHHhcccccccC
Confidence 89999999999999999999999999999999999999999999998 33 48999999999999999998765432211
Q ss_pred c-------------c------hHHHHHHHHHHHHHHHhcC---------CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 344 N-------------H------LHERLGLIRNAKLRLEEKG---------VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 344 ~-------------~------l~e~~~~I~~a~~~L~e~g---------RepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
. . ..+....+..++..|++.. .+.+++|||+.||+|..+|++.+.++++.+
T Consensus 91 ~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~~~~~~eIA~~lgis~~tv~~~~~ra~~~l 169 (179)
T PRK11924 91 SDDALEPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLL 169 (179)
T ss_pred cccccccccCCccCCHHHHHhhHHHHHHHHHHHHhCCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 0 0 1112234556666664332 344999999999999999999999987654
No 84
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=99.63 E-value=1.8e-15 Score=138.24 Aligned_cols=130 Identities=17% Similarity=0.147 Sum_probs=105.2
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhccccc-
Q 014764 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR- 341 (419)
Q Consensus 263 ~~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~ir- 341 (419)
..||+.|+..|.+.|+.++.+|+++..+++|++||+|+.+|+++.+|++.. .|.+|++.+++|.+.++++...+..+
T Consensus 6 ~~af~~l~~~~~~~l~~~~~~~~~~~~daeDl~Qevfl~l~~~~~~~~~~~--~f~~wl~~iarn~~~~~~r~~~~~~~~ 83 (179)
T PRK12543 6 QEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNR--PFRFWLIGLVIKQIHSWRRKRWRRFRI 83 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--ChHHHHHHHHHHHHHHHHHhhcccccc
Confidence 379999999999999999999999999999999999999999999999765 79999999999999999876542111
Q ss_pred --------------Cccch--HHHHHHHHHHHHHHHhcCC---------CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 342 --------------LPNHL--HERLGLIRNAKLRLEEKGV---------TPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 342 --------------ip~~l--~e~~~~I~~a~~~L~e~gR---------epS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
.|... .+....+..++..|++..| +.+++|||+.||||+++|+..+.++++.+
T Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~i~~l~~~e~~s~~EIA~~lgis~~tV~~~l~ra~~~L 161 (179)
T PRK12543 84 FEKAEEQRKPVSIDFSEDVLSKESNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKKL 161 (179)
T ss_pred ccccccccccccccChHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHccCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 01111 1223456677777755443 34999999999999999999999987654
No 85
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=99.62 E-value=3.2e-15 Score=149.64 Aligned_cols=130 Identities=23% Similarity=0.217 Sum_probs=105.1
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhccccc--
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR-- 341 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~ir-- 341 (419)
.+|++|+..|.+.|+.+|.+++++..++||++||+|+.+|+.+++|++. ..|.+|++++++|.+++++|+..+...
T Consensus 19 ~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~ 96 (339)
T PRK08241 19 DAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGR--SSLRTWLYRIATNVCLDALEGRARRPLPT 96 (339)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhhhccccc--cchHHHHHHHHHHHHHHHHHhhccccCcc
Confidence 8999999999999999999999999999999999999999999999853 379999999999999999997653211
Q ss_pred -C-----------------------cc-----------ch---HHH-HHHHHHHHHHHHhcCCCc---------cHHHHH
Q 014764 342 -L-----------------------PN-----------HL---HER-LGLIRNAKLRLEEKGVTP---------SVDRIA 373 (419)
Q Consensus 342 -i-----------------------p~-----------~l---~e~-~~~I~~a~~~L~e~gRep---------S~eEIA 373 (419)
. +. .. .+. ...+..++..|++..|.+ +++|||
T Consensus 97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA 176 (339)
T PRK08241 97 DLGAPAADPVDELVERPEVPWLEPYPDALLDPAAADPAARVVARESVRLAFVAALQHLPPRQRAVLILRDVLGWSAAEVA 176 (339)
T ss_pred ccCCCcCcccccccccccccccCCCCcccccccCCChHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhHHhhCCCHHHHH
Confidence 0 00 00 011 123666777776545444 999999
Q ss_pred HHcCCCHHHHHHHHHHhCcccc
Q 014764 374 EYLNMSQKKVRNATEAIGKVFS 395 (419)
Q Consensus 374 e~LGIS~etVr~~l~rark~lS 395 (419)
+.||+|+++|+.++.++++.+-
T Consensus 177 ~~lgis~~tVk~~l~RAr~~Lr 198 (339)
T PRK08241 177 ELLDTSVAAVNSALQRARATLA 198 (339)
T ss_pred HHhCCCHHHHHHHHHHHHHHHh
Confidence 9999999999999999986653
No 86
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=99.62 E-value=2.5e-15 Score=135.43 Aligned_cols=131 Identities=13% Similarity=0.146 Sum_probs=106.0
Q ss_pred HHHHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhccccc
Q 014764 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 341 (419)
Q Consensus 262 ~~~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~ir 341 (419)
+...|..|+..|.+.|+.+|.++.++..++||++||+|+.+|+.+.+|+... .|.+|++++++|.+++++|+..+...
T Consensus 4 ~~~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~~~~ 81 (164)
T PRK12547 4 CSKNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGT--NLKAWLFTILRNEFYSQMRKRGREVQ 81 (164)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCcc--cHHHHHHHHHHHHHHHHHHhhccccc
Confidence 4578999999999999999999999999999999999999999999998643 69999999999999999997654321
Q ss_pred Cc---------cc----hHHHHHHHHHHHHHHHhcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 342 LP---------NH----LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 342 ip---------~~----l~e~~~~I~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
.. .. .......+..++..|++..|. .+++|||+.||+|+++|++.+.++++.+
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~~L 156 (164)
T PRK12547 82 DSDGVFTARVAVHPAQYGSLDLQDFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRL 156 (164)
T ss_pred cccccccccCCCCchhhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 10 00 111234567777777554443 4999999999999999999999997643
No 87
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=99.62 E-value=4.5e-15 Score=138.58 Aligned_cols=128 Identities=10% Similarity=0.040 Sum_probs=101.9
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccC-
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL- 342 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~iri- 342 (419)
.||+.|+..|.+.++.++. +.++..++||++||+|+.+|+.+++|++.. .|.+|++.+++|.+++++|+..+....
T Consensus 25 ~a~~~l~~~y~~~l~~~~~-~~~~~~~AEDivQevflkl~~~~~~~~~~~--~~~~WL~~Iarn~~id~~Rk~~~~~~~~ 101 (196)
T PRK12535 25 AALTEFIRETQDDVWRLLA-HLGGHDIADDLTQETYLRVMSALPRFAARS--SARTWLLSLARRVWVDNIRHDMARPRKS 101 (196)
T ss_pred HHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHHhhhcCCcc--cHHHHHHHHHHHHHHHHHHhhccCCCcc
Confidence 8999999999999999975 567888999999999999999999998643 799999999999999999976432210
Q ss_pred -------------ccc--hHHHHHHHHHHHHHHHhcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 343 -------------PNH--LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 343 -------------p~~--l~e~~~~I~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
|.. ..+....+..++..|++..++ .+++|||+.||+|+++|+..+.++++.+
T Consensus 102 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIAe~lgis~~tV~~~l~Rar~~L 177 (196)
T PRK12535 102 ATEYEDAAATTASNETTGSWSEWIDVRTLIDALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSRVARARADL 177 (196)
T ss_pred cccccccccccCCcchhHHHHHHHHHHHHHHcCCHHHHHHhhhHHHhCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 000 112224566777777554443 3999999999999999999999987654
No 88
>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=99.60 E-value=2.6e-15 Score=132.08 Aligned_cols=128 Identities=22% Similarity=0.206 Sum_probs=101.3
Q ss_pred HHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccC--
Q 014764 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL-- 342 (419)
Q Consensus 265 A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~iri-- 342 (419)
||+.|+..|.+.|+.++.++.++..++||++||+|+++|+.+.+|++.. +|.+|++.++++.+.+++++..+....
T Consensus 2 a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~~--~~~~wl~~i~r~~~~d~~r~~~~~~~~~~ 79 (161)
T TIGR02985 2 AFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEVE--SFKAYLFTIVKNRSLNYLRHKQVEEKYQE 79 (161)
T ss_pred hHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhccccc--cHHHHHHHHHHHHHHHHHHHHHhHhHHHH
Confidence 7999999999999999999998889999999999999999999998644 799999999999999999876532110
Q ss_pred --------------ccc---hHHHHHHHHHHHHHHHhc---------CCCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 343 --------------PNH---LHERLGLIRNAKLRLEEK---------GVTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 343 --------------p~~---l~e~~~~I~~a~~~L~e~---------gRepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
|.. ..+....+..++..|++. ..+.++.|||+.||+|..+|+..+.++++.+
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~il~l~~~~~~~~~eIA~~lgis~~tv~~~~~ra~~~L 157 (161)
T TIGR02985 80 EILEIEVDELSENDPEEELEAKELQLIIYKAIEKLPEQCRKIFILSRFEGKSYKEIAEELGISVKTVEYHISKALKEL 157 (161)
T ss_pred HHHhhcccccCCCCcHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 000 011223355555555332 2345999999999999999999999987543
No 89
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=99.60 E-value=6e-15 Score=132.06 Aligned_cols=129 Identities=13% Similarity=0.096 Sum_probs=102.9
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccC
Q 014764 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (419)
Q Consensus 263 ~~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~iri 342 (419)
..||+.|+..|.+.|+.++.+++++..+++|++||+|+.+|+.+++|++. .|.||++.+++|.+++++|+..+....
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 599999999999999999876542211
Q ss_pred ----------ccc-----hHHHHHHHHHHHHHHHhcCC---------CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 343 ----------PNH-----LHERLGLIRNAKLRLEEKGV---------TPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 343 ----------p~~-----l~e~~~~I~~a~~~L~e~gR---------epS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
+.. ..+....+..++..|++..+ +.+++|||+.||+|.++|+..+.++++.+
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 000 11122334455566654333 34999999999999999999999998654
No 90
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=99.59 E-value=4e-15 Score=136.19 Aligned_cols=131 Identities=14% Similarity=-0.002 Sum_probs=102.4
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccC--CCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccc
Q 014764 263 SLAREKLVMSNVRLVMSIAQRYDN--MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340 (419)
Q Consensus 263 ~~A~e~LIe~yl~LV~sIAkry~~--~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~i 340 (419)
..+|+.|+..|.+.|+.++.++++ +..++||++||+|+.+|+.+++|+......|.||++++++|.+++++|+..+..
T Consensus 12 ~~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~~Rk~~~~~ 91 (178)
T PRK12529 12 RDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSWRRRQSLEL 91 (178)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 379999999999999998665555 467899999999999999999997543347999999999999999998754211
Q ss_pred c-------C-------ccc---hHHHHHHHHHHHHHHHhcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014764 341 R-------L-------PNH---LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKV 393 (419)
Q Consensus 341 r-------i-------p~~---l~e~~~~I~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~~l~rark~ 393 (419)
. . |.. ..+....|..++..|++..|. .|++|||+.||+|+++|+..+.++...
T Consensus 92 ~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~rAl~~ 170 (178)
T PRK12529 92 AWLEALATLPEPLHPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQAYVT 170 (178)
T ss_pred hhhhHhhhccCcCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 0 0 111 122334577788888655444 399999999999999999999988643
No 91
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=99.59 E-value=6.5e-15 Score=132.53 Aligned_cols=126 Identities=10% Similarity=0.048 Sum_probs=101.8
Q ss_pred HHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCc--
Q 014764 266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP-- 343 (419)
Q Consensus 266 ~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip-- 343 (419)
|+.|++.|.+.|+.+|.++.++..++||++||+|+.+|+.++.|++. .|.+|++++++|.+.+++|+..+.....
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wL~~i~~n~~~d~~R~~~~~~~~~~~ 79 (165)
T PRK09644 3 IEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYHTFIDFVRKEKKVSFVGTD 79 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc---chHHHHHHHHHHHHHHHHHhhhhccccchh
Confidence 67899999999999999999999999999999999999999999863 6999999999999999999876432211
Q ss_pred ----------cc---hHHHHHHHHHHHHHHHhcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 344 ----------NH---LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 344 ----------~~---l~e~~~~I~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
.. ..+....+..++..|++..+. .+++|||+.||+|+++|+..++++++.+
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 00 011224456666666543333 3999999999999999999999998755
No 92
>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=99.59 E-value=8.5e-15 Score=130.80 Aligned_cols=130 Identities=15% Similarity=0.073 Sum_probs=104.7
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhccccc-
Q 014764 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR- 341 (419)
Q Consensus 263 ~~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~ir- 341 (419)
..+|+.|+..|.+.|+.++.+++++..+++|++||+|+.+|+.+++|+. .+ .|.+|++.+++|.+++++++..+...
T Consensus 5 ~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~-~~-~~~~wl~~i~~n~~~d~~rk~~~~~~~ 82 (162)
T TIGR02983 5 EEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRD-PD-APDAYVRRVLVNLARSRWRRRRLLELP 82 (162)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCC-cc-cHHHHHHHHHHHHHHHHHHhhcccccc
Confidence 3799999999999999999999999999999999999999999999964 33 89999999999999999987653110
Q ss_pred ---Ccc----c---hHHHHHHHHHHHHHHHhcCC---------CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 342 ---LPN----H---LHERLGLIRNAKLRLEEKGV---------TPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 342 ---ip~----~---l~e~~~~I~~a~~~L~e~gR---------epS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
.+. . .......+..++..|++..+ +.+++|||+.||+|.++|+..+.++++.+
T Consensus 83 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ra~~~L 154 (162)
T TIGR02983 83 TRELPDAAAPDPAPDVALRAALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARL 154 (162)
T ss_pred ccccCcccCCccchhHHHHHHHHHHHHhCCHHHHHHhhhHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 010 0 11233456667777754333 34999999999999999999999998755
No 93
>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=99.58 E-value=1e-14 Score=125.26 Aligned_cols=126 Identities=29% Similarity=0.342 Sum_probs=101.9
Q ss_pred HHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccC--
Q 014764 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL-- 342 (419)
Q Consensus 265 A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~iri-- 342 (419)
|++.|+..|.++|+++++++..+..+++|++||++++++++++.|++. ..|.+|++.++++.+.+++++..+ .+.
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 789999999999999999999988999999999999999999999988 489999999999999999998763 110
Q ss_pred ------------ccc---hHHHHHHHHHHHHHHHhc---------CCCccHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014764 343 ------------PNH---LHERLGLIRNAKLRLEEK---------GVTPSVDRIAEYLNMSQKKVRNATEAIGKV 393 (419)
Q Consensus 343 ------------p~~---l~e~~~~I~~a~~~L~e~---------gRepS~eEIAe~LGIS~etVr~~l~rark~ 393 (419)
+.. .......+..++..|++. ..+.+..|||+.||+|..+|++++.++++.
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 000 112223455555555332 244599999999999999999999988654
No 94
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=99.58 E-value=1.1e-14 Score=134.38 Aligned_cols=129 Identities=16% Similarity=0.198 Sum_probs=104.8
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccC-
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL- 342 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~iri- 342 (419)
.++..++..|.+.|+++|.+++++..++||++||+|+.+|+.+++|++.. .|.+|++++++|.++++++++.+....
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 57889999999999999999999999999999999999999999998654 699999999999999999876542211
Q ss_pred -----------ccc-hHHHHHHHHHHHHHHHhcCC---------CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 343 -----------PNH-LHERLGLIRNAKLRLEEKGV---------TPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 343 -----------p~~-l~e~~~~I~~a~~~L~e~gR---------epS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
+.. .......+..++..|++..| +.+++|||+.||+|+++|+..+.++++.+
T Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RAr~~L 155 (182)
T PRK12540 83 DGSYAKTLKSQPGQNAHLEFEEFRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKL 155 (182)
T ss_pred cccccccccCCCchHHHHHHHHHHHHHHhCCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 000 11122446777777754333 34999999999999999999999998765
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=99.57 E-value=1.1e-14 Score=144.44 Aligned_cols=129 Identities=21% Similarity=0.201 Sum_probs=104.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccC-
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL- 342 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~iri- 342 (419)
.||+.|+..|.+.|+++|.+++++..++||++||+|+.+|+.+.+|++.. .|.+|++++++|.|++++|+..+....
T Consensus 5 ~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~~--~~~~WL~~Ia~n~~~d~~Rk~~~~~~~~ 82 (324)
T TIGR02960 5 AAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGRS--SVRTWLYRIATNACLDALEARQRRPRPV 82 (324)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCccc--chHHHHHHHHHHHHHHHHHhccCCcCcc
Confidence 79999999999999999999999999999999999999999999998643 799999999999999999876532110
Q ss_pred -------------------------cc-----------c------hHHH-HHHHHHHHHHHHhcCCCc---------cHH
Q 014764 343 -------------------------PN-----------H------LHER-LGLIRNAKLRLEEKGVTP---------SVD 370 (419)
Q Consensus 343 -------------------------p~-----------~------l~e~-~~~I~~a~~~L~e~gRep---------S~e 370 (419)
+. . ..+. ...+..++..|++..|.+ +++
T Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~ 162 (324)
T TIGR02960 83 GLGAPSADGTAAASEAAEVTWLEPLPDLTLDLDDPAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRDVLGWRAA 162 (324)
T ss_pred ccCCCCCcccccccccccccccCCCCccccccccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHHhCCCHH
Confidence 00 0 0111 123566777776555444 999
Q ss_pred HHHHHcCCCHHHHHHHHHHhCccc
Q 014764 371 RIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 371 EIAe~LGIS~etVr~~l~rark~l 394 (419)
|||+.||+|+++|++++.++++.+
T Consensus 163 EIA~~lgis~~tV~~~l~Rar~~L 186 (324)
T TIGR02960 163 ETAELLGTSTASVNSALQRARATL 186 (324)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHHH
Confidence 999999999999999999998655
No 96
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=99.57 E-value=6.5e-15 Score=133.58 Aligned_cols=128 Identities=16% Similarity=0.085 Sum_probs=101.1
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhccccc--
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR-- 341 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~ir-- 341 (419)
.||..|+..|.+.|+.++.+++++..+++|++||+|+.+|+. ..|... ..|.+|++++++|.+++++|+..+...
T Consensus 10 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~~~d~~Rk~~~~~~~~ 86 (172)
T PRK12523 10 ELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRRAALEQAYL 86 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 799999999999999999999999999999999999999987 456543 279999999999999999987643210
Q ss_pred -----C-------ccc---hHHHHHHHHHHHHHHHhcC---------CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 342 -----L-------PNH---LHERLGLIRNAKLRLEEKG---------VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 342 -----i-------p~~---l~e~~~~I~~a~~~L~e~g---------RepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
. |.. ..+....+..++..|++.. .+.+++|||+.||+|+++|+..+.++.+.+
T Consensus 87 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~~ 163 (172)
T PRK12523 87 AELALVPEAEQPSPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGLRQC 163 (172)
T ss_pred HHHhhcccccCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 0 010 0122235667777775433 344999999999999999999999987665
No 97
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=99.57 E-value=1.6e-14 Score=137.42 Aligned_cols=129 Identities=15% Similarity=0.153 Sum_probs=104.9
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccC
Q 014764 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (419)
Q Consensus 263 ~~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~iri 342 (419)
..+|+.|+..|.+.++.++.++.++..++||++||+|+.+|+.+.+|++. .|.+|++++++|.++++++++.+....
T Consensus 17 ~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~~---~~~aWL~~IarN~~~d~~Rk~~~~~~~ 93 (216)
T PRK12533 17 GERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRGD---NARPWLLAIVRHTWYSEWRRRANAHEV 93 (216)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCcc---chHhHHHHHHHHHHHHHHHhhcccccc
Confidence 37999999999999999999999999999999999999999999999752 599999999999999999876532110
Q ss_pred ------cc------------c------hHHHHHHHHHHHHHHHhcCCC---------ccHHHHHHHcCCCHHHHHHHHHH
Q 014764 343 ------PN------------H------LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 343 ------p~------------~------l~e~~~~I~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~~l~r 389 (419)
.. . ..+....+..++..|++..|. .+++|||+.||||+++|+..+++
T Consensus 94 ~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y~eg~s~~EIAe~LgiS~~tVk~~L~R 173 (216)
T PRK12533 94 AAPDTLDDADSLDDWQPAGEDPLALLLRAEDVRLVNAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRLAR 173 (216)
T ss_pred cccccccccccccccccCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHhHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 00 0 112234577777777554443 49999999999999999999999
Q ss_pred hCccc
Q 014764 390 IGKVF 394 (419)
Q Consensus 390 ark~l 394 (419)
+++.+
T Consensus 174 Ar~~L 178 (216)
T PRK12533 174 ARRRL 178 (216)
T ss_pred HHHHH
Confidence 98755
No 98
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=99.56 E-value=7.2e-15 Score=131.22 Aligned_cols=121 Identities=15% Similarity=0.081 Sum_probs=96.2
Q ss_pred HHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhccccc-C-------
Q 014764 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR-L------- 342 (419)
Q Consensus 271 e~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~ir-i------- 342 (419)
+.|.+.|+.+|.+++++..++||++||+|+.+|+++++|++. .|.+|++++++|.+++++|+..+... .
T Consensus 2 ~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~~~~~~~ 78 (160)
T PRK09642 2 QTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFR---GLKTWMARIATNHAIDYKRKKARENEELSLCKETE 78 (160)
T ss_pred chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcccccccc---hhHHHHHHHHHHHHHHHHHHhcccccccccchhhh
Confidence 578999999999999999999999999999999999999853 59999999999999999997654211 0
Q ss_pred --------ccch---HHHHHHHHHHHHHHHhcCC---------CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 343 --------PNHL---HERLGLIRNAKLRLEEKGV---------TPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 343 --------p~~l---~e~~~~I~~a~~~L~e~gR---------epS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
|... .+....+..++..|++..| +.|++|||+.||+|+++|++.+.++++.+
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 1112346667777755433 34999999999999999999999998654
No 99
>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=99.56 E-value=1.7e-14 Score=131.41 Aligned_cols=132 Identities=17% Similarity=0.091 Sum_probs=101.6
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcc----CCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhc-
Q 014764 263 SLAREKLVMSNVRLVMSIAQRYD----NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENS- 337 (419)
Q Consensus 263 ~~A~e~LIe~yl~LV~sIAkry~----~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~- 337 (419)
..|++.|+..|.+.|+.+|++|. ++..++||++||+|+.+|+++.+|++..+..|.+|++.+++|.+.+++++..
T Consensus 6 ~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r~~~~ 85 (189)
T TIGR02984 6 QEALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNVLADALRRHLG 85 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHHHHHHHHHH
Confidence 37999999999999999999874 3567899999999999999999998765558999999999999999998652
Q ss_pred ---ccc--cCc-------------------------cc---hHHHHHHHHHHHHHHHhcC---------CCccHHHHHHH
Q 014764 338 ---RTL--RLP-------------------------NH---LHERLGLIRNAKLRLEEKG---------VTPSVDRIAEY 375 (419)
Q Consensus 338 ---r~i--rip-------------------------~~---l~e~~~~I~~a~~~L~e~g---------RepS~eEIAe~ 375 (419)
+.. ..+ .. ..+....|..++..|++.. .+.+++|||+.
T Consensus 86 ~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vi~l~~~~g~s~~eIA~~ 165 (189)
T TIGR02984 86 AQKRDIRREQSLDAGGRLDESSVRLAAQLAADGPSPSQVAARREAAVRLAQALAKLPEDYREVILLRHLEGLSFAEVAER 165 (189)
T ss_pred HHhhhcccccCCCcccccCCcchhHHHHccCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCHHHHHHH
Confidence 110 000 00 0111234556666664322 34599999999
Q ss_pred cCCCHHHHHHHHHHhCccc
Q 014764 376 LNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 376 LGIS~etVr~~l~rark~l 394 (419)
||||.++|+..+.++++.+
T Consensus 166 lgis~~~v~~~l~Ra~~~L 184 (189)
T TIGR02984 166 MDRSEGAVSMLWVRGLARL 184 (189)
T ss_pred HCcCHHHHHHHHHHHHHHH
Confidence 9999999999999987643
No 100
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=99.56 E-value=1.8e-14 Score=129.04 Aligned_cols=127 Identities=15% Similarity=0.057 Sum_probs=101.5
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccc---
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL--- 340 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~i--- 340 (419)
.||+.|+++|.+.|+.++.+++++..++||++||+|+.+|+..+.|++ + .|.+|++++++|.+++++|+..+..
T Consensus 4 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~--~-~~~~wl~~i~~n~~~d~~R~~~~~~~~~ 80 (161)
T PRK12528 4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQI--I-EPRAFLTTIAKRVLCNHYRRQDLERAYL 80 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhccccccc--c-CHHHHHHHHHHHHHHHHHHHHHHHHhhH
Confidence 699999999999999999999999899999999999999999888764 2 6999999999999999998754211
Q ss_pred ----cCcc----c------hHHHHHHHHHHHHHHHhcC---------CCccHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014764 341 ----RLPN----H------LHERLGLIRNAKLRLEEKG---------VTPSVDRIAEYLNMSQKKVRNATEAIGKV 393 (419)
Q Consensus 341 ----rip~----~------l~e~~~~I~~a~~~L~e~g---------RepS~eEIAe~LGIS~etVr~~l~rark~ 393 (419)
..+. . ..+....+..++..|++.. .+.+++|||+.||+|.++|+..+.++.+.
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~~g~s~~EIA~~l~is~~tV~~~l~ra~~~ 156 (161)
T PRK12528 81 EALAQLPERVAPSEEERAIILETLVELDQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAMR 156 (161)
T ss_pred HHhhccccccCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 0110 0 1122245667777775433 34499999999999999999999998653
No 101
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=99.55 E-value=2.1e-14 Score=128.53 Aligned_cols=127 Identities=17% Similarity=0.110 Sum_probs=101.0
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCc
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip 343 (419)
.+|+.|++.|.+.|+.+|.++.++..+++|++||+|+.+|++ .|+.. ..|.+|++++++|.+.+++++..+.....
T Consensus 3 ~~f~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fi~~~~~--~~~~~--~~~~~wl~~i~rn~~~d~~rk~~~~~~~~ 78 (166)
T PRK09639 3 ETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKGI--ENEKGWLIKSARNVAYNYLRSEKRRRARI 78 (166)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH--hcccc--cchHHHHHHHHHHHHHHHHHHhccccccc
Confidence 689999999999999999999999999999999999999999 67643 37999999999999999998766432110
Q ss_pred ---------------cc---hHHHHHHHHHHHHHHHhcC--------CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 344 ---------------NH---LHERLGLIRNAKLRLEEKG--------VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 344 ---------------~~---l~e~~~~I~~a~~~L~e~g--------RepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
.. ..+....+..++..|++.. .+.+++|||+.||+|..+|+..+.++++.+
T Consensus 79 ~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~~g~s~~eIA~~lgis~~tV~~~i~ra~~~L 155 (166)
T PRK09639 79 LGEFQWQEVDNEPSPEEIWIRKEEITKVQEVLAKMTERDRTVLLLRFSGYSYKEIAEALGIKESSVGTTLARAKKKF 155 (166)
T ss_pred cchhhhhhccCCCChHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 00 0122234566666664322 455999999999999999999999987654
No 102
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=99.54 E-value=3.7e-14 Score=130.60 Aligned_cols=127 Identities=19% Similarity=0.148 Sum_probs=101.5
Q ss_pred HHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCcc-
Q 014764 266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPN- 344 (419)
Q Consensus 266 ~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~- 344 (419)
++.|++.|.+.|+.++.++.++..+++|++||+|+.+|+.+..|++. .+|.+|++++++|.+.+++|+..+....+.
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~aeDi~QEvflkl~~~~~~~~~~--~~~~~wL~~i~~n~~~d~~Rk~~~~~~~~~~ 80 (181)
T PRK09637 3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDG--SSIKSWLYQIANNTIIDFYRKKNRSEELPDD 80 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHhHHHhccc--cchHHHHHHHHHHHHHHHHHhccccCCcchh
Confidence 67899999999999999999999999999999999999999999853 379999999999999999987664332211
Q ss_pred -------c----hHHHHHHHHHHHHHHHhcC---------CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 345 -------H----LHERLGLIRNAKLRLEEKG---------VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 345 -------~----l~e~~~~I~~a~~~L~e~g---------RepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
. ..+....+..++..|++.. .+.+++|||+.||+|.++|+..+.++++.+
T Consensus 81 ~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~~~~EIA~~lgis~~tV~~~l~Rar~~L 150 (181)
T PRK09637 81 LLFEDEEREENAKKELAPCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKL 150 (181)
T ss_pred hhccCCChhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 0 1122234555556664333 344999999999999999999999987654
No 103
>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=99.54 E-value=2.7e-14 Score=126.15 Aligned_cols=122 Identities=20% Similarity=0.202 Sum_probs=97.3
Q ss_pred HHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccC-------
Q 014764 270 VMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL------- 342 (419)
Q Consensus 270 Ie~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~iri------- 342 (419)
+++|.+.|+.++.+++++..+++|++||+|+.+|+.+++|++ + +|.||++.++++.+.+++++..+....
T Consensus 1 y~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~--~-~f~~wl~~i~~~~~~d~~r~~~~~~~~~~~~~~~ 77 (154)
T TIGR02950 1 YREYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD--S-SIKPWLFRIARNAFIDWYRKDKKIQTIDDDAIGD 77 (154)
T ss_pred CchHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC--C-chHHHHHHHHHHHHHHHHHHhhhhccccHhhhhh
Confidence 357899999999999998899999999999999999999997 3 799999999999999999875532211
Q ss_pred --------ccc---hHHHHHHHHHHHHHHHhcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 343 --------PNH---LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 343 --------p~~---l~e~~~~I~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
|.. ..+....+..++..|++..+. .+++|||+.||+|+++|+..+.++++.+
T Consensus 78 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~L 149 (154)
T TIGR02950 78 LEQHPVESPEHHLLIKIEQEEITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARKEL 149 (154)
T ss_pred ccccccCChhHHHHHHHHHHHHHHHHHhCCHhheeeeeehhhccCcHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 000 011224567777777644333 4999999999999999999999987654
No 104
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=99.54 E-value=3.8e-14 Score=131.22 Aligned_cols=132 Identities=17% Similarity=0.139 Sum_probs=104.7
Q ss_pred HHHHHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccc
Q 014764 261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340 (419)
Q Consensus 261 ~~~~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~i 340 (419)
....+|+.|+..|.+.|+.+|.+++++..++||++||+|+.+|+.++.|++.. .|.+|++++++|.+.+..+...+..
T Consensus 20 ~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~~--~~~~wL~~Iarn~~~~~~r~~~~~~ 97 (188)
T PRK12517 20 SKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEK--AAKAWLITILRRENARRFERKQFDL 97 (188)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCcc--chHHHHHHHHHHHHHHHHHHhccCc
Confidence 35589999999999999999999999999999999999999999999998653 7999999999999888776543211
Q ss_pred -c-----Ccc---c---hHHHHHHHHHHHHHHHhcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 341 -R-----LPN---H---LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 341 -r-----ip~---~---l~e~~~~I~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
. .+. . .......+..++..|++..+. .+++|||+.||||+++|+.++.++++.+
T Consensus 98 ~~~~~~~~~~~~~~~~e~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~L 172 (188)
T PRK12517 98 VDIEDDSIEDDASHSSEEEMEQEWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARNQL 172 (188)
T ss_pred cCcccccccCccccChhHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 0 000 0 111123467777777654444 3999999999999999999999998654
No 105
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=99.53 E-value=3.7e-14 Score=131.13 Aligned_cols=126 Identities=15% Similarity=0.211 Sum_probs=99.2
Q ss_pred HHHHHHhHHHHHHHHHHccCCCCC-hhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCc--
Q 014764 267 EKLVMSNVRLVMSIAQRYDNMGAD-MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP-- 343 (419)
Q Consensus 267 e~LIe~yl~LV~sIAkry~~~g~d-~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip-- 343 (419)
+..+..|.+.|+.+|.+++++..+ +||++||+|+.+|+++++|++. + .|.+|++++++|.+++++|++.+.....
T Consensus 8 ~~~~~~~~~~l~~~a~~~~~~~~~~AEDivQevfl~~~~~~~~~~~~-~-~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~~~ 85 (195)
T PRK12532 8 DAELIESRKLLLHFARLQLPDHPDLAEDLVQETLLSAYSAGDSFQGR-A-LVNSWLFAILKNKIIDALRQIGRQRKVFTL 85 (195)
T ss_pred hhhHHHHHHHHHHHHHHHcCChhhhHHHHHHHHHHHHHHhccccccc-c-hHHHHHHHHHHHHHHHHHHHhccccccccc
Confidence 456788999999999999998888 9999999999999999999864 3 7999999999999999999865422110
Q ss_pred --------------------------------cc---hHHHHHHHHHHHHHHHhcCC---------CccHHHHHHHcCCC
Q 014764 344 --------------------------------NH---LHERLGLIRNAKLRLEEKGV---------TPSVDRIAEYLNMS 379 (419)
Q Consensus 344 --------------------------------~~---l~e~~~~I~~a~~~L~e~gR---------epS~eEIAe~LGIS 379 (419)
.. ..+....+..++..|++..| +.+++|||+.||+|
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~L~~~~g~s~~EIA~~lgis 165 (195)
T PRK12532 86 LDDELLDEAFESHFSQNGHWTPEGQPQHWNTPEKSLNNNEFQKILQSCLYNLPENTARVFTLKEILGFSSDEIQQMCGIS 165 (195)
T ss_pred ccccccchhhhhhhccccccccccCccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHHhCCCHHHHHHHHCCC
Confidence 00 01112346666777754333 34999999999999
Q ss_pred HHHHHHHHHHhCccc
Q 014764 380 QKKVRNATEAIGKVF 394 (419)
Q Consensus 380 ~etVr~~l~rark~l 394 (419)
+++|+..+.++++.+
T Consensus 166 ~~tVk~~l~Rar~~L 180 (195)
T PRK12532 166 TSNYHTIMHRARESL 180 (195)
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999999987654
No 106
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=99.53 E-value=3.1e-14 Score=133.03 Aligned_cols=125 Identities=15% Similarity=0.127 Sum_probs=99.0
Q ss_pred HHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCc---c
Q 014764 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP---N 344 (419)
Q Consensus 268 ~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip---~ 344 (419)
.++..|.+.|+.+|.+++++..++||++||+|+.+|+.+++|++.. .|.+|++++++|.+++++|+..+....+ .
T Consensus 12 ~~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~~--~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~~~ 89 (201)
T PRK12545 12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQS--AHKTWVFGILRNKLIDTLRARQRTVNLSALDA 89 (201)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhccccc--hHHHHHHHHHHHHHHHHHHhhccccccccccc
Confidence 3488899999999999999999999999999999999999998763 6999999999999999999866432111 0
Q ss_pred -----------------------------chH------HHHHHHHHHHHHHHhcC---------CCccHHHHHHHcCCCH
Q 014764 345 -----------------------------HLH------ERLGLIRNAKLRLEEKG---------VTPSVDRIAEYLNMSQ 380 (419)
Q Consensus 345 -----------------------------~l~------e~~~~I~~a~~~L~e~g---------RepS~eEIAe~LGIS~ 380 (419)
... +....+..++..|++.. .+.+++|||+.||+|+
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 000 11123556666665433 3449999999999999
Q ss_pred HHHHHHHHHhCccc
Q 014764 381 KKVRNATEAIGKVF 394 (419)
Q Consensus 381 etVr~~l~rark~l 394 (419)
++|+..+.++++.+
T Consensus 170 ~tVk~~l~RAr~~L 183 (201)
T PRK12545 170 NHCSVLLYRARTRL 183 (201)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999998654
No 107
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=99.53 E-value=4.9e-14 Score=132.50 Aligned_cols=128 Identities=20% Similarity=0.176 Sum_probs=103.3
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccc--c
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL--R 341 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~i--r 341 (419)
.+|+.|+..|.+.++.++.++.++..+++|++||+|+.+|+.+.+|++ + +|.+|++++++|.+++++|+..+.. .
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 799999999999999999999999999999999999999999999975 3 6999999999999999999765311 0
Q ss_pred Cc-----------c--c---hHHHHHHHHHHHHHHHhcC---------CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 342 LP-----------N--H---LHERLGLIRNAKLRLEEKG---------VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 342 ip-----------~--~---l~e~~~~I~~a~~~L~e~g---------RepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
.+ . . ..+....+..++..|++.. .+.+++|||+.||+|+++|+..+.++++.+
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 00 0 0 0112234566666664433 344999999999999999999999998655
No 108
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=99.52 E-value=5.2e-14 Score=130.16 Aligned_cols=125 Identities=10% Similarity=0.089 Sum_probs=98.6
Q ss_pred HHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCc----
Q 014764 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP---- 343 (419)
Q Consensus 268 ~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip---- 343 (419)
.-|..|.+.++.+|.+++++..++||++||+|+.+|+.+.+|++.. +|.+|++++++|.+++++|++.+.....
T Consensus 11 ~~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~~--~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~~~~~ 88 (189)
T PRK12530 11 LEIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQS--ALKTWIFAILKNKIIDLIRYRKRFVNESELIE 88 (189)
T ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCCc--cHHHHHHHHHHHHHHHHHHhhccCCCcccccc
Confidence 3467788999999999999989999999999999999999998653 7999999999999999999765432110
Q ss_pred ---------------------cc--h-------HHHHHHHHHHHHHHHhcCCC---------ccHHHHHHHcCCCHHHHH
Q 014764 344 ---------------------NH--L-------HERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVR 384 (419)
Q Consensus 344 ---------------------~~--l-------~e~~~~I~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr 384 (419)
.. . .+....+..++..|++..|+ .|++|||+.||+|+++|+
T Consensus 89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tVk 168 (189)
T PRK12530 89 EDSPNSFFDEKGHWKPEYYEPSEWQEVENTVYKEEFWLIFEACLNHLPAQQARVFMMREYLELSSEQICQECDISTSNLH 168 (189)
T ss_pred cccchhhhcccccccccccCCccccCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHhHHHHcCCCHHHHHHHHCCCHHHHH
Confidence 00 0 01112356677777654443 499999999999999999
Q ss_pred HHHHHhCccc
Q 014764 385 NATEAIGKVF 394 (419)
Q Consensus 385 ~~l~rark~l 394 (419)
..+.++++.+
T Consensus 169 ~~l~RAr~~L 178 (189)
T PRK12530 169 VLLYRARLQL 178 (189)
T ss_pred HHHHHHHHHH
Confidence 9999998654
No 109
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=99.52 E-value=3.8e-13 Score=130.21 Aligned_cols=78 Identities=17% Similarity=0.207 Sum_probs=71.8
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCC--ChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhccccc
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGA--DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 341 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~--d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~ir 341 (419)
.|++.|++.|.++|+++|.+++++.. +++|++||||+++|+++++|++.+|.+|.+|++++|+|.+++++|+..+...
T Consensus 18 ~AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~awl~~Iirn~~iDylRk~~~~~~ 97 (237)
T PRK08311 18 ELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELVIKRRLIDYFRKESKHNL 97 (237)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccc
Confidence 79999999999999999999998765 5999999999999999999999988789999999999999999998776433
No 110
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=99.51 E-value=5.6e-14 Score=132.40 Aligned_cols=126 Identities=13% Similarity=0.127 Sum_probs=99.4
Q ss_pred HHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCcc--
Q 014764 267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPN-- 344 (419)
Q Consensus 267 e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~-- 344 (419)
..++..|.+.|+.+|++++++..++||++||+|+.+|+.+.+|++. + +|.+|++++++|.+++++|+..+....+.
T Consensus 21 ~~~~~~~~~~l~~~~~~~~~d~~~AEDivQEvfikl~~~~~~~~~~-~-~~~~WL~~IarN~~~d~~Rk~~~~~~~~~~~ 98 (206)
T PRK12544 21 PVFLEDLRKQMIKFATLQLSDLHLAEDAVQEALIGALKNADSFAGR-A-AFKTWVFAILKNKIIDLLRQKKRHVSASSLL 98 (206)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHHHHhcCCc-c-cHHHHHHHHHHHHHHHHHHhhcccccccccc
Confidence 4688899999999999999999999999999999999999999865 2 79999999999999999997654221110
Q ss_pred -----------------------------c---h---HHHHHHHHHHHHHHHhcCC---------CccHHHHHHHcCCCH
Q 014764 345 -----------------------------H---L---HERLGLIRNAKLRLEEKGV---------TPSVDRIAEYLNMSQ 380 (419)
Q Consensus 345 -----------------------------~---l---~e~~~~I~~a~~~L~e~gR---------epS~eEIAe~LGIS~ 380 (419)
. . .+....+..++..|++..| +.+++|||+.||+|+
T Consensus 99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~L~~L~~~~r~v~~L~~~~g~s~~EIAe~lgis~ 178 (206)
T PRK12544 99 RDEEEEEDFEELFDESGHWQKDERPQAWGNPEESLEQEQFWRIFEACLDGLPAKYARVFMMREFIELETNEICHAVDLSV 178 (206)
T ss_pred cccchhhHHHHhhcccccccccccccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCH
Confidence 0 0 0111235556666654333 349999999999999
Q ss_pred HHHHHHHHHhCccc
Q 014764 381 KKVRNATEAIGKVF 394 (419)
Q Consensus 381 etVr~~l~rark~l 394 (419)
++|+..+.++++.+
T Consensus 179 ~tV~~~l~RAr~~L 192 (206)
T PRK12544 179 SNLNVLLYRARLRL 192 (206)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999998755
No 111
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=99.51 E-value=1.2e-13 Score=128.25 Aligned_cols=128 Identities=17% Similarity=0.204 Sum_probs=101.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCc
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip 343 (419)
++++.|+. |.+.|+++|.+++++..++||++||+|+.+|+.+..|+... .|.+|++.+++|.+++++|+..+.....
T Consensus 8 ~~~~~l~~-~~~~l~~~a~~~l~~~~~AEDivQevfl~l~~~~~~~~~~~--~~~awL~~ia~n~~~d~~Rk~~r~~~~~ 84 (188)
T PRK12546 8 DPRDELVE-HLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEGT--NLRAWLFTILRNTFYSDRRKHKREVPDP 84 (188)
T ss_pred hHHHHHHH-HHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHhccCCCc--chHHHHHHHHHHHHHHHHHHhcccccCc
Confidence 56777766 77999999999999999999999999999999999998643 7999999999999999999866422110
Q ss_pred ------------cc-hHHHHHHHHHHHHHHHhcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 344 ------------NH-LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 344 ------------~~-l~e~~~~I~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
.. .......+..++..|++..+. .+++|||+.||||..+|+..+.++++.+
T Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~v~~L~~~~g~s~~EIA~~LgiS~~tVk~~l~Rar~~L 157 (188)
T PRK12546 85 EGVHAASLAVKPAHDGRLAMSDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARL 157 (188)
T ss_pred ccccccccccCCcchhHHHHHHHHHHHHhCCHHHhHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 00 011124567777777654443 3999999999999999999999998654
No 112
>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=99.51 E-value=6.2e-14 Score=129.69 Aligned_cols=126 Identities=15% Similarity=0.153 Sum_probs=99.9
Q ss_pred HHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCc---
Q 014764 267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP--- 343 (419)
Q Consensus 267 e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip--- 343 (419)
.+++..|.+.|+.++.+++++..+++|++||+|+.+|+...+|++.. +|.+|++++++|.+++++|+..+....+
T Consensus 5 ~~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~~--~~~~wL~~iarn~~~d~~R~~~r~~~~~~~~ 82 (188)
T TIGR02943 5 PQELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGRS--ALKTWLFAILKNKIIDALRAKGREVKVSDLD 82 (188)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhcccc--HHHHHHHHHHHHHHHHHHHhhcccCCccccc
Confidence 35678899999999999999999999999999999999999998653 8999999999999999999765432111
Q ss_pred cc---------------------------------hHHHHHHHHHHHHHHHhcC---------CCccHHHHHHHcCCCHH
Q 014764 344 NH---------------------------------LHERLGLIRNAKLRLEEKG---------VTPSVDRIAEYLNMSQK 381 (419)
Q Consensus 344 ~~---------------------------------l~e~~~~I~~a~~~L~e~g---------RepS~eEIAe~LGIS~e 381 (419)
.. ..+....+..++..|++.. .+.+++|||+.||+|++
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 00 0011234566666665433 33499999999999999
Q ss_pred HHHHHHHHhCccc
Q 014764 382 KVRNATEAIGKVF 394 (419)
Q Consensus 382 tVr~~l~rark~l 394 (419)
+|+.++.++++.+
T Consensus 163 tvk~rl~Rar~~L 175 (188)
T TIGR02943 163 NCHVLLYRARLSL 175 (188)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999998765
No 113
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=99.50 E-value=1.2e-13 Score=125.65 Aligned_cols=128 Identities=17% Similarity=0.157 Sum_probs=100.6
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhccccc-
Q 014764 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR- 341 (419)
Q Consensus 263 ~~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~ir- 341 (419)
..||+.|++.|.+.++.++.++.++..++||++||.|+.+|+. ..|++-. .|.+|++++++|.+++++|+..+...
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 3565443 69999999999999999986542110
Q ss_pred ------C-----cc--ch---HHHHHHHHHHHHHHHhcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014764 342 ------L-----PN--HL---HERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKV 393 (419)
Q Consensus 342 ------i-----p~--~l---~e~~~~I~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~~l~rark~ 393 (419)
. +. .. .+....+..++..|++..++ .+++|||+.||+|+++|+..+.++.+.
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 1 11 01 12234567777777554443 499999999999999999999998753
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=99.49 E-value=8.2e-14 Score=126.62 Aligned_cols=122 Identities=20% Similarity=0.200 Sum_probs=97.0
Q ss_pred HHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccc-----
Q 014764 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH----- 345 (419)
Q Consensus 271 e~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~----- 345 (419)
..|.+.++.++.++.++..++||++||+|+.+|+++.+|+.. .+|.+|++.+++|.+++++|+..+...++..
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~l~~~~~~~~~~--~~f~~wl~~iarn~~~d~~Rk~~~~~~~~~~~~~~~ 79 (170)
T TIGR02959 2 DEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDG--QKIQSWLYQIARNTIIDFYRSKSRSVELPESLLAAD 79 (170)
T ss_pred chHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhccCccccchhhcccC
Confidence 468899999999999999999999999999999999999864 3899999999999999999987654332211
Q ss_pred -------hHHHHHHHHHHHHHHHhcC---------CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 346 -------LHERLGLIRNAKLRLEEKG---------VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 346 -------l~e~~~~I~~a~~~L~e~g---------RepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
..+....+..++..|++.. .+.+++|||+.||+|+++|+..+.++++.+
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 1112233555556664332 344999999999999999999999998655
No 115
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=99.48 E-value=1.3e-13 Score=127.22 Aligned_cols=127 Identities=18% Similarity=0.175 Sum_probs=100.2
Q ss_pred HHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCc--
Q 014764 266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP-- 343 (419)
Q Consensus 266 ~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip-- 343 (419)
.+..+..|.+.|+.+|.++.++..++||++||+|+.+|+.+..|+... +|.+|++.+++|.++++++++.+.....
T Consensus 6 ~~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~~--~~~~WL~~Iarn~~id~~Rk~~~~~~~~~~ 83 (182)
T PRK12511 6 KRFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSGG--NLRTWLMSILHNAFIDELRRRRVEARRADE 83 (182)
T ss_pred hhhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCcc--chHHHHHHHHHHHHHHHHHhhccccccccc
Confidence 344577889999999999999999999999999999999999998643 7999999999999999998765421110
Q ss_pred ----------cc--hHHHHHHHHHHHHHHHhcCC---------CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 344 ----------NH--LHERLGLIRNAKLRLEEKGV---------TPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 344 ----------~~--l~e~~~~I~~a~~~L~e~gR---------epS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
.. .......+..++..|++..| +.+++|||+.||||+++|+..+.++++.+
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 11123446677777755433 34999999999999999999999998654
No 116
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=99.47 E-value=1.8e-13 Score=131.69 Aligned_cols=127 Identities=13% Similarity=0.080 Sum_probs=99.1
Q ss_pred HHHHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhccccc
Q 014764 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 341 (419)
Q Consensus 262 ~~~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~ir 341 (419)
...+|+.+++.| +.+++++.+++++..++||++||+|+.+|+. |+... .|.+|++++++|.+++++|++.+...
T Consensus 16 ~~~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~~---~~~~~--~~~~WL~~IarN~~id~~Rk~k~~~~ 89 (228)
T PRK06704 16 NHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQK---YSNKD--ICMTLVYKIARNRWLDQIKSKSVHEK 89 (228)
T ss_pred CHHHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH---cCccc--cHHHHHHHHHHHHHHHHHhccccccc
Confidence 337899888888 7899999999999999999999999999986 55432 59999999999999999997654322
Q ss_pred Cccc---------hHHHHHHHHHHHHHHHhcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 342 LPNH---------LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 342 ip~~---------l~e~~~~I~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
+... ..+....+..++..|+...|. .|++|||+.||+|+++|+..+.++++.+
T Consensus 90 ~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~R~v~lL~~~eg~S~~EIAe~LgiS~~tVksrL~Rark~L 160 (228)
T PRK06704 90 IRDQITFEEPHEKIADLHEMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRL 160 (228)
T ss_pred cccccccCChHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHhhCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 2110 112234456677777554444 3999999999999999999999998765
No 117
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=99.42 E-value=7e-13 Score=118.55 Aligned_cols=124 Identities=15% Similarity=0.166 Sum_probs=95.2
Q ss_pred HHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhccccc------
Q 014764 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR------ 341 (419)
Q Consensus 268 ~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~ir------ 341 (419)
.++..|.+.++.+|.++.++..++||++||+|+++|+....|++. .|.+|++.+++|.+++++|+..+...
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 357788899999999999999999999999999999998877653 58999999999999999987653211
Q ss_pred ----Ccc---c------hHHHHHHHHHHHHHHHhcC---------CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 342 ----LPN---H------LHERLGLIRNAKLRLEEKG---------VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 342 ----ip~---~------l~e~~~~I~~a~~~L~e~g---------RepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
.+. . ..+....+..++..|++.. .+.+++|||+.||+|.++|+..+.++.+.+
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~EIA~~lgis~~tV~~~l~ra~~~l 153 (163)
T PRK07037 79 DGLDVPSPEASPEAALINRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALVHC 153 (163)
T ss_pred cccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 010 0 1112234566666664433 344999999999999999999999887543
No 118
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=99.42 E-value=7.6e-13 Score=119.74 Aligned_cols=127 Identities=12% Similarity=0.014 Sum_probs=98.5
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccc---
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL--- 340 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~i--- 340 (419)
.+|..++..|.+.++.++.+++++..++||++||+|+.+|+....++. + .|.+|++++++|.+++++|+.....
T Consensus 9 ~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~~--~-~~~~wl~~Iarn~~~d~~Rr~~~~~~~~ 85 (168)
T PRK12525 9 TLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI--R-EPRALLTTIARRLMYEGWRRQDLERAYL 85 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCcccc--c-CHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 689999999999999999999999999999999999999986655542 2 7999999999999999998643210
Q ss_pred ----cC-------ccc---hHHHHHHHHHHHHHHHhcC---------CCccHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014764 341 ----RL-------PNH---LHERLGLIRNAKLRLEEKG---------VTPSVDRIAEYLNMSQKKVRNATEAIGKV 393 (419)
Q Consensus 341 ----ri-------p~~---l~e~~~~I~~a~~~L~e~g---------RepS~eEIAe~LGIS~etVr~~l~rark~ 393 (419)
.. |.. ..+....+..++..|++.. .+.+++|||+.||+|+++|+..+.++.+.
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~eg~s~~EIA~~l~is~~tV~~~l~ra~~~ 161 (168)
T PRK12525 86 QSLAEAPEAVQPSPEEQWMVIETLLAIDRLLDGLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAFKC 161 (168)
T ss_pred HHHhcccccccCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 00 100 1112344666666675433 34499999999999999999999988654
No 119
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=99.42 E-value=5.8e-13 Score=118.98 Aligned_cols=121 Identities=16% Similarity=0.082 Sum_probs=94.2
Q ss_pred HHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccC--------
Q 014764 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL-------- 342 (419)
Q Consensus 271 e~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~iri-------- 342 (419)
..|.+.++.++.+++++..++||++||+|+.+|+....|++ + +|.||++.+++|.+++++|++......
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~--~-~~~~wL~~ia~n~~~d~~R~~~~~~~~~~~~~~~~ 78 (159)
T PRK12527 2 ENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQI--E-HPRAFLYRTALNLVVDRHRRHRVRQAEPLEVLDEE 78 (159)
T ss_pred hhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhccccccc--c-chHHHHHHHHHHHHHHHHHHHhcccccchhhhhcc
Confidence 57888999999999998899999999999999999998864 2 799999999999999999865422110
Q ss_pred -----c--cch---HHHHHHHHHHHHHHHhcC---------CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 343 -----P--NHL---HERLGLIRNAKLRLEEKG---------VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 343 -----p--~~l---~e~~~~I~~a~~~L~e~g---------RepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
+ ... .+....+..++..|++.. .+.+++|||+.||+|+++|+..+.++++.+
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~ra~~~L 149 (159)
T PRK12527 79 ERLHSPSPQTRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHC 149 (159)
T ss_pred ccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 0 000 112234667777775433 344999999999999999999999987654
No 120
>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=101.47 Aligned_cols=70 Identities=27% Similarity=0.418 Sum_probs=66.5
Q ss_pred HHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcc
Q 014764 269 LVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSR 338 (419)
Q Consensus 269 LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r 338 (419)
|++.|.++|+.++.+|++++.+++|++||++++||+++.+||++++..|.+|++.+++|.+.++++++.+
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 7899999999999999999999999999999999999999999998889999999999999999987754
No 121
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=99.38 E-value=1.6e-12 Score=128.29 Aligned_cols=127 Identities=17% Similarity=0.075 Sum_probs=98.3
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccc---
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL--- 340 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~i--- 340 (419)
..+..|++.|.+.++.+|++++++..++||++||+|+. |.....|+. ..|.+|++++++|.|++++|+..+..
T Consensus 4 ~~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~-~~~~~~~~~---~~~~~WL~~Ia~n~~~d~lR~~~~~~~~~ 79 (293)
T PRK09636 4 ADAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQI---RDPRAWLTRVVTRLCLDRLRSARHRRETY 79 (293)
T ss_pred cHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHhcccccc---cCHHHHHHHHHHHHHHHHHHhhhcccccc
Confidence 35778999999999999999999999999999999999 555667752 37999999999999999999754321
Q ss_pred ---cCccc----------h---HHH-HHHHHHHHHHHHhcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 341 ---RLPNH----------L---HER-LGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 341 ---rip~~----------l---~e~-~~~I~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
..+.. . .+. ...+..++..|++..|.+ +++|||+.||+|+++|+++++++++.+
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 11111 0 111 123566677775544443 999999999999999999999998765
No 122
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=99.34 E-value=3.7e-12 Score=126.38 Aligned_cols=128 Identities=11% Similarity=-0.049 Sum_probs=99.6
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccc---
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL--- 340 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~i--- 340 (419)
..+..+++.|.+.++.+|++++++..++||++||+|+.+|++...+ . ..|.+|++++++|.|++++|+..+..
T Consensus 5 ~~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~---~-~~~~aWL~~Ia~n~~id~lRk~~~rr~~~ 80 (290)
T PRK09635 5 DPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGD---I-DDERGWLIVVTSRLCLDHIKSASTRRERP 80 (290)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCccc---c-ccHHHHHHHHHHHHHHHHHhhhhccCcCc
Confidence 5789999999999999999999999999999999999999987543 1 26999999999999999998743211
Q ss_pred -----cCcc--------c--h---HH-HHHHHHHHHHHHHhcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCc
Q 014764 341 -----RLPN--------H--L---HE-RLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGK 392 (419)
Q Consensus 341 -----rip~--------~--l---~e-~~~~I~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~~l~rark 392 (419)
..|. . . .+ ....+..++..|++..|.+ +++|||+.||+|+.+|+.+++++++
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 0110 0 0 11 1134566666665444443 9999999999999999999999987
Q ss_pred ccc
Q 014764 393 VFS 395 (419)
Q Consensus 393 ~lS 395 (419)
.+-
T Consensus 161 ~Lr 163 (290)
T PRK09635 161 KIN 163 (290)
T ss_pred HHH
Confidence 654
No 123
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=99.32 E-value=4.8e-12 Score=124.50 Aligned_cols=123 Identities=17% Similarity=0.081 Sum_probs=93.3
Q ss_pred HHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccc------c
Q 014764 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL------R 341 (419)
Q Consensus 268 ~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~i------r 341 (419)
++++.|.+.++.+|++++++..++||++||+|+.+++. .|+.. ..|.+|++++++|.+++++|+..+.. .
T Consensus 1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~~--~~~~awL~~Ia~n~~ld~lR~~~~~~~~~~~~~ 76 (281)
T TIGR02957 1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQI--ENPKAYLTKVVTRRCIDVLRSARARREVYVGPW 76 (281)
T ss_pred ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Ccccc--cCHHHHHHHHHHHHHHHHHHHhhhcccccCCCC
Confidence 37899999999999999999999999999999998775 55433 37999999999999999998764221 1
Q ss_pred Cccc----------hH---HHH-HHHHHHHHHHHhcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 342 LPNH----------LH---ERL-GLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 342 ip~~----------l~---e~~-~~I~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
++.. .. +.. ..+..++..|++..|. .+++|||+.||+|+.+|+++++++++.+
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 2111 00 111 1244556666443433 3999999999999999999999998765
No 124
>PRK09191 two-component response regulator; Provisional
Probab=99.31 E-value=6.5e-12 Score=119.11 Aligned_cols=122 Identities=13% Similarity=0.036 Sum_probs=94.3
Q ss_pred HHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCcc
Q 014764 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPN 344 (419)
Q Consensus 265 A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~ 344 (419)
+|..|+.+|.+.|+++|.++.++..+++|++||+|+.+|+...+|++.. .|.+|+++++++........ ...+.
T Consensus 2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~~--~~~~wl~~~~~~~~~~~~~~----~~~~~ 75 (261)
T PRK09191 2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEAS--SPRVGLYRLFHRLWSSAGAN----DPEPG 75 (261)
T ss_pred chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCCc--chhhHHHHHHHHHhcccccc----CCCCC
Confidence 5889999999999999999999999999999999999999999998653 69999999998753322111 00010
Q ss_pred chHHHHHHHHHHHHHHHhcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 345 HLHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 345 ~l~e~~~~I~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
......+..++..|++..|. .|++|||+.||+|+++|+..+.++++.+
T Consensus 76 --~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l 132 (261)
T PRK09191 76 --SPFEARAERRLAGLTPLPRQAFLLTALEGFSVEEAAEILGVDPAEAEALLDDARAEI 132 (261)
T ss_pred --CCchHHHHHHHHhCCHHHhHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 01112566777777544443 4999999999999999999998887543
No 125
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=99.24 E-value=2e-11 Score=107.19 Aligned_cols=112 Identities=16% Similarity=0.118 Sum_probs=84.0
Q ss_pred HHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhh-----cCCCCCCchhhHHHHHHHhhHHHHHHHhcccc
Q 014764 266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEK-----FDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340 (419)
Q Consensus 266 ~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIer-----FDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~i 340 (419)
|+.|+..|.++++.+|.+|.. .+|+ ||.|+.+|..+.+ |++. ..|.||++++++|.+++++|++.+..
T Consensus 1 f~~~~~~y~~~l~~~~~~~~~----~~~~-qdvf~~~w~~~~~~~~~~~~~~--~~~~~wL~~iarN~~id~~Rk~~~~~ 73 (142)
T TIGR03209 1 FEEIYMNFKNTIDIFTRKYNL----YYDY-NDILYHLWIILKKIDLNKFNTE--NDLEKYISTSLKRYCLDICNKKNRDK 73 (142)
T ss_pred ChHHHHHHHHHHHHHHHHhcc----hhhH-HHHHHHHHHHHHHhhhhhcCch--hHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 468999999999999999965 2344 9999999999865 5543 37999999999999999998765321
Q ss_pred cCc-------------cc--hHHHHHHHHHHHHHHHhcCCC---------ccHHHHHHHcCCCHHHHH
Q 014764 341 RLP-------------NH--LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVR 384 (419)
Q Consensus 341 rip-------------~~--l~e~~~~I~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr 384 (419)
... .. ..+....+..++..|++..|. .|++|||+.||+|+++|+
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 110 00 111224577777777654444 399999999999999996
No 126
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=99.20 E-value=3.3e-11 Score=107.16 Aligned_cols=106 Identities=13% Similarity=0.093 Sum_probs=78.4
Q ss_pred CCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCc----------------------
Q 014764 286 NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP---------------------- 343 (419)
Q Consensus 286 ~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip---------------------- 343 (419)
++..++||++||+|+.+|+.+..+ + +..|.+|++++++|.+++++|+..+.....
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 347999999999999999998765321110
Q ss_pred ------cch------HHHHHHHHHHHHHHHhcCC---------CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 344 ------NHL------HERLGLIRNAKLRLEEKGV---------TPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 344 ------~~l------~e~~~~I~~a~~~L~e~gR---------epS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
... .+....+..++..|++..| +.+++|||+.||+|+++|+.++.++++.+
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 1122346667777754333 34999999999999999999999987654
No 127
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=98.87 E-value=3.2e-08 Score=91.82 Aligned_cols=130 Identities=22% Similarity=0.126 Sum_probs=90.1
Q ss_pred HHHHHHHHHhHHHHHHHHHHccC---CCCChhh--HhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcc
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDN---MGADMAD--LVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSR 338 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~---~g~d~ED--LVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r 338 (419)
.|++.|+..|.+.+..+|.++.. .+.+.+| |++|+|+.+++.-...+......|..|+..++++.++++.|.+.+
T Consensus 17 ~A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~~lv~ea~lrl~~~~~~~~~~~~~~f~~~~~~~~rr~lid~~R~~~a 96 (185)
T PF07638_consen 17 AALDQLFERYYPELRRLARRRLRRERRGHDLQDTALVHEAFLRLARRGRFVQFSDRRHFWALLARIMRRKLIDHARRRQA 96 (185)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccccCCchhHHHHHHHHHHHHhccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 89999999999999999997653 2344444 577888888774433233322379999999999999999986654
Q ss_pred cccC------c---------cchHHHHHHHHHHHHHHHh------------cCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 339 TLRL------P---------NHLHERLGLIRNAKLRLEE------------KGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 339 ~iri------p---------~~l~e~~~~I~~a~~~L~e------------~gRepS~eEIAe~LGIS~etVr~~l~rar 391 (419)
..+- + ....+....+.++...|.. ...+.|++|||+.||||+.+|+..+..++
T Consensus 97 ~KRg~~~~~~~l~~~~~~~~~~~~~~~~~l~e~l~~L~~l~~~~~~~v~l~~~~Gls~~EIA~~lgiS~~tV~r~l~~aR 176 (185)
T PF07638_consen 97 QKRGGDQVRVELDERADSGDEPSPEELLELEEALERLLALDPRQRRVVELRFFEGLSVEEIAERLGISERTVRRRLRRAR 176 (185)
T ss_pred HhcCCCCcccchhhhhccccCCCHHHHHHHHHHHHHHHccCHHHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3321 1 0112223344444444422 12345999999999999999999999887
Q ss_pred cc
Q 014764 392 KV 393 (419)
Q Consensus 392 k~ 393 (419)
..
T Consensus 177 ~~ 178 (185)
T PF07638_consen 177 AW 178 (185)
T ss_pred HH
Confidence 53
No 128
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=98.64 E-value=7.8e-08 Score=76.82 Aligned_cols=67 Identities=33% Similarity=0.322 Sum_probs=54.5
Q ss_pred HHHHHHHHHHHHHH-hcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCCCCCCCCcccccCCC
Q 014764 348 ERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSVIHC 418 (419)
Q Consensus 348 e~~~~I~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~~l~rark~lSLD~~~~~~~d~~~~~tl~d~IaD 418 (419)
+.+++|.+++..|. .+||.||.+|||+.|||+++.|+.++..+...+|||.+... +++.++.|+|+|
T Consensus 1 E~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~----~~~~~l~~~i~d 68 (78)
T PF04539_consen 1 EKLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGD----EDDSTLGDFIED 68 (78)
T ss_dssp HHHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSS----SSSEEGGGSSB-
T ss_pred ChHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecC----CCCCchhheecC
Confidence 45788999999995 68999999999999999999999999999999999987743 334588888876
No 129
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=97.69 E-value=0.00061 Score=70.17 Aligned_cols=134 Identities=18% Similarity=0.287 Sum_probs=77.0
Q ss_pred hHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHh
Q 014764 226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRG 305 (419)
Q Consensus 226 ~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrA 305 (419)
.+...|.+.+|++||.+|+|..+|++.++++..+..... ..++-... +.+ +| ..+...
T Consensus 220 ~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~------------~~SLd~~~---~~~-~~------~~l~d~ 277 (367)
T PRK09210 220 RVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQE------------PVSLETPI---GEE-DD------SHLGDF 277 (367)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcC------------CCCcCCCC---CCC-Cc------chhhhh
Confidence 366788899999999999999999999998874332100 11111111 000 11 011111
Q ss_pred HhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccchHHHHHHHHHHHHHHHhcCCCccHHHHHHHcCCCHHHHHH
Q 014764 306 IEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRN 385 (419)
Q Consensus 306 IerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~l~e~~~~I~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~ 385 (419)
+. |..............++..+.++|. .+.+..+.|...++.|. .|.+.|++|||+.||||.++|++
T Consensus 278 i~--d~~~~~p~~~~~~~~~~~~l~~~l~----------~L~~rEr~Vl~lrygl~-~~~~~tl~EIa~~lgvs~erVrQ 344 (367)
T PRK09210 278 IE--DQDATSPADHAAYELLKEQLEDVLD----------TLTDREENVLRLRFGLD-DGRTRTLEEVGKVFGVTRERIRQ 344 (367)
T ss_pred cc--CCCCCCHHHHHHHHHHHHHHHHHHH----------hCCHHHHHHHHHHhccC-CCCCccHHHHHHHHCCCHHHHHH
Confidence 21 1111112333333444443333331 23344555666555552 24677999999999999999999
Q ss_pred HHHHhCccc
Q 014764 386 ATEAIGKVF 394 (419)
Q Consensus 386 ~l~rark~l 394 (419)
+..++..++
T Consensus 345 i~~~Al~kL 353 (367)
T PRK09210 345 IEAKALRKL 353 (367)
T ss_pred HHHHHHHHH
Confidence 988875443
No 130
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=97.67 E-value=0.00051 Score=69.75 Aligned_cols=134 Identities=22% Similarity=0.294 Sum_probs=76.6
Q ss_pred hHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHh
Q 014764 226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRG 305 (419)
Q Consensus 226 ~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrA 305 (419)
.+...|...+|++|+.+|+|..+|++.+++...+... ..+.++-... +.+ ++ ..+...
T Consensus 177 ~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~------------~~~~SLd~~~---~~~-~~------~~l~d~ 234 (324)
T PRK07921 177 RIKRELHQQLGREATDEELAEESGIPEEKIADLLEHS------------RDPVSLDMPV---GSD-EE------APLGDF 234 (324)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHc------------CCCceecCCC---CCC-CC------chHHHH
Confidence 3667888999999999999999999999877632110 0111221111 101 01 012222
Q ss_pred HhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccchHHHHHHHHHHHHHHHhcCCCccHHHHHHHcCCCHHHHHH
Q 014764 306 IEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRN 385 (419)
Q Consensus 306 IerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~l~e~~~~I~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~ 385 (419)
+.. +..............+..+..+|. .+.++.+.|...++.|. .+.+.|.+|||+.||||.+.|++
T Consensus 235 l~d--~~~~~pe~~~~~~~~~~~l~~~L~----------~L~eREr~Vl~~rygl~-~~~~~Tl~eIa~~lgvS~eRVrQ 301 (324)
T PRK07921 235 IED--SEATSAENAVIAGLLHTDIRSVLA----------TLDEREQQVIRLRFGLD-DGQPRTLDQIGKLFGLSRERVRQ 301 (324)
T ss_pred hcC--CCCCCHHHHHHHHHHHHHHHHHHH----------hCCHHHHHHHHHHHhcC-CCCCcCHHHHHHHHCCCHHHHHH
Confidence 221 111112223333333333333331 24445566666666653 14556999999999999999999
Q ss_pred HHHHhCccc
Q 014764 386 ATEAIGKVF 394 (419)
Q Consensus 386 ~l~rark~l 394 (419)
+..++.+++
T Consensus 302 Ie~~Al~KL 310 (324)
T PRK07921 302 IEREVMSKL 310 (324)
T ss_pred HHHHHHHHH
Confidence 988876544
No 131
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=97.59 E-value=0.0011 Score=71.26 Aligned_cols=133 Identities=19% Similarity=0.269 Sum_probs=75.8
Q ss_pred hHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHh
Q 014764 226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRG 305 (419)
Q Consensus 226 ~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrA 305 (419)
..+..|.+.+|++|+.+|+|..+|++.++++..+... .-+.++-..+.. + +| ..+...
T Consensus 362 ~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~------------~~~~SLD~~i~~---d-~~------~~l~d~ 419 (509)
T PRK05901 362 RIERELLQELGREPTPEELAKEMGFTPEKVREIQKYN------------REPISLDKTIGK---E-GD------SQFGDF 419 (509)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhc------------CCCccccccccc---C-Cc------ccHHHh
Confidence 3667888999999999999999999999877632210 001111111100 0 01 012222
Q ss_pred HhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccchHHHHHHHHHHHHHHHhcCCCccHHHHHHHcCCCHHHHHH
Q 014764 306 IEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRN 385 (419)
Q Consensus 306 IerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~l~e~~~~I~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~ 385 (419)
+. |+..............+..+..+|. .+.++.+.|...++.|.. +...|+.|||+.||||.++|++
T Consensus 420 l~--D~~~~~p~~~~~~~~l~~~L~~aL~----------~L~eREr~VI~lRyGL~~-~e~~TL~EIa~~lGVSrERVRQ 486 (509)
T PRK05901 420 IE--DSEAVSPVDAVSFTLLQDQLQEVLE----------TLSEREAGVIRMRFGLTD-GQPKTLDEIGQVYGVTRERIRQ 486 (509)
T ss_pred cc--CCCCCCHHHHHHHHHHHHHHHHHHh----------hCCHHHHHHHHHHhhccC-CCCCCHHHHHHHHCCCHHHHHH
Confidence 21 1111111222222233332222221 244556667777776632 4567999999999999999999
Q ss_pred HHHHhCcc
Q 014764 386 ATEAIGKV 393 (419)
Q Consensus 386 ~l~rark~ 393 (419)
+..++...
T Consensus 487 Ie~kAL~K 494 (509)
T PRK05901 487 IESKTLRK 494 (509)
T ss_pred HHHHHHHH
Confidence 98887544
No 132
>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=97.56 E-value=0.0013 Score=63.29 Aligned_cols=132 Identities=19% Similarity=0.199 Sum_probs=70.6
Q ss_pred HHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHH-HHHHHHh
Q 014764 227 HKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGG-LIGLLRG 305 (419)
Q Consensus 227 ~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG-~IgLlrA 305 (419)
+..+|...+|++||.+|+|..+|++.+++...+.. +... ...++.+++. -..+...
T Consensus 92 ~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~-------------------~~~~----~SLd~~~~~~~~~~l~d~ 148 (238)
T TIGR02393 92 AERQLTQELGREPTDEELAERMGMPAEKVREIKKI-------------------AQEP----ISLETPIGEEEDSFLGDF 148 (238)
T ss_pred HHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHH-------------------hccC----CCcCCCCCCCCcccHHHH
Confidence 56778889999999999999999999987763221 1111 1111111100 0012222
Q ss_pred HhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccchHHHHHHHHHHHHHHHhcCCCccHHHHHHHcCCCHHHHHH
Q 014764 306 IEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRN 385 (419)
Q Consensus 306 IerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~l~e~~~~I~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~ 385 (419)
+. |+..............+..+..++. .+| +..+.+....+.|. .+.+.|++|||+.||||.++|++
T Consensus 149 l~--d~~~~~p~~~~~~~~~~~~l~~~l~------~L~----~~er~vl~l~ygl~-~~~~~t~~EIA~~lgis~~~V~q 215 (238)
T TIGR02393 149 IE--DTSIESPDDYAAKELLREQLDEVLE------TLT----ERERKVLRMRYGLL-DGRPHTLEEVGKEFNVTRERIRQ 215 (238)
T ss_pred hc--CCCCCChHHHHHHHHHHHHHHHHHH------hCC----HHHHHHHHHHhCCC-CCCCccHHHHHHHHCCCHHHHHH
Confidence 22 1111111122222222222222221 222 23334444443331 13567999999999999999999
Q ss_pred HHHHhCccc
Q 014764 386 ATEAIGKVF 394 (419)
Q Consensus 386 ~l~rark~l 394 (419)
+..++.+.+
T Consensus 216 ~~~~al~kL 224 (238)
T TIGR02393 216 IESKALRKL 224 (238)
T ss_pred HHHHHHHHH
Confidence 999887654
No 133
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=97.44 E-value=0.0021 Score=62.81 Aligned_cols=60 Identities=23% Similarity=0.262 Sum_probs=40.2
Q ss_pred hhhHHHHHHhhcCCCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHH
Q 014764 190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSIL 259 (419)
Q Consensus 190 ~~~l~~yl~~i~~~~lLt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l 259 (419)
...+-.|++..... |....+.+.++. .+..+|.+.+|++|+.+|+|..+|++.+++...+
T Consensus 88 r~~i~~~lr~~~~~----pr~~~~~~~~l~------~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~ 147 (257)
T PRK05911 88 KAAIIDDLRKQDWV----PRSVHQKANKLA------DAMDSLRQSLGKEPTDGELCEYLNISQQELSGWF 147 (257)
T ss_pred HHHHHHHHHhcCCC----CHHHHHHHHHHH------HHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHH
Confidence 34455555554432 233334444443 3556788999999999999999999999887643
No 134
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=97.39 E-value=0.003 Score=65.45 Aligned_cols=132 Identities=17% Similarity=0.262 Sum_probs=72.6
Q ss_pred HHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhH
Q 014764 227 HKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGI 306 (419)
Q Consensus 227 ~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAI 306 (419)
+...|.+.+|++|+.+|+|..+|++.++++..+.. ...+.++-.... .+ +| ..+...+
T Consensus 228 a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~------------~~~~~SLd~~i~---~~-~~------~~l~d~l 285 (373)
T PRK07406 228 TTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKS------------AQLPISLETPIG---KE-ED------SRLGDFI 285 (373)
T ss_pred HHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh------------cCCCcccCCCCC---CC-Cc------ccHHHhc
Confidence 56788899999999999999999999987653110 011122211111 01 11 0122222
Q ss_pred hhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccchHHHHHHHHHHHHHHHhcCCCccHHHHHHHcCCCHHHHHHH
Q 014764 307 EKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNA 386 (419)
Q Consensus 307 erFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~l~e~~~~I~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~~ 386 (419)
. +.... ..........+..+..++. .+.+..+.|...++.+. .+...|++|||+.||||.++|+++
T Consensus 286 ~--d~~~~-pee~~~~~~~~~~L~~aL~----------~L~~rEr~IL~lrygl~-~~~~~Tl~EIA~~lgiS~eRVRQi 351 (373)
T PRK07406 286 E--ADGET-PEDDVAKNLLREDLEGVLA----------TLSPRERDVLRLRYGLD-DGRMKTLEEIGQIFNVTRERIRQI 351 (373)
T ss_pred C--CCCCC-HHHHHHHHHHHHHHHHHHH----------cCCHHHHHHHHHHHhcC-CCCCCCHHHHHHHHCcCHHHHHHH
Confidence 1 11111 1112222222222222221 23344555566555542 134569999999999999999999
Q ss_pred HHHhCccc
Q 014764 387 TEAIGKVF 394 (419)
Q Consensus 387 l~rark~l 394 (419)
..++.+++
T Consensus 352 e~rAL~KL 359 (373)
T PRK07406 352 EAKALRKL 359 (373)
T ss_pred HHHHHHHH
Confidence 99886554
No 135
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=97.33 E-value=0.0021 Score=67.50 Aligned_cols=135 Identities=16% Similarity=0.261 Sum_probs=76.3
Q ss_pred chhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHH
Q 014764 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLL 303 (419)
Q Consensus 224 l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLl 303 (419)
++.++..|.+.+|+.|+.+|+|..+|++.++++..+... +...++-..... +-+. .+.
T Consensus 264 lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~l~~~------------~~~~SLd~~vg~---~~d~-------~l~ 321 (415)
T PRK07598 264 IKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLRV------------PRSVSLETKVGK---DKDT-------ELG 321 (415)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHc------------cCCcccccccCC---Cccc-------cHH
Confidence 445667788899999999999999999999988754321 112222222211 1010 111
Q ss_pred HhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccchHHHHHHHHHHHHHHHhcCCCccHHHHHHHcCCCHHHH
Q 014764 304 RGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKV 383 (419)
Q Consensus 304 rAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~l~e~~~~I~~a~~~L~e~gRepS~eEIAe~LGIS~etV 383 (419)
..+.. +..+ .-........+..+..+|. . +.+..+.+...++.|. .+.+.|++|||+.||+|.++|
T Consensus 322 d~l~~--~~~~-pee~~~~~~l~~~L~~~L~------~----L~~reR~VI~LRygl~-d~~~~Tl~EIA~~LGvS~erV 387 (415)
T PRK07598 322 DLLET--DDIS-PEEMLMRESLQRDLQHLLA------D----LTSRERDVIRMRFGLA-DGHTYSLAEIGRALDLSRERV 387 (415)
T ss_pred HhccC--CCCC-HHHHHHHHHHHHHHHHHHH------h----CCHHHHHHHHHHHhcC-CCCCCCHHHHHHHHCcCHHHH
Confidence 11211 1111 1111111222222222221 1 2334455555555553 256779999999999999999
Q ss_pred HHHHHHhCccc
Q 014764 384 RNATEAIGKVF 394 (419)
Q Consensus 384 r~~l~rark~l 394 (419)
++++++|.+.+
T Consensus 388 Rqie~rAl~KL 398 (415)
T PRK07598 388 RQIESKALQKL 398 (415)
T ss_pred HHHHHHHHHHH
Confidence 99999987554
No 136
>PRK05949 RNA polymerase sigma factor; Validated
Probab=97.33 E-value=0.0029 Score=64.29 Aligned_cols=135 Identities=19% Similarity=0.276 Sum_probs=72.7
Q ss_pred chhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHH
Q 014764 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLL 303 (419)
Q Consensus 224 l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLl 303 (419)
+..+...+...+|++|+.+|+|..+|++.+++...+... .-+.++-... +.+.+. .+.
T Consensus 180 l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~------------~~~~SLd~~~---~~~~~~-------~l~ 237 (327)
T PRK05949 180 IKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMA------------RQPISLDVRV---GDNQDT-------ELS 237 (327)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHh------------ccccccCCCc---CCCCCc-------cHH
Confidence 344566788899999999999999999998877632211 0011221111 001010 111
Q ss_pred HhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccchHHHHHHHHHHHHHHHhcCCCccHHHHHHHcCCCHHHH
Q 014764 304 RGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKV 383 (419)
Q Consensus 304 rAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~l~e~~~~I~~a~~~L~e~gRepS~eEIAe~LGIS~etV 383 (419)
..+.. .... ..........+..+..++. .+.+..+.|...++.|. .+.+.|++|||+.||||.++|
T Consensus 238 ~~l~d--~~~~-pe~~~~~~~~~~~L~~~L~----------~L~~rer~Vi~lr~gl~-~~e~~Tl~EIa~~lgiS~erV 303 (327)
T PRK05949 238 ELLED--EGPS-PDQYITQELLRQDLNNLLA----------ELTPQQREVLTLRFGLE-DGKELSLAKVGERLNLSRERV 303 (327)
T ss_pred hhcCC--CCCC-HHHHHHHHHHHHHHHHHHH----------hCCHHHHHHHHHHhccC-CCCCCCHHHHHHHHCcCHHHH
Confidence 11111 1111 1111111112222222221 13334455555555552 145679999999999999999
Q ss_pred HHHHHHhCccc
Q 014764 384 RNATEAIGKVF 394 (419)
Q Consensus 384 r~~l~rark~l 394 (419)
++++.++.+.+
T Consensus 304 rq~~~rAl~kL 314 (327)
T PRK05949 304 RQLEHQALAHL 314 (327)
T ss_pred HHHHHHHHHHH
Confidence 99999887544
No 137
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=97.30 E-value=0.00073 Score=65.99 Aligned_cols=63 Identities=24% Similarity=0.399 Sum_probs=41.3
Q ss_pred hhhhHHHHHHhhcCCCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 014764 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (419)
Q Consensus 189 ~~~~l~~yl~~i~~~~lLt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~ 258 (419)
+.+.+..|++.....-.+ |....+.++++. .+...|.+.+|++|+.+|+|..+|++.++++..
T Consensus 87 Ir~~i~~~lr~~~~~vr~-pr~~~~~~~~~~------~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~ 149 (256)
T PRK07408 87 IRGEIQHYLRDKSPTVRI-PRRWQELQRQAK------KVRQELRQELGRQPTDQEIAQALDISLEEWQEI 149 (256)
T ss_pred HHHHHHHHHHHcCCeeee-CHHHHHHHHHHH------HHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHH
Confidence 445555666653321111 222233444443 366788999999999999999999999987763
No 138
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=97.30 E-value=0.0056 Score=60.18 Aligned_cols=152 Identities=19% Similarity=0.197 Sum_probs=85.1
Q ss_pred hhHHHHHHhhcCCCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHH
Q 014764 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (419)
Q Consensus 191 ~~l~~yl~~i~~~~lLt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LI 270 (419)
..+-+||++-. +.--|.-..++.+++. .+...|+.++||+|+++|+|..+|++.++....+.....
T Consensus 87 Gei~d~LR~~~--~v~vpR~~~~~~~~i~------~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~------ 152 (247)
T COG1191 87 GEILDYLRKND--SVKVPRSLRELGRRIE------EAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAING------ 152 (247)
T ss_pred HHHHHHHHhCC--CccCcHHHHHHHHHHH------HHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhcc------
Confidence 45667777766 2223344444555544 366789999999999999999999999987765443321
Q ss_pred HHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccchHHHH
Q 014764 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL 350 (419)
Q Consensus 271 e~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~l~e~~ 350 (419)
..+.++.........+ + +... -+..+..+..+...+.+...+. . +.++.
T Consensus 153 ----~~~~sld~~~~~~~d~--~------------~~~~---~~~~~~~~~~~~~~~~l~~ai~------~----L~ERE 201 (247)
T COG1191 153 ----SQLLSLDEDVLKDDDD--D------------VDDQ---IENPDDGVEKEELLEILKEAIE------P----LPERE 201 (247)
T ss_pred ----ccccchhhhhcccccc--c------------hhhc---cccchhHHHHHHHHHHHHHHHH------c----cCHHH
Confidence 1122222211111000 0 0000 1112333333334443333332 1 22333
Q ss_pred HHHHHHHHHHHhcCCCccHHHHHHHcCCCHHHHHHHHHHhCc
Q 014764 351 GLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGK 392 (419)
Q Consensus 351 ~~I~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~~l~rark 392 (419)
+.|...++ ..+.|..|||+.||||+.+|.++..++-+
T Consensus 202 k~Vl~l~y-----~eelt~kEI~~~LgISes~VSql~kkai~ 238 (247)
T COG1191 202 KLVLVLRY-----KEELTQKEIAEVLGISESRVSRLHKKAIK 238 (247)
T ss_pred HHHHHHHH-----HhccCHHHHHHHhCccHHHHHHHHHHHHH
Confidence 33333332 34569999999999999999999877654
No 139
>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=97.30 E-value=9.1e-05 Score=52.10 Aligned_cols=33 Identities=30% Similarity=0.483 Sum_probs=30.6
Q ss_pred hhHHHHHHhhcCCCCCCHHHHHHHHHHHHccCc
Q 014764 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS 223 (419)
Q Consensus 191 ~~l~~yl~~i~~~~lLt~~eE~eL~rkik~Gd~ 223 (419)
|.++.||++|.++|+||++||.+|+++++.|+.
T Consensus 2 D~l~~Yl~ei~~~~LLt~eeE~~LA~~i~~g~~ 34 (37)
T PF00140_consen 2 DSLRLYLKEIGRYPLLTAEEEIELARRIRKGDE 34 (37)
T ss_dssp HHHHHHHHHHHHS-EETTHHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhHH
Confidence 689999999999999999999999999999986
No 140
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=97.28 E-value=0.004 Score=62.07 Aligned_cols=30 Identities=17% Similarity=0.268 Sum_probs=26.7
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
.+.|++|||+.||||.++|+++++++.+.+
T Consensus 244 ~~~t~~EIa~~lgvs~~~V~q~~~~Al~kL 273 (289)
T PRK07500 244 DGATLEALGEELGISKERVRQIEARALEKL 273 (289)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 566999999999999999999999987654
No 141
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=97.12 E-value=0.0021 Score=63.19 Aligned_cols=63 Identities=21% Similarity=0.272 Sum_probs=42.2
Q ss_pred hhhhHHHHHHhhcCCCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 014764 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (419)
Q Consensus 189 ~~~~l~~yl~~i~~~~lLt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~ 258 (419)
+...+..|+++....-.+ |....+++.+++. +..+|.+.+|++|+.+|+|..+|++.+++...
T Consensus 101 Irg~I~~~lr~~~~~ir~-Pr~~~~~~~~i~~------~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~ 163 (264)
T PRK07122 101 IMGEVRRHFRDNSWSVKV-PRRLKELHLRLGR------ATAELSQRLGRAPTASELAAELGMDREEVVEG 163 (264)
T ss_pred HHHHHHHHHHHcCCcccc-CHHHHHHHHHHHH------HHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 444555666654321111 2333445555543 56788899999999999999999999987764
No 142
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=97.09 E-value=0.0024 Score=64.59 Aligned_cols=135 Identities=20% Similarity=0.290 Sum_probs=72.0
Q ss_pred chhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHH
Q 014764 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLL 303 (419)
Q Consensus 224 l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLl 303 (419)
++.+...+...+|++|+.+|+|..+|++.+++...+... .-..++-... +.+ +| ..+.
T Consensus 170 l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~------------~~~~SLd~~~---~~~-~~------~~l~ 227 (317)
T PRK07405 170 IKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERA------------RQPLSLDLRV---GDN-QD------TELG 227 (317)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHc------------CCCeeecCCC---CCC-CC------ccHH
Confidence 344667788899999999999999999988876532110 0011111111 001 01 0111
Q ss_pred HhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccchHHHHHHHHHHHHHHHhcCCCccHHHHHHHcCCCHHHH
Q 014764 304 RGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKV 383 (419)
Q Consensus 304 rAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~l~e~~~~I~~a~~~L~e~gRepS~eEIAe~LGIS~etV 383 (419)
..+. |.... ........-.+..+..++. . +.+..+.|...++.|. .+.+.|++|||+.||||.++|
T Consensus 228 ~~~~--d~~~~-pe~~~~~~~~~~~l~~al~------~----L~~rer~Vi~lr~gl~-~~~~~Tl~EIa~~lgiS~erV 293 (317)
T PRK07405 228 ELLE--DTGAS-PEDFATQSSLQLDLERLME------D----LTPQQKEVIALRFGLE-DGQPLTLAKIGERLNISRERV 293 (317)
T ss_pred Hhhc--CCCCC-HHHHHHHHHHHHHHHHHHH------c----CCHHHHHHHHHHhhcC-CCCCcCHHHHHHHHCcCHHHH
Confidence 1111 11110 1111111112222222221 1 3334455555555552 145679999999999999999
Q ss_pred HHHHHHhCccc
Q 014764 384 RNATEAIGKVF 394 (419)
Q Consensus 384 r~~l~rark~l 394 (419)
++++.++.+.+
T Consensus 294 Rqi~~rAl~kL 304 (317)
T PRK07405 294 RQIEREALSKL 304 (317)
T ss_pred HHHHHHHHHHH
Confidence 99999887544
No 143
>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=97.07 E-value=0.0031 Score=62.96 Aligned_cols=133 Identities=20% Similarity=0.266 Sum_probs=71.4
Q ss_pred hHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHh
Q 014764 226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRG 305 (419)
Q Consensus 226 ~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrA 305 (419)
....++...+|++|+.+++|..+|++.+++...+... ..+.++-... +.+.++ .+...
T Consensus 165 k~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~------------~~~~SLd~~~---~~~~~~-------~~~~~ 222 (298)
T TIGR02997 165 KVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRA------------RQPVSLDAPV---GDEEDT-------ELGDL 222 (298)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHc------------ccCcccCCCc---CCCCcc-------hHHHh
Confidence 3556777889999999999999999999887642210 0111111111 000000 01111
Q ss_pred HhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccchHHHHHHHHHHHHHHHhcCCCccHHHHHHHcCCCHHHHHH
Q 014764 306 IEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRN 385 (419)
Q Consensus 306 IerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~l~e~~~~I~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~ 385 (419)
+.. ... ...........+..+..++. . +.+..+.|...++.|. .+.+.|++|||+.||+|.++|++
T Consensus 223 ~~~--~~~-~pe~~~~~~~~~~~L~~~L~------~----L~~rer~Vi~lr~gl~-~~~~~Tl~EIa~~lgiS~erVrq 288 (298)
T TIGR02997 223 LED--DGE-SPEEQVERESLRQDLESLLA------E----LTPRERQVLRLRFGLD-GGEPLTLAEIGRRLNLSRERVRQ 288 (298)
T ss_pred ccC--CCC-CHHHHHHHHHHHHHHHHHHH------c----CCHHHHHHHHHHhccC-CCCCcCHHHHHHHHCcCHHHHHH
Confidence 111 111 11222222222222222221 1 2333444555544442 13456999999999999999999
Q ss_pred HHHHhCccc
Q 014764 386 ATEAIGKVF 394 (419)
Q Consensus 386 ~l~rark~l 394 (419)
++.++.+.+
T Consensus 289 ~~~rAl~kL 297 (298)
T TIGR02997 289 IEAKALRKL 297 (298)
T ss_pred HHHHHHHHc
Confidence 999987653
No 144
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=96.93 E-value=0.0098 Score=65.34 Aligned_cols=132 Identities=15% Similarity=0.245 Sum_probs=73.3
Q ss_pred hHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhH-HHHHHHH
Q 014764 226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQG-GLIGLLR 304 (419)
Q Consensus 226 ~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQE-G~IgLlr 304 (419)
.+..++.+.+|++|+.+++|..+|++.++++..+. ++.... ..++-+.+ +-..+..
T Consensus 471 ~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~-------------------~~~~~~----Sld~~i~~~~~~~l~d 527 (619)
T PRK05658 471 RISRQMLQEIGREPTPEELAERLGMPEDKVRKVLK-------------------IAKEPI----SLETPIGDDEDSHLGD 527 (619)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH-------------------hcCCCC----cCCCCCCCCCCCchhh
Confidence 35677889999999999999999999998876322 222211 11111100 0001111
Q ss_pred hHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccchHHHHHHHHHHHHHHHhcCCCccHHHHHHHcCCCHHHHH
Q 014764 305 GIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVR 384 (419)
Q Consensus 305 AIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~l~e~~~~I~~a~~~L~e~gRepS~eEIAe~LGIS~etVr 384 (419)
.+. |......+........+..+...+ ..+.++.+.|...++.+. .+...|.+|||+.||||.++|+
T Consensus 528 ~i~--d~~~~~p~~~~~~~~~~~~l~~~l----------~~L~~rE~~Vl~~r~g~~-~~~~~tl~ei~~~lgvs~eRVr 594 (619)
T PRK05658 528 FIE--DKNAELPIDAAIQESLREATTDVL----------ASLTPREAKVLRMRFGID-MNTDHTLEEVGKQFDVTRERIR 594 (619)
T ss_pred hcC--CCCCCChHHHHHHHHHHHHHHHHH----------HcCCHHHHHHHHHhcCCC-CCCCccHHHHHHHhCCCHHHHH
Confidence 111 111111222222222333222222 123344555666655542 1355699999999999999999
Q ss_pred HHHHHhCcc
Q 014764 385 NATEAIGKV 393 (419)
Q Consensus 385 ~~l~rark~ 393 (419)
++..++.++
T Consensus 595 Qie~~al~k 603 (619)
T PRK05658 595 QIEAKALRK 603 (619)
T ss_pred HHHHHHHHH
Confidence 998887544
No 145
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=96.92 E-value=0.027 Score=55.19 Aligned_cols=34 Identities=38% Similarity=0.470 Sum_probs=29.4
Q ss_pred hhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 014764 225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (419)
Q Consensus 225 ~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~ 258 (419)
+.+...|+..+|++|+.+++|..+|++.+++...
T Consensus 121 ~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~ 154 (268)
T PRK06288 121 ERAIAMLEARLGRTPSDEEIADELGISLEEYNSL 154 (268)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHH
Confidence 3466788899999999999999999999887763
No 146
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=96.88 E-value=0.0074 Score=58.52 Aligned_cols=34 Identities=18% Similarity=0.256 Sum_probs=28.8
Q ss_pred HHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHh
Q 014764 227 HKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (419)
Q Consensus 227 ~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~ 260 (419)
+...+.+.+|++|+.+++|..+|++.++++..+.
T Consensus 114 ~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~ 147 (251)
T PRK07670 114 AIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMN 147 (251)
T ss_pred HHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 4556778899999999999999999999887443
No 147
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=96.79 E-value=0.0047 Score=59.56 Aligned_cols=60 Identities=22% Similarity=0.354 Sum_probs=40.9
Q ss_pred hhhhHHHHHHhhcCCCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 014764 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (419)
Q Consensus 189 ~~~~l~~yl~~i~~~~lLt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~ 258 (419)
+.+.+-.|++.....| ........+++ .+...|.+.+|++|+.+|+|..+|++.+++.+.
T Consensus 78 Ir~~il~~lr~~~~~~----r~vr~~~~~i~------~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~ 137 (231)
T PRK12427 78 IRGAILDELRELDWRP----RRLRQKTHKTN------DAIREIAKRLGHEPNFEEISAELNLTAEEYQEY 137 (231)
T ss_pred HHHHHHHHHHhcCCCC----HHHHHHHHHHH------HHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHH
Confidence 3345556666544322 22333444443 356788899999999999999999999987664
No 148
>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=96.78 E-value=0.014 Score=56.75 Aligned_cols=63 Identities=16% Similarity=0.264 Sum_probs=40.7
Q ss_pred hhhhHHHHHHhhcCCCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHH
Q 014764 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSIL 259 (419)
Q Consensus 189 ~~~~l~~yl~~i~~~~lLt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l 259 (419)
+.+.+..|++...... + |....+++.++.. +..++...+|++|+.+|+|..+|++.+++...+
T Consensus 95 irn~~~~~lr~~~~ir-~-p~~~~~~~~~~~~------~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~ 157 (254)
T TIGR02850 95 IIGEIRRYLRDNNPIR-V-SRSLRDIAYKALQ------VRDKLISENSKEPTVSEIAKELKVPQEEVVFAL 157 (254)
T ss_pred HHHHHHHHHHhCCCcc-C-chHHHHHHHHHHH------HHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHH
Confidence 3345555555533111 1 2333444444443 456788899999999999999999999877643
No 149
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=96.78 E-value=0.019 Score=58.85 Aligned_cols=144 Identities=21% Similarity=0.335 Sum_probs=83.5
Q ss_pred HHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHHHhHHHHHHHHHHccCCC-
Q 014764 210 EVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMG- 288 (419)
Q Consensus 210 eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~yl~LV~sIAkry~~~g- 288 (419)
..++++.+++. ....|.+.+|++|+.+++|+.+|++.++++..+..... ..++-.....+.
T Consensus 183 h~~e~~nkl~r------~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~------------~~SLd~~ig~ded 244 (342)
T COG0568 183 HQVELINKLRR------VKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASE------------PISLDTPIGDDED 244 (342)
T ss_pred HHHHHHHHHHH------HHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhccc------------CcccCCcCCCCcc
Confidence 44555555554 56678888999999999999999999987763322111 122222211110
Q ss_pred CChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHH-HHhhHHHHHHHhcccccCccchHHHHHHHHHHHHHHHhcCCCc
Q 014764 289 ADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW-IRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTP 367 (419)
Q Consensus 289 ~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~-Irn~I~~~Lrd~~r~irip~~l~e~~~~I~~a~~~L~e~gRep 367 (419)
....|++.+. . +....-.+... .+..+...+.. .+.++...|...+..+. .+...
T Consensus 245 ~~l~d~leD~---------~-----~~~p~~~~~~~~~~~~~~~~L~~---------~Lt~rE~~Vi~~R~gl~-~~~~~ 300 (342)
T COG0568 245 SELGDFLEDD---------K-----SVSPEDAVERESLKEDLNEVLAE---------ALTERERRVIRLRFGLD-DGEPK 300 (342)
T ss_pred cHHHHHhhcC---------C-----cCCHHHHHHHHHHHHHHHHHHHh---------cCCHHHHHHHHHHhccC-CCCcc
Confidence 0122333332 1 11122222221 12222222211 15556677777777775 24456
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHhCcccc
Q 014764 368 SVDRIAEYLNMSQKKVRNATEAIGKVFS 395 (419)
Q Consensus 368 S~eEIAe~LGIS~etVr~~l~rark~lS 395 (419)
|.+||++++|||.+.|+++...+.+++.
T Consensus 301 TLeevg~~~~isrERvRQIE~kAl~KLr 328 (342)
T COG0568 301 TLEELGEEFGISRERVRQIEAKALRKLR 328 (342)
T ss_pred hHHHHHHHhCCcHHHHHHHHHHHHHHHH
Confidence 9999999999999999999988866553
No 150
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=96.74 E-value=0.0034 Score=49.92 Aligned_cols=34 Identities=35% Similarity=0.555 Sum_probs=27.8
Q ss_pred hHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHH
Q 014764 226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSIL 259 (419)
Q Consensus 226 ~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l 259 (419)
.++.+|.+.+||+|+.+|+|..+|++.++++..+
T Consensus 8 ~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l 41 (78)
T PF04539_consen 8 RARRELEQELGREPTDEEIAEELGISVEEVRELL 41 (78)
T ss_dssp HHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHH
Confidence 4778999999999999999999999999988744
No 151
>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=96.60 E-value=0.02 Score=54.30 Aligned_cols=33 Identities=30% Similarity=0.429 Sum_probs=28.7
Q ss_pred hHHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 014764 226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (419)
Q Consensus 226 ~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~ 258 (419)
.+...|...+|++|+.+|+|..+|++.++++..
T Consensus 87 ~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~ 119 (224)
T TIGR02479 87 RAIRELEARLGREPTEEEIAEELGMDLKEYRQA 119 (224)
T ss_pred HHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHH
Confidence 356678889999999999999999999987764
No 152
>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=96.37 E-value=0.036 Score=52.81 Aligned_cols=42 Identities=33% Similarity=0.515 Sum_probs=32.1
Q ss_pred HHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 014764 211 VVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (419)
Q Consensus 211 E~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~ 258 (419)
...+..++.. ....|...+|++|+.+|+|..+|++.+++...
T Consensus 92 ~~~~~~~~~~------~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~ 133 (231)
T TIGR02885 92 LKELARKIRY------MKEELSKELGREPTINELAEALGVSPEEIVMA 133 (231)
T ss_pred HHHHHHHHHH------HHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHH
Confidence 3445555543 45578888999999999999999999887653
No 153
>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=96.07 E-value=0.0094 Score=57.77 Aligned_cols=32 Identities=25% Similarity=0.332 Sum_probs=27.6
Q ss_pred HHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 014764 227 HKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (419)
Q Consensus 227 ~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~ 258 (419)
+...++..+|++|+.+++|..++++.+++...
T Consensus 121 ~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~~ 152 (255)
T TIGR02941 121 AIDELTDHLQRSPKIIEIADHLGLSEEEVLEI 152 (255)
T ss_pred HHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 45678888999999999999999999987653
No 154
>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=96.05 E-value=0.024 Score=44.74 Aligned_cols=47 Identities=26% Similarity=0.208 Sum_probs=40.3
Q ss_pred HHHHHHHHHhHHHHHHHHHHccC------CCCChhhHhhHHHHHHHHhHhhcC
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDN------MGADMADLVQGGLIGLLRGIEKFD 310 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~------~g~d~EDLVQEG~IgLlrAIerFD 310 (419)
.|.++++..|.|++.+++.|-.. ++.--+|+-|+--..|+++|-+|+
T Consensus 13 ~A~~~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kLi~~I~~F~ 65 (65)
T PF12645_consen 13 EAMEEILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKLIEAILKFE 65 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHHHHHHHccC
Confidence 89999999999999999987331 233459999999999999999995
No 155
>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=95.97 E-value=0.01 Score=56.23 Aligned_cols=31 Identities=29% Similarity=0.506 Sum_probs=27.1
Q ss_pred HHHHHHHhhCCCCchHHHHHHhcCChHHHHH
Q 014764 227 HKLRLKERLGCEPSMEQLAASLRISRPELQS 257 (419)
Q Consensus 227 ~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~ 257 (419)
....++..+|++|+.+|+|..+|++.+++..
T Consensus 95 ~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~ 125 (227)
T TIGR02980 95 ATEELTQRLGRSPTIAEIAEELGVSEEEVVE 125 (227)
T ss_pred HHHHHHHHHCCCCCHHHHHHHhCCCHHHHHH
Confidence 4567888899999999999999999998764
No 156
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=95.96 E-value=0.12 Score=51.44 Aligned_cols=29 Identities=17% Similarity=0.216 Sum_probs=25.8
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKV 393 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~rark~ 393 (419)
.+.|+.|||+.||||.++|+++.+++.+.
T Consensus 247 ~~~Tl~EIA~~lgvS~~rVrqi~~~Al~k 275 (284)
T PRK06596 247 DKSTLQELAAEYGVSAERVRQIEKNAMKK 275 (284)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 56799999999999999999999888654
No 157
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=95.95 E-value=0.056 Score=51.79 Aligned_cols=30 Identities=17% Similarity=0.181 Sum_probs=26.3
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
.+.|++|||+.||+|.++|+..+.++.+.+
T Consensus 199 ~g~s~~EIA~~lgis~~tV~~~~~ra~~~L 228 (236)
T PRK06986 199 EELNLKEIGAVLGVSESRVSQIHSQAIKRL 228 (236)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 456999999999999999999999887644
No 158
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=95.75 E-value=0.026 Score=57.32 Aligned_cols=31 Identities=10% Similarity=0.221 Sum_probs=27.6
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
..+.|++|||+.||+|.++|+++++++.+.+
T Consensus 280 ~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kL 310 (325)
T PRK05657 280 YEAATLEDVAREIGLTRERVRQIQVEALRRL 310 (325)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 3567999999999999999999999998655
No 159
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=95.64 E-value=0.047 Score=53.12 Aligned_cols=32 Identities=25% Similarity=0.370 Sum_probs=27.7
Q ss_pred HHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 014764 227 HKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (419)
Q Consensus 227 ~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~ 258 (419)
+..++...+|++|+.+|+|..+|++.+++...
T Consensus 128 ~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~~ 159 (258)
T PRK08215 128 VREKLINENSKEPTVEEIAKELEVPREEVVFA 159 (258)
T ss_pred HHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHH
Confidence 45578889999999999999999999987653
No 160
>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=95.36 E-value=0.0057 Score=45.35 Aligned_cols=30 Identities=27% Similarity=0.172 Sum_probs=23.1
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKV 393 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~rark~ 393 (419)
..+.|+.|||+.+|+|..+|+..+.++++.
T Consensus 24 ~~g~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 24 FQGMSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp TS---HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred HHCcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 455699999999999999999999998654
No 161
>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=95.31 E-value=0.05 Score=53.87 Aligned_cols=31 Identities=13% Similarity=0.217 Sum_probs=27.6
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
..+.|+.|||+.||+|.++|+.++.++.+.+
T Consensus 240 ~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkL 270 (285)
T TIGR02394 240 YEPATLEEVAAEVGLTRERVRQIQVEALKKL 270 (285)
T ss_pred CCCccHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4566999999999999999999999998655
No 162
>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=95.25 E-value=0.32 Score=47.86 Aligned_cols=30 Identities=13% Similarity=0.176 Sum_probs=25.7
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKV 393 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~rark~ 393 (419)
+.+.|+.|||+.||||.++|+++..++.+.
T Consensus 234 ~~~~t~~eIA~~lgvS~~~V~q~~~~Al~k 263 (270)
T TIGR02392 234 DDKLTLQELAAEYGVSAERIRQIEKNAMKK 263 (270)
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 346799999999999999999998887544
No 163
>PRK05572 sporulation sigma factor SigF; Validated
Probab=95.12 E-value=0.33 Score=47.10 Aligned_cols=30 Identities=23% Similarity=0.235 Sum_probs=26.3
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
.+.|+.|||+.+|+|..+|..+..++.+.+
T Consensus 217 ~~~s~~eIA~~lgis~~~V~~~~~ral~kL 246 (252)
T PRK05572 217 KDKTQSEVAKRLGISQVQVSRLEKKILKQM 246 (252)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 467999999999999999999999886543
No 164
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=93.78 E-value=0.12 Score=37.81 Aligned_cols=30 Identities=27% Similarity=0.203 Sum_probs=25.6
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKV 393 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~rark~ 393 (419)
..+.|+.|||+.||+|.++|+++..++.+.
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~~~~~al~k 47 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTVRRILKRALKK 47 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHHHHHHHHHHHH
Confidence 567799999999999999999999887543
No 165
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=90.55 E-value=0.8 Score=36.07 Aligned_cols=44 Identities=30% Similarity=0.369 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHH-HhcCCCccHHHHHHHcCCC-HHHHHHHHHHhC
Q 014764 348 ERLGLIRNAKLRL-EEKGVTPSVDRIAEYLNMS-QKKVRNATEAIG 391 (419)
Q Consensus 348 e~~~~I~~a~~~L-~e~gRepS~eEIAe~LGIS-~etVr~~l~rar 391 (419)
+...++..++... .+.|..||+.|||+.+|++ ..+|...+....
T Consensus 6 ~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le 51 (65)
T PF01726_consen 6 ERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALE 51 (65)
T ss_dssp HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 3344555555444 5679999999999999997 999999987654
No 166
>PHA02547 55 RNA polymerase sigma factor; Provisional
Probab=90.40 E-value=0.9 Score=42.51 Aligned_cols=64 Identities=14% Similarity=0.295 Sum_probs=50.2
Q ss_pred HHHHHHHHHHccCCCCC---hhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhc
Q 014764 274 VRLVMSIAQRYDNMGAD---MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENS 337 (419)
Q Consensus 274 l~LV~sIAkry~~~g~d---~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~ 337 (419)
+..+..+.++|--++.. -+|+|.+|....++.++.||+.+...+-+|++.++-+...+.|....
T Consensus 47 mkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~kEk 113 (179)
T PHA02547 47 MKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIKKEK 113 (179)
T ss_pred HHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHHHHH
Confidence 34444455555333333 78999999999999999999999989999999999998888776554
No 167
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=88.98 E-value=0.25 Score=47.95 Aligned_cols=31 Identities=23% Similarity=0.075 Sum_probs=26.6
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
..+.|++|||+.||||.++|+..++++.+.+
T Consensus 219 ~~g~s~~eIA~~l~is~~tV~~~~~ra~~kL 249 (257)
T PRK08583 219 IENLSQKETGERLGISQMHVSRLQRQAIKKL 249 (257)
T ss_pred hCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 3566999999999999999999999886543
No 168
>PRK06930 positive control sigma-like factor; Validated
Probab=88.96 E-value=0.25 Score=45.89 Aligned_cols=30 Identities=30% Similarity=0.389 Sum_probs=26.6
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
.+.|+.|||+.||+|.++|+..+.++++.+
T Consensus 129 eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kL 158 (170)
T PRK06930 129 YGLSYSEIADYLNIKKSTVQSMIERAEKKI 158 (170)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 456999999999999999999999987654
No 169
>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=88.85 E-value=0.42 Score=36.41 Aligned_cols=30 Identities=17% Similarity=0.203 Sum_probs=26.7
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKV 393 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~rark~ 393 (419)
-|..+..|||+.||||..++...++++.++
T Consensus 21 PR~~tl~elA~~lgis~st~~~~LRrae~k 50 (53)
T PF04967_consen 21 PRRITLEELAEELGISKSTVSEHLRRAERK 50 (53)
T ss_pred CCcCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 478899999999999999999999988543
No 170
>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=87.72 E-value=0.93 Score=36.79 Aligned_cols=26 Identities=27% Similarity=0.340 Sum_probs=23.1
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHH
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~r 389 (419)
..+.|+.|||+.||+|+.+|+..+..
T Consensus 30 ~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 30 EAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 35679999999999999999999874
No 171
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=87.05 E-value=3.4 Score=42.85 Aligned_cols=127 Identities=11% Similarity=-0.009 Sum_probs=79.8
Q ss_pred HHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhcccccCccch
Q 014764 267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHL 346 (419)
Q Consensus 267 e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~l 346 (419)
+..+..-.+.+..---+|.++-.-+||.+||+|+...+..-+=-+-+ .-.+|++-.-||.-++.+|+..+....+.+.
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 33444444555555556667666799999999976655554433333 4689999999999999998877654433321
Q ss_pred HHHH--HHH---------------HHHHH-------------HHH-hcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccc
Q 014764 347 HERL--GLI---------------RNAKL-------------RLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFS 395 (419)
Q Consensus 347 ~e~~--~~I---------------~~a~~-------------~L~-e~gRepS~eEIAe~LGIS~etVr~~l~rark~lS 395 (419)
.... .++ .+.+. .|. ..--+.|..|||...=+++.++.+++.++++.+.
T Consensus 86 ~~~~e~~e~~~a~~~~d~~i~Dd~LRLiFvccHPal~~~~riALtLR~v~GLs~~eIArAFLv~e~am~QRivRAK~ri~ 165 (415)
T COG4941 86 LLSDEDEEMEEAEALDDEHIRDDRLRLIFVCCHPALPPEQRIALTLRLVGGLSTAEIARAFLVPEAAMAQRIVRAKARIR 165 (415)
T ss_pred cccccchhhhccccccccccchhhHHhhhhhcCCCCChhhHHHHHHHHHcCCcHHHHHHHHcCCcHHHHHHHHHHHHHHH
Confidence 1110 000 00000 000 0012339999999999999999999999886653
No 172
>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=86.39 E-value=0.52 Score=33.06 Aligned_cols=29 Identities=31% Similarity=0.255 Sum_probs=25.1
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKV 393 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~rark~ 393 (419)
.+.+..+||+.+|++..+|...+.++...
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 55699999999999999999998887543
No 173
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=85.51 E-value=0.91 Score=32.51 Aligned_cols=31 Identities=26% Similarity=0.276 Sum_probs=26.5
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCcccc
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVFS 395 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~rark~lS 395 (419)
.+.+..|||+.||+|..+|+..+.++...+-
T Consensus 17 ~g~s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 17 EGLTNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 3459999999999999999999998866554
No 174
>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=85.40 E-value=3.1 Score=32.12 Aligned_cols=42 Identities=24% Similarity=0.187 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHhcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 350 LGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 350 ~~~I~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~~l~rar 391 (419)
.....+++..|.+.+..++..+||+.||++..+|-..+++..
T Consensus 6 ~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~ 47 (60)
T PF01325_consen 6 EEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLA 47 (60)
T ss_dssp HHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHH
Confidence 345567777787777888999999999999999999987753
No 175
>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=84.76 E-value=2.7 Score=30.22 Aligned_cols=26 Identities=27% Similarity=0.309 Sum_probs=20.7
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
-..++.|||+.+|+|..+|.+++++.
T Consensus 16 ~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 16 GRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 34699999999999999999988753
No 176
>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=84.38 E-value=2.9 Score=30.79 Aligned_cols=37 Identities=19% Similarity=0.224 Sum_probs=27.1
Q ss_pred HHHHHHhcCCCccHHHHHHHcCCCHHHHHHHHHHhCc
Q 014764 356 AKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGK 392 (419)
Q Consensus 356 a~~~L~e~gRepS~eEIAe~LGIS~etVr~~l~rark 392 (419)
.+..|......+|.+|||+.||+|..+|++.+.....
T Consensus 5 il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~ 41 (55)
T PF08279_consen 5 ILKLLLESKEPITAKELAEELGVSRRTIRRDIKELRE 41 (55)
T ss_dssp HHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3344533344489999999999999999999877654
No 177
>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=82.62 E-value=1.2 Score=32.13 Aligned_cols=30 Identities=23% Similarity=0.304 Sum_probs=25.9
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
.+.+..|||+.||+|..+|+..+.++.+.+
T Consensus 14 ~~~s~~eia~~l~~s~~tv~~~~~~~~~~l 43 (57)
T cd06170 14 EGKTNKEIADILGISEKTVKTHLRNIMRKL 43 (57)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHh
Confidence 346999999999999999999999876544
No 178
>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=82.46 E-value=4 Score=30.72 Aligned_cols=46 Identities=30% Similarity=0.421 Sum_probs=33.9
Q ss_pred cCccchHHHHHHHHHHHHHHHhcCC-CccHHHHHHHcCCCHHHHHHH
Q 014764 341 RLPNHLHERLGLIRNAKLRLEEKGV-TPSVDRIAEYLNMSQKKVRNA 386 (419)
Q Consensus 341 rip~~l~e~~~~I~~a~~~L~e~gR-epS~eEIAe~LGIS~etVr~~ 386 (419)
.+|....+++....+....|...|. .++-.|||+.+|++..+|+.=
T Consensus 2 ~Ip~~ti~RL~~Y~r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRKD 48 (50)
T PF06971_consen 2 KIPKATIRRLPLYLRYLEQLKEEGVERVSSQELAEALGITPAQVRKD 48 (50)
T ss_dssp S-SHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHcCCeeECHHHHHHHHCCCHHHhccc
Confidence 3566677777777888888876665 459999999999999999864
No 179
>PRK04217 hypothetical protein; Provisional
Probab=82.33 E-value=1.1 Score=39.10 Aligned_cols=30 Identities=13% Similarity=0.096 Sum_probs=26.5
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
.+.|++|||+.||||..+|+..+.++.+.+
T Consensus 57 eGlS~~EIAk~LGIS~sTV~r~L~RArkkL 86 (110)
T PRK04217 57 EGLTQEEAGKRMGVSRGTVWRALTSARKKV 86 (110)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 456999999999999999999999887654
No 180
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=81.52 E-value=3.9 Score=29.36 Aligned_cols=27 Identities=19% Similarity=0.228 Sum_probs=21.5
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
....|..|||+.+|+|..+|...+...
T Consensus 15 ~~~~t~~ela~~~~is~~tv~~~l~~L 41 (48)
T PF13412_consen 15 NPRITQKELAEKLGISRSTVNRYLKKL 41 (48)
T ss_dssp CTTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred cCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 344899999999999999999998764
No 181
>PRK00118 putative DNA-binding protein; Validated
Probab=81.38 E-value=1.1 Score=38.65 Aligned_cols=29 Identities=28% Similarity=0.290 Sum_probs=25.6
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKV 393 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~rark~ 393 (419)
.+.|+.|||+.+|+|..+|...+.++++.
T Consensus 32 eg~S~~EIAe~lGIS~~TV~r~L~RArkk 60 (104)
T PRK00118 32 DDYSLGEIAEEFNVSRQAVYDNIKRTEKL 60 (104)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 46699999999999999999999887643
No 182
>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=80.59 E-value=3.2 Score=32.47 Aligned_cols=27 Identities=26% Similarity=0.307 Sum_probs=22.9
Q ss_pred HhcCCCccHHHHHHHcCCCHHHHHHHH
Q 014764 361 EEKGVTPSVDRIAEYLNMSQKKVRNAT 387 (419)
Q Consensus 361 ~e~gRepS~eEIAe~LGIS~etVr~~l 387 (419)
.+.+...+..+||+.||++..+|+.=-
T Consensus 17 ~~~~g~i~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 17 KESNGKIKLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred HHhCCCccHHHHHHHHCCCHHHHHHHh
Confidence 345778899999999999999998753
No 183
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=80.44 E-value=2.4 Score=41.12 Aligned_cols=35 Identities=26% Similarity=0.290 Sum_probs=29.5
Q ss_pred cCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccc
Q 014764 363 KGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLD 397 (419)
Q Consensus 363 ~gRepS~eEIAe~LGIS~etVr~~l~rark~lSLD 397 (419)
..++.|.+|||+.|++++.||++...+..+++-+.
T Consensus 155 ia~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLgv~ 189 (217)
T PRK13719 155 YSFGFSHEYIAQLLNITVGSSKNKISEILKFFGIS 189 (217)
T ss_pred HHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 35678999999999999999999998887666543
No 184
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=79.92 E-value=1.2 Score=33.47 Aligned_cols=33 Identities=30% Similarity=0.302 Sum_probs=26.7
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSL 396 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~rark~lSL 396 (419)
..+.+..|||+.||+++.+|+..+..+.+++-+
T Consensus 16 ~~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~ 48 (58)
T PF00196_consen 16 AQGMSNKEIAEELGISEKTVKSHRRRIMKKLGV 48 (58)
T ss_dssp HTTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred HhcCCcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence 456699999999999999999999888766544
No 185
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=79.26 E-value=2.6 Score=28.96 Aligned_cols=24 Identities=21% Similarity=0.433 Sum_probs=19.1
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 367 PSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 367 pS~eEIAe~LGIS~etVr~~l~ra 390 (419)
.|.+|||..+|++.++|...+...
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l 26 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKL 26 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHH
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHH
Confidence 378999999999999999988764
No 186
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=77.24 E-value=3 Score=30.04 Aligned_cols=26 Identities=23% Similarity=0.192 Sum_probs=18.4
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHH
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~r 389 (419)
..+.|+.|||+.||++..||..-+++
T Consensus 18 ~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 18 EQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp CS---HHHHHHHTT--HHHHHHHHHH
T ss_pred HcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 35679999999999999999988765
No 187
>PHA02591 hypothetical protein; Provisional
Probab=77.10 E-value=2.7 Score=34.67 Aligned_cols=34 Identities=29% Similarity=0.339 Sum_probs=25.8
Q ss_pred HHHHHHHHHhcCCCccHHHHHHHcCCCHHHHHHHHH
Q 014764 353 IRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATE 388 (419)
Q Consensus 353 I~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~~l~ 388 (419)
+......|- .++.|+++||+.||++..+|++.++
T Consensus 48 ~~~vA~eL~--eqGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 48 LISVTHELA--RKGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred HHHHHHHHH--HcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 334444443 2567999999999999999999875
No 188
>PRK14082 hypothetical protein; Provisional
Probab=76.70 E-value=9 Score=30.48 Aligned_cols=55 Identities=11% Similarity=0.016 Sum_probs=42.5
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhH
Q 014764 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 320 (419)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTY 320 (419)
...+.|+..+.|.|.+-... .+..+.|||.||--+.+++.+..++-..+..|.-|
T Consensus 9 ~e~e~ii~~FepkIkKsL~~--T~yqeREDLeQElk~Ki~eK~~~~~~~e~PGF~ef 63 (65)
T PRK14082 9 EEIEHLIENFSPMIKKKLSN--TSYQEREDLEQELKIKIIEKADMLLCQEVPGFWEF 63 (65)
T ss_pred HHHHHHHHHccHHHHHHHhc--CChhhHHHHHHHHHHHHHHHHHHhhcccCCcHHHh
Confidence 56788999999988765543 24567899999999999999999876665556544
No 189
>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=76.52 E-value=2.1 Score=38.74 Aligned_cols=31 Identities=16% Similarity=0.072 Sum_probs=26.2
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
.++.|++|||+.||+|..+|+.++.++.+.+
T Consensus 19 ~~GlTq~EIAe~LgiS~stV~~~e~ra~kkL 49 (137)
T TIGR00721 19 EKGLSQKEIAKELKTTRANVSAIEKRAMENI 49 (137)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHhHHHHH
Confidence 3567999999999999999999888876443
No 190
>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=76.45 E-value=4.7 Score=29.68 Aligned_cols=32 Identities=22% Similarity=0.347 Sum_probs=24.6
Q ss_pred HHHhcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 359 RLEEKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 359 ~L~e~gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
.+...+...+..|||+.+|++..+|..++..-
T Consensus 11 ~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL 42 (52)
T PF09339_consen 11 ALAESGGPLTLSEIARALGLPKSTVHRLLQTL 42 (52)
T ss_dssp CHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 34444555699999999999999999988653
No 191
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=75.98 E-value=3.3 Score=39.35 Aligned_cols=33 Identities=12% Similarity=0.157 Sum_probs=29.0
Q ss_pred hcCCCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 362 EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 362 e~gRepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
+.-|.++..|||+.|||+..++.+.+++|.+++
T Consensus 174 d~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl 206 (215)
T COG3413 174 DYPRRVSLKDLAKELGISKSTLSEHLRRAERKL 206 (215)
T ss_pred CCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 345888999999999999999999999997654
No 192
>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=74.41 E-value=7.2 Score=28.09 Aligned_cols=21 Identities=24% Similarity=0.243 Sum_probs=16.9
Q ss_pred ccHHHHHHHcCCCHHHHHHHH
Q 014764 367 PSVDRIAEYLNMSQKKVRNAT 387 (419)
Q Consensus 367 pS~eEIAe~LGIS~etVr~~l 387 (419)
.++.+||+.+|||..||...+
T Consensus 22 ~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 22 MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp --HHHHHHHTTS-HHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHH
Confidence 799999999999999998875
No 193
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=73.92 E-value=4 Score=37.09 Aligned_cols=29 Identities=17% Similarity=0.170 Sum_probs=25.1
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCc
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGK 392 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~rark 392 (419)
..+.|++|||+.||+|..+|+..+.++.+
T Consensus 19 ~~GlTq~EIAe~LGiS~~tVs~ie~ra~k 47 (141)
T PRK03975 19 ERGLTQQEIADILGTSRANVSSIEKRARE 47 (141)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 35679999999999999999998877654
No 194
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=73.20 E-value=6.5 Score=34.66 Aligned_cols=32 Identities=22% Similarity=0.217 Sum_probs=26.1
Q ss_pred HHHhcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 359 RLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 359 ~L~e~gRepS~eEIAe~LGIS~etVr~~l~rar 391 (419)
.|...+| .++.|||+.+|+|..+|.+++.+..
T Consensus 16 ~L~~d~r-~~~~eia~~lglS~~~v~~Ri~~L~ 47 (154)
T COG1522 16 LLQEDAR-ISNAELAERVGLSPSTVLRRIKRLE 47 (154)
T ss_pred HHHHhCC-CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3444455 8999999999999999999987753
No 195
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=72.68 E-value=3.3 Score=29.88 Aligned_cols=25 Identities=24% Similarity=0.170 Sum_probs=18.7
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 366 TPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 366 epS~eEIAe~LGIS~etVr~~l~ra 390 (419)
+.|+.+||+.+|+|..+|.+.+.+-
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 5699999999999999999987664
No 196
>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=71.69 E-value=2.9 Score=36.01 Aligned_cols=31 Identities=26% Similarity=0.278 Sum_probs=23.6
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
....|..|||+.+|||...|.+.++++.+.+
T Consensus 31 ~eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L 61 (101)
T PF04297_consen 31 EEDLSLSEIAEELGISRQAVYDSIKRAEKKL 61 (101)
T ss_dssp TS---HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4566999999999999999999999987543
No 197
>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=70.73 E-value=9.5 Score=31.36 Aligned_cols=33 Identities=33% Similarity=0.420 Sum_probs=23.6
Q ss_pred HHHhcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 359 RLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 359 ~L~e~gRepS~eEIAe~LGIS~etVr~~l~rar 391 (419)
.+-..|+.+|..++|..+|++.++|+.++....
T Consensus 31 r~LA~G~PVt~~~LA~a~g~~~e~v~~~L~~~p 63 (77)
T PF12324_consen 31 RLLAKGQPVTVEQLAAALGWPVEEVRAALAAMP 63 (77)
T ss_dssp HHHTTTS-B-HHHHHHHHT--HHHHHHHHHH-T
T ss_pred HHHHcCCCcCHHHHHHHHCCCHHHHHHHHHhCC
Confidence 333459999999999999999999999998763
No 198
>PF14502 HTH_41: Helix-turn-helix domain
Probab=70.09 E-value=5.6 Score=29.88 Aligned_cols=34 Identities=18% Similarity=0.358 Sum_probs=27.9
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhC--cccccc
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAIG--KVFSLD 397 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~rar--k~lSLD 397 (419)
.|-|++.|.++.++++.++|++++.... ..+.|.
T Consensus 4 dRi~tI~e~~~~~~vs~GtiQ~Alk~Le~~gaI~Le 39 (48)
T PF14502_consen 4 DRIPTISEYSEKFGVSRGTIQNALKFLEENGAIKLE 39 (48)
T ss_pred cccCCHHHHHHHhCcchhHHHHHHHHHHHCCcEEee
Confidence 4678999999999999999999988653 455554
No 199
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=70.04 E-value=9.6 Score=30.70 Aligned_cols=35 Identities=29% Similarity=0.260 Sum_probs=23.8
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCccccccc
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDR 398 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~rark~lSLD~ 398 (419)
.+..|+.|+|+.||++..+|.++++.-...+|+|.
T Consensus 29 ~~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~ 63 (80)
T PF13744_consen 29 ERGLTQAELAERLGISQPRVSRLENGKIDDFSLDT 63 (80)
T ss_dssp CCT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHH
T ss_pred HcCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHH
Confidence 57889999999999999999998864445566654
No 200
>PF13730 HTH_36: Helix-turn-helix domain
Probab=70.01 E-value=5.6 Score=29.21 Aligned_cols=27 Identities=30% Similarity=0.523 Sum_probs=23.1
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
+--|+++.||+.+|++..+|.+++..-
T Consensus 23 ~~~pS~~~la~~~g~s~~Tv~~~i~~L 49 (55)
T PF13730_consen 23 GCFPSQETLAKDLGVSRRTVQRAIKEL 49 (55)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 345699999999999999999988654
No 201
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=69.83 E-value=5.2 Score=29.43 Aligned_cols=23 Identities=17% Similarity=0.215 Sum_probs=20.3
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHh
Q 014764 368 SVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 368 S~eEIAe~LGIS~etVr~~l~ra 390 (419)
|+.+||+.+|+|..+|..++...
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~~ 23 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNGP 23 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTTC
T ss_pred CHHHHHHHHCcCHHHHHHHHhCC
Confidence 67899999999999999998643
No 202
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=69.46 E-value=12 Score=29.40 Aligned_cols=32 Identities=25% Similarity=0.376 Sum_probs=25.6
Q ss_pred HHhcCC-CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 360 LEEKGV-TPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 360 L~e~gR-epS~eEIAe~LGIS~etVr~~l~rar 391 (419)
|...+. +.+..|||+.||++..+|...+....
T Consensus 15 L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~ 47 (68)
T smart00550 15 LENSGDETSTALQLAKNLGLPKKEVNRVLYSLE 47 (68)
T ss_pred HHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 344444 48999999999999999999987643
No 203
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=69.17 E-value=7.1 Score=36.07 Aligned_cols=33 Identities=21% Similarity=0.137 Sum_probs=28.2
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSL 396 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~rark~lSL 396 (419)
..+.|..|||+.|++|..||+..+.+..+++-+
T Consensus 163 ~~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~v 195 (216)
T PRK10840 163 AEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGV 195 (216)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 467899999999999999999998887666544
No 204
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=69.06 E-value=6.6 Score=37.28 Aligned_cols=34 Identities=29% Similarity=0.309 Sum_probs=29.2
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCcccccc
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLD 397 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~rark~lSLD 397 (419)
.++.+.+|||+.|++|++||+.......+++-+.
T Consensus 161 a~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~v~ 194 (211)
T COG2197 161 AEGLSNKEIAEELNLSEKTVKTHVSNILRKLGVR 194 (211)
T ss_pred HCCCCHHHHHHHHCCCHhHHHHHHHHHHHHcCCC
Confidence 5677999999999999999999988887766554
No 205
>PF12728 HTH_17: Helix-turn-helix domain
Probab=68.36 E-value=5.5 Score=28.89 Aligned_cols=23 Identities=26% Similarity=0.222 Sum_probs=20.5
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHh
Q 014764 368 SVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 368 S~eEIAe~LGIS~etVr~~l~ra 390 (419)
|.+|+|+.|||+..+|....+..
T Consensus 3 t~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 3 TVKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcC
Confidence 78999999999999999987644
No 206
>PRK13870 transcriptional regulator TraR; Provisional
Probab=68.31 E-value=4.3 Score=39.30 Aligned_cols=31 Identities=23% Similarity=0.253 Sum_probs=27.1
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
..+.|..|||.+||||+.||+-.+..+.+++
T Consensus 186 A~GKT~~EIa~ILgISe~TV~~Hl~na~~KL 216 (234)
T PRK13870 186 AVGKTMEEIADVEGVKYNSVRVKLREAMKRF 216 (234)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHc
Confidence 3455999999999999999999999887764
No 207
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=68.28 E-value=6.8 Score=36.93 Aligned_cols=33 Identities=15% Similarity=0.182 Sum_probs=28.2
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSL 396 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~rark~lSL 396 (419)
..+.|.+|||+.||+|+.||+..+.+...++-.
T Consensus 150 a~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~v 182 (207)
T PRK15411 150 MAGQGTIQISDQMNIKAKTVSSHKGNIKRKIKT 182 (207)
T ss_pred HcCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCC
Confidence 467799999999999999999999887666544
No 208
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=66.67 E-value=7.5 Score=28.20 Aligned_cols=26 Identities=31% Similarity=0.409 Sum_probs=22.9
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 366 epS~eEIAe~LGIS~etVr~~l~rar 391 (419)
-||..|||+.+|+|..+|+.++....
T Consensus 20 l~s~~~la~~~~vs~~tv~~~l~~L~ 45 (60)
T smart00345 20 LPSERELAAQLGVSRTTVREALSRLE 45 (60)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 34999999999999999999988754
No 209
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=66.08 E-value=12 Score=27.09 Aligned_cols=23 Identities=26% Similarity=0.263 Sum_probs=21.4
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHH
Q 014764 367 PSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 367 pS~eEIAe~LGIS~etVr~~l~r 389 (419)
.|..+||+.+|++..+|..++.+
T Consensus 28 ~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 28 RSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHh
Confidence 69999999999999999999865
No 210
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=65.96 E-value=2.8 Score=36.82 Aligned_cols=29 Identities=21% Similarity=0.291 Sum_probs=26.4
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014764 368 SVDRIAEYLNMSQKKVRNATEAIGKVFSL 396 (419)
Q Consensus 368 S~eEIAe~LGIS~etVr~~l~rark~lSL 396 (419)
++.|+++.||||.-||++++...-..+.+
T Consensus 51 nlKe~e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 51 NLKEMEKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred CHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence 88999999999999999999988777766
No 211
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=65.66 E-value=19 Score=28.73 Aligned_cols=35 Identities=17% Similarity=0.192 Sum_probs=27.2
Q ss_pred HHHHHHhcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 356 AKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 356 a~~~L~e~gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
.+..+.......+..|||+.+|++..+|...+...
T Consensus 10 Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L 44 (91)
T smart00346 10 VLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTL 44 (91)
T ss_pred HHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 33344433356899999999999999999998765
No 212
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=65.30 E-value=5.4 Score=38.76 Aligned_cols=31 Identities=23% Similarity=0.265 Sum_probs=27.2
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCcccc
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVFS 395 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~rark~lS 395 (419)
.+.|..|||++||||+.||+..+..+.+++-
T Consensus 193 ~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~ 223 (240)
T PRK10188 193 EGKTSAEIAMILSISENTVNFHQKNMQKKFN 223 (240)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 4569999999999999999999998877653
No 213
>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=65.11 E-value=5.3 Score=38.43 Aligned_cols=31 Identities=19% Similarity=0.275 Sum_probs=27.1
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCcccc
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVFS 395 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~rark~lS 395 (419)
.+.|..|||++||+|+.||+..+.++.+++-
T Consensus 185 ~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~ 215 (232)
T TIGR03541 185 LGRRQADIAAILGISERTVENHLRSARRKLG 215 (232)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHC
Confidence 4569999999999999999999999876553
No 214
>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=64.86 E-value=5.3 Score=39.33 Aligned_cols=32 Identities=25% Similarity=0.253 Sum_probs=27.6
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVFSL 396 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~rark~lSL 396 (419)
.+.|..|||+.||||+.||+..+..+.+++-.
T Consensus 204 ~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v 235 (247)
T TIGR03020 204 DGKTNEEIAAILGISSLTVKNHLQHIFKKLDV 235 (247)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence 56799999999999999999999988766543
No 215
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=64.78 E-value=9.3 Score=36.32 Aligned_cols=34 Identities=21% Similarity=0.177 Sum_probs=28.6
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCcccccc
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLD 397 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~rark~lSLD 397 (419)
.++.|.+|||+.|+||+.||+.......+++-+.
T Consensus 147 ~~G~snkeIA~~L~iS~~TV~~h~~~I~~KLgv~ 180 (207)
T PRK11475 147 SRGYSMPQIAEQLERNIKTIRAHKFNVMSKLGVS 180 (207)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCC
Confidence 4577999999999999999999988877665443
No 216
>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=64.74 E-value=8.2 Score=26.89 Aligned_cols=23 Identities=30% Similarity=0.397 Sum_probs=20.6
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHh
Q 014764 368 SVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 368 S~eEIAe~LGIS~etVr~~l~ra 390 (419)
|.+|+|+.||++..++.+..+..
T Consensus 3 t~~e~a~~lgis~~ti~~~~~~g 25 (49)
T TIGR01764 3 TVEEAAEYLGVSKDTVYRLIHEG 25 (49)
T ss_pred CHHHHHHHHCCCHHHHHHHHHcC
Confidence 78999999999999999987654
No 217
>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=64.36 E-value=13 Score=28.34 Aligned_cols=30 Identities=17% Similarity=0.359 Sum_probs=24.8
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKV 393 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~rark~ 393 (419)
.+..++.|||+.||+|..++++.+......
T Consensus 17 ~~~~~~~ela~~l~~S~rti~~~i~~L~~~ 46 (59)
T PF08280_consen 17 NKWITLKELAKKLNISERTIKNDINELNEF 46 (59)
T ss_dssp HTSBBHHHHHHHCTS-HHHHHHHHHHHHTT
T ss_pred CCCCcHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 567899999999999999999998776543
No 218
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=63.97 E-value=5.9 Score=34.38 Aligned_cols=30 Identities=20% Similarity=0.170 Sum_probs=27.3
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
.+.+++|.|+.||||..|+..++..|++++
T Consensus 56 egl~QeeaA~~MgVSR~T~~ril~~ARkKi 85 (106)
T PF02001_consen 56 EGLSQEEAAERMGVSRPTFQRILESARKKI 85 (106)
T ss_pred cCCCHHHHHHHcCCcHHHHHHHHHHHHHHH
Confidence 457999999999999999999999998765
No 219
>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=63.83 E-value=20 Score=29.58 Aligned_cols=42 Identities=29% Similarity=0.254 Sum_probs=32.0
Q ss_pred HHHHHHHHHHH-HhcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 350 LGLIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 350 ~~~I~~a~~~L-~e~gRepS~eEIAe~LGIS~etVr~~l~rar 391 (419)
...|..++-.+ .+.++.+.-++||+.|+++..+|++.|....
T Consensus 6 q~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le 48 (78)
T PF03444_consen 6 QREILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADLE 48 (78)
T ss_pred HHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHH
Confidence 34444444444 4568888999999999999999999987653
No 220
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=63.40 E-value=18 Score=30.63 Aligned_cols=39 Identities=21% Similarity=0.225 Sum_probs=28.0
Q ss_pred HHHHHHHHhc--CCCccHHHHHHHcCCCHHHHHHHHHHhCc
Q 014764 354 RNAKLRLEEK--GVTPSVDRIAEYLNMSQKKVRNATEAIGK 392 (419)
Q Consensus 354 ~~a~~~L~e~--gRepS~eEIAe~LGIS~etVr~~l~rark 392 (419)
+....+|... ....|.+|||+.||+++..+..++....+
T Consensus 9 ~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~lekil~~tqr 49 (97)
T COG4367 9 QRTKQELQANFELCPLSDEEIATALNWTEVKLEKILQVTQR 49 (97)
T ss_pred HHHHHHHHHhhhhccccHHHHHHHhCCCHHHHHHHHHHhhc
Confidence 3444455432 34459999999999999999999865543
No 221
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=61.93 E-value=1e+02 Score=33.49 Aligned_cols=24 Identities=21% Similarity=0.264 Sum_probs=20.8
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHH
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATE 388 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~ 388 (419)
+..+..+||+.+|+.+.||..+..
T Consensus 368 kPLtlkdVAe~lglHeSTVSRa~~ 391 (481)
T PRK12469 368 KPLVLRDVAEELGLHESTISRATG 391 (481)
T ss_pred cCCcHHHHHHHhCCCcchhhHHhc
Confidence 334999999999999999999864
No 222
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=61.53 E-value=5.9 Score=37.98 Aligned_cols=26 Identities=19% Similarity=0.116 Sum_probs=21.6
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
++...++||..||||+.||+......
T Consensus 156 ~G~~NKqIA~dLgiS~rTVe~HRanv 181 (202)
T COG4566 156 RGLMNKQIAFDLGISERTVELHRANV 181 (202)
T ss_pred cCcccHHHHHHcCCchhhHHHHHHHH
Confidence 45589999999999999999865544
No 223
>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=61.49 E-value=34 Score=31.03 Aligned_cols=54 Identities=15% Similarity=0.075 Sum_probs=38.5
Q ss_pred CccchHHHHHHHHHHHHHHH-hcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccc
Q 014764 342 LPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFS 395 (419)
Q Consensus 342 ip~~l~e~~~~I~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~~l~rark~lS 395 (419)
-|.-..+......+....|. ..++..|+.||++.+||++..|...++..+-.++
T Consensus 21 Cp~C~~~~e~~f~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~IreGRL~~~ 75 (137)
T TIGR03826 21 CPSCYEEEEREFEKVYKFLRKHENRQATVSEIVEETGVSEKLILKFIREGRLQLK 75 (137)
T ss_pred CHHHhHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCCeecc
Confidence 34445555555555555563 3466789999999999999999999887764443
No 224
>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=61.10 E-value=38 Score=25.75 Aligned_cols=48 Identities=23% Similarity=0.247 Sum_probs=37.4
Q ss_pred CCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHH
Q 014764 206 LTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECS 263 (419)
Q Consensus 206 Lt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~ 263 (419)
||+.|..-|...+..|=. ..-|.-+.+++|..+|+|...+...|..+.
T Consensus 1 LT~~Q~e~L~~A~~~GYf----------d~PR~~tl~elA~~lgis~st~~~~LRrae 48 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYF----------DVPRRITLEELAEELGISKSTVSEHLRRAE 48 (53)
T ss_pred CCHHHHHHHHHHHHcCCC----------CCCCcCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 567777667777888776 445778899999999999998888776543
No 225
>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=60.78 E-value=11 Score=28.99 Aligned_cols=27 Identities=22% Similarity=0.166 Sum_probs=23.5
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~rar 391 (419)
++-++.|||+.||++..+|.+-..+-.
T Consensus 12 ~G~~~~eIA~~Lg~~~~TV~~W~~r~~ 38 (58)
T PF06056_consen 12 QGWSIKEIAEELGVPRSTVYSWKDRYK 38 (58)
T ss_pred cCCCHHHHHHHHCCChHHHHHHHHhhC
Confidence 577999999999999999999876654
No 226
>PRK09483 response regulator; Provisional
Probab=60.65 E-value=13 Score=33.44 Aligned_cols=33 Identities=24% Similarity=0.256 Sum_probs=28.4
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSL 396 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~rark~lSL 396 (419)
..+.+..|||+.|+++..||+....+..+++.+
T Consensus 161 ~~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~v 193 (217)
T PRK09483 161 TKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNI 193 (217)
T ss_pred HCCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence 355699999999999999999999988777654
No 227
>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=60.23 E-value=28 Score=25.95 Aligned_cols=26 Identities=19% Similarity=0.424 Sum_probs=23.0
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 366 epS~eEIAe~LGIS~etVr~~l~rar 391 (419)
.++..|||+.+|++..+|..++....
T Consensus 25 ~~s~~ela~~~g~s~~tv~r~l~~L~ 50 (67)
T cd00092 25 PLTRQEIADYLGLTRETVSRTLKELE 50 (67)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 46999999999999999999987654
No 228
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=60.19 E-value=19 Score=32.42 Aligned_cols=27 Identities=11% Similarity=0.182 Sum_probs=23.6
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~rar 391 (419)
-..++.|||+.+|+|+.+|+.++++..
T Consensus 22 ~R~s~~eiA~~lglS~~tV~~Ri~rL~ 48 (153)
T PRK11179 22 ARTPYAELAKQFGVSPGTIHVRVEKMK 48 (153)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 345999999999999999999988754
No 229
>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=60.05 E-value=43 Score=28.39 Aligned_cols=66 Identities=8% Similarity=-0.045 Sum_probs=40.0
Q ss_pred hhHHHHHHHhhHHHHHHHhcccccCccchHHHHHHHHHHHHHHHhcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 318 STYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 318 STYa~~~Irn~I~~~Lrd~~r~irip~~l~e~~~~I~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~~l~rar 391 (419)
.+|....+.+.+.+.+........+..... . .+..|.. ....+..|||+.+|++..+|...+....
T Consensus 2 ~~~~l~~~~~~~~~~~~~~l~~~~lt~~q~----~---iL~~l~~-~~~~t~~ela~~~~~~~~tvs~~l~~Le 67 (118)
T TIGR02337 2 LPLALLQAREAAMSFFRPILAQHGLTEQQW----R---ILRILAE-QGSMEFTQLANQACILRPSLTGILARLE 67 (118)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHcCCCHHHH----H---HHHHHHH-cCCcCHHHHHHHhCCCchhHHHHHHHHH
Confidence 456666666666666655443333321111 1 2222322 3457999999999999999998887653
No 230
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=59.77 E-value=12 Score=35.72 Aligned_cols=33 Identities=12% Similarity=0.231 Sum_probs=28.0
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSL 396 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~rark~lSL 396 (419)
.++.|..|||+.|++|..||+..+.++.+++-+
T Consensus 146 AqGkTnKEIAe~L~IS~rTVkth~srImkKLgV 178 (198)
T PRK15201 146 ASGYHLSETAALLSLSEEQTKSLRRSIMRKLHV 178 (198)
T ss_pred HCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 457799999999999999999998887766544
No 231
>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=59.76 E-value=21 Score=26.93 Aligned_cols=27 Identities=22% Similarity=0.284 Sum_probs=23.2
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
...++++|||+.+|+|..||+.-+...
T Consensus 12 ~~~~s~~ela~~~~VS~~TiRRDl~~L 38 (57)
T PF08220_consen 12 KGKVSVKELAEEFGVSEMTIRRDLNKL 38 (57)
T ss_pred cCCEEHHHHHHHHCcCHHHHHHHHHHH
Confidence 457799999999999999999877653
No 232
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=59.15 E-value=97 Score=33.29 Aligned_cols=23 Identities=30% Similarity=0.356 Sum_probs=20.4
Q ss_pred CccHHHHHHHcCCCHHHHHHHHH
Q 014764 366 TPSVDRIAEYLNMSQKKVRNATE 388 (419)
Q Consensus 366 epS~eEIAe~LGIS~etVr~~l~ 388 (419)
..+..+||+.+|+.+.||..+..
T Consensus 343 PLtlkdvAe~lglheSTVSRav~ 365 (455)
T PRK05932 343 PLVLKDIAEELGMHESTISRATT 365 (455)
T ss_pred CccHHHHHHHhCCCccchhhhhc
Confidence 34999999999999999999864
No 233
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=59.03 E-value=9.7 Score=28.20 Aligned_cols=31 Identities=23% Similarity=0.259 Sum_probs=26.1
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCcccc
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVFS 395 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~rark~lS 395 (419)
.+.+..|||..+|++..+|...+.....++.
T Consensus 18 ~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~ 48 (65)
T COG2771 18 QGKSNKEIARILGISEETVKTHLRNIYRKLG 48 (65)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 3479999999999999999999888765543
No 234
>PRK13239 alkylmercury lyase; Provisional
Probab=58.96 E-value=20 Score=34.59 Aligned_cols=29 Identities=31% Similarity=0.328 Sum_probs=27.0
Q ss_pred cCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 363 KGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 363 ~gRepS~eEIAe~LGIS~etVr~~l~rar 391 (419)
.|+.||+.+||+.+|+++++|+.+++...
T Consensus 33 ~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 33 KGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 69999999999999999999999998754
No 235
>PRK10403 transcriptional regulator NarP; Provisional
Probab=58.90 E-value=15 Score=32.41 Aligned_cols=33 Identities=21% Similarity=0.252 Sum_probs=29.2
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCcccccc
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLD 397 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~rark~lSLD 397 (419)
.+.+.+|||+.||++..||+..+.+..+++.+.
T Consensus 167 ~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~ 199 (215)
T PRK10403 167 QGLSNKQIASVLNISEQTVKVHIRNLLRKLNVR 199 (215)
T ss_pred CCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCCC
Confidence 458999999999999999999999988877664
No 236
>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=58.45 E-value=12 Score=25.79 Aligned_cols=23 Identities=22% Similarity=0.229 Sum_probs=20.3
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHh
Q 014764 368 SVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 368 S~eEIAe~LGIS~etVr~~l~ra 390 (419)
+..|+|+.|||+..+|.......
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~g 24 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKEG 24 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcC
Confidence 67899999999999999987654
No 237
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=58.10 E-value=18 Score=34.23 Aligned_cols=26 Identities=27% Similarity=0.316 Sum_probs=22.5
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 366 epS~eEIAe~LGIS~etVr~~l~rar 391 (419)
+.|+.|||+.||.++.||++.+....
T Consensus 61 g~Ti~EIAeelG~TeqTir~hlkget 86 (182)
T COG1318 61 GMTISEIAEELGRTEQTVRNHLKGET 86 (182)
T ss_pred cCcHHHHHHHhCCCHHHHHHHHhcch
Confidence 44999999999999999999987543
No 238
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=58.03 E-value=1.3e+02 Score=30.55 Aligned_cols=27 Identities=15% Similarity=0.318 Sum_probs=22.9
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
+-..|+.|||+.+|+++.|+++.....
T Consensus 249 ~~~~tq~eva~v~~vtevTIrnrykel 275 (285)
T COG1405 249 GERRTQKEVAKVAGVTEVTIRNRYKEL 275 (285)
T ss_pred CCchHHHHHHHHhCCeeeHHHHHHHHH
Confidence 345599999999999999999998544
No 239
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=57.37 E-value=13 Score=35.56 Aligned_cols=32 Identities=22% Similarity=0.236 Sum_probs=27.3
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVFSL 396 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~rark~lSL 396 (419)
.+.|..|||+.|++|+.||+..+.++.+++-+
T Consensus 169 ~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v 200 (216)
T PRK10100 169 IGASNNEIARSLFISENTVKTHLYNLFKKIAV 200 (216)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 36799999999999999999999887665544
No 240
>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=57.14 E-value=20 Score=29.93 Aligned_cols=41 Identities=27% Similarity=0.261 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHHhcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 350 LGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 350 ~~~I~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
..+|..++..-.....++++.+|++.|+++..+|+.++...
T Consensus 49 ~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L 89 (102)
T PF08784_consen 49 QDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFL 89 (102)
T ss_dssp HHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHH
Confidence 34444444442223567899999999999999999998754
No 241
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=57.03 E-value=16 Score=31.99 Aligned_cols=33 Identities=21% Similarity=0.172 Sum_probs=28.3
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCcccccc
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLD 397 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~rark~lSLD 397 (419)
.+.+.+|||+.|+++..||+..+.++.+++.+.
T Consensus 163 ~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~~ 195 (211)
T PRK15369 163 EGYTNRDIAEQLSISIKTVETHRLNMMRKLDVH 195 (211)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 345899999999999999999999988776554
No 242
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=56.90 E-value=23 Score=29.44 Aligned_cols=25 Identities=20% Similarity=0.314 Sum_probs=22.6
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 366 TPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 366 epS~eEIAe~LGIS~etVr~~l~ra 390 (419)
..+..|||+.+|++..+|.+++.+.
T Consensus 17 ~~~~~~la~~l~~s~~tv~~~l~~L 41 (108)
T smart00344 17 RISLAELAKKVGLSPSTVHNRVKRL 41 (108)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4689999999999999999998775
No 243
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=56.47 E-value=16 Score=25.50 Aligned_cols=25 Identities=20% Similarity=0.340 Sum_probs=22.3
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 367 PSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 367 pS~eEIAe~LGIS~etVr~~l~rar 391 (419)
++..|||+.+|++..+|...+....
T Consensus 9 ~s~~~la~~l~~s~~tv~~~l~~L~ 33 (48)
T smart00419 9 LTRQEIAELLGLTRETVSRTLKRLE 33 (48)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 5899999999999999999887654
No 244
>PRK15320 transcriptional activator SprB; Provisional
Probab=56.36 E-value=15 Score=35.74 Aligned_cols=32 Identities=9% Similarity=0.020 Sum_probs=27.0
Q ss_pred cCCCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 363 KGVTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 363 ~gRepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
+..+.|.+|||+.|++|.++|.....+...++
T Consensus 176 LAkG~SNKEIAekL~LS~KTVSTYKnRLLeKL 207 (251)
T PRK15320 176 LSSGHPAIELAKKFGLGTKTVSIYRKKVMYRL 207 (251)
T ss_pred HHcCCCHHHHHHHhccchhhHHHHHHHHHHHc
Confidence 35677999999999999999999988876544
No 245
>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=56.29 E-value=17 Score=28.34 Aligned_cols=27 Identities=19% Similarity=0.201 Sum_probs=21.7
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
...+|..|||..+|+++++|+.++..-
T Consensus 12 ~~~~S~~eLa~~~~~s~~~ve~mL~~l 38 (69)
T PF09012_consen 12 RGRVSLAELAREFGISPEAVEAMLEQL 38 (69)
T ss_dssp S-SEEHHHHHHHTT--HHHHHHHHHHH
T ss_pred cCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 567899999999999999999998764
No 246
>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=55.56 E-value=14 Score=28.24 Aligned_cols=26 Identities=31% Similarity=0.390 Sum_probs=20.5
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
+-|+..+||+.+|+|..+|++++...
T Consensus 23 ~lps~~~la~~~~vsr~tvr~al~~L 48 (64)
T PF00392_consen 23 RLPSERELAERYGVSRTTVREALRRL 48 (64)
T ss_dssp BE--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred EeCCHHHHHHHhccCCcHHHHHHHHH
Confidence 34599999999999999999998874
No 247
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=55.04 E-value=34 Score=23.89 Aligned_cols=27 Identities=26% Similarity=0.373 Sum_probs=23.8
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~rar 391 (419)
..++..+||+.+|++..+|...+....
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~L~ 39 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNKLE 39 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 358999999999999999999987754
No 248
>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=54.83 E-value=37 Score=24.68 Aligned_cols=37 Identities=14% Similarity=0.198 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHhcCCCccHHHHHHHcCCCHHHHHHHHHH
Q 014764 351 GLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 351 ~~I~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~~l~r 389 (419)
..|..|+..+. .|. .++.+.|+..|||..|+..++..
T Consensus 3 e~l~~Ai~~v~-~g~-~S~r~AA~~ygVp~sTL~~r~~g 39 (45)
T PF05225_consen 3 EDLQKAIEAVK-NGK-MSIRKAAKKYGVPRSTLRRRLRG 39 (45)
T ss_dssp HHHHHHHHHHH-TTS-S-HHHHHHHHT--HHHHHHHHHH
T ss_pred HHHHHHHHHHH-hCC-CCHHHHHHHHCcCHHHHHHHHcC
Confidence 34666776665 244 89999999999999999977654
No 249
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=54.67 E-value=28 Score=31.72 Aligned_cols=26 Identities=8% Similarity=0.059 Sum_probs=23.0
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 366 epS~eEIAe~LGIS~etVr~~l~rar 391 (419)
..++.|||+.+|+|..+|.+++++..
T Consensus 28 R~s~~eiA~~lglS~~tv~~Ri~rL~ 53 (164)
T PRK11169 28 RISNVELSKRVGLSPTPCLERVRRLE 53 (164)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 45899999999999999999988753
No 250
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=54.42 E-value=19 Score=31.98 Aligned_cols=33 Identities=27% Similarity=0.204 Sum_probs=29.2
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCcccccc
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLD 397 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~rark~lSLD 397 (419)
.+.+.+|||+.|+++..+|+..+.++++++.+.
T Consensus 163 ~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl~~~ 195 (210)
T PRK09935 163 SGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLH 195 (210)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCCC
Confidence 458999999999999999999999998877654
No 251
>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=54.12 E-value=35 Score=28.42 Aligned_cols=27 Identities=22% Similarity=0.277 Sum_probs=23.3
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
...+|..|||+.+|++..+|..++...
T Consensus 45 ~~~is~~eLa~~~g~sr~tVsr~L~~L 71 (95)
T TIGR01610 45 QDRVTATVIAELTGLSRTHVSDAIKSL 71 (95)
T ss_pred CCccCHHHHHHHHCcCHHHHHHHHHHH
Confidence 445699999999999999999987764
No 252
>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=53.11 E-value=13 Score=27.85 Aligned_cols=26 Identities=19% Similarity=0.132 Sum_probs=19.6
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHH
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~r 389 (419)
..+++..+||..+||+..||.+++..
T Consensus 20 e~g~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 20 EEGESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp HCTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 45569999999999999999998764
No 253
>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=52.47 E-value=40 Score=27.79 Aligned_cols=25 Identities=16% Similarity=0.263 Sum_probs=22.1
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHH
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~r 389 (419)
..+++.+||+.+|+|..+|...+..
T Consensus 18 ~~~ti~dvA~~~gvS~~TVsr~L~~ 42 (80)
T TIGR02844 18 TKATVRETAKVFGVSKSTVHKDVTE 42 (80)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHhcC
Confidence 5679999999999999999998753
No 254
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=52.41 E-value=1.8e+02 Score=29.87 Aligned_cols=126 Identities=14% Similarity=0.134 Sum_probs=71.0
Q ss_pred HhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCC
Q 014764 233 ERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSS 312 (419)
Q Consensus 233 ~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~ 312 (419)
++.+.+-|..|+...++++.+|+.+.++-=.++++..+..+.--.--+..||+.+ ....--+|++-.-+-+....||--
T Consensus 159 Rq~~~pRT~kEI~~~anv~kKEIgr~~K~i~~~l~~s~~~~s~~t~~~m~RFCs~-L~L~~~~q~aA~e~a~ka~~~~~~ 237 (308)
T KOG1597|consen 159 RQEDVPRTFKEISAVANVSKKEIGRCVKLIGEALETSVDLISISTGDFMPRFCSN-LGLPKSAQEAATEIAEKAEEMDIR 237 (308)
T ss_pred HhcCCCchHHHHHHHHcCCHHHHHHHHHHHHHHHhccchhhhhhHHHHHHHHHHh-cCCCHHHHHHHHHHHHHHHHhccc
Confidence 4678899999999999999999988655444445444444421122334445432 222223344433333444334322
Q ss_pred CCCchhhHHHHHHHhhHHHHHHHhcccccCccchHHHHHHHHHHHHHHHhcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 313 KGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 313 rG~rFSTYa~~~Irn~I~~~Lrd~~r~irip~~l~e~~~~I~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
.| |-|..+.. .+......|. +..-+.+||.+.+|+.+.|+++.....
T Consensus 238 ~g--------------------------RsPiSIAA---a~IYmisqls--~~kkt~keI~~vtgVaE~TIr~sYK~L 284 (308)
T KOG1597|consen 238 AG--------------------------RSPISIAA---AAIYMISQLS--DEKKTQKEIGEVTGVAEVTIRNSYKDL 284 (308)
T ss_pred cC--------------------------CCchhHHH---HHHHHHHHhc--cCcccHHHHHHHhhhhHHHHHHHHHHH
Confidence 11 22333221 1222222332 234499999999999999999976644
No 255
>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=52.11 E-value=17 Score=27.94 Aligned_cols=26 Identities=27% Similarity=0.360 Sum_probs=23.0
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
...|..|||+.+|++..+|...+..-
T Consensus 21 ~~~t~~eIa~~l~i~~~~v~~~L~~L 46 (68)
T PF01978_consen 21 GPATAEEIAEELGISRSTVYRALKSL 46 (68)
T ss_dssp CHEEHHHHHHHHTSSHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 45699999999999999999998764
No 256
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=51.63 E-value=1.8e+02 Score=29.38 Aligned_cols=26 Identities=19% Similarity=0.308 Sum_probs=22.6
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014764 368 SVDRIAEYLNMSQKKVRNATEAIGKV 393 (419)
Q Consensus 368 S~eEIAe~LGIS~etVr~~l~rark~ 393 (419)
|.+|||+..|++..+|+++.+...+.
T Consensus 278 t~keIa~v~~Vs~~tI~~~ykel~~~ 303 (310)
T PRK00423 278 TQREVAEVAGVTEVTVRNRYKELAEK 303 (310)
T ss_pred CHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 99999999999999999987765543
No 257
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=50.78 E-value=13 Score=37.84 Aligned_cols=37 Identities=16% Similarity=0.112 Sum_probs=29.9
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCc----cccccccc
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGK----VFSLDREA 400 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~rark----~lSLD~~~ 400 (419)
..+.|+.|||++||+|.-+|.+++..|++ .+.++.+.
T Consensus 27 ~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~I~I~~~~ 67 (318)
T PRK15418 27 HDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQINSRF 67 (318)
T ss_pred hcCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEEEEEeCCC
Confidence 35679999999999999999999999874 34555443
No 258
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=50.77 E-value=16 Score=34.13 Aligned_cols=33 Identities=15% Similarity=0.224 Sum_probs=26.6
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC--ccccccc
Q 014764 366 TPSVDRIAEYLNMSQKKVRNATEAIG--KVFSLDR 398 (419)
Q Consensus 366 epS~eEIAe~LGIS~etVr~~l~rar--k~lSLD~ 398 (419)
+.|.+|||+.||||+.||+..+.... +.++.+-
T Consensus 177 g~s~~eIa~~l~iS~~Tv~~~~~~~~~~~~~~~~~ 211 (225)
T PRK10046 177 QHTAETVAQALTISRTTARRYLEYCASRHLIIAEI 211 (225)
T ss_pred CcCHHHHHHHhCccHHHHHHHHHHHHhCCeEEEEe
Confidence 56999999999999999999988754 3445443
No 259
>PRK12423 LexA repressor; Provisional
Probab=50.49 E-value=44 Score=31.49 Aligned_cols=32 Identities=25% Similarity=0.448 Sum_probs=25.9
Q ss_pred HHhcCCCccHHHHHHHcC-CCHHHHHHHHHHhC
Q 014764 360 LEEKGVTPSVDRIAEYLN-MSQKKVRNATEAIG 391 (419)
Q Consensus 360 L~e~gRepS~eEIAe~LG-IS~etVr~~l~rar 391 (419)
+.+.+-.||..|||+.+| .+..+|+..+.+..
T Consensus 19 i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~ 51 (202)
T PRK12423 19 IAQAGQPPSLAEIAQAFGFASRSVARKHVQALA 51 (202)
T ss_pred HHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 345567799999999999 59999998877643
No 260
>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=50.04 E-value=14 Score=25.91 Aligned_cols=23 Identities=17% Similarity=0.310 Sum_probs=19.1
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHh
Q 014764 368 SVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 368 S~eEIAe~LGIS~etVr~~l~ra 390 (419)
|+.|+|+.+||+..+++......
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~G 23 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYEREG 23 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHTT
T ss_pred CHHHHHHHHCCCHHHHHHHHHCC
Confidence 57899999999999999987654
No 261
>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=49.95 E-value=38 Score=24.96 Aligned_cols=26 Identities=19% Similarity=0.279 Sum_probs=22.2
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 366 epS~eEIAe~LGIS~etVr~~l~rar 391 (419)
.++..|||+.++++..+|..++.+..
T Consensus 21 ~~t~~~la~~l~~~~~~vs~~v~~L~ 46 (62)
T PF12802_consen 21 ELTQSELAERLGISKSTVSRIVKRLE 46 (62)
T ss_dssp GEEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 37999999999999999999988754
No 262
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=49.59 E-value=20 Score=33.82 Aligned_cols=34 Identities=21% Similarity=0.160 Sum_probs=28.2
Q ss_pred cCCCccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014764 363 KGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSL 396 (419)
Q Consensus 363 ~gRepS~eEIAe~LGIS~etVr~~l~rark~lSL 396 (419)
...+.|.+|||+.||+|..||+..+....+..=+
T Consensus 175 ~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~~~ 208 (239)
T PRK10430 175 QDYEFSTDELANAVNISRVSCRKYLIWLVNCHIL 208 (239)
T ss_pred CCCCcCHHHHHHHhCchHHHHHHHHHHHHhCCEE
Confidence 4577899999999999999999999887554333
No 263
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=49.34 E-value=63 Score=30.61 Aligned_cols=58 Identities=28% Similarity=0.259 Sum_probs=46.4
Q ss_pred CCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHHHhHH
Q 014764 205 LLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVR 275 (419)
Q Consensus 205 lLt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~yl~ 275 (419)
.||+.|..-|-.+.+.|=. ..-|.-+..++|+.+|+|...+.+.|.+ |-++|+..+..
T Consensus 155 ~LTdrQ~~vL~~A~~~GYF----------d~PR~~~l~dLA~~lGISkst~~ehLRr---Ae~Kl~~~~~~ 212 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYF----------DYPRRVSLKDLAKELGISKSTLSEHLRR---AERKLIEAYFD 212 (215)
T ss_pred cCCHHHHHHHHHHHHcCCC----------CCCccCCHHHHHHHhCCCHHHHHHHHHH---HHHHHHHHhhh
Confidence 5999998888888999877 4456677899999999999999887774 66677766543
No 264
>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=48.83 E-value=39 Score=31.36 Aligned_cols=40 Identities=18% Similarity=0.238 Sum_probs=30.1
Q ss_pred HHHHHHHHHH-HhcCCCccHHHHHHHcCCC-HHHHHHHHHHh
Q 014764 351 GLIRNAKLRL-EEKGVTPSVDRIAEYLNMS-QKKVRNATEAI 390 (419)
Q Consensus 351 ~~I~~a~~~L-~e~gRepS~eEIAe~LGIS-~etVr~~l~ra 390 (419)
.+|...+... .+.+..||..|||+.+|++ ..+|...+.+.
T Consensus 9 ~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L 50 (199)
T TIGR00498 9 QEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKAL 50 (199)
T ss_pred HHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHH
Confidence 3444444444 3457778999999999998 99999988764
No 265
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=47.98 E-value=20 Score=25.22 Aligned_cols=23 Identities=13% Similarity=0.180 Sum_probs=20.0
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHh
Q 014764 368 SVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 368 S~eEIAe~LGIS~etVr~~l~ra 390 (419)
+..|+|+.+|++..+|+......
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHHCC
Confidence 67899999999999999886554
No 266
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=47.88 E-value=14 Score=31.63 Aligned_cols=30 Identities=10% Similarity=0.035 Sum_probs=26.6
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
.+.+++|.|..||||..|+.+++..+++++
T Consensus 48 ~~l~QeeAA~rMgISr~Tfwr~l~sAR~Kv 77 (99)
T COG1342 48 EGLTQEEAALRMGISRQTFWRLLTSARKKV 77 (99)
T ss_pred hhccHHHHHHHhcccHHHHHHHHHHHHHHH
Confidence 456999999999999999999999988654
No 267
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=47.54 E-value=44 Score=28.01 Aligned_cols=41 Identities=24% Similarity=0.178 Sum_probs=28.4
Q ss_pred ccchHHHHHHHHHHHHHHHhcCCCccHHHHHHHcCCCHHHHHHH
Q 014764 343 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNA 386 (419)
Q Consensus 343 p~~l~e~~~~I~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~~ 386 (419)
|..+.....+++-+..-|. .+.|+.|||+.+|+|.-||-..
T Consensus 29 ~~E~~~l~~R~~va~~lL~---~g~syreIa~~tgvS~aTItRv 69 (87)
T PF01371_consen 29 PDELEALAQRWQVAKELLD---EGKSYREIAEETGVSIATITRV 69 (87)
T ss_dssp HHHHHHHHHHHHHHHHHHH---TTSSHHHHHHHHTSTHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHH---CCCCHHHHHHHhCCCHHHHHHH
Confidence 4444444555555544443 4679999999999999998765
No 268
>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=47.38 E-value=45 Score=24.47 Aligned_cols=25 Identities=36% Similarity=0.488 Sum_probs=22.3
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 367 PSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 367 pS~eEIAe~LGIS~etVr~~l~rar 391 (419)
++..+||+.+|+|..+|..++....
T Consensus 26 ~~~~~la~~~~is~~~v~~~l~~L~ 50 (66)
T cd07377 26 PSERELAEELGVSRTTVREALRELE 50 (66)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4799999999999999999988753
No 269
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=47.10 E-value=52 Score=29.04 Aligned_cols=40 Identities=20% Similarity=0.122 Sum_probs=30.7
Q ss_pred HHHHHHHHHHhcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 352 LIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 352 ~I~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~~l~rar 391 (419)
...+++..+...+..++..+||+.||++..+|...+.+..
T Consensus 8 dyL~~I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~ 47 (142)
T PRK03902 8 DYIEQIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLD 47 (142)
T ss_pred HHHHHHHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHH
Confidence 3455555565556677999999999999999999987643
No 270
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=47.08 E-value=30 Score=27.11 Aligned_cols=27 Identities=22% Similarity=0.185 Sum_probs=22.1
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
...++..|||+.+|++..+|+..+...
T Consensus 13 ~~p~~T~eiA~~~gls~~~aR~yL~~L 39 (62)
T PF04703_consen 13 NGPLKTREIADALGLSIYQARYYLEKL 39 (62)
T ss_dssp TS-EEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 556799999999999999999998764
No 271
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=46.93 E-value=19 Score=28.21 Aligned_cols=22 Identities=14% Similarity=0.280 Sum_probs=19.2
Q ss_pred ccHHHHHHHcCCCHHHHHHHHH
Q 014764 367 PSVDRIAEYLNMSQKKVRNATE 388 (419)
Q Consensus 367 pS~eEIAe~LGIS~etVr~~l~ 388 (419)
++..|||+.+|+|..+|..++.
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln 22 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLN 22 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHC
Confidence 3688999999999999998764
No 272
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=46.72 E-value=53 Score=28.55 Aligned_cols=39 Identities=13% Similarity=0.088 Sum_probs=29.3
Q ss_pred HHHHHHHHHH-hcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 352 LIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 352 ~I~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
.+.+++..+. .....+++++||+.+|+++.++....+..
T Consensus 10 ~i~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 10 TIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3455555564 34566899999999999999998877654
No 273
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=46.32 E-value=34 Score=29.67 Aligned_cols=31 Identities=19% Similarity=0.111 Sum_probs=26.7
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014764 366 TPSVDRIAEYLNMSQKKVRNATEAIGKVFSL 396 (419)
Q Consensus 366 epS~eEIAe~LGIS~etVr~~l~rark~lSL 396 (419)
+.+.++||+.+|++..+|+..+.++++++..
T Consensus 156 ~~~~~~ia~~l~~s~~tv~~~~~~~~~kl~~ 186 (202)
T PRK09390 156 GLSNKVIARDLDISPRTVEVYRANVMTKMQA 186 (202)
T ss_pred cCchHHHHHHcCCCHHHHHHHHHHHHHHHcc
Confidence 3489999999999999999999888776644
No 274
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=46.11 E-value=61 Score=28.98 Aligned_cols=28 Identities=25% Similarity=0.367 Sum_probs=24.3
Q ss_pred cCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 363 KGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 363 ~gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
-.+-||+.|+|..+||.+.||.++.+..
T Consensus 32 GdkLPSvRelA~~~~VNpnTv~raY~eL 59 (125)
T COG1725 32 GDKLPSVRELAKDLGVNPNTVQRAYQEL 59 (125)
T ss_pred CCCCCcHHHHHHHhCCCHHHHHHHHHHH
Confidence 3577899999999999999999987653
No 275
>PRK09480 slmA division inhibitor protein; Provisional
Probab=45.88 E-value=1.9e+02 Score=25.80 Aligned_cols=72 Identities=18% Similarity=0.028 Sum_probs=47.1
Q ss_pred HhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHH
Q 014764 233 ERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLR 304 (419)
Q Consensus 233 ~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlr 304 (419)
+.-|...|..++|..+|+++..+..-...-.+-+..+++.+..-+............+..+.++..+-.++.
T Consensus 25 ~~~G~~~ti~~Ia~~agvs~gt~Y~~F~~K~~L~~~v~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ 96 (194)
T PRK09480 25 SPPGERITTAKLAARVGVSEAALYRHFPSKARMFEGLIEFIEESLFSRINQILKDEKDTLARARLILLLLLG 96 (194)
T ss_pred hcCCCccCHHHHHHHhCCCHhHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHccCCCHHHHHHHHHHHHHH
Confidence 333578899999999999999999877766666667776665555444433333333455555555544444
No 276
>PF13551 HTH_29: Winged helix-turn helix
Probab=45.51 E-value=66 Score=26.27 Aligned_cols=42 Identities=14% Similarity=0.209 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHhcCC-CccHHHHHHHc-------CCCHHHHHHHHHHh
Q 014764 349 RLGLIRNAKLRLEEKGV-TPSVDRIAEYL-------NMSQKKVRNATEAI 390 (419)
Q Consensus 349 ~~~~I~~a~~~L~e~gR-epS~eEIAe~L-------GIS~etVr~~l~ra 390 (419)
....|......-+..+. ..+..+|++.| .+|..+|..++++.
T Consensus 62 ~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~~~ 111 (112)
T PF13551_consen 62 QRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILKRA 111 (112)
T ss_pred HHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHHHC
Confidence 33444544444432332 45889999865 78999999998764
No 277
>PRK10651 transcriptional regulator NarL; Provisional
Probab=45.38 E-value=32 Score=30.43 Aligned_cols=33 Identities=18% Similarity=0.189 Sum_probs=28.8
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCcccccc
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLD 397 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~rark~lSLD 397 (419)
.+.+.+|||+.|+++..||+..+.+..+++.+.
T Consensus 169 ~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl~~~ 201 (216)
T PRK10651 169 QGLPNKMIARRLDITESTVKVHVKHMLKKMKLK 201 (216)
T ss_pred cCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCCC
Confidence 456999999999999999999999988777654
No 278
>PF13518 HTH_28: Helix-turn-helix domain
Probab=45.01 E-value=28 Score=24.82 Aligned_cols=25 Identities=24% Similarity=0.198 Sum_probs=21.9
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 367 PSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 367 pS~eEIAe~LGIS~etVr~~l~rar 391 (419)
.|+.+||+.+||+..+|...+.+-.
T Consensus 13 ~s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 13 ESVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred CCHHHHHHHHCCCHhHHHHHHHHHH
Confidence 3999999999999999999877653
No 279
>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=44.68 E-value=27 Score=25.28 Aligned_cols=25 Identities=20% Similarity=0.238 Sum_probs=20.3
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHH
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~r 389 (419)
.+.|..|+|+.+|++..+|...+.-
T Consensus 8 ~gls~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 8 KGLSQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred cCCCHHHHHHHhCCCcchhHHHhcC
Confidence 5679999999999999999998764
No 280
>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=44.26 E-value=38 Score=31.09 Aligned_cols=26 Identities=23% Similarity=0.173 Sum_probs=23.5
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 366 epS~eEIAe~LGIS~etVr~~l~rar 391 (419)
..|.+|||+.|||+...|+.++..-.
T Consensus 28 ~~tdEeLa~~Lgi~~~~VRk~L~~L~ 53 (158)
T TIGR00373 28 EFTDEEISLELGIKLNEVRKALYALY 53 (158)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 67999999999999999999987653
No 281
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=43.79 E-value=17 Score=27.22 Aligned_cols=32 Identities=13% Similarity=0.016 Sum_probs=19.0
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVFSL 396 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~rark~lSL 396 (419)
+..|..++|+.+|++..++......-...+++
T Consensus 9 ~~it~~~La~~~gis~~tl~~~~~~~~~~~~~ 40 (63)
T PF13443_consen 9 RGITQKDLARKTGISRSTLSRILNGKPSNPSL 40 (63)
T ss_dssp TT--HHHHHHHHT--HHHHHHHHTTT-----H
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcccccccH
Confidence 55699999999999999999987644234443
No 282
>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=43.23 E-value=22 Score=21.77 Aligned_cols=21 Identities=29% Similarity=0.273 Sum_probs=18.1
Q ss_pred CccHHHHHHHcCCCHHHHHHH
Q 014764 366 TPSVDRIAEYLNMSQKKVRNA 386 (419)
Q Consensus 366 epS~eEIAe~LGIS~etVr~~ 386 (419)
..+..+||+.+|++..+|.+.
T Consensus 21 ~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 21 GESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCCHHHHHHHHCCCHHHHHHh
Confidence 349999999999999998764
No 283
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=42.47 E-value=46 Score=29.80 Aligned_cols=27 Identities=30% Similarity=0.358 Sum_probs=23.4
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
....|.+|||+.||++..+|..+++.-
T Consensus 40 ~~~~tvdelae~lnr~rStv~rsl~~L 66 (126)
T COG3355 40 NGPLTVDELAEILNRSRSTVYRSLQNL 66 (126)
T ss_pred cCCcCHHHHHHHHCccHHHHHHHHHHH
Confidence 456699999999999999999988763
No 284
>PHA02943 hypothetical protein; Provisional
Probab=42.34 E-value=71 Score=29.77 Aligned_cols=25 Identities=32% Similarity=0.381 Sum_probs=21.5
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 366 TPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 366 epS~eEIAe~LGIS~etVr~~l~ra 390 (419)
..|..|||+.||+|-++|+.++...
T Consensus 24 ~~TtseIAkaLGlS~~qa~~~LyvL 48 (165)
T PHA02943 24 CKTTSRIANKLGVSHSMARNALYQL 48 (165)
T ss_pred CccHHHHHHHHCCCHHHHHHHHHHH
Confidence 4579999999999999999987643
No 285
>PF11251 DUF3050: Protein of unknown function (DUF3050); InterPro: IPR024423 This family of proteins has no known function.
Probab=41.93 E-value=1.1e+02 Score=30.26 Aligned_cols=101 Identities=12% Similarity=0.179 Sum_probs=55.6
Q ss_pred hhHHHHHHhhcCCCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHH
Q 014764 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (419)
Q Consensus 191 ~~l~~yl~~i~~~~lLt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LI 270 (419)
+-+++|++.+....- ....-..++..++.|..+..+. .. .+-+ .+-..++
T Consensus 80 SHFElYl~AM~e~GA-dt~~I~~fl~~~~~g~~v~~Al---~~-~~~p-------------------------~~~~~Fv 129 (232)
T PF11251_consen 80 SHFELYLDAMEEVGA-DTSPIDRFLSLLREGTSVFEAL---QQ-ADVP-------------------------EPAKRFV 129 (232)
T ss_pred cHHHHHHHHHHHcCC-ChHHHHHHHHHHHcCCCHHHHH---Hh-cCCC-------------------------HHHHHHH
Confidence 467888887765442 3444567889999997722211 11 1111 1222222
Q ss_pred HHhHHH-----HHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHHH
Q 014764 271 MSNVRL-----VMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWI 325 (419)
Q Consensus 271 e~yl~L-----V~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~I 325 (419)
..-..+ .+.+|.-|+- -.||||-+=|.++++.+ .+.+..-..|.-|+-|.|
T Consensus 130 ~~Tf~~i~~~~~H~iAAaFtf---GREdlIP~MF~~il~~~-~~~~~~~~~f~yYL~RHI 185 (232)
T PF11251_consen 130 RFTFEIIAEGKPHEIAAAFTF---GREDLIPDMFRSILKDL-NIPPGQLPTFRYYLERHI 185 (232)
T ss_pred HHHHHHHhcCCHHHHHHHHHh---ccccchHHHHHHHHHHh-cCCccccHHHHHHHHhhh
Confidence 222222 3456655542 23899999999999999 444443234554444443
No 286
>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]
Probab=41.77 E-value=48 Score=31.65 Aligned_cols=33 Identities=21% Similarity=0.071 Sum_probs=27.8
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSL 396 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~rark~lSL 396 (419)
.++.+..|||++|++|.+|+.-++.++....+.
T Consensus 16 ~~Glt~gEIAdELNvSreTa~WL~~r~~~~~~~ 48 (203)
T COG0856 16 SKGLTTGEIADELNVSRETATWLLTRAFKKESV 48 (203)
T ss_pred HCCCcHHHhhhhhhhhHHHHHHHHhhhhhccCC
Confidence 577899999999999999999999887654443
No 287
>PRK13558 bacterio-opsin activator; Provisional
Probab=41.68 E-value=19 Score=39.39 Aligned_cols=30 Identities=13% Similarity=0.140 Sum_probs=26.8
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKV 393 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~rark~ 393 (419)
-|+.|.+|||+.||||..++.++++++.++
T Consensus 628 pr~~~~~e~a~~l~is~~t~~~~lr~a~~~ 657 (665)
T PRK13558 628 PRRVEGEELAESMGISRSTFHQHLRAAERK 657 (665)
T ss_pred CccCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 367799999999999999999999998654
No 288
>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=41.58 E-value=54 Score=28.37 Aligned_cols=28 Identities=21% Similarity=0.363 Sum_probs=25.2
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~rar 391 (419)
....|..|||+.+||+..+|-.++++..
T Consensus 69 ~pd~tl~Ela~~l~Vs~~ti~~~Lkrlg 96 (119)
T PF01710_consen 69 NPDATLRELAERLGVSPSTIWRALKRLG 96 (119)
T ss_pred CCCcCHHHHHHHcCCCHHHHHHHHHHcC
Confidence 5677999999999999999999998865
No 289
>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=41.53 E-value=33 Score=26.48 Aligned_cols=24 Identities=21% Similarity=0.372 Sum_probs=22.1
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 368 SVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 368 S~eEIAe~LGIS~etVr~~l~rar 391 (419)
|.++||..+|++..+|.+.++...
T Consensus 30 t~~~iA~~~g~sr~tv~r~l~~l~ 53 (76)
T PF13545_consen 30 TQEEIADMLGVSRETVSRILKRLK 53 (76)
T ss_dssp SHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 999999999999999999988754
No 290
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=41.36 E-value=49 Score=31.04 Aligned_cols=26 Identities=19% Similarity=0.151 Sum_probs=23.4
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 366 epS~eEIAe~LGIS~etVr~~l~rar 391 (419)
..|.+|||+.|||+...|+.++....
T Consensus 36 ~~tdeeLA~~Lgi~~~~VRk~L~~L~ 61 (178)
T PRK06266 36 EVTDEEIAEQTGIKLNTVRKILYKLY 61 (178)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 67999999999999999999987653
No 291
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=41.21 E-value=1.5e+02 Score=25.93 Aligned_cols=27 Identities=4% Similarity=0.028 Sum_probs=23.4
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~rar 391 (419)
...+..|||+.+|++..+|-.++.+.-
T Consensus 53 ~~~t~~eLa~~l~i~~~tvsr~l~~Le 79 (144)
T PRK11512 53 ACITPVELKKVLSVDLGALTRMLDRLV 79 (144)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 457999999999999999999887653
No 292
>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=41.06 E-value=36 Score=24.46 Aligned_cols=26 Identities=27% Similarity=0.317 Sum_probs=21.8
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
...+..|||+.+|++..+|...+...
T Consensus 14 ~~~~~~el~~~l~~s~~~vs~hL~~L 39 (47)
T PF01022_consen 14 GPLTVSELAEELGLSQSTVSHHLKKL 39 (47)
T ss_dssp SSEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCchhhHHHhccccchHHHHHHHHH
Confidence 55699999999999999999988754
No 293
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=41.03 E-value=40 Score=24.08 Aligned_cols=28 Identities=25% Similarity=0.234 Sum_probs=23.9
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~rar 391 (419)
....+..+|++.+|++..+|..+++...
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~ 35 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLR 35 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3456999999999999999999988754
No 294
>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=40.71 E-value=63 Score=27.01 Aligned_cols=23 Identities=9% Similarity=0.037 Sum_probs=20.3
Q ss_pred CCccHHHHHHHcCCCHHHHHHHH
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNAT 387 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l 387 (419)
.+.|..|||+.+|+|..||..+.
T Consensus 49 ~G~S~~eIA~~LgISrsTIyRi~ 71 (88)
T TIGR02531 49 QGKTYSDIEAETGASTATISRVK 71 (88)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHH
Confidence 45699999999999999999954
No 295
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=40.68 E-value=31 Score=26.21 Aligned_cols=24 Identities=17% Similarity=0.206 Sum_probs=21.0
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 368 SVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 368 S~eEIAe~LGIS~etVr~~l~rar 391 (419)
|+.|+|+.+|||..+|+.-.....
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 678999999999999999877653
No 296
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=40.63 E-value=24 Score=36.26 Aligned_cols=37 Identities=19% Similarity=0.152 Sum_probs=29.7
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCc----cccccccc
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGK----VFSLDREA 400 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~rark----~lSLD~~~ 400 (419)
..+.|+.|||+.||||.-+|...+..+++ .++++.+.
T Consensus 24 ~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I~i~~~~ 64 (321)
T COG2390 24 VEGLTQSEIAERLGISRATVSRLLAKAREEGIVKISINSPV 64 (321)
T ss_pred hcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEEEeCCCC
Confidence 45679999999999999999999998874 34555443
No 297
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=40.56 E-value=77 Score=26.25 Aligned_cols=38 Identities=11% Similarity=0.111 Sum_probs=27.3
Q ss_pred HHHHHHHHH-hcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 353 IRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 353 I~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
+..+...+. .....++.++||+.+|+|..++..+....
T Consensus 7 ~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 7 IQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 344444443 34566899999999999999998876553
No 298
>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=39.79 E-value=77 Score=23.80 Aligned_cols=27 Identities=26% Similarity=0.273 Sum_probs=22.9
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
+...|..|||+.+|++..+|...+...
T Consensus 22 ~~~~t~~ela~~l~~~~~t~s~hL~~L 48 (61)
T PF12840_consen 22 NGPMTVSELAEELGISQSTVSYHLKKL 48 (61)
T ss_dssp CSTBEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 567799999999999999999987764
No 299
>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=39.78 E-value=70 Score=30.76 Aligned_cols=29 Identities=10% Similarity=0.140 Sum_probs=24.6
Q ss_pred hcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 362 EKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 362 e~gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
......+..|||+.+|++..+|..++...
T Consensus 20 ~~~~~~~l~eia~~lglpksT~~RlL~tL 48 (248)
T TIGR02431 20 AERPRLTLTDVAEATGLTRAAARRFLLTL 48 (248)
T ss_pred cCCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 33556799999999999999999998764
No 300
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=39.35 E-value=56 Score=30.85 Aligned_cols=49 Identities=24% Similarity=0.328 Sum_probs=36.5
Q ss_pred cCccchHHHHHHHHHHHHHHHhcC-CCccHHHHHHHcCCCHHHHHHHHHH
Q 014764 341 RLPNHLHERLGLIRNAKLRLEEKG-VTPSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 341 rip~~l~e~~~~I~~a~~~L~e~g-RepS~eEIAe~LGIS~etVr~~l~r 389 (419)
.+|.....+..+..+....|...| ..++..|+|+.+|++..+|+.=+..
T Consensus 6 ~~~~~~~~r~~~~~~il~~l~~~~~~~vs~~~L~~~~~v~~~tirrDl~~ 55 (213)
T PRK05472 6 KIPEATIKRLPLYYRYLKELKEEGVERVSSKELAEALGVDSAQIRKDLSY 55 (213)
T ss_pred cCCHHHHHHhHHHHHHHHHHHHcCCcEEeHHHHHHHhCcCHHHHHHHHHH
Confidence 466666666666666777776655 3569999999999999999885543
No 301
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=39.25 E-value=1.4e+02 Score=25.99 Aligned_cols=28 Identities=11% Similarity=0.132 Sum_probs=23.6
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~rar 391 (419)
+...+..|||+.+|++..+|...+.+..
T Consensus 44 ~~~~t~~eLa~~l~~~~~tvt~~v~~Le 71 (144)
T PRK03573 44 PPEQSQIQLAKAIGIEQPSLVRTLDQLE 71 (144)
T ss_pred CCCCCHHHHHHHhCCChhhHHHHHHHHH
Confidence 3456899999999999999999887753
No 302
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=39.13 E-value=2.8e+02 Score=30.84 Aligned_cols=22 Identities=23% Similarity=0.184 Sum_probs=19.8
Q ss_pred cHHHHHHHcCCCHHHHHHHHHH
Q 014764 368 SVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 368 S~eEIAe~LGIS~etVr~~l~r 389 (419)
|..|||+..|+|..+|-+..+.
T Consensus 376 si~eLA~~~~vS~aTV~Rf~kk 397 (638)
T PRK14101 376 PIVDIARKADVSQPTVIRFCRS 397 (638)
T ss_pred cHHHHHHHhCCCHHHHHHHHHH
Confidence 9999999999999999887554
No 303
>PRK09726 antitoxin HipB; Provisional
Probab=38.59 E-value=56 Score=26.58 Aligned_cols=24 Identities=13% Similarity=0.145 Sum_probs=20.8
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHH
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATE 388 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~ 388 (419)
++.|..|+|+.+|++..+|.+...
T Consensus 24 ~gltq~elA~~~gvs~~tis~~e~ 47 (88)
T PRK09726 24 NGWTQSELAKKIGIKQATISNFEN 47 (88)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHC
Confidence 467999999999999999998765
No 304
>PRK04841 transcriptional regulator MalT; Provisional
Probab=38.57 E-value=25 Score=39.64 Aligned_cols=33 Identities=12% Similarity=0.197 Sum_probs=27.8
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCcccccc
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLD 397 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~rark~lSLD 397 (419)
++.|.+|||+.|+||+.||+..+..+..++-+.
T Consensus 852 ~g~~~~~ia~~l~~s~~tv~~h~~~~~~kl~v~ 884 (903)
T PRK04841 852 SGYSNEQIAGELDVAATTIKTHIRNLYQKLGIA 884 (903)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 455999999999999999999999887665443
No 305
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=38.54 E-value=47 Score=23.77 Aligned_cols=42 Identities=24% Similarity=0.304 Sum_probs=19.2
Q ss_pred CCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhH
Q 014764 203 EELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (419)
Q Consensus 203 ~~lLt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~ 261 (419)
++-||++|-.++......|. +..++|..+|.+...+...+..
T Consensus 2 ~~~Lt~~eR~~I~~l~~~G~-----------------s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQGM-----------------SIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ----------HHHHHHCS--------------------HHHHHHHTT--HHHHHHHHHH
T ss_pred ccchhhhHHHHHHHHHHcCC-----------------CHHHHHHHHCcCcHHHHHHHhc
Confidence 34577777666666666665 4678888888888877765543
No 306
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=38.50 E-value=66 Score=31.81 Aligned_cols=38 Identities=18% Similarity=0.292 Sum_probs=27.4
Q ss_pred HHHHHHHHHHhcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 352 LIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 352 ~I~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
+.......|...+ .++..|||+.+|+|..||++-+...
T Consensus 18 R~~~Il~~L~~~~-~vtv~eLa~~l~VS~~TIRRDL~~L 55 (269)
T PRK09802 18 RREQIIQRLRQQG-SVQVNDLSALYGVSTVTIRNDLAFL 55 (269)
T ss_pred HHHHHHHHHHHcC-CEeHHHHHHHHCCCHHHHHHHHHHH
Confidence 3344444454434 4899999999999999998876543
No 307
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=38.45 E-value=47 Score=29.49 Aligned_cols=33 Identities=18% Similarity=0.134 Sum_probs=28.4
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCcccccc
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLD 397 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~rark~lSLD 397 (419)
.+.+.+|||+.++++..+|+....+.++++..+
T Consensus 157 ~g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl~~~ 189 (204)
T PRK09958 157 DGKDNNDIAEKMFISNKTVSTYKSRLMEKLECK 189 (204)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCCC
Confidence 456999999999999999999999988776543
No 308
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=38.38 E-value=72 Score=29.21 Aligned_cols=41 Identities=20% Similarity=0.105 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHhcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 351 GLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 351 ~~I~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~~l~rar 391 (419)
.....+++.+......+...+||+.||++..+|.+++++..
T Consensus 9 edYL~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~ 49 (154)
T COG1321 9 EDYLETIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLE 49 (154)
T ss_pred HHHHHHHHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHH
Confidence 34455666665556667999999999999999988887653
No 309
>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=38.09 E-value=42 Score=24.01 Aligned_cols=25 Identities=8% Similarity=0.217 Sum_probs=22.0
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHH
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~r 389 (419)
+..|+.++|+.+|++..+|......
T Consensus 14 ~gltq~~lA~~~gvs~~~vs~~e~g 38 (58)
T TIGR03070 14 LGLTQADLADLAGVGLRFIRDVENG 38 (58)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 4679999999999999999998753
No 310
>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=38.00 E-value=33 Score=28.30 Aligned_cols=26 Identities=23% Similarity=0.165 Sum_probs=19.0
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 366 epS~eEIAe~LGIS~etVr~~l~rar 391 (419)
+.|+.|||+.||.|...|.+++....
T Consensus 3 G~tq~eIA~~lGks~s~Vs~~l~Ll~ 28 (93)
T PF08535_consen 3 GWTQEEIAKRLGKSRSWVSNHLALLD 28 (93)
T ss_dssp T--HHHHHHHTT--HHHHHHHHGGGS
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHc
Confidence 45899999999999999999987543
No 311
>PF13551 HTH_29: Winged helix-turn helix
Probab=37.81 E-value=36 Score=27.90 Aligned_cols=24 Identities=21% Similarity=0.265 Sum_probs=22.0
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 368 SVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 368 S~eEIAe~LGIS~etVr~~l~rar 391 (419)
+..+||+.+|++..+|.+.+++..
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~ 37 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYR 37 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHH
Confidence 699999999999999999988754
No 312
>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=37.58 E-value=41 Score=26.99 Aligned_cols=26 Identities=27% Similarity=0.305 Sum_probs=22.0
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 366 epS~eEIAe~LGIS~etVr~~l~rar 391 (419)
.++.+|||+.+|+|...|++++..-.
T Consensus 25 ~~s~~eiA~~~~i~~~~l~kil~~L~ 50 (83)
T PF02082_consen 25 PVSSKEIAERLGISPSYLRKILQKLK 50 (83)
T ss_dssp -BEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHh
Confidence 37999999999999999999988754
No 313
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=37.43 E-value=52 Score=25.53 Aligned_cols=20 Identities=35% Similarity=0.539 Sum_probs=17.1
Q ss_pred CCCccHHHHHHHcCCCHHHH
Q 014764 364 GVTPSVDRIAEYLNMSQKKV 383 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etV 383 (419)
+...|..|||+.+|++..++
T Consensus 52 ~~~~t~~eIa~~~~Vs~~tI 71 (71)
T PF00382_consen 52 GVPRTLKEIAEAAGVSEKTI 71 (71)
T ss_dssp TSSSSHHHHHHHCTSSHHHH
T ss_pred CCCcCHHHHHHHhCCCCCcC
Confidence 45559999999999999875
No 314
>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=37.40 E-value=40 Score=28.39 Aligned_cols=27 Identities=26% Similarity=0.250 Sum_probs=22.8
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhCc
Q 014764 366 TPSVDRIAEYLNMSQKKVRNATEAIGK 392 (419)
Q Consensus 366 epS~eEIAe~LGIS~etVr~~l~rark 392 (419)
..+..+||+.||+|..++-.....|.+
T Consensus 71 ~~~~~~I~~~l~~S~~t~yr~~~~Al~ 97 (100)
T PF07374_consen 71 KLTWEQIAEELNISRRTYYRIHKKALK 97 (100)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 348999999999999999988777643
No 315
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=36.85 E-value=85 Score=23.61 Aligned_cols=58 Identities=17% Similarity=0.236 Sum_probs=33.4
Q ss_pred CCchHHHHHHhcCChHHHHHHHhHHH-HHHHHHHHHhHHHHHHHHHHcc-CCCCChhhHhhHH
Q 014764 238 EPSMEQLAASLRISRPELQSILMECS-LAREKLVMSNVRLVMSIAQRYD-NMGADMADLVQGG 298 (419)
Q Consensus 238 ~p~~~e~A~~~~~s~~eLr~~l~~~~-~A~e~LIe~yl~LV~sIAkry~-~~g~d~EDLVQEG 298 (419)
+++.+++|..+|++...|.+.+.... ......+.. ..+.. |..+. ......+|+.++.
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~~~~s~~~~~~~--~r~~~-a~~~l~~~~~~~~~ia~~~ 60 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKETGTTPKQYLRD--RRLER-ARRLLRDTDLSVTEIALRV 60 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHhCcCHHHHHHH--HHHHH-HHHHHHcCCCCHHHHHHHh
Confidence 46889999999999999988776432 112222111 11222 33332 3346777777665
No 316
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=36.84 E-value=70 Score=31.46 Aligned_cols=34 Identities=21% Similarity=0.218 Sum_probs=26.7
Q ss_pred HHHHHhcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 357 KLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 357 ~~~L~e~gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
+..+...+...+..|||+.||++..+|..++...
T Consensus 31 L~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL 64 (271)
T PRK10163 31 LQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVL 64 (271)
T ss_pred HHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3334444556799999999999999999998764
No 317
>PRK00215 LexA repressor; Validated
Probab=36.82 E-value=95 Score=28.92 Aligned_cols=31 Identities=35% Similarity=0.485 Sum_probs=26.3
Q ss_pred HhcCCCccHHHHHHHcCC-CHHHHHHHHHHhC
Q 014764 361 EEKGVTPSVDRIAEYLNM-SQKKVRNATEAIG 391 (419)
Q Consensus 361 ~e~gRepS~eEIAe~LGI-S~etVr~~l~rar 391 (419)
...+..++..|||+.+|+ +..+|..++....
T Consensus 18 ~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~ 49 (205)
T PRK00215 18 EETGYPPSRREIADALGLRSPSAVHEHLKALE 49 (205)
T ss_pred HHhCCCCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 445778899999999999 9999999887643
No 318
>PRK09480 slmA division inhibitor protein; Provisional
Probab=36.29 E-value=83 Score=28.16 Aligned_cols=40 Identities=20% Similarity=0.227 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHHH-Hhc-CCCccHHHHHHHcCCCHHHHHHH
Q 014764 347 HERLGLIRNAKLRL-EEK-GVTPSVDRIAEYLNMSQKKVRNA 386 (419)
Q Consensus 347 ~e~~~~I~~a~~~L-~e~-gRepS~eEIAe~LGIS~etVr~~ 386 (419)
.....+|..+...| ... |...|+++||+..||+.+++-..
T Consensus 9 ~~~r~~Il~aa~~l~~~~~G~~~ti~~Ia~~agvs~gt~Y~~ 50 (194)
T PRK09480 9 GERREQILQALAQMLESPPGERITTAKLAARVGVSEAALYRH 50 (194)
T ss_pred hhHHHHHHHHHHHHHHhcCCCccCHHHHHHHhCCCHhHHHHH
Confidence 33444555554454 443 78889999999999999998764
No 319
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=36.13 E-value=2.2e+02 Score=26.61 Aligned_cols=25 Identities=12% Similarity=0.240 Sum_probs=22.2
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 367 PSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 367 pS~eEIAe~LGIS~etVr~~l~rar 391 (419)
+|+++||..||++.++|.+.++..+
T Consensus 185 lt~~~iA~~lG~sr~tvsR~l~~l~ 209 (235)
T PRK11161 185 MTRGDIGNYLGLTVETISRLLGRFQ 209 (235)
T ss_pred ccHHHHHHHhCCcHHHHHHHHHHHH
Confidence 5999999999999999999887654
No 320
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=35.79 E-value=70 Score=31.32 Aligned_cols=33 Identities=18% Similarity=0.314 Sum_probs=25.4
Q ss_pred HHHHHhcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 357 KLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 357 ~~~L~e~gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
+..|.+ ...+++.|+|+.+|+|..||++-+...
T Consensus 11 l~~L~~-~~~v~v~eLa~~l~VS~~TIRRDL~~L 43 (256)
T PRK10434 11 LEYLQK-QGKTSVEELAQYFDTTGTTIRKDLVIL 43 (256)
T ss_pred HHHHHH-cCCEEHHHHHHHHCCCHHHHHHHHHHH
Confidence 333443 345899999999999999999877653
No 321
>PHA01976 helix-turn-helix protein
Probab=35.75 E-value=41 Score=25.38 Aligned_cols=26 Identities=4% Similarity=-0.008 Sum_probs=21.1
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHH
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~r 389 (419)
.+..|..|+|+.+|++..+|.+....
T Consensus 13 ~~glt~~~lA~~~gvs~~~v~~~e~g 38 (67)
T PHA01976 13 ARAWSAPELSRRAGVRHSLIYDFEAD 38 (67)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 35678999999999999999887643
No 322
>PF04963 Sigma54_CBD: Sigma-54 factor, core binding domain; InterPro: IPR007046 This domain makes a direct interaction with the core RNA polymerase, to form an enhancer dependent holoenzyme []. The centre of this domain contains a very weak similarity to a helix-turn-helix motif, which may represent a DNA binding domain.; GO: 0003677 DNA binding, 0006352 transcription initiation, DNA-dependent; PDB: 2K9L_A 2K9M_A.
Probab=35.47 E-value=99 Score=29.09 Aligned_cols=24 Identities=33% Similarity=0.477 Sum_probs=0.0
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 368 SVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 368 S~eEIAe~LGIS~etVr~~l~rar 391 (419)
.+.+||+.+|++.++|+.++...+
T Consensus 121 ~~~~ia~~l~~s~~~v~~~~~~Ir 144 (194)
T PF04963_consen 121 DYKKIAKKLGISEEEVQEAIELIR 144 (194)
T ss_dssp ------------------------
T ss_pred hhcccccccccccccccccccccc
Confidence 567788889999999988887654
No 323
>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=35.07 E-value=57 Score=23.32 Aligned_cols=41 Identities=17% Similarity=0.328 Sum_probs=28.1
Q ss_pred CCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHh
Q 014764 203 EELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (419)
Q Consensus 203 ~~lLt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~ 260 (419)
.+-+++++..++.+....|. +..++|+.+|+|+..+...+.
T Consensus 3 p~~~~~~~~~~i~~l~~~G~-----------------si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 3 PPKLSKEQIEEIKELYAEGM-----------------SIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp SSSSSHCCHHHHHHHHHTT-------------------HHHHHHHTTS-HHHHHHHHC
T ss_pred CCCCCHHHHHHHHHHHHCCC-----------------CHHHHHHHHCcCHHHHHHHHh
Confidence 34566665566777777774 478999999999998877653
No 324
>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=35.06 E-value=45 Score=25.21 Aligned_cols=22 Identities=14% Similarity=0.238 Sum_probs=19.6
Q ss_pred cHHHHHHHcCCCHHHHHHHHHH
Q 014764 368 SVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 368 S~eEIAe~LGIS~etVr~~l~r 389 (419)
+..|+|+.+||+..+++.....
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh
Confidence 6789999999999999988654
No 325
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=34.82 E-value=67 Score=32.47 Aligned_cols=40 Identities=30% Similarity=0.299 Sum_probs=31.3
Q ss_pred HHHHHHHHHH-HhcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 351 GLIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 351 ~~I~~a~~~L-~e~gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
..+..++-.| .+..+.+.=+|||+.+|..+++|++.|+..
T Consensus 9 keIL~aLi~LY~~~~r~IKgeeIA~~l~rnpGTVRNqmq~L 49 (294)
T COG2524 9 KEILQALINLYRRKKRPIKGEEIAEVLNRNPGTVRNQMQSL 49 (294)
T ss_pred HHHHHHHHHHHHhcCCCcchHHHHHHHccCcchHHHHHHHH
Confidence 4455555555 345777799999999999999999998764
No 326
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=34.76 E-value=64 Score=30.86 Aligned_cols=27 Identities=15% Similarity=0.321 Sum_probs=24.2
Q ss_pred cCCCccHHHHHHHcCCCHHHHHHHHHH
Q 014764 363 KGVTPSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 363 ~gRepS~eEIAe~LGIS~etVr~~l~r 389 (419)
-.+-|+-.|+|+.+|+|..||++++..
T Consensus 32 G~~LPsE~eLa~~~~VSR~TVR~Al~~ 58 (241)
T PRK10079 32 GDYLPAEQQLAARYEVNRHTLRRAIDQ 58 (241)
T ss_pred CCcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 357789999999999999999999865
No 327
>PF13309 HTH_22: HTH domain
Probab=34.15 E-value=94 Score=24.15 Aligned_cols=20 Identities=30% Similarity=0.353 Sum_probs=18.2
Q ss_pred cHHHHHHHcCCCHHHHHHHH
Q 014764 368 SVDRIAEYLNMSQKKVRNAT 387 (419)
Q Consensus 368 S~eEIAe~LGIS~etVr~~l 387 (419)
+...+|+.||||..||-+.+
T Consensus 44 av~~vA~~L~iS~~TVY~YL 63 (64)
T PF13309_consen 44 AVEYVAEKLGISRATVYRYL 63 (64)
T ss_pred HHHHHHHHHCCCHHHHHHHc
Confidence 89999999999999998764
No 328
>PF13730 HTH_36: Helix-turn-helix domain
Probab=33.99 E-value=1.5e+02 Score=21.50 Aligned_cols=25 Identities=44% Similarity=0.627 Sum_probs=21.3
Q ss_pred hCCCCchHHHHHHhcCChHHHHHHH
Q 014764 235 LGCEPSMEQLAASLRISRPELQSIL 259 (419)
Q Consensus 235 lg~~p~~~e~A~~~~~s~~eLr~~l 259 (419)
.++-|+.+.+|..+|+++..+++.+
T Consensus 22 ~~~~pS~~~la~~~g~s~~Tv~~~i 46 (55)
T PF13730_consen 22 GGCFPSQETLAKDLGVSRRTVQRAI 46 (55)
T ss_pred CCCCcCHHHHHHHHCcCHHHHHHHH
Confidence 4588999999999999999888643
No 329
>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=33.98 E-value=58 Score=25.04 Aligned_cols=26 Identities=23% Similarity=0.317 Sum_probs=22.9
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 366 epS~eEIAe~LGIS~etVr~~l~rar 391 (419)
..+..|||+.+|+|..+|...+....
T Consensus 13 ~~~~~eLa~~l~vS~~tv~~~l~~L~ 38 (69)
T TIGR00122 13 PFSGEKLGEALGMSRTAVNKHIQTLR 38 (69)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45799999999999999999988764
No 330
>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=33.94 E-value=98 Score=22.58 Aligned_cols=24 Identities=29% Similarity=0.387 Sum_probs=22.2
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 367 PSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 367 pS~eEIAe~LGIS~etVr~~l~ra 390 (419)
++..||++.+|++..+|...+...
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~L 44 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKL 44 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHHH
Confidence 899999999999999999988775
No 331
>TIGR01636 phage_rinA phage transcriptional activator, RinA family. This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.
Probab=33.87 E-value=46 Score=29.50 Aligned_cols=25 Identities=16% Similarity=0.088 Sum_probs=22.1
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 367 PSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 367 pS~eEIAe~LGIS~etVr~~l~rar 391 (419)
.|..+||..||+|..+|......+.
T Consensus 101 ~t~~~Ia~~l~iS~~t~~r~r~~~l 125 (134)
T TIGR01636 101 LTLVGLAQQLFISKSTAYRLRNHII 125 (134)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 4999999999999999998877653
No 332
>PF06970 RepA_N: Replication initiator protein A (RepA) N-terminus; InterPro: IPR010724 This entry represents the N terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids []. Most proteins in this entry are bacterial, but archaeal and eukaryotic members are also included.
Probab=33.83 E-value=43 Score=27.17 Aligned_cols=21 Identities=33% Similarity=0.483 Sum_probs=19.6
Q ss_pred cHHHHHHHcCCCHHHHHHHHH
Q 014764 368 SVDRIAEYLNMSQKKVRNATE 388 (419)
Q Consensus 368 S~eEIAe~LGIS~etVr~~l~ 388 (419)
|++||++.||++..+|.+++.
T Consensus 54 s~eel~~~L~~s~~tv~~~~k 74 (76)
T PF06970_consen 54 SIEELMELLNCSKSTVIKAKK 74 (76)
T ss_pred eHHHHHHHHCCCHHHHHHHHH
Confidence 999999999999999998865
No 333
>COG2902 NAD-specific glutamate dehydrogenase [Amino acid transport and metabolism]
Probab=33.19 E-value=1.1e+03 Score=29.63 Aligned_cols=30 Identities=23% Similarity=0.303 Sum_probs=25.6
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHhCcccccc
Q 014764 368 SVDRIAEYLNMSQKKVRNATEAIGKVFSLD 397 (419)
Q Consensus 368 S~eEIAe~LGIS~etVr~~l~rark~lSLD 397 (419)
.+-+||+..|++..+|.+........+++|
T Consensus 1468 dii~ia~~~~~~~~~~Ak~yf~v~~~~~~~ 1497 (1592)
T COG2902 1468 DIIDIADITGIDVAEVAKAYFAVSDALGLD 1497 (1592)
T ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHhCch
Confidence 788899999999999999887777777766
No 334
>PF14493 HTH_40: Helix-turn-helix domain
Probab=33.14 E-value=70 Score=26.18 Aligned_cols=28 Identities=11% Similarity=0.122 Sum_probs=24.1
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~rar 391 (419)
..+.|++|||+.-|+++.||.+.+..+.
T Consensus 11 ~~G~si~eIA~~R~L~~sTI~~HL~~~~ 38 (91)
T PF14493_consen 11 QKGLSIEEIAKIRGLKESTIYGHLAELI 38 (91)
T ss_pred HcCCCHHHHHHHcCCCHHHHHHHHHHHH
Confidence 3567999999999999999999887653
No 335
>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=32.84 E-value=37 Score=28.96 Aligned_cols=23 Identities=22% Similarity=0.166 Sum_probs=20.0
Q ss_pred CCccHHHHHHHcCCCHHHHHHHH
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNAT 387 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l 387 (419)
.+.|+.|||+.+|||..+|-+.-
T Consensus 54 ~~~tQrEIa~~lGiS~atIsR~s 76 (94)
T TIGR01321 54 GNMSQREIASKLGVSIATITRGS 76 (94)
T ss_pred CCCCHHHHHHHhCCChhhhhHHH
Confidence 56799999999999999987653
No 336
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=32.67 E-value=49 Score=25.00 Aligned_cols=21 Identities=14% Similarity=0.308 Sum_probs=19.0
Q ss_pred cHHHHHHHcCCCHHHHHHHHH
Q 014764 368 SVDRIAEYLNMSQKKVRNATE 388 (419)
Q Consensus 368 S~eEIAe~LGIS~etVr~~l~ 388 (419)
+..|+|+.+||+..+++....
T Consensus 2 s~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 678999999999999998865
No 337
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=32.00 E-value=71 Score=28.10 Aligned_cols=33 Identities=21% Similarity=0.210 Sum_probs=27.9
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCcccccc
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLD 397 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~rark~lSLD 397 (419)
.+.+.++||+.|+++..+|+....+.++++...
T Consensus 151 ~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~~~ 183 (196)
T PRK10360 151 QGMAVKEIAAELGLSPKTVHVHRANLMEKLGVS 183 (196)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 346999999999999999999998887766543
No 338
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=31.88 E-value=66 Score=28.94 Aligned_cols=27 Identities=22% Similarity=0.292 Sum_probs=24.4
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhCc
Q 014764 366 TPSVDRIAEYLNMSQKKVRNATEAIGK 392 (419)
Q Consensus 366 epS~eEIAe~LGIS~etVr~~l~rark 392 (419)
.++.++||+.||++...|+.++.....
T Consensus 15 ~~~dedLa~~l~i~~n~vRkiL~~L~e 41 (147)
T smart00531 15 CVTEEDLAELLGIKQKQLRKILYLLYD 41 (147)
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHHHh
Confidence 679999999999999999999987654
No 339
>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=31.80 E-value=60 Score=22.90 Aligned_cols=22 Identities=18% Similarity=0.339 Sum_probs=17.7
Q ss_pred cHHHHHHHcCCCHHHHHHHHHH
Q 014764 368 SVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 368 S~eEIAe~LGIS~etVr~~l~r 389 (419)
...+.|+.|||+..++...+..
T Consensus 20 n~~~aA~~Lgisr~tL~~klkk 41 (42)
T PF02954_consen 20 NVSKAARLLGISRRTLYRKLKK 41 (42)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHHHh
Confidence 6789999999999999988753
No 340
>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=31.67 E-value=55 Score=24.89 Aligned_cols=22 Identities=9% Similarity=0.335 Sum_probs=19.3
Q ss_pred cHHHHHHHcCCCHHHHHHHHHH
Q 014764 368 SVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 368 S~eEIAe~LGIS~etVr~~l~r 389 (419)
++.|+|+.+||+..+++.....
T Consensus 2 ~i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 2 TIKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh
Confidence 6789999999999999987654
No 341
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=31.62 E-value=45 Score=25.19 Aligned_cols=26 Identities=23% Similarity=0.219 Sum_probs=20.6
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
.+.|..++|+.+|++..+|.++..--
T Consensus 13 ~gls~~~lA~~~g~s~s~v~~iE~G~ 38 (64)
T PF13560_consen 13 AGLSQAQLADRLGVSQSTVSRIERGR 38 (64)
T ss_dssp HTS-HHHHHHHHTS-HHHHHHHHTTS
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHCCC
Confidence 46799999999999999999987643
No 342
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=31.60 E-value=96 Score=24.94 Aligned_cols=24 Identities=8% Similarity=0.248 Sum_probs=20.7
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHH
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATE 388 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~ 388 (419)
...|++|+|+.+|++.+|+-.+..
T Consensus 13 ~~ltQ~elA~~vgVsRQTi~~iEk 36 (68)
T COG1476 13 LGLTQEELAKLVGVSRQTIIAIEK 36 (68)
T ss_pred hCcCHHHHHHHcCcCHHHHHHHHc
Confidence 356999999999999999988754
No 343
>PRK04217 hypothetical protein; Provisional
Probab=31.48 E-value=2.1e+02 Score=24.89 Aligned_cols=29 Identities=14% Similarity=0.158 Sum_probs=23.3
Q ss_pred chHHHHHHhcCChHHHHHHHhHHHHHHHH
Q 014764 240 SMEQLAASLRISRPELQSILMECSLAREK 268 (419)
Q Consensus 240 ~~~e~A~~~~~s~~eLr~~l~~~~~A~e~ 268 (419)
+.+|+|..+|+|...+...+......+.+
T Consensus 60 S~~EIAk~LGIS~sTV~r~L~RArkkLre 88 (110)
T PRK04217 60 TQEEAGKRMGVSRGTVWRALTSARKKVAQ 88 (110)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 68899999999999999988865554433
No 344
>COG2344 AT-rich DNA-binding protein [General function prediction only]
Probab=31.39 E-value=1e+02 Score=29.78 Aligned_cols=49 Identities=24% Similarity=0.349 Sum_probs=39.9
Q ss_pred ccCccchHHHHHHHHHHHHHHHhcCCC-ccHHHHHHHcCCCHHHHHHHHH
Q 014764 340 LRLPNHLHERLGLIRNAKLRLEEKGVT-PSVDRIAEYLNMSQKKVRNATE 388 (419)
Q Consensus 340 irip~~l~e~~~~I~~a~~~L~e~gRe-pS~eEIAe~LGIS~etVr~~l~ 388 (419)
..+|.....++....+....|...+.+ ++-+|||+.+|++..+|++=+.
T Consensus 5 ~~IP~AT~kRL~~YyR~le~l~a~~v~rvsS~els~~~~vdsatIRrDfS 54 (211)
T COG2344 5 KKIPKATAKRLPLYYRVLERLHASGVERVSSKELSEALGVDSATIRRDFS 54 (211)
T ss_pred ccCCHHHHHHhHHHHHHHHHHHHcCCceecHHHHHHHhCCCHHHHhhhhH
Confidence 367888888888888888888655544 5999999999999999998654
No 345
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=31.38 E-value=97 Score=30.11 Aligned_cols=27 Identities=22% Similarity=0.410 Sum_probs=23.9
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
...++..|||+.||+|..||++-+...
T Consensus 16 ~~~~~~~eLa~~l~VS~~TiRRdL~~L 42 (240)
T PRK10411 16 HTSLTTEALAEQLNVSKETIRRDLNEL 42 (240)
T ss_pred cCCCcHHHHHHHHCcCHHHHHHHHHHH
Confidence 457899999999999999999988764
No 346
>PF11740 KfrA_N: Plasmid replication region DNA-binding N-term; InterPro: IPR021104 The KfrA family of protiens are encoded on plasmids, generally in or near gene clusters invloved in stable inheritance functions. These proteins are thought to form an all-helical structure, consisting of an N-terminal helix-turn-helix DNA binding domain and an extended coiled-coil tail. The best-characterised KfrA protein, encoded on the broad host-range Plasmid RK2, is a site-specific DNA-binding protein whose operator overlaps its own promoter. The DNA-binding domain is essential for function, while the coiled-coil domain is probably responsible for formation of multimers, and may provide an example of a bridge to host structures required for plasmid partitioning []. This entry represents the N-terminal DNA-binding domain.
Probab=31.13 E-value=1.4e+02 Score=25.34 Aligned_cols=41 Identities=20% Similarity=0.158 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHhcCCCccHHHHHHHcC-CCHHHHHHHHHHhC
Q 014764 351 GLIRNAKLRLEEKGVTPSVDRIAEYLN-MSQKKVRNATEAIG 391 (419)
Q Consensus 351 ~~I~~a~~~L~e~gRepS~eEIAe~LG-IS~etVr~~l~rar 391 (419)
..|..+...|...|+.||+.-|-+.|| -|..+|...++.-+
T Consensus 4 e~V~~Aa~~L~~~G~~pT~~~Vr~~lG~GS~~ti~~~l~~w~ 45 (120)
T PF11740_consen 4 EDVIEAADELLAAGKKPTVRAVRERLGGGSMSTISKHLKEWR 45 (120)
T ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHHCCCCHHHHHHHHHHHH
Confidence 467788888888899999999999999 99999999988754
No 347
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=30.89 E-value=7.9e+02 Score=27.45 Aligned_cols=134 Identities=10% Similarity=0.034 Sum_probs=68.0
Q ss_pred CCCchHHHHHHhcCChHHHHHHHhHH-----------HHHHHHHHHHhHHHHHHHHHHcc-CCCCChhhHhhHHHHHHHH
Q 014764 237 CEPSMEQLAASLRISRPELQSILMEC-----------SLAREKLVMSNVRLVMSIAQRYD-NMGADMADLVQGGLIGLLR 304 (419)
Q Consensus 237 ~~p~~~e~A~~~~~s~~eLr~~l~~~-----------~~A~e~LIe~yl~LV~sIAkry~-~~g~d~EDLVQEG~IgLlr 304 (419)
...+..+++...+++.+++...+..+ ..+++.+.+.-...+..+-.++- ..|...++|.+-
T Consensus 376 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~h~~~p~~~g~~~~~l~~~------- 448 (614)
T PRK10512 376 GAVNLADFAWARQLNGEGMRALLQQPGYIQAGDSLLSAPVAARWQRKLLDTLATYHEQHRDEPGPGRERLRRM------- 448 (614)
T ss_pred cCCCHHHHHHHhcCCHHHHHHHhccCCeEEEccEEECHHHHHHHHHHHHHHHHHHHHHCCcccCCCHHHHHhh-------
Confidence 56677888888888888887655332 23344444444444443333332 234555554321
Q ss_pred hHhhcCCCCCCchhhHHHHHHHhhHHHHHHHhc------ccccCccch---HHHHHHHHHHHHHHHhcCCCccHHHHHHH
Q 014764 305 GIEKFDSSKGFKISTYVYWWIRQGVSRALVENS------RTLRLPNHL---HERLGLIRNAKLRLEEKGVTPSVDRIAEY 375 (419)
Q Consensus 305 AIerFDp~rG~rFSTYa~~~Irn~I~~~Lrd~~------r~irip~~l---~e~~~~I~~a~~~L~e~gRepS~eEIAe~ 375 (419)
+..|+...+.+.+.+.+.... ..+++|.+. ......+...+..+-. ...|...|+++.
T Consensus 449 ------------~~~~~~~~~~~~~l~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~-~~p~~~~~~~~~ 515 (614)
T PRK10512 449 ------------ALPMEDEALVLLLIEKMRESGDIHSHHGWLHLPDHKAGFSEEQQALWQKAEPLFG-DEPWWVRDLAKE 515 (614)
T ss_pred ------------cccCCCHHHHHHHHHHHHhCCCEEEeCCEEECCCCCCCCCHHHHHHHHHHHHHHh-cCCCCHHHHHHH
Confidence 111111122233333333222 123334331 2222222222222111 356799999999
Q ss_pred cCCCHHHHHHHHHHh
Q 014764 376 LNMSQKKVRNATEAI 390 (419)
Q Consensus 376 LGIS~etVr~~l~ra 390 (419)
+|++...+++++...
T Consensus 516 l~~~~~~~~~~l~~l 530 (614)
T PRK10512 516 TGTDEQAMRLTLRQA 530 (614)
T ss_pred hCCCHHHHHHHHHHH
Confidence 999999998888765
No 348
>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=30.88 E-value=49 Score=29.72 Aligned_cols=26 Identities=15% Similarity=0.135 Sum_probs=23.0
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 366 epS~eEIAe~LGIS~etVr~~l~rar 391 (419)
..|++|||..+|++.++|-.+++..+
T Consensus 143 ~~t~~~iA~~lG~tretvsR~l~~l~ 168 (193)
T TIGR03697 143 RLSHQAIAEAIGSTRVTITRLLGDLR 168 (193)
T ss_pred CCCHHHHHHHhCCcHHHHHHHHHHHH
Confidence 35999999999999999999987754
No 349
>cd06445 ATase The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases are specific for repair of guanines with O6-alkyl adducts, however human ATase is not limited to O6-methylguanine, repairing many other adducts at the O6-position of guanine as well. ATase is widely distributed among species. Most ATases have N- and C-terminal domains. The C-terminal domain contains the conserved active-site cysteine motif (PCHR), the O6-alkylguanine binding channel, and the helix-turn-helix (HTH) DNA-binding motif. The active site is located near the recognition helix of the HTH motif. While the C-terminal domain of ATase contains residues that are necessary for DNA binding and alkyl transfer, the function of the N-terminal domain is still unknown. Removal of the N-terminal domain abolishes the activity of
Probab=30.82 E-value=86 Score=25.17 Aligned_cols=30 Identities=17% Similarity=0.146 Sum_probs=24.6
Q ss_pred hcCCCccHHHHHHHcCC--CHHHHHHHHHHhC
Q 014764 362 EKGVTPSVDRIAEYLNM--SQKKVRNATEAIG 391 (419)
Q Consensus 362 e~gRepS~eEIAe~LGI--S~etVr~~l~rar 391 (419)
..|+..|+.+||+.+|. ....|-.++....
T Consensus 13 P~G~v~TYg~iA~~~g~p~~~R~Vg~al~~np 44 (79)
T cd06445 13 PYGEVTTYGQIAKLAGTPKAARAVGSALARNP 44 (79)
T ss_pred CCCCcCcHHHHHHHHCCCCcHHHHHHHHHhCC
Confidence 35888999999999999 5778888876554
No 350
>PRK11569 transcriptional repressor IclR; Provisional
Probab=30.77 E-value=99 Score=30.39 Aligned_cols=33 Identities=6% Similarity=0.124 Sum_probs=26.3
Q ss_pred HHHHhcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 358 LRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 358 ~~L~e~gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
..+.+.....+..|||+.+|++..+|..++...
T Consensus 35 ~~l~~~~~~~~lseia~~lglpksTv~RlL~tL 67 (274)
T PRK11569 35 EWIAESNGSVALTELAQQAGLPNSTTHRLLTTM 67 (274)
T ss_pred HHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 333344556799999999999999999998764
No 351
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=30.45 E-value=73 Score=22.08 Aligned_cols=27 Identities=15% Similarity=0.064 Sum_probs=20.2
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
....++++||+.+|+|......+.+..
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~ 32 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFKKE 32 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 456799999999999999999888765
No 352
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=30.36 E-value=95 Score=28.83 Aligned_cols=27 Identities=30% Similarity=0.482 Sum_probs=22.9
Q ss_pred CCccHHHHHHHc--CCCHHHHHHHHHHhC
Q 014764 365 VTPSVDRIAEYL--NMSQKKVRNATEAIG 391 (419)
Q Consensus 365 RepS~eEIAe~L--GIS~etVr~~l~rar 391 (419)
-.+++.+||+.+ +||.++|++.+....
T Consensus 38 ~~~d~~~iak~l~p~is~~ev~~sL~~L~ 66 (171)
T PF14394_consen 38 FAPDPEWIAKRLRPKISAEEVRDSLEFLE 66 (171)
T ss_pred CCCCHHHHHHHhcCCCCHHHHHHHHHHHH
Confidence 344899999999 999999999987653
No 353
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=30.31 E-value=1.1e+02 Score=25.94 Aligned_cols=25 Identities=20% Similarity=0.221 Sum_probs=22.1
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHH
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~r 389 (419)
-+.|.++||+.||+|.+.|.+++..
T Consensus 22 ~~ls~~~ia~dL~~s~~~le~vL~l 46 (89)
T PF10078_consen 22 SGLSLEQIAADLGTSPEHLEQVLNL 46 (89)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 4679999999999999999998653
No 354
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=30.02 E-value=61 Score=28.67 Aligned_cols=28 Identities=14% Similarity=0.317 Sum_probs=24.2
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~rar 391 (419)
|..++..|||+.+|+|...|++++..-.
T Consensus 23 g~~~s~~~ia~~~~is~~~vrk~l~~L~ 50 (141)
T PRK11014 23 GRMTSISEVTEVYGVSRNHMVKIINQLS 50 (141)
T ss_pred CCccCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4557999999999999999999987653
No 355
>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=29.90 E-value=58 Score=25.24 Aligned_cols=24 Identities=17% Similarity=0.264 Sum_probs=21.5
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHH
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATE 388 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~ 388 (419)
+..|..++|+.+|++..+|...+.
T Consensus 17 ~~~t~~~lA~~~gis~~tis~~~~ 40 (78)
T TIGR02607 17 LGLSIRALAKALGVSRSTLSRIVN 40 (78)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHc
Confidence 567999999999999999999876
No 356
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=29.56 E-value=76 Score=30.07 Aligned_cols=26 Identities=23% Similarity=0.308 Sum_probs=23.4
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHH
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~r 389 (419)
.+-||-.|+|+.+|+|..||++++..
T Consensus 22 ~~LPsE~eLa~~~gVSR~TVR~Al~~ 47 (233)
T TIGR02404 22 DYLPSEHELMDQYGASRETVRKALNL 47 (233)
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 46789999999999999999999865
No 357
>TIGR02612 mob_myst_A mobile mystery protein A. Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).
Probab=29.54 E-value=2e+02 Score=26.41 Aligned_cols=25 Identities=16% Similarity=0.228 Sum_probs=21.2
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHH
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~r 389 (419)
.+.|..|+|+.+||+..+|......
T Consensus 37 lGmTq~eLAerlGVS~~tIs~iE~G 61 (150)
T TIGR02612 37 LGMSGAQLAGRLGVTPQRVEALEKS 61 (150)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 4668999999999999999988764
No 358
>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=28.90 E-value=1e+02 Score=28.92 Aligned_cols=25 Identities=24% Similarity=0.360 Sum_probs=23.0
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 366 TPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 366 epS~eEIAe~LGIS~etVr~~l~ra 390 (419)
.+|..|||+.||++..+|...+...
T Consensus 15 ~~t~~eLA~~lgis~~tV~~~L~~L 39 (203)
T TIGR02702 15 QATAAALAEALAISPQAVRRHLKDL 39 (203)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4899999999999999999998875
No 359
>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=28.88 E-value=63 Score=30.49 Aligned_cols=26 Identities=27% Similarity=0.382 Sum_probs=23.5
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHH
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~r 389 (419)
.+-||-.|+|+.+|+|..||++++..
T Consensus 30 ~~LPsE~eLa~~~~VSR~TvR~Al~~ 55 (238)
T TIGR02325 30 DYLPAEMQLAERFGVNRHTVRRAIAA 55 (238)
T ss_pred CcCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 46789999999999999999999865
No 360
>PHA00675 hypothetical protein
Probab=28.86 E-value=1.2e+02 Score=25.03 Aligned_cols=22 Identities=18% Similarity=0.150 Sum_probs=19.9
Q ss_pred cHHHHHHHcCCCHHHHHHHHHH
Q 014764 368 SVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 368 S~eEIAe~LGIS~etVr~~l~r 389 (419)
++.+||+.+|+|..+|.++...
T Consensus 41 s~~~IA~~fGVsrstV~~I~~g 62 (78)
T PHA00675 41 SYAVLAEKFEQSKGAIAKICRY 62 (78)
T ss_pred cHHHHHHHhCCCHHHHHHHHcc
Confidence 9999999999999999998643
No 361
>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=28.80 E-value=1.3e+02 Score=29.97 Aligned_cols=86 Identities=24% Similarity=0.220 Sum_probs=53.6
Q ss_pred HHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHh
Q 014764 228 KLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIE 307 (419)
Q Consensus 228 ~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIe 307 (419)
--++.+-+|+-|+.++....+++.-+++. |-++.+.++..+.+.|.+.++|...-.-+=++.+.
T Consensus 33 ~~r~~ew~~~AP~LeediAl~~ia~DelG----------------HAr~ly~ll~el~g~G~~~d~la~~R~~~~~rn~~ 96 (263)
T PF05138_consen 33 GQRLSEWCGHAPSLEEDIALANIAQDELG----------------HARLLYRLLEELEGEGRDEDDLAFLRDAREFRNLL 96 (263)
T ss_dssp HHHHHTGGGGSSSHHHHHHHHHHHHHHHH----------------HHHHHHHHHHHCHCCCHHHHHHHHHHHTTCS-SSG
T ss_pred hhHHhHHHhhCCCHHHHHHHHHHHHHHHH----------------HHHHHHHHHHHHhccCCChhHHHhhcccchhhhhh
Confidence 34566779999999887766655555544 45678888888877776766665554333333333
Q ss_pred hcCCCCCCchhhHHHHHHHhhHHHHH
Q 014764 308 KFDSSKGFKISTYVYWWIRQGVSRAL 333 (419)
Q Consensus 308 rFDp~rG~rFSTYa~~~Irn~I~~~L 333 (419)
-|+ ..+..|+..++++-+.+..
T Consensus 97 l~e----~p~~dwa~~v~r~~l~d~~ 118 (263)
T PF05138_consen 97 LFE----QPNGDWADTVARQFLFDRA 118 (263)
T ss_dssp GGG----S---SHHHHHHHHHHHHHH
T ss_pred hhc----cCCCCHHHHHHHHHHHHHH
Confidence 333 2566888888888665543
No 362
>PRK14999 histidine utilization repressor; Provisional
Probab=28.67 E-value=86 Score=29.97 Aligned_cols=26 Identities=15% Similarity=0.211 Sum_probs=23.3
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHH
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~r 389 (419)
.+-|+..|+|+.+|+|..||++++..
T Consensus 34 ~~LPsE~eLa~~~gVSR~TVR~Al~~ 59 (241)
T PRK14999 34 DRIPSEAELVAQYGFSRMTINRALRE 59 (241)
T ss_pred CcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 46789999999999999999999865
No 363
>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=28.48 E-value=1.4e+02 Score=23.66 Aligned_cols=26 Identities=15% Similarity=0.083 Sum_probs=19.5
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHH
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~r 389 (419)
-...|..|||+.+|+|..+|-+..+.
T Consensus 32 ~~~~si~elA~~~~vS~sti~Rf~kk 57 (77)
T PF01418_consen 32 IAFMSISELAEKAGVSPSTIVRFCKK 57 (77)
T ss_dssp HCT--HHHHHHHCTS-HHHHHHHHHH
T ss_pred HHHccHHHHHHHcCCCHHHHHHHHHH
Confidence 35669999999999999999887654
No 364
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=28.42 E-value=1.1e+02 Score=27.95 Aligned_cols=40 Identities=10% Similarity=0.135 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHHH-HhcC-CCccHHHHHHHcCCCHHHHHHH
Q 014764 347 HERLGLIRNAKLRL-EEKG-VTPSVDRIAEYLNMSQKKVRNA 386 (419)
Q Consensus 347 ~e~~~~I~~a~~~L-~e~g-RepS~eEIAe~LGIS~etVr~~ 386 (419)
.+...+|.++...| .+.| ...|+++||+..|+|.+++-..
T Consensus 10 ~~~r~~Il~aa~~lf~~~G~~~~ti~~Ia~~agvsk~t~Y~~ 51 (213)
T PRK09975 10 LKTRQELIETAIAQFALRGVSNTTLNDIADAANVTRGAIYWH 51 (213)
T ss_pred HHHHHHHHHHHHHHHHHcCcccCCHHHHHHHcCCCHHHHHHH
Confidence 33445555555555 5566 5689999999999999999774
No 365
>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=28.37 E-value=42 Score=23.97 Aligned_cols=19 Identities=21% Similarity=0.163 Sum_probs=16.8
Q ss_pred HHHHHcCCCHHHHHHHHHH
Q 014764 371 RIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 371 EIAe~LGIS~etVr~~l~r 389 (419)
|||+.+|++..+|..++..
T Consensus 2 ~lA~~~gvs~~tvs~~l~g 20 (52)
T cd01392 2 DIARAAGVSVATVSRVLNG 20 (52)
T ss_pred cHHHHHCcCHHHHHHHHcC
Confidence 7999999999999998764
No 366
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=28.35 E-value=3.6e+02 Score=22.66 Aligned_cols=23 Identities=17% Similarity=0.244 Sum_probs=20.2
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHh
Q 014764 368 SVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 368 S~eEIAe~LGIS~etVr~~l~ra 390 (419)
...+.|+.|||+..+++..+++.
T Consensus 70 n~s~AAr~LGIsRsTL~rKLkr~ 92 (95)
T PRK00430 70 NQTRAALMLGINRGTLRKKLKKY 92 (95)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHh
Confidence 68899999999999999888753
No 367
>PF01035 DNA_binding_1: 6-O-methylguanine DNA methyltransferase, DNA binding domain; InterPro: IPR014048 Synonym(s): 6-O-methylguanine-DNA methyltransferase, O-6-methylguanine-DNA-alkyltransferase This entry represents the DNA binding region of 6-O-methylguanine-DNA methyltransferases. The repair of DNA containing O6-alkylated guanine is carried out by DNA-[protein]-cysteine S-methyltransferase (2.1.1.63 from EC). The major mutagenic and carcinogenic effect of methylating agents in DNA is the formation of O6-alkylguanine. The alkyl group at the O-6 position is transferred to a cysteine residue in the enzyme []. This is a suicide reaction since the enzyme is irreversibly inactivated and the methylated protein accumulates as a dead-end product. Most, but not all of the methyltransferases are also able to repair O-4-methylthymine. DNA-[protein]-cysteine S-methyltransferases are widely distributed and are found in various prokaryotic and eukaryotic sources [].; GO: 0003824 catalytic activity, 0006281 DNA repair; PDB: 1SFE_A 1T39_B 1T38_A 1EH7_A 1EH6_A 1YFH_C 1EH8_A 1QNT_A 2KIM_A 2KIF_A ....
Probab=28.21 E-value=74 Score=26.07 Aligned_cols=38 Identities=18% Similarity=0.180 Sum_probs=27.1
Q ss_pred HHHHHHHHHHhcCCCccHHHHHHHcC--CCHHHHHHHHHHh
Q 014764 352 LIRNAKLRLEEKGVTPSVDRIAEYLN--MSQKKVRNATEAI 390 (419)
Q Consensus 352 ~I~~a~~~L~e~gRepS~eEIAe~LG--IS~etVr~~l~ra 390 (419)
++.+++..++ .|+..|+.+||+.+| -....|-.++...
T Consensus 6 ~V~~~v~~IP-~G~v~TYg~iA~~~g~p~~ar~Vg~al~~n 45 (85)
T PF01035_consen 6 RVWEAVRQIP-YGKVTTYGEIARLLGRPKAARAVGSALARN 45 (85)
T ss_dssp HHHHHHTTS--TT-BEEHHHHHHHTT-TTCHHHHHHHHHTS
T ss_pred HHHHHHHcCC-CCceEeHHHHHHHHhhcccHHHHHHHhccc
Confidence 3444444433 588889999999999 8888888888764
No 368
>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=28.21 E-value=1.3e+02 Score=23.30 Aligned_cols=43 Identities=37% Similarity=0.397 Sum_probs=26.5
Q ss_pred HHHHHHhhCCCCchHHHHHHhcCChHHHH-HHHhHHHHHHHHHHH
Q 014764 228 KLRLKERLGCEPSMEQLAASLRISRPELQ-SILMECSLAREKLVM 271 (419)
Q Consensus 228 ~~~l~~~lg~~p~~~e~A~~~~~s~~eLr-~~l~~~~~A~e~LIe 271 (419)
..+|.+.+|.. +..++|+.+|++...+. .....+.--.+.|+.
T Consensus 3 i~rl~~~~g~~-~~~~lA~~lgis~st~s~~~~~r~~~P~~~l~~ 46 (66)
T PF07022_consen 3 IERLKEALGVK-SDKELAERLGISKSTLSNNWKKRGSIPAEWLIK 46 (66)
T ss_dssp HHHHHHHHT-S-SCHHHHCCTT--HHHHH-HHHHSSS--HHHHHH
T ss_pred HHHHHHHhCCC-CHHHHHHHhCcCHHHhhHHHHhCCCCCHHHHHH
Confidence 45677777766 67899999999999988 555554333444443
No 369
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=28.06 E-value=77 Score=30.52 Aligned_cols=26 Identities=31% Similarity=0.402 Sum_probs=23.7
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHH
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~r 389 (419)
.+-|+-.|+|+.+|+|..||++++..
T Consensus 29 ~~LPsE~eLa~~f~VSR~TvRkAL~~ 54 (236)
T COG2188 29 DKLPSERELAEQFGVSRMTVRKALDE 54 (236)
T ss_pred CCCCCHHHHHHHHCCcHHHHHHHHHH
Confidence 57789999999999999999999865
No 370
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=27.76 E-value=82 Score=20.92 Aligned_cols=24 Identities=17% Similarity=0.231 Sum_probs=20.7
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHH
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATE 388 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~ 388 (419)
+..+..++|+.+|++..+|.....
T Consensus 9 ~~~s~~~la~~~~i~~~~i~~~~~ 32 (56)
T smart00530 9 KGLTQEELAEKLGVSRSTLSRIEN 32 (56)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHC
Confidence 456999999999999999988654
No 371
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=27.73 E-value=61 Score=30.75 Aligned_cols=26 Identities=12% Similarity=0.441 Sum_probs=23.1
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
+-|+..|||+.+|+|..+|++++.+-
T Consensus 30 ~LPsE~eLae~~gVSRt~VReAL~~L 55 (239)
T PRK04984 30 ILPAERELSELIGVTRTTLREVLQRL 55 (239)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 44689999999999999999999874
No 372
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=27.69 E-value=1.3e+02 Score=29.34 Aligned_cols=27 Identities=19% Similarity=0.234 Sum_probs=23.6
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
....+..|||+.+|+|..||++-+...
T Consensus 17 ~~~~~~~ela~~l~vS~~TirRdL~~L 43 (251)
T PRK13509 17 LGFVTVEKVIERLGISPATARRDINKL 43 (251)
T ss_pred cCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 566799999999999999999887754
No 373
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=27.67 E-value=92 Score=29.25 Aligned_cols=27 Identities=7% Similarity=0.107 Sum_probs=22.7
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
|...+..|+|+.+|+|...|++++.+-
T Consensus 28 G~~L~e~eLae~lgVSRtpVREAL~~L 54 (224)
T PRK11534 28 DEKLRMSLLTSRYALGVGPLREALSQL 54 (224)
T ss_pred CCcCCHHHHHHHHCCChHHHHHHHHHH
Confidence 555577899999999999999998874
No 374
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=27.58 E-value=1.5e+02 Score=28.82 Aligned_cols=29 Identities=21% Similarity=0.257 Sum_probs=24.6
Q ss_pred hcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 362 EKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 362 e~gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
..+...+..|||+.+|++..+|..++...
T Consensus 22 ~~~~~ls~~eia~~lgl~kstv~RlL~tL 50 (263)
T PRK09834 22 RLDGGATVGLLAELTGLHRTTVRRLLETL 50 (263)
T ss_pred hcCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 34455799999999999999999998764
No 375
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=27.45 E-value=1.5e+02 Score=26.26 Aligned_cols=25 Identities=28% Similarity=0.223 Sum_probs=22.3
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHH
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~r 389 (419)
++.|+.+||+.||+|+..|.+.+.-
T Consensus 21 eG~Sq~~iA~LLGltqaAVS~Yls~ 45 (119)
T COG2522 21 EGLSQYRIAKLLGLTQAAVSQYLSG 45 (119)
T ss_pred cCCcHHHHHHHhCCCHHHHHHHHcc
Confidence 4789999999999999999998754
No 376
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=27.37 E-value=61 Score=29.47 Aligned_cols=25 Identities=12% Similarity=0.221 Sum_probs=22.4
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 367 PSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 367 pS~eEIAe~LGIS~etVr~~l~rar 391 (419)
.|+++||..+|++.++|...+..-.
T Consensus 150 ~t~~~iA~~lG~tretvsR~l~~l~ 174 (202)
T PRK13918 150 ATHDELAAAVGSVRETVTKVIGELS 174 (202)
T ss_pred CCHHHHHHHhCccHHHHHHHHHHHH
Confidence 4999999999999999999887754
No 377
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=27.37 E-value=99 Score=29.24 Aligned_cols=26 Identities=19% Similarity=0.172 Sum_probs=23.3
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHH
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~r 389 (419)
.+-||..|+|+.+|+|..||++++..
T Consensus 23 ~~LPsE~eLa~~~~VSR~TVR~Al~~ 48 (230)
T TIGR02018 23 HRIPSEHELVAQYGCSRMTVNRALRE 48 (230)
T ss_pred CcCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 45779999999999999999999865
No 378
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=27.16 E-value=1.1e+02 Score=24.64 Aligned_cols=50 Identities=24% Similarity=0.327 Sum_probs=36.2
Q ss_pred CchHHHHHHhcCChHHHHHHHhHHHHHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHH
Q 014764 239 PSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGG 298 (419)
Q Consensus 239 p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG 298 (419)
-|-+++|...|+|++.+...-.+ =+...+.+.+.+|+-| +...||+++..
T Consensus 15 ltQ~elA~~vgVsRQTi~~iEkg-------ky~Psl~La~kia~~f---~~~iedIF~~~ 64 (68)
T COG1476 15 LTQEELAKLVGVSRQTIIAIEKG-------KYNPSLELALKIARVF---GKTIEDIFQLE 64 (68)
T ss_pred cCHHHHHHHcCcCHHHHHHHHcC-------CCCchHHHHHHHHHHh---CCCHHHHHhhh
Confidence 56789999999999887764332 1234466778888887 47889998854
No 379
>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=27.09 E-value=44 Score=24.71 Aligned_cols=21 Identities=19% Similarity=0.256 Sum_probs=18.6
Q ss_pred ccHHHHHHHcCCCHHHHHHHH
Q 014764 367 PSVDRIAEYLNMSQKKVRNAT 387 (419)
Q Consensus 367 pS~eEIAe~LGIS~etVr~~l 387 (419)
.++.|+|+.||++...|-..+
T Consensus 4 i~V~elAk~l~v~~~~ii~~l 24 (54)
T PF04760_consen 4 IRVSELAKELGVPSKEIIKKL 24 (54)
T ss_dssp E-TTHHHHHHSSSHHHHHHHH
T ss_pred eEHHHHHHHHCcCHHHHHHHH
Confidence 478899999999999999988
No 380
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=27.01 E-value=91 Score=31.13 Aligned_cols=28 Identities=14% Similarity=0.210 Sum_probs=23.8
Q ss_pred cCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 363 KGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 363 ~gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
.+-.+.+.|||+.|||+++.|...+...
T Consensus 22 ~qp~v~q~eIA~~lgiT~QaVsehiK~L 49 (260)
T COG1497 22 RQPRVKQKEIAKKLGITLQAVSEHIKEL 49 (260)
T ss_pred hCCCCCHHHHHHHcCCCHHHHHHHHHHH
Confidence 4566799999999999999999987654
No 381
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=26.91 E-value=73 Score=24.34 Aligned_cols=22 Identities=9% Similarity=0.170 Sum_probs=19.2
Q ss_pred cHHHHHHHcCCCHHHHHHHHHH
Q 014764 368 SVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 368 S~eEIAe~LGIS~etVr~~l~r 389 (419)
+..|+|+.+||+..+++.....
T Consensus 2 ~i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 2 TIGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh
Confidence 5789999999999999987554
No 382
>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=26.82 E-value=1.3e+02 Score=23.52 Aligned_cols=26 Identities=23% Similarity=0.436 Sum_probs=18.0
Q ss_pred HHhhCCCCchHHHHHHhcCC-hHHHHH
Q 014764 232 KERLGCEPSMEQLAASLRIS-RPELQS 257 (419)
Q Consensus 232 ~~~lg~~p~~~e~A~~~~~s-~~eLr~ 257 (419)
-+..|.+||..|+|..+|++ ..-+..
T Consensus 19 ~~~~G~~Pt~rEIa~~~g~~S~~tv~~ 45 (65)
T PF01726_consen 19 IEENGYPPTVREIAEALGLKSTSTVQR 45 (65)
T ss_dssp HHHHSS---HHHHHHHHTSSSHHHHHH
T ss_pred HHHcCCCCCHHHHHHHhCCCChHHHHH
Confidence 34789999999999999996 655554
No 383
>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=26.42 E-value=1.6e+02 Score=25.26 Aligned_cols=26 Identities=23% Similarity=0.254 Sum_probs=23.0
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 366 epS~eEIAe~LGIS~etVr~~l~rar 391 (419)
.++.+|||+.+|+|...|.+++..-.
T Consensus 25 ~~s~~eia~~~~i~~~~v~~il~~L~ 50 (132)
T TIGR00738 25 PVSVKEIAERQGISRSYLEKILRTLR 50 (132)
T ss_pred cCcHHHHHHHHCcCHHHHHHHHHHHH
Confidence 56999999999999999999987643
No 384
>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=26.28 E-value=1.7e+02 Score=20.70 Aligned_cols=23 Identities=17% Similarity=0.039 Sum_probs=20.1
Q ss_pred CCCccHHHHHHHcCCCHHHHHHH
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNA 386 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~ 386 (419)
....|..+||+.+|++...+...
T Consensus 14 ~~~~s~~~Ia~~~gvs~~~~y~~ 36 (47)
T PF00440_consen 14 YEAVSIRDIARRAGVSKGSFYRY 36 (47)
T ss_dssp TTTSSHHHHHHHHTSCHHHHHHH
T ss_pred HHhCCHHHHHHHHccchhhHHHH
Confidence 46789999999999999998764
No 385
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=26.05 E-value=3.4e+02 Score=23.46 Aligned_cols=34 Identities=18% Similarity=0.188 Sum_probs=27.6
Q ss_pred HHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHH
Q 014764 229 LRLKERLGCEPSMEQLAASLRISRPELQSILMEC 262 (419)
Q Consensus 229 ~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~ 262 (419)
.-+.+.+..+++.+++|..+|+|...|.....+.
T Consensus 16 ~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 16 DWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3456667788999999999999999988876653
No 386
>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=25.87 E-value=81 Score=27.24 Aligned_cols=28 Identities=18% Similarity=0.178 Sum_probs=24.1
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~rar 391 (419)
+..++..|||+.+|+|...|.+++....
T Consensus 23 ~~~~s~~eia~~l~is~~~v~~~l~~L~ 50 (130)
T TIGR02944 23 SQPYSAAEIAEQTGLNAPTVSKILKQLS 50 (130)
T ss_pred CCCccHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3456999999999999999999987754
No 387
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=25.56 E-value=70 Score=30.69 Aligned_cols=26 Identities=19% Similarity=0.386 Sum_probs=23.0
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
+-|+..|||+.+|+|...|++++.+.
T Consensus 33 ~LpsE~eLa~~lgVSRtpVREAL~~L 58 (254)
T PRK09464 33 KLPPERELAKQFDVSRPSLREAIQRL 58 (254)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 34589999999999999999999874
No 388
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=25.50 E-value=1.4e+02 Score=28.98 Aligned_cols=27 Identities=19% Similarity=0.236 Sum_probs=23.2
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
....+..|||+.+|+|..+|..++...
T Consensus 17 ~~~l~l~ela~~~glpksT~~RlL~tL 43 (246)
T COG1414 17 PGGLSLAELAERLGLPKSTVHRLLQTL 43 (246)
T ss_pred CCCCCHHHHHHHhCcCHHHHHHHHHHH
Confidence 344589999999999999999998764
No 389
>PHA00542 putative Cro-like protein
Probab=25.30 E-value=80 Score=25.58 Aligned_cols=26 Identities=19% Similarity=0.124 Sum_probs=22.7
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
++.|..|+|+.+||+..+|...+...
T Consensus 30 ~glTq~elA~~lgIs~~tIsr~e~g~ 55 (82)
T PHA00542 30 AGWSQEQIADATDVSQPTICRIYSGR 55 (82)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHcCC
Confidence 56799999999999999999987544
No 390
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=24.99 E-value=1.2e+02 Score=26.33 Aligned_cols=26 Identities=23% Similarity=0.355 Sum_probs=23.3
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 366 epS~eEIAe~LGIS~etVr~~l~rar 391 (419)
.+|+.|||+.+.+|...++.+++...
T Consensus 19 ~vtl~elA~~l~cS~Rn~r~lLkkm~ 44 (115)
T PF12793_consen 19 EVTLDELAELLFCSRRNARTLLKKMQ 44 (115)
T ss_pred ceeHHHHHHHhCCCHHHHHHHHHHHH
Confidence 45999999999999999999998754
No 391
>PRK00901 methylated-DNA--protein-cysteine methyltransferase; Provisional
Probab=24.96 E-value=1.4e+02 Score=27.37 Aligned_cols=67 Identities=16% Similarity=0.119 Sum_probs=39.5
Q ss_pred hHHHHHHHhcccccCccch--HHHHHHHHHHHHHHHhcCCCccHHHHHHHcCCCH--HHHHHHHHHhCcccccc
Q 014764 328 GVSRALVENSRTLRLPNHL--HERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQ--KKVRNATEAIGKVFSLD 397 (419)
Q Consensus 328 ~I~~~Lrd~~r~irip~~l--~e~~~~I~~a~~~L~e~gRepS~eEIAe~LGIS~--etVr~~l~rark~lSLD 397 (419)
.+..|+........+|-.. .....++.+++...+ .|+..||.|||+.+|-+. ..|-+++. +|++.+-
T Consensus 51 ~l~~Yf~G~~~~f~lpl~~~gt~fq~~Vw~~l~~Ip-~G~t~tY~~lA~~~g~p~a~RAVg~A~~--~NP~~ii 121 (155)
T PRK00901 51 QLEEYFEGKRKKFDLPLAPQGTEFQKKVWKALQEIP-YGETRSYKEIAVNIGNPKACRAVGLANN--KNPIPIF 121 (155)
T ss_pred HHHHHHcCCCcCCceeecCCCChHHHHHHHHHccCC-CCCcCCHHHHHHHHCCCchHHHHHHHHH--hCCCCCc
Confidence 3444555444333344332 234455565554443 689999999999999865 55655554 3555543
No 392
>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=24.79 E-value=80 Score=26.03 Aligned_cols=27 Identities=33% Similarity=0.356 Sum_probs=19.5
Q ss_pred hCCCCchHHHHHHhcCChHHHHHHHhH
Q 014764 235 LGCEPSMEQLAASLRISRPELQSILME 261 (419)
Q Consensus 235 lg~~p~~~e~A~~~~~s~~eLr~~l~~ 261 (419)
.|++.+.+++|.++|++.++++..+..
T Consensus 35 ~G~PVt~~~LA~a~g~~~e~v~~~L~~ 61 (77)
T PF12324_consen 35 KGQPVTVEQLAAALGWPVEEVRAALAA 61 (77)
T ss_dssp TTS-B-HHHHHHHHT--HHHHHHHHHH
T ss_pred cCCCcCHHHHHHHHCCCHHHHHHHHHh
Confidence 377899999999999999999887654
No 393
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=24.72 E-value=1.3e+02 Score=29.33 Aligned_cols=27 Identities=30% Similarity=0.341 Sum_probs=23.3
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
.-..|..|||++|||+..+|+..|..-
T Consensus 23 ~g~~sa~elA~~Lgis~~avR~HL~~L 49 (218)
T COG2345 23 SGPVSADELAEELGISPMAVRRHLDDL 49 (218)
T ss_pred cCCccHHHHHHHhCCCHHHHHHHHHHH
Confidence 345599999999999999999998764
No 394
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=24.59 E-value=1e+02 Score=28.95 Aligned_cols=27 Identities=33% Similarity=0.351 Sum_probs=22.4
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
|...+..+||+.+|+|...|++++.+-
T Consensus 32 G~~L~e~~La~~lgVSRtpVREAL~~L 58 (221)
T PRK11414 32 GARLITKNLAEQLGMSITPVREALLRL 58 (221)
T ss_pred CCccCHHHHHHHHCCCchhHHHHHHHH
Confidence 444466899999999999999999875
No 395
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=24.52 E-value=1.6e+02 Score=21.80 Aligned_cols=25 Identities=16% Similarity=0.226 Sum_probs=15.8
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHH
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~r 389 (419)
+..|+.++|+.+|++..++.....-
T Consensus 11 ~~lt~~~~a~~~~i~~~~i~~~e~g 35 (64)
T PF12844_consen 11 KGLTQKDLAEKLGISRSTISKIENG 35 (64)
T ss_dssp CT--HHHHHHHHTS-HHHHHHHHTT
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 4557888888888887777776543
No 396
>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=24.52 E-value=4e+02 Score=23.00 Aligned_cols=42 Identities=21% Similarity=0.232 Sum_probs=27.1
Q ss_pred CCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHHHhHHHHHHH
Q 014764 238 EPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSI 280 (419)
Q Consensus 238 ~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~yl~LV~sI 280 (419)
.-|..|+|..+|+|+..+...+..+...+. =++.-+.++...
T Consensus 33 DlSlsEIAe~~~iSRqaV~d~ikr~~~~L~-~yE~kL~l~~k~ 74 (101)
T PF04297_consen 33 DLSLSEIAEELGISRQAVYDSIKRAEKKLE-EYEEKLGLVEKF 74 (101)
T ss_dssp ---HHHHHHHCTS-HHHHHHHHHHHHHHHH-HHHHHH-HHHHH
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH-HHHHHHhhHHHH
Confidence 348899999999999999999988766542 234444444433
No 397
>PRK03837 transcriptional regulator NanR; Provisional
Probab=24.51 E-value=76 Score=30.00 Aligned_cols=26 Identities=23% Similarity=0.441 Sum_probs=23.1
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
+-|+..+||+.+|+|...|++++.+.
T Consensus 36 ~Lp~E~~Lae~~gVSRt~VREAL~~L 61 (241)
T PRK03837 36 QLPSERELMAFFGVGRPAVREALQAL 61 (241)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 44599999999999999999999874
No 398
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=24.41 E-value=3e+02 Score=20.45 Aligned_cols=38 Identities=24% Similarity=0.216 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHhcCCCccHHHHHHHcCC-CHHHHHHHHHHh
Q 014764 351 GLIRNAKLRLEEKGVTPSVDRIAEYLNM-SQKKVRNATEAI 390 (419)
Q Consensus 351 ~~I~~a~~~L~e~gRepS~eEIAe~LGI-S~etVr~~l~ra 390 (419)
.++..+...+... ..++.|||..+|+ +........+..
T Consensus 37 ~r~~~a~~~l~~~--~~~~~~ia~~~g~~s~~~f~r~Fk~~ 75 (84)
T smart00342 37 RRLERARRLLRDT--DLSVTEIALRVGFSSQSYFSRAFKKL 75 (84)
T ss_pred HHHHHHHHHHHcC--CCCHHHHHHHhCCCChHHHHHHHHHH
Confidence 3466666666532 6799999999999 999888876553
No 399
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=24.39 E-value=6.5e+02 Score=24.33 Aligned_cols=44 Identities=14% Similarity=0.026 Sum_probs=26.0
Q ss_pred HHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCCCCchhhHHHHH
Q 014764 280 IAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324 (419)
Q Consensus 280 IAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~rG~rFSTYa~~~ 324 (419)
|...|.......+++.+...|..-.-...|... |..|..|+...
T Consensus 206 I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk~~-G~T~~~yi~~~ 249 (302)
T PRK09685 206 IDQSIQEEILRPEWIAGELGISVRSLYRLFAEQ-GLVVAQYIRNR 249 (302)
T ss_pred HHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHc-CCCHHHHHHHH
Confidence 333444434778888887776665555566543 55566655543
No 400
>PRK11050 manganese transport regulator MntR; Provisional
Probab=24.30 E-value=2e+02 Score=25.92 Aligned_cols=28 Identities=21% Similarity=0.112 Sum_probs=24.2
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~rar 391 (419)
+...+..|||+.+|++..+|..++.+..
T Consensus 49 ~~~~t~~eLA~~l~is~stVsr~l~~Le 76 (152)
T PRK11050 49 VGEARQVDIAARLGVSQPTVAKMLKRLA 76 (152)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4457999999999999999999987754
No 401
>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=24.22 E-value=1.8e+02 Score=24.76 Aligned_cols=26 Identities=12% Similarity=0.240 Sum_probs=20.6
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 366 epS~eEIAe~LGIS~etVr~~l~rar 391 (419)
+-++.|||...|+|...|.+++...+
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 55899999999999999999998764
No 402
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=24.20 E-value=85 Score=30.01 Aligned_cols=27 Identities=19% Similarity=0.308 Sum_probs=23.8
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
.+-||-.|+|+.+|+|..||++++...
T Consensus 27 ~~LPsE~eL~~~~~VSR~TvR~Al~~L 53 (240)
T PRK09764 27 DALPTESALQTEFGVSRVTVRQALRQL 53 (240)
T ss_pred CcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 356799999999999999999998753
No 403
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=24.17 E-value=1e+02 Score=28.55 Aligned_cols=27 Identities=33% Similarity=0.385 Sum_probs=23.2
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
|...+..++|+.+|+|...|++++.+-
T Consensus 32 G~~L~e~~La~~lgVSRtpVReAL~~L 58 (212)
T TIGR03338 32 GAKLNESDIAARLGVSRGPVREAFRAL 58 (212)
T ss_pred CCEecHHHHHHHhCCChHHHHHHHHHH
Confidence 555588899999999999999998875
No 404
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=24.13 E-value=2e+02 Score=22.87 Aligned_cols=34 Identities=21% Similarity=0.234 Sum_probs=26.6
Q ss_pred HHHHHhcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 357 KLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 357 ~~~L~e~gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
...+......+++++||+.++++.++|...+..+
T Consensus 51 l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~l~~~ 84 (105)
T PF01399_consen 51 LRQLSKPYSSISISEIAKALQLSEEEVESILIDL 84 (105)
T ss_dssp HHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred HHHHHHHhcccchHHHHHHhccchHHHHHHHHHH
Confidence 3334345678899999999999999999988765
No 405
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=24.11 E-value=1.6e+02 Score=21.47 Aligned_cols=25 Identities=20% Similarity=0.271 Sum_probs=21.4
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 366 TPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 366 epS~eEIAe~LGIS~etVr~~l~ra 390 (419)
..+..|||+.++++..++-..+...
T Consensus 17 ~~~~~~la~~~~~~~~~~t~~i~~L 41 (59)
T PF01047_consen 17 GITQSELAEKLGISRSTVTRIIKRL 41 (59)
T ss_dssp SEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCHHHHHHHHCCChhHHHHHHHHH
Confidence 4799999999999999999988765
No 406
>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=24.09 E-value=1.8e+02 Score=27.04 Aligned_cols=26 Identities=12% Similarity=0.215 Sum_probs=23.3
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 366 epS~eEIAe~LGIS~etVr~~l~rar 391 (419)
..+.+|||+.+|++..+|..++..+.
T Consensus 120 g~s~~~iA~~lg~s~~~V~r~l~l~~ 145 (187)
T TIGR00180 120 SMTQEDLAKKIGKSRAHITNLLRLLK 145 (187)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHc
Confidence 45899999999999999999988765
No 407
>smart00351 PAX Paired Box domain.
Probab=24.04 E-value=73 Score=27.87 Aligned_cols=27 Identities=15% Similarity=-0.050 Sum_probs=23.8
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhCc
Q 014764 366 TPSVDRIAEYLNMSQKKVRNATEAIGK 392 (419)
Q Consensus 366 epS~eEIAe~LGIS~etVr~~l~rark 392 (419)
+.+..+||+.+||+..+|...+++...
T Consensus 33 G~s~~~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 33 GVRPCDISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 458999999999999999999988654
No 408
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=23.96 E-value=1.5e+02 Score=28.78 Aligned_cols=26 Identities=12% Similarity=0.180 Sum_probs=23.1
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
...+..|||+.+|++..+|..++..-
T Consensus 27 ~~l~l~eia~~lgl~kstv~Rll~tL 52 (257)
T PRK15090 27 REIGITELSQRVMMSKSTVYRFLQTM 52 (257)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 45799999999999999999998764
No 409
>TIGR03337 phnR transcriptional regulator protein. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.
Probab=23.90 E-value=86 Score=29.42 Aligned_cols=27 Identities=22% Similarity=0.374 Sum_probs=23.7
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
.+-|+..|+|+.+|+|.-+|++++...
T Consensus 23 ~~lPsE~eLa~~~~Vsr~Tvr~Al~~L 49 (231)
T TIGR03337 23 DKLPSERDLGERFNTTRVTIREALQQL 49 (231)
T ss_pred CcCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 356799999999999999999998764
No 410
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=23.86 E-value=1.5e+02 Score=29.57 Aligned_cols=39 Identities=13% Similarity=0.177 Sum_probs=27.8
Q ss_pred HHHHHHHHHHhcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 352 LIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 352 ~I~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
.+.+....|....-..+..+||+.+|+|...|++++++-
T Consensus 184 Av~~IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkL 222 (251)
T TIGR02787 184 AVEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKL 222 (251)
T ss_pred HHHHHHHHhccccccccHHHHHHHHCCCHHHHHHHHHHH
Confidence 344444444332234689999999999999999998874
No 411
>PRK06424 transcription factor; Provisional
Probab=23.78 E-value=1.8e+02 Score=26.45 Aligned_cols=26 Identities=8% Similarity=0.061 Sum_probs=22.9
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHH
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~r 389 (419)
.++.|++|+|+.+|++..+|..+...
T Consensus 95 ~~GLSQ~eLA~~iGvs~stIskiE~G 120 (144)
T PRK06424 95 RLSMSQADLAAKIFERKNVIASIERG 120 (144)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 46789999999999999999998753
No 412
>PRK13239 alkylmercury lyase; Provisional
Probab=23.76 E-value=80 Score=30.54 Aligned_cols=27 Identities=30% Similarity=0.323 Sum_probs=23.7
Q ss_pred hCCCCchHHHHHHhcCChHHHHHHHhH
Q 014764 235 LGCEPSMEQLAASLRISRPELQSILME 261 (419)
Q Consensus 235 lg~~p~~~e~A~~~~~s~~eLr~~l~~ 261 (419)
.|++|+.+++|..+|.+.++++..|..
T Consensus 33 ~G~pvt~~~lA~~~~~~~~~v~~~L~~ 59 (206)
T PRK13239 33 KGRPVSVTTLAAALGWPVEEVEAVLEA 59 (206)
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 688999999999999999998876554
No 413
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=23.75 E-value=84 Score=29.99 Aligned_cols=26 Identities=19% Similarity=0.330 Sum_probs=23.4
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHH
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~r 389 (419)
.+-|+-.|+|+.+|+|..||++++..
T Consensus 31 ~kLPsE~eLa~~~~VSR~TvR~Al~~ 56 (241)
T PRK11402 31 QQIPTENELCTQYNVSRITIRKAISD 56 (241)
T ss_pred CcCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 46789999999999999999999864
No 414
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=23.73 E-value=1.4e+02 Score=28.80 Aligned_cols=26 Identities=31% Similarity=0.404 Sum_probs=22.7
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
+-|+..|+|+.+|||...|++++.+-
T Consensus 32 ~LpsE~eLa~~~gVSRtpVREAL~~L 57 (257)
T PRK10225 32 RLPPEREIAEMLDVTRTVVREALIML 57 (257)
T ss_pred cCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 33479999999999999999999874
No 415
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=23.71 E-value=1.2e+02 Score=28.58 Aligned_cols=32 Identities=31% Similarity=0.391 Sum_probs=26.7
Q ss_pred HHHhcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 359 RLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 359 ~L~e~gRepS~eEIAe~LGIS~etVr~~l~rar 391 (419)
.+...| +.|.+|||+.|||....|+.++.+..
T Consensus 26 ~l~~kg-e~tDeela~~l~i~~~~vrriL~~L~ 57 (176)
T COG1675 26 ALLEKG-ELTDEELAELLGIKKNEVRRILYALY 57 (176)
T ss_pred HHHhcC-CcChHHHHHHhCccHHHHHHHHHHHH
Confidence 344434 78999999999999999999998764
No 416
>PF09824 ArsR: ArsR transcriptional regulator; InterPro: IPR014517 Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family.
Probab=23.50 E-value=35 Score=31.76 Aligned_cols=30 Identities=33% Similarity=0.673 Sum_probs=21.9
Q ss_pred ccccccccccchhHHHHHHhhHh-HHHhhhccc
Q 014764 95 NSIEEESSELDYSVEALLLLQKS-MLEKQWNLS 126 (419)
Q Consensus 95 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~ 126 (419)
++|++.-.+ ...++|.+|.|. |+|-||..|
T Consensus 34 ~El~e~~G~--d~~~~L~~LkK~gLiE~qWrmP 64 (160)
T PF09824_consen 34 EELEEKYGK--DVRESLLILKKGGLIESQWRMP 64 (160)
T ss_pred HHHHHHHCc--CHHHHHHHHHHcCchhhccccC
Confidence 445444322 338999999885 999999988
No 417
>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=23.43 E-value=98 Score=23.13 Aligned_cols=42 Identities=26% Similarity=0.389 Sum_probs=28.6
Q ss_pred CCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhHH
Q 014764 204 ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMEC 262 (419)
Q Consensus 204 ~lLt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~~ 262 (419)
..||.++-.++++.+..|.. ..++|...|++...+...+..-
T Consensus 5 ~~LTl~eK~~iI~~~e~g~s-----------------~~~ia~~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 5 KSLTLEEKLEIIKRLEEGES-----------------KRDIAREFGVSRSTVSTILKNK 46 (53)
T ss_dssp SS--HHHHHHHHHHHHCTT------------------HHHHHHHHT--CCHHHHHHHCH
T ss_pred ccCCHHHHHHHHHHHHcCCC-----------------HHHHHHHhCCCHHHHHHHHHhH
Confidence 34888999999999888764 6678888888888887766653
No 418
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.33 E-value=91 Score=27.11 Aligned_cols=28 Identities=25% Similarity=0.290 Sum_probs=23.9
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCc
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAIGK 392 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~rark 392 (419)
...|..|||+..+||...|.+-+.++-.
T Consensus 32 dDlSl~EIAee~~VSRqAIyDnIKr~~~ 59 (105)
T COG2739 32 DDLSLSEIAEEFNVSRQAIYDNIKRTEK 59 (105)
T ss_pred hhccHHHHHHHhCccHHHHHHHHHHHHH
Confidence 4559999999999999999998877643
No 419
>PRK15044 transcriptional regulator SirC; Provisional
Probab=23.23 E-value=3.7e+02 Score=27.49 Aligned_cols=60 Identities=17% Similarity=0.132 Sum_probs=40.5
Q ss_pred HHHHHHhhcCCCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhH
Q 014764 193 LKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (419)
Q Consensus 193 l~~yl~~i~~~~lLt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~ 261 (419)
+..|++.....+.|......... +....-+.+.+..+++.+++|..+|+|+.-|.+....
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 45566654444444443332222 2244456778889999999999999999999987765
No 420
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=23.07 E-value=1.4e+02 Score=29.08 Aligned_cols=27 Identities=19% Similarity=0.186 Sum_probs=23.2
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
...++..|+|+.+|+|+.||++=+...
T Consensus 19 ~~~v~v~eLa~~~~VS~~TIRRDL~~L 45 (252)
T PRK10681 19 SDKLHLKDAAALLGVSEMTIRRDLNAH 45 (252)
T ss_pred cCCCcHHHHHHHhCCCHHHHHHHHHHh
Confidence 456899999999999999998877653
No 421
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=22.87 E-value=1.3e+02 Score=29.36 Aligned_cols=26 Identities=15% Similarity=0.217 Sum_probs=22.2
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHH
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~r 389 (419)
...+++.|||+.+|+|..||++-+..
T Consensus 17 ~~~~~~~ela~~l~vS~~TiRRdL~~ 42 (252)
T PRK10906 17 QGYVSTEELVEHFSVSPQTIRRDLND 42 (252)
T ss_pred cCCEeHHHHHHHhCCCHHHHHHHHHH
Confidence 45689999999999999999986544
No 422
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=22.83 E-value=1.4e+02 Score=22.02 Aligned_cols=32 Identities=16% Similarity=0.041 Sum_probs=26.2
Q ss_pred HHhcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 360 LEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 360 L~e~gRepS~eEIAe~LGIS~etVr~~l~rar 391 (419)
|..+...++.+.||...||+..+|.++.+...
T Consensus 13 L~~LR~~~~~~~La~~FgIs~stvsri~~~~~ 44 (53)
T PF13613_consen 13 LMYLRLNLTFQDLAYRFGISQSTVSRIFHEWI 44 (53)
T ss_pred HHHHHcCCcHhHHhhheeecHHHHHHHHHHHH
Confidence 33445678999999999999999999887653
No 423
>PF13309 HTH_22: HTH domain
Probab=22.81 E-value=3.4e+02 Score=21.01 Aligned_cols=58 Identities=21% Similarity=0.269 Sum_probs=40.2
Q ss_pred HhhhhHHHHHHhhcCC-CCCCHHHHHHHHHHHH-ccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHH
Q 014764 188 LIQNRLKGYVKGVVSE-ELLTHAEVVRLSKKIK-TGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQS 257 (419)
Q Consensus 188 ~~~~~l~~yl~~i~~~-~lLt~~eE~eL~rkik-~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~ 257 (419)
.+.+.++.++..+... ..|+.++-.++++.+. .|-. .---+-+.+|..+|+|+..+..
T Consensus 2 ~i~~~i~~~~~~~~~~~~~l~~~~k~~iV~~L~~~G~F------------~lKgav~~vA~~L~iS~~TVY~ 61 (64)
T PF13309_consen 2 LIESIIEEVIAEVGKPPSRLSKEEKKEIVRQLYEKGIF------------LLKGAVEYVAEKLGISRATVYR 61 (64)
T ss_pred hHHHHHHHHHHHhCCChhhCCHHHHHHHHHHHHHCCCc------------ccCcHHHHHHHHHCCCHHHHHH
Confidence 4566778888877544 5688888888888764 4544 1223457888999999887654
No 424
>PRK10072 putative transcriptional regulator; Provisional
Probab=22.79 E-value=91 Score=26.47 Aligned_cols=26 Identities=19% Similarity=0.160 Sum_probs=22.0
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
.+.|+.|+|+.+|++..+|.+-...-
T Consensus 45 ~glTQ~elA~~lGvS~~TVs~WE~G~ 70 (96)
T PRK10072 45 TGLKIDDFARVLGVSVAMVKEWESRR 70 (96)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcCC
Confidence 46699999999999999999986543
No 425
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=22.64 E-value=85 Score=29.69 Aligned_cols=26 Identities=12% Similarity=0.441 Sum_probs=23.0
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
+-|+..+||+.+|+|...|++++.+-
T Consensus 29 ~LpsE~~La~~lgVSRtpVREAL~~L 54 (235)
T TIGR02812 29 ILPAERELSELIGVTRTTLREVLQRL 54 (235)
T ss_pred cCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 34589999999999999999999874
No 426
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=22.63 E-value=2.8e+02 Score=25.97 Aligned_cols=25 Identities=20% Similarity=0.204 Sum_probs=22.0
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 367 PSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 367 pS~eEIAe~LGIS~etVr~~l~rar 391 (419)
.+.+|||+.+|++.++|.+.+....
T Consensus 170 ~t~~~lA~~lG~sretvsR~L~~L~ 194 (226)
T PRK10402 170 EKHTQAAEYLGVSYRHLLYVLAQFI 194 (226)
T ss_pred chHHHHHHHHCCcHHHHHHHHHHHH
Confidence 3889999999999999999887654
No 427
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=22.52 E-value=1.7e+02 Score=21.81 Aligned_cols=29 Identities=17% Similarity=0.203 Sum_probs=22.0
Q ss_pred cCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 363 KGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 363 ~gRepS~eEIAe~LGIS~etVr~~l~rar 391 (419)
....++..+||+.+|++..+|...++...
T Consensus 15 ~~~~~t~~~l~~~~~~~~~~vs~~i~~L~ 43 (68)
T PF13463_consen 15 SDGPMTQSDLAERLGISKSTVSRIIKKLE 43 (68)
T ss_dssp -TS-BEHHHHHHHTT--HHHHHHHHHHHH
T ss_pred cCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 35677999999999999999999888764
No 428
>PRK09954 putative kinase; Provisional
Probab=22.51 E-value=1.6e+02 Score=29.77 Aligned_cols=26 Identities=19% Similarity=0.227 Sum_probs=23.2
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 366 epS~eEIAe~LGIS~etVr~~l~rar 391 (419)
..+..|||+.||+|..+|..++.+..
T Consensus 17 ~~s~~~la~~l~~s~~~v~~~i~~L~ 42 (362)
T PRK09954 17 LIQQNEIADILQISRSRVAAHIMDLM 42 (362)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 57999999999999999999988643
No 429
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=22.40 E-value=87 Score=30.12 Aligned_cols=26 Identities=23% Similarity=0.360 Sum_probs=22.9
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
+-|+..|||+.+|||...|++++.+.
T Consensus 25 ~LpsE~eLae~~gVSRtpVREAL~~L 50 (253)
T PRK10421 25 KLPAERQLAMQLGVSRNSLREALAKL 50 (253)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 34589999999999999999999874
No 430
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=22.30 E-value=81 Score=28.77 Aligned_cols=31 Identities=13% Similarity=0.156 Sum_probs=25.0
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhC--cccccc
Q 014764 367 PSVDRIAEYLNMSQKKVRNATEAIG--KVFSLD 397 (419)
Q Consensus 367 pS~eEIAe~LGIS~etVr~~l~rar--k~lSLD 397 (419)
.|.+|||+.+|++.++|.++++... ..+.++
T Consensus 169 ~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~~~ 201 (211)
T PRK11753 169 ITRQEIGRIVGCSREMVGRVLKMLEDQGLISAH 201 (211)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEec
Confidence 5899999999999999999987654 344444
No 431
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=22.20 E-value=3.5e+02 Score=23.57 Aligned_cols=34 Identities=18% Similarity=0.188 Sum_probs=26.5
Q ss_pred CCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHH
Q 014764 238 EPSMEQLAASLRISRPELQSILMECSLAREKLVM 271 (419)
Q Consensus 238 ~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe 271 (419)
.-+.+|+|..+|+|...++..+..+......++.
T Consensus 127 g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~ 160 (166)
T PRK09639 127 GYSYKEIAEALGIKESSVGTTLARAKKKFRKIYE 160 (166)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3468999999999999999988876665555444
No 432
>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=22.12 E-value=84 Score=22.93 Aligned_cols=21 Identities=19% Similarity=0.404 Sum_probs=18.0
Q ss_pred cHHHHHHHcCCCHHHHHHHHH
Q 014764 368 SVDRIAEYLNMSQKKVRNATE 388 (419)
Q Consensus 368 S~eEIAe~LGIS~etVr~~l~ 388 (419)
..++||+.|||+...|..=..
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 678999999999999987543
No 433
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=21.95 E-value=3.8e+02 Score=23.43 Aligned_cols=31 Identities=16% Similarity=0.142 Sum_probs=23.7
Q ss_pred chHHHHHHhcCChHHHHHHHhHHHHHHHHHH
Q 014764 240 SMEQLAASLRISRPELQSILMECSLAREKLV 270 (419)
Q Consensus 240 ~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LI 270 (419)
+.+++|..+|+|...+...+..+...+...+
T Consensus 146 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 146 SYEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5789999999999999988876555444333
No 434
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=21.95 E-value=7.2e+02 Score=23.95 Aligned_cols=38 Identities=11% Similarity=0.156 Sum_probs=28.5
Q ss_pred HHHHHHHHHH-hcCCCccHHHHHHHcCCCHHHHHHHHHH
Q 014764 352 LIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 352 ~I~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~~l~r 389 (419)
.+.+++..+. ......+++++|+.+|+|...+..+.+.
T Consensus 184 ~i~~~~~~i~~~~~~~isl~~lA~~~~lS~~~l~r~Fk~ 222 (290)
T PRK10572 184 RVREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQ 222 (290)
T ss_pred HHHHHHHHHHhcccCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3555555563 4567789999999999999998887654
No 435
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=21.76 E-value=91 Score=29.83 Aligned_cols=26 Identities=27% Similarity=0.446 Sum_probs=23.0
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
+-|+..|||+.+|+|...|++++.+-
T Consensus 30 ~LPsE~eLa~~~gVSRtpVREAL~~L 55 (251)
T PRK09990 30 ALPSERRLCEKLGFSRSALREGLTVL 55 (251)
T ss_pred cCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 44589999999999999999999874
No 436
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=21.71 E-value=58 Score=26.11 Aligned_cols=31 Identities=19% Similarity=0.267 Sum_probs=24.2
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~rark~l 394 (419)
...++.+++|+.+++|..++.+.+...++.+
T Consensus 28 ~~~~s~~~la~~~~iS~sti~~~i~~l~~~l 58 (87)
T PF05043_consen 28 NEYVSIEDLAEELFISRSTIYRDIKKLNKYL 58 (87)
T ss_dssp -SEEEHHHHHHHHT--HHHHHHHHHHHHHHH
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 5677999999999999999999998876543
No 437
>TIGR03076 near_not_gcvH Chlamydial GcvH-like protein upstream region protein. The H protein (GcvH) of the glycine cleavage system shuttles the methylamine group of glycine from the P protein to the T protein. Most Chlamydia but lack the P and T proteins, and have a single homolog of GcvH that appears deeply split from canonical GcvH in molecular phylogenetic trees. The protein family modeled here is observed so far only in the Chlamydiae, always as part of a two-gene operon, upstream of the homolog of GcvH. Its function is unknown.
Probab=21.53 E-value=4.2e+02 Score=29.47 Aligned_cols=128 Identities=13% Similarity=0.138 Sum_probs=65.9
Q ss_pred HHHHHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhHhhcCCCC-CCchhhHHHHHHHhhHHHHHHHhccc
Q 014764 261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSK-GFKISTYVYWWIRQGVSRALVENSRT 339 (419)
Q Consensus 261 ~~~~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAIerFDp~r-G~rFSTYa~~~Irn~I~~~Lrd~~r~ 339 (419)
++..|+-+|+..-..+-..+.+.+....-.+--|-+++.+.=-+-+.-|-..- ..-|..+....+-..+++.|.++...
T Consensus 159 egf~aRV~LFLeEkkfphy~LrqmLeYrrqmfnLp~D~~L~~g~dL~LFGY~~i~DWFg~~yvs~v~e~ll~fi~EQkk~ 238 (686)
T TIGR03076 159 EGFAARVRLFLEEKKFPHYVLRQMLEYRRQMFNLPVDGSLAQGKDLRLFGYRNIKDWFGDAYVSAAVEALLRFIDEQKKN 238 (686)
T ss_pred HHHHHHHHHHHhhccCCHHHHHHHHHHHHHhccCCCChhHhhcccceeeccccHHHhhhHHHHHHHHHHHHHHHHHhccc
Confidence 45567777775544333333332221111111233444333212222232110 11466666777788888899888877
Q ss_pred ccCccchHHHHHHHHHHHHHHHhcCCCc----cHHH----HHHHcCCCHHHHHHHHH
Q 014764 340 LRLPNHLHERLGLIRNAKLRLEEKGVTP----SVDR----IAEYLNMSQKKVRNATE 388 (419)
Q Consensus 340 irip~~l~e~~~~I~~a~~~L~e~gRep----S~eE----IAe~LGIS~etVr~~l~ 388 (419)
+-+|..-.....-++++.....++.+.+ |.+| -=..|||++.+.-++-+
T Consensus 239 v~mps~~EA~~Df~dkaq~af~~~sk~~~~~ls~~e~v~s~~~fmgv~esef~~myR 295 (686)
T TIGR03076 239 IAMPSLKEAQQDFYDKAKQAFTKLSKHAEFNLTFDQFVSSYFSFMGVSESEFFNMYR 295 (686)
T ss_pred ccCCcHHHHHHHHHHHHHHHHHHhccCCCcCcCHHHHHHHHHHHhCCcHHHHHHHHH
Confidence 7666543333344555555555444333 5444 44578999988766543
No 438
>PRK01381 Trp operon repressor; Provisional
Probab=21.51 E-value=89 Score=26.93 Aligned_cols=22 Identities=14% Similarity=0.087 Sum_probs=18.3
Q ss_pred CCccHHHHHHHcCCCHHHHHHH
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNA 386 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~ 386 (419)
.+.|+.|||+.||+|..+|-.-
T Consensus 54 g~~sQREIa~~lGvSiaTITRg 75 (99)
T PRK01381 54 GELSQREIKQELGVGIATITRG 75 (99)
T ss_pred CCcCHHHHHHHhCCceeeehhh
Confidence 3579999999999998887553
No 439
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=21.44 E-value=77 Score=23.94 Aligned_cols=32 Identities=19% Similarity=0.390 Sum_probs=24.7
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhCcccccc
Q 014764 366 TPSVDRIAEYLNMSQKKVRNATEAIGKVFSLD 397 (419)
Q Consensus 366 epS~eEIAe~LGIS~etVr~~l~rark~lSLD 397 (419)
.-+..+.|+.|+|...||+.++.++.+.+-+|
T Consensus 12 ~~n~~~tA~~L~iHrNTl~yRl~ki~~l~g~d 43 (59)
T PF13556_consen 12 NGNISKTARALHIHRNTLRYRLKKIEELLGLD 43 (59)
T ss_dssp TT-HHHHHHHHTS-HHHHHHHHHHHHHHHS--
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHCcC
Confidence 34889999999999999999999988766555
No 440
>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=21.32 E-value=1.8e+02 Score=29.23 Aligned_cols=25 Identities=12% Similarity=0.268 Sum_probs=21.1
Q ss_pred CccHHHHHHHcC--CCHHHHHHHHHHh
Q 014764 366 TPSVDRIAEYLN--MSQKKVRNATEAI 390 (419)
Q Consensus 366 epS~eEIAe~LG--IS~etVr~~l~ra 390 (419)
..++.+||+.++ ||.++|++.+...
T Consensus 137 ~~~~~~ia~~l~p~is~~ev~~sL~~L 163 (271)
T TIGR02147 137 ADDPEELAKRCFPKISAEQVKESLDLL 163 (271)
T ss_pred CCCHHHHHHHhCCCCCHHHHHHHHHHH
Confidence 447889999998 9999999998764
No 441
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=21.30 E-value=1.6e+02 Score=27.92 Aligned_cols=26 Identities=31% Similarity=0.378 Sum_probs=21.8
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
...|..||+++||+|...|...++..
T Consensus 40 ~Pmtl~Ei~E~lg~Sks~vS~~lkkL 65 (177)
T COG1510 40 KPLTLDEIAEALGMSKSNVSMGLKKL 65 (177)
T ss_pred CCccHHHHHHHHCCCcchHHHHHHHH
Confidence 34499999999999999998887643
No 442
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=21.27 E-value=4e+02 Score=25.12 Aligned_cols=23 Identities=30% Similarity=0.443 Sum_probs=21.4
Q ss_pred cHHHHHHHc-CCCHHHHHHHHHHh
Q 014764 368 SVDRIAEYL-NMSQKKVRNATEAI 390 (419)
Q Consensus 368 S~eEIAe~L-GIS~etVr~~l~ra 390 (419)
|...||+.+ ||++.+|+..+...
T Consensus 72 SN~~La~r~~G~s~~tlrR~l~~L 95 (177)
T PF03428_consen 72 SNAQLAERLNGMSERTLRRHLARL 95 (177)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHH
Confidence 999999999 99999999998764
No 443
>COG0350 Ada Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=21.20 E-value=1.9e+02 Score=26.78 Aligned_cols=50 Identities=20% Similarity=0.132 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHHHhcCCCccHHHHHHHcCCCH--HHHHHHHHHhCccccccccc
Q 014764 348 ERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQ--KKVRNATEAIGKVFSLDREA 400 (419)
Q Consensus 348 e~~~~I~~a~~~L~e~gRepS~eEIAe~LGIS~--etVr~~l~rark~lSLD~~~ 400 (419)
....++..++...+ .|...||.|||+.+|-+. ..|-.++ .+|+++|=-|+
T Consensus 88 ~Fq~~Vw~aL~~IP-~Get~TY~eiA~~ig~p~a~rAVG~A~--~~NPl~IiIPC 139 (168)
T COG0350 88 GFQGRVWQALREIP-YGETVTYGEIARRLGRPTAVRAVGNAN--GANPLPIIIPC 139 (168)
T ss_pred hHHHHHHHHHhcCC-CCCcEeHHHHHHHhCCCcHHHHHHHHh--ccCCceEEecC
Confidence 34455555554443 688999999999999932 2344433 45777764433
No 444
>smart00753 PAM PCI/PINT associated module.
Probab=21.19 E-value=2.6e+02 Score=22.09 Aligned_cols=35 Identities=23% Similarity=0.246 Sum_probs=27.2
Q ss_pred HHHHHHhcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 356 AKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 356 a~~~L~e~gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
....+......++.++||+.++++.+.|...+..+
T Consensus 14 ~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~ 48 (88)
T smart00753 14 NLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKA 48 (88)
T ss_pred HHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHH
Confidence 34444445678899999999999999988877654
No 445
>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=21.19 E-value=2.6e+02 Score=22.09 Aligned_cols=35 Identities=23% Similarity=0.246 Sum_probs=27.2
Q ss_pred HHHHHHhcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 356 AKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 356 a~~~L~e~gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
....+......++.++||+.++++.+.|...+..+
T Consensus 14 ~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~ 48 (88)
T smart00088 14 NLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKA 48 (88)
T ss_pred HHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHH
Confidence 34444445678899999999999999988877654
No 446
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=21.18 E-value=3.7e+02 Score=23.43 Aligned_cols=33 Identities=15% Similarity=0.093 Sum_probs=25.6
Q ss_pred CchHHHHHHhcCChHHHHHHHhHHHHHHHHHHH
Q 014764 239 PSMEQLAASLRISRPELQSILMECSLAREKLVM 271 (419)
Q Consensus 239 p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe 271 (419)
-+.+|+|..+|+|...++..+..+.....+.+.
T Consensus 142 ~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~ 174 (179)
T PRK11924 142 LSYREIAEILGVPVGTVKSRLRRARQLLRECLE 174 (179)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 357899999999999999988876665544443
No 447
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=21.15 E-value=1.2e+02 Score=20.18 Aligned_cols=25 Identities=16% Similarity=0.246 Sum_probs=21.0
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHH
Q 014764 365 VTPSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~~l~r 389 (419)
...+..++|+.+|++..+|...+..
T Consensus 11 ~~~s~~~~a~~~~~~~~~v~~~~~g 35 (58)
T cd00093 11 KGLTQEELAEKLGVSRSTISRIENG 35 (58)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHcC
Confidence 3568999999999999999887653
No 448
>PF02885 Glycos_trans_3N: Glycosyl transferase family, helical bundle domain Prosite entry for Thymidine and pyrimidine-nucleoside phosphorylases; InterPro: IPR017459 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. The glycosyl transferase family includes anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase (2.4.2.2 from EC) catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism. This N-terminal domain is found in various family 3 glycosyl transferases, including anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism.; PDB: 2DSJ_B 2ELC_B 2BPQ_A 1ZVW_B 3QR9_B 1V8G_B 2WK5_C 2J0F_C 2WK6_B 1UOU_A ....
Probab=21.12 E-value=2.5e+02 Score=21.59 Aligned_cols=31 Identities=23% Similarity=0.172 Sum_probs=23.2
Q ss_pred HHHHHHhhcCCCCCCHHHHHHHHHHHHccCc
Q 014764 193 LKGYVKGVVSEELLTHAEVVRLSKKIKTGLS 223 (419)
Q Consensus 193 l~~yl~~i~~~~lLt~~eE~eL~rkik~Gd~ 223 (419)
+..||+.+....-||.+|..+++..+-.|..
T Consensus 2 ~~~~l~~l~~g~~Ls~~e~~~~~~~i~~g~~ 32 (66)
T PF02885_consen 2 IKEILKKLRDGEDLSREEAKAAFDAILDGEV 32 (66)
T ss_dssp HHHHHHHHHTT----HHHHHHHHHHHHTTSS
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHHHHHcCCC
Confidence 5678888888889999999999999999875
No 449
>PRK03887 methylated-DNA--protein-cysteine methyltransferase; Provisional
Probab=20.91 E-value=2.3e+02 Score=26.83 Aligned_cols=29 Identities=24% Similarity=0.289 Sum_probs=23.9
Q ss_pred hcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 362 EKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 362 e~gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
+.|+..||.+||+.+|.+...|-.++.+.
T Consensus 106 P~G~v~TYgqIA~~~G~aaRAVG~Al~~N 134 (175)
T PRK03887 106 KRGEVITYGELAKALNTSPRAVGGAMKRN 134 (175)
T ss_pred CCCCCCcHHHHHHHHCchHHHHHHHHHhC
Confidence 35899999999999998877777776654
No 450
>PF01498 HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in []. Tc3 is a member of the Tc1/mariner family of transposable elements. This entry also includes histone-lysine N-methyltransferase SETMAR, which is a SET domain and mariner transposase fusion gene-containing protein. This histone methyltransferase has sequence-specific DNA-binding activity and recognises the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element. This protein has DNA nicking activity, and has in vivo end joining activity and may mediate genomic integration of foreign DNA [, , , ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated, 0015074 DNA integration; PDB: 3K9K_B 3F2K_B 3K9J_B 1U78_A.
Probab=20.89 E-value=1.1e+02 Score=23.51 Aligned_cols=28 Identities=25% Similarity=0.316 Sum_probs=18.6
Q ss_pred CCCccHHHHHHHc-----CCCHHHHHHHHHHhC
Q 014764 364 GVTPSVDRIAEYL-----NMSQKKVRNATEAIG 391 (419)
Q Consensus 364 gRepS~eEIAe~L-----GIS~etVr~~l~rar 391 (419)
.+..|..||+..| +||..||+..++...
T Consensus 11 ~p~~s~~~i~~~l~~~~~~vS~~TI~r~L~~~g 43 (72)
T PF01498_consen 11 NPRISAREIAQELQEAGISVSKSTIRRRLREAG 43 (72)
T ss_dssp -----HHHHHHHT---T--S-HHHHHHHHHHT-
T ss_pred CCCCCHHHHHHHHHHccCCcCHHHHHHHHHHcC
Confidence 4456999999998 899999999998764
No 451
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=20.81 E-value=1e+02 Score=29.98 Aligned_cols=27 Identities=30% Similarity=0.389 Sum_probs=24.4
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
.+-|+-.|+|+.+|+|...|++++..-
T Consensus 32 ~~LP~EreLae~fgVSR~~vREAl~~L 58 (241)
T COG2186 32 DRLPSERELAERFGVSRTVVREALKRL 58 (241)
T ss_pred CCCCCHHHHHHHHCCCcHHHHHHHHHH
Confidence 577899999999999999999998763
No 452
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=20.80 E-value=6.2e+02 Score=22.74 Aligned_cols=74 Identities=14% Similarity=0.091 Sum_probs=47.3
Q ss_pred HHhhC-CCCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHHHhHHHHHHHHHHccCCCCChhhHhhHHHHHHHHhH
Q 014764 232 KERLG-CEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGI 306 (419)
Q Consensus 232 ~~~lg-~~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~yl~LV~sIAkry~~~g~d~EDLVQEG~IgLlrAI 306 (419)
-.+-| ...|..++|+.+|+|...+..-...=.+-+..+++.+..........+.. ..+..+-+.+.+...+...
T Consensus 21 f~e~G~~~~s~~~IA~~agvs~~~lY~hF~sKe~L~~av~~~~~~~~~~~~~~~~~-~~~~~e~l~~~~~~~~~~~ 95 (202)
T TIGR03613 21 FSRFGFHGTSLEQIAELAGVSKTNLLYYFPSKDALYLAVLRQILDIWLSPLKAFTE-DFAPLAAIKAYIRAKLEMS 95 (202)
T ss_pred HHHhCcccCCHHHHHHHhCCCHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcc-CCCHHHHHHHHHHHHHHHH
Confidence 33444 44788999999999999999877765566777777666555444444432 3344555555555544444
No 453
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=20.76 E-value=3.5e+02 Score=25.25 Aligned_cols=36 Identities=17% Similarity=0.177 Sum_probs=28.6
Q ss_pred chHHHHHHhcCChHHHHHHHhHHHHHHHHHHHHhHH
Q 014764 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVR 275 (419)
Q Consensus 240 ~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~yl~ 275 (419)
+.+|+|..+|++...++..+..+...+.+.+..+.|
T Consensus 156 s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~~~~~ 191 (203)
T PRK09647 156 SYEEIAATLGVKLGTVRSRIHRGRQQLRAALAAHAP 191 (203)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhch
Confidence 579999999999999999888877766665555443
No 454
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=20.56 E-value=4.1e+02 Score=23.12 Aligned_cols=33 Identities=21% Similarity=0.195 Sum_probs=26.8
Q ss_pred chHHHHHHhcCChHHHHHHHhHHHHHHHHHHHH
Q 014764 240 SMEQLAASLRISRPELQSILMECSLAREKLVMS 272 (419)
Q Consensus 240 ~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~ 272 (419)
+.+|+|..+|+|...++..+..+..+....+..
T Consensus 123 s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~~ 155 (159)
T PRK12527 123 SHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQ 155 (159)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 589999999999999999888777666555544
No 455
>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=20.55 E-value=3.3e+02 Score=22.77 Aligned_cols=43 Identities=23% Similarity=0.246 Sum_probs=30.1
Q ss_pred CCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHH
Q 014764 205 LLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQS 257 (419)
Q Consensus 205 lLt~~eE~eL~rkik~Gd~l~~~~~~l~~~lg~~p~~~e~A~~~~~s~~eLr~ 257 (419)
++||.|-..+..+++- .++-|...-+..|+|..+|+|--.+-+
T Consensus 26 L~T~~E~~~l~~R~~v----------a~~lL~~g~syreIa~~tgvS~aTItR 68 (87)
T PF01371_consen 26 LCTPDELEALAQRWQV----------AKELLDEGKSYREIAEETGVSIATITR 68 (87)
T ss_dssp HSSHHHHHHHHHHHHH----------HHHHHHTTSSHHHHHHHHTSTHHHHHH
T ss_pred hCCHHHHHHHHHHHHH----------HHHHHHCCCCHHHHHHHhCCCHHHHHH
Confidence 4678887777766552 223455566789999999998776554
No 456
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=20.54 E-value=3.2e+02 Score=24.73 Aligned_cols=36 Identities=17% Similarity=0.096 Sum_probs=27.8
Q ss_pred CCchHHHHHHhcCChHHHHHHHhHHHHHHHHHHHHh
Q 014764 238 EPSMEQLAASLRISRPELQSILMECSLAREKLVMSN 273 (419)
Q Consensus 238 ~p~~~e~A~~~~~s~~eLr~~l~~~~~A~e~LIe~y 273 (419)
.-+..|+|..+|+|...++..+..+.......+..|
T Consensus 157 g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~ 192 (194)
T PRK12519 157 GLSQSEIAKRLGIPLGTVKARARQGLLKLRELLQDL 192 (194)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 346899999999999999998887666555555443
No 457
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=20.53 E-value=1.8e+02 Score=23.97 Aligned_cols=33 Identities=15% Similarity=0.139 Sum_probs=26.7
Q ss_pred HHHHHhhCCCCchHHHHHHhcCChHHHHHHHhH
Q 014764 229 LRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (419)
Q Consensus 229 ~~l~~~lg~~p~~~e~A~~~~~s~~eLr~~l~~ 261 (419)
.-+.+.+..+++.+++|..+++|...|.+...+
T Consensus 12 ~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~ 44 (107)
T PRK10219 12 AWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRT 44 (107)
T ss_pred HHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 345566778899999999999999988876664
No 458
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=20.50 E-value=1.4e+02 Score=30.92 Aligned_cols=27 Identities=22% Similarity=0.343 Sum_probs=23.8
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEAI 390 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~ra 390 (419)
.+-|+..++|+.+|+|..+|++++...
T Consensus 27 ~~lps~r~la~~~~vsr~tv~~a~~~L 53 (431)
T PRK15481 27 DSLPPVRELASELGVNRNTVAAAYKRL 53 (431)
T ss_pred CcCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 566799999999999999999997653
No 459
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=20.18 E-value=3.4e+02 Score=25.60 Aligned_cols=25 Identities=28% Similarity=0.383 Sum_probs=22.3
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 367 PSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 367 pS~eEIAe~LGIS~etVr~~l~rar 391 (419)
+|+++||..+|++.++|.++++..+
T Consensus 180 lt~~~IA~~lGisretlsR~L~~L~ 204 (230)
T PRK09391 180 MSRRDIADYLGLTIETVSRALSQLQ 204 (230)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4899999999999999999887654
No 460
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=20.08 E-value=1.5e+02 Score=24.83 Aligned_cols=26 Identities=19% Similarity=0.219 Sum_probs=19.8
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014764 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (419)
Q Consensus 366 epS~eEIAe~LGIS~etVr~~l~rar 391 (419)
..+.++||+.+|++..+|+.++..-.
T Consensus 27 ~l~de~la~~~~l~~~~vRkiL~~L~ 52 (105)
T PF02002_consen 27 ELTDEDLAKKLGLKPKEVRKILYKLY 52 (105)
T ss_dssp -B-HHHHHHTT-S-HHHHHHHHHHHH
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 46999999999999999999987754
No 461
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=20.05 E-value=1.3e+02 Score=29.44 Aligned_cols=26 Identities=23% Similarity=0.327 Sum_probs=22.3
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHH
Q 014764 364 GVTPSVDRIAEYLNMSQKKVRNATEA 389 (419)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~~l~r 389 (419)
...++++|+|+.+|+|+.||++=+..
T Consensus 17 ~g~v~v~eLa~~~~VS~~TIRRDL~~ 42 (253)
T COG1349 17 KGKVSVEELAELFGVSEMTIRRDLNE 42 (253)
T ss_pred cCcEEHHHHHHHhCCCHHHHHHhHHH
Confidence 45689999999999999999985543
Done!