Query 014852
Match_columns 417
No_of_seqs 225 out of 1815
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 09:08:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014852.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014852hhsearch_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 1.1E-40 2.3E-45 342.7 23.6 215 191-405 60-317 (415)
2 PRK07406 RNA polymerase sigma 100.0 3E-39 6.5E-44 328.9 23.7 215 191-405 63-278 (373)
3 TIGR02997 Sig70-cyanoRpoD RNA 100.0 1.1E-38 2.4E-43 315.1 23.8 211 192-402 2-213 (298)
4 PRK05949 RNA polymerase sigma 100.0 1.4E-38 3E-43 319.1 24.0 216 190-405 17-233 (327)
5 PRK07405 RNA polymerase sigma 100.0 1.9E-37 4.2E-42 309.5 23.7 214 191-404 8-222 (317)
6 PRK05901 RNA polymerase sigma 100.0 7.8E-36 1.7E-40 313.4 20.4 203 190-405 210-413 (509)
7 PRK07921 RNA polymerase sigma 100.0 1.6E-34 3.4E-39 289.7 21.0 202 191-405 26-228 (324)
8 COG0568 RpoD DNA-directed RNA 100.0 3.2E-34 7E-39 287.4 18.1 223 190-412 8-251 (342)
9 PRK09210 RNA polymerase sigma 100.0 8.7E-33 1.9E-37 281.1 20.2 177 189-405 94-271 (367)
10 PRK05658 RNA polymerase sigma 100.0 1.1E-30 2.4E-35 281.5 20.4 178 192-406 345-523 (619)
11 PRK07500 rpoH2 RNA polymerase 100.0 2.1E-28 4.6E-33 241.5 21.3 174 191-404 6-187 (289)
12 PRK06596 RNA polymerase factor 100.0 3.4E-28 7.3E-33 239.4 20.8 176 184-403 10-189 (284)
13 PRK05657 RNA polymerase sigma 100.0 1.2E-27 2.5E-32 240.1 20.9 177 187-403 49-226 (325)
14 TIGR02392 rpoH_proteo alternat 100.0 1.6E-27 3.4E-32 232.5 20.6 171 192-403 2-177 (270)
15 PRK07122 RNA polymerase sigma 100.0 1.6E-27 3.4E-32 232.5 17.9 140 264-403 40-182 (264)
16 TIGR02850 spore_sigG RNA polym 99.9 1E-26 2.3E-31 224.6 20.1 162 201-403 11-173 (254)
17 TIGR02393 RpoD_Cterm RNA polym 99.9 3.2E-27 7E-32 225.9 14.9 140 265-404 1-141 (238)
18 PRK07408 RNA polymerase sigma 99.9 2.2E-26 4.8E-31 223.1 19.6 140 264-403 25-168 (256)
19 PRK08215 sporulation sigma fac 99.9 1.7E-25 3.6E-30 216.5 19.4 162 201-403 14-176 (258)
20 COG1191 FliA DNA-directed RNA 99.9 2.4E-25 5.1E-30 215.7 17.9 161 204-406 4-168 (247)
21 TIGR02394 rpoS_proteo RNA poly 99.9 9E-25 1.9E-29 214.6 20.5 175 188-402 10-185 (285)
22 TIGR02941 Sigma_B RNA polymera 99.9 1.2E-23 2.6E-28 202.9 19.8 162 204-405 8-173 (255)
23 PRK05911 RNA polymerase sigma 99.9 1E-23 2.2E-28 204.7 19.0 136 264-402 23-164 (257)
24 TIGR02885 spore_sigF RNA polym 99.9 1.5E-23 3.2E-28 199.1 17.4 141 262-403 9-150 (231)
25 PRK06288 RNA polymerase sigma 99.9 9.5E-23 2.1E-27 198.5 18.9 159 200-401 6-171 (268)
26 TIGR02980 SigBFG RNA polymeras 99.9 8.3E-23 1.8E-27 193.2 17.3 139 263-401 2-143 (227)
27 PRK05572 sporulation sigma fac 99.9 2.8E-22 6.1E-27 193.4 19.8 165 197-402 5-170 (252)
28 PRK08583 RNA polymerase sigma 99.9 8.5E-22 1.8E-26 190.2 19.4 160 204-403 8-171 (257)
29 PRK07670 RNA polymerase sigma 99.9 2.4E-21 5.2E-26 186.8 18.5 136 264-402 22-163 (251)
30 PRK05803 sporulation sigma fac 99.9 2.2E-21 4.8E-26 185.0 15.8 163 192-394 17-223 (233)
31 PRK12427 flagellar biosynthesi 99.9 1.2E-20 2.6E-25 180.7 16.6 136 264-403 15-156 (231)
32 TIGR02479 FliA_WhiG RNA polyme 99.8 3.8E-20 8.3E-25 175.1 15.0 130 269-401 1-136 (224)
33 TIGR02846 spore_sigmaK RNA pol 99.8 1.6E-19 3.5E-24 171.8 15.8 163 192-394 15-222 (227)
34 PRK06986 fliA flagellar biosyn 99.8 2.4E-19 5.3E-24 171.1 15.9 138 261-401 5-148 (236)
35 PRK08301 sporulation sigma fac 99.8 1.9E-19 4E-24 171.3 14.8 159 196-394 23-226 (234)
36 TIGR02835 spore_sigmaE RNA pol 99.8 2.4E-18 5.1E-23 164.4 14.6 159 196-394 23-226 (234)
37 PRK09646 RNA polymerase sigma 99.8 1.6E-18 3.5E-23 160.3 11.9 153 201-394 7-186 (194)
38 PRK09648 RNA polymerase sigma 99.8 8E-18 1.7E-22 154.4 13.9 148 206-394 6-183 (189)
39 PRK05602 RNA polymerase sigma 99.7 1.2E-17 2.5E-22 153.0 12.9 130 264-394 20-172 (186)
40 PRK12513 RNA polymerase sigma 99.7 1.7E-17 3.6E-22 152.9 13.6 129 264-394 26-183 (194)
41 PRK11922 RNA polymerase sigma 99.7 2.1E-17 4.5E-22 157.5 13.6 152 201-394 7-193 (231)
42 PRK08295 RNA polymerase factor 99.7 1.5E-17 3.3E-22 154.0 12.2 131 264-394 24-198 (208)
43 TIGR02859 spore_sigH RNA polym 99.7 4.3E-17 9.2E-22 149.8 13.6 131 264-394 19-193 (198)
44 PRK12514 RNA polymerase sigma 99.7 2.9E-17 6.4E-22 149.2 12.0 130 264-394 19-173 (179)
45 PRK06759 RNA polymerase factor 99.7 2.2E-17 4.8E-22 145.9 10.9 129 264-394 4-150 (154)
46 PRK09640 RNA polymerase sigma 99.7 5.9E-17 1.3E-21 149.0 13.8 144 249-394 7-178 (188)
47 PRK12524 RNA polymerase sigma 99.7 2.5E-17 5.5E-22 152.5 11.3 130 264-394 26-180 (196)
48 PRK11923 algU RNA polymerase s 99.7 4.9E-17 1.1E-21 149.5 13.0 147 206-394 2-182 (193)
49 PRK13919 putative RNA polymera 99.7 3.2E-17 6.9E-22 149.7 11.6 130 264-394 23-179 (186)
50 PRK12534 RNA polymerase sigma 99.7 3.2E-17 6.9E-22 150.0 11.2 130 264-394 25-181 (187)
51 PRK12531 RNA polymerase sigma 99.7 3.9E-17 8.6E-22 151.0 11.9 130 264-394 27-185 (194)
52 PRK06811 RNA polymerase factor 99.7 4.7E-17 1E-21 149.9 12.0 130 264-394 18-175 (189)
53 TIGR02952 Sig70_famx2 RNA poly 99.7 4.5E-17 9.8E-22 145.7 11.4 132 262-394 9-166 (170)
54 TIGR02948 SigW_bacill RNA poly 99.7 7.1E-17 1.5E-21 146.8 12.8 129 264-394 18-180 (187)
55 PRK12537 RNA polymerase sigma 99.7 5.1E-17 1.1E-21 148.7 11.9 130 264-394 23-177 (182)
56 PRK12519 RNA polymerase sigma 99.7 8.2E-17 1.8E-21 148.1 12.5 129 264-394 29-185 (194)
57 TIGR02895 spore_sigI RNA polym 99.7 1.5E-16 3.3E-21 151.9 14.3 120 265-384 10-141 (218)
58 TIGR02954 Sig70_famx3 RNA poly 99.7 1E-16 2.2E-21 144.4 12.3 129 264-394 16-163 (169)
59 PRK12538 RNA polymerase sigma 99.7 9.3E-17 2E-21 154.1 12.5 130 264-394 63-215 (233)
60 PRK12536 RNA polymerase sigma 99.7 2E-16 4.4E-21 144.6 14.0 129 264-394 21-173 (181)
61 PRK09643 RNA polymerase sigma 99.7 1.4E-16 3.1E-21 147.4 12.4 129 264-394 27-178 (192)
62 PRK09638 RNA polymerase sigma 99.7 1.6E-16 3.5E-21 143.6 12.4 129 264-394 18-170 (176)
63 PRK12526 RNA polymerase sigma 99.7 1.7E-16 3.8E-21 148.6 12.6 130 264-394 38-197 (206)
64 PRK09649 RNA polymerase sigma 99.7 1.8E-16 3.8E-21 146.0 12.5 130 264-396 24-176 (185)
65 TIGR02939 RpoE_Sigma70 RNA pol 99.7 2.7E-16 5.8E-21 143.3 13.4 129 264-394 20-182 (190)
66 PRK09641 RNA polymerase sigma 99.7 2.9E-16 6.2E-21 142.8 13.0 129 264-394 18-180 (187)
67 PRK12539 RNA polymerase sigma 99.7 5.3E-16 1.1E-20 142.2 13.4 129 264-394 21-175 (184)
68 PRK12542 RNA polymerase sigma 99.7 1.4E-16 3E-21 146.0 8.9 134 261-394 6-166 (185)
69 COG1595 RpoE DNA-directed RNA 99.7 6.9E-16 1.5E-20 141.3 12.6 135 258-394 9-171 (182)
70 PRK09652 RNA polymerase sigma 99.7 4.1E-16 8.9E-21 140.0 10.8 131 262-394 8-172 (182)
71 TIGR02999 Sig-70_X6 RNA polyme 99.7 4.6E-16 1E-20 141.4 10.8 129 264-394 17-178 (183)
72 PRK12515 RNA polymerase sigma 99.7 6.1E-16 1.3E-20 142.1 11.5 129 264-394 22-175 (189)
73 PRK12512 RNA polymerase sigma 99.7 1.2E-15 2.7E-20 139.2 13.4 129 264-394 22-175 (184)
74 TIGR02989 Sig-70_gvs1 RNA poly 99.7 6.9E-16 1.5E-20 136.8 11.0 128 265-394 2-155 (159)
75 PRK09415 RNA polymerase factor 99.6 9E-16 2E-20 140.2 11.6 131 262-394 14-171 (179)
76 PRK12520 RNA polymerase sigma 99.6 6.6E-16 1.4E-20 142.2 10.2 128 265-394 3-175 (191)
77 TIGR03001 Sig-70_gmx1 RNA poly 99.6 1.2E-15 2.5E-20 147.8 12.2 129 264-394 39-205 (244)
78 PRK12522 RNA polymerase sigma 99.6 1.4E-15 3E-20 137.7 11.3 129 264-394 3-163 (173)
79 TIGR02947 SigH_actino RNA poly 99.6 1.4E-15 2.9E-20 140.3 11.3 130 263-394 10-175 (193)
80 PRK12543 RNA polymerase sigma 99.6 1.3E-15 2.8E-20 139.0 10.9 132 261-394 4-161 (179)
81 PRK09645 RNA polymerase sigma 99.6 1.3E-15 2.9E-20 137.4 10.7 132 262-394 7-162 (173)
82 PRK12516 RNA polymerase sigma 99.6 1.7E-15 3.7E-20 140.2 11.0 131 262-394 8-160 (187)
83 PRK12540 RNA polymerase sigma 99.6 1.8E-15 3.9E-20 139.4 11.1 150 264-417 5-178 (182)
84 PRK12518 RNA polymerase sigma 99.6 2.8E-15 6.1E-20 135.4 11.9 129 263-394 10-164 (175)
85 PRK11924 RNA polymerase sigma 99.6 3.8E-15 8.3E-20 133.3 12.7 130 263-394 12-169 (179)
86 PRK08241 RNA polymerase factor 99.6 3.8E-15 8.3E-20 148.9 13.2 130 264-395 19-198 (339)
87 PRK12547 RNA polymerase sigma 99.6 4.7E-15 1E-19 133.5 11.4 130 263-394 5-156 (164)
88 TIGR02983 SigE-fam_strep RNA p 99.6 4.6E-15 9.9E-20 132.4 11.1 131 262-394 4-154 (162)
89 PRK12535 RNA polymerase sigma 99.6 7.7E-15 1.7E-19 136.9 12.9 128 264-394 25-177 (196)
90 TIGR02985 Sig70_bacteroi1 RNA 99.6 2.6E-15 5.5E-20 132.0 9.0 128 265-394 2-157 (161)
91 PRK12541 RNA polymerase sigma 99.6 6.3E-15 1.4E-19 131.7 11.2 129 263-394 4-156 (161)
92 TIGR02937 sigma70-ECF RNA poly 99.6 6.3E-15 1.4E-19 126.3 10.1 128 265-394 2-154 (158)
93 PRK12529 RNA polymerase sigma 99.6 4E-15 8.7E-20 136.0 9.2 134 261-394 10-171 (178)
94 PRK09644 RNA polymerase sigma 99.6 7.1E-15 1.5E-19 132.1 10.5 126 266-394 3-152 (165)
95 TIGR02960 SigX5 RNA polymerase 99.6 8.1E-15 1.8E-19 145.2 11.1 131 262-394 3-186 (324)
96 PRK12533 RNA polymerase sigma 99.6 1.5E-14 3.3E-19 137.5 12.2 131 261-394 15-178 (216)
97 TIGR02984 Sig-70_plancto1 RNA 99.6 1.8E-14 3.9E-19 131.0 11.5 133 262-394 5-184 (189)
98 PRK12523 RNA polymerase sigma 99.6 7.8E-15 1.7E-19 132.9 8.4 128 264-394 10-163 (172)
99 PRK09642 RNA polymerase sigma 99.6 8E-15 1.7E-19 130.8 8.2 121 271-394 2-150 (160)
100 PRK09639 RNA polymerase sigma 99.6 1.6E-14 3.5E-19 129.1 9.9 127 264-394 3-155 (166)
101 PRK12517 RNA polymerase sigma 99.5 2.9E-14 6.2E-19 131.9 11.1 132 261-394 20-172 (188)
102 TIGR02950 SigM_subfam RNA poly 99.5 2.4E-14 5.2E-19 126.3 9.6 122 270-394 1-149 (154)
103 PRK12528 RNA polymerase sigma 99.5 2.5E-14 5.3E-19 127.9 9.7 128 264-394 4-157 (161)
104 PRK09637 RNA polymerase sigma 99.5 4.4E-14 9.6E-19 129.9 11.2 127 266-394 3-150 (181)
105 PRK09647 RNA polymerase sigma 99.5 4.5E-14 9.7E-19 132.7 10.8 130 262-394 26-182 (203)
106 PRK12532 RNA polymerase sigma 99.5 3.8E-14 8.3E-19 130.8 10.2 126 267-394 8-180 (195)
107 PRK12545 RNA polymerase sigma 99.5 3.6E-14 7.9E-19 132.4 9.8 124 269-394 13-183 (201)
108 PRK08311 putative RNA polymera 99.5 3.7E-13 8.1E-18 130.2 17.0 77 264-340 18-96 (237)
109 PRK12530 RNA polymerase sigma 99.5 5.4E-14 1.2E-18 129.9 9.9 125 268-394 11-178 (189)
110 PRK12546 RNA polymerase sigma 99.5 1.3E-13 2.7E-18 128.0 11.9 128 264-394 8-157 (188)
111 PRK12544 RNA polymerase sigma 99.5 6.9E-14 1.5E-18 131.7 10.1 126 267-394 21-192 (206)
112 TIGR02943 Sig70_famx1 RNA poly 99.5 6.8E-14 1.5E-18 129.3 9.6 125 268-394 6-175 (188)
113 PRK09651 RNA polymerase sigma 99.5 1.3E-13 2.8E-18 125.3 11.0 129 263-394 9-163 (172)
114 TIGR02959 SigZ RNA polymerase 99.5 7.3E-14 1.6E-18 126.8 9.3 122 271-394 2-144 (170)
115 PRK12511 RNA polymerase sigma 99.5 1.4E-13 3.1E-18 126.9 10.1 126 267-394 7-155 (182)
116 PRK06704 RNA polymerase factor 99.5 2.4E-13 5.2E-18 130.8 10.6 134 255-394 9-160 (228)
117 PRK07037 extracytoplasmic-func 99.4 6.9E-13 1.5E-17 118.5 9.4 124 268-394 2-153 (163)
118 PRK12527 RNA polymerase sigma 99.4 6.9E-13 1.5E-17 118.4 8.6 121 271-394 2-149 (159)
119 PRK12525 RNA polymerase sigma 99.4 1E-12 2.2E-17 118.8 9.3 127 264-393 9-161 (168)
120 PF04542 Sigma70_r2: Sigma-70 99.4 1.2E-12 2.6E-17 100.9 7.9 70 269-338 1-70 (71)
121 PRK09636 RNA polymerase sigma 99.4 1.7E-12 3.6E-17 128.0 9.6 128 264-395 4-160 (293)
122 PRK09191 two-component respons 99.3 6.4E-12 1.4E-16 119.0 9.3 122 265-394 2-132 (261)
123 PRK09635 sigI RNA polymerase s 99.3 7E-12 1.5E-16 124.4 9.5 129 264-396 5-164 (290)
124 TIGR02957 SigX4 RNA polymerase 99.3 6.1E-12 1.3E-16 123.7 8.9 124 268-395 1-153 (281)
125 TIGR03209 P21_Cbot clostridium 99.2 2.7E-11 5.9E-16 106.3 7.8 112 266-384 1-141 (142)
126 PRK09047 RNA polymerase factor 99.2 3.2E-11 6.8E-16 107.2 7.5 106 286-394 2-150 (161)
127 PF07638 Sigma70_ECF: ECF sigm 98.8 4.2E-08 9.1E-13 90.9 12.5 130 264-393 17-178 (185)
128 PF04539 Sigma70_r3: Sigma-70 98.5 1.6E-07 3.4E-12 75.0 5.8 67 348-414 1-68 (78)
129 PRK09210 RNA polymerase sigma 97.6 0.00087 1.9E-08 69.0 13.4 133 226-394 220-353 (367)
130 PRK07921 RNA polymerase sigma 97.6 0.0012 2.6E-08 67.1 13.8 133 226-394 177-310 (324)
131 PRK05901 RNA polymerase sigma 97.6 0.0011 2.3E-08 71.2 13.9 133 226-394 362-495 (509)
132 TIGR02393 RpoD_Cterm RNA polym 97.6 0.0014 3E-08 63.1 13.0 133 226-394 91-224 (238)
133 PF00140 Sigma70_r1_2: Sigma-7 97.4 5.5E-05 1.2E-09 53.2 1.3 33 191-223 2-34 (37)
134 PRK07406 RNA polymerase sigma 97.3 0.0045 9.9E-08 64.1 14.2 132 227-394 228-359 (373)
135 PRK07500 rpoH2 RNA polymerase 97.3 0.0043 9.3E-08 61.8 13.4 30 365-394 244-273 (289)
136 PRK07598 RNA polymerase sigma 97.3 0.0015 3.3E-08 68.5 10.3 135 224-394 264-398 (415)
137 PRK05911 RNA polymerase sigma 97.3 0.0045 9.8E-08 60.5 12.9 60 189-258 87-146 (257)
138 PRK07408 RNA polymerase sigma 97.2 0.00091 2E-08 65.3 7.8 63 189-258 87-149 (256)
139 PRK05949 RNA polymerase sigma 97.2 0.004 8.7E-08 63.3 12.5 135 224-394 180-314 (327)
140 COG0568 RpoD DNA-directed RNA 97.1 0.0075 1.6E-07 61.8 13.4 48 346-394 280-327 (342)
141 COG1191 FliA DNA-directed RNA 97.1 0.01 2.2E-07 58.4 13.7 153 190-393 86-239 (247)
142 PRK07405 RNA polymerase sigma 97.0 0.0042 9.1E-08 62.8 9.8 135 224-394 170-304 (317)
143 TIGR02997 Sig70-cyanoRpoD RNA 97.0 0.006 1.3E-07 60.8 10.7 132 226-394 165-297 (298)
144 PRK07670 RNA polymerase sigma 96.9 0.0083 1.8E-07 58.1 10.7 33 227-259 114-146 (251)
145 PRK07122 RNA polymerase sigma 96.9 0.018 3.9E-07 56.6 13.1 63 189-258 101-163 (264)
146 PRK06288 RNA polymerase sigma 96.9 0.011 2.4E-07 57.8 11.5 34 224-257 120-153 (268)
147 PRK12427 flagellar biosynthesi 96.7 0.0099 2.1E-07 57.3 9.9 60 189-258 78-137 (231)
148 PRK05658 RNA polymerase sigma 96.7 0.016 3.5E-07 63.6 12.3 131 226-394 471-604 (619)
149 TIGR02850 spore_sigG RNA polym 96.5 0.036 7.7E-07 53.9 11.9 62 189-258 95-156 (254)
150 TIGR02479 FliA_WhiG RNA polyme 96.4 0.036 7.8E-07 52.6 11.4 34 225-258 86-119 (224)
151 TIGR02980 SigBFG RNA polymeras 96.2 0.011 2.4E-07 56.0 6.3 31 227-257 95-125 (227)
152 TIGR02941 Sigma_B RNA polymera 96.2 0.0096 2.1E-07 57.7 6.0 31 227-257 121-151 (255)
153 PF04539 Sigma70_r3: Sigma-70 96.2 0.013 2.7E-07 46.6 5.6 35 225-259 7-41 (78)
154 PF12645 HTH_16: Helix-turn-he 96.1 0.023 4.9E-07 44.9 6.6 47 264-310 13-65 (65)
155 PRK06596 RNA polymerase factor 96.1 0.19 4.2E-06 49.9 14.8 30 365-394 247-276 (284)
156 PRK06986 fliA flagellar biosyn 96.0 0.066 1.4E-06 51.3 10.6 31 227-257 100-130 (236)
157 PF08281 Sigma70_r4_2: Sigma-7 95.8 0.003 6.5E-08 46.8 0.7 27 367-393 27-53 (54)
158 PRK05657 RNA polymerase sigma 95.8 0.056 1.2E-06 54.9 10.0 30 365-394 281-310 (325)
159 TIGR02885 spore_sigF RNA polym 95.5 0.067 1.5E-06 50.9 8.7 31 227-257 102-132 (231)
160 TIGR02394 rpoS_proteo RNA poly 95.4 0.11 2.3E-06 51.5 10.1 30 365-394 241-270 (285)
161 PRK08215 sporulation sigma fac 95.4 0.08 1.7E-06 51.5 8.8 32 227-258 128-159 (258)
162 TIGR02392 rpoH_proteo alternat 95.2 0.6 1.3E-05 45.9 14.5 30 365-394 235-264 (270)
163 PRK05572 sporulation sigma fac 94.2 0.29 6.2E-06 47.5 9.3 30 365-394 217-246 (252)
164 PF04545 Sigma70_r4: Sigma-70, 93.5 0.14 3.1E-06 37.4 4.4 30 364-393 18-47 (50)
165 PF01726 LexA_DNA_bind: LexA D 91.8 0.51 1.1E-05 37.2 5.8 44 348-391 6-51 (65)
166 PRK08583 RNA polymerase sigma 90.5 0.16 3.5E-06 49.2 2.2 30 365-394 220-249 (257)
167 PF13404 HTH_AsnC-type: AsnC-t 90.3 0.65 1.4E-05 33.5 4.7 34 356-390 8-41 (42)
168 PRK06930 positive control sigm 90.2 0.18 3.8E-06 46.8 2.1 29 366-394 130-158 (170)
169 PHA02547 55 RNA polymerase sig 89.7 1 2.2E-05 42.1 6.6 65 273-337 46-113 (179)
170 cd06171 Sigma70_r4 Sigma70, re 89.3 0.27 6E-06 34.5 2.1 29 365-393 25-53 (55)
171 PF04967 HTH_10: HTH DNA bindi 87.6 0.55 1.2E-05 35.8 2.8 31 363-393 20-50 (53)
172 TIGR03879 near_KaiC_dom probab 87.0 1.1 2.4E-05 36.4 4.4 26 365-390 31-56 (73)
173 smart00421 HTH_LUXR helix_turn 86.8 0.65 1.4E-05 33.3 2.8 29 367-395 19-47 (58)
174 PF08279 HTH_11: HTH domain; 86.5 1.8 4E-05 31.9 5.1 40 355-394 4-43 (55)
175 PRK00118 putative DNA-binding 85.7 0.45 9.7E-06 41.1 1.6 29 366-394 33-61 (104)
176 PF06971 Put_DNA-bind_N: Putat 85.7 2.5 5.4E-05 31.9 5.4 46 341-386 2-48 (50)
177 PF13412 HTH_24: Winged helix- 85.5 2.2 4.8E-05 30.7 5.0 35 356-391 8-42 (48)
178 PHA02591 hypothetical protein; 84.9 1.9 4.2E-05 35.5 4.8 35 353-389 48-82 (83)
179 cd06170 LuxR_C_like C-terminal 84.3 0.92 2E-05 32.7 2.6 28 367-394 16-43 (57)
180 PF01325 Fe_dep_repress: Iron 84.0 3.9 8.4E-05 31.6 6.0 41 351-391 7-47 (60)
181 PF10668 Phage_terminase: Phag 82.6 2.5 5.4E-05 33.1 4.4 29 361-389 17-45 (60)
182 PF13936 HTH_38: Helix-turn-he 82.2 2.3 5E-05 30.7 3.9 24 366-389 20-43 (44)
183 PRK04217 hypothetical protein; 82.2 1 2.2E-05 39.3 2.3 29 366-394 58-86 (110)
184 PF00196 GerE: Bacterial regul 81.4 0.98 2.1E-05 34.0 1.8 31 366-396 18-48 (58)
185 COG4941 Predicted RNA polymera 81.1 7.6 0.00017 40.4 8.5 126 267-394 8-164 (415)
186 PF00325 Crp: Bacterial regula 80.5 1.7 3.8E-05 29.8 2.5 25 367-391 3-27 (32)
187 PRK11179 DNA-binding transcrip 79.7 3.5 7.5E-05 37.1 5.1 34 357-391 15-48 (153)
188 PF02796 HTH_7: Helix-turn-hel 78.9 4.6 9.9E-05 29.1 4.5 21 367-387 22-42 (45)
189 PF09339 HTH_IclR: IclR helix- 78.4 3.7 8.1E-05 30.2 4.0 36 355-390 7-42 (52)
190 COG1522 Lrp Transcriptional re 78.0 4.1 8.9E-05 35.9 4.9 36 355-391 12-47 (154)
191 PRK13719 conjugal transfer tra 78.0 3 6.6E-05 40.5 4.3 34 364-397 156-189 (217)
192 PF13744 HTH_37: Helix-turn-he 76.9 5.2 0.00011 32.2 4.8 35 364-398 29-63 (80)
193 PF13384 HTH_23: Homeodomain-l 76.7 2.2 4.8E-05 30.7 2.4 26 366-391 17-42 (50)
194 PRK14082 hypothetical protein; 76.4 8 0.00017 30.8 5.5 55 264-320 9-63 (65)
195 TIGR00721 tfx DNA-binding prot 75.8 3.3 7.1E-05 37.5 3.7 30 365-394 20-49 (137)
196 PRK11169 leucine-responsive tr 73.9 4.9 0.00011 36.6 4.4 34 357-391 20-53 (164)
197 PRK03975 tfx putative transcri 73.6 3.9 8.4E-05 37.2 3.6 29 365-393 20-48 (141)
198 PF06056 Terminase_5: Putative 73.1 8.9 0.00019 29.6 5.0 26 366-391 13-38 (58)
199 COG3413 Predicted DNA binding 73.1 4.4 9.5E-05 38.5 4.0 33 362-394 174-206 (215)
200 smart00550 Zalpha Z-DNA-bindin 72.6 9.2 0.0002 30.0 5.1 35 357-391 12-47 (68)
201 PF13730 HTH_36: Helix-turn-he 72.5 4.6 9.9E-05 29.7 3.2 26 365-390 24-49 (55)
202 PF08280 HTH_Mga: M protein tr 71.8 7.3 0.00016 29.7 4.2 31 364-394 17-47 (59)
203 PF00356 LacI: Bacterial regul 71.5 3.9 8.5E-05 30.1 2.6 23 368-390 1-23 (46)
204 PF12728 HTH_17: Helix-turn-he 71.3 4.4 9.6E-05 29.4 2.8 23 368-390 3-25 (51)
205 PF12324 HTH_15: Helix-turn-he 71.0 11 0.00023 31.1 5.2 30 362-391 34-63 (77)
206 PF14502 HTH_41: Helix-turn-he 70.6 5.7 0.00012 29.8 3.2 34 364-397 4-39 (48)
207 PF04297 UPF0122: Putative hel 69.7 3.4 7.3E-05 35.6 2.2 31 364-394 31-61 (101)
208 smart00345 HTH_GNTR helix_turn 69.6 6 0.00013 28.7 3.3 28 365-392 19-46 (60)
209 PF13542 HTH_Tnp_ISL3: Helix-t 69.1 9.6 0.00021 27.6 4.3 23 367-389 28-50 (52)
210 smart00346 HTH_ICLR helix_turn 69.0 15 0.00033 29.3 5.8 38 354-391 8-45 (91)
211 TIGR01764 excise DNA binding d 68.8 5.9 0.00013 27.6 3.0 23 368-390 3-25 (49)
212 COG2197 CitB Response regulato 68.2 7.1 0.00015 37.1 4.3 34 364-397 161-194 (211)
213 PRK15411 rcsA colanic acid cap 68.2 7 0.00015 36.9 4.2 32 365-396 151-182 (207)
214 PRK10840 transcriptional regul 67.7 7.8 0.00017 35.8 4.4 32 365-396 164-195 (216)
215 PRK13870 transcriptional regul 67.1 4.3 9.4E-05 39.3 2.6 27 368-394 190-216 (234)
216 PF03444 HrcA_DNA-bdg: Winged 66.2 31 0.00067 28.5 7.0 43 350-392 6-49 (78)
217 PF00392 GntR: Bacterial regul 66.0 10 0.00022 28.9 4.0 27 365-391 23-49 (64)
218 cd04762 HTH_MerR-trunc Helix-T 64.9 7.9 0.00017 26.7 3.0 24 368-391 2-25 (49)
219 PF02001 DUF134: Protein of un 64.6 5.3 0.00011 34.7 2.4 29 366-394 57-85 (106)
220 PRK11475 DNA-binding transcrip 64.3 9.6 0.00021 36.2 4.3 32 365-396 148-179 (207)
221 TIGR03541 reg_near_HchA LuxR f 64.3 5.1 0.00011 38.5 2.5 29 367-395 187-215 (232)
222 PRK10188 DNA-binding transcrip 64.0 5.4 0.00012 38.7 2.6 29 367-395 195-223 (240)
223 smart00344 HTH_ASNC helix_turn 63.9 15 0.00031 30.6 4.9 34 357-391 9-42 (108)
224 PRK13239 alkylmercury lyase; P 63.2 16 0.00034 35.4 5.5 32 359-391 30-61 (206)
225 TIGR03020 EpsA transcriptional 63.0 5.5 0.00012 39.2 2.5 30 367-396 206-235 (247)
226 PF08220 HTH_DeoR: DeoR-like h 63.0 17 0.00038 27.4 4.7 31 359-390 8-38 (57)
227 COG4566 TtrR Response regulato 61.8 5.9 0.00013 38.0 2.3 22 368-389 159-180 (202)
228 TIGR03826 YvyF flagellar opero 61.1 20 0.00044 32.4 5.6 53 342-394 21-74 (137)
229 smart00420 HTH_DEOR helix_turn 60.9 24 0.00052 24.7 5.0 26 366-391 14-39 (53)
230 PF05225 HTH_psq: helix-turn-h 60.7 24 0.00052 25.6 4.9 38 351-390 3-40 (45)
231 COG2771 CsgD DNA-binding HTH d 60.3 9 0.0002 28.4 2.7 29 367-395 20-48 (65)
232 COG4367 Uncharacterized protei 60.1 25 0.00055 29.8 5.5 38 354-391 9-48 (97)
233 cd00092 HTH_CRP helix_turn_hel 60.1 25 0.00053 26.3 5.2 26 366-391 25-50 (67)
234 PRK09483 response regulator; P 59.8 14 0.0003 33.2 4.4 31 366-396 163-193 (217)
235 PF04967 HTH_10: HTH DNA bindi 59.6 40 0.00086 25.7 6.1 47 206-262 1-47 (53)
236 TIGR02844 spore_III_D sporulat 59.4 26 0.00056 28.9 5.4 25 365-389 18-42 (80)
237 PRK15201 fimbriae regulatory p 58.8 13 0.00029 35.4 4.1 32 365-396 147-178 (198)
238 smart00419 HTH_CRP helix_turn_ 58.4 14 0.0003 25.8 3.3 26 367-392 9-34 (48)
239 TIGR02337 HpaR homoprotocatech 58.4 47 0.001 28.1 7.2 66 318-391 2-67 (118)
240 PRK10403 transcriptional regul 58.3 16 0.00035 32.2 4.5 32 366-397 168-199 (215)
241 PRK15369 two component system 58.0 15 0.00032 32.1 4.2 30 367-396 165-194 (211)
242 PRK12423 LexA repressor; Provi 57.7 27 0.00059 32.9 6.1 33 360-392 19-52 (202)
243 PF09012 FeoC: FeoC like trans 57.2 21 0.00045 27.9 4.4 28 364-391 12-39 (69)
244 PF13551 HTH_29: Winged helix- 57.1 34 0.00073 28.0 6.0 43 348-390 61-111 (112)
245 PRK10100 DNA-binding transcrip 56.9 14 0.0003 35.3 4.1 31 366-396 170-200 (216)
246 TIGR00373 conserved hypothetic 56.4 19 0.0004 33.1 4.6 35 356-391 19-53 (158)
247 PF08784 RPA_C: Replication pr 56.2 21 0.00045 29.8 4.6 42 349-390 48-89 (102)
248 PRK09935 transcriptional regul 55.8 17 0.00038 32.2 4.3 31 367-397 165-195 (210)
249 TIGR00498 lexA SOS regulatory 55.7 27 0.00058 32.5 5.7 42 350-391 8-51 (199)
250 PRK10046 dpiA two-component re 55.1 21 0.00045 33.4 4.8 26 366-391 177-202 (225)
251 cd07377 WHTH_GntR Winged helix 54.9 29 0.00062 25.5 4.7 25 367-391 26-50 (66)
252 PRK00423 tfb transcription ini 54.8 1.6E+02 0.0034 29.8 11.4 27 368-394 278-304 (310)
253 cd04761 HTH_MerR-SF Helix-Turn 54.6 15 0.00033 25.9 3.0 24 368-391 2-25 (49)
254 PF13518 HTH_28: Helix-turn-he 53.3 17 0.00037 25.9 3.2 24 368-391 14-37 (52)
255 PF13309 HTH_22: HTH domain 53.2 54 0.0012 25.5 6.1 34 354-387 27-63 (64)
256 PF01978 TrmB: Sugar-specific 53.1 16 0.00034 28.1 3.1 26 366-391 22-47 (68)
257 TIGR01610 phage_O_Nterm phage 53.0 37 0.00079 28.3 5.5 28 364-391 45-72 (95)
258 PRK15418 transcriptional regul 52.4 12 0.00025 38.2 2.8 35 365-399 28-66 (318)
259 PF12802 MarR_2: MarR family; 52.0 38 0.00082 25.0 5.0 35 357-391 11-46 (62)
260 PRK09390 fixJ response regulat 52.0 25 0.00053 30.5 4.5 30 367-396 157-186 (202)
261 COG1318 Predicted transcriptio 51.3 26 0.00057 33.1 4.7 23 368-390 63-85 (182)
262 PF00376 MerR: MerR family reg 51.2 18 0.0004 25.4 2.9 23 368-390 1-23 (38)
263 PRK06266 transcription initiat 51.2 28 0.00061 32.6 5.0 34 357-391 28-61 (178)
264 PRK15320 transcriptional activ 50.4 21 0.00046 34.7 4.1 32 365-396 178-209 (251)
265 COG1342 Predicted DNA-binding 50.1 13 0.00027 32.0 2.2 29 366-394 49-77 (99)
266 PF04218 CENP-B_N: CENP-B N-te 50.0 16 0.00034 27.4 2.6 25 365-389 21-45 (53)
267 smart00354 HTH_LACI helix_turn 49.7 16 0.00034 28.6 2.6 22 367-388 1-22 (70)
268 PRK09802 DNA-binding transcrip 48.6 37 0.00081 33.6 5.7 38 352-390 18-55 (269)
269 PF13411 MerR_1: MerR HTH fami 48.6 20 0.00043 27.3 3.0 24 368-391 2-25 (69)
270 KOG1597 Transcription initiati 48.3 3E+02 0.0065 28.3 11.9 127 232-390 158-284 (308)
271 PRK10079 phosphonate metabolis 47.8 29 0.00062 33.2 4.6 39 351-389 19-58 (241)
272 PRK10430 DNA-binding transcrip 47.1 21 0.00044 33.7 3.5 30 363-392 175-204 (239)
273 PRK10651 transcriptional regul 47.0 30 0.00064 30.6 4.3 31 367-397 171-201 (216)
274 cd00569 HTH_Hin_like Helix-tur 46.9 18 0.0004 22.2 2.2 19 368-386 23-41 (42)
275 PF13545 HTH_Crp_2: Crp-like h 46.6 20 0.00043 27.7 2.8 24 368-391 30-53 (76)
276 PF01381 HTH_3: Helix-turn-hel 46.2 25 0.00053 25.5 3.1 25 365-389 8-32 (55)
277 COG2390 DeoR Transcriptional r 45.7 42 0.00091 34.5 5.7 28 365-392 25-52 (321)
278 PF02082 Rrf2: Transcriptional 45.4 36 0.00078 27.3 4.2 27 366-392 25-51 (83)
279 PRK03902 manganese transport t 45.3 57 0.0012 28.7 5.8 39 353-391 9-47 (142)
280 PRK10434 srlR DNA-bindng trans 45.2 41 0.00089 32.9 5.3 37 353-390 7-43 (256)
281 COG2524 Predicted transcriptio 44.8 37 0.0008 34.2 4.9 42 350-391 8-50 (294)
282 PF07374 DUF1492: Protein of u 44.4 26 0.00056 29.5 3.3 26 367-392 72-97 (100)
283 PRK11161 fumarate/nitrate redu 44.3 1.4E+02 0.0029 27.9 8.6 25 367-391 185-209 (235)
284 PF04703 FaeA: FaeA-like prote 44.2 36 0.00078 26.7 3.8 28 364-391 13-40 (62)
285 PF09862 DUF2089: Protein of u 43.9 19 0.00042 31.6 2.5 29 368-396 51-79 (113)
286 PF13551 HTH_29: Winged helix- 43.7 24 0.00053 28.9 3.1 24 368-391 14-37 (112)
287 smart00531 TFIIE Transcription 43.4 34 0.00073 30.8 4.1 33 359-392 9-41 (147)
288 PF12840 HTH_20: Helix-turn-he 43.0 56 0.0012 24.6 4.7 28 364-391 22-49 (61)
289 PF01022 HTH_5: Bacterial regu 42.9 36 0.00078 24.4 3.4 27 365-391 14-40 (47)
290 PF13936 HTH_38: Helix-turn-he 42.9 36 0.00078 24.4 3.4 41 204-261 3-43 (44)
291 cd01104 HTH_MlrA-CarA Helix-Tu 42.2 30 0.00065 26.2 3.1 23 368-390 2-24 (68)
292 COG2188 PhnF Transcriptional r 42.2 34 0.00074 32.9 4.2 29 361-389 26-54 (236)
293 PRK05472 redox-sensing transcr 42.1 62 0.0013 30.5 5.9 50 341-390 6-56 (213)
294 PF01710 HTH_Tnp_IS630: Transp 42.0 53 0.0011 28.4 5.0 29 364-392 69-97 (119)
295 COG0856 Orotate phosphoribosyl 42.0 41 0.00089 32.1 4.5 34 364-397 16-49 (203)
296 PF13443 HTH_26: Cro/C1-type H 41.9 19 0.00041 26.9 1.9 32 365-396 9-40 (63)
297 TIGR02404 trehalos_R_Bsub treh 41.8 36 0.00078 32.3 4.2 27 363-389 21-47 (233)
298 PHA02943 hypothetical protein; 41.7 74 0.0016 29.7 6.0 24 367-390 25-48 (165)
299 TIGR02431 pcaR_pcaU beta-ketoa 41.5 64 0.0014 31.0 6.0 35 357-391 15-49 (248)
300 PF01371 Trp_repressor: Trp re 41.5 47 0.001 27.8 4.3 39 345-386 31-69 (87)
301 TIGR03070 couple_hipB transcri 41.4 52 0.0011 23.5 4.2 25 365-389 14-38 (58)
302 cd00090 HTH_ARSR Arsenical Res 40.9 68 0.0015 23.5 4.9 25 367-391 21-45 (78)
303 PRK10163 DNA-binding transcrip 40.8 55 0.0012 32.1 5.5 38 354-391 28-65 (271)
304 PRK14101 bifunctional glucokin 40.6 2.7E+02 0.0059 30.9 11.4 22 368-389 376-397 (638)
305 smart00418 HTH_ARSR helix_turn 40.5 41 0.00089 24.0 3.6 27 365-391 9-35 (66)
306 PRK11511 DNA-binding transcrip 40.5 77 0.0017 27.5 5.8 39 352-390 10-49 (127)
307 PRK10411 DNA-binding transcrip 40.4 62 0.0013 31.4 5.7 36 355-391 8-43 (240)
308 PRK14999 histidine utilization 40.4 45 0.00096 31.9 4.7 28 363-390 33-60 (241)
309 PF00382 TFIIB: Transcription 40.4 44 0.00096 25.9 3.9 20 364-383 52-71 (71)
310 COG1476 Predicted transcriptio 40.3 45 0.00097 26.8 3.8 23 366-388 14-36 (68)
311 COG1725 Predicted transcriptio 40.2 27 0.00059 31.2 2.9 32 359-390 28-59 (125)
312 COG2344 AT-rich DNA-binding pr 40.1 63 0.0014 31.2 5.5 49 340-388 5-54 (211)
313 PRK09958 DNA-binding transcrip 39.8 43 0.00094 29.7 4.3 31 366-396 158-188 (204)
314 PRK13558 bacterio-opsin activa 39.7 21 0.00046 39.0 2.6 31 364-394 628-658 (665)
315 COG3413 Predicted DNA binding 39.7 1E+02 0.0023 29.1 7.0 57 205-274 155-211 (215)
316 PRK00215 LexA repressor; Valid 39.7 83 0.0018 29.3 6.3 31 361-391 18-49 (205)
317 TIGR02531 yecD_yerC TrpR-relat 39.6 31 0.00067 28.8 3.0 21 367-387 51-71 (88)
318 COG3355 Predicted transcriptio 39.3 56 0.0012 29.3 4.7 27 364-390 40-66 (126)
319 COG1321 TroR Mn-dependent tran 39.0 74 0.0016 29.1 5.6 42 351-392 9-50 (154)
320 TIGR01636 phage_rinA phage tra 39.0 35 0.00075 30.2 3.4 25 367-391 101-125 (134)
321 PHA01976 helix-turn-helix prot 38.8 35 0.00076 25.8 3.0 26 364-389 13-38 (67)
322 PRK09480 slmA division inhibit 38.6 2.8E+02 0.006 24.7 9.4 72 233-304 25-96 (194)
323 PRK09480 slmA division inhibit 38.3 87 0.0019 28.0 6.1 37 349-385 11-49 (194)
324 smart00422 HTH_MERR helix_turn 38.2 36 0.00078 25.8 3.0 22 368-389 2-23 (70)
325 PHA00675 hypothetical protein 38.0 75 0.0016 26.3 4.8 22 368-389 41-62 (78)
326 TIGR02325 C_P_lyase_phnF phosp 37.9 50 0.0011 31.1 4.6 27 364-390 30-56 (238)
327 PF13730 HTH_36: Helix-turn-he 37.7 1.1E+02 0.0024 22.1 5.5 25 235-259 22-46 (55)
328 PRK10681 DNA-binding transcrip 37.5 74 0.0016 31.0 5.8 36 355-391 11-46 (252)
329 TIGR03697 NtcA_cyano global ni 37.1 34 0.00073 30.8 3.1 25 367-391 144-168 (193)
330 cd04764 HTH_MlrA-like_sg1 Heli 37.0 40 0.00088 25.7 3.1 23 368-390 2-24 (67)
331 PF02796 HTH_7: Helix-turn-hel 37.0 50 0.0011 23.6 3.4 41 203-260 3-43 (45)
332 cd06445 ATase The DNA repair p 36.7 59 0.0013 26.1 4.2 38 353-391 5-44 (79)
333 PRK11512 DNA-binding transcrip 36.6 2E+02 0.0043 25.2 7.9 26 366-391 54-79 (144)
334 PRK03573 transcriptional regul 36.3 1.7E+02 0.0036 25.5 7.4 28 364-391 44-71 (144)
335 PRK10219 DNA-binding transcrip 36.2 1E+02 0.0022 25.5 5.7 37 353-389 7-44 (107)
336 TIGR00122 birA_repr_reg BirA b 36.1 44 0.00096 25.7 3.2 26 366-391 13-38 (69)
337 PRK10360 DNA-binding transcrip 36.0 34 0.00075 30.1 3.0 30 367-396 153-182 (196)
338 PF08535 KorB: KorB domain; I 35.9 35 0.00076 28.1 2.8 25 367-391 4-28 (93)
339 PF13560 HTH_31: Helix-turn-he 35.8 64 0.0014 24.4 4.0 26 366-391 14-39 (64)
340 TIGR02018 his_ut_repres histid 35.4 62 0.0014 30.6 4.8 27 363-389 22-48 (230)
341 PRK04841 transcriptional regul 35.3 32 0.0007 38.8 3.2 30 367-396 854-883 (903)
342 TIGR03337 phnR transcriptional 35.1 47 0.001 31.2 3.9 28 363-390 22-49 (231)
343 PRK09764 DNA-binding transcrip 34.6 63 0.0014 30.9 4.7 27 364-390 27-53 (240)
344 PRK11014 transcriptional repre 34.6 42 0.00092 29.6 3.3 28 364-391 23-50 (141)
345 COG1349 GlpR Transcriptional r 34.5 60 0.0013 31.8 4.6 35 354-389 8-42 (253)
346 COG1675 TFA1 Transcription ini 34.2 63 0.0014 30.5 4.5 36 355-391 22-57 (176)
347 PRK09726 antitoxin HipB; Provi 34.2 75 0.0016 25.8 4.4 24 365-388 24-47 (88)
348 PRK06424 transcription factor; 33.8 96 0.0021 28.2 5.5 39 350-389 82-120 (144)
349 PRK11569 transcriptional repre 33.5 83 0.0018 30.9 5.5 37 355-391 32-68 (274)
350 TIGR01321 TrpR trp operon repr 33.5 90 0.002 26.6 4.9 24 365-388 54-77 (94)
351 PF01726 LexA_DNA_bind: LexA D 33.2 86 0.0019 24.5 4.4 26 232-257 19-45 (65)
352 PF11740 KfrA_N: Plasmid repli 33.1 1.2E+02 0.0026 25.7 5.8 42 351-392 4-46 (120)
353 smart00342 HTH_ARAC helix_turn 32.9 94 0.002 23.3 4.6 58 238-298 1-60 (84)
354 TIGR02702 SufR_cyano iron-sulf 32.9 80 0.0017 29.6 5.0 26 366-391 15-40 (203)
355 PF01035 DNA_binding_1: 6-O-me 32.5 55 0.0012 26.8 3.4 39 351-390 5-45 (85)
356 PF06970 RepA_N: Replication i 32.5 47 0.001 27.0 2.9 21 368-388 54-74 (76)
357 PRK10512 selenocysteinyl-tRNA- 32.5 6.6E+02 0.014 28.0 12.8 27 365-391 505-531 (614)
358 cd04763 HTH_MlrA-like Helix-Tu 32.1 51 0.0011 25.2 3.0 22 368-389 2-23 (68)
359 PF11176 DUF2962: Protein of u 31.8 1.7E+02 0.0037 26.8 6.8 91 191-314 49-143 (155)
360 smart00342 HTH_ARAC helix_turn 31.8 64 0.0014 24.3 3.5 24 367-390 2-25 (84)
361 PRK13918 CRP/FNR family transc 31.6 41 0.0009 30.5 2.8 25 367-391 150-174 (202)
362 PF10078 DUF2316: Uncharacteri 31.6 91 0.002 26.3 4.5 25 366-390 23-47 (89)
363 PRK13509 transcriptional repre 31.5 98 0.0021 30.2 5.5 34 356-390 10-43 (251)
364 PF02002 TFIIE_alpha: TFIIE al 31.2 68 0.0015 26.8 3.8 26 366-391 27-52 (105)
365 PRK09834 DNA-binding transcrip 30.9 1.1E+02 0.0023 29.9 5.7 34 358-391 18-51 (263)
366 PF13404 HTH_AsnC-type: AsnC-t 30.8 1.2E+02 0.0026 21.7 4.5 23 239-261 18-40 (42)
367 PF02954 HTH_8: Bacterial regu 30.8 64 0.0014 22.8 3.1 22 368-389 20-41 (42)
368 TIGR00180 parB_part ParB-like 30.7 1.2E+02 0.0025 28.2 5.7 25 367-391 121-145 (187)
369 PF00440 TetR_N: Bacterial reg 30.7 1.3E+02 0.0029 21.3 4.8 31 356-386 5-36 (47)
370 TIGR02607 antidote_HigA addict 30.3 57 0.0012 25.3 3.0 25 365-389 17-41 (78)
371 smart00351 PAX Paired Box doma 29.8 50 0.0011 28.9 2.9 26 367-392 34-59 (125)
372 PRK09954 putative kinase; Prov 29.5 90 0.002 31.6 5.1 35 356-391 8-42 (362)
373 PRK04984 fatty acid metabolism 29.4 60 0.0013 30.8 3.6 28 364-391 29-56 (239)
374 cd01392 HTH_LacI Helix-turn-he 29.3 40 0.00086 24.1 1.8 19 371-389 2-20 (52)
375 PRK10225 DNA-binding transcrip 28.8 95 0.0021 29.8 4.9 27 365-391 32-58 (257)
376 PRK00901 methylated-DNA--prote 28.7 1.1E+02 0.0023 28.2 4.9 66 328-396 51-120 (155)
377 PF13463 HTH_27: Winged helix 28.5 1.1E+02 0.0024 22.8 4.3 29 363-391 15-43 (68)
378 TIGR02325 C_P_lyase_phnF phosp 28.5 1.2E+02 0.0025 28.6 5.4 43 213-272 16-59 (238)
379 TIGR00738 rrf2_super rrf2 fami 28.5 1.1E+02 0.0024 26.2 4.8 26 366-391 25-50 (132)
380 PF04760 IF2_N: Translation in 28.5 40 0.00088 24.9 1.8 21 367-387 4-24 (54)
381 PRK10072 putative transcriptio 28.4 62 0.0013 27.5 3.1 26 366-391 46-71 (96)
382 TIGR02944 suf_reg_Xantho FeS a 28.4 63 0.0014 27.9 3.3 28 364-391 23-50 (130)
383 PRK11402 DNA-binding transcrip 28.4 61 0.0013 30.9 3.5 27 363-389 30-56 (241)
384 PF04218 CENP-B_N: CENP-B N-te 28.2 69 0.0015 23.9 3.0 42 204-262 5-46 (53)
385 PRK09975 DNA-binding transcrip 28.2 1.4E+02 0.003 27.4 5.7 38 348-385 11-50 (213)
386 smart00530 HTH_XRE Helix-turn- 28.2 79 0.0017 21.0 3.2 24 365-388 9-32 (56)
387 PRK11753 DNA-binding transcrip 27.8 56 0.0012 29.8 3.0 25 367-391 169-193 (211)
388 PRK09464 pdhR transcriptional 27.5 61 0.0013 31.1 3.3 27 365-391 33-59 (254)
389 COG2522 Predicted transcriptio 27.4 1.6E+02 0.0034 26.2 5.5 26 366-391 22-47 (119)
390 TIGR02787 codY_Gpos GTP-sensin 27.4 1.2E+02 0.0025 30.3 5.2 41 350-391 182-223 (251)
391 PRK10421 DNA-binding transcrip 27.3 66 0.0014 30.9 3.5 27 365-391 25-51 (253)
392 PF01399 PCI: PCI domain; Int 27.3 1.6E+02 0.0036 23.4 5.4 36 355-390 49-84 (105)
393 PF01418 HTH_6: Helix-turn-hel 27.2 1.5E+02 0.0032 23.5 5.0 26 364-389 32-57 (77)
394 PRK10906 DNA-binding transcrip 27.2 1E+02 0.0022 30.2 4.8 34 355-389 9-42 (252)
395 PRK00430 fis global DNA-bindin 27.1 3.8E+02 0.0082 22.5 8.2 23 368-390 70-92 (95)
396 PF01047 MarR: MarR family; I 26.8 1.4E+02 0.003 21.8 4.5 25 367-391 18-42 (59)
397 COG1497 Predicted transcriptio 26.8 1E+02 0.0023 30.7 4.7 31 360-390 19-49 (260)
398 PRK15481 transcriptional regul 26.8 90 0.0019 32.3 4.6 30 361-390 24-53 (431)
399 PF00165 HTH_AraC: Bacterial r 26.7 93 0.002 21.5 3.3 27 364-390 6-32 (42)
400 PRK11511 DNA-binding transcrip 26.6 2.9E+02 0.0064 23.8 7.2 35 228-262 15-49 (127)
401 PF05138 PaaA_PaaC: Phenylacet 26.4 1.4E+02 0.0031 29.6 5.7 106 207-332 11-117 (263)
402 COG2188 PhnF Transcriptional r 26.2 1.3E+02 0.0028 28.9 5.3 44 212-272 14-58 (236)
403 COG1414 IclR Transcriptional r 26.2 1.4E+02 0.003 29.1 5.5 35 357-391 10-44 (246)
404 COG1405 SUA7 Transcription ini 26.1 1.3E+02 0.0027 30.5 5.3 27 365-391 250-276 (285)
405 PF13022 HTH_Tnp_1_2: Helix-tu 26.1 1.2E+02 0.0026 27.8 4.7 26 363-388 31-56 (142)
406 PRK03837 transcriptional regul 26.0 69 0.0015 30.3 3.3 27 365-391 36-62 (241)
407 PF13556 HTH_30: PucR C-termin 25.9 56 0.0012 24.7 2.2 30 368-397 14-43 (59)
408 PHA00542 putative Cro-like pro 25.9 72 0.0016 25.9 3.0 26 365-390 30-55 (82)
409 PRK10402 DNA-binding transcrip 25.8 2.1E+02 0.0046 26.8 6.6 25 367-391 170-194 (226)
410 PRK15044 transcriptional regul 25.8 2.8E+02 0.006 28.4 7.7 60 193-261 172-231 (295)
411 PF00392 GntR: Bacterial regul 25.6 2E+02 0.0044 21.6 5.3 35 213-257 8-43 (64)
412 PF14493 HTH_40: Helix-turn-he 25.4 1.2E+02 0.0025 24.9 4.2 26 366-391 13-38 (91)
413 TIGR02404 trehalos_R_Bsub treh 25.2 1.4E+02 0.0031 28.2 5.3 43 213-272 8-51 (233)
414 PRK15090 DNA-binding transcrip 25.1 1.3E+02 0.0028 29.1 5.1 27 365-391 27-53 (257)
415 PRK09990 DNA-binding transcrip 24.9 1E+02 0.0022 29.5 4.3 28 364-391 29-56 (251)
416 PRK09391 fixK transcriptional 24.9 2.2E+02 0.0049 26.8 6.6 25 367-391 180-204 (230)
417 COG0350 Ada Methylated DNA-pro 24.9 1.9E+02 0.004 26.9 5.8 47 348-397 88-136 (168)
418 PRK11402 DNA-binding transcrip 24.7 1.5E+02 0.0032 28.3 5.4 36 213-258 17-53 (241)
419 COG2944 Predicted transcriptio 24.6 1.1E+02 0.0023 26.7 3.9 26 366-391 57-82 (104)
420 smart00753 PAM PCI/PINT associ 24.6 2E+02 0.0044 22.7 5.4 37 354-390 12-48 (88)
421 smart00088 PINT motif in prote 24.6 2E+02 0.0044 22.7 5.4 37 354-390 12-48 (88)
422 PRK09639 RNA polymerase sigma 24.5 2.9E+02 0.0063 24.1 6.9 35 238-272 127-161 (166)
423 COG2186 FadR Transcriptional r 24.4 77 0.0017 30.7 3.4 29 362-390 30-58 (241)
424 PRK15431 ferrous iron transpor 24.3 1.9E+02 0.0042 23.9 5.1 36 354-390 5-40 (78)
425 COG1476 Predicted transcriptio 24.2 1.2E+02 0.0027 24.3 3.9 50 239-298 15-64 (68)
426 PF08765 Mor: Mor transcriptio 24.1 1.8E+02 0.0039 24.7 5.2 26 367-392 73-98 (108)
427 PRK11534 DNA-binding transcrip 24.1 1.2E+02 0.0025 28.5 4.4 28 364-391 28-55 (224)
428 TIGR02612 mob_myst_A mobile my 23.8 2.8E+02 0.0062 25.3 6.7 24 366-389 38-61 (150)
429 TIGR02812 fadR_gamma fatty aci 23.7 80 0.0017 29.9 3.3 27 365-391 29-55 (235)
430 PF09824 ArsR: ArsR transcript 23.7 34 0.00074 31.8 0.7 30 95-126 34-64 (160)
431 PF13613 HTH_Tnp_4: Helix-turn 23.7 1.3E+02 0.0029 22.2 3.8 34 359-392 12-45 (53)
432 PF07022 Phage_CI_repr: Bacter 23.6 1.8E+02 0.0039 22.4 4.7 52 229-281 4-56 (66)
433 PF05043 Mga: Mga helix-turn-h 23.6 48 0.001 26.6 1.5 31 364-394 28-58 (87)
434 PRK04217 hypothetical protein; 23.4 3.7E+02 0.0081 23.4 7.1 49 204-270 41-90 (110)
435 PRK09652 RNA polymerase sigma 23.4 3.3E+02 0.0071 23.8 7.0 31 240-270 146-176 (182)
436 COG2739 Uncharacterized protei 23.0 93 0.002 27.0 3.2 27 366-392 33-59 (105)
437 PF06784 UPF0240: Uncharacteri 22.8 1.5E+02 0.0033 27.9 4.9 39 353-391 120-161 (179)
438 PRK11050 manganese transport r 22.7 2.2E+02 0.0048 25.6 5.8 29 364-392 49-77 (152)
439 PRK12527 RNA polymerase sigma 22.6 3.4E+02 0.0074 23.6 6.9 35 239-273 122-156 (159)
440 PRK09685 DNA-binding transcrip 22.5 7.1E+02 0.015 24.1 10.5 33 288-321 214-246 (302)
441 PRK11924 RNA polymerase sigma 22.5 3.2E+02 0.0069 23.8 6.8 34 239-272 142-175 (179)
442 PRK14999 histidine utilization 22.5 1.8E+02 0.004 27.7 5.6 44 212-272 19-63 (241)
443 TIGR02010 IscR iron-sulfur clu 22.5 94 0.002 27.3 3.3 27 365-391 24-50 (135)
444 PRK09647 RNA polymerase sigma 22.3 3E+02 0.0065 25.7 6.8 36 240-275 156-191 (203)
445 cd00093 HTH_XRE Helix-turn-hel 22.3 99 0.0021 20.6 2.8 24 366-389 12-35 (58)
446 PRK01381 Trp operon repressor; 22.3 81 0.0018 27.2 2.7 21 366-386 55-75 (99)
447 PF12793 SgrR_N: Sugar transpo 22.2 1.5E+02 0.0032 25.8 4.4 26 366-391 19-44 (115)
448 TIGR02018 his_ut_repres histid 22.1 1.8E+02 0.0038 27.5 5.3 43 213-272 9-52 (230)
449 PF00046 Homeobox: Homeobox do 22.1 2E+02 0.0043 20.9 4.5 21 368-388 29-49 (57)
450 PRK11523 DNA-binding transcrip 22.0 1.4E+02 0.003 28.7 4.7 27 365-391 31-57 (253)
451 COG1356 tfx Transcriptional re 22.0 62 0.0014 29.3 2.0 27 365-391 22-48 (143)
452 COG1654 BirA Biotin operon rep 22.0 1E+02 0.0023 25.3 3.2 29 363-391 16-44 (79)
453 PRK10219 DNA-binding transcrip 22.0 1.7E+02 0.0036 24.2 4.6 34 228-261 11-44 (107)
454 PF04545 Sigma70_r4: Sigma-70, 22.0 3E+02 0.0065 19.6 6.1 24 238-261 20-43 (50)
455 COG3415 Transposase and inacti 21.7 97 0.0021 28.1 3.2 31 364-394 19-49 (138)
456 PRK11552 putative DNA-binding 21.7 2.5E+02 0.0055 26.5 6.3 35 351-385 17-51 (225)
457 PRK04424 fatty acid biosynthes 21.7 1.6E+02 0.0034 27.5 4.8 33 355-388 11-43 (185)
458 cd04766 HTH_HspR Helix-Turn-He 21.6 97 0.0021 25.3 3.0 22 368-389 3-24 (91)
459 PRK12519 RNA polymerase sigma 21.6 2.8E+02 0.0061 25.0 6.4 35 239-273 158-192 (194)
460 PF08006 DUF1700: Protein of u 21.5 2.8E+02 0.006 25.5 6.3 60 326-389 3-63 (181)
461 COG2345 Predicted transcriptio 21.3 1.7E+02 0.0037 28.6 5.0 26 365-390 24-49 (218)
462 COG4565 CitB Response regulato 21.2 1.7E+02 0.0036 28.8 4.8 38 354-391 161-198 (224)
463 TIGR00270 conserved hypothetic 21.2 2.5E+02 0.0055 25.7 5.9 25 364-388 80-104 (154)
464 cd00131 PAX Paired Box domain 21.1 2.2E+02 0.0047 25.1 5.3 30 367-396 34-63 (128)
465 PF05930 Phage_AlpA: Prophage 21.0 1E+02 0.0022 22.6 2.7 25 367-391 4-28 (51)
466 TIGR03338 phnR_burk phosphonat 21.0 97 0.0021 28.7 3.2 28 364-391 32-59 (212)
467 PF04297 UPF0122: Putative hel 20.9 5.2E+02 0.011 22.2 7.4 41 238-279 33-73 (101)
468 PF07900 DUF1670: Protein of u 20.8 2.2E+02 0.0048 27.9 5.6 39 353-391 92-130 (220)
469 PRK08359 transcription factor; 20.7 2.2E+02 0.0047 26.9 5.4 24 364-387 96-119 (176)
470 PRK09392 ftrB transcriptional 20.3 88 0.0019 29.3 2.8 24 368-391 175-198 (236)
471 PRK11414 colanic acid/biofilm 20.3 1.4E+02 0.003 28.0 4.1 28 364-391 32-59 (221)
No 1
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=100.00 E-value=1.1e-40 Score=342.73 Aligned_cols=215 Identities=37% Similarity=0.645 Sum_probs=201.1
Q ss_pred hhHHHHHHhhcccCCCCHHHHHHHHHHHHccCc--------------------chhHHHHHHHhhCCCCchHHHHHHhc-
Q 014852 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS--------------------LDDHKLRLKERLGCEPSMEQLAASLR- 249 (417)
Q Consensus 191 ~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~--------------------l~~~~~~l~~~lg~eps~~e~A~~~~- 249 (417)
|.++.||.+|++.|+||++||++|.++++.+.. |++.+.+|++.+|++|+..+||.++|
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 799999999999999999999999999999988 88899999999999999999996555
Q ss_pred ---------------------CChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhh
Q 014852 250 ---------------------ISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEK 308 (417)
Q Consensus 250 ---------------------~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAier 308 (417)
++.++|...+..|..|+++||.+|+++|+++|++|.+++.+++||+|||++|||+|+++
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 45555556667788999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHH
Q 014852 309 FDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNAT 387 (417)
Q Consensus 309 FD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL 387 (417)
|||.+|++|+||++||||+.|.+++.++.+.+++|.++.+.+++++++...|. .+||.||..|||+.|||++++|+.++
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 68999999999999999999999999
Q ss_pred HHhCcccccccccCCCCC
Q 014852 388 EAIGKVFSLDREAFPSLN 405 (417)
Q Consensus 388 ~rark~LSLD~~~~~s~~ 405 (417)
..++..+|||.++..+.+
T Consensus 300 ~~~~~~~SLd~~vg~~~d 317 (415)
T PRK07598 300 LRVPRSVSLETKVGKDKD 317 (415)
T ss_pred HHccCCcccccccCCCcc
Confidence 999999999998875544
No 2
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=3e-39 Score=328.92 Aligned_cols=215 Identities=37% Similarity=0.590 Sum_probs=206.7
Q ss_pred hhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHH
Q 014852 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (417)
Q Consensus 191 ~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LI 270 (417)
+.+..||++|+++|+||++||.+|+++++.|..+++.+..|.+.+|++|+..+||..+|++..+|+.++..|..|++.||
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 014852 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL 350 (417)
Q Consensus 271 e~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~ 350 (417)
.+|+++|+++|++|.+++.+++||+|||+||||+++++||+.+|++|+|||+||||+.|.++|+++.+.+++|.++.+..
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-HcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCCC
Q 014852 351 GLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLN 405 (417)
Q Consensus 351 ~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~s~~ 405 (417)
.++.++...|. .+||.||.+|||+.||+++++|..++..+...+|||.+...+.+
T Consensus 223 ~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~ 278 (373)
T PRK07406 223 SRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEED 278 (373)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCc
Confidence 99999999995 58999999999999999999999998888889999999865443
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=1.1e-38 Score=315.14 Aligned_cols=211 Identities=39% Similarity=0.660 Sum_probs=203.0
Q ss_pred hHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHH
Q 014852 192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM 271 (417)
Q Consensus 192 ~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe 271 (417)
.+..||++|...|+||++||.+|+++++.|..+++.+..|.+.+|++|+..+||++++++..+|...+..|..|++.||.
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 014852 272 SNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG 351 (417)
Q Consensus 272 ~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~ 351 (417)
+|+++|+++|++|.+++.+++||+||||+|||+|+++|||.+|++|+||++||||+.|.+++.++.+.+++|.++.....
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 HHHHHHHHH-HHcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCC
Q 014852 352 LIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFP 402 (417)
Q Consensus 352 kI~~a~~~L-~e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~ 402 (417)
+++++...+ ..+|+.||.+|||+.||+++++|..++......+|||.+...
T Consensus 162 ~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~ 213 (298)
T TIGR02997 162 KIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGD 213 (298)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCC
Confidence 999998888 458999999999999999999999999999899999998754
No 4
>PRK05949 RNA polymerase sigma factor; Validated
Probab=100.00 E-value=1.4e-38 Score=319.14 Aligned_cols=216 Identities=33% Similarity=0.608 Sum_probs=207.3
Q ss_pred hhhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHH
Q 014852 190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKL 269 (417)
Q Consensus 190 ~~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~L 269 (417)
.|.+..|+++|+..|+||++||.+|+++++.|..+++.+..|...+|++|+..+||..+++++.+|...+..|..|++.|
T Consensus 17 ~d~~~~yl~~i~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~~L 96 (327)
T PRK05949 17 ADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQKM 96 (327)
T ss_pred CCHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHHHH
Confidence 37888999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHH
Q 014852 270 VMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHER 349 (417)
Q Consensus 270 Ie~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~ 349 (417)
|.+|+++|+++|++|.+++.+++||+||||+|||+++++||+++|++|+|||+||||+.|.+++.++.+.+|+|.++.+.
T Consensus 97 i~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~~~~~~ 176 (327)
T PRK05949 97 IEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK 176 (327)
T ss_pred HHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHH-HHcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCCC
Q 014852 350 LGLIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLN 405 (417)
Q Consensus 350 ~~kI~~a~~~L-~e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~s~~ 405 (417)
++.++++...+ ..+||+||.+|||+.||+++++|..++..+...+|||.+..++.+
T Consensus 177 ~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~ 233 (327)
T PRK05949 177 LNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQD 233 (327)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCC
Confidence 99999999998 568999999999999999999999999999999999998765433
No 5
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=1.9e-37 Score=309.53 Aligned_cols=214 Identities=37% Similarity=0.642 Sum_probs=205.4
Q ss_pred hhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHH
Q 014852 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (417)
Q Consensus 191 ~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LI 270 (417)
+.+..||++|+..|+||++||.+|+++++.|..+++.+..|.+.+|++|+..+||.++++++.+|...+..|..|++.||
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 67889999999999999999999999999999999999999999999999999999999999999999999989999999
Q ss_pred HHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHH
Q 014852 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL 350 (417)
Q Consensus 271 e~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~ 350 (417)
..|+++|+++|++|.+++.+++||+||||+|||+++++||+.+|++|+|||+||||+.|.++|.++.+.+|+|.++....
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-HcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCC
Q 014852 351 GLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSL 404 (417)
Q Consensus 351 ~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~s~ 404 (417)
.+++++...+. .+|+.||.+|||+.+|++.++|..++......+|||.+..++.
T Consensus 168 ~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~ 222 (317)
T PRK07405 168 NKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQ 222 (317)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCC
Confidence 99999999984 5899999999999999999999999999889999998875443
No 6
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=100.00 E-value=7.8e-36 Score=313.42 Aligned_cols=203 Identities=34% Similarity=0.568 Sum_probs=182.3
Q ss_pred hhhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHH
Q 014852 190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKL 269 (417)
Q Consensus 190 ~~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~L 269 (417)
.+.+..||++|+.+|+||++||.+|+++++.|+.+++.. . ...+|+ .....+|+..+..+..|++.|
T Consensus 210 ~d~l~~YL~~i~~~~lLt~eEE~~La~~i~~g~~~~~~~---~-------~~~~~~---~~~~~~l~~~~~~g~~Ar~~L 276 (509)
T PRK05901 210 ADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEELL---A-------EGEKLD---PELRRDLQWIGRDGKRAKNHL 276 (509)
T ss_pred ccHHHHHHHHhccCCCCCHHHHHHHHHHHHhCCchhhhh---h-------hcccch---hhhhhhhhhhccchHHHHHHH
Confidence 478999999999999999999999999999998744421 1 112233 224567888888899999999
Q ss_pred HHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHH
Q 014852 270 VMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHER 349 (417)
Q Consensus 270 Ie~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~ 349 (417)
|.+|++||+++|++|.++|++++||||||+|||++|+++|||++|++|+|||+||||+.|.++|+++.+.+|+|.++.+.
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-HcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCCC
Q 014852 350 LGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLN 405 (417)
Q Consensus 350 ~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~s~~ 405 (417)
.++|.++...|. .+||.||.+|||+.||++++.|..++......+|||.++..+.+
T Consensus 357 i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~ 413 (509)
T PRK05901 357 INKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGD 413 (509)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCc
Confidence 999999999994 68999999999999999999999999988899999998865544
No 7
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=100.00 E-value=1.6e-34 Score=289.67 Aligned_cols=202 Identities=34% Similarity=0.585 Sum_probs=179.8
Q ss_pred hhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHH
Q 014852 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (417)
Q Consensus 191 ~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LI 270 (417)
+.+..||++|+.+|+||++||.+|+++++.|..++.. +|...+++.. ...+|+..+..|..|++.||
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 1111111111 34578888889999999999
Q ss_pred HHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHH
Q 014852 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL 350 (417)
Q Consensus 271 e~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~ 350 (417)
..|+++|+++|++|.+++.+++||+|||+||||+|+++|||++|++|+|||+||||+.|.++|+++.+.+++|.++.+..
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-HcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCCC
Q 014852 351 GLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLN 405 (417)
Q Consensus 351 ~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~s~~ 405 (417)
+++.++...|. .+||.||.+|||+.||+++++|..++..+...+|||.+...+.+
T Consensus 173 ~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~ 228 (324)
T PRK07921 173 NKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEE 228 (324)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCC
Confidence 99999999995 68999999999999999999999999888889999998754433
No 8
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=100.00 E-value=3.2e-34 Score=287.40 Aligned_cols=223 Identities=36% Similarity=0.531 Sum_probs=196.3
Q ss_pred hhhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHH-hhCCCCchH---------------HHHHHhcCCh-
Q 014852 190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKE-RLGCEPSME---------------QLAASLRISR- 252 (417)
Q Consensus 190 ~~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~-~lg~eps~~---------------e~A~~~~~s~- 252 (417)
.+.+..|+..++..++++.+++..+.+.+.....+......+.. .++..|+.. +++..+...+
T Consensus 8 ~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Ee 87 (342)
T COG0568 8 ADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEEE 87 (342)
T ss_pred hhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHHH
Confidence 47889999999999999999999999999887776666667766 677888876 4444444444
Q ss_pred HHHHHHhhhh---HHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhH
Q 014852 253 PELQSILMEC---SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGV 329 (417)
Q Consensus 253 ~eLr~~l~~~---~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i 329 (417)
..|..++..+ ..|..+||.+|+++|++||++|.++|..+.||||||+|||++|+++|||++|++|+|||+||||+.|
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 5566667655 4499999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhccccccCccHHHHHHHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCCCCCC
Q 014852 330 SRALVENSRTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLP 408 (417)
Q Consensus 330 ~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~s~~~~~ 408 (417)
.++|.++.+.+|+|.|+.+..+++.++...|. +.+++|+++|||+.||++.++|+..+.++..++|||.+++.+.++..
T Consensus 168 ~raI~~q~rtIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd~~ig~ded~~l 247 (342)
T COG0568 168 TRAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDDEDSEL 247 (342)
T ss_pred HHHHHHhcchhhHhHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccCCcCCCCcccHH
Confidence 99999999999999999999999999999995 46999999999999999999999999999999999999987765544
Q ss_pred CCcc
Q 014852 409 GETH 412 (417)
Q Consensus 409 ~d~l 412 (417)
++-+
T Consensus 248 ~d~l 251 (342)
T COG0568 248 GDFL 251 (342)
T ss_pred HHHh
Confidence 4433
No 9
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=8.7e-33 Score=281.07 Aligned_cols=177 Identities=37% Similarity=0.616 Sum_probs=168.5
Q ss_pred hhhhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHH
Q 014852 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREK 268 (417)
Q Consensus 189 ~~~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~ 268 (417)
..+.++.||++|+..|+||++++.+|+++++.||. .|++.
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 35799999999999999999999999999999987 89999
Q ss_pred HHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHH
Q 014852 269 LVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHE 348 (417)
Q Consensus 269 LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e 348 (417)
||..|+++|+++|++|.+++.+++||+|||+||||+|+++||+.+|++|+|||+||||+.|.++|+++.+.+++|.++.+
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-HcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCCC
Q 014852 349 RLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLN 405 (417)
Q Consensus 349 ~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~s~~ 405 (417)
..+++.++...|. .+||.||.+|||+.||+++++|++++..+...+|||.++..+.+
T Consensus 214 ~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~ 271 (367)
T PRK09210 214 TINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDD 271 (367)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCCCc
Confidence 9999999999984 68999999999999999999999999998889999998865544
No 10
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=99.97 E-value=1.1e-30 Score=281.45 Aligned_cols=178 Identities=32% Similarity=0.608 Sum_probs=164.5
Q ss_pred hHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHH
Q 014852 192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM 271 (417)
Q Consensus 192 ~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe 271 (417)
.+..||+++...+.|++++...++++++.|+. .+..|+++||.
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 55678888888899999999999999998875 12268999999
Q ss_pred HhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHH
Q 014852 272 SNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG 351 (417)
Q Consensus 272 ~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~ 351 (417)
.|++||+++|++|.++|++++||+|||+|||++|+++|||.+|++|+|||+||||++|.++|+++.+.+++|.++.+..+
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-HHcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCCCC
Q 014852 352 LIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNG 406 (417)
Q Consensus 352 kI~~a~~~L-~e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~s~~~ 406 (417)
++.++...| .++||+||.+|||+.||+|+++|+.++..+..++|||.+..++.+.
T Consensus 468 k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~Sld~~i~~~~~~ 523 (619)
T PRK05658 468 KLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDS 523 (619)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCcCCCCCCCCCCC
Confidence 999999998 5689999999999999999999999999999999999998665543
No 11
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=99.96 E-value=2.1e-28 Score=241.53 Aligned_cols=174 Identities=24% Similarity=0.351 Sum_probs=151.1
Q ss_pred hhHHHHHHhhcccCCCCHHHHHHHHHHHH-ccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHH
Q 014852 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIK-TGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKL 269 (417)
Q Consensus 191 ~~~~~yl~~i~~~~lLt~~eE~eLirk~k-~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~L 269 (417)
+.+..||++|...|+||+++|.+|+++++ .||. .|++.|
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 46677999999999999999999999974 7887 899999
Q ss_pred HHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHH-
Q 014852 270 VMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHE- 348 (417)
Q Consensus 270 Ie~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e- 348 (417)
|..|+|+|+++|++|.+++.+++||+||||+|||+++++||+.+|.+|+|||+|||++.|.++++++.+.+|+|.+...
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 9999999999999999999999999999999999999999999999999999999999999999998888899988554
Q ss_pred -HHHHHHHHHHHHH----HcCCCccHHHHHHHcCCCHHHHHHHHHH-hCcccccccccCCCC
Q 014852 349 -RLGLIRNAKLRLE----EKGVTPSVDRIAEYLNMSQKKVRNATEA-IGKVFSLDREAFPSL 404 (417)
Q Consensus 349 -~~~kI~~a~~~L~----e~gRepS~eEIAe~LGIS~etVr~aL~r-ark~LSLD~~~~~s~ 404 (417)
...++.++...+. .+++.||.+|||+.||+++++|..++.. ....+|||.+..++.
T Consensus 126 ~~~~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~ 187 (289)
T PRK07500 126 ALFFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEED 187 (289)
T ss_pred HHHHHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCCCC
Confidence 2234444444442 4789999999999999999999877543 447899999876443
No 12
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=99.96 E-value=3.4e-28 Score=239.42 Aligned_cols=176 Identities=30% Similarity=0.471 Sum_probs=153.2
Q ss_pred cchhhhhhhHHHHHHhhcccCCCCHHHHHHHHHHH-HccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhh
Q 014852 184 ISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKI-KTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMEC 262 (417)
Q Consensus 184 ~~~e~~~~~~~~yl~~i~~~~lLt~~eE~eLirk~-k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~ 262 (417)
.+|+ +.+..|++++...|++++++|.+|+.+. +.||.
T Consensus 10 ~~~~---~~~~~y~~~~~~~~~l~~~~e~~l~~~~~~~Gd~--------------------------------------- 47 (284)
T PRK06596 10 LSPE---GNLDAYIQAVNKIPMLTAEEEYMLAKRLREHGDL--------------------------------------- 47 (284)
T ss_pred CCCc---cHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCCH---------------------------------------
Confidence 4555 5888999999999999999999999984 68887
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc
Q 014852 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (417)
Q Consensus 263 ~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl 342 (417)
.|++.||..|+++|+++|++|.+++.+++||+|||++||++|+++||+++|++|+|||+|||++.|.++++++.+.+++
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 8999999999999999999999999999999999999999999999999999999999999999999999998777888
Q ss_pred CccHHH--HHHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC-cccccccccCCC
Q 014852 343 PNHLHE--RLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG-KVFSLDREAFPS 403 (417)
Q Consensus 343 p~~~~e--~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar-k~LSLD~~~~~s 403 (417)
|.+... ....+.++...+. .++.||.+|||+.||+++++|.+++.... ..+|||.+..++
T Consensus 127 p~~~~~~~~~~~~~~~~~~l~-~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~ 189 (284)
T PRK06596 127 ATTKAQRKLFFNLRKAKKRLG-WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDD 189 (284)
T ss_pred cchHHHHHHHHHHHHHHHHhc-cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCC
Confidence 887532 3344555555554 46889999999999999999999876544 688999987543
No 13
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=99.96 E-value=1.2e-27 Score=240.09 Aligned_cols=177 Identities=35% Similarity=0.571 Sum_probs=164.1
Q ss_pred hhhhhhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHH
Q 014852 187 ELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAR 266 (417)
Q Consensus 187 e~~~~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Ar 266 (417)
+.+.+.+++|+++|+..|+||++++..|+++++.||. .|+
T Consensus 49 ~~~~~~~~~y~~~~~~~~~l~~~ee~~li~~~~~Gd~----------------------------------------~A~ 88 (325)
T PRK05657 49 QRVLDATQLYLNEIGYSPLLTAEEEVYFARRALRGDF----------------------------------------AAR 88 (325)
T ss_pred cccccHHHHHHHHHhcCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHH
Confidence 3455899999999999999999999999999999998 899
Q ss_pred HHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccH
Q 014852 267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHL 346 (417)
Q Consensus 267 e~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~ 346 (417)
+.||.+|.++|+++|++|++++.+++||+||||||+|+++++||+.+|++|+||++||||..|.++++++.+.+++|.++
T Consensus 89 ~~Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~~i~~~~r~ir~p~~~ 168 (325)
T PRK05657 89 QRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHV 168 (325)
T ss_pred HHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHcCCccccCHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred HHHHHHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCC
Q 014852 347 HERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPS 403 (417)
Q Consensus 347 ~e~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~s 403 (417)
...++.+.++...|. ..++.|+.+|||+.||++++.|+.++......+|||.+...+
T Consensus 169 ~~~l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~~~~ 226 (325)
T PRK05657 169 VKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGD 226 (325)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCCCCC
Confidence 888777888888885 478999999999999999999999998777788999876543
No 14
>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=1.6e-27 Score=232.55 Aligned_cols=171 Identities=29% Similarity=0.496 Sum_probs=147.2
Q ss_pred hHHHHHHhhcccCCCCHHHHHHHHHH-HHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHH
Q 014852 192 RLKGYVKGVVSEELLTHAEVVRLSKK-IKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (417)
Q Consensus 192 ~~~~yl~~i~~~~lLt~~eE~eLirk-~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LI 270 (417)
.+..||+++..+|+|+++++.+|+++ .+.||. .|++.||
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 014852 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLH--E 348 (417)
Q Consensus 271 e~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~--e 348 (417)
..|+++|+++|++|.+++.+++||+|||++||++|+++||+++|++|+|||+|||+++|.+++++..+.+++|.... +
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 99999999999999999999999999999999999999999999999999999999999999998876678886643 3
Q ss_pred HHHHHHHHHHHHHHcCCCc-cHHHHHHHcCCCHHHHHHHHHHhC-cccccccccCCC
Q 014852 349 RLGLIRNAKLRLEEKGVTP-SVDRIAEYLNMSQKKVRNATEAIG-KVFSLDREAFPS 403 (417)
Q Consensus 349 ~~~kI~~a~~~L~e~gRep-S~eEIAe~LGIS~etVr~aL~rar-k~LSLD~~~~~s 403 (417)
...++..+...+. .++.| +.+|||+.||+++++|.+++.... ..+|||.+..++
T Consensus 122 ~~~~~~~~~~~~~-~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~~ 177 (270)
T TIGR02392 122 LFFNLRKMKKRLQ-GWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDD 177 (270)
T ss_pred HHHHHHHHHHHHh-cCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCCC
Confidence 3445555555553 12555 699999999999999999876554 478999987553
No 15
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=99.95 E-value=1.6e-27 Score=232.48 Aligned_cols=140 Identities=26% Similarity=0.368 Sum_probs=131.8
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccC
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp 343 (417)
.++++||..|+++|+++|++|.++|.+.+||+|||+|||++|+++|||++|++|+|||+||||+.|.++++++.+.+++|
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--hCcccccccccCCC
Q 014852 344 NHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEA--IGKVFSLDREAFPS 403 (417)
Q Consensus 344 ~~~~e~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~r--ark~LSLD~~~~~s 403 (417)
.++.+...++.++...|. .+|+.||.+|||+.||+++++|.+++.. ....+|||.+..++
T Consensus 120 r~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~ 182 (264)
T PRK07122 120 RRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSG 182 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccccccCC
Confidence 999999999999999995 6899999999999999999999998865 34689999987543
No 16
>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=1e-26 Score=224.61 Aligned_cols=162 Identities=33% Similarity=0.443 Sum_probs=151.2
Q ss_pred cccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHH
Q 014852 201 VSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSI 280 (417)
Q Consensus 201 ~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sI 280 (417)
...|+|+++++.+|+.+++.||. .|++.|+..|.++|+++
T Consensus 11 ~~~~~l~~~~~~~li~~~~~gd~----------------------------------------~a~~~L~~~~~~~v~~~ 50 (254)
T TIGR02850 11 SKLPVLKNQEMRELFIRMQSGDT----------------------------------------TAREKLINGNLRLVLSV 50 (254)
T ss_pred cCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhHHHHHHH
Confidence 56799999999999999999987 89999999999999999
Q ss_pred HHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHH
Q 014852 281 AQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRL 360 (417)
Q Consensus 281 A~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L 360 (417)
|++|.+++.+++||+||||+|||+++++||+.+|.+|+||+++||+|.|.+++++.. .+++|.+..+...++.++...|
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 999999999999999999999999999999999999999999999999999999965 7899999999989999998888
Q ss_pred H-HcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCC
Q 014852 361 E-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPS 403 (417)
Q Consensus 361 ~-e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~s 403 (417)
. ++|+.||.+|||+.||+++++|..++......+|||++...+
T Consensus 130 ~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~ 173 (254)
T TIGR02850 130 ISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYND 173 (254)
T ss_pred HHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCC
Confidence 4 589999999999999999999999999888889999887543
No 17
>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=3.2e-27 Score=225.92 Aligned_cols=140 Identities=41% Similarity=0.699 Sum_probs=132.4
Q ss_pred HHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCc
Q 014852 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPN 344 (417)
Q Consensus 265 Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~ 344 (417)
|+++||..|+++|+++|++|.+++.+++||+|||+|||++|+++|||.+|++|+|||+||||+.|.++++++.+.+++|.
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-HcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCC
Q 014852 345 HLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSL 404 (417)
Q Consensus 345 ~~~e~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~s~ 404 (417)
++.+..+++.++...|. ..|+.||.+|||+.||++.++|.+++......+|||.+...+.
T Consensus 81 ~~~~~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~ 141 (238)
T TIGR02393 81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEE 141 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCCCCCC
Confidence 99999999999999995 5899999999999999999999999888888999999875443
No 18
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=99.95 E-value=2.2e-26 Score=223.09 Aligned_cols=140 Identities=32% Similarity=0.444 Sum_probs=129.4
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCC-CCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNM-GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~-g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl 342 (417)
.|+++||..|+++|+++|++|.+. +.+++||+|||+||||+|+++|||++|++|+|||++||++.|.++++++...+++
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 899999999999999999999865 6679999999999999999999999999999999999999999999999999999
Q ss_pred CccHHHHHHHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHH--hCcccccccccCCC
Q 014852 343 PNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEA--IGKVFSLDREAFPS 403 (417)
Q Consensus 343 p~~~~e~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~r--ark~LSLD~~~~~s 403 (417)
|.++.+..+++.++...|. .+|++||.+|||+.||+++++|..++.. ....+|||.+...+
T Consensus 105 pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~~ 168 (256)
T PRK07408 105 PRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQD 168 (256)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCCC
Confidence 9999999999999999995 5899999999999999999999998653 34688999987543
No 19
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=99.94 E-value=1.7e-25 Score=216.53 Aligned_cols=162 Identities=32% Similarity=0.457 Sum_probs=150.0
Q ss_pred cccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHH
Q 014852 201 VSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSI 280 (417)
Q Consensus 201 ~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sI 280 (417)
...|+|+++++..|+.+++.||. .|++.|+..|.++|+++
T Consensus 14 ~~~~~l~~~~~~~l~~~~~~gd~----------------------------------------~a~~~l~~~~~~~v~~~ 53 (258)
T PRK08215 14 SKLPVLKNEEMRELFERMQNGDK----------------------------------------EAREKLINGNLRLVLSV 53 (258)
T ss_pred CCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHH
Confidence 35689999999999999999987 89999999999999999
Q ss_pred HHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHH
Q 014852 281 AQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRL 360 (417)
Q Consensus 281 A~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L 360 (417)
|++|.+++.+++||+|||++|||+++++||+.+|.+|.||+++||++.|.+++++.. .+++|.+......++.++...+
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 999999999999999999999999999999999999999999999999999999985 7899999998888888888888
Q ss_pred H-HcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCC
Q 014852 361 E-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPS 403 (417)
Q Consensus 361 ~-e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~s 403 (417)
. ..|+.|+..|||+.||+++++|...+......+|||.+..++
T Consensus 133 ~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~ 176 (258)
T PRK08215 133 INENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHD 176 (258)
T ss_pred HHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCC
Confidence 4 589999999999999999999999998887888999887544
No 20
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=99.93 E-value=2.4e-25 Score=215.68 Aligned_cols=161 Identities=34% Similarity=0.487 Sum_probs=147.3
Q ss_pred CCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHH
Q 014852 204 ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQR 283 (417)
Q Consensus 204 ~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~R 283 (417)
+.++..+...++...+.|+. .++ .||++|+|||.++|++
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 45677777788888888887 888 9999999999999999
Q ss_pred ccCCCC-ChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHH-
Q 014852 284 YDNMGA-DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE- 361 (417)
Q Consensus 284 y~~~g~-e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~- 361 (417)
|.+.+. +.|||+|.|+|||++|+++||+++|.+|+|||.++|+++|++++|++. .+++|+.+++..+++..+++.|.
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 999999999999999999999999999999999999999999999999 99999999999999999999995
Q ss_pred HcCCCccHHHHHHHcCCCHHHHHHHHHHhC--cccccccccCCCCCC
Q 014852 362 EKGVTPSVDRIAEYLNMSQKKVRNATEAIG--KVFSLDREAFPSLNG 406 (417)
Q Consensus 362 e~gRepS~eEIAe~LGIS~etVr~aL~rar--k~LSLD~~~~~s~~~ 406 (417)
++||+||..|||+.|||+.+.|..++.... ..+|+|+....+++.
T Consensus 122 el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~d~ 168 (247)
T COG1191 122 ELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDD 168 (247)
T ss_pred HhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhcccccc
Confidence 699999999999999999999999998876 788999877654443
No 21
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=99.93 E-value=9e-25 Score=214.60 Aligned_cols=175 Identities=35% Similarity=0.578 Sum_probs=163.0
Q ss_pred hhhhhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHH
Q 014852 188 LIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLARE 267 (417)
Q Consensus 188 ~~~~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are 267 (417)
.+.+.+++||++|..+|.|+.+++.+|+++++.||. .|++
T Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~gd~----------------------------------------~a~~ 49 (285)
T TIGR02394 10 RVADVTQLYLREIGFKPLLTAEEEIAYARRALAGDF----------------------------------------EARK 49 (285)
T ss_pred CcchHHHHHHHHHhccCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHH
Confidence 567899999999999999999999999999999998 8999
Q ss_pred HHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHH
Q 014852 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLH 347 (417)
Q Consensus 268 ~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~ 347 (417)
.||..|.++|+++|.+|.+++.+++||+||||||||+++++||+.+|++|+||+.|+++..+.++++++.+.+++|..+.
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 99999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred HHHHHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCC
Q 014852 348 ERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFP 402 (417)
Q Consensus 348 e~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~ 402 (417)
+..+.+.+....+. ..++.|+..++|+.||++++.|..++..+.+.+|+|.+...
T Consensus 130 ~~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~~~ 185 (285)
T TIGR02394 130 KELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDD 185 (285)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCCCC
Confidence 88888777776664 46899999999999999999999999888888999876543
No 22
>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=99.92 E-value=1.2e-23 Score=202.90 Aligned_cols=162 Identities=27% Similarity=0.330 Sum_probs=148.3
Q ss_pred CCCCHHHHHHHHHHHHc-cCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHH
Q 014852 204 ELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQ 282 (417)
Q Consensus 204 ~lLt~~eE~eLirk~k~-Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~ 282 (417)
|.|++.++.+|+.+++. ||. .|++.|+..|.++|+.+|+
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 67999999999999988 576 8999999999999999999
Q ss_pred HccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHH-
Q 014852 283 RYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE- 361 (417)
Q Consensus 283 Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~- 361 (417)
+|.+++.++|||+||||++||+++++|++..|.+|.||+++||+|.|.+++++....+++|..+.+...++..+...+.
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 9999999999999999999999999999999999999999999999999999998888999999999999999999985
Q ss_pred HcCCCccHHHHHHHcCCCHHHHHHHHHHhC--cccccccccCCCCC
Q 014852 362 EKGVTPSVDRIAEYLNMSQKKVRNATEAIG--KVFSLDREAFPSLN 405 (417)
Q Consensus 362 e~gRepS~eEIAe~LGIS~etVr~aL~rar--k~LSLD~~~~~s~~ 405 (417)
.+|+.|+..|||+.||++.+.+..++.... ..+|||.++..+++
T Consensus 128 ~~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~~~ 173 (255)
T TIGR02941 128 HLQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSD 173 (255)
T ss_pred HhCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCCCC
Confidence 579999999999999999999998877653 57899988765433
No 23
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=99.92 E-value=1e-23 Score=204.71 Aligned_cols=136 Identities=25% Similarity=0.391 Sum_probs=123.5
Q ss_pred HHHHHHHHHhHHHHHHHHHHcc---CCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc
Q 014852 264 LAREKLVMSNVRLVMSIAQRYD---NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~---~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i 340 (417)
.|++.||..|+|+|+++|++|. ..+.+.+||+|||+||||+|+++|||++|++|+||+.+|||++|.+++++..
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 7999999999999999999985 2456899999999999999999999999999999999999999999999876
Q ss_pred ccCccHHHHHHHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHHhC--cccccccccCC
Q 014852 341 RLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIG--KVFSLDREAFP 402 (417)
Q Consensus 341 rlp~~~~e~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rar--k~LSLD~~~~~ 402 (417)
++|.++.+..+++..+...|. .+||.||.+|||+.||+++++|..++..+. ..+|||.+...
T Consensus 100 ~~pr~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~Sld~~~~~ 164 (257)
T PRK05911 100 WVPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPC 164 (257)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHHhhccceeeccccCCC
Confidence 489999999999999999885 589999999999999999999999987665 36899987643
No 24
>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=99.91 E-value=1.5e-23 Score=199.05 Aligned_cols=141 Identities=35% Similarity=0.437 Sum_probs=131.1
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc
Q 014852 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 341 (417)
Q Consensus 262 ~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir 341 (417)
+..|++.|+..|.++|+++|.+|.+++.+++||+||||+|||+++++||+.+|.+|.||+++||+|.|.++++++. .++
T Consensus 9 d~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~lr~~~-~i~ 87 (231)
T TIGR02885 9 DKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDDG-IIK 87 (231)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-CeE
Confidence 3489999999999999999999999999999999999999999999999999889999999999999999999986 789
Q ss_pred cCccHHHHHHHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCC
Q 014852 342 LPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPS 403 (417)
Q Consensus 342 lp~~~~e~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~s 403 (417)
+|.++.+...++.++...|. ++|+.||.+|||+.||+++++|..++..+....|||.+..++
T Consensus 88 ~p~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~ 150 (231)
T TIGR02885 88 VSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQD 150 (231)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCC
Confidence 99999999999999988885 579999999999999999999999988888889999877543
No 25
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=99.90 E-value=9.5e-23 Score=198.49 Aligned_cols=159 Identities=28% Similarity=0.362 Sum_probs=141.5
Q ss_pred hcccCCCCHHHHHHHHHHHH-ccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHH
Q 014852 200 VVSEELLTHAEVVRLSKKIK-TGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVM 278 (417)
Q Consensus 200 i~~~~lLt~~eE~eLirk~k-~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~ 278 (417)
-+.+|+||.++|.+|+++++ .||. .|++.|+..|.++|+
T Consensus 6 ~~~~~~~~~~~e~~l~~~~~~~~d~----------------------------------------~a~~~l~~~y~~lv~ 45 (268)
T PRK06288 6 SGKIPKYAQQDETELWREYKKTGDP----------------------------------------KIREYLILKYSPLVK 45 (268)
T ss_pred cCCCccccchHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHH
Confidence 36789999999999999976 4565 899999999999999
Q ss_pred HHHHHcc-C--CCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHH
Q 014852 279 SIAQRYD-N--MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRN 355 (417)
Q Consensus 279 sIA~Ry~-~--~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~ 355 (417)
.+|++|. + .+.+++||+||||+|||+++++||+.+|.+|+||+++||+|.|.+++|+.. ++|.++......+.+
T Consensus 46 ~~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i~d~~R~~~---~~p~~~~~~~~~i~~ 122 (268)
T PRK06288 46 YVAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSID---WIPRSVRQKARQIER 122 (268)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC---ccCHHHHHHHHHHHH
Confidence 9999986 2 567899999999999999999999998899999999999999999998653 689998888889999
Q ss_pred HHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHHhC--cccccccccC
Q 014852 356 AKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIG--KVFSLDREAF 401 (417)
Q Consensus 356 a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rar--k~LSLD~~~~ 401 (417)
+...|. .+++.||.+|||+.||++.+.|..++..+. ..+|||++..
T Consensus 123 ~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~ 171 (268)
T PRK06288 123 AIAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWF 171 (268)
T ss_pred HHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhc
Confidence 999995 589999999999999999999999987653 5689988764
No 26
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=99.90 E-value=8.3e-23 Score=193.23 Aligned_cols=139 Identities=39% Similarity=0.485 Sum_probs=130.4
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc
Q 014852 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (417)
Q Consensus 263 ~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl 342 (417)
..|++.|+..|.++|+++|++|.+++.++|||+|||++|||+++++||+.+|.+|+||+++||++.|.++++++.+.+++
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 37999999999999999999999999999999999999999999999999999999999999999999999999888999
Q ss_pred CccHHHHHHHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHHhCc--ccccccccC
Q 014852 343 PNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGK--VFSLDREAF 401 (417)
Q Consensus 343 p~~~~e~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rark--~LSLD~~~~ 401 (417)
|.++.+...++.++...+. ..|+.|+..|+|+.||+++++|.+++..... .+|||++..
T Consensus 82 ~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~ 143 (227)
T TIGR02980 82 PRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIE 143 (227)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCC
Confidence 9999999999999999884 5789999999999999999999998887765 889998875
No 27
>PRK05572 sporulation sigma factor SigF; Validated
Probab=99.90 E-value=2.8e-22 Score=193.39 Aligned_cols=165 Identities=36% Similarity=0.452 Sum_probs=151.3
Q ss_pred HHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHH
Q 014852 197 VKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRL 276 (417)
Q Consensus 197 l~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~L 276 (417)
++.-...|.|+++++.+|+.+++.|+. .|++.|+..|.++
T Consensus 5 ~~~~~~~~~l~~~~~~~li~~~~~gd~----------------------------------------~a~~~L~~~y~~~ 44 (252)
T PRK05572 5 VKNKKKKPQLKDEENKELIKKSQDGDQ----------------------------------------EARDTLVEKNLRL 44 (252)
T ss_pred hccCcCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhHHH
Confidence 345567899999999999999999987 8999999999999
Q ss_pred HHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHH
Q 014852 277 VMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNA 356 (417)
Q Consensus 277 V~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a 356 (417)
|+++|++|.+++.+++||+||||+++|+++++|++.+|.+|.||+++||++.|.+++++.. .+++|..+.....++.++
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 9999999999999999999999999999999999988889999999999999999999874 779999999999999999
Q ss_pred HHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCC
Q 014852 357 KLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFP 402 (417)
Q Consensus 357 ~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~ 402 (417)
...+. +.||.|+..|||+.||++++.|..++.......||+.+..+
T Consensus 124 ~~~l~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~ 170 (252)
T PRK05572 124 KDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHE 170 (252)
T ss_pred HHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCccc
Confidence 98884 57999999999999999999999998887788899887653
No 28
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=99.89 E-value=8.5e-22 Score=190.20 Aligned_cols=160 Identities=28% Similarity=0.342 Sum_probs=146.1
Q ss_pred CCCCHHHHHHHHHHHHc-cCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHH
Q 014852 204 ELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQ 282 (417)
Q Consensus 204 ~lLt~~eE~eLirk~k~-Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~ 282 (417)
|.|+++++.+|+.+++. ||. .|++.|+..|.++|+++|+
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 77999999999999885 787 8999999999999999999
Q ss_pred HccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHH-
Q 014852 283 RYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE- 361 (417)
Q Consensus 283 Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~- 361 (417)
+|.+++.+++||+||||++||+++++||+..|.+|.||+++||+|.|.+++++....+++|.++.+..+++..+...+.
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 9999999999999999999999999999998889999999999999999999998889999999999999999988885
Q ss_pred HcCCCccHHHHHHHcCCCHHHHHHHHHHhC--cccccccccCCC
Q 014852 362 EKGVTPSVDRIAEYLNMSQKKVRNATEAIG--KVFSLDREAFPS 403 (417)
Q Consensus 362 e~gRepS~eEIAe~LGIS~etVr~aL~rar--k~LSLD~~~~~s 403 (417)
..++.|+..|+|+.+|++.+.|..++.... ..+|+|.+...+
T Consensus 128 ~~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~ 171 (257)
T PRK08583 128 ELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEAD 171 (257)
T ss_pred HhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCC
Confidence 578999999999999999999988876543 578898877544
No 29
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=99.87 E-value=2.4e-21 Score=186.84 Aligned_cols=136 Identities=25% Similarity=0.375 Sum_probs=123.4
Q ss_pred HHHHHHHHHhHHHHHHHHHHccC---CCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~---~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i 340 (417)
.|++.||..|.++|+++|++|.+ ++.+++||+||||+|||+++++||+.+|.+|.||+++||+|.|.++++++.
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 688999999999999999999999999999999999999999999999865
Q ss_pred ccCccHHHHHHHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHH--hCcccccccccCC
Q 014852 341 RLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEA--IGKVFSLDREAFP 402 (417)
Q Consensus 341 rlp~~~~e~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~r--ark~LSLD~~~~~ 402 (417)
++|....+...+++++...+. ..|+.|+.+|||+.||+++++|+.++.. ....+|||++...
T Consensus 99 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~ 163 (251)
T PRK07670 99 WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHD 163 (251)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCccccC
Confidence 688888888888888888884 5899999999999999999999999864 3468899988643
No 30
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=99.87 E-value=2.2e-21 Score=184.97 Aligned_cols=163 Identities=28% Similarity=0.364 Sum_probs=136.1
Q ss_pred hHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHH
Q 014852 192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM 271 (417)
Q Consensus 192 ~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe 271 (417)
++..|+.++...|+||++++..|+..++.|+. .|++.|+.
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 014852 272 SNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR-L-------- 342 (417)
Q Consensus 272 ~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir-l-------- 342 (417)
.|.++|+++|.+|.+++.+++|++||+||++|+++++|++++|.+|.||+++|++|.+++++|+..+..+ .
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 9999999999999999999999999999999999999999888899999999999999999987653210 0
Q ss_pred -------------Cc---cHH------HHHHHHHHHHHHHHHcC-------------CCccHHHHHHHcCCCHHHHHHHH
Q 014852 343 -------------PN---HLH------ERLGLIRNAKLRLEEKG-------------VTPSVDRIAEYLNMSQKKVRNAT 387 (417)
Q Consensus 343 -------------p~---~~~------e~~~kI~~a~~~L~e~g-------------RepS~eEIAe~LGIS~etVr~aL 387 (417)
+. ... .....+..++..|++.. .+.|++|||+.||+|.++|++++
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 00 000 11234666666664322 34589999999999999999999
Q ss_pred HHhCccc
Q 014852 388 EAIGKVF 394 (417)
Q Consensus 388 ~rark~L 394 (417)
+++++.+
T Consensus 217 ~rA~~kL 223 (233)
T PRK05803 217 KRALKKL 223 (233)
T ss_pred HHHHHHH
Confidence 8887654
No 31
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=99.85 E-value=1.2e-20 Score=180.73 Aligned_cols=136 Identities=20% Similarity=0.270 Sum_probs=119.3
Q ss_pred HHHHHHHHHhHHHHHHHHHHccC---CCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~---~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i 340 (417)
.-...|+..|+|+|..+|++|.. .+.+.+||+|||+||||+|+++||+..| +|+||+++||+|.|.+++++..
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 34568899999999999999874 4679999999999999999999998666 8999999999999999998854
Q ss_pred ccCccHHHHHHHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHH--hCcccccccccCCC
Q 014852 341 RLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEA--IGKVFSLDREAFPS 403 (417)
Q Consensus 341 rlp~~~~e~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~r--ark~LSLD~~~~~s 403 (417)
+.|..+....+++.++...|. .+|++||.+|||+.||+++++|.+++.. +...+|||++..++
T Consensus 91 ~~~r~vr~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~ 156 (231)
T PRK12427 91 WRPRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALE 156 (231)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccCC
Confidence 468888888899999999984 5899999999999999999999998764 34688999987554
No 32
>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=99.84 E-value=3.8e-20 Score=175.14 Aligned_cols=130 Identities=33% Similarity=0.464 Sum_probs=117.2
Q ss_pred HHHHhHHHHHHHHHHccC---CCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCcc
Q 014852 269 LVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH 345 (417)
Q Consensus 269 LIe~yl~LV~sIA~Ry~~---~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~ 345 (417)
|+..|.++|+++|.+|.+ ++.+++||+||||+|||+++++||+++|.+|+||+++||+|.+.+++++.. ++|..
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--cccccccccC
Q 014852 346 LHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIG--KVFSLDREAF 401 (417)
Q Consensus 346 ~~e~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rar--k~LSLD~~~~ 401 (417)
.....+++.++...|. .+|+.|+.+|||+.||++++.|..++..+. ..+|+|+...
T Consensus 78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~ 136 (224)
T TIGR02479 78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLE 136 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCccc
Confidence 8888999999999995 589999999999999999999999987554 4678887554
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=1.6e-19 Score=171.75 Aligned_cols=163 Identities=26% Similarity=0.367 Sum_probs=131.7
Q ss_pred hHHHHHHhhcc-cCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHH
Q 014852 192 RLKGYVKGVVS-EELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (417)
Q Consensus 192 ~~~~yl~~i~~-~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LI 270 (417)
++-+|+-.-++ .+.|++.++.+|+.+++.|+. .|++.|+
T Consensus 15 ~~~~~~~~~~~~~~~~~~~~~~~li~~~~~gd~----------------------------------------~af~~l~ 54 (227)
T TIGR02846 15 FLVGYVTNNGSFPQPLSEEEEKKYLDRLKEGDE----------------------------------------EARNVLI 54 (227)
T ss_pred HHHHHHHHHHhCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHH
Confidence 44567666554 456999999999999999997 8999999
Q ss_pred HHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc-c-------
Q 014852 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR-L------- 342 (417)
Q Consensus 271 e~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir-l------- 342 (417)
+.|.+.|+++|.+|.++..++||++||+|+++|+++++|+++.+.+|.||++++++|.+++++|+..+..+ .
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 99999999999999999999999999999999999999999888789999999999999999987654211 0
Q ss_pred --------------Cc---c------HHHHHHHHHHHHHHHHHcC-------------CCccHHHHHHHcCCCHHHHHHH
Q 014852 343 --------------PN---H------LHERLGLIRNAKLRLEEKG-------------VTPSVDRIAEYLNMSQKKVRNA 386 (417)
Q Consensus 343 --------------p~---~------~~e~~~kI~~a~~~L~e~g-------------RepS~eEIAe~LGIS~etVr~a 386 (417)
+. . ..+....+..++..|++.. .+.|++|||+.||+|+++|+..
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 0011233666677764322 3458999999999999999999
Q ss_pred HHHhCccc
Q 014852 387 TEAIGKVF 394 (417)
Q Consensus 387 L~rark~L 394 (417)
++++++.+
T Consensus 215 ~~rAl~~L 222 (227)
T TIGR02846 215 EKRALMKL 222 (227)
T ss_pred HHHHHHHH
Confidence 99987654
No 34
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=99.82 E-value=2.4e-19 Score=171.07 Aligned_cols=138 Identities=28% Similarity=0.400 Sum_probs=120.7
Q ss_pred hhHHHHHHHHHHhHHHHHHHHHHcc---CCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhc
Q 014852 261 ECSLAREKLVMSNVRLVMSIAQRYD---NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENS 337 (417)
Q Consensus 261 ~~~~Are~LIe~yl~LV~sIA~Ry~---~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~ 337 (417)
+|..++++|+..|.++|+++|.+|. +++.+++||+||||+|||+++++||+..|.+|.||+++||+|.|.++++++.
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 4567899999999999999999997 6789999999999999999999999998889999999999999999999875
Q ss_pred cccccCccHHHHHHHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHHhC--cccccccccC
Q 014852 338 RTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIG--KVFSLDREAF 401 (417)
Q Consensus 338 r~irlp~~~~e~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rar--k~LSLD~~~~ 401 (417)
++|..+......+.++...+. ..+++|+.+|||+.||++++.|..++.... ..+|++....
T Consensus 85 ---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~ 148 (236)
T PRK06986 85 ---WVPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRG 148 (236)
T ss_pred ---CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccc
Confidence 367777776677777777774 579999999999999999999999887643 4668887643
No 35
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=99.82 E-value=1.9e-19 Score=171.31 Aligned_cols=159 Identities=26% Similarity=0.443 Sum_probs=129.2
Q ss_pred HHHhhccc-CCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhH
Q 014852 196 YVKGVVSE-ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNV 274 (417)
Q Consensus 196 yl~~i~~~-~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl 274 (417)
|+++.... +.+++..+.+|+.+++.||. .|++.|+..|.
T Consensus 23 ~~~~~~~~~~~~~~~~~~~L~~~~~~gd~----------------------------------------~af~~l~~~y~ 62 (234)
T PRK08301 23 YIGGSEALPPPLSKEEEEYLLNKLPKGDE----------------------------------------AVRSLLIERNL 62 (234)
T ss_pred HhccccccCCcCCHHHHHHHHHHHHccCH----------------------------------------HHHHHHHHHhH
Confidence 66666444 44888888999999999987 89999999999
Q ss_pred HHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc---c--C------
Q 014852 275 RLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR---L--P------ 343 (417)
Q Consensus 275 ~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir---l--p------ 343 (417)
++|+.+|.+|.+++.+++|++||+|+++|+++++|++..+++|.||++++++|.+++++|++.+... . +
T Consensus 63 ~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~~d~lRk~~~~~~~~~~~~~~~~~~~ 142 (234)
T PRK08301 63 RLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLRRNNKVKAEVSFDEPLNIDWD 142 (234)
T ss_pred HHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHHHHHHhccccccccccccccccC
Confidence 9999999999999999999999999999999999999887789999999999999999997654211 0 0
Q ss_pred ------------c-cH------H-HHHHHHHHHHHHHHHc-------------CCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 344 ------------N-HL------H-ERLGLIRNAKLRLEEK-------------GVTPSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 344 ------------~-~~------~-e~~~kI~~a~~~L~e~-------------gRepS~eEIAe~LGIS~etVr~aL~ra 390 (417)
. .. . .....+..++..|++. ..+.|++|||+.||||+++|++.++++
T Consensus 143 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA 222 (234)
T PRK08301 143 GNELLLSDVLGTDNDIIYKDIEDEVDRKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRI 222 (234)
T ss_pred CCcccHHHhccCcccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 0 00 0 0123467777777442 235699999999999999999999998
Q ss_pred Cccc
Q 014852 391 GKVF 394 (417)
Q Consensus 391 rk~L 394 (417)
++.+
T Consensus 223 ~~~L 226 (234)
T PRK08301 223 IKRL 226 (234)
T ss_pred HHHH
Confidence 7654
No 36
>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=2.4e-18 Score=164.43 Aligned_cols=159 Identities=29% Similarity=0.445 Sum_probs=127.6
Q ss_pred HHHhhc-ccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhH
Q 014852 196 YVKGVV-SEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNV 274 (417)
Q Consensus 196 yl~~i~-~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl 274 (417)
|+.+-. .-+.|++.++.+|+..++.|+. .|++.|+..|.
T Consensus 23 ~~~~~~~~~~~~~~~~~~~l~~~~~~~d~----------------------------------------~a~~~l~~~y~ 62 (234)
T TIGR02835 23 YIGGSEALPPPLTGEEEEALLQKLTQGDE----------------------------------------SAKSTLIERNL 62 (234)
T ss_pred HhcccccCCCcCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhH
Confidence 444433 3366888888899999999887 89999999999
Q ss_pred HHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc-cC----------
Q 014852 275 RLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR-LP---------- 343 (417)
Q Consensus 275 ~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir-lp---------- 343 (417)
+.|+++|.+|.+++.++|||+||+|+++|+++++|++..+++|.||++++++|.+++++++..+... .+
T Consensus 63 ~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~~d~~Rk~~r~~~~~~~~~~~~~~~~ 142 (234)
T TIGR02835 63 RLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEILMYLRRNNKTRSEVSFDEPLNVDWD 142 (234)
T ss_pred HHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHhccccCcccccccccCCCC
Confidence 9999999999999999999999999999999999998887789999999999999999997654211 00
Q ss_pred ------------c-----cH---HHHHHHHHHHHHHHHHc-------------CCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 344 ------------N-----HL---HERLGLIRNAKLRLEEK-------------GVTPSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 344 ------------~-----~~---~e~~~kI~~a~~~L~e~-------------gRepS~eEIAe~LGIS~etVr~aL~ra 390 (417)
. .. ......+..++..|++. +.+.|++|||+.||+|+++|+.+++++
T Consensus 143 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra 222 (234)
T TIGR02835 143 GNELLLSDVLGTDSDIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRI 222 (234)
T ss_pred CCcchHHHhcCCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 0 00 01123467777777431 145799999999999999999999988
Q ss_pred Cccc
Q 014852 391 GKVF 394 (417)
Q Consensus 391 rk~L 394 (417)
++.+
T Consensus 223 ~~~L 226 (234)
T TIGR02835 223 LKRL 226 (234)
T ss_pred HHHH
Confidence 7644
No 37
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=99.77 E-value=1.6e-18 Score=160.26 Aligned_cols=153 Identities=11% Similarity=0.083 Sum_probs=123.6
Q ss_pred cccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHH
Q 014852 201 VSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSI 280 (417)
Q Consensus 201 ~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sI 280 (417)
...|+..+.++..|+..+..|+. .|++.|++.|.++|+++
T Consensus 7 ~~~~~~~~~~~~~li~~~~~g~~----------------------------------------~a~~~l~~~y~~~l~~~ 46 (194)
T PRK09646 7 MTGPPAESPDLDALLRRVARGDQ----------------------------------------DAFAELYDRTSSRVYGL 46 (194)
T ss_pred ccCCCCCcccHHHHHHHHHccCH----------------------------------------HHHHHHHHHHHHHHHHH
Confidence 34566666677788888888876 89999999999999999
Q ss_pred HHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc---------Cc---cH--
Q 014852 281 AQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL---------PN---HL-- 346 (417)
Q Consensus 281 A~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl---------p~---~~-- 346 (417)
|.+|+++..++||++||+||++|+++++|++.+| .|.+|++.+++|.++++++.+.+..+. .. ..
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 9999999999999999999999999999998776 899999999999999999876532110 00 00
Q ss_pred ----HHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 347 ----HERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 347 ----~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
.+....+..++..|++..|. .|++|||+.||+|+++|+..++++++.+
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 11223466777777554444 3999999999999999999999998754
No 38
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=99.76 E-value=8e-18 Score=154.44 Aligned_cols=148 Identities=18% Similarity=0.129 Sum_probs=119.7
Q ss_pred CCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHcc
Q 014852 206 LTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYD 285 (417)
Q Consensus 206 Lt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~ 285 (417)
+|+.+...|+..++.|+. .|++.|+..|.+.|+.+|.++.
T Consensus 6 ~~~~~~~~l~~~~~~gd~----------------------------------------~a~~~l~~~~~~~l~~~~~~~~ 45 (189)
T PRK09648 6 DTGEELDALVAEAVAGDR----------------------------------------RALREVLEIIRPLVVRYCRARL 45 (189)
T ss_pred CCchHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHHHHHHh
Confidence 477777788888888887 8999999999999999999987
Q ss_pred CC----CCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc-----Cc------c-----
Q 014852 286 NM----GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL-----PN------H----- 345 (417)
Q Consensus 286 ~~----g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl-----p~------~----- 345 (417)
++ +.+++|++||+|+++|+++.+|++.. .+|.||++.+++|.+++++++..+.... +. .
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 46899999999999999999998653 4899999999999999999986653211 10 0
Q ss_pred -HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 346 -LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 346 -~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
..+....+..++..|++..|++ +++|||+.||+|+.+|+..++++++.|
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 1112234677777776655553 999999999999999999999988654
No 39
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=99.75 E-value=1.2e-17 Score=152.99 Aligned_cols=130 Identities=14% Similarity=0.134 Sum_probs=107.3
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc--
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR-- 341 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir-- 341 (417)
.|++.|+..|.++|+.+|.++++++.+++|++||+|+++|+++.+|++.. .+|.+|++++++|.+.++++++.....
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 89999999999999999999999999999999999999999999999863 489999999999999999987653210
Q ss_pred cCc---------c---HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 342 LPN---------H---LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 342 lp~---------~---~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
.+. . ..+....+..++..|++..|+ .+++|||+.||+|..+|+..++++++.+
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 012234467777777655554 3999999999999999999999998765
No 40
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=99.75 E-value=1.7e-17 Score=152.90 Aligned_cols=129 Identities=14% Similarity=0.120 Sum_probs=107.5
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccC
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp 343 (417)
.|++.|+..|.+.|+++|.++.++..++||++||+|+++|+++.+|++.. .|.+|++++++|.+++++++..+....+
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 89999999999999999999999999999999999999999999999754 7999999999999999998776432211
Q ss_pred c------------c--------HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 344 N------------H--------LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 344 ~------------~--------~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
. . ..+....+..++..|++..|.+ |++|||+.||+|+++|++.++++++.+
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 0112245777788886655553 999999999999999999999998765
No 41
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=99.74 E-value=2.1e-17 Score=157.52 Aligned_cols=152 Identities=19% Similarity=0.206 Sum_probs=127.3
Q ss_pred cccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHH
Q 014852 201 VSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSI 280 (417)
Q Consensus 201 ~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sI 280 (417)
...|+|++..+..|+.+++.|+. .|++.|+..|.+.|+++
T Consensus 7 ~~~~~~~~~~~~~l~~~~~~gd~----------------------------------------~a~~~l~~~y~~~l~~~ 46 (231)
T PRK11922 7 SRPPPLSAASDRELVARVLAGDE----------------------------------------AAFEALMRRHNRRLYRT 46 (231)
T ss_pred CCCCCcCcccHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHH
Confidence 45688999999999999999987 89999999999999999
Q ss_pred HHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCc----------------
Q 014852 281 AQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPN---------------- 344 (417)
Q Consensus 281 A~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~---------------- 344 (417)
+.++.++..++|||+||+|+++|+++++|++.. .|.||++++++|.+++++|+..+....+.
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 999999999999999999999999999999863 89999999999999999987664322110
Q ss_pred ----c------HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 345 ----H------LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 345 ----~------~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
. ..+....+..++..|++..|++ |++|||+.||+|.++|+++++++++.+
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 0112234777888886655553 999999999999999999999998655
No 42
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=99.74 E-value=1.5e-17 Score=154.05 Aligned_cols=131 Identities=28% Similarity=0.347 Sum_probs=102.5
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccC
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp 343 (417)
.|++.|++.|.++|+.+|.+|.++..++||++||+|+++|+++.+|++.+|.+|.||++.++++.+.++++...+..+.+
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 89999999999999999999999999999999999999999999999987679999999999999999887543321110
Q ss_pred -----------------------------ccH------HHHHHHH-HHHHHHHHHcCC--------CccHHHHHHHcCCC
Q 014852 344 -----------------------------NHL------HERLGLI-RNAKLRLEEKGV--------TPSVDRIAEYLNMS 379 (417)
Q Consensus 344 -----------------------------~~~------~e~~~kI-~~a~~~L~e~gR--------epS~eEIAe~LGIS 379 (417)
... .+....+ ..++..|++..| +.|++|||+.||+|
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 0011122 223345443333 34999999999999
Q ss_pred HHHHHHHHHHhCccc
Q 014852 380 QKKVRNATEAIGKVF 394 (417)
Q Consensus 380 ~etVr~aL~rark~L 394 (417)
+++|+.+++++++.+
T Consensus 184 ~~tV~~~l~rar~~L 198 (208)
T PRK08295 184 VKSIDNALQRVKRKL 198 (208)
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999999998765
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=149.76 Aligned_cols=131 Identities=26% Similarity=0.345 Sum_probs=102.9
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc-
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL- 342 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl- 342 (417)
.|++.|+..|.+.|+.+|.++.++..+++||+||+|+++|+++.+|++..+.+|.||++++|++.+.++++...+..+.
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 8999999999999999999999999999999999999999999999998767999999999999888777643211000
Q ss_pred -------------------------------CccH---HHHHHHHHHHHHHH-HHcCC--------CccHHHHHHHcCCC
Q 014852 343 -------------------------------PNHL---HERLGLIRNAKLRL-EEKGV--------TPSVDRIAEYLNMS 379 (417)
Q Consensus 343 -------------------------------p~~~---~e~~~kI~~a~~~L-~e~gR--------epS~eEIAe~LGIS 379 (417)
|... .+....+.+++..| ++..+ +.|++|||+.||+|
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 11123355666664 22222 24999999999999
Q ss_pred HHHHHHHHHHhCccc
Q 014852 380 QKKVRNATEAIGKVF 394 (417)
Q Consensus 380 ~etVr~aL~rark~L 394 (417)
+++|+.+++++++.+
T Consensus 179 ~~tV~~~l~r~r~~L 193 (198)
T TIGR02859 179 VKSIDNALQRVKRKL 193 (198)
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999999998765
No 44
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=99.73 E-value=2.9e-17 Score=149.24 Aligned_cols=130 Identities=14% Similarity=0.063 Sum_probs=105.8
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc-cc
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL-RL 342 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i-rl 342 (417)
.|+..|+..|.+.|+.+|.++.++..+++|++||+|+++|+++++|++..+ .|.||++.+++|.+++++++..+.. ..
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 899999999999999999999999999999999999999999999997554 7999999999999999998755321 00
Q ss_pred ------------CccH---HHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 343 ------------PNHL---HERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 343 ------------p~~~---~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
|... .+....+..++..|++..|+ .|++|||+.||+|+++|+..++++++.+
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 0000 11223466777777654444 3999999999999999999999998765
No 45
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=99.73 E-value=2.2e-17 Score=145.90 Aligned_cols=129 Identities=19% Similarity=0.187 Sum_probs=105.4
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc---
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL--- 340 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i--- 340 (417)
.||+.|++.|.++|++++.++ ++..++||++||+|+++|+++++|++..| +|.+|++.+++|.++++++++.+..
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 45679999999999999999999998776 8999999999999999999874211
Q ss_pred ---ccCcc---HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 341 ---RLPNH---LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 341 ---rlp~~---~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
..|.. ..+....+..++..|++..|. .|++|||+.||+|+++|+.++.++++.+
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 11222 222345577777777654444 4999999999999999999999998654
No 46
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=99.72 E-value=5.9e-17 Score=148.97 Aligned_cols=144 Identities=17% Similarity=0.225 Sum_probs=117.0
Q ss_pred cCChHHHHHHhhh----hHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHH
Q 014852 249 RISRPELQSILME----CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324 (417)
Q Consensus 249 ~~s~~eLr~~l~~----~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~ 324 (417)
.+++++|...++. +..|++.|+..|.+.|+++|.+|.++..+++|++||+|+++|+++++|++. + +|.||++++
T Consensus 7 ~~~~~~li~~~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~~~~~~~~~-~-~~~~wl~~i 84 (188)
T PRK09640 7 ELNDEELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGK-S-KFKTWLYSI 84 (188)
T ss_pred CCCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHHHhcCC-C-cchHHHHHH
Confidence 3456666666653 688999999999999999999999999999999999999999999999964 3 899999999
Q ss_pred HHhhHHHHHHhhccccccC---------c---c---HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCH
Q 014852 325 IRQGVSRALVENSRTLRLP---------N---H---LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQ 380 (417)
Q Consensus 325 IR~~i~~~Ird~~r~irlp---------~---~---~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~ 380 (417)
++|.+++++++..+..... . . ..+....+..++..|++..|++ +++|||+.||||.
T Consensus 85 a~n~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~lgis~ 164 (188)
T PRK09640 85 TYNECITQYRKERRKRRLMDALSLDPLEEASEEKAPKPEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMGL 164 (188)
T ss_pred HHHHHHHHHHHhcccccCcchhhhcccccccccccccHHHHHHHHHHHHhcChhheeeeeeHHhcCCCHHHHHHHHCCCH
Confidence 9999999998754321111 0 0 1122355788888887666654 9999999999999
Q ss_pred HHHHHHHHHhCccc
Q 014852 381 KKVRNATEAIGKVF 394 (417)
Q Consensus 381 etVr~aL~rark~L 394 (417)
++|+..+.+|++.+
T Consensus 165 ~tV~~~l~Ra~~~L 178 (188)
T PRK09640 165 SATKMRYKRALDKL 178 (188)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999998654
No 47
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=99.72 E-value=2.5e-17 Score=152.52 Aligned_cols=130 Identities=19% Similarity=0.233 Sum_probs=106.2
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc-c-
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL-R- 341 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i-r- 341 (417)
.|++.|+..|.+.|+.+|.++.++..+++|++||+|+++|+.+.+|++..+ .|.||+++++++.++++++++.+.. .
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 899999999999999999999999999999999999999999999986444 8999999999999999998754321 1
Q ss_pred --cC------c---c---HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 342 --LP------N---H---LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 342 --lp------~---~---~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
.+ . . ..+....+..++..|++..|. .+++|||+.||+|..+|+++++++++.+
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 00 0 0 011224467777777654443 4999999999999999999999998766
No 48
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=99.72 E-value=4.9e-17 Score=149.48 Aligned_cols=147 Identities=20% Similarity=0.250 Sum_probs=119.1
Q ss_pred CCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHcc
Q 014852 206 LTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYD 285 (417)
Q Consensus 206 Lt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~ 285 (417)
||+..+..|+..++.||. .+++.|+..|.+.|+.+++++.
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---c--C------------cc---
Q 014852 286 NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR---L--P------------NH--- 345 (417)
Q Consensus 286 ~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir---l--p------------~~--- 345 (417)
++..+++|++||+|+++|+++.+|++.. .|.+|++++++|.++++++++.+... . . ..
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 9999999999999999999999999875 69999999999999999986543211 0 0 00
Q ss_pred -----HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 346 -----LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 346 -----~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
..+....+..++..|++..|.+ +++|||+.||+|+++|+..+.++++.|
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 0011234666777776555543 999999999999999999999998755
No 49
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=99.72 E-value=3.2e-17 Score=149.65 Aligned_cols=130 Identities=15% Similarity=0.167 Sum_probs=106.4
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc-c
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR-L 342 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir-l 342 (417)
.|++.|+..|.+.|+.++.++.+++.+++|++||+|+++|+++++|++..+ .|.+|++++++|.+++++++..+... +
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 899999999999999999999988899999999999999999999997654 79999999999999999987653211 1
Q ss_pred ------C------cc-----HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 343 ------P------NH-----LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 343 ------p------~~-----~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
+ .. .......+..++..|++..|.+ +++|||+.||+|+++|+..++++++.+
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 0111234677777776545443 999999999999999999999998765
No 50
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=99.72 E-value=3.2e-17 Score=149.98 Aligned_cols=130 Identities=15% Similarity=0.068 Sum_probs=106.4
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc--
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR-- 341 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir-- 341 (417)
.+++.|+..|.+.|+++|.++.++..++||++||+|+++|+++++|++.++ .|.||++++++|.+++++++..+...
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 899999999999999999999999999999999999999999999998765 79999999999999999987643210
Q ss_pred ----cC---------cc---HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 342 ----LP---------NH---LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 342 ----lp---------~~---~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
.+ .. ..+....+..++..|++..+. .+++|||+.||+|+++|+.+++++++.|
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 112234566777777554333 4999999999999999999999998765
No 51
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=99.72 E-value=3.9e-17 Score=151.02 Aligned_cols=130 Identities=15% Similarity=0.114 Sum_probs=105.6
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc-cc
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL-RL 342 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i-rl 342 (417)
.+++.|+..|.+.|+.+|.++.++..+++|++||+|+.+|+.+++|++..+ .|.||++++++|.+++++++..+.. ..
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 899999999999999999999999889999999999999999999997655 7999999999999999998765321 10
Q ss_pred ------Cc---------c-HH---HHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 343 ------PN---------H-LH---ERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 343 ------p~---------~-~~---e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
+. . .. .....+..++..|++..|. .+++|||+.||||+++|+..++++++.+
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 1123466667777554444 3999999999999999999999998765
No 52
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=99.72 E-value=4.7e-17 Score=149.95 Aligned_cols=130 Identities=18% Similarity=0.176 Sum_probs=104.6
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCC---CCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNM---GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~---g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i 340 (417)
.|++.|+..|.+.|+.++.++.++ ..++||++||+|+++|+++++|+++.+ .|.||++++++|.+.++++++.+..
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 357999999999999999999997655 8999999999999999998766432
Q ss_pred ccC---c-------c------HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 341 RLP---N-------H------LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 341 rlp---~-------~------~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
... . . ..+....+..++..|++..|. .+++|||+.||+|..+|++.+.++++.+
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 111223466777777554443 4999999999999999999999998654
No 53
>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=4.5e-17 Score=145.69 Aligned_cols=132 Identities=15% Similarity=0.067 Sum_probs=107.3
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc
Q 014852 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 341 (417)
Q Consensus 262 ~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir 341 (417)
+..|++.|+..|.+.++.++.++.++..++||++||+|+++|+++++|+...+ +|.+|++++++|.++++++.+.+...
T Consensus 9 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~~R~~~~~~~ 87 (170)
T TIGR02952 9 EEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVNDYFRGSKRHPL 87 (170)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHHHHHhcCCCCC
Confidence 33899999999999999999999988899999999999999999999997655 89999999999999999997654322
Q ss_pred cCc-----------cH------HHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 342 LPN-----------HL------HERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 342 lp~-----------~~------~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
.+. .. .+....+..++..|++..|. .+++|||+.||||+++|+..++++++.+
T Consensus 88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~eIA~~l~is~~tv~~~l~ra~~~L 166 (170)
T TIGR02952 88 FSLDVFKELLSNEPNPEEAILKEEANEKLLKALKILTPKQQHVIALRFGQNLPIAEVARILGKTEGAVKILQFRAIKKL 166 (170)
T ss_pred CcHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 110 00 11224466777777654444 3999999999999999999999998654
No 54
>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=7.1e-17 Score=146.79 Aligned_cols=129 Identities=19% Similarity=0.161 Sum_probs=105.4
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccC
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp 343 (417)
.|+.+|+..|.+.|+.+|.+|.++..+++|++||+|+++|+++.+|++.. +|.||++++++|.+.+++++..+.....
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 89999999999999999999999999999999999999999999999876 7999999999999999998754321100
Q ss_pred c-------------------c---H---HHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHH
Q 014852 344 N-------------------H---L---HERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 344 ~-------------------~---~---~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~r 389 (417)
. . . .+....+.+++..|++..|.+ +++|||+.||+|+++|+..+++
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 0 0 011233666777776555443 9999999999999999999999
Q ss_pred hCccc
Q 014852 390 IGKVF 394 (417)
Q Consensus 390 ark~L 394 (417)
+++.+
T Consensus 176 ar~~L 180 (187)
T TIGR02948 176 GREAL 180 (187)
T ss_pred HHHHH
Confidence 98755
No 55
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=99.71 E-value=5.1e-17 Score=148.67 Aligned_cols=130 Identities=21% Similarity=0.239 Sum_probs=107.0
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccC
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp 343 (417)
.|++.|+..|.+.|+.++.+++++..+++|++||+|+.+|+.+++|++..+ .|.+|++++++|.+++++++..+.....
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 899999999999999999999999999999999999999999999987554 7999999999999999999876432211
Q ss_pred c----------cH------HHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 344 N----------HL------HERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 344 ~----------~~------~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
. .. .+....+..++..|++..|. .+++|||+.||||+++|+..++++++.+
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 00 11223466777777654444 3999999999999999999999998654
No 56
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=99.71 E-value=8.2e-17 Score=148.11 Aligned_cols=129 Identities=22% Similarity=0.229 Sum_probs=104.1
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc-
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL- 342 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl- 342 (417)
.|++.|+..|.+.|+.++.++.++..+++|++||+|+++|+. ..|++..+ .|.||++++++|.++++++++.+....
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 899999999999999999999999999999999999999976 67887665 899999999999999999876542110
Q ss_pred -----------Cc-c------HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 343 -----------PN-H------LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 343 -----------p~-~------~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
+. . ..+....+..++..|++..++ .+++|||+.||+|+.+|+..++++++.+
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 00 0 011224467777777654444 3999999999999999999999988654
No 57
>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=99.70 E-value=1.5e-16 Score=151.95 Aligned_cols=120 Identities=19% Similarity=0.205 Sum_probs=100.9
Q ss_pred HHHHHHHHhHHHHHHHHHHccCCC--CChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcc---c
Q 014852 265 AREKLVMSNVRLVMSIAQRYDNMG--ADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSR---T 339 (417)
Q Consensus 265 Are~LIe~yl~LV~sIA~Ry~~~g--~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r---~ 339 (417)
.+++||..|.|+|.++|.+|+++. .+.||++|+|+||||+|+++||+++|.+|.|||.++|++++.+++|+..+ .
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 399999999999999999998664 58999999999999999999999999999999999999999999999873 4
Q ss_pred cccCccHHHHHHHHHHHHHHHH-HcCCCccHHHHHHH------cCCCHHHHH
Q 014852 340 LRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEY------LNMSQKKVR 384 (417)
Q Consensus 340 irlp~~~~e~~~kI~~a~~~L~-e~gRepS~eEIAe~------LGIS~etVr 384 (417)
+++|+...+....+..+...+. ..++.++.+||+.. .||+.+.+-
T Consensus 90 v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~~~~~L~~~gi~~~dLv 141 (218)
T TIGR02895 90 LYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILEYKKLLKQFGIEFVELV 141 (218)
T ss_pred eeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcCCcHHHHh
Confidence 4677665555556666666664 46888888888764 488877763
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=1e-16 Score=144.45 Aligned_cols=129 Identities=18% Similarity=0.146 Sum_probs=106.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccC
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp 343 (417)
.|++.|+..|.+.|++++.++.++..++||++||+|+.+|+.+.+|++.. +|.||++.+++|.+++++++..+....+
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 89999999999999999999999999999999999999999999999754 7999999999999999998765432211
Q ss_pred cc----------HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 344 NH----------LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 344 ~~----------~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
.. ..+....+..++..|++..|+ .|++|||+.||+|+++|+..+.++++.+
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 011123566777777655554 3999999999999999999999998754
No 59
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=99.70 E-value=9.3e-17 Score=154.12 Aligned_cols=130 Identities=21% Similarity=0.228 Sum_probs=107.2
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc--c
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL--R 341 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i--r 341 (417)
.|++.|+..|.+.|+.++.+++++..++||++||+|+++|+.+++|++..+ .|.+|++++++|.+++++|++.+.. .
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 899999999999999999999999999999999999999999999987655 7999999999999999998753211 0
Q ss_pred c-------CccH-----HHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 342 L-------PNHL-----HERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 342 l-------p~~~-----~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
. +... .+....+..++..|++..|++ +++|||+.||+|+++|+..++++++.|
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 1 1100 112234677788886655553 999999999999999999999998755
No 60
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=99.70 E-value=2e-16 Score=144.60 Aligned_cols=129 Identities=16% Similarity=0.159 Sum_probs=105.4
Q ss_pred HHHHHHHHHhHHHHHHHHHHcc-CCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc
Q 014852 264 LAREKLVMSNVRLVMSIAQRYD-NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~-~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl 342 (417)
.|++.|+..|.+.|+.++.++. ++..++||++||+|+.+|+.++.|++.. +|.+|++.+++|.+++++|+..+....
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 8999999999999999999876 4578999999999999999999999753 799999999999999999986432211
Q ss_pred C--------------ccHHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 343 P--------------NHLHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 343 p--------------~~~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
. ....+....+..++..|++..+.+ +++|||+.||+|+++|+..++++++.+
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 011223345777777776555543 999999999999999999999998765
No 61
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=99.69 E-value=1.4e-16 Score=147.40 Aligned_cols=129 Identities=18% Similarity=0.203 Sum_probs=107.6
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccC
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp 343 (417)
.+++.|++.|.+.|++++.++.++..++||++||+|+.+|+.+++|++.. +|.+|++++++|.+++++|+..+....+
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 89999999999999999999999999999999999999999999999764 7999999999999999998765322111
Q ss_pred -----------ccH---HHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 344 -----------NHL---HERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 344 -----------~~~---~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
... .+....+..++..|++..|.+ +++|||+.||+|..+|+..++++++.+
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 111 122345777777886655543 999999999999999999999998765
No 62
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=99.69 E-value=1.6e-16 Score=143.57 Aligned_cols=129 Identities=16% Similarity=0.147 Sum_probs=106.5
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccC
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp 343 (417)
.|++.|+..|.+.|+.+|.++.++..+++|++||+|+++|+++++|++.. +|.+|++.+++|.+++++++..+.....
T Consensus 18 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~~~ 95 (176)
T PRK09638 18 AALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGRS--KFSTWLISIASRLYKDHLRKQKREKLRL 95 (176)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHhcCCcc--cHHHHHHHHHHHHHHHHHHHhccccchh
Confidence 89999999999999999999999999999999999999999999998753 8999999999999999999765422110
Q ss_pred ----------c--c---HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 344 ----------N--H---LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 344 ----------~--~---~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
. . .......+..++..|++..|.+ +++|||+.||+|+.+|+..+.++++.+
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 1112345677777776655553 999999999999999999999988654
No 63
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=99.69 E-value=1.7e-16 Score=148.55 Aligned_cols=130 Identities=18% Similarity=0.156 Sum_probs=106.0
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc-
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL- 342 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl- 342 (417)
.++++|+..|.+.|++++.++.++..+++|++||+|+.+|+++++|++.++ .|.||++++++|.+++++++..+....
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 899999999999999999999999899999999999999999999998766 699999999999999999876532110
Q ss_pred ------C--c-------c---HHH--HHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014852 343 ------P--N-------H---LHE--RLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKV 393 (417)
Q Consensus 343 ------p--~-------~---~~e--~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~ 393 (417)
+ . . ... ....+..++..|++..|. .|++|||+.||+|+.+|+..++++++.
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 113466777777554444 399999999999999999999999876
Q ss_pred c
Q 014852 394 F 394 (417)
Q Consensus 394 L 394 (417)
+
T Consensus 197 L 197 (206)
T PRK12526 197 L 197 (206)
T ss_pred H
Confidence 5
No 64
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=99.69 E-value=1.8e-16 Score=145.99 Aligned_cols=130 Identities=16% Similarity=0.139 Sum_probs=106.5
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc-
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL- 342 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl- 342 (417)
.|++.|+..|.+.++.++. +.++..++||++||+|+.+|+.+++|++.. .|.+|++++++|.+++++++..+....
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 577788999999999999999999999653 899999999999999999875432211
Q ss_pred ----Ccc---------HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014852 343 ----PNH---------LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVFSL 396 (417)
Q Consensus 343 ----p~~---------~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~LSL 396 (417)
+.. ..+....+..++..|++..|++ |++|||+.||+|+++|+..+.++++.+--
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 110 0122345777888887666654 99999999999999999999999987643
No 65
>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=2.7e-16 Score=143.35 Aligned_cols=129 Identities=20% Similarity=0.226 Sum_probs=105.1
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc-
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL- 342 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl- 342 (417)
.|++.|+..|.+.|+.+|.++.++..+++|++||+|+++|+++++|++.. +|.+|++++++|.+++++++..+....
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 89999999999999999999999999999999999999999999999763 799999999999999999765432210
Q ss_pred ---------------------Ccc---HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHH
Q 014852 343 ---------------------PNH---LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 343 ---------------------p~~---~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~r 389 (417)
|.. ..+....+..++..|++..|.+ +++|||+.||+++.+|++.+++
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 000 0111234666777776555543 9999999999999999999999
Q ss_pred hCccc
Q 014852 390 IGKVF 394 (417)
Q Consensus 390 ark~L 394 (417)
+++.|
T Consensus 178 ar~~L 182 (190)
T TIGR02939 178 AREAI 182 (190)
T ss_pred HHHHH
Confidence 98765
No 66
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=99.69 E-value=2.9e-16 Score=142.82 Aligned_cols=129 Identities=22% Similarity=0.189 Sum_probs=105.0
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc-
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL- 342 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl- 342 (417)
.|++.|+..|.++|+.+|.++.++..+++|++||+|++||+++++|++.. .|.+|++++++|.+++++++..+....
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 89999999999999999999999999999999999999999999999754 799999999999999999876532110
Q ss_pred ---------------Cc---c------HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHH
Q 014852 343 ---------------PN---H------LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 343 ---------------p~---~------~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~r 389 (417)
+. . ..+....+..++..|++..++ .+++|||+.||||+++|++.+++
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 00 0 011123466677777554444 39999999999999999999999
Q ss_pred hCccc
Q 014852 390 IGKVF 394 (417)
Q Consensus 390 ark~L 394 (417)
+++.+
T Consensus 176 ar~~L 180 (187)
T PRK09641 176 GREAL 180 (187)
T ss_pred HHHHH
Confidence 98654
No 67
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=99.68 E-value=5.3e-16 Score=142.20 Aligned_cols=129 Identities=21% Similarity=0.187 Sum_probs=104.9
Q ss_pred HHHHHHHHHhHHHHHHHHH----HccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccc
Q 014852 264 LAREKLVMSNVRLVMSIAQ----RYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRT 339 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~----Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ 339 (417)
.||+.|+..|.+.|+.++. ++.++..+++|++||+|+.+|+.++.|++.. .|.+|++++++|.+++++++..+.
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 5557889999999999999999999999764 799999999999999999875532
Q ss_pred c-ccC---------cc---HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 340 L-RLP---------NH---LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 340 i-rlp---------~~---~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
. ..+ .. ..+....+..++..|++..|+ .+++|||+.||+|+++|+..++++++.+
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 00 122334577778888665554 3999999999999999999999998754
No 68
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=99.67 E-value=1.4e-16 Score=145.98 Aligned_cols=134 Identities=18% Similarity=0.147 Sum_probs=109.6
Q ss_pred hhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc
Q 014852 261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340 (417)
Q Consensus 261 ~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i 340 (417)
++..|++.|+..|.+.|+.+|.+++++..++||++||+|+.+|+++.+|++..+..|.||++++++|.+++++++..+..
T Consensus 6 gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn~~~d~~Rk~~~~~ 85 (185)
T PRK12542 6 NDYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRKNKRHE 85 (185)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 45589999999999999999999999999999999999999999999998754448999999999999999998865432
Q ss_pred cc----C--------ccH------HHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014852 341 RL----P--------NHL------HERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKV 393 (417)
Q Consensus 341 rl----p--------~~~------~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~ 393 (417)
.. + ... ......+..++..|++..|++ +++|||+.||+|+++|+..+.++++.
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~ 165 (185)
T PRK12542 86 TFLEEYERESIEAVDENIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARKR 165 (185)
T ss_pred hhhhhccccchhhhhccHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 11 0 000 011234677777887656554 99999999999999999999999876
Q ss_pred c
Q 014852 394 F 394 (417)
Q Consensus 394 L 394 (417)
+
T Consensus 166 L 166 (185)
T PRK12542 166 V 166 (185)
T ss_pred H
Confidence 5
No 69
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=99.66 E-value=6.9e-16 Score=141.35 Aligned_cols=135 Identities=24% Similarity=0.251 Sum_probs=112.4
Q ss_pred HhhhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhc
Q 014852 258 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENS 337 (417)
Q Consensus 258 ~l~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~ 337 (417)
....+..++..++..|.+.++.++.+++++..++|||+||+|+.+|+++..| ...+ .|.||++++++|.+++++|+..
T Consensus 9 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~~~-~~~~wl~~Ia~n~~iD~~R~~~ 86 (182)
T COG1595 9 ALRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RGRS-SFKAWLYRIARNLAIDRLRKRK 86 (182)
T ss_pred HHhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CCCC-chHHHHHHHHHHHHHHHHHHhc
Confidence 3445668999999999999999999999988899999999999999999999 4444 8999999999999999999776
Q ss_pred ccccc-C-------------ccH-----HHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHH
Q 014852 338 RTLRL-P-------------NHL-----HERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 338 r~irl-p-------------~~~-----~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~r 389 (417)
+.... . ... .+....+..++..|++..|++ |++|||+.||||+++|+..+++
T Consensus 87 r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~~~gls~~EIA~~l~i~~~tVks~l~r 166 (182)
T COG1595 87 RRRARVEEADLLPEEADPAPDLAELLLAEEELERLRRALARLPPRQREAFLLRYLEGLSYEEIAEILGISVGTVKSRLHR 166 (182)
T ss_pred ccccccccccccccccCcccccchHHHHHHHHHHHHHHHHhCCHHHhHHhhhHhhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 53221 0 001 233456888888887766664 9999999999999999999999
Q ss_pred hCccc
Q 014852 390 IGKVF 394 (417)
Q Consensus 390 ark~L 394 (417)
++..+
T Consensus 167 a~~~l 171 (182)
T COG1595 167 ARKKL 171 (182)
T ss_pred HHHHH
Confidence 98755
No 70
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=99.66 E-value=4.1e-16 Score=139.95 Aligned_cols=131 Identities=24% Similarity=0.189 Sum_probs=104.4
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc
Q 014852 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 341 (417)
Q Consensus 262 ~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir 341 (417)
+..|++.|+..|.++|+.++.+|.+++.+++|++||++++||+++++|+ . +.+|.||++.++++.+.+++++..+...
T Consensus 8 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~-~-~~~~~~~l~~~~~~~~~~~~r~~~~~~~ 85 (182)
T PRK09652 8 DRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR-G-GAAFYTWLYRIARNTAINYLRKQGRRPP 85 (182)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcC-C-CcchHHHHHHHHHHHHHHHHHcccCCCC
Confidence 4489999999999999999999999999999999999999999999999 3 3489999999999999999987654322
Q ss_pred cC-------c---------c---H------HHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHH
Q 014852 342 LP-------N---------H---L------HERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNAT 387 (417)
Q Consensus 342 lp-------~---------~---~------~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL 387 (417)
.+ . . . .+....+..++..|++..|. .+++|||+.||+|+.+|+..+
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~tV~~~l 165 (182)
T PRK09652 86 ASDVDAEEAEDFDLADALRDISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRI 165 (182)
T ss_pred ccccccccccccccccccccccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 11 0 0 0 01223455666666443333 399999999999999999999
Q ss_pred HHhCccc
Q 014852 388 EAIGKVF 394 (417)
Q Consensus 388 ~rark~L 394 (417)
+++++.+
T Consensus 166 ~ra~~~L 172 (182)
T PRK09652 166 FRAREAL 172 (182)
T ss_pred HHHHHHH
Confidence 9988654
No 71
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=99.66 E-value=4.6e-16 Score=141.44 Aligned_cols=129 Identities=19% Similarity=0.187 Sum_probs=100.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCC-----ChhhhhhhHHHHHHH-HHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhc
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGA-----DMADLVQGGLIGLLR-GIEKFDSSKGFKISTYVYWWIRQGVSRALVENS 337 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~-----e~EDLIQEG~IgLik-AierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~ 337 (417)
.|++.|+..|.+.|+.+|.+|.++.. +++|++||+|+.+|+ ...+|++. + .|.+|++.+++|.+++++++..
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 78889754 3 7999999999999999998754
Q ss_pred cccc------c------Cc---cHHHHHHHHHHHHHH---HHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 338 RTLR------L------PN---HLHERLGLIRNAKLR---LEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 338 r~ir------l------p~---~~~e~~~kI~~a~~~---L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~ra 390 (417)
+..+ . +. ...+....+..+... |++..|+ .|++|||+.||||+++|+..++++
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 3211 0 00 111222233444344 6554444 399999999999999999999999
Q ss_pred Cccc
Q 014852 391 GKVF 394 (417)
Q Consensus 391 rk~L 394 (417)
++.+
T Consensus 175 r~~L 178 (183)
T TIGR02999 175 RAWL 178 (183)
T ss_pred HHHH
Confidence 8654
No 72
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=99.66 E-value=6.1e-16 Score=142.14 Aligned_cols=129 Identities=16% Similarity=0.146 Sum_probs=105.0
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc-
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL- 342 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl- 342 (417)
.|++.|+..|.+.++.++.++.++..+++|++||+|+.+|+++.+|++.. .|.||++++++|.+.+++++..+....
T Consensus 22 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~~~ 99 (189)
T PRK12515 22 TAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGRS--QVSTWLLSIARFKALSALRRRKHEEIDD 99 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCCC--ChHHHHHHHHHHHHHHHHHccCCCCCcc
Confidence 89999999999999999999999999999999999999999999999753 899999999999999999875432110
Q ss_pred ------Cc------cH---HHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 343 ------PN------HL---HERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 343 ------p~------~~---~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
+. .. .+....+..++..|++..|+ .+++|||+.||+|+++|++.+.++++.+
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 01123466677777654544 3999999999999999999999998765
No 73
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=99.66 E-value=1.2e-15 Score=139.16 Aligned_cols=129 Identities=19% Similarity=0.162 Sum_probs=105.0
Q ss_pred HHHHHHHHHhHHHHHHHHHHccC----CCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccc
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDN----MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRT 339 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~----~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ 339 (417)
.|++.|+..|.+.|+.+|.++++ +..+++|++||+|+.+|+..++|+... .|.+|++.+++|.+.++++++.+.
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 89999999999999999999875 346899999999999999999998743 799999999999999999876543
Q ss_pred ccc---------Ccc---HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 340 LRL---------PNH---LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 340 irl---------p~~---~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
... +.. .......+.+++..|++..|++ +++|||+.||+|..+|+..++++++.+
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 1122355777777776655553 999999999999999999999998765
No 74
>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=6.9e-16 Score=136.82 Aligned_cols=128 Identities=16% Similarity=0.173 Sum_probs=105.0
Q ss_pred HHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc-C
Q 014852 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL-P 343 (417)
Q Consensus 265 Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl-p 343 (417)
|++.++..|.+.|+.+|.++.++..++||++||+++.+|+++++|++.. .|.+|++++++|.++++++++.+.... .
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 799999999999999999986643221 0
Q ss_pred cc----------------HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 344 NH----------------LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 344 ~~----------------~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
.. ..+....+..++..|++..+. .+++|||+.||||.++|+..++++++.+
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 011223366667777554443 3999999999999999999999998765
No 75
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=99.65 E-value=9e-16 Score=140.24 Aligned_cols=131 Identities=12% Similarity=0.124 Sum_probs=107.7
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc
Q 014852 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 341 (417)
Q Consensus 262 ~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir 341 (417)
+..|++.|+..|.+.|++++.+++++..+++|++||+|+.+|+++++|++.. .|.+|++++++|.+++++|+..+...
T Consensus 14 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~~--~~~awl~~ia~n~~~d~~Rk~~~~~~ 91 (179)
T PRK09415 14 KEDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKS--SLKTWLYRIAINHCKDYLKSWHNKKV 91 (179)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCCc--ccHHHHHHHHHHHHHHHHHhhccccc
Confidence 4479999999999999999999999999999999999999999999998753 79999999999999999987532211
Q ss_pred cC---------------cc---HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 342 LP---------------NH---LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 342 lp---------------~~---~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
.+ .. ..+....+..++..|++..|++ |++|||+.||||+++|+..+.++++.+
T Consensus 92 ~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tv~~~l~Ra~~~L 171 (179)
T PRK09415 92 IVTEDIFTYMESQKESVEEEVIQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELL 171 (179)
T ss_pred cccccccccccccccCcHHHHHHHHHHHHHHHHHHhCCHHHhhHhHhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 10 00 1122345677777787666664 999999999999999999999998765
No 76
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=99.64 E-value=6.6e-16 Score=142.17 Aligned_cols=128 Identities=15% Similarity=0.137 Sum_probs=106.0
Q ss_pred HHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCc
Q 014852 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPN 344 (417)
Q Consensus 265 Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~ 344 (417)
+|+.|+..|.+.|+.+|.+++++..++||++||.|+.+|+.+++|++.. +|.||++++++|.+++++++..+......
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 6899999999999999999999999999999999999999999998654 79999999999999999998654322110
Q ss_pred ------------------------------cH------HHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCC
Q 014852 345 ------------------------------HL------HERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMS 379 (417)
Q Consensus 345 ------------------------------~~------~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS 379 (417)
.. .+....+..++..|++..|.+ |++|||+.||+|
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 011234677777786655554 999999999999
Q ss_pred HHHHHHHHHHhCccc
Q 014852 380 QKKVRNATEAIGKVF 394 (417)
Q Consensus 380 ~etVr~aL~rark~L 394 (417)
+++|+..++++++.+
T Consensus 161 ~~tV~~~l~Rar~~L 175 (191)
T PRK12520 161 ATNAWVLLYRARMRL 175 (191)
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999999998765
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=1.2e-15 Score=147.78 Aligned_cols=129 Identities=15% Similarity=0.058 Sum_probs=105.2
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHH-------HHhhcCCCCCCchhhHHHHHHHhhHHHHHHhh
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLR-------GIEKFDSSKGFKISTYVYWWIRQGVSRALVEN 336 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLik-------AierFD~~rG~rFsTYA~~~IR~~i~~~Ird~ 336 (417)
.||..|++.|.+.|+.++.+++++..++||++||+|+.+|. .+++|++.. .|.||++++++|.++++++++
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 788899753 799999999999999999876
Q ss_pred ccccccC---------------ccH-H------HHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHH
Q 014852 337 SRTLRLP---------------NHL-H------ERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRN 385 (417)
Q Consensus 337 ~r~irlp---------------~~~-~------e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~ 385 (417)
.+...+. ... . +....+.+++..|++..|++ |++|||+.||||+++|+.
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 12234777888887655553 999999999999999999
Q ss_pred HHHHhCccc
Q 014852 386 ATEAIGKVF 394 (417)
Q Consensus 386 aL~rark~L 394 (417)
.++++++.+
T Consensus 197 rl~RAr~~L 205 (244)
T TIGR03001 197 WVAQARERL 205 (244)
T ss_pred HHHHHHHHH
Confidence 999988654
No 78
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=99.64 E-value=1.4e-15 Score=137.75 Aligned_cols=129 Identities=16% Similarity=0.116 Sum_probs=105.3
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc-
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL- 342 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl- 342 (417)
..+++|+..|.++|+.+|.+|.++..++||++||+|+.+|+++++|++.. +|.+|++.+++|.+++++|++.+....
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 46899999999999999999999999999999999999999999999864 899999999999999999876542110
Q ss_pred --------------------Ccc--HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 343 --------------------PNH--LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 343 --------------------p~~--~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rar 391 (417)
+.. ..+....+..++..|++..+. .+++|||+.||+|+++|+..+.+++
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 011223466777777654444 3999999999999999999999998
Q ss_pred ccc
Q 014852 392 KVF 394 (417)
Q Consensus 392 k~L 394 (417)
+.|
T Consensus 161 ~~L 163 (173)
T PRK12522 161 KQM 163 (173)
T ss_pred HHH
Confidence 765
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=140.30 Aligned_cols=130 Identities=17% Similarity=0.157 Sum_probs=107.5
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc
Q 014852 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (417)
Q Consensus 263 ~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl 342 (417)
..+|+.|+..|.+.|+.+|.+++++..+++|++||+|+.+|+.+.+|++.. +|.+|++++++|.+++++++..+....
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 478999999999999999999999999999999999999999999998654 799999999999999999876543211
Q ss_pred C--c------------c------HH-------HHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHH
Q 014852 343 P--N------------H------LH-------ERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNA 386 (417)
Q Consensus 343 p--~------------~------~~-------e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~a 386 (417)
. . . .. .....+..++..|++..|++ |++|||+.||||+++|+..
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 0 0 00 11245677888887666654 9999999999999999999
Q ss_pred HHHhCccc
Q 014852 387 TEAIGKVF 394 (417)
Q Consensus 387 L~rark~L 394 (417)
++++++.+
T Consensus 168 l~Rar~~L 175 (193)
T TIGR02947 168 LHRGRKQL 175 (193)
T ss_pred HHHHHHHH
Confidence 99998755
No 80
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=99.63 E-value=1.3e-15 Score=139.03 Aligned_cols=132 Identities=17% Similarity=0.138 Sum_probs=107.4
Q ss_pred hhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc
Q 014852 261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340 (417)
Q Consensus 261 ~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i 340 (417)
++..|+..|+..|.+.|+.++.+|+++..+++|++||+|+.+|+++.+|++.. .|.+|++.+++|.+.++++...+..
T Consensus 4 ~d~~af~~l~~~~~~~l~~~~~~~~~~~~daeDl~Qevfl~l~~~~~~~~~~~--~f~~wl~~iarn~~~~~~r~~~~~~ 81 (179)
T PRK12543 4 GDQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNR--PFRFWLIGLVIKQIHSWRRKRWRRF 81 (179)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--ChHHHHHHHHHHHHHHHHHhhcccc
Confidence 34579999999999999999999999999999999999999999999999875 7999999999999999887644211
Q ss_pred c---------------cCccH--HHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 341 R---------------LPNHL--HERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 341 r---------------lp~~~--~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
+ .|... .+....+..++..|++..|++ |++|||+.||||+++|+..++++++.+
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~i~~l~~~e~~s~~EIA~~lgis~~tV~~~l~ra~~~L 161 (179)
T PRK12543 82 RIFEKAEEQRKPVSIDFSEDVLSKESNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKKL 161 (179)
T ss_pred ccccccccccccccccChHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHccCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 1 11111 122345677777776655543 999999999999999999999988655
No 81
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=99.63 E-value=1.3e-15 Score=137.40 Aligned_cols=132 Identities=15% Similarity=0.099 Sum_probs=106.6
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc
Q 014852 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 341 (417)
Q Consensus 262 ~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir 341 (417)
+..+++.|+..|.+.|+++|.+++++..++||++||.|+.+|+..++|++..+ .|.+|++++++|.+++++++..+...
T Consensus 7 ~~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~~~~~~~~~~~-~~~~wL~~iarn~~~d~~Rk~~~~~~ 85 (173)
T PRK09645 7 EAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTGR-SARAWLFTVARNLVIDERRSARARPV 85 (173)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-cHHHHHHHHHHHHHHHHHHhhccccc
Confidence 44799999999999999999999998899999999999999999999975433 79999999999999999987543211
Q ss_pred --------cCc-----cHH--HHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 342 --------LPN-----HLH--ERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 342 --------lp~-----~~~--e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
.+. ... .....+..++..|++..|++ +++|||+.||+|+++|+..++++++.+
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~L 162 (173)
T PRK09645 86 EGGDDVLGVPEQSAPDEVDRALDRLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRAL 162 (173)
T ss_pred ccccccccCCCCCCchHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 110 111 11234677777776655553 999999999999999999999998654
No 82
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=99.63 E-value=1.7e-15 Score=140.18 Aligned_cols=131 Identities=11% Similarity=0.137 Sum_probs=107.9
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc
Q 014852 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 341 (417)
Q Consensus 262 ~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir 341 (417)
+..+|..|+..|.+.++.+|.+++++..++||++||.|+.+|+..++|+... .|.+|++++++|.++++++++.+...
T Consensus 8 ~~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~~--~~~awL~~Ia~n~~~d~~R~~~~~~~ 85 (187)
T PRK12516 8 GTPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGT--NMKAWLFTILRNEFYSQMRKRGREVQ 85 (187)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCcc--cHHHHHHHHHHHHHHHHHHhhcCCcc
Confidence 4479999999999999999999999999999999999999999999998654 79999999999999999998654221
Q ss_pred cCc------------c-HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 342 LPN------------H-LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 342 lp~------------~-~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
... . .......+..++..|++..|++ +++|||+.||||+++|+..+.++++.|
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~i~~L~~~~g~s~~EIA~~Lgis~~tVk~~l~Rar~~L 160 (187)
T PRK12516 86 DTDGMFTEQLAVHPSQYGTLDLQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRL 160 (187)
T ss_pred ccccccccccCCCcchhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 100 0 1112345777888886655553 999999999999999999999998655
No 83
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=99.63 E-value=1.8e-15 Score=139.40 Aligned_cols=150 Identities=16% Similarity=0.194 Sum_probs=116.4
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc-
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL- 342 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl- 342 (417)
.++..++..|.+.|+++|.+++++..++||++||+|+.+|+..++|++.. .|.+|++++++|.++++++++.+....
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 57889999999999999999999999999999999999999999998764 799999999999999999876542210
Q ss_pred -----------Ccc-HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc--ccccc
Q 014852 343 -----------PNH-LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF--SLDRE 399 (417)
Q Consensus 343 -----------p~~-~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L--SLD~~ 399 (417)
+.. .......+..++..|++..|++ |++|||+.||+|+++|+..++++++.| .|...
T Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~ 162 (182)
T PRK12540 83 DGSYAKTLKSQPGQNAHLEFEEFRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLYVD 162 (182)
T ss_pred cccccccccCCCchHHHHHHHHHHHHHHhCCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 000 1112245677788886655553 999999999999999999999998765 22211
Q ss_pred cCCCCCCCCCCccccccC
Q 014852 400 AFPSLNGLPGETHHIHCG 417 (417)
Q Consensus 400 ~~~s~~~~~~d~l~d~l~ 417 (417)
. ..+..++++..+++|
T Consensus 163 ~--~~~~~~~~~~~~~~~ 178 (182)
T PRK12540 163 G--AEDFGPDDTVRAVIG 178 (182)
T ss_pred c--ccccCCCcccccccC
Confidence 1 222356677777776
No 84
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=99.62 E-value=2.8e-15 Score=135.37 Aligned_cols=129 Identities=17% Similarity=0.129 Sum_probs=102.8
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc-
Q 014852 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR- 341 (417)
Q Consensus 263 ~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir- 341 (417)
..|++.|+..|.+.|+.++.++.+ ..+++|++||+|+.+|+.++.|++.. .|.+|++++++|.+++++|+..+...
T Consensus 10 ~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~ia~n~~~d~~R~~~~~~~~ 86 (175)
T PRK12518 10 RQSFRQLYRRYQQKVRSTLYQLCG-RELLDDLVQEVFLRVWKGLPKLRNPA--YFSTWLYRITWNVATDARRQFAQRPSR 86 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcC-HhHHHHHHHHHHHHHHHhHHhhCCcc--cHHHHHHHHHHHHHHHHHHHhhccccc
Confidence 389999999999999999999874 47899999999999999999999753 79999999999999999987543110
Q ss_pred ---cC--------c--c-H--HHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 342 ---LP--------N--H-L--HERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 342 ---lp--------~--~-~--~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
.+ . . . .+....+..++..|++..|.+ |++|||+.||+|+++|+..++++++.+
T Consensus 87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L 164 (175)
T PRK12518 87 IQDDSLNDQPSRPSDTPDLMQLHYQDLVQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYARRQL 164 (175)
T ss_pred hhcccccccccCCCCcHHHHHHHHHHHHHHHHHhCCHHHeeeeeehHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 00 0 0 0 011133566677776655553 999999999999999999999998765
No 85
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=99.62 E-value=3.8e-15 Score=133.33 Aligned_cols=130 Identities=19% Similarity=0.127 Sum_probs=104.6
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc
Q 014852 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (417)
Q Consensus 263 ~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl 342 (417)
..|++.|++.|.+.|+++|.++.++..+++|++||+|++||+++++|+ .. ..|.+|++.++++.+.++++...+....
T Consensus 12 ~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~-~~-~~~~~~l~~i~~~~~~d~~r~~~~~~~~ 89 (179)
T PRK11924 12 KEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN-GK-GSARTWLLTIARNVCYDLLRRRRREKAV 89 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC-Cc-chHHHHHHHHHHHHHHHHHHhccccccc
Confidence 389999999999999999999999999999999999999999999999 33 3899999999999999999875543211
Q ss_pred Cc-------------c------HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 343 PN-------------H------LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 343 p~-------------~------~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
.. . ..+....+..++..|++..+. .+++|||+.||+|..+|++.++++++.+
T Consensus 90 ~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~~~~~~eIA~~lgis~~tv~~~~~ra~~~l 169 (179)
T PRK11924 90 LSDDALEPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLL 169 (179)
T ss_pred CcccccccccCCccCCHHHHHhhHHHHHHHHHHHHhCCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 00 0 111223456666666544443 3999999999999999999999988654
No 86
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=99.62 E-value=3.8e-15 Score=148.89 Aligned_cols=130 Identities=23% Similarity=0.224 Sum_probs=106.8
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc--
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR-- 341 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir-- 341 (417)
.+++.|+..|.+.|+++|.+++++..++||++||.|+.+|+.+++|++.. .|.+|++++++|.+++++|++.+...
T Consensus 19 ~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~~~~~~~~~~--~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~ 96 (339)
T PRK08241 19 DAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGRS--SLRTWLYRIATNVCLDALEGRARRPLPT 96 (339)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhhhcccccc--chHHHHHHHHHHHHHHHHHhhccccCcc
Confidence 89999999999999999999999999999999999999999999998543 79999999999999999987543210
Q ss_pred -c-----------------------Cc-----------cH---HHH-HHHHHHHHHHHHHcCCCc---------cHHHHH
Q 014852 342 -L-----------------------PN-----------HL---HER-LGLIRNAKLRLEEKGVTP---------SVDRIA 373 (417)
Q Consensus 342 -l-----------------------p~-----------~~---~e~-~~kI~~a~~~L~e~gRep---------S~eEIA 373 (417)
. +. .. .+. ...+..++..|++..|++ +++|||
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 123667788887666664 999999
Q ss_pred HHcCCCHHHHHHHHHHhCcccc
Q 014852 374 EYLNMSQKKVRNATEAIGKVFS 395 (417)
Q Consensus 374 e~LGIS~etVr~aL~rark~LS 395 (417)
+.||+|+++|+..++++++.+.
T Consensus 177 ~~lgis~~tVk~~l~RAr~~Lr 198 (339)
T PRK08241 177 ELLDTSVAAVNSALQRARATLA 198 (339)
T ss_pred HHhCCCHHHHHHHHHHHHHHHh
Confidence 9999999999999999987664
No 87
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=99.61 E-value=4.7e-15 Score=133.54 Aligned_cols=130 Identities=12% Similarity=0.128 Sum_probs=106.8
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc
Q 014852 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (417)
Q Consensus 263 ~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl 342 (417)
...|..|+..|.+.|+.+|.++.++..++||++||+|+.+|+...+|+... .|.+|++++++|.+++++++..+....
T Consensus 5 ~~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~~~~~ 82 (164)
T PRK12547 5 SKNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGT--NLKAWLFTILRNEFYSQMRKRGREVQD 82 (164)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCcc--cHHHHHHHHHHHHHHHHHHhhcccccc
Confidence 478999999999999999999999999999999999999999999998654 799999999999999999876542211
Q ss_pred C---------cc----HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 343 P---------NH----LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 343 p---------~~----~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
. .. .......+..++..|++..|++ +++|||+.||||+++|++.++++++.+
T Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~~L 156 (164)
T PRK12547 83 SDGVFTARVAVHPAQYGSLDLQDFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRL 156 (164)
T ss_pred ccccccccCCCCchhhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 0 00 0112345677788886655553 999999999999999999999998654
No 88
>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=99.60 E-value=4.6e-15 Score=132.37 Aligned_cols=131 Identities=15% Similarity=0.081 Sum_probs=106.8
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc-
Q 014852 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL- 340 (417)
Q Consensus 262 ~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i- 340 (417)
+..+++.|+..|.+.|+.++.+++++..+++|++||+|+.+|+.+++|+. .+ .|.+|++.+++|.+++++++..+..
T Consensus 4 ~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~-~~-~~~~wl~~i~~n~~~d~~rk~~~~~~ 81 (162)
T TIGR02983 4 TEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRD-PD-APDAYVRRVLVNLARSRWRRRRLLEL 81 (162)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCC-cc-cHHHHHHHHHHHHHHHHHHhhccccc
Confidence 45899999999999999999999999999999999999999999999964 33 8999999999999999998765311
Q ss_pred ---ccCc----c---HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 341 ---RLPN----H---LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 341 ---rlp~----~---~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
..+. . .......+..++..|++..|++ +++|||+.||+|+++|+..+.++++.+
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ra~~~L 154 (162)
T TIGR02983 82 PTRELPDAAAPDPAPDVALRAALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARL 154 (162)
T ss_pred cccccCcccCCccchhHHHHHHHHHHHHhCCHHHHHHhhhHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 0010 0 1123345777777776655543 999999999999999999999998765
No 89
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=99.60 E-value=7.7e-15 Score=136.86 Aligned_cols=128 Identities=10% Similarity=0.049 Sum_probs=103.4
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc-
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL- 342 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl- 342 (417)
.+++.|+..|.+.++.++. +.++..++||++||.|+.+|+..++|++.. .|.+|++.+++|.+++++|+..+..+.
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 799999999999999999975432110
Q ss_pred -------------Ccc--HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 343 -------------PNH--LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 343 -------------p~~--~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
|.. ..+....+..++..|++..|++ +++|||+.||+|+++|+..++++++.|
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 1112245677777776655554 999999999999999999999998654
No 90
>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=132.00 Aligned_cols=128 Identities=22% Similarity=0.214 Sum_probs=101.7
Q ss_pred HHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc--
Q 014852 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL-- 342 (417)
Q Consensus 265 Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl-- 342 (417)
|++.|+..|.+.|+.++.++.++..++||++||+|+++|+.+.+|++.. +|.+|++.++++.+.+++++..+....
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 7899999999999999999999989999999999999999999998754 899999999999999988876532110
Q ss_pred --------------Ccc---HHHHHHHHHHHHHHHHHcCC---------CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 343 --------------PNH---LHERLGLIRNAKLRLEEKGV---------TPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 343 --------------p~~---~~e~~~kI~~a~~~L~e~gR---------epS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
|.. ..+....+..++..|++..+ +.++.|||+.||+|+.+|+..++++++.+
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 01122345666665543333 34999999999999999999999997654
No 91
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=99.60 E-value=6.3e-15 Score=131.75 Aligned_cols=129 Identities=13% Similarity=0.105 Sum_probs=104.3
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc
Q 014852 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (417)
Q Consensus 263 ~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl 342 (417)
..|++.|+..|.+.|+.++.+++++..+++|++||+|+.+|+.+++|++. .|.||++++++|.+++++++..+....
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 47999999999999999999999999999999999999999999999863 599999999999999999876532111
Q ss_pred ----------Ccc-----HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 343 ----------PNH-----LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 343 ----------p~~-----~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
+.. ..+....+..++..|++..|.+ +++|||+.||+|+++|+..++++++.+
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 1112233455666676555543 999999999999999999999998755
No 92
>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=99.59 E-value=6.3e-15 Score=126.28 Aligned_cols=128 Identities=28% Similarity=0.353 Sum_probs=102.7
Q ss_pred HHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcc------
Q 014852 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSR------ 338 (417)
Q Consensus 265 Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r------ 338 (417)
|++.|+..|.++|+++++++..++.+++|++||++++++++++.|++. .+|.+|+..++++.+.+++++..+
T Consensus 2 a~~~l~~~~~~~v~~~~~~~~~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~rk~~~~~~~~~ 79 (158)
T TIGR02937 2 AFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRRLRRELD 79 (158)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHHHHHHHHhccCCcchh
Confidence 789999999999999999999988999999999999999999999998 489999999999999999988763
Q ss_pred cc-cc------Ccc---HHHHHHHHHHHHHHHHHcCC---------CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 339 TL-RL------PNH---LHERLGLIRNAKLRLEEKGV---------TPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 339 ~i-rl------p~~---~~e~~~kI~~a~~~L~e~gR---------epS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
.. .. +.. .......+..++..|++..+ +.+..|||+.||+|+.+|++++.++++.+
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~ii~~~~~~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl 154 (158)
T TIGR02937 80 LLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154 (158)
T ss_pred hhhhcccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 00 00 000 11223445666666643332 34999999999999999999999987543
No 93
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=99.59 E-value=4e-15 Score=136.02 Aligned_cols=134 Identities=13% Similarity=-0.005 Sum_probs=105.1
Q ss_pred hhHHHHHHHHHHhHHHHHHHHHHccC--CCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcc
Q 014852 261 ECSLAREKLVMSNVRLVMSIAQRYDN--MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSR 338 (417)
Q Consensus 261 ~~~~Are~LIe~yl~LV~sIA~Ry~~--~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r 338 (417)
++..+|+.|+..|.+.|+.++.++++ +..++||++||.|+.+|+..++|+......|.||++++++|.+++++++..+
T Consensus 10 ~d~~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~~Rk~~~ 89 (178)
T PRK12529 10 ADRDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSWRRRQSL 89 (178)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHHHHHHHH
Confidence 44589999999999999998665555 4678999999999999999999985433489999999999999999987542
Q ss_pred ccc-------c-------Ccc---HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCc
Q 014852 339 TLR-------L-------PNH---LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGK 392 (417)
Q Consensus 339 ~ir-------l-------p~~---~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark 392 (417)
... . |.. ..+....|..++..|++..|.+ |++|||+.||+|+++|+..++++..
T Consensus 90 ~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~rAl~ 169 (178)
T PRK12529 90 ELAWLEALATLPEPLHPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQAYV 169 (178)
T ss_pred HhhhhhHhhhccCcCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 110 0 111 1123345788888887766664 9999999999999999999998875
Q ss_pred cc
Q 014852 393 VF 394 (417)
Q Consensus 393 ~L 394 (417)
.+
T Consensus 170 ~~ 171 (178)
T PRK12529 170 TC 171 (178)
T ss_pred HH
Confidence 43
No 94
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=99.58 E-value=7.1e-15 Score=132.13 Aligned_cols=126 Identities=10% Similarity=0.058 Sum_probs=103.2
Q ss_pred HHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccC--
Q 014852 266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP-- 343 (417)
Q Consensus 266 re~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp-- 343 (417)
++.|++.|.+.|+.+|.++.++..++||++||+|+.+|+.+++|++. .|.+|++++++|.+.+++++..+.....
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 6999999999999999999866432111
Q ss_pred ----------ccH---HHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 344 ----------NHL---HERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 344 ----------~~~---~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
... .+....+..++..|++..|++ +++|||+.||+|+++|+.+++++++.+
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Rar~~L 152 (165)
T PRK09644 80 EIEAIQAESTEEYVVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRL 152 (165)
T ss_pred HHhhhcccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 110 112245666777776555553 999999999999999999999998765
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=99.58 E-value=8.1e-15 Score=145.17 Aligned_cols=131 Identities=21% Similarity=0.201 Sum_probs=107.2
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc
Q 014852 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 341 (417)
Q Consensus 262 ~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir 341 (417)
+..|++.|+..|.+.|+++|.+++++..++||++||.|+.+|+.+++|++.. .|.+|++++++|.+++++|++.+...
T Consensus 3 d~~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~~--~~~~WL~~Ia~n~~~d~~Rk~~~~~~ 80 (324)
T TIGR02960 3 DGAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGRS--SVRTWLYRIATNACLDALEARQRRPR 80 (324)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCccc--chHHHHHHHHHHHHHHHHHhccCCcC
Confidence 3479999999999999999999999999999999999999999999999753 79999999999999999987543211
Q ss_pred --------------------------cCc-----------c-----H-HHH-HHHHHHHHHHHHHcCCCc---------c
Q 014852 342 --------------------------LPN-----------H-----L-HER-LGLIRNAKLRLEEKGVTP---------S 368 (417)
Q Consensus 342 --------------------------lp~-----------~-----~-~e~-~~kI~~a~~~L~e~gRep---------S 368 (417)
.+. . . .+. ...+..++..|++..|.+ +
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s 160 (324)
T TIGR02960 81 PVGLGAPSADGTAAASEAAEVTWLEPLPDLTLDLDDPAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRDVLGWR 160 (324)
T ss_pred ccccCCCCCcccccccccccccccCCCCccccccccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHHhCCC
Confidence 000 0 0 111 123667788887666664 9
Q ss_pred HHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 369 VDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 369 ~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
++|||+.||+|+++|++.++++++.|
T Consensus 161 ~~EIA~~lgis~~tV~~~l~Rar~~L 186 (324)
T TIGR02960 161 AAETAELLGTSTASVNSALQRARATL 186 (324)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 99999999999999999999998765
No 96
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=99.57 E-value=1.5e-14 Score=137.47 Aligned_cols=131 Identities=15% Similarity=0.149 Sum_probs=107.3
Q ss_pred hhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc
Q 014852 261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340 (417)
Q Consensus 261 ~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i 340 (417)
....+|+.|+..|.+.++.++.++.++..++||++||+|+.+|+.+++|++. .|.+|++++++|.++++++++.+..
T Consensus 15 ~~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~~---~~~aWL~~IarN~~~d~~Rk~~~~~ 91 (216)
T PRK12533 15 ARGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRGD---NARPWLLAIVRHTWYSEWRRRANAH 91 (216)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCcc---chHhHHHHHHHHHHHHHHHhhcccc
Confidence 4457999999999999999999999999999999999999999999999853 5999999999999999998764321
Q ss_pred c------cC------------cc------HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHH
Q 014852 341 R------LP------------NH------LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNAT 387 (417)
Q Consensus 341 r------lp------------~~------~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL 387 (417)
. .. .. ..+....+..++..|++..|++ |++|||+.||||+++|+..+
T Consensus 92 ~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y~eg~s~~EIAe~LgiS~~tVk~~L 171 (216)
T PRK12533 92 EVAAPDTLDDADSLDDWQPAGEDPLALLLRAEDVRLVNAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRL 171 (216)
T ss_pred cccccccccccccccccccCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHhHhhhHHhcCCCHHHHHHHHCCCHHHHHHHH
Confidence 1 00 00 1122345777777886655554 99999999999999999999
Q ss_pred HHhCccc
Q 014852 388 EAIGKVF 394 (417)
Q Consensus 388 ~rark~L 394 (417)
+++++.|
T Consensus 172 ~RAr~~L 178 (216)
T PRK12533 172 ARARRRL 178 (216)
T ss_pred HHHHHHH
Confidence 9998765
No 97
>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=99.57 E-value=1.8e-14 Score=130.99 Aligned_cols=133 Identities=19% Similarity=0.115 Sum_probs=103.2
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHcc----CCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhc
Q 014852 262 CSLAREKLVMSNVRLVMSIAQRYD----NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENS 337 (417)
Q Consensus 262 ~~~Are~LIe~yl~LV~sIA~Ry~----~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~ 337 (417)
+..|++.|+..|.+.|+.+|++|. ++..++||++||+|+.+|+++.+|++..+.+|.+|++++++|.+.+++++..
T Consensus 5 ~~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r~~~ 84 (189)
T TIGR02984 5 DQEALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNVLADALRRHL 84 (189)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHHHHHHHHH
Confidence 458999999999999999999874 3567899999999999999999999765558999999999999999998651
Q ss_pred ----ccc----cc-----------------------Ccc---HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHH
Q 014852 338 ----RTL----RL-----------------------PNH---LHERLGLIRNAKLRLEEKGVT---------PSVDRIAE 374 (417)
Q Consensus 338 ----r~i----rl-----------------------p~~---~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe 374 (417)
+.. .+ |.. ..+....+..++..|++..|. .+++|||+
T Consensus 85 ~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vi~l~~~~g~s~~eIA~ 164 (189)
T TIGR02984 85 GAQKRDIRREQSLDAGGRLDESSVRLAAQLAADGPSPSQVAARREAAVRLAQALAKLPEDYREVILLRHLEGLSFAEVAE 164 (189)
T ss_pred HHHhhhcccccCCCcccccCCcchhHHHHccCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCHHHHHH
Confidence 100 00 000 011223466666666544433 39999999
Q ss_pred HcCCCHHHHHHHHHHhCccc
Q 014852 375 YLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 375 ~LGIS~etVr~aL~rark~L 394 (417)
.||||+++|+..++++++.+
T Consensus 165 ~lgis~~~v~~~l~Ra~~~L 184 (189)
T TIGR02984 165 RMDRSEGAVSMLWVRGLARL 184 (189)
T ss_pred HHCcCHHHHHHHHHHHHHHH
Confidence 99999999999999988654
No 98
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=99.56 E-value=7.8e-15 Score=132.90 Aligned_cols=128 Identities=16% Similarity=0.099 Sum_probs=102.2
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc---
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL--- 340 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i--- 340 (417)
.|+..|+..|.+.|+.++.+++++..+++|++||+|+.+|+. ..|.... .|.+|++++++|.++++++++.+..
T Consensus 10 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~~--~~~~wL~~Iarn~~~d~~Rk~~~~~~~~ 86 (172)
T PRK12523 10 ELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTPR--EPRAFLAAVAKGLMFDHFRRAALEQAYL 86 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcch--hHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 799999999999999999999999999999999999999986 4566442 7999999999999999998754311
Q ss_pred -c---c-----C--ccH---HHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 341 -R---L-----P--NHL---HERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 341 -r---l-----p--~~~---~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
. . + ... .+....+..++..|++..|. .+++|||+.||+|+++|+..+.++++.+
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 0 0 110 12224567777777654544 3999999999999999999999988765
No 99
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=99.56 E-value=8e-15 Score=130.78 Aligned_cols=121 Identities=15% Similarity=0.078 Sum_probs=97.6
Q ss_pred HHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc-c-------
Q 014852 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR-L------- 342 (417)
Q Consensus 271 e~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir-l------- 342 (417)
+.|.+.|+.+|.+++++..++||++||+|+.+|+++++|++. .|.||++++++|.+++++++..+... .
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 578999999999999999999999999999999999999863 59999999999999999987653211 0
Q ss_pred --------CccH---HHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 343 --------PNHL---HERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 343 --------p~~~---~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
|... .+....+..++..|++..|.+ |++|||+.||+|+++|++.++++++.+
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 111234677777776655553 999999999999999999999998755
No 100
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=99.55 E-value=1.6e-14 Score=129.14 Aligned_cols=127 Identities=17% Similarity=0.107 Sum_probs=101.3
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccC
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp 343 (417)
.+++.|++.|.+.|+.+|.++.++..+++|++||+|+.+|++ .|++. ..|.+|++++++|.+.+++++..+.....
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 67654 38999999999999999998766432110
Q ss_pred ---------------cc---HHHHHHHHHHHHHHHHHcCC--------CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 344 ---------------NH---LHERLGLIRNAKLRLEEKGV--------TPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 344 ---------------~~---~~e~~~kI~~a~~~L~e~gR--------epS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
.. ..+....+..++..|++..| ..+++|||+.||+|+.+|+..+.++++.+
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 01122346666666654333 34999999999999999999999998654
No 101
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=99.55 E-value=2.9e-14 Score=131.93 Aligned_cols=132 Identities=17% Similarity=0.149 Sum_probs=106.2
Q ss_pred hhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc
Q 014852 261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340 (417)
Q Consensus 261 ~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i 340 (417)
.+..+++.|+..|.+.|+.+|.+++++..+++|++||+|+.+|+.++.|++.. .|.+|++++++|.+.+.++...+..
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 45689999999999999999999999999999999999999999999998753 7999999999999887765543211
Q ss_pred -cc-----C-----cc-HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 341 -RL-----P-----NH-LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 341 -rl-----p-----~~-~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
.. + .. .......+..++..|++..|.+ +++|||+.||||+.+|+..++++++.+
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 00 0 00 1111234777888887655553 999999999999999999999998765
No 102
>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=2.4e-14 Score=126.31 Aligned_cols=122 Identities=20% Similarity=0.194 Sum_probs=98.3
Q ss_pred HHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc-------
Q 014852 270 VMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL------- 342 (417)
Q Consensus 270 Ie~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl------- 342 (417)
+++|.+.|+.++.+++++..+++|++||+|+.+|+.+++|++ + +|.||++.++++.+.+++++..+....
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 357899999999999999999999999999999999999997 3 899999999999999999875432211
Q ss_pred --------CccH---HHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 343 --------PNHL---HERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 343 --------p~~~---~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
|... .+....+..++..|++..+++ +++|||+.||+|+.+|+..++++++.+
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 0000 112245777788886655543 999999999999999999999998654
No 103
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=99.54 E-value=2.5e-14 Score=127.95 Aligned_cols=128 Identities=15% Similarity=0.073 Sum_probs=102.9
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc---
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL--- 340 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i--- 340 (417)
.|++.|++.|.+.|+.++.+++++..++||++||.|+.+|+..+.|++. .|.+|++++++|.+++++++..+..
T Consensus 4 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~~~~~ 80 (161)
T PRK12528 4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQII---EPRAFLTTIAKRVLCNHYRRQDLERAYL 80 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhcccccccc---CHHHHHHHHHHHHHHHHHHHHHHHHhhH
Confidence 6899999999999999999999999999999999999999998887642 6999999999999999998754211
Q ss_pred ----ccCc----c------HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 341 ----RLPN----H------LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 341 ----rlp~----~------~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
..+. . ..+....+..++..|++..|++ +++|||+.||+|+++|+..++++++.+
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~~g~s~~EIA~~l~is~~tV~~~l~ra~~~~ 157 (161)
T PRK12528 81 EALAQLPERVAPSEEERAIILETLVELDQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAMRC 157 (161)
T ss_pred HHhhccccccCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 0110 0 0122245667777776655543 999999999999999999999987643
No 104
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=99.53 E-value=4.4e-14 Score=129.94 Aligned_cols=127 Identities=19% Similarity=0.163 Sum_probs=102.4
Q ss_pred HHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCc-
Q 014852 266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPN- 344 (417)
Q Consensus 266 re~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~- 344 (417)
++.|++.|.+.|+.++.++.++..++||++||.|+.+|+.+..|+... +|.+|++++++|.+++++++..+....+.
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~aeDi~QEvflkl~~~~~~~~~~~--~~~~wL~~i~~n~~~d~~Rk~~~~~~~~~~ 80 (181)
T PRK09637 3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDGS--SIKSWLYQIANNTIIDFYRKKNRSEELPDD 80 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHhHHHhcccc--chHHHHHHHHHHHHHHHHHhccccCCcchh
Confidence 678999999999999999999999999999999999999999998643 89999999999999999987654332211
Q ss_pred -------c----HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 345 -------H----LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 345 -------~----~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
. ..+....+..++..|++..|. .+++|||+.||+|+++|+..+.++++.+
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 1 112223455666666554444 3999999999999999999999988654
No 105
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=99.53 E-value=4.5e-14 Score=132.67 Aligned_cols=130 Identities=19% Similarity=0.190 Sum_probs=105.1
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc-
Q 014852 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL- 340 (417)
Q Consensus 262 ~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i- 340 (417)
+..+++.|+..|.+.++.++.++.++..+++|++||+|+.+|+...+|++ + +|.+|++++++|.+++++++..+..
T Consensus 26 d~~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~~~d~~Rk~~~~~~ 102 (203)
T PRK09647 26 TMPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNLFLDMVRRRARIRM 102 (203)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHHHHHHHHhcccCcc
Confidence 44799999999999999999999999999999999999999999999985 3 6999999999999999998764311
Q ss_pred -ccC-----------c--cH---HHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 341 -RLP-----------N--HL---HERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 341 -rlp-----------~--~~---~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
..+ . .. .+....+..++..|++..+. .+++|||+.||||+++|++.+.++++.|
T Consensus 103 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~L~~~~r~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RArk~L 182 (203)
T PRK09647 103 EALPEDYDRVPGDEPNPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQL 182 (203)
T ss_pred ccccccccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 000 0 00 11223466667777554444 3999999999999999999999998765
No 106
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=99.53 E-value=3.8e-14 Score=130.85 Aligned_cols=126 Identities=15% Similarity=0.219 Sum_probs=100.3
Q ss_pred HHHHHHhHHHHHHHHHHccCCCCC-hhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccC--
Q 014852 267 EKLVMSNVRLVMSIAQRYDNMGAD-MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP-- 343 (417)
Q Consensus 267 e~LIe~yl~LV~sIA~Ry~~~g~e-~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp-- 343 (417)
+..+..|.+.|+.+|.+++++..+ +||++||+|+.+|+++++|++. + +|.+|++++++|.++++++++.+.....
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 9999999999999999999865 3 8999999999999999999865422110
Q ss_pred --------------------------------cc---HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCC
Q 014852 344 --------------------------------NH---LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMS 379 (417)
Q Consensus 344 --------------------------------~~---~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS 379 (417)
.. ..+....+..++..|++..|++ |++|||+.||+|
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 0111234667777776555443 999999999999
Q ss_pred HHHHHHHHHHhCccc
Q 014852 380 QKKVRNATEAIGKVF 394 (417)
Q Consensus 380 ~etVr~aL~rark~L 394 (417)
+++|+..++++++.+
T Consensus 166 ~~tVk~~l~Rar~~L 180 (195)
T PRK12532 166 TSNYHTIMHRARESL 180 (195)
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999999998654
No 107
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=99.52 E-value=3.6e-14 Score=132.42 Aligned_cols=124 Identities=15% Similarity=0.115 Sum_probs=99.8
Q ss_pred HHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccC---c-
Q 014852 269 LVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP---N- 344 (417)
Q Consensus 269 LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp---~- 344 (417)
++..|.+.|+.+|.+++++..++||++||+|+.+|+.+++|++.. .|.||++++++|.+++++++..+....+ .
T Consensus 13 ~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~~--~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~~~~ 90 (201)
T PRK12545 13 YLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQS--AHKTWVFGILRNKLIDTLRARQRTVNLSALDAE 90 (201)
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhccccc--hHHHHHHHHHHHHHHHHHHhhcccccccccccc
Confidence 488899999999999999999999999999999999999999764 7999999999999999999765432110 0
Q ss_pred ----------------------------cHH------HHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHH
Q 014852 345 ----------------------------HLH------ERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQK 381 (417)
Q Consensus 345 ----------------------------~~~------e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~e 381 (417)
... +....+..++..|++..|. .+++|||+.||+|++
T Consensus 91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~v~~L~~~eg~s~~EIA~~lgis~~ 170 (201)
T PRK12545 91 LDGEALLDRELFKDNGHWAAHAKPRPWPKPETILQQQQFWTLFETCLDHLPEQIGRVFMMREFLDFEIDDICTELTLTAN 170 (201)
T ss_pred cchhhhhhhhhhcccccccccccCcCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHH
Confidence 000 1112356677777654544 399999999999999
Q ss_pred HHHHHHHHhCccc
Q 014852 382 KVRNATEAIGKVF 394 (417)
Q Consensus 382 tVr~aL~rark~L 394 (417)
+|+..+.++++.|
T Consensus 171 tVk~~l~RAr~~L 183 (201)
T PRK12545 171 HCSVLLYRARTRL 183 (201)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999998755
No 108
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=99.52 E-value=3.7e-13 Score=130.18 Aligned_cols=77 Identities=17% Similarity=0.220 Sum_probs=71.6
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCC--ChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGA--DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~--e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i 340 (417)
.|++.|+..|.|+|+++|.+++++.. +++|++||||+++|+++++|++++|.+|.+|++++|+|.+++++|++.+..
T Consensus 18 ~AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~awl~~Iirn~~iDylRk~~~~~ 96 (237)
T PRK08311 18 ELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELVIKRRLIDYFRKESKHN 96 (237)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHhhccc
Confidence 89999999999999999999998765 599999999999999999999998889999999999999999999877643
No 109
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=99.51 E-value=5.4e-14 Score=129.91 Aligned_cols=125 Identities=11% Similarity=0.109 Sum_probs=99.9
Q ss_pred HHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc-----
Q 014852 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL----- 342 (417)
Q Consensus 268 ~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl----- 342 (417)
.-|..|.+.++.+|.+++++..++||++||+|+.+|+.+++|++.. +|.+|++++++|.+++++|++.+....
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 3467788999999999999999999999999999999999998764 799999999999999999976542211
Q ss_pred ---C-----------------cc--H-------HHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHH
Q 014852 343 ---P-----------------NH--L-------HERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVR 384 (417)
Q Consensus 343 ---p-----------------~~--~-------~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr 384 (417)
+ .. . .+....+..++..|++..|++ |++|||+.||+|+++|+
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 0 00 0 011123567778887655554 99999999999999999
Q ss_pred HHHHHhCccc
Q 014852 385 NATEAIGKVF 394 (417)
Q Consensus 385 ~aL~rark~L 394 (417)
..++++++.+
T Consensus 169 ~~l~RAr~~L 178 (189)
T PRK12530 169 VLLYRARLQL 178 (189)
T ss_pred HHHHHHHHHH
Confidence 9999998754
No 110
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=99.51 E-value=1.3e-13 Score=128.04 Aligned_cols=128 Identities=16% Similarity=0.194 Sum_probs=103.2
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc-
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL- 342 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl- 342 (417)
++++.|.. |.+.|+++|.++.++..++||++||.|+.+|+.+..|+... .|.+|++++++|.+++++++..+....
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 799999999999999999886642210
Q ss_pred C-----------cc-HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 343 P-----------NH-LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 343 p-----------~~-~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
. .. .......+..++..|++..|.+ +++|||+.||||+.+|+..++++++.+
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 0 00 0112245677888887655554 999999999999999999999998654
No 111
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=99.50 E-value=6.9e-14 Score=131.68 Aligned_cols=126 Identities=13% Similarity=0.124 Sum_probs=100.7
Q ss_pred HHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccC---
Q 014852 267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP--- 343 (417)
Q Consensus 267 e~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp--- 343 (417)
..++..|.+.|+.+|++++++..+++|++||+|+.+|+.+.+|++.. +|.+|++++++|.+++++++..+....+
T Consensus 21 ~~~~~~~~~~l~~~~~~~~~d~~~AEDivQEvfikl~~~~~~~~~~~--~~~~WL~~IarN~~~d~~Rk~~~~~~~~~~~ 98 (206)
T PRK12544 21 PVFLEDLRKQMIKFATLQLSDLHLAEDAVQEALIGALKNADSFAGRA--AFKTWVFAILKNKIIDLLRQKKRHVSASSLL 98 (206)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHHHHhcCCcc--cHHHHHHHHHHHHHHHHHHhhcccccccccc
Confidence 46788899999999999999999999999999999999999998653 7999999999999999999765422111
Q ss_pred -------------------------------ccH---HHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCH
Q 014852 344 -------------------------------NHL---HERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQ 380 (417)
Q Consensus 344 -------------------------------~~~---~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~ 380 (417)
... .+....+..++..|++..|++ +++|||+.||+|+
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 000 011123566677776555543 9999999999999
Q ss_pred HHHHHHHHHhCccc
Q 014852 381 KKVRNATEAIGKVF 394 (417)
Q Consensus 381 etVr~aL~rark~L 394 (417)
++|+..++++++.+
T Consensus 179 ~tV~~~l~RAr~~L 192 (206)
T PRK12544 179 SNLNVLLYRARLRL 192 (206)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999998765
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=99.50 E-value=6.8e-14 Score=129.30 Aligned_cols=125 Identities=15% Similarity=0.154 Sum_probs=100.5
Q ss_pred HHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccC---c
Q 014852 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP---N 344 (417)
Q Consensus 268 ~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp---~ 344 (417)
+++..|.+.|+.++.+++++..+++|++||+|+.+|+...+|++.. +|.+|++++++|.+++++++..+....+ .
T Consensus 6 ~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~~--~~~~wL~~iarn~~~d~~R~~~r~~~~~~~~~ 83 (188)
T TIGR02943 6 QELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGRS--ALKTWLFAILKNKIIDALRAKGREVKVSDLDD 83 (188)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhcccc--HHHHHHHHHHHHHHHHHHHhhcccCCcccccc
Confidence 5678899999999999999999999999999999999999999753 8999999999999999998765432111 0
Q ss_pred c---------------------------------HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHH
Q 014852 345 H---------------------------------LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKK 382 (417)
Q Consensus 345 ~---------------------------------~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~et 382 (417)
. ..+....+..++..|++..|+ .+++|||+.||+|+++
T Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~lgis~~t 163 (188)
T TIGR02943 84 ELDDEAFNALFTQNGHWAQHGQPQHWNTPEKQLENKEFWEVFEACLYHLPEQTARVFMMREVLGFESDEICQELEISTSN 163 (188)
T ss_pred ccccchhhhhhccccchhccccccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHhCCCHHH
Confidence 0 001123466677777654444 3999999999999999
Q ss_pred HHHHHHHhCccc
Q 014852 383 VRNATEAIGKVF 394 (417)
Q Consensus 383 Vr~aL~rark~L 394 (417)
|+..+.++++.+
T Consensus 164 vk~rl~Rar~~L 175 (188)
T TIGR02943 164 CHVLLYRARLSL 175 (188)
T ss_pred HHHHHHHHHHHH
Confidence 999999998765
No 113
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=99.50 E-value=1.3e-13 Score=125.32 Aligned_cols=129 Identities=17% Similarity=0.152 Sum_probs=102.3
Q ss_pred HHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc--
Q 014852 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL-- 340 (417)
Q Consensus 263 ~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i-- 340 (417)
..|+..|++.|.+.++.++.++.++..++||++||.|+.+|+. ..|++.. +|.+|++++++|.+++++++..+..
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 4799999999999999999999999999999999999999998 3565443 6999999999999999998654211
Q ss_pred -----cc-----Ccc--H---HHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 341 -----RL-----PNH--L---HERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 341 -----rl-----p~~--~---~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
.. +.. . .+....+..++..|++..|++ +++|||+.||+|+++|+..++++++.+
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~ 163 (172)
T PRK09651 86 LEMLALMPEGGAPSPEERESQLETLQLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKATEHC 163 (172)
T ss_pred hhHHhhccccCCCChHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhhhccCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 00 110 1 122345677777886655554 999999999999999999999987643
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=99.50 E-value=7.3e-14 Score=126.83 Aligned_cols=122 Identities=20% Similarity=0.214 Sum_probs=97.8
Q ss_pred HHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCcc-----
Q 014852 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH----- 345 (417)
Q Consensus 271 e~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~----- 345 (417)
..|.+.++.++.++.++..++||++||+|+.+|+++++|+... +|.+|++.+++|.+++++++..+...++..
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~l~~~~~~~~~~~--~f~~wl~~iarn~~~d~~Rk~~~~~~~~~~~~~~~ 79 (170)
T TIGR02959 2 DEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDGQ--KIQSWLYQIARNTIIDFYRSKSRSVELPESLLAAD 79 (170)
T ss_pred chHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCcc--cHHHHHHHHHHHHHHHHHHhccCccccchhhcccC
Confidence 4688999999999999999999999999999999999999743 899999999999999999987654332211
Q ss_pred -------HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 346 -------LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 346 -------~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
..+....+..++..|++..|+ .+++|||+.||+|+.+|+..++++++.+
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 111223456666666544443 3999999999999999999999998655
No 115
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=99.48 E-value=1.4e-13 Score=126.91 Aligned_cols=126 Identities=18% Similarity=0.181 Sum_probs=101.1
Q ss_pred HHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccC---
Q 014852 267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP--- 343 (417)
Q Consensus 267 e~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp--- 343 (417)
+..+..+.+.|+.+|.++.++..+++|++||.|+.+|+.+.+|+... +|.+|++++++|.++++++++.+.....
T Consensus 7 ~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~~--~~~~WL~~Iarn~~id~~Rk~~~~~~~~~~~ 84 (182)
T PRK12511 7 RFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSGG--NLRTWLMSILHNAFIDELRRRRVEARRADEL 84 (182)
T ss_pred hhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCcc--chHHHHHHHHHHHHHHHHHhhccccccccch
Confidence 44577889999999999999999999999999999999999998653 7999999999999999998765421100
Q ss_pred ---------cc--HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 344 ---------NH--LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 344 ---------~~--~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
.. .......+..++..|++..|++ |++|||+.||||+++|+..++++++.+
T Consensus 85 ~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~eg~s~~EIA~~lgis~~tV~~~l~Rar~~L 155 (182)
T PRK12511 85 AVLADASLPAAQEHAVRLAQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAAL 155 (182)
T ss_pred hhccccCCCcchHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHHHHH
Confidence 00 1112344677777776655553 999999999999999999999998755
No 116
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=99.46 E-value=2.4e-13 Score=130.77 Aligned_cols=134 Identities=13% Similarity=0.080 Sum_probs=103.3
Q ss_pred HHHHhhhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHH
Q 014852 255 LQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALV 334 (417)
Q Consensus 255 Lr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ir 334 (417)
|++.+..+..+++.+++.| +.+++++.+++++..++|||+||+|+.+|+. |+... .|.+|++++++|.++++++
T Consensus 9 ~~~~~~~~~~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~~---~~~~~--~~~~WL~~IarN~~id~~R 82 (228)
T PRK06704 9 LKNHIDMNHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQK---YSNKD--ICMTLVYKIARNRWLDQIK 82 (228)
T ss_pred HhcccCCCHHHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH---cCccc--cHHHHHHHHHHHHHHHHHh
Confidence 3334444447888888888 7899999999999999999999999999986 55433 6999999999999999999
Q ss_pred hhccccccCc--------c-HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 335 ENSRTLRLPN--------H-LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 335 d~~r~irlp~--------~-~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
++.+...... . ..+....+..++..|++..|.+ |++|||+.||+|+++|+..++++++.+
T Consensus 83 k~k~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~R~v~lL~~~eg~S~~EIAe~LgiS~~tVksrL~Rark~L 160 (228)
T PRK06704 83 SKSVHEKIRDQITFEEPHEKIADLHEMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRL 160 (228)
T ss_pred ccccccccccccccCChHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHhhCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 7654322111 0 1122344677777776655554 999999999999999999999999765
No 117
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=99.42 E-value=6.9e-13 Score=118.46 Aligned_cols=124 Identities=15% Similarity=0.164 Sum_probs=96.3
Q ss_pred HHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc------
Q 014852 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR------ 341 (417)
Q Consensus 268 ~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir------ 341 (417)
.++..|.+.++.+|.++.++..++||++||+|+++|+....|++. .|.+|++.+++|.+++++++..+...
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 357788999999999999999999999999999999988877653 58999999999999999987653211
Q ss_pred ----cCc---c------HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 342 ----LPN---H------LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 342 ----lp~---~------~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
.+. . ..+....+..++..|++..|. .+++|||+.||+|+.+|+..+.++++.+
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 110 0 111223456666777554444 3999999999999999999999887654
No 118
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=99.40 E-value=6.9e-13 Score=118.36 Aligned_cols=121 Identities=16% Similarity=0.085 Sum_probs=95.0
Q ss_pred HHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc--------
Q 014852 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL-------- 342 (417)
Q Consensus 271 e~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl-------- 342 (417)
..|.+.++..+.+++++..++||++||+|+.+|+..+.|++ + +|.||++.+++|.++++++++......
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 56888999999999999899999999999999999998875 3 799999999999999999865321110
Q ss_pred -----Cc--cH---HHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 343 -----PN--HL---HERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 343 -----p~--~~---~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
|. .. .+....+..++..|++..+. .+++|||+.||+|+++|+..+.++++.+
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 00 00 11223467777777654444 3999999999999999999999988654
No 119
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=99.40 E-value=1e-12 Score=118.85 Aligned_cols=127 Identities=12% Similarity=0.022 Sum_probs=99.2
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc---
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL--- 340 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i--- 340 (417)
.++..++..|.+.++.++.+++++..+++|++||.|+.+|+..+.++. + .|.+|++++++|.+++++++.....
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 689999999999999999999999999999999999999986555542 2 7999999999999999988643110
Q ss_pred ----c-------cCcc---HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014852 341 ----R-------LPNH---LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKV 393 (417)
Q Consensus 341 ----r-------lp~~---~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~ 393 (417)
. .|.. ..+....+..++..|++..|.+ |++|||+.||+|+++|+..+.++.+.
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 0 0100 1112344667777776545443 99999999999999999999988754
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=1.2e-12 Score=100.94 Aligned_cols=70 Identities=27% Similarity=0.418 Sum_probs=66.7
Q ss_pred HHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcc
Q 014852 269 LVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSR 338 (417)
Q Consensus 269 LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r 338 (417)
|++.|.++|++++.+|++++.++||++||++++||+++++||+++|..|.+|++.++++.+.+.++++.+
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 7899999999999999999999999999999999999999999998899999999999999999988754
No 121
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=99.37 E-value=1.7e-12 Score=128.01 Aligned_cols=128 Identities=17% Similarity=0.074 Sum_probs=100.3
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc---
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL--- 340 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i--- 340 (417)
..+..|++.|.+.++.+|++++++..++||++||+|+. |.....|+. ..|.+|++++++|.|++++|+..+..
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 45778999999999999999999999999999999999 555677752 37999999999999999998754211
Q ss_pred ---ccCcc----------H---HHH-HHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 341 ---RLPNH----------L---HER-LGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 341 ---rlp~~----------~---~e~-~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
..+.. . .+. ...+..++..|++.+|.+ +++|||+.||+|+.+|+++++++++.+
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 01110 0 111 123667777776666654 999999999999999999999998766
Q ss_pred c
Q 014852 395 S 395 (417)
Q Consensus 395 S 395 (417)
.
T Consensus 160 r 160 (293)
T PRK09636 160 R 160 (293)
T ss_pred H
Confidence 3
No 122
>PRK09191 two-component response regulator; Provisional
Probab=99.31 E-value=6.4e-12 Score=119.02 Aligned_cols=122 Identities=13% Similarity=0.047 Sum_probs=95.9
Q ss_pred HHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCc
Q 014852 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPN 344 (417)
Q Consensus 265 Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~ 344 (417)
++..|+..|.+.++++|.++.++..+++|++||+|+.+|+...+|++.. .|.+|+++++++........ ...+.
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 5789999999999999999999999999999999999999999998754 79999999998754322111 01011
Q ss_pred cHHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 345 HLHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 345 ~~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
. .....+..++..|++.+|.+ |++|||+.||+|+++|+..++++++.+
T Consensus 76 ~--~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l 132 (261)
T PRK09191 76 S--PFEARAERRLAGLTPLPRQAFLLTALEGFSVEEAAEILGVDPAEAEALLDDARAEI 132 (261)
T ss_pred C--CchHHHHHHHHhCCHHHhHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 0 11125777777776655553 999999999999999999999887654
No 123
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=99.30 E-value=7e-12 Score=124.36 Aligned_cols=129 Identities=11% Similarity=-0.051 Sum_probs=101.3
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc---
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL--- 340 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i--- 340 (417)
..+..+++.|.+.++.+|++++++..++||++||+|+.+|++...+ . ..|.+|++++++|.|++++++..+..
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 5788999999999999999999999999999999999999986542 2 26999999999999999998743210
Q ss_pred -----ccC-----c-----cH---HH-HHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCc
Q 014852 341 -----RLP-----N-----HL---HE-RLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGK 392 (417)
Q Consensus 341 -----rlp-----~-----~~---~e-~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark 392 (417)
..| . .. .+ ....+..++..|++..|.+ +++|||+.||+|+.+|+..++++++
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~al~~~L~~L~p~~R~vf~L~~~~g~s~~EIA~~Lgis~~tVr~~l~RAr~ 160 (290)
T PRK09635 81 QDIAAWHDGDASVSSVDPADRVTLDDEVRLALLIMLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARR 160 (290)
T ss_pred ccccccCccccCCCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHHhCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 011 0 00 11 1234667777776656654 9999999999999999999999987
Q ss_pred cccc
Q 014852 393 VFSL 396 (417)
Q Consensus 393 ~LSL 396 (417)
.+.-
T Consensus 161 ~Lr~ 164 (290)
T PRK09635 161 KINE 164 (290)
T ss_pred HHHh
Confidence 7643
No 124
>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=99.30 E-value=6.1e-12 Score=123.65 Aligned_cols=124 Identities=17% Similarity=0.099 Sum_probs=95.2
Q ss_pred HHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc------c
Q 014852 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL------R 341 (417)
Q Consensus 268 ~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i------r 341 (417)
++++.|.+.++.+|++++++..++||++||+|+.+++. .|+... .|.+|++++++|.+++++++..+.. .
T Consensus 1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~~~--~~~awL~~Ia~n~~ld~lR~~~~~~~~~~~~~ 76 (281)
T TIGR02957 1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQIE--NPKAYLTKVVTRRCIDVLRSARARREVYVGPW 76 (281)
T ss_pred ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Cccccc--CHHHHHHHHHHHHHHHHHHHhhhcccccCCCC
Confidence 37899999999999999999999999999999998775 555433 7999999999999999998754211 1
Q ss_pred cCcc----------HH---HHH-HHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCcccc
Q 014852 342 LPNH----------LH---ERL-GLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVFS 395 (417)
Q Consensus 342 lp~~----------~~---e~~-~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~LS 395 (417)
+|.. .. +.. ..+..++..|++..|.+ +++|||+.||+|+.+|+++++++++.+-
T Consensus 77 ~~e~~~~~~~~~~~~~~~~e~~~~~l~~~l~~L~~~~R~v~~L~~~~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr 153 (281)
T TIGR02957 77 LPEPLLTTSADPAESVELAESLSMAYLLLLERLSPLERAVFVLREVFDYPYEEIASIVGKSEANCRQLVSRARRHLD 153 (281)
T ss_pred CCcccCCCCCChHHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 1111 00 111 22455666676555553 9999999999999999999999987663
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=99.22 E-value=2.7e-11 Score=106.30 Aligned_cols=112 Identities=16% Similarity=0.118 Sum_probs=85.2
Q ss_pred HHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhh-----cCCCCCCchhhHHHHHHHhhHHHHHHhhcccc
Q 014852 266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEK-----FDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340 (417)
Q Consensus 266 re~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAier-----FD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i 340 (417)
|+.|+..|.++++.+|.+|.. .+|+ ||.|+.+|+.+.+ |++. ..|.||++++++|.++++++++.+..
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--HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHH
Q 014852 341 RLP-------------NH--LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVR 384 (417)
Q Consensus 341 rlp-------------~~--~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr 384 (417)
... .. ..+....+..++..|++..|++ |++|||+.||||+++|+
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 1112245777888887766654 99999999999999996
No 126
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=99.20 E-value=3.2e-11 Score=107.17 Aligned_cols=106 Identities=13% Similarity=0.101 Sum_probs=79.7
Q ss_pred CCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccC----------------------
Q 014852 286 NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP---------------------- 343 (417)
Q Consensus 286 ~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp---------------------- 343 (417)
++..+++|++||+|+.+|+..+.+ + +..|.+|++++++|.+++++|++.+.....
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 355679999999999999998863 3 337999999999999999998765321110
Q ss_pred ------ccH------HHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 344 ------NHL------HERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 344 ------~~~------~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
... .+....+..++..|++..|.+ +++|||+.||||+++|+..++++++.+
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 112244677777776655553 999999999999999999999998654
No 127
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=98.83 E-value=4.2e-08 Score=90.92 Aligned_cols=130 Identities=22% Similarity=0.142 Sum_probs=89.5
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCC---CCChhh--hhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcc
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNM---GADMAD--LVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSR 338 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~---g~e~ED--LIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r 338 (417)
.|++.|+..|.+.++.+|.++... +.+.+| |++|.|+.+++.....+...-..|..|+..++++.++++.|.+..
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 899999999999999999987632 334444 577888877774332233322379999999999999999986654
Q ss_pred cccc------C---------ccHHHHHHHHHHHHHHHHHcC------------CCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 339 TLRL------P---------NHLHERLGLIRNAKLRLEEKG------------VTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 339 ~irl------p---------~~~~e~~~kI~~a~~~L~e~g------------RepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
..+- + ....+....+.++...|.... -..|++|||+.||||+.+|+..+..++
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 3221 1 011223334555555442211 123999999999999999999999887
Q ss_pred cc
Q 014852 392 KV 393 (417)
Q Consensus 392 k~ 393 (417)
..
T Consensus 177 ~~ 178 (185)
T PF07638_consen 177 AW 178 (185)
T ss_pred HH
Confidence 54
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=98.53 E-value=1.6e-07 Score=74.98 Aligned_cols=67 Identities=31% Similarity=0.316 Sum_probs=53.4
Q ss_pred HHHHHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCCCCCCCCcccc
Q 014852 348 ERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHI 414 (417)
Q Consensus 348 e~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~s~~~~~~d~l~d 414 (417)
+.+++|.++...|. .+||.||.+|||+.|||+++.|+.++..++..+||+.+...+.+...++.+.|
T Consensus 1 E~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~~~~l~~~i~d 68 (78)
T PF04539_consen 1 EKLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDEDDSTLGDFIED 68 (78)
T ss_dssp HHHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSSSEEGGGSSB-
T ss_pred ChHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCCCCchhheecC
Confidence 35688999999995 68999999999999999999999999999999999998877655544444443
No 129
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=97.61 E-value=0.00087 Score=68.98 Aligned_cols=133 Identities=17% Similarity=0.252 Sum_probs=77.2
Q ss_pred hHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhH-HHHHHH
Q 014852 226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGG-LIGLLR 304 (417)
Q Consensus 226 ~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG-~IgLik 304 (417)
.+...|.+.+|++|+.+++|..+|++.++++..+... .. ....++.+.++ -..+..
T Consensus 220 ~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~-------------------~~----~~SLd~~~~~~~~~~l~d 276 (367)
T PRK09210 220 RVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIA-------------------QE----PVSLETPIGEEDDSHLGD 276 (367)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHh-------------------cC----CCCcCCCCCCCCcchhhh
Confidence 3567788999999999999999999999877643221 11 11111111110 011111
Q ss_pred HHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHH
Q 014852 305 GIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVR 384 (417)
Q Consensus 305 AierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr 384 (417)
.+. |.....+........++..+..++. . +.++.+.|...+..|. .|...|++|||+.||||.++|+
T Consensus 277 ~i~--d~~~~~p~~~~~~~~~~~~l~~~l~------~----L~~rEr~Vl~lrygl~-~~~~~tl~EIa~~lgvs~erVr 343 (367)
T PRK09210 277 FIE--DQDATSPADHAAYELLKEQLEDVLD------T----LTDREENVLRLRFGLD-DGRTRTLEEVGKVFGVTRERIR 343 (367)
T ss_pred hcc--CCCCCCHHHHHHHHHHHHHHHHHHH------h----CCHHHHHHHHHHhccC-CCCCccHHHHHHHHCCCHHHHH
Confidence 111 1111223444444444544444332 1 3333455555555543 2466799999999999999999
Q ss_pred HHHHHhCccc
Q 014852 385 NATEAIGKVF 394 (417)
Q Consensus 385 ~aL~rark~L 394 (417)
++...|..+|
T Consensus 344 Qi~~~Al~kL 353 (367)
T PRK09210 344 QIEAKALRKL 353 (367)
T ss_pred HHHHHHHHHH
Confidence 9988776544
No 130
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=97.59 E-value=0.0012 Score=67.08 Aligned_cols=133 Identities=20% Similarity=0.241 Sum_probs=75.8
Q ss_pred hHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhh-HHHHHHH
Q 014852 226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQG-GLIGLLR 304 (417)
Q Consensus 226 ~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQE-G~IgLik 304 (417)
.+...|...+|++|+.+|+|..+|++.+++...+. .+.. ....++.+.+ +-..+..
T Consensus 177 ~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~-------------------~~~~----~~SLd~~~~~~~~~~l~d 233 (324)
T PRK07921 177 RIKRELHQQLGREATDEELAEESGIPEEKIADLLE-------------------HSRD----PVSLDMPVGSDEEAPLGD 233 (324)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHH-------------------HcCC----CceecCCCCCCCCchHHH
Confidence 36678889999999999999999999988764321 1111 1111111111 0011222
Q ss_pred HHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHH
Q 014852 305 GIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVR 384 (417)
Q Consensus 305 AierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr 384 (417)
.+.. .........+.....+..+..++. .+.++...|...+..|. .+...|.+|||+.||||.++|+
T Consensus 234 ~l~d--~~~~~pe~~~~~~~~~~~l~~~L~----------~L~eREr~Vl~~rygl~-~~~~~Tl~eIa~~lgvS~eRVr 300 (324)
T PRK07921 234 FIED--SEATSAENAVIAGLLHTDIRSVLA----------TLDEREQQVIRLRFGLD-DGQPRTLDQIGKLFGLSRERVR 300 (324)
T ss_pred HhcC--CCCCCHHHHHHHHHHHHHHHHHHH----------hCCHHHHHHHHHHHhcC-CCCCcCHHHHHHHHCCCHHHHH
Confidence 2221 111112333333333443333331 23344455666666553 1455699999999999999999
Q ss_pred HHHHHhCccc
Q 014852 385 NATEAIGKVF 394 (417)
Q Consensus 385 ~aL~rark~L 394 (417)
++..++.++|
T Consensus 301 QIe~~Al~KL 310 (324)
T PRK07921 301 QIEREVMSKL 310 (324)
T ss_pred HHHHHHHHHH
Confidence 9988876554
No 131
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=97.58 E-value=0.0011 Score=71.22 Aligned_cols=133 Identities=18% Similarity=0.273 Sum_probs=76.5
Q ss_pred hHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhh-HHHHHHH
Q 014852 226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQG-GLIGLLR 304 (417)
Q Consensus 226 ~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQE-G~IgLik 304 (417)
.++..|...+|++|+.+|+|..+|++.+++...+. +......+++.+.+ +-..+..
T Consensus 362 ~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~-----------------------~~~~~~SLD~~i~~d~~~~l~d 418 (509)
T PRK05901 362 RIERELLQELGREPTPEELAKEMGFTPEKVREIQK-----------------------YNREPISLDKTIGKEGDSQFGD 418 (509)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH-----------------------hcCCCcccccccccCCcccHHH
Confidence 35677889999999999999999999988765321 11112222222211 1111212
Q ss_pred HHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHH
Q 014852 305 GIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVR 384 (417)
Q Consensus 305 AierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr 384 (417)
.+. |.....+.........+..+..++. .+.++...|...++.|.. +...|.+|||+.||||.++|+
T Consensus 419 ~l~--D~~~~~p~~~~~~~~l~~~L~~aL~----------~L~eREr~VI~lRyGL~~-~e~~TL~EIa~~lGVSrERVR 485 (509)
T PRK05901 419 FIE--DSEAVSPVDAVSFTLLQDQLQEVLE----------TLSEREAGVIRMRFGLTD-GQPKTLDEIGQVYGVTRERIR 485 (509)
T ss_pred hcc--CCCCCCHHHHHHHHHHHHHHHHHHh----------hCCHHHHHHHHHHhhccC-CCCCCHHHHHHHHCCCHHHHH
Confidence 111 1111112233333333333333321 234445666666666632 456699999999999999999
Q ss_pred HHHHHhCccc
Q 014852 385 NATEAIGKVF 394 (417)
Q Consensus 385 ~aL~rark~L 394 (417)
++..++...|
T Consensus 486 QIe~kAL~KL 495 (509)
T PRK05901 486 QIESKTLRKL 495 (509)
T ss_pred HHHHHHHHHH
Confidence 9988776543
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=97.55 E-value=0.0014 Score=63.07 Aligned_cols=133 Identities=18% Similarity=0.194 Sum_probs=71.1
Q ss_pred hHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHH-HHHHH
Q 014852 226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGL-IGLLR 304 (417)
Q Consensus 226 ~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~-IgLik 304 (417)
.+...+...+|++|+.+++|..+|++.+++...... +. .....++.++++- ..+..
T Consensus 91 ~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~-------------------~~----~~~SLd~~~~~~~~~~l~d 147 (238)
T TIGR02393 91 KAERQLTQELGREPTDEELAERMGMPAEKVREIKKI-------------------AQ----EPISLETPIGEEEDSFLGD 147 (238)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHH-------------------hc----cCCCcCCCCCCCCcccHHH
Confidence 356778889999999999999999999987643211 11 1122222221110 01222
Q ss_pred HHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHH
Q 014852 305 GIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVR 384 (417)
Q Consensus 305 AierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr 384 (417)
.+.. +..............+..+..++. .+| +....|......|.. +.+.|++|||+.||||.++|+
T Consensus 148 ~l~d--~~~~~p~~~~~~~~~~~~l~~~l~------~L~----~~er~vl~l~ygl~~-~~~~t~~EIA~~lgis~~~V~ 214 (238)
T TIGR02393 148 FIED--TSIESPDDYAAKELLREQLDEVLE------TLT----ERERKVLRMRYGLLD-GRPHTLEEVGKEFNVTRERIR 214 (238)
T ss_pred HhcC--CCCCChHHHHHHHHHHHHHHHHHH------hCC----HHHHHHHHHHhCCCC-CCCccHHHHHHHHCCCHHHHH
Confidence 2221 111111222222222222222221 222 223334444333311 355699999999999999999
Q ss_pred HHHHHhCccc
Q 014852 385 NATEAIGKVF 394 (417)
Q Consensus 385 ~aL~rark~L 394 (417)
++..++.+.|
T Consensus 215 q~~~~al~kL 224 (238)
T TIGR02393 215 QIESKALRKL 224 (238)
T ss_pred HHHHHHHHHH
Confidence 9999887655
No 133
>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=97.43 E-value=5.5e-05 Score=53.21 Aligned_cols=33 Identities=30% Similarity=0.483 Sum_probs=30.7
Q ss_pred hhHHHHHHhhcccCCCCHHHHHHHHHHHHccCc
Q 014852 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS 223 (417)
Q Consensus 191 ~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~ 223 (417)
|.++.||++|+.+|+||++||.+|+++++.|+.
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 134
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=97.31 E-value=0.0045 Score=64.12 Aligned_cols=132 Identities=17% Similarity=0.268 Sum_probs=71.8
Q ss_pred HHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHH
Q 014852 227 HKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGI 306 (417)
Q Consensus 227 ~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAi 306 (417)
+...|...+|++|+.+++|..+|++.++++..+.. ...+.++-..+. .+ +| ..+...+
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 56678899999999999999999999887642110 011112111110 00 01 0122222
Q ss_pred hhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHH
Q 014852 307 EKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNA 386 (417)
Q Consensus 307 erFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~a 386 (417)
. +.... ..........+..+..++. . +.+..+.|...+..|.. +...|.+|||+.||||.++|+++
T Consensus 286 ~--d~~~~-pee~~~~~~~~~~L~~aL~------~----L~~rEr~IL~lrygl~~-~~~~Tl~EIA~~lgiS~eRVRQi 351 (373)
T PRK07406 286 E--ADGET-PEDDVAKNLLREDLEGVLA------T----LSPRERDVLRLRYGLDD-GRMKTLEEIGQIFNVTRERIRQI 351 (373)
T ss_pred C--CCCCC-HHHHHHHHHHHHHHHHHHH------c----CCHHHHHHHHHHHhcCC-CCCCCHHHHHHHHCcCHHHHHHH
Confidence 1 11111 2222222222222222221 1 23334555555554421 34569999999999999999999
Q ss_pred HHHhCccc
Q 014852 387 TEAIGKVF 394 (417)
Q Consensus 387 L~rark~L 394 (417)
..++.++|
T Consensus 352 e~rAL~KL 359 (373)
T PRK07406 352 EAKALRKL 359 (373)
T ss_pred HHHHHHHH
Confidence 99887654
No 135
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=97.30 E-value=0.0043 Score=61.81 Aligned_cols=30 Identities=17% Similarity=0.268 Sum_probs=26.5
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
.+.|++|||+.||||.++|+++++++.+.+
T Consensus 244 ~~~t~~EIa~~lgvs~~~V~q~~~~Al~kL 273 (289)
T PRK07500 244 DGATLEALGEELGISKERVRQIEARALEKL 273 (289)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 455999999999999999999999887655
No 136
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=97.27 E-value=0.0015 Score=68.51 Aligned_cols=135 Identities=16% Similarity=0.261 Sum_probs=76.0
Q ss_pred chhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHH
Q 014852 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLL 303 (417)
Q Consensus 224 l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLi 303 (417)
+.+++..|.+.+|+.|+.+|+|+.+|++.++++..+... +...++-..... +-+. .+.
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 445667788899999999999999999999988653321 112222222211 1000 111
Q ss_pred HHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHH
Q 014852 304 RGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKV 383 (417)
Q Consensus 304 kAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etV 383 (417)
..+. ++..+ .-........+..+..++. . +.+..+.+......|. .+...|++|||+.||+|.++|
T Consensus 322 d~l~--~~~~~-pee~~~~~~l~~~L~~~L~------~----L~~reR~VI~LRygl~-d~~~~Tl~EIA~~LGvS~erV 387 (415)
T PRK07598 322 DLLE--TDDIS-PEEMLMRESLQRDLQHLLA------D----LTSRERDVIRMRFGLA-DGHTYSLAEIGRALDLSRERV 387 (415)
T ss_pred Hhcc--CCCCC-HHHHHHHHHHHHHHHHHHH------h----CCHHHHHHHHHHHhcC-CCCCCCHHHHHHHHCcCHHHH
Confidence 1121 11111 1111112222222222221 1 2333445555555553 256679999999999999999
Q ss_pred HHHHHHhCccc
Q 014852 384 RNATEAIGKVF 394 (417)
Q Consensus 384 r~aL~rark~L 394 (417)
++++++|.+.|
T Consensus 388 Rqie~rAl~KL 398 (415)
T PRK07598 388 RQIESKALQKL 398 (415)
T ss_pred HHHHHHHHHHH
Confidence 99999987654
No 137
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=97.26 E-value=0.0045 Score=60.47 Aligned_cols=60 Identities=25% Similarity=0.277 Sum_probs=40.0
Q ss_pred hhhhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 014852 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (417)
Q Consensus 189 ~~~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~ 258 (417)
+...+-.|++.....| ....+.+.++. .+...|++.+|++|+.+++|..+|++.+++...
T Consensus 87 Ir~~i~~~lr~~~~~p----r~~~~~~~~l~------~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~ 146 (257)
T PRK05911 87 IKAAIIDDLRKQDWVP----RSVHQKANKLA------DAMDSLRQSLGKEPTDGELCEYLNISQQELSGW 146 (257)
T ss_pred HHHHHHHHHHhcCCCC----HHHHHHHHHHH------HHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHH
Confidence 3345555665554422 23333444443 355678889999999999999999999987654
No 138
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=97.24 E-value=0.00091 Score=65.26 Aligned_cols=63 Identities=24% Similarity=0.399 Sum_probs=41.1
Q ss_pred hhhhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 014852 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (417)
Q Consensus 189 ~~~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~ 258 (417)
+.+.+..|++.....-.+ |....+.+++++ .+...|.+.+|++|+.+++|..+|++.+++...
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 445566666654432112 122223444443 366788999999999999999999999987653
No 139
>PRK05949 RNA polymerase sigma factor; Validated
Probab=97.23 E-value=0.004 Score=63.29 Aligned_cols=135 Identities=19% Similarity=0.276 Sum_probs=72.0
Q ss_pred chhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHH
Q 014852 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLL 303 (417)
Q Consensus 224 l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLi 303 (417)
+..+...+...+|++|+.+++|..+|++.+++...+... .-+.++-... +.+.+. .+.
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 344566778889999999999999999998876532111 0011211111 001000 111
Q ss_pred HHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHH
Q 014852 304 RGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKV 383 (417)
Q Consensus 304 kAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etV 383 (417)
..+.. ...+ ..........+..+..++. . +.+..+.|...+..|. .+...|++|||+.||||.++|
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------E----LTPQQREVLTLRFGLE-DGKELSLAKVGERLNLSRERV 303 (327)
T ss_pred hhcCC--CCCC-HHHHHHHHHHHHHHHHHHH------h----CCHHHHHHHHHHhccC-CCCCCCHHHHHHHHCcCHHHH
Confidence 11111 1111 1111111222222222221 1 2233445555555453 135569999999999999999
Q ss_pred HHHHHHhCccc
Q 014852 384 RNATEAIGKVF 394 (417)
Q Consensus 384 r~aL~rark~L 394 (417)
++++.++.+.|
T Consensus 304 rq~~~rAl~kL 314 (327)
T PRK05949 304 RQLEHQALAHL 314 (327)
T ss_pred HHHHHHHHHHH
Confidence 99999887654
No 140
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=97.14 E-value=0.0075 Score=61.80 Aligned_cols=48 Identities=19% Similarity=0.344 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 346 LHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 346 ~~e~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
+.++...|...+..+. .+...|.+||++.+|||.+.|+++...+...+
T Consensus 280 Lt~rE~~Vi~~R~gl~-~~~~~TLeevg~~~~isrERvRQIE~kAl~KL 327 (342)
T COG0568 280 LTERERRVIRLRFGLD-DGEPKTLEELGEEFGISRERVRQIEAKALRKL 327 (342)
T ss_pred CCHHHHHHHHHHhccC-CCCcchHHHHHHHhCCcHHHHHHHHHHHHHHH
Confidence 4555566777777775 24455999999999999999999988876554
No 141
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=97.13 E-value=0.01 Score=58.40 Aligned_cols=153 Identities=19% Similarity=0.187 Sum_probs=84.0
Q ss_pred hhhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHH
Q 014852 190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKL 269 (417)
Q Consensus 190 ~~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~L 269 (417)
-..+-.||++.. +.--|.-..++.+++. .+..+|+..+|++|+.+|+|..+|++.+++...+.....
T Consensus 86 ~Gei~d~LR~~~--~v~vpR~~~~~~~~i~------~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~----- 152 (247)
T COG1191 86 RGEILDYLRKND--SVKVPRSLRELGRRIE------EAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAING----- 152 (247)
T ss_pred HHHHHHHHHhCC--CccCcHHHHHHHHHHH------HHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhcc-----
Confidence 346667787776 2222333344444444 366789999999999999999999999987654433211
Q ss_pred HHHhHHHHHHHHHHccCCCCC-hhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHH
Q 014852 270 VMSNVRLVMSIAQRYDNMGAD-MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHE 348 (417)
Q Consensus 270 Ie~yl~LV~sIA~Ry~~~g~e-~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e 348 (417)
..+.++.......+.. ..|. .+.++..+-.+...+.+..++. . +.+
T Consensus 153 -----~~~~sld~~~~~~~d~~~~~~------------------~~~~~~~~~~~~~~~~l~~ai~------~----L~E 199 (247)
T COG1191 153 -----SQLLSLDEDVLKDDDDDVDDQ------------------IENPDDGVEKEELLEILKEAIE------P----LPE 199 (247)
T ss_pred -----ccccchhhhhccccccchhhc------------------cccchhHHHHHHHHHHHHHHHH------c----cCH
Confidence 1122222111111000 0111 1113333334444443333332 1 222
Q ss_pred HHHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014852 349 RLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKV 393 (417)
Q Consensus 349 ~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rark~ 393 (417)
+.+.|..... ..+.|..|||+.||||+.+|.++..++.+.
T Consensus 200 REk~Vl~l~y-----~eelt~kEI~~~LgISes~VSql~kkai~k 239 (247)
T COG1191 200 REKLVLVLRY-----KEELTQKEIAEVLGISESRVSRLHKKAIKK 239 (247)
T ss_pred HHHHHHHHHH-----HhccCHHHHHHHhCccHHHHHHHHHHHHHH
Confidence 2233333322 234589999999999999998887776543
No 142
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=96.98 E-value=0.0042 Score=62.77 Aligned_cols=135 Identities=20% Similarity=0.280 Sum_probs=71.5
Q ss_pred chhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHH
Q 014852 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLL 303 (417)
Q Consensus 224 l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLi 303 (417)
+..++..+...+|++|+.+++|..+|++.+++...+... .-..++-... +.+. | ..+.
T Consensus 170 l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~------------~~~~SLd~~~---~~~~-~------~~l~ 227 (317)
T PRK07405 170 IKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERA------------RQPLSLDLRV---GDNQ-D------TELG 227 (317)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHc------------CCCeeecCCC---CCCC-C------ccHH
Confidence 444666778899999999999999999988766431100 0011111110 0000 0 0111
Q ss_pred HHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHH
Q 014852 304 RGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKV 383 (417)
Q Consensus 304 kAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etV 383 (417)
..+. |... .........-.+..+..++. . +.+..+.|......|. .+...|++|||+.||||.++|
T Consensus 228 ~~~~--d~~~-~pe~~~~~~~~~~~l~~al~------~----L~~rer~Vi~lr~gl~-~~~~~Tl~EIa~~lgiS~erV 293 (317)
T PRK07405 228 ELLE--DTGA-SPEDFATQSSLQLDLERLME------D----LTPQQKEVIALRFGLE-DGQPLTLAKIGERLNISRERV 293 (317)
T ss_pred Hhhc--CCCC-CHHHHHHHHHHHHHHHHHHH------c----CCHHHHHHHHHHhhcC-CCCCcCHHHHHHHHCcCHHHH
Confidence 1111 1111 01222221222222222221 1 2333455555555553 135569999999999999999
Q ss_pred HHHHHHhCccc
Q 014852 384 RNATEAIGKVF 394 (417)
Q Consensus 384 r~aL~rark~L 394 (417)
++++.+|.+.|
T Consensus 294 Rqi~~rAl~kL 304 (317)
T PRK07405 294 RQIEREALSKL 304 (317)
T ss_pred HHHHHHHHHHH
Confidence 99999887654
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=96.96 E-value=0.006 Score=60.83 Aligned_cols=132 Identities=19% Similarity=0.229 Sum_probs=70.6
Q ss_pred hHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhh-HHHHHHH
Q 014852 226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQG-GLIGLLR 304 (417)
Q Consensus 226 ~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQE-G~IgLik 304 (417)
.....+...+|++|+.+++|..+|++.+++...+.. +.+.. ..+..+.+ +-..+..
T Consensus 165 k~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~-------------------~~~~~----SLd~~~~~~~~~~~~~ 221 (298)
T TIGR02997 165 KVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQR-------------------ARQPV----SLDAPVGDEEDTELGD 221 (298)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHH-------------------cccCc----ccCCCcCCCCcchHHH
Confidence 345667788999999999999999999987753211 11111 11111110 0001111
Q ss_pred HHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHH
Q 014852 305 GIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVR 384 (417)
Q Consensus 305 AierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr 384 (417)
.+.. ... ...........+..+..++. .+| +..+.|......|. .+...|++|||+.||||.++|+
T Consensus 222 ~~~~--~~~-~pe~~~~~~~~~~~L~~~L~------~L~----~rer~Vi~lr~gl~-~~~~~Tl~EIa~~lgiS~erVr 287 (298)
T TIGR02997 222 LLED--DGE-SPEEQVERESLRQDLESLLA------ELT----PRERQVLRLRFGLD-GGEPLTLAEIGRRLNLSRERVR 287 (298)
T ss_pred hccC--CCC-CHHHHHHHHHHHHHHHHHHH------cCC----HHHHHHHHHHhccC-CCCCcCHHHHHHHHCcCHHHHH
Confidence 1111 111 12222322223332222221 122 33344444444442 1344599999999999999999
Q ss_pred HHHHHhCccc
Q 014852 385 NATEAIGKVF 394 (417)
Q Consensus 385 ~aL~rark~L 394 (417)
++++++.+.+
T Consensus 288 q~~~rAl~kL 297 (298)
T TIGR02997 288 QIEAKALRKL 297 (298)
T ss_pred HHHHHHHHHc
Confidence 9999987654
No 144
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=96.89 E-value=0.0083 Score=58.12 Aligned_cols=33 Identities=18% Similarity=0.285 Sum_probs=27.9
Q ss_pred HHHHHHHhhCCCCchHHHHHHhcCChHHHHHHh
Q 014852 227 HKLRLKERLGCEPSMEQLAASLRISRPELQSIL 259 (417)
Q Consensus 227 ~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l 259 (417)
+...+.+.+|++|+.+++|..+|++.++++..+
T Consensus 114 ~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~ 146 (251)
T PRK07670 114 AIEKLEQRYMRNVTPKEVAAELGMTEEEVEATM 146 (251)
T ss_pred HHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 455677889999999999999999999877543
No 145
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=96.87 E-value=0.018 Score=56.61 Aligned_cols=63 Identities=21% Similarity=0.272 Sum_probs=41.9
Q ss_pred hhhhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 014852 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (417)
Q Consensus 189 ~~~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~ 258 (417)
+...+..||.+....-.+ |....+++.+++. +..++.+.+|++|+.+++|..+|++.+++...
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 445566666664432112 1223345555543 56678889999999999999999999987653
No 146
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=96.86 E-value=0.011 Score=57.81 Aligned_cols=34 Identities=38% Similarity=0.470 Sum_probs=29.0
Q ss_pred chhHHHHHHHhhCCCCchHHHHHHhcCChHHHHH
Q 014852 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQS 257 (417)
Q Consensus 224 l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~ 257 (417)
+..+...|+..+|++|+.+++|..+|++.+++..
T Consensus 120 i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~ 153 (268)
T PRK06288 120 IERAIAMLEARLGRTPSDEEIADELGISLEEYNS 153 (268)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHH
Confidence 3346678899999999999999999999988664
No 147
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=96.74 E-value=0.0099 Score=57.27 Aligned_cols=60 Identities=22% Similarity=0.354 Sum_probs=40.3
Q ss_pred hhhhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 014852 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (417)
Q Consensus 189 ~~~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~ 258 (417)
+.+.+-.|++.....| ........+++ .+...+...+|++|+.+++|+.+|++.+++...
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 3345555666554333 22233344443 356788899999999999999999999987653
No 148
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=96.69 E-value=0.016 Score=63.58 Aligned_cols=131 Identities=15% Similarity=0.266 Sum_probs=73.5
Q ss_pred hHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhH-HHHHHH
Q 014852 226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGG-LIGLLR 304 (417)
Q Consensus 226 ~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG-~IgLik 304 (417)
.+...+.+.+|++|+.+++|..+|++.++++..+. ++.. ....++-+.+. -..+.
T Consensus 471 ~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~-------------------~~~~----~~Sld~~i~~~~~~~l~- 526 (619)
T PRK05658 471 RISRQMLQEIGREPTPEELAERLGMPEDKVRKVLK-------------------IAKE----PISLETPIGDDEDSHLG- 526 (619)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH-------------------hcCC----CCcCCCCCCCCCCCchh-
Confidence 35667889999999999999999999998775322 2221 12222211110 00111
Q ss_pred HHhhcCCCC--CCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHH
Q 014852 305 GIEKFDSSK--GFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKK 382 (417)
Q Consensus 305 AierFD~~r--G~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~et 382 (417)
.|-++. ..++........+..+...+ ..+.++...|...+..|. .+...|.+|||+.||||.++
T Consensus 527 ---d~i~d~~~~~p~~~~~~~~~~~~l~~~l----------~~L~~rE~~Vl~~r~g~~-~~~~~tl~ei~~~lgvs~eR 592 (619)
T PRK05658 527 ---DFIEDKNAELPIDAAIQESLREATTDVL----------ASLTPREAKVLRMRFGID-MNTDHTLEEVGKQFDVTRER 592 (619)
T ss_pred ---hhcCCCCCCChHHHHHHHHHHHHHHHHH----------HcCCHHHHHHHHHhcCCC-CCCCccHHHHHHHhCCCHHH
Confidence 121221 11233333333333222222 123334455555555442 13456999999999999999
Q ss_pred HHHHHHHhCccc
Q 014852 383 VRNATEAIGKVF 394 (417)
Q Consensus 383 Vr~aL~rark~L 394 (417)
|+++...+.+.|
T Consensus 593 VrQie~~al~kL 604 (619)
T PRK05658 593 IRQIEAKALRKL 604 (619)
T ss_pred HHHHHHHHHHHH
Confidence 999988776543
No 149
>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=96.48 E-value=0.036 Score=53.88 Aligned_cols=62 Identities=15% Similarity=0.232 Sum_probs=39.7
Q ss_pred hhhhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 014852 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (417)
Q Consensus 189 ~~~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~ 258 (417)
+.+.+..|++..... .+ |....+++.++.. +..++...+|++|+.+++|+.+|++.+++...
T Consensus 95 irn~~~~~lr~~~~i-r~-p~~~~~~~~~~~~------~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~ 156 (254)
T TIGR02850 95 IIGEIRRYLRDNNPI-RV-SRSLRDIAYKALQ------VRDKLISENSKEPTVSEIAKELKVPQEEVVFA 156 (254)
T ss_pred HHHHHHHHHHhCCCc-cC-chHHHHHHHHHHH------HHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHH
Confidence 334555566554321 12 2223334444432 45678888999999999999999999987654
No 150
>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=96.44 E-value=0.036 Score=52.57 Aligned_cols=34 Identities=29% Similarity=0.443 Sum_probs=28.6
Q ss_pred hhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 014852 225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (417)
Q Consensus 225 ~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~ 258 (417)
..+...|+..+|++|+.+++|+.+|++.++++..
T Consensus 86 ~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~ 119 (224)
T TIGR02479 86 ERAIRELEARLGREPTEEEIAEELGMDLKEYRQA 119 (224)
T ss_pred HHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHH
Confidence 3456678889999999999999999999887653
No 151
>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=96.17 E-value=0.011 Score=55.98 Aligned_cols=31 Identities=29% Similarity=0.506 Sum_probs=26.7
Q ss_pred HHHHHHHhhCCCCchHHHHHHhcCChHHHHH
Q 014852 227 HKLRLKERLGCEPSMEQLAASLRISRPELQS 257 (417)
Q Consensus 227 ~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~ 257 (417)
+...++..+|++|+.+++|..+|++.+++..
T Consensus 95 ~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~ 125 (227)
T TIGR02980 95 ATEELTQRLGRSPTIAEIAEELGVSEEEVVE 125 (227)
T ss_pred HHHHHHHHHCCCCCHHHHHHHhCCCHHHHHH
Confidence 4567888899999999999999999988653
No 152
>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=96.16 E-value=0.0096 Score=57.66 Aligned_cols=31 Identities=23% Similarity=0.299 Sum_probs=26.7
Q ss_pred HHHHHHHhhCCCCchHHHHHHhcCChHHHHH
Q 014852 227 HKLRLKERLGCEPSMEQLAASLRISRPELQS 257 (417)
Q Consensus 227 ~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~ 257 (417)
+...++..+|++|+.+++|..++++.+++..
T Consensus 121 ~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~ 151 (255)
T TIGR02941 121 AIDELTDHLQRSPKIIEIADHLGLSEEEVLE 151 (255)
T ss_pred HHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 4557888899999999999999999988664
No 153
>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=96.15 E-value=0.013 Score=46.61 Aligned_cols=35 Identities=34% Similarity=0.564 Sum_probs=27.9
Q ss_pred hhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHh
Q 014852 225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSIL 259 (417)
Q Consensus 225 ~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l 259 (417)
.+++..|.+.+||+|+.+|+|..+|++.++++..+
T Consensus 7 ~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l 41 (78)
T PF04539_consen 7 ERARRELEQELGREPTDEEIAEELGISVEEVRELL 41 (78)
T ss_dssp HHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHH
Confidence 34778899999999999999999999999987643
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=96.08 E-value=0.023 Score=44.86 Aligned_cols=47 Identities=26% Similarity=0.221 Sum_probs=40.4
Q ss_pred HHHHHHHHHhHHHHHHHHHHcc----C--CCCChhhhhhhHHHHHHHHHhhcC
Q 014852 264 LAREKLVMSNVRLVMSIAQRYD----N--MGADMADLVQGGLIGLLRGIEKFD 310 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~----~--~g~e~EDLIQEG~IgLikAierFD 310 (417)
.|.++++..|.|++.+++.|-. + .+.--+|+-|+--..|++++-+|+
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 9999999999999999999833 1 234458999999999999999996
No 155
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=96.06 E-value=0.19 Score=49.91 Aligned_cols=30 Identities=17% Similarity=0.231 Sum_probs=26.1
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
.+.|++|||+.||||.++|+++...+.+.|
T Consensus 247 ~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kL 276 (284)
T PRK06596 247 DKSTLQELAAEYGVSAERVRQIEKNAMKKL 276 (284)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 466999999999999999999998876543
No 156
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=95.95 E-value=0.066 Score=51.26 Aligned_cols=31 Identities=29% Similarity=0.413 Sum_probs=26.3
Q ss_pred HHHHHHHhhCCCCchHHHHHHhcCChHHHHH
Q 014852 227 HKLRLKERLGCEPSMEQLAASLRISRPELQS 257 (417)
Q Consensus 227 ~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~ 257 (417)
....+...+|++|+.+++|..+|++.+++..
T Consensus 100 ~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~ 130 (236)
T PRK06986 100 AIRQLEQELGREPTDTEVAEKLGLSLEEYRE 130 (236)
T ss_pred HHHHHHHHHCCCCCHHHHHHHcCCCHHHHHH
Confidence 4456777899999999999999999988664
No 157
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=95.85 E-value=0.003 Score=46.84 Aligned_cols=27 Identities=30% Similarity=0.287 Sum_probs=22.3
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAIGKV 393 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~rark~ 393 (417)
.|++|||+.+|+|+.+|+..+.++++.
T Consensus 27 ~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 27 MSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp --HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 499999999999999999999998754
No 158
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=95.82 E-value=0.056 Score=54.87 Aligned_cols=30 Identities=10% Similarity=0.273 Sum_probs=26.9
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
...|++|||+.||||.++|+++++++++.|
T Consensus 281 e~~s~~EIA~~Lgis~~tV~~~~~rAl~kL 310 (325)
T PRK05657 281 EAATLEDVAREIGLTRERVRQIQVEALRRL 310 (325)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 456999999999999999999999998765
No 159
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=95.52 E-value=0.067 Score=50.87 Aligned_cols=31 Identities=35% Similarity=0.531 Sum_probs=26.6
Q ss_pred HHHHHHHhhCCCCchHHHHHHhcCChHHHHH
Q 014852 227 HKLRLKERLGCEPSMEQLAASLRISRPELQS 257 (417)
Q Consensus 227 ~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~ 257 (417)
....+...+|++|+.+++|+.+|++.+++..
T Consensus 102 ~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~ 132 (231)
T TIGR02885 102 MKEELSKELGREPTINELAEALGVSPEEIVM 132 (231)
T ss_pred HHHHHHHHHCcCCCHHHHHHHHCcCHHHHHH
Confidence 4556788899999999999999999988654
No 160
>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=95.42 E-value=0.11 Score=51.46 Aligned_cols=30 Identities=13% Similarity=0.268 Sum_probs=26.8
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
...|++|||+.||||+++|+.+++++++.+
T Consensus 241 e~~s~~EIA~~Lgis~~tVk~~l~rAlkkL 270 (285)
T TIGR02394 241 EPATLEEVAAEVGLTRERVRQIQVEALKKL 270 (285)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 445999999999999999999999998765
No 161
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=95.36 E-value=0.08 Score=51.50 Aligned_cols=32 Identities=25% Similarity=0.370 Sum_probs=27.4
Q ss_pred HHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 014852 227 HKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (417)
Q Consensus 227 ~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~ 258 (417)
+..++...+|++|+.+++|..+|++.+++...
T Consensus 128 ~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~~ 159 (258)
T PRK08215 128 VREKLINENSKEPTVEEIAKELEVPREEVVFA 159 (258)
T ss_pred HHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHH
Confidence 45578889999999999999999999987643
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=95.22 E-value=0.6 Score=45.87 Aligned_cols=30 Identities=13% Similarity=0.197 Sum_probs=25.4
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
...|++|||+.||||.++|+++...+.+.+
T Consensus 235 ~~~t~~eIA~~lgvS~~~V~q~~~~Al~kL 264 (270)
T TIGR02392 235 DKLTLQELAAEYGVSAERIRQIEKNAMKKL 264 (270)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 456999999999999999999888776543
No 163
>PRK05572 sporulation sigma factor SigF; Validated
Probab=94.21 E-value=0.29 Score=47.46 Aligned_cols=30 Identities=23% Similarity=0.235 Sum_probs=25.9
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
...|++|||+.||+|..+|+.+.+++.+.+
T Consensus 217 ~~~s~~eIA~~lgis~~~V~~~~~ral~kL 246 (252)
T PRK05572 217 KDKTQSEVAKRLGISQVQVSRLEKKILKQM 246 (252)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 346999999999999999999998887654
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=93.47 E-value=0.14 Score=37.41 Aligned_cols=30 Identities=27% Similarity=0.203 Sum_probs=25.3
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014852 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKV 393 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~aL~rark~ 393 (417)
....|+.|||+.||+|.++|+++..++.+.
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 455699999999999999999999887643
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=91.79 E-value=0.51 Score=37.17 Aligned_cols=44 Identities=30% Similarity=0.369 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHH-HHcCCCccHHHHHHHcCCC-HHHHHHHHHHhC
Q 014852 348 ERLGLIRNAKLRL-EEKGVTPSVDRIAEYLNMS-QKKVRNATEAIG 391 (417)
Q Consensus 348 e~~~kI~~a~~~L-~e~gRepS~eEIAe~LGIS-~etVr~aL~rar 391 (417)
+...+|..++... .+.|..||+.|||+.+|++ ..+|...+.+..
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 4445555555554 6689999999999999997 999999988764
No 166
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=90.50 E-value=0.16 Score=49.17 Aligned_cols=30 Identities=23% Similarity=0.128 Sum_probs=25.9
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
.+.|++|||+.||||+++|+..++++++.+
T Consensus 220 ~g~s~~eIA~~l~is~~tV~~~~~ra~~kL 249 (257)
T PRK08583 220 ENLSQKETGERLGISQMHVSRLQRQAIKKL 249 (257)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 345999999999999999999999887644
No 167
>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=90.31 E-value=0.65 Score=33.47 Aligned_cols=34 Identities=29% Similarity=0.341 Sum_probs=24.3
Q ss_pred HHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 356 AKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 356 a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~ra 390 (417)
.+..|...+| .++.+||+.+|+|..+|.+++.+.
T Consensus 8 Il~~Lq~d~r-~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 8 ILRLLQEDGR-RSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHH-TT-S-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHcCC-ccHHHHHHHHCcCHHHHHHHHHHh
Confidence 3444555555 589999999999999999988764
No 168
>PRK06930 positive control sigma-like factor; Validated
Probab=90.24 E-value=0.18 Score=46.84 Aligned_cols=29 Identities=31% Similarity=0.415 Sum_probs=25.8
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
+.|+.|||+.||+|+++|+..+.++++.+
T Consensus 130 g~s~~EIA~~lgiS~~tVk~~l~Ra~~kL 158 (170)
T PRK06930 130 GLSYSEIADYLNIKKSTVQSMIERAEKKI 158 (170)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 34999999999999999999999988654
No 169
>PHA02547 55 RNA polymerase sigma factor; Provisional
Probab=89.66 E-value=1 Score=42.13 Aligned_cols=65 Identities=14% Similarity=0.277 Sum_probs=50.7
Q ss_pred hHHHHHHHHHHccCCCCC---hhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhc
Q 014852 273 NVRLVMSIAQRYDNMGAD---MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENS 337 (417)
Q Consensus 273 yl~LV~sIA~Ry~~~g~e---~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~ 337 (417)
.+..+..+.++|--++.. -+|+|.+|...+++.++.||+.+...+-+|+..++-++..+.|..+.
T Consensus 46 imkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~kEk 113 (179)
T PHA02547 46 IMKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIKKEK 113 (179)
T ss_pred HHHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHHHHH
Confidence 344445555555433333 68999999999999999999999999999999999988888776554
No 170
>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=89.33 E-value=0.27 Score=34.50 Aligned_cols=29 Identities=31% Similarity=0.255 Sum_probs=24.9
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKV 393 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~rark~ 393 (417)
...+..+||+.||++..+|...+.+++..
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 34589999999999999999999887643
No 171
>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=87.64 E-value=0.55 Score=35.75 Aligned_cols=31 Identities=16% Similarity=0.178 Sum_probs=27.0
Q ss_pred cCCCccHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014852 363 KGVTPSVDRIAEYLNMSQKKVRNATEAIGKV 393 (417)
Q Consensus 363 ~gRepS~eEIAe~LGIS~etVr~aL~rark~ 393 (417)
.-|..+..|||+.|||+..++...++++-++
T Consensus 20 ~PR~~tl~elA~~lgis~st~~~~LRrae~k 50 (53)
T PF04967_consen 20 VPRRITLEELAEELGISKSTVSEHLRRAERK 50 (53)
T ss_pred CCCcCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 3477899999999999999999999988643
No 172
>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=87.01 E-value=1.1 Score=36.40 Aligned_cols=26 Identities=27% Similarity=0.316 Sum_probs=22.7
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~ra 390 (417)
...|+.|||+.||+|+.+|+..+..-
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~~~ 56 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLKGE 56 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcC
Confidence 44599999999999999999998753
No 173
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=86.76 E-value=0.65 Score=33.29 Aligned_cols=29 Identities=28% Similarity=0.329 Sum_probs=25.7
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhCcccc
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAIGKVFS 395 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~rark~LS 395 (417)
.+..|||+.||+|..+|+..+.++.+.+.
T Consensus 19 ~s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 19 LTNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 48999999999999999999998876654
No 174
>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=86.47 E-value=1.8 Score=31.85 Aligned_cols=40 Identities=18% Similarity=0.149 Sum_probs=28.9
Q ss_pred HHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 355 NAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 355 ~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
..+..|.......|.+|||+.||||..||++.+.......
T Consensus 4 ~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 4 QILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 3444563334448999999999999999999988775433
No 175
>PRK00118 putative DNA-binding protein; Validated
Probab=85.75 E-value=0.45 Score=41.06 Aligned_cols=29 Identities=28% Similarity=0.346 Sum_probs=25.3
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
+.|+.|||+.+|+|..+|...+.++++.+
T Consensus 33 g~S~~EIAe~lGIS~~TV~r~L~RArkkL 61 (104)
T PRK00118 33 DYSLGEIAEEFNVSRQAVYDNIKRTEKLL 61 (104)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 45999999999999999999999887543
No 176
>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=85.68 E-value=2.5 Score=31.85 Aligned_cols=46 Identities=30% Similarity=0.421 Sum_probs=35.3
Q ss_pred ccCccHHHHHHHHHHHHHHHHHcCCC-ccHHHHHHHcCCCHHHHHHH
Q 014852 341 RLPNHLHERLGLIRNAKLRLEEKGVT-PSVDRIAEYLNMSQKKVRNA 386 (417)
Q Consensus 341 rlp~~~~e~~~kI~~a~~~L~e~gRe-pS~eEIAe~LGIS~etVr~a 386 (417)
.+|....+++....+++..|...|.+ ++-.|||+.+|++..+|+.=
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 46777777888888888899877765 58999999999999999864
No 177
>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=85.55 E-value=2.2 Score=30.68 Aligned_cols=35 Identities=20% Similarity=0.160 Sum_probs=25.1
Q ss_pred HHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 356 AKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 356 a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
.+..|.+.++ .|..|||+.+|+|..+|...+....
T Consensus 8 Il~~l~~~~~-~t~~ela~~~~is~~tv~~~l~~L~ 42 (48)
T PF13412_consen 8 ILNYLRENPR-ITQKELAEKLGISRSTVNRYLKKLE 42 (48)
T ss_dssp HHHHHHHCTT-S-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHcCC-CCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 3344544444 7999999999999999999987653
No 178
>PHA02591 hypothetical protein; Provisional
Probab=84.89 E-value=1.9 Score=35.54 Aligned_cols=35 Identities=34% Similarity=0.472 Sum_probs=26.9
Q ss_pred HHHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHH
Q 014852 353 IRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 353 I~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~r 389 (417)
+......|.+.| .|+++||+.||++.++|++.++-
T Consensus 48 ~~~vA~eL~eqG--lSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 48 LISVTHELARKG--FTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred HHHHHHHHHHcC--CCHHHHHHHhCCCHHHHHHHHhc
Confidence 445555565444 59999999999999999998753
No 179
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=84.29 E-value=0.92 Score=32.68 Aligned_cols=28 Identities=25% Similarity=0.361 Sum_probs=25.2
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
.+..|||+.||++..+|+..++++++.+
T Consensus 16 ~s~~eia~~l~~s~~tv~~~~~~~~~~l 43 (57)
T cd06170 16 KTNKEIADILGISEKTVKTHLRNIMRKL 43 (57)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHh
Confidence 4999999999999999999999887654
No 180
>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=83.98 E-value=3.9 Score=31.55 Aligned_cols=41 Identities=24% Similarity=0.214 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 351 GLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 351 ~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
....+++..|.+.+..++..+||+.||++..+|-..+.+..
T Consensus 7 e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~ 47 (60)
T PF01325_consen 7 EDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLA 47 (60)
T ss_dssp HHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHH
Confidence 34566777777777788999999999999999999988754
No 181
>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=82.64 E-value=2.5 Score=33.12 Aligned_cols=29 Identities=24% Similarity=0.281 Sum_probs=23.8
Q ss_pred HHcCCCccHHHHHHHcCCCHHHHHHHHHH
Q 014852 361 EEKGVTPSVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 361 ~e~gRepS~eEIAe~LGIS~etVr~aL~r 389 (417)
.+.+...+..+||+.|||+..||+..-..
T Consensus 17 ~~~~g~i~lkdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 17 KESNGKIKLKDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred HHhCCCccHHHHHHHHCCCHHHHHHHhhh
Confidence 34566789999999999999999987443
No 182
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=82.22 E-value=2.3 Score=30.66 Aligned_cols=24 Identities=25% Similarity=0.239 Sum_probs=17.5
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHH
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~r 389 (417)
..|+.|||+.||++..||.+.+.+
T Consensus 20 G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 20 GMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ---HHHHHHHTT--HHHHHHHHHH
T ss_pred CCCHHHHHHHHCcCcHHHHHHHhc
Confidence 369999999999999999988765
No 183
>PRK04217 hypothetical protein; Provisional
Probab=82.15 E-value=1 Score=39.30 Aligned_cols=29 Identities=14% Similarity=0.121 Sum_probs=25.9
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
+.|++|||+.||||..+|+..+.++++.|
T Consensus 58 GlS~~EIAk~LGIS~sTV~r~L~RArkkL 86 (110)
T PRK04217 58 GLTQEEAGKRMGVSRGTVWRALTSARKKV 86 (110)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 45999999999999999999999887655
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=81.36 E-value=0.98 Score=33.96 Aligned_cols=31 Identities=32% Similarity=0.333 Sum_probs=25.4
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATEAIGKVFSL 396 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~rark~LSL 396 (417)
.-+..|||+.||+++.+|+..+..+.+.+-+
T Consensus 18 G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~ 48 (58)
T PF00196_consen 18 GMSNKEIAEELGISEKTVKSHRRRIMKKLGV 48 (58)
T ss_dssp TS-HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred cCCcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence 3489999999999999999999888776644
No 185
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=81.13 E-value=7.6 Score=40.37 Aligned_cols=126 Identities=11% Similarity=-0.010 Sum_probs=76.8
Q ss_pred HHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccH
Q 014852 267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHL 346 (417)
Q Consensus 267 e~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~ 346 (417)
+..+..-.+.+..---+|+++-.-+||.+||+|+...+.--+=-+-+ .=..|++-.-|+.-++.+|+..+....+.+.
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 33344444555555556667666799999999865544333222323 4578999999999999998877544333321
Q ss_pred HHHH--HH---------------HHHHHHH-----HHHcCC---------CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 347 HERL--GL---------------IRNAKLR-----LEEKGV---------TPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 347 ~e~~--~k---------------I~~a~~~-----L~e~gR---------epS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
.... .+ +.+.+.. |+..+| ..|..|||...=+++.++.+++-+++..+
T Consensus 86 ~~~~e~~e~~~a~~~~d~~i~Dd~LRLiFvccHPal~~~~riALtLR~v~GLs~~eIArAFLv~e~am~QRivRAK~ri 164 (415)
T COG4941 86 LLSDEDEEMEEAEALDDEHIRDDRLRLIFVCCHPALPPEQRIALTLRLVGGLSTAEIARAFLVPEAAMAQRIVRAKARI 164 (415)
T ss_pred cccccchhhhccccccccccchhhHHhhhhhcCCCCChhhHHHHHHHHHcCCcHHHHHHHHcCCcHHHHHHHHHHHHHH
Confidence 1100 00 1111111 011111 13999999999999999999999988655
No 186
>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=80.50 E-value=1.7 Score=29.80 Aligned_cols=25 Identities=20% Similarity=0.405 Sum_probs=19.7
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~rar 391 (417)
.|.+|||..+|++.++|-..+...+
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l~ 27 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKLE 27 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHHH
Confidence 3789999999999999999887654
No 187
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=79.69 E-value=3.5 Score=37.13 Aligned_cols=34 Identities=15% Similarity=0.140 Sum_probs=27.7
Q ss_pred HHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 357 KLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 357 ~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
+..|...+| .++.|||+.+|+|+.+|+.++++..
T Consensus 15 l~~Lq~d~R-~s~~eiA~~lglS~~tV~~Ri~rL~ 48 (153)
T PRK11179 15 LEALMENAR-TPYAELAKQFGVSPGTIHVRVEKMK 48 (153)
T ss_pred HHHHHHcCC-CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 444555565 4899999999999999999998765
No 188
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=78.92 E-value=4.6 Score=29.12 Aligned_cols=21 Identities=24% Similarity=0.243 Sum_probs=16.9
Q ss_pred ccHHHHHHHcCCCHHHHHHHH
Q 014852 367 PSVDRIAEYLNMSQKKVRNAT 387 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL 387 (417)
.|+.+||+.+||+..||...+
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 689999999999999998875
No 189
>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=78.39 E-value=3.7 Score=30.22 Aligned_cols=36 Identities=19% Similarity=0.259 Sum_probs=26.7
Q ss_pred HHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 355 NAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 355 ~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~ra 390 (417)
..+..+.+.+...+..|||+.+|++..+|..++...
T Consensus 7 ~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL 42 (52)
T PF09339_consen 7 RILEALAESGGPLTLSEIARALGLPKSTVHRLLQTL 42 (52)
T ss_dssp HHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 334444555556799999999999999999988754
No 190
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=77.96 E-value=4.1 Score=35.89 Aligned_cols=36 Identities=19% Similarity=0.149 Sum_probs=28.9
Q ss_pred HHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 355 NAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 355 ~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
+.+..|+..+| .++.|||+.+|+|..+|.+++.+..
T Consensus 12 ~IL~~L~~d~r-~~~~eia~~lglS~~~v~~Ri~~L~ 47 (154)
T COG1522 12 RILRLLQEDAR-ISNAELAERVGLSPSTVLRRIKRLE 47 (154)
T ss_pred HHHHHHHHhCC-CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 34445666666 7999999999999999999988754
No 191
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=77.96 E-value=3 Score=40.48 Aligned_cols=34 Identities=26% Similarity=0.319 Sum_probs=28.5
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCcccccc
Q 014852 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLD 397 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD 397 (417)
.+..|.+|||+.|++++.||++.+....+++.+.
T Consensus 156 a~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLgv~ 189 (217)
T PRK13719 156 SFGFSHEYIAQLLNITVGSSKNKISEILKFFGIS 189 (217)
T ss_pred HCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 4456999999999999999999998887766543
No 192
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=76.89 E-value=5.2 Score=32.24 Aligned_cols=35 Identities=29% Similarity=0.260 Sum_probs=23.6
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCccccccc
Q 014852 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDR 398 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~ 398 (417)
.+..|+.|+|+.||++..+|.++++.-...+|+|.
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 56789999999999999999998764445566653
No 193
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=76.74 E-value=2.2 Score=30.75 Aligned_cols=26 Identities=23% Similarity=0.151 Sum_probs=18.6
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~rar 391 (417)
..|+.+||+.||+|..||.+.+.+-+
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT---
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHcc
Confidence 34899999999999999999977653
No 194
>PRK14082 hypothetical protein; Provisional
Probab=76.43 E-value=8 Score=30.77 Aligned_cols=55 Identities=11% Similarity=0.016 Sum_probs=43.3
Q ss_pred HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhH
Q 014852 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 320 (417)
Q Consensus 264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTY 320 (417)
...+.|+..+.|.+.+-... .+..+.|||.||--|.+++-++.++...+.-|.-|
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 56778999999988765443 24567899999999999999999987776666544
No 195
>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=75.83 E-value=3.3 Score=37.46 Aligned_cols=30 Identities=17% Similarity=0.083 Sum_probs=25.8
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
+..|++|||+.||+|..+|+..+.++++.+
T Consensus 20 ~GlTq~EIAe~LgiS~stV~~~e~ra~kkL 49 (137)
T TIGR00721 20 KGLSQKEIAKELKTTRANVSAIEKRAMENI 49 (137)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHhHHHHH
Confidence 456999999999999999999988876544
No 196
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=73.87 E-value=4.9 Score=36.64 Aligned_cols=34 Identities=12% Similarity=0.119 Sum_probs=27.4
Q ss_pred HHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 357 KLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 357 ~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
+..|+..+| .|+.|||+.+|+|..+|.+++++..
T Consensus 20 L~~Lq~d~R-~s~~eiA~~lglS~~tv~~Ri~rL~ 53 (164)
T PRK11169 20 LNELQKDGR-ISNVELSKRVGLSPTPCLERVRRLE 53 (164)
T ss_pred HHHhccCCC-CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 334555555 4889999999999999999988754
No 197
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=73.62 E-value=3.9 Score=37.16 Aligned_cols=29 Identities=17% Similarity=0.154 Sum_probs=24.6
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKV 393 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~rark~ 393 (417)
...|++|||+.||+|..+|...+.++++.
T Consensus 20 ~GlTq~EIAe~LGiS~~tVs~ie~ra~kk 48 (141)
T PRK03975 20 RGLTQQEIADILGTSRANVSSIEKRAREN 48 (141)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 45699999999999999999988776643
No 198
>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=73.14 E-value=8.9 Score=29.56 Aligned_cols=26 Identities=23% Similarity=0.192 Sum_probs=22.9
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~rar 391 (417)
.-++.|||+.||++..||.+...+-.
T Consensus 13 G~~~~eIA~~Lg~~~~TV~~W~~r~~ 38 (58)
T PF06056_consen 13 GWSIKEIAEELGVPRSTVYSWKDRYK 38 (58)
T ss_pred CCCHHHHHHHHCCChHHHHHHHHhhC
Confidence 45899999999999999999887765
No 199
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=73.07 E-value=4.4 Score=38.50 Aligned_cols=33 Identities=12% Similarity=0.157 Sum_probs=29.1
Q ss_pred HcCCCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 362 EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 362 e~gRepS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
+.-|..+.+|||+.|||+..++.+.+++|.+++
T Consensus 174 d~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl 206 (215)
T COG3413 174 DYPRRVSLKDLAKELGISKSTLSEHLRRAERKL 206 (215)
T ss_pred CCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 345788999999999999999999999998655
No 200
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=72.64 E-value=9.2 Score=30.02 Aligned_cols=35 Identities=23% Similarity=0.267 Sum_probs=27.3
Q ss_pred HHHHHHcCC-CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 357 KLRLEEKGV-TPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 357 ~~~L~e~gR-epS~eEIAe~LGIS~etVr~aL~rar 391 (417)
+..|...|. ..+..|||+.||++..+|+..+....
T Consensus 12 L~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~ 47 (68)
T smart00550 12 LEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLE 47 (68)
T ss_pred HHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 334444444 47999999999999999999988654
No 201
>PF13730 HTH_36: Helix-turn-helix domain
Probab=72.55 E-value=4.6 Score=29.69 Aligned_cols=26 Identities=27% Similarity=0.459 Sum_probs=22.8
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~ra 390 (417)
--||++.||+.+|++..||.+++...
T Consensus 24 ~~pS~~~la~~~g~s~~Tv~~~i~~L 49 (55)
T PF13730_consen 24 CFPSQETLAKDLGVSRRTVQRAIKEL 49 (55)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 34799999999999999999998764
No 202
>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=71.75 E-value=7.3 Score=29.67 Aligned_cols=31 Identities=19% Similarity=0.423 Sum_probs=25.2
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
.+..++.|||+.||+|..+|++.+......+
T Consensus 17 ~~~~~~~ela~~l~~S~rti~~~i~~L~~~f 47 (59)
T PF08280_consen 17 NKWITLKELAKKLNISERTIKNDINELNEFF 47 (59)
T ss_dssp HTSBBHHHHHHHCTS-HHHHHHHHHHHHTT-
T ss_pred CCCCcHHHHHHHHCCCHHHHHHHHHHHHHHh
Confidence 5667999999999999999999988776543
No 203
>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=71.53 E-value=3.9 Score=30.09 Aligned_cols=23 Identities=17% Similarity=0.215 Sum_probs=20.3
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHh
Q 014852 368 SVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 368 S~eEIAe~LGIS~etVr~aL~ra 390 (417)
|++|||+.+|+|..||..+++--
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 67999999999999999987654
No 204
>PF12728 HTH_17: Helix-turn-helix domain
Probab=71.32 E-value=4.4 Score=29.41 Aligned_cols=23 Identities=26% Similarity=0.222 Sum_probs=20.6
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHh
Q 014852 368 SVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 368 S~eEIAe~LGIS~etVr~aL~ra 390 (417)
|.+|+|+.|||+..+|.......
T Consensus 3 t~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 3 TVKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcC
Confidence 78999999999999999987654
No 205
>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=70.96 E-value=11 Score=31.11 Aligned_cols=30 Identities=30% Similarity=0.397 Sum_probs=22.6
Q ss_pred HcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 362 EKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 362 e~gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
..|+.+|..++|..+|++.++|+.++..+.
T Consensus 34 A~G~PVt~~~LA~a~g~~~e~v~~~L~~~p 63 (77)
T PF12324_consen 34 AKGQPVTVEQLAAALGWPVEEVRAALAAMP 63 (77)
T ss_dssp TTTS-B-HHHHHHHHT--HHHHHHHHHH-T
T ss_pred HcCCCcCHHHHHHHHCCCHHHHHHHHHhCC
Confidence 349999999999999999999999998774
No 206
>PF14502 HTH_41: Helix-turn-helix domain
Probab=70.56 E-value=5.7 Score=29.83 Aligned_cols=34 Identities=18% Similarity=0.358 Sum_probs=27.9
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhC--cccccc
Q 014852 364 GVTPSVDRIAEYLNMSQKKVRNATEAIG--KVFSLD 397 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~aL~rar--k~LSLD 397 (417)
.|-||+.|.++.++++.++|.+++.... ..+.|.
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 4678999999999999999999998765 344444
No 207
>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=69.71 E-value=3.4 Score=35.59 Aligned_cols=31 Identities=26% Similarity=0.278 Sum_probs=23.5
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
....|..|||+.+|||...|...+.++.+.+
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 3446999999999999999999999987654
No 208
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=69.63 E-value=6 Score=28.70 Aligned_cols=28 Identities=29% Similarity=0.355 Sum_probs=24.0
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCc
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAIGK 392 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~rark 392 (417)
+-||..|||+.+|+|..+|+.++....+
T Consensus 19 ~l~s~~~la~~~~vs~~tv~~~l~~L~~ 46 (60)
T smart00345 19 KLPSERELAAQLGVSRTTVREALSRLEA 46 (60)
T ss_pred cCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3359999999999999999999887653
No 209
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=69.12 E-value=9.6 Score=27.59 Aligned_cols=23 Identities=26% Similarity=0.263 Sum_probs=21.2
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHH
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~r 389 (417)
.|..+||+.+|++..+|.+++..
T Consensus 28 ~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 28 RSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHh
Confidence 59999999999999999998765
No 210
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=69.01 E-value=15 Score=29.28 Aligned_cols=38 Identities=16% Similarity=0.147 Sum_probs=28.8
Q ss_pred HHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 354 RNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 354 ~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
...+..|.......+..|||+.+|++..+|...+....
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~ 45 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQ 45 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 33444454443467999999999999999999988754
No 211
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=68.77 E-value=5.9 Score=27.61 Aligned_cols=23 Identities=30% Similarity=0.397 Sum_probs=20.7
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHh
Q 014852 368 SVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 368 S~eEIAe~LGIS~etVr~aL~ra 390 (417)
|.+|+|+.|||+..+|.+..+..
T Consensus 3 t~~e~a~~lgis~~ti~~~~~~g 25 (49)
T TIGR01764 3 TVEEAAEYLGVSKDTVYRLIHEG 25 (49)
T ss_pred CHHHHHHHHCCCHHHHHHHHHcC
Confidence 78999999999999999987654
No 212
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=68.22 E-value=7.1 Score=37.05 Aligned_cols=34 Identities=29% Similarity=0.309 Sum_probs=28.1
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCcccccc
Q 014852 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLD 397 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD 397 (417)
.+..|.+|||+.|++|++||+.......+++-+.
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 3445999999999999999999988877766543
No 213
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=68.15 E-value=7 Score=36.86 Aligned_cols=32 Identities=16% Similarity=0.224 Sum_probs=27.1
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVFSL 396 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~rark~LSL 396 (417)
...|.+|||+.||+|+.||+..+.+...++..
T Consensus 151 ~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~v 182 (207)
T PRK15411 151 AGQGTIQISDQMNIKAKTVSSHKGNIKRKIKT 182 (207)
T ss_pred cCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCC
Confidence 34589999999999999999999887766644
No 214
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=67.71 E-value=7.8 Score=35.77 Aligned_cols=32 Identities=22% Similarity=0.136 Sum_probs=27.4
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVFSL 396 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~rark~LSL 396 (417)
...|.+|||+.|++|..||+..+....+++.+
T Consensus 164 ~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~v 195 (216)
T PRK10840 164 EGFLVTEIAKKLNRSIKTISSQKKSAMMKLGV 195 (216)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 44699999999999999999999887776654
No 215
>PRK13870 transcriptional regulator TraR; Provisional
Probab=67.08 E-value=4.3 Score=39.28 Aligned_cols=27 Identities=22% Similarity=0.263 Sum_probs=25.2
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 368 SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 368 S~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
|..|||.+||||+.||+..+..++++|
T Consensus 190 T~~EIa~ILgISe~TV~~Hl~na~~KL 216 (234)
T PRK13870 190 TMEEIADVEGVKYNSVRVKLREAMKRF 216 (234)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHc
Confidence 899999999999999999999888775
No 216
>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=66.16 E-value=31 Score=28.45 Aligned_cols=43 Identities=28% Similarity=0.258 Sum_probs=32.6
Q ss_pred HHHHHHHHHHH-HHcCCCccHHHHHHHcCCCHHHHHHHHHHhCc
Q 014852 350 LGLIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKVRNATEAIGK 392 (417)
Q Consensus 350 ~~kI~~a~~~L-~e~gRepS~eEIAe~LGIS~etVr~aL~rark 392 (417)
...|..++-.+ .+.++.+.-++||+.|+++..||++.|.....
T Consensus 6 q~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~ 49 (78)
T PF03444_consen 6 QREILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADLEE 49 (78)
T ss_pred HHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHHH
Confidence 34444444444 45688889999999999999999999887643
No 217
>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=66.03 E-value=10 Score=28.92 Aligned_cols=27 Identities=30% Similarity=0.365 Sum_probs=21.1
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
+-|+..+||+.+|+|..+|++++....
T Consensus 23 ~lps~~~la~~~~vsr~tvr~al~~L~ 49 (64)
T PF00392_consen 23 RLPSERELAERYGVSRTTVREALRRLE 49 (64)
T ss_dssp BE--HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred EeCCHHHHHHHhccCCcHHHHHHHHHH
Confidence 446999999999999999999988753
No 218
>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=64.93 E-value=7.9 Score=26.74 Aligned_cols=24 Identities=21% Similarity=0.205 Sum_probs=20.9
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 368 SVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 368 S~eEIAe~LGIS~etVr~aL~rar 391 (417)
+..|+|+.|||+..+|........
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcCC
Confidence 678999999999999999877653
No 219
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=64.61 E-value=5.3 Score=34.68 Aligned_cols=29 Identities=21% Similarity=0.197 Sum_probs=26.5
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
..+++|-|+.||||..|+..++..|++++
T Consensus 57 gl~QeeaA~~MgVSR~T~~ril~~ARkKi 85 (106)
T PF02001_consen 57 GLSQEEAAERMGVSRPTFQRILESARKKI 85 (106)
T ss_pred CCCHHHHHHHcCCcHHHHHHHHHHHHHHH
Confidence 35999999999999999999999999765
No 220
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=64.30 E-value=9.6 Score=36.19 Aligned_cols=32 Identities=22% Similarity=0.179 Sum_probs=27.2
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVFSL 396 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~rark~LSL 396 (417)
+..|.+|||+.|+||+.||+.......+++.+
T Consensus 148 ~G~snkeIA~~L~iS~~TV~~h~~~I~~KLgv 179 (207)
T PRK11475 148 RGYSMPQIAEQLERNIKTIRAHKFNVMSKLGV 179 (207)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 34599999999999999999998887776654
No 221
>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=64.27 E-value=5.1 Score=38.52 Aligned_cols=29 Identities=21% Similarity=0.286 Sum_probs=26.0
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhCcccc
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAIGKVFS 395 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~rark~LS 395 (417)
.|..|||+.||||+.||+..+..+.+++-
T Consensus 187 ~t~~eIa~~l~is~~Tv~~~l~~~~~kl~ 215 (232)
T TIGR03541 187 RRQADIAAILGISERTVENHLRSARRKLG 215 (232)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHC
Confidence 49999999999999999999999887653
No 222
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=63.96 E-value=5.4 Score=38.73 Aligned_cols=29 Identities=24% Similarity=0.318 Sum_probs=26.1
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhCcccc
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAIGKVFS 395 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~rark~LS 395 (417)
.|..|||++||||+.||+..+..+.+++.
T Consensus 195 ~t~~eIa~~l~is~~TV~~h~~~~~~KL~ 223 (240)
T PRK10188 195 KTSAEIAMILSISENTVNFHQKNMQKKFN 223 (240)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 49999999999999999999999887764
No 223
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=63.86 E-value=15 Score=30.59 Aligned_cols=34 Identities=18% Similarity=0.239 Sum_probs=26.5
Q ss_pred HHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 357 KLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 357 ~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
+..|...++ .+..|||+.+|++..+|.+.+.+..
T Consensus 9 l~~L~~~~~-~~~~~la~~l~~s~~tv~~~l~~L~ 42 (108)
T smart00344 9 LEELQKDAR-ISLAELAKKVGLSPSTVHNRVKRLE 42 (108)
T ss_pred HHHHHHhCC-CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 344444444 6899999999999999999987754
No 224
>PRK13239 alkylmercury lyase; Provisional
Probab=63.16 E-value=16 Score=35.38 Aligned_cols=32 Identities=31% Similarity=0.316 Sum_probs=28.6
Q ss_pred HHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 359 RLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 359 ~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
.|. .||.||..+||+.+|+++++|+.+++...
T Consensus 30 ~la-~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 30 LLA-KGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred HHH-cCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 344 79999999999999999999999998865
No 225
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=63.01 E-value=5.5 Score=39.22 Aligned_cols=30 Identities=27% Similarity=0.314 Sum_probs=26.3
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAIGKVFSL 396 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~rark~LSL 396 (417)
.|..|||+.||||+.||+..+..+.+++-.
T Consensus 206 ~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v 235 (247)
T TIGR03020 206 KTNEEIAAILGISSLTVKNHLQHIFKKLDV 235 (247)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence 499999999999999999999988766543
No 226
>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=63.00 E-value=17 Score=27.41 Aligned_cols=31 Identities=26% Similarity=0.319 Sum_probs=24.8
Q ss_pred HHHHcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 359 RLEEKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 359 ~L~e~gRepS~eEIAe~LGIS~etVr~aL~ra 390 (417)
.|.. ...++.+|+|+.+|+|..||+.-+...
T Consensus 8 ~l~~-~~~~s~~ela~~~~VS~~TiRRDl~~L 38 (57)
T PF08220_consen 8 LLKE-KGKVSVKELAEEFGVSEMTIRRDLNKL 38 (57)
T ss_pred HHHH-cCCEEHHHHHHHHCcCHHHHHHHHHHH
Confidence 3443 346799999999999999999877654
No 227
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=61.83 E-value=5.9 Score=38.00 Aligned_cols=22 Identities=23% Similarity=0.172 Sum_probs=19.0
Q ss_pred cHHHHHHHcCCCHHHHHHHHHH
Q 014852 368 SVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 368 S~eEIAe~LGIS~etVr~aL~r 389 (417)
..++||..||||+.||+.....
T Consensus 159 ~NKqIA~dLgiS~rTVe~HRan 180 (202)
T COG4566 159 MNKQIAFDLGISERTVELHRAN 180 (202)
T ss_pred ccHHHHHHcCCchhhHHHHHHH
Confidence 7899999999999999876443
No 228
>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=61.10 E-value=20 Score=32.43 Aligned_cols=53 Identities=15% Similarity=0.081 Sum_probs=39.2
Q ss_pred cCccHHHHHHHHHHHHHHHHH-cCCCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 342 LPNHLHERLGLIRNAKLRLEE-KGVTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 342 lp~~~~e~~~kI~~a~~~L~e-~gRepS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
-|.-..+......++..-|.+ .++..|+.||++.+||+++.|...++..+-.+
T Consensus 21 Cp~C~~~~e~~f~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~IreGRL~~ 74 (137)
T TIGR03826 21 CPSCYEEEEREFEKVYKFLRKHENRQATVSEIVEETGVSEKLILKFIREGRLQL 74 (137)
T ss_pred CHHHhHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCCeec
Confidence 355555555556666666643 46678999999999999999999988877444
No 229
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=60.87 E-value=24 Score=24.69 Aligned_cols=26 Identities=27% Similarity=0.429 Sum_probs=23.5
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~rar 391 (417)
.++..+||+.+|++..+|...+....
T Consensus 14 ~~s~~~l~~~l~~s~~tv~~~l~~L~ 39 (53)
T smart00420 14 KVSVEELAELLGVSEMTIRRDLNKLE 39 (53)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 48999999999999999999987764
No 230
>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=60.70 E-value=24 Score=25.65 Aligned_cols=38 Identities=13% Similarity=0.175 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 351 GLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 351 ~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~ra 390 (417)
..+..|+..+. .|. .|+.+.|+..|||..|+..++...
T Consensus 3 e~l~~Ai~~v~-~g~-~S~r~AA~~ygVp~sTL~~r~~g~ 40 (45)
T PF05225_consen 3 EDLQKAIEAVK-NGK-MSIRKAAKKYGVPRSTLRRRLRGK 40 (45)
T ss_dssp HHHHHHHHHHH-TTS-S-HHHHHHHHT--HHHHHHHHHHT
T ss_pred HHHHHHHHHHH-hCC-CCHHHHHHHHCcCHHHHHHHHcCC
Confidence 34667777776 355 899999999999999999776543
No 231
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=60.28 E-value=9 Score=28.36 Aligned_cols=29 Identities=24% Similarity=0.306 Sum_probs=24.9
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhCcccc
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAIGKVFS 395 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~rark~LS 395 (417)
.+..|||..||++..+|+..+..+..++.
T Consensus 20 ~s~~eia~~l~is~~tV~~h~~~i~~Kl~ 48 (65)
T COG2771 20 KSNKEIARILGISEETVKTHLRNIYRKLG 48 (65)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 58999999999999999999887765543
No 232
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.12 E-value=25 Score=29.78 Aligned_cols=38 Identities=21% Similarity=0.211 Sum_probs=27.2
Q ss_pred HHHHHHHHH--cCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 354 RNAKLRLEE--KGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 354 ~~a~~~L~e--~gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
+.-.++|.. ..-..|++|||+.||+++..+..++....
T Consensus 9 ~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~lekil~~tq 48 (97)
T COG4367 9 QRTKQELQANFELCPLSDEEIATALNWTEVKLEKILQVTQ 48 (97)
T ss_pred HHHHHHHHHhhhhccccHHHHHHHhCCCHHHHHHHHHHhh
Confidence 334445543 12345999999999999999999986543
No 233
>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=60.05 E-value=25 Score=26.27 Aligned_cols=26 Identities=19% Similarity=0.424 Sum_probs=23.1
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~rar 391 (417)
.++..|||+.+|++..+|...+....
T Consensus 25 ~~s~~ela~~~g~s~~tv~r~l~~L~ 50 (67)
T cd00092 25 PLTRQEIADYLGLTRETVSRTLKELE 50 (67)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 35999999999999999999987665
No 234
>PRK09483 response regulator; Provisional
Probab=59.83 E-value=14 Score=33.23 Aligned_cols=31 Identities=26% Similarity=0.303 Sum_probs=27.1
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATEAIGKVFSL 396 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~rark~LSL 396 (417)
..+.+|||+.|++++.||+..++...+++.+
T Consensus 163 G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~v 193 (217)
T PRK09483 163 GQKVNEISEQLNLSPKTVNSYRYRMFSKLNI 193 (217)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence 3589999999999999999999988877754
No 235
>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=59.59 E-value=40 Score=25.65 Aligned_cols=47 Identities=23% Similarity=0.251 Sum_probs=36.3
Q ss_pred CCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhh
Q 014852 206 LTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMEC 262 (417)
Q Consensus 206 Lt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~ 262 (417)
||+.|..-|..++..|=. ..-|.-+..++|..+|+|...+-..+..+
T Consensus 1 LT~~Q~e~L~~A~~~GYf----------d~PR~~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYF----------DVPRRITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred CCHHHHHHHHHHHHcCCC----------CCCCcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 677777777778888776 44566789999999999998877766544
No 236
>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=59.38 E-value=26 Score=28.87 Aligned_cols=25 Identities=16% Similarity=0.263 Sum_probs=21.9
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHH
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~r 389 (417)
..+++.+||+.+|+|..||...+..
T Consensus 18 ~~~ti~dvA~~~gvS~~TVsr~L~~ 42 (80)
T TIGR02844 18 TKATVRETAKVFGVSKSTVHKDVTE 42 (80)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHhcC
Confidence 4579999999999999999998754
No 237
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=58.80 E-value=13 Score=35.36 Aligned_cols=32 Identities=13% Similarity=0.233 Sum_probs=27.0
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVFSL 396 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~rark~LSL 396 (417)
+..|.+|||+.|++|+.||+..+..+.+++.+
T Consensus 147 qGkTnKEIAe~L~IS~rTVkth~srImkKLgV 178 (198)
T PRK15201 147 SGYHLSETAALLSLSEEQTKSLRRSIMRKLHV 178 (198)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 34589999999999999999998888766644
No 238
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=58.45 E-value=14 Score=25.77 Aligned_cols=26 Identities=23% Similarity=0.368 Sum_probs=22.8
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhCc
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAIGK 392 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~rark 392 (417)
++..|||+.+|++..+|...+....+
T Consensus 9 ~s~~~la~~l~~s~~tv~~~l~~L~~ 34 (48)
T smart00419 9 LTRQEIAELLGLTRETVSRTLKRLEK 34 (48)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 58999999999999999999887653
No 239
>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=58.42 E-value=47 Score=28.13 Aligned_cols=66 Identities=8% Similarity=-0.037 Sum_probs=40.5
Q ss_pred hhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 318 STYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 318 sTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
.+|....+.+.+.+.+........+.... ..++..|.. ....++.|||+.+|++..+|-..+....
T Consensus 2 ~~~~l~~~~~~~~~~~~~~l~~~~lt~~q-------~~iL~~l~~-~~~~t~~ela~~~~~~~~tvs~~l~~Le 67 (118)
T TIGR02337 2 LPLALLQAREAAMSFFRPILAQHGLTEQQ-------WRILRILAE-QGSMEFTQLANQACILRPSLTGILARLE 67 (118)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHcCCCHHH-------HHHHHHHHH-cCCcCHHHHHHHhCCCchhHHHHHHHHH
Confidence 45666667776666665544333332111 122233333 2346899999999999999988877654
No 240
>PRK10403 transcriptional regulator NarP; Provisional
Probab=58.33 E-value=16 Score=32.25 Aligned_cols=32 Identities=22% Similarity=0.276 Sum_probs=28.4
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhCcccccc
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATEAIGKVFSLD 397 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~rark~LSLD 397 (417)
..|.+|||+.||++..||+..+.+.++++.+.
T Consensus 168 g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~ 199 (215)
T PRK10403 168 GLSNKQIASVLNISEQTVKVHIRNLLRKLNVR 199 (215)
T ss_pred CCCHHHHHHHcCCCHHHHHHHHHHHHHHcCCC
Confidence 36899999999999999999999998887654
No 241
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=57.96 E-value=15 Score=32.09 Aligned_cols=30 Identities=23% Similarity=0.217 Sum_probs=26.8
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAIGKVFSL 396 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~rark~LSL 396 (417)
.+.+|||+.|+++..||+..+.++++++..
T Consensus 165 ~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~ 194 (211)
T PRK15369 165 YTNRDIAEQLSISIKTVETHRLNMMRKLDV 194 (211)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 479999999999999999999998887754
No 242
>PRK12423 LexA repressor; Provisional
Probab=57.72 E-value=27 Score=32.92 Aligned_cols=33 Identities=24% Similarity=0.447 Sum_probs=26.9
Q ss_pred HHHcCCCccHHHHHHHcC-CCHHHHHHHHHHhCc
Q 014852 360 LEEKGVTPSVDRIAEYLN-MSQKKVRNATEAIGK 392 (417)
Q Consensus 360 L~e~gRepS~eEIAe~LG-IS~etVr~aL~rark 392 (417)
+.+.|..||..|||+.+| .+..+|+..+.+..+
T Consensus 19 i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~ 52 (202)
T PRK12423 19 IAQAGQPPSLAEIAQAFGFASRSVARKHVQALAE 52 (202)
T ss_pred HHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 455677799999999999 599999988876543
No 243
>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=57.20 E-value=21 Score=27.86 Aligned_cols=28 Identities=18% Similarity=0.140 Sum_probs=21.9
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 364 GVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
...+|..|||..+|+++++|+..+..--
T Consensus 12 ~~~~S~~eLa~~~~~s~~~ve~mL~~l~ 39 (69)
T PF09012_consen 12 RGRVSLAELAREFGISPEAVEAMLEQLI 39 (69)
T ss_dssp S-SEEHHHHHHHTT--HHHHHHHHHHHH
T ss_pred cCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 5568999999999999999999987643
No 244
>PF13551 HTH_29: Winged helix-turn helix
Probab=57.08 E-value=34 Score=28.03 Aligned_cols=43 Identities=16% Similarity=0.232 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHHHHHcCC-CccHHHHHHHc-------CCCHHHHHHHHHHh
Q 014852 348 ERLGLIRNAKLRLEEKGV-TPSVDRIAEYL-------NMSQKKVRNATEAI 390 (417)
Q Consensus 348 e~~~kI~~a~~~L~e~gR-epS~eEIAe~L-------GIS~etVr~aL~ra 390 (417)
+....|.+....-+..|. ..+..+|++.| .++..+|..++++.
T Consensus 61 ~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~~~ 111 (112)
T PF13551_consen 61 EQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILKRA 111 (112)
T ss_pred HHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHHHC
Confidence 333445555444443343 45889999865 68999999998764
No 245
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=56.87 E-value=14 Score=35.26 Aligned_cols=31 Identities=23% Similarity=0.210 Sum_probs=26.6
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATEAIGKVFSL 396 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~rark~LSL 396 (417)
..|.+|||+.|++|+.||+..+.++.+++-+
T Consensus 170 G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v 200 (216)
T PRK10100 170 GASNNEIARSLFISENTVKTHLYNLFKKIAV 200 (216)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 3589999999999999999999888766544
No 246
>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=56.39 E-value=19 Score=33.10 Aligned_cols=35 Identities=26% Similarity=0.225 Sum_probs=27.7
Q ss_pred HHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 356 AKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 356 a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
++..|...+ ..|.+|||+.|||+...|+.++....
T Consensus 19 Vl~aL~~~~-~~tdEeLa~~Lgi~~~~VRk~L~~L~ 53 (158)
T TIGR00373 19 VLFSLGIKG-EFTDEEISLELGIKLNEVRKALYALY 53 (158)
T ss_pred HHHHHhccC-CCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 344455434 67999999999999999999988764
No 247
>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=56.17 E-value=21 Score=29.76 Aligned_cols=42 Identities=26% Similarity=0.237 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 349 RLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 349 ~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~ra 390 (417)
...+|..++..-......+++.+|++.|++++.+|+.++...
T Consensus 48 ~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L 89 (102)
T PF08784_consen 48 LQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFL 89 (102)
T ss_dssp HHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHH
Confidence 344555555542223445799999999999999999998765
No 248
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=55.77 E-value=17 Score=32.15 Aligned_cols=31 Identities=29% Similarity=0.239 Sum_probs=28.1
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhCcccccc
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAIGKVFSLD 397 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~rark~LSLD 397 (417)
.+.+|||+.|+++..||+..+.++++++.+.
T Consensus 165 ~s~~eIa~~l~~s~~tv~~~~~~~~~kl~~~ 195 (210)
T PRK09935 165 LSNKEIADQLLLSNKTVSAHKSNIYGKLGLH 195 (210)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHcCCC
Confidence 6899999999999999999999999887553
No 249
>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=55.72 E-value=27 Score=32.47 Aligned_cols=42 Identities=17% Similarity=0.208 Sum_probs=31.8
Q ss_pred HHHHHHHHHHH-HHcCCCccHHHHHHHcCCC-HHHHHHHHHHhC
Q 014852 350 LGLIRNAKLRL-EEKGVTPSVDRIAEYLNMS-QKKVRNATEAIG 391 (417)
Q Consensus 350 ~~kI~~a~~~L-~e~gRepS~eEIAe~LGIS-~etVr~aL~rar 391 (417)
..+|...+... .+.+..||..|||+.+|++ ..+|...+.+..
T Consensus 8 q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~ 51 (199)
T TIGR00498 8 QQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALE 51 (199)
T ss_pred HHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHH
Confidence 34455555544 4467779999999999998 999999887654
No 250
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=55.11 E-value=21 Score=33.42 Aligned_cols=26 Identities=19% Similarity=0.275 Sum_probs=23.2
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~rar 391 (417)
..|.+|||+.||||+.||+..+....
T Consensus 177 g~s~~eIa~~l~iS~~Tv~~~~~~~~ 202 (225)
T PRK10046 177 QHTAETVAQALTISRTTARRYLEYCA 202 (225)
T ss_pred CcCHHHHHHHhCccHHHHHHHHHHHH
Confidence 45999999999999999999987765
No 251
>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=54.95 E-value=29 Score=25.54 Aligned_cols=25 Identities=36% Similarity=0.488 Sum_probs=22.5
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~rar 391 (417)
++..+||+.+|++..+|..++....
T Consensus 26 ~~~~~la~~~~is~~~v~~~l~~L~ 50 (66)
T cd07377 26 PSERELAEELGVSRTTVREALRELE 50 (66)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 5799999999999999999988764
No 252
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=54.79 E-value=1.6e+02 Score=29.84 Aligned_cols=27 Identities=19% Similarity=0.321 Sum_probs=23.0
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 368 SVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 368 S~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
|++|||+..|+++.+|+++.....+.+
T Consensus 278 t~keIa~v~~Vs~~tI~~~ykel~~~l 304 (310)
T PRK00423 278 TQREVAEVAGVTEVTVRNRYKELAEKL 304 (310)
T ss_pred CHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence 999999999999999998877665543
No 253
>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=54.63 E-value=15 Score=25.89 Aligned_cols=24 Identities=13% Similarity=0.112 Sum_probs=20.6
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 368 SVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 368 S~eEIAe~LGIS~etVr~aL~rar 391 (417)
+..|+|+.+|++..+|+.......
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHHCCC
Confidence 578999999999999998866553
No 254
>PF13518 HTH_28: Helix-turn-helix domain
Probab=53.27 E-value=17 Score=25.91 Aligned_cols=24 Identities=25% Similarity=0.213 Sum_probs=21.8
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 368 SVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 368 S~eEIAe~LGIS~etVr~aL~rar 391 (417)
|+.+||+.+||+..+|...+....
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHH
Confidence 999999999999999999887654
No 255
>PF13309 HTH_22: HTH domain
Probab=53.17 E-value=54 Score=25.53 Aligned_cols=34 Identities=29% Similarity=0.372 Sum_probs=24.8
Q ss_pred HHHHHHHHHcCC---CccHHHHHHHcCCCHHHHHHHH
Q 014852 354 RNAKLRLEEKGV---TPSVDRIAEYLNMSQKKVRNAT 387 (417)
Q Consensus 354 ~~a~~~L~e~gR---epS~eEIAe~LGIS~etVr~aL 387 (417)
.+++..|.+.|- .-++..+|+.||||..||-+.+
T Consensus 27 ~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TVY~YL 63 (64)
T PF13309_consen 27 KEIVRQLYEKGIFLLKGAVEYVAEKLGISRATVYRYL 63 (64)
T ss_pred HHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHHHHHc
Confidence 344556665442 1289999999999999998764
No 256
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=53.10 E-value=16 Score=28.10 Aligned_cols=26 Identities=27% Similarity=0.392 Sum_probs=22.8
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~rar 391 (417)
..|..|||+.+|++..+|...+....
T Consensus 22 ~~t~~eIa~~l~i~~~~v~~~L~~L~ 47 (68)
T PF01978_consen 22 PATAEEIAEELGISRSTVYRALKSLE 47 (68)
T ss_dssp HEEHHHHHHHHTSSHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 46999999999999999999987653
No 257
>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=53.02 E-value=37 Score=28.28 Aligned_cols=28 Identities=21% Similarity=0.273 Sum_probs=23.5
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 364 GVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
...+|..|||+.+|++..+|..++....
T Consensus 45 ~~~is~~eLa~~~g~sr~tVsr~L~~Le 72 (95)
T TIGR01610 45 QDRVTATVIAELTGLSRTHVSDAIKSLA 72 (95)
T ss_pred CCccCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3446999999999999999999887643
No 258
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=52.37 E-value=12 Score=38.15 Aligned_cols=35 Identities=17% Similarity=0.153 Sum_probs=28.6
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCc----ccccccc
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAIGK----VFSLDRE 399 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~rark----~LSLD~~ 399 (417)
...|+.|||++||+|.-+|.+++..|++ .+.++.+
T Consensus 28 ~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~I~I~~~ 66 (318)
T PRK15418 28 DGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQINSR 66 (318)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEEEEEeCC
Confidence 3459999999999999999999999985 3455544
No 259
>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=52.04 E-value=38 Score=24.99 Aligned_cols=35 Identities=17% Similarity=0.209 Sum_probs=25.5
Q ss_pred HHHHHHcCC-CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 357 KLRLEEKGV-TPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 357 ~~~L~e~gR-epS~eEIAe~LGIS~etVr~aL~rar 391 (417)
+..|...+. .++..|||+.++++..+|...+.+..
T Consensus 11 L~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~ 46 (62)
T PF12802_consen 11 LMALARHPGEELTQSELAERLGISKSTVSRIVKRLE 46 (62)
T ss_dssp HHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 334443333 37999999999999999999887754
No 260
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=51.97 E-value=25 Score=30.53 Aligned_cols=30 Identities=20% Similarity=0.127 Sum_probs=26.2
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAIGKVFSL 396 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~rark~LSL 396 (417)
.+.++||+.+|++..+|+..+.++++++..
T Consensus 157 ~~~~~ia~~l~~s~~tv~~~~~~~~~kl~~ 186 (202)
T PRK09390 157 LSNKVIARDLDISPRTVEVYRANVMTKMQA 186 (202)
T ss_pred CchHHHHHHcCCCHHHHHHHHHHHHHHHcc
Confidence 378999999999999999999998877643
No 261
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=51.34 E-value=26 Score=33.07 Aligned_cols=23 Identities=30% Similarity=0.423 Sum_probs=21.1
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHh
Q 014852 368 SVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 368 S~eEIAe~LGIS~etVr~aL~ra 390 (417)
|+.|||+.||.++.||++.+...
T Consensus 63 Ti~EIAeelG~TeqTir~hlkge 85 (182)
T COG1318 63 TISEIAEELGRTEQTVRNHLKGE 85 (182)
T ss_pred cHHHHHHHhCCCHHHHHHHHhcc
Confidence 89999999999999999998654
No 262
>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=51.18 E-value=18 Score=25.40 Aligned_cols=23 Identities=17% Similarity=0.310 Sum_probs=19.2
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHh
Q 014852 368 SVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 368 S~eEIAe~LGIS~etVr~aL~ra 390 (417)
|+.|+|+.+||+..+++......
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 57899999999999999987664
No 263
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=51.16 E-value=28 Score=32.65 Aligned_cols=34 Identities=24% Similarity=0.189 Sum_probs=27.2
Q ss_pred HHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 357 KLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 357 ~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
+..|...| ..|.+|||+.|||+...|+..+....
T Consensus 28 l~~L~~~g-~~tdeeLA~~Lgi~~~~VRk~L~~L~ 61 (178)
T PRK06266 28 LKALIKKG-EVTDEEIAEQTGIKLNTVRKILYKLY 61 (178)
T ss_pred HHHHHHcC-CcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 33454434 67999999999999999999988754
No 264
>PRK15320 transcriptional activator SprB; Provisional
Probab=50.40 E-value=21 Score=34.70 Aligned_cols=32 Identities=9% Similarity=0.071 Sum_probs=26.7
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVFSL 396 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~rark~LSL 396 (417)
...|.+|||+.|++|.+||...+.+...++-+
T Consensus 178 kG~SNKEIAekL~LS~KTVSTYKnRLLeKLgA 209 (251)
T PRK15320 178 SGHPAIELAKKFGLGTKTVSIYRKKVMYRLGM 209 (251)
T ss_pred cCCCHHHHHHHhccchhhHHHHHHHHHHHcCC
Confidence 34589999999999999999998887765544
No 265
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=50.10 E-value=13 Score=31.97 Aligned_cols=29 Identities=10% Similarity=0.058 Sum_probs=26.0
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
+.+++|-|..||||..|+-+++..+++++
T Consensus 49 ~l~QeeAA~rMgISr~Tfwr~l~sAR~Kv 77 (99)
T COG1342 49 GLTQEEAALRMGISRQTFWRLLTSARKKV 77 (99)
T ss_pred hccHHHHHHHhcccHHHHHHHHHHHHHHH
Confidence 45899999999999999999999998654
No 266
>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=50.05 E-value=16 Score=27.43 Aligned_cols=25 Identities=20% Similarity=0.147 Sum_probs=18.6
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHH
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~r 389 (417)
..++..+||..+||+..||..++..
T Consensus 21 ~g~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 21 EGESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp CTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 3449999999999999999998754
No 267
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=49.65 E-value=16 Score=28.59 Aligned_cols=22 Identities=14% Similarity=0.280 Sum_probs=19.1
Q ss_pred ccHHHHHHHcCCCHHHHHHHHH
Q 014852 367 PSVDRIAEYLNMSQKKVRNATE 388 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~ 388 (417)
+++.|||+.+|++..+|..+++
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln 22 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLN 22 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHC
Confidence 3688999999999999988764
No 268
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=48.64 E-value=37 Score=33.55 Aligned_cols=38 Identities=18% Similarity=0.270 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 352 LIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 352 kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~ra 390 (417)
+....+..|...++ ++..|||+.||+|+.||++-+...
T Consensus 18 R~~~Il~~L~~~~~-vtv~eLa~~l~VS~~TIRRDL~~L 55 (269)
T PRK09802 18 RREQIIQRLRQQGS-VQVNDLSALYGVSTVTIRNDLAFL 55 (269)
T ss_pred HHHHHHHHHHHcCC-EeHHHHHHHHCCCHHHHHHHHHHH
Confidence 34445555655454 899999999999999998877654
No 269
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=48.57 E-value=20 Score=27.29 Aligned_cols=24 Identities=17% Similarity=0.206 Sum_probs=21.3
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 368 SVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 368 S~eEIAe~LGIS~etVr~aL~rar 391 (417)
|..|+|+.+|||..+|+.......
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 578999999999999999987664
No 270
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=48.28 E-value=3e+02 Score=28.28 Aligned_cols=127 Identities=14% Similarity=0.134 Sum_probs=71.2
Q ss_pred HHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCC
Q 014852 232 KERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDS 311 (417)
Q Consensus 232 ~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~ 311 (417)
=++.+.+-+..|+...++++-.|+.+.++---++++..+..+---.-.+..||+.+ +.+.--+|++-.-+-+...-||-
T Consensus 158 CRq~~~pRT~kEI~~~anv~kKEIgr~~K~i~~~l~~s~~~~s~~t~~~m~RFCs~-L~L~~~~q~aA~e~a~ka~~~~~ 236 (308)
T KOG1597|consen 158 CRQEDVPRTFKEISAVANVSKKEIGRCVKLIGEALETSVDLISISTGDFMPRFCSN-LGLPKSAQEAATEIAEKAEEMDI 236 (308)
T ss_pred HHhcCCCchHHHHHHHHcCCHHHHHHHHHHHHHHHhccchhhhhhHHHHHHHHHHh-cCCCHHHHHHHHHHHHHHHHhcc
Confidence 34567788999999999999999887555444444444433311122334444432 22233334443333344443433
Q ss_pred CCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 312 SKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 312 ~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~ra 390 (417)
-.| |-|-.+. ..+......|.. ..-+++||.+.+|+.+.||++...-.
T Consensus 237 ~~g--------------------------RsPiSIA---Aa~IYmisqls~--~kkt~keI~~vtgVaE~TIr~sYK~L 284 (308)
T KOG1597|consen 237 RAG--------------------------RSPISIA---AAAIYMISQLSD--EKKTQKEIGEVTGVAEVTIRNSYKDL 284 (308)
T ss_pred ccC--------------------------CCchhHH---HHHHHHHHHhcc--CcccHHHHHHHhhhhHHHHHHHHHHH
Confidence 222 2243332 223333444432 23389999999999999999976544
No 271
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=47.76 E-value=29 Score=33.24 Aligned_cols=39 Identities=10% Similarity=0.189 Sum_probs=29.3
Q ss_pred HHHHHHHH-HHHHcCCCccHHHHHHHcCCCHHHHHHHHHH
Q 014852 351 GLIRNAKL-RLEEKGVTPSVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 351 ~kI~~a~~-~L~e~gRepS~eEIAe~LGIS~etVr~aL~r 389 (417)
..|++.+. .+..-.+-||..|+|+.+|+|..||++++..
T Consensus 19 ~~L~~~I~~~~~~G~~LPsE~eLa~~~~VSR~TVR~Al~~ 58 (241)
T PRK10079 19 AKLEQELRQHYRCGDYLPAEQQLAARYEVNRHTLRRAIDQ 58 (241)
T ss_pred HHHHHHHhcccCCCCcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 33444332 3444567899999999999999999999875
No 272
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=47.08 E-value=21 Score=33.70 Aligned_cols=30 Identities=20% Similarity=0.158 Sum_probs=25.9
Q ss_pred cCCCccHHHHHHHcCCCHHHHHHHHHHhCc
Q 014852 363 KGVTPSVDRIAEYLNMSQKKVRNATEAIGK 392 (417)
Q Consensus 363 ~gRepS~eEIAe~LGIS~etVr~aL~rark 392 (417)
.....|.+|||+.||+|+.||+..+.+..+
T Consensus 175 ~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~ 204 (239)
T PRK10430 175 QDYEFSTDELANAVNISRVSCRKYLIWLVN 204 (239)
T ss_pred CCCCcCHHHHHHHhCchHHHHHHHHHHHHh
Confidence 355679999999999999999999987744
No 273
>PRK10651 transcriptional regulator NarL; Provisional
Probab=47.00 E-value=30 Score=30.63 Aligned_cols=31 Identities=19% Similarity=0.229 Sum_probs=27.5
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhCcccccc
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAIGKVFSLD 397 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~rark~LSLD 397 (417)
.+.++||+.|+++..||+..+.++++++.+.
T Consensus 171 ~~~~~ia~~l~is~~tV~~~~~~l~~Kl~~~ 201 (216)
T PRK10651 171 LPNKMIARRLDITESTVKVHVKHMLKKMKLK 201 (216)
T ss_pred CCHHHHHHHcCCCHHHHHHHHHHHHHHcCCC
Confidence 4899999999999999999999988877654
No 274
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=46.89 E-value=18 Score=22.18 Aligned_cols=19 Identities=32% Similarity=0.329 Sum_probs=17.4
Q ss_pred cHHHHHHHcCCCHHHHHHH
Q 014852 368 SVDRIAEYLNMSQKKVRNA 386 (417)
Q Consensus 368 S~eEIAe~LGIS~etVr~a 386 (417)
+..+||+.+|++..+|.+.
T Consensus 23 s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 23 SVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CHHHHHHHHCCCHHHHHHh
Confidence 8999999999999999765
No 275
>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=46.65 E-value=20 Score=27.70 Aligned_cols=24 Identities=21% Similarity=0.372 Sum_probs=22.2
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 368 SVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 368 S~eEIAe~LGIS~etVr~aL~rar 391 (417)
|.++||..+|++..+|.+.++..+
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 999999999999999999988765
No 276
>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=46.16 E-value=25 Score=25.47 Aligned_cols=25 Identities=20% Similarity=0.238 Sum_probs=19.9
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHH
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~r 389 (417)
+..|+.|+|+.+|++..+|..++.-
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 3458999999999999999998765
No 277
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=45.73 E-value=42 Score=34.46 Aligned_cols=28 Identities=21% Similarity=0.170 Sum_probs=25.2
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCc
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAIGK 392 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~rark 392 (417)
...|+.|||+.||||.-+|...+..+++
T Consensus 25 ~gltQ~eIA~~LgiSR~~v~rlL~~Ar~ 52 (321)
T COG2390 25 EGLTQSEIAERLGISRATVSRLLAKARE 52 (321)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3459999999999999999999999884
No 278
>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=45.40 E-value=36 Score=27.31 Aligned_cols=27 Identities=30% Similarity=0.334 Sum_probs=22.5
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhCc
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATEAIGK 392 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~rark 392 (417)
.+|.+|||+.+|+|...|+.++....+
T Consensus 25 ~~s~~eiA~~~~i~~~~l~kil~~L~~ 51 (83)
T PF02082_consen 25 PVSSKEIAERLGISPSYLRKILQKLKK 51 (83)
T ss_dssp -BEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHhh
Confidence 379999999999999999999887653
No 279
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=45.28 E-value=57 Score=28.74 Aligned_cols=39 Identities=21% Similarity=0.159 Sum_probs=30.0
Q ss_pred HHHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 353 IRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 353 I~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
..+++..+...+..++..+||+.||++..+|...+....
T Consensus 9 yL~~I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~ 47 (142)
T PRK03902 9 YIEQIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLD 47 (142)
T ss_pred HHHHHHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHH
Confidence 445555555555667999999999999999999887654
No 280
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=45.21 E-value=41 Score=32.93 Aligned_cols=37 Identities=19% Similarity=0.359 Sum_probs=27.9
Q ss_pred HHHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 353 IRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 353 I~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~ra 390 (417)
....+..|.+.+ .++..|+|+.+|+|+.||++-+...
T Consensus 7 ~~~Il~~L~~~~-~v~v~eLa~~l~VS~~TIRRDL~~L 43 (256)
T PRK10434 7 QAAILEYLQKQG-KTSVEELAQYFDTTGTTIRKDLVIL 43 (256)
T ss_pred HHHHHHHHHHcC-CEEHHHHHHHHCCCHHHHHHHHHHH
Confidence 344444555544 4899999999999999999887654
No 281
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=44.76 E-value=37 Score=34.24 Aligned_cols=42 Identities=29% Similarity=0.239 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 350 LGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 350 ~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
...+..++-.|. +..|...-+|||+.+|..++|||+.|+..+
T Consensus 8 QkeIL~aLi~LY~~~~r~IKgeeIA~~l~rnpGTVRNqmq~Lk 50 (294)
T COG2524 8 QKEILQALINLYRRKKRPIKGEEIAEVLNRNPGTVRNQMQSLK 50 (294)
T ss_pred HHHHHHHHHHHHHhcCCCcchHHHHHHHccCcchHHHHHHHHH
Confidence 345566666664 467777889999999999999999988764
No 282
>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=44.36 E-value=26 Score=29.53 Aligned_cols=26 Identities=27% Similarity=0.258 Sum_probs=22.5
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhCc
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAIGK 392 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~rark 392 (417)
.+..+||+.||+|..++......|.+
T Consensus 72 ~~~~~I~~~l~~S~~t~yr~~~~Al~ 97 (100)
T PF07374_consen 72 LTWEQIAEELNISRRTYYRIHKKALK 97 (100)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 48899999999999999988877754
No 283
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=44.26 E-value=1.4e+02 Score=27.95 Aligned_cols=25 Identities=12% Similarity=0.240 Sum_probs=22.4
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~rar 391 (417)
.|+++||..||++.++|-+.+...+
T Consensus 185 lt~~~iA~~lG~sr~tvsR~l~~l~ 209 (235)
T PRK11161 185 MTRGDIGNYLGLTVETISRLLGRFQ 209 (235)
T ss_pred ccHHHHHHHhCCcHHHHHHHHHHHH
Confidence 5899999999999999999887655
No 284
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=44.19 E-value=36 Score=26.70 Aligned_cols=28 Identities=21% Similarity=0.169 Sum_probs=22.5
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 364 GVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
...++-.|||+.+|++.-+++..+....
T Consensus 13 ~~p~~T~eiA~~~gls~~~aR~yL~~Le 40 (62)
T PF04703_consen 13 NGPLKTREIADALGLSIYQARYYLEKLE 40 (62)
T ss_dssp TS-EEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 5557999999999999999999987653
No 285
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=43.88 E-value=19 Score=31.61 Aligned_cols=29 Identities=21% Similarity=0.291 Sum_probs=26.4
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014852 368 SVDRIAEYLNMSQKKVRNATEAIGKVFSL 396 (417)
Q Consensus 368 S~eEIAe~LGIS~etVr~aL~rark~LSL 396 (417)
+.+|+++.||||..||++++...-..+.+
T Consensus 51 nlKe~e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 51 NLKEMEKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred CHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence 69999999999999999999988777766
No 286
>PF13551 HTH_29: Winged helix-turn helix
Probab=43.74 E-value=24 Score=28.88 Aligned_cols=24 Identities=21% Similarity=0.265 Sum_probs=22.0
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 368 SVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 368 S~eEIAe~LGIS~etVr~aL~rar 391 (417)
+..+||+.+|++..||.+.+++..
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~ 37 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYR 37 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHH
Confidence 699999999999999999988755
No 287
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=43.43 E-value=34 Score=30.82 Aligned_cols=33 Identities=24% Similarity=0.332 Sum_probs=26.9
Q ss_pred HHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhCc
Q 014852 359 RLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGK 392 (417)
Q Consensus 359 ~L~e~gRepS~eEIAe~LGIS~etVr~aL~rark 392 (417)
.|-..+ .++.++||+.||++..+|+.++.....
T Consensus 9 ~L~~~~-~~~dedLa~~l~i~~n~vRkiL~~L~e 41 (147)
T smart00531 9 ALMRNG-CVTEEDLAELLGIKQKQLRKILYLLYD 41 (147)
T ss_pred HHHhcC-CcCHHHHHHHhCCCHHHHHHHHHHHHh
Confidence 343333 679999999999999999999988764
No 288
>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=42.97 E-value=56 Score=24.59 Aligned_cols=28 Identities=25% Similarity=0.254 Sum_probs=23.2
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 364 GVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
+...|..|||+.+|++..++...+....
T Consensus 22 ~~~~t~~ela~~l~~~~~t~s~hL~~L~ 49 (61)
T PF12840_consen 22 NGPMTVSELAEELGISQSTVSYHLKKLE 49 (61)
T ss_dssp CSTBEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 5667999999999999999998877654
No 289
>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=42.87 E-value=36 Score=24.44 Aligned_cols=27 Identities=26% Similarity=0.293 Sum_probs=22.2
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
...+..|||+.+|++..+|...+...+
T Consensus 14 ~~~~~~el~~~l~~s~~~vs~hL~~L~ 40 (47)
T PF01022_consen 14 GPLTVSELAEELGLSQSTVSHHLKKLR 40 (47)
T ss_dssp SSEEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCchhhHHHhccccchHHHHHHHHHH
Confidence 456999999999999999998877654
No 290
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=42.86 E-value=36 Score=24.42 Aligned_cols=41 Identities=24% Similarity=0.333 Sum_probs=19.4
Q ss_pred CCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhh
Q 014852 204 ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (417)
Q Consensus 204 ~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~ 261 (417)
+-||++|-.++......|. +..++|..+|.+...+.+.+..
T Consensus 3 ~~Lt~~eR~~I~~l~~~G~-----------------s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQGM-----------------SIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ---------HHHHHHCS--------------------HHHHHHHTT--HHHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcCC-----------------CHHHHHHHHCcCcHHHHHHHhc
Confidence 4577777666666666654 4778888888888887766553
No 291
>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=42.19 E-value=30 Score=26.20 Aligned_cols=23 Identities=13% Similarity=0.218 Sum_probs=20.1
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHh
Q 014852 368 SVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 368 S~eEIAe~LGIS~etVr~aL~ra 390 (417)
+..|+|+.+||+..+++......
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~~ 24 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERRY 24 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHhC
Confidence 57899999999999999987643
No 292
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=42.16 E-value=34 Score=32.94 Aligned_cols=29 Identities=28% Similarity=0.337 Sum_probs=25.3
Q ss_pred HHcCCCccHHHHHHHcCCCHHHHHHHHHH
Q 014852 361 EEKGVTPSVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 361 ~e~gRepS~eEIAe~LGIS~etVr~aL~r 389 (417)
+.-.+-|+-.|+|+.+|||..||++++..
T Consensus 26 ~~G~~LPsE~eLa~~f~VSR~TvRkAL~~ 54 (236)
T COG2188 26 PPGDKLPSERELAEQFGVSRMTVRKALDE 54 (236)
T ss_pred CCCCCCCCHHHHHHHHCCcHHHHHHHHHH
Confidence 44457789999999999999999999875
No 293
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=42.13 E-value=62 Score=30.54 Aligned_cols=50 Identities=26% Similarity=0.363 Sum_probs=38.4
Q ss_pred ccCccHHHHHHHHHHHHHHHHHcCC-CccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 341 RLPNHLHERLGLIRNAKLRLEEKGV-TPSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 341 rlp~~~~e~~~kI~~a~~~L~e~gR-epS~eEIAe~LGIS~etVr~aL~ra 390 (417)
.+|.....+..+..+.+..|.+.|. .++..|+|+.+|++..+|+.=+...
T Consensus 6 ~~~~~~~~r~~~~~~il~~l~~~~~~~vs~~~L~~~~~v~~~tirrDl~~l 56 (213)
T PRK05472 6 KIPEATIKRLPLYYRYLKELKEEGVERVSSKELAEALGVDSAQIRKDLSYF 56 (213)
T ss_pred cCCHHHHHHhHHHHHHHHHHHHcCCcEEeHHHHHHHhCcCHHHHHHHHHHH
Confidence 4676666677777777778877662 4699999999999999998865443
No 294
>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=41.97 E-value=53 Score=28.40 Aligned_cols=29 Identities=21% Similarity=0.327 Sum_probs=25.2
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCc
Q 014852 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGK 392 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~aL~rark 392 (417)
....|..|||+.|||+..+|-.++++..-
T Consensus 69 ~pd~tl~Ela~~l~Vs~~ti~~~Lkrlg~ 97 (119)
T PF01710_consen 69 NPDATLRELAERLGVSPSTIWRALKRLGI 97 (119)
T ss_pred CCCcCHHHHHHHcCCCHHHHHHHHHHcCc
Confidence 55569999999999999999999988753
No 295
>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]
Probab=41.95 E-value=41 Score=32.09 Aligned_cols=34 Identities=21% Similarity=0.062 Sum_probs=27.8
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCcccccc
Q 014852 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLD 397 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD 397 (417)
.+..|..|||++||+|.+|+.-++.++....+-.
T Consensus 16 ~~Glt~gEIAdELNvSreTa~WL~~r~~~~~~~~ 49 (203)
T COG0856 16 SKGLTTGEIADELNVSRETATWLLTRAFKKESVP 49 (203)
T ss_pred HCCCcHHHhhhhhhhhHHHHHHHHhhhhhccCCC
Confidence 4567999999999999999999998876554433
No 296
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=41.91 E-value=19 Score=26.95 Aligned_cols=32 Identities=13% Similarity=0.016 Sum_probs=18.0
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVFSL 396 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~rark~LSL 396 (417)
+..|+.++|+.+|++..++....+.-...+++
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 34489999999999999998887643233333
No 297
>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=41.79 E-value=36 Score=32.27 Aligned_cols=27 Identities=22% Similarity=0.283 Sum_probs=23.9
Q ss_pred cCCCccHHHHHHHcCCCHHHHHHHHHH
Q 014852 363 KGVTPSVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 363 ~gRepS~eEIAe~LGIS~etVr~aL~r 389 (417)
-.+-||..|+|+.+|+|..||++++..
T Consensus 21 G~~LPsE~eLa~~~gVSR~TVR~Al~~ 47 (233)
T TIGR02404 21 GDYLPSEHELMDQYGASRETVRKALNL 47 (233)
T ss_pred CCCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 346789999999999999999999875
No 298
>PHA02943 hypothetical protein; Provisional
Probab=41.67 E-value=74 Score=29.66 Aligned_cols=24 Identities=33% Similarity=0.404 Sum_probs=21.1
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~ra 390 (417)
.|..|||+.||+|-++|+.++...
T Consensus 25 ~TtseIAkaLGlS~~qa~~~LyvL 48 (165)
T PHA02943 25 KTTSRIANKLGVSHSMARNALYQL 48 (165)
T ss_pred ccHHHHHHHHCCCHHHHHHHHHHH
Confidence 478999999999999999987654
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=41.52 E-value=64 Score=31.03 Aligned_cols=35 Identities=9% Similarity=0.044 Sum_probs=27.1
Q ss_pred HHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 357 KLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 357 ~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
++.+.......+..|||+.+|+|..++..++....
T Consensus 15 L~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~ 49 (248)
T TIGR02431 15 IEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLV 49 (248)
T ss_pred HHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 33344445567999999999999999999987643
No 300
>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=41.46 E-value=47 Score=27.83 Aligned_cols=39 Identities=23% Similarity=0.104 Sum_probs=25.5
Q ss_pred cHHHHHHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHH
Q 014852 345 HLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNA 386 (417)
Q Consensus 345 ~~~e~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~a 386 (417)
.......++.-+...|. ...|+.|||+.+|+|.-||-..
T Consensus 31 E~~~l~~R~~va~~lL~---~g~syreIa~~tgvS~aTItRv 69 (87)
T PF01371_consen 31 ELEALAQRWQVAKELLD---EGKSYREIAEETGVSIATITRV 69 (87)
T ss_dssp HHHHHHHHHHHHHHHHH---TTSSHHHHHHHHTSTHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHH---CCCCHHHHHHHhCCCHHHHHHH
Confidence 33334444444433443 3459999999999999998654
No 301
>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=41.36 E-value=52 Score=23.46 Aligned_cols=25 Identities=8% Similarity=0.217 Sum_probs=21.5
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHH
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~r 389 (417)
+..|++++|+.+|++..+|......
T Consensus 14 ~gltq~~lA~~~gvs~~~vs~~e~g 38 (58)
T TIGR03070 14 LGLTQADLADLAGVGLRFIRDVENG 38 (58)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 4568999999999999999998653
No 302
>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=40.88 E-value=68 Score=23.46 Aligned_cols=25 Identities=28% Similarity=0.361 Sum_probs=22.7
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~rar 391 (417)
.+..|||+.+|++..+|...+....
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~L~ 45 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKLE 45 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHHHH
Confidence 7999999999999999999987754
No 303
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=40.76 E-value=55 Score=32.14 Aligned_cols=38 Identities=18% Similarity=0.156 Sum_probs=28.9
Q ss_pred HHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 354 RNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 354 ~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
...++.+...+...+..|||+.||+|..+|..++....
T Consensus 28 l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~ 65 (271)
T PRK10163 28 IAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQ 65 (271)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 33344444445667999999999999999999987654
No 304
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=40.59 E-value=2.7e+02 Score=30.87 Aligned_cols=22 Identities=23% Similarity=0.184 Sum_probs=19.0
Q ss_pred cHHHHHHHcCCCHHHHHHHHHH
Q 014852 368 SVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 368 S~eEIAe~LGIS~etVr~aL~r 389 (417)
|..|||+..|+|..+|-+..+.
T Consensus 376 si~eLA~~~~vS~aTV~Rf~kk 397 (638)
T PRK14101 376 PIVDIARKADVSQPTVIRFCRS 397 (638)
T ss_pred cHHHHHHHhCCCHHHHHHHHHH
Confidence 9999999999999999776443
No 305
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=40.53 E-value=41 Score=23.99 Aligned_cols=27 Identities=26% Similarity=0.252 Sum_probs=23.5
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
...+..+|++.+|++..+|..+++...
T Consensus 9 ~~~~~~~i~~~l~is~~~v~~~l~~L~ 35 (66)
T smart00418 9 GELCVCELAEILGLSQSTVSHHLKKLR 35 (66)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHHH
Confidence 446899999999999999999988764
No 306
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=40.52 E-value=77 Score=27.50 Aligned_cols=39 Identities=13% Similarity=0.103 Sum_probs=28.1
Q ss_pred HHHHHHHHHHH-cCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 352 LIRNAKLRLEE-KGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 352 kI~~a~~~L~e-~gRepS~eEIAe~LGIS~etVr~aL~ra 390 (417)
.+.+++.-+.. ....+++++||+.+|+++.++.......
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 34555555543 4556899999999999999997766543
No 307
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=40.43 E-value=62 Score=31.44 Aligned_cols=36 Identities=19% Similarity=0.235 Sum_probs=27.6
Q ss_pred HHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 355 NAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 355 ~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
..+..|.+ ...++.+|||+.||+|+.||++-+....
T Consensus 8 ~Il~~l~~-~~~~~~~eLa~~l~VS~~TiRRdL~~L~ 43 (240)
T PRK10411 8 AIVDLLLN-HTSLTTEALAEQLNVSKETIRRDLNELQ 43 (240)
T ss_pred HHHHHHHH-cCCCcHHHHHHHHCcCHHHHHHHHHHHH
Confidence 33444544 3468999999999999999999887653
No 308
>PRK14999 histidine utilization repressor; Provisional
Probab=40.42 E-value=45 Score=31.91 Aligned_cols=28 Identities=14% Similarity=0.236 Sum_probs=24.4
Q ss_pred cCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 363 KGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 363 ~gRepS~eEIAe~LGIS~etVr~aL~ra 390 (417)
-.+-||..|+|+.+|+|..||++++...
T Consensus 33 G~~LPsE~eLa~~~gVSR~TVR~Al~~L 60 (241)
T PRK14999 33 HDRIPSEAELVAQYGFSRMTINRALREL 60 (241)
T ss_pred CCcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 3467899999999999999999998753
No 309
>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=40.35 E-value=44 Score=25.92 Aligned_cols=20 Identities=35% Similarity=0.539 Sum_probs=16.9
Q ss_pred CCCccHHHHHHHcCCCHHHH
Q 014852 364 GVTPSVDRIAEYLNMSQKKV 383 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etV 383 (417)
+-..|.+|||+.+|+++.+|
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 44459999999999999886
No 310
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=40.27 E-value=45 Score=26.84 Aligned_cols=23 Identities=9% Similarity=0.232 Sum_probs=19.7
Q ss_pred CccHHHHHHHcCCCHHHHHHHHH
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATE 388 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~ 388 (417)
..|++|+|+.+|++.+||-.+..
T Consensus 14 ~ltQ~elA~~vgVsRQTi~~iEk 36 (68)
T COG1476 14 GLTQEELAKLVGVSRQTIIAIEK 36 (68)
T ss_pred CcCHHHHHHHcCcCHHHHHHHHc
Confidence 35999999999999999987643
No 311
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=40.20 E-value=27 Score=31.18 Aligned_cols=32 Identities=25% Similarity=0.374 Sum_probs=26.3
Q ss_pred HHHHcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 359 RLEEKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 359 ~L~e~gRepS~eEIAe~LGIS~etVr~aL~ra 390 (417)
.|.+-.+-||+.|+|..+||++.||.++.+-.
T Consensus 28 ~l~pGdkLPSvRelA~~~~VNpnTv~raY~eL 59 (125)
T COG1725 28 ELKPGDKLPSVRELAKDLGVNPNTVQRAYQEL 59 (125)
T ss_pred CcCCCCCCCcHHHHHHHhCCCHHHHHHHHHHH
Confidence 34445677999999999999999999987654
No 312
>COG2344 AT-rich DNA-binding protein [General function prediction only]
Probab=40.07 E-value=63 Score=31.23 Aligned_cols=49 Identities=24% Similarity=0.349 Sum_probs=41.0
Q ss_pred cccCccHHHHHHHHHHHHHHHHHcCCC-ccHHHHHHHcCCCHHHHHHHHH
Q 014852 340 LRLPNHLHERLGLIRNAKLRLEEKGVT-PSVDRIAEYLNMSQKKVRNATE 388 (417)
Q Consensus 340 irlp~~~~e~~~kI~~a~~~L~e~gRe-pS~eEIAe~LGIS~etVr~aL~ 388 (417)
..+|....+++....+....|...+.+ ++-+|||+.+|++..+||+=..
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 368888888888899999988765654 5889999999999999988654
No 313
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=39.79 E-value=43 Score=29.65 Aligned_cols=31 Identities=19% Similarity=0.169 Sum_probs=27.4
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATEAIGKVFSL 396 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~rark~LSL 396 (417)
..+.+|||+.++++..||+..+.+.++++..
T Consensus 158 g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl~~ 188 (204)
T PRK09958 158 GKDNNDIAEKMFISNKTVSTYKSRLMEKLEC 188 (204)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence 3489999999999999999999999887754
No 314
>PRK13558 bacterio-opsin activator; Provisional
Probab=39.74 E-value=21 Score=38.97 Aligned_cols=31 Identities=13% Similarity=0.157 Sum_probs=27.4
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
-|+.|.+|||+.|||+..|+.+.++++.+++
T Consensus 628 pr~~~~~e~a~~l~is~~t~~~~lr~a~~~l 658 (665)
T PRK13558 628 PRRVEGEELAESMGISRSTFHQHLRAAERKL 658 (665)
T ss_pred CccCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 3667999999999999999999999987654
No 315
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=39.68 E-value=1e+02 Score=29.10 Aligned_cols=57 Identities=28% Similarity=0.265 Sum_probs=43.9
Q ss_pred CCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhH
Q 014852 205 LLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNV 274 (417)
Q Consensus 205 lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl 274 (417)
.||+.|..-|-.++..|=. ..-|.-+..++|+.+|+|...+.+.+.. |..+|+..+.
T Consensus 155 ~LTdrQ~~vL~~A~~~GYF----------d~PR~~~l~dLA~~lGISkst~~ehLRr---Ae~Kl~~~~~ 211 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYF----------DYPRRVSLKDLAKELGISKSTLSEHLRR---AERKLIEAYF 211 (215)
T ss_pred cCCHHHHHHHHHHHHcCCC----------CCCccCCHHHHHHHhCCCHHHHHHHHHH---HHHHHHHHhh
Confidence 5999998888888898876 3445678899999999999887776654 4556666554
No 316
>PRK00215 LexA repressor; Validated
Probab=39.67 E-value=83 Score=29.31 Aligned_cols=31 Identities=35% Similarity=0.485 Sum_probs=26.5
Q ss_pred HHcCCCccHHHHHHHcCC-CHHHHHHHHHHhC
Q 014852 361 EEKGVTPSVDRIAEYLNM-SQKKVRNATEAIG 391 (417)
Q Consensus 361 ~e~gRepS~eEIAe~LGI-S~etVr~aL~rar 391 (417)
...+..++..|||+.+|+ +..+|..++....
T Consensus 18 ~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~ 49 (205)
T PRK00215 18 EETGYPPSRREIADALGLRSPSAVHEHLKALE 49 (205)
T ss_pred HHhCCCCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 446778899999999999 9999999887654
No 317
>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=39.58 E-value=31 Score=28.84 Aligned_cols=21 Identities=10% Similarity=0.082 Sum_probs=19.1
Q ss_pred ccHHHHHHHcCCCHHHHHHHH
Q 014852 367 PSVDRIAEYLNMSQKKVRNAT 387 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL 387 (417)
.|..|||+.+|+|..||..+.
T Consensus 51 ~S~~eIA~~LgISrsTIyRi~ 71 (88)
T TIGR02531 51 KTYSDIEAETGASTATISRVK 71 (88)
T ss_pred CCHHHHHHHHCcCHHHHHHHH
Confidence 499999999999999999944
No 318
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=39.29 E-value=56 Score=29.29 Aligned_cols=27 Identities=30% Similarity=0.358 Sum_probs=23.2
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 364 GVTPSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~aL~ra 390 (417)
....|.+|||+.||++..+|..+++..
T Consensus 40 ~~~~tvdelae~lnr~rStv~rsl~~L 66 (126)
T COG3355 40 NGPLTVDELAEILNRSRSTVYRSLQNL 66 (126)
T ss_pred cCCcCHHHHHHHHCccHHHHHHHHHHH
Confidence 455699999999999999998887754
No 319
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=38.96 E-value=74 Score=29.13 Aligned_cols=42 Identities=19% Similarity=0.124 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhCc
Q 014852 351 GLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGK 392 (417)
Q Consensus 351 ~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rark 392 (417)
....+++..+...+..+...+||+.|||+..+|...+++..+
T Consensus 9 edYL~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~ 50 (154)
T COG1321 9 EDYLETIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLER 50 (154)
T ss_pred HHHHHHHHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHHH
Confidence 344556666655556679999999999999999888877543
No 320
>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=38.96 E-value=35 Score=30.25 Aligned_cols=25 Identities=16% Similarity=0.088 Sum_probs=22.1
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~rar 391 (417)
.|..+||..||+|..+|......+.
T Consensus 101 ~t~~~Ia~~l~iS~~t~~r~r~~~l 125 (134)
T TIGR01636 101 LTLVGLAQQLFISKSTAYRLRNHII 125 (134)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 4999999999999999998877664
No 321
>PHA01976 helix-turn-helix protein
Probab=38.76 E-value=35 Score=25.78 Aligned_cols=26 Identities=4% Similarity=-0.008 Sum_probs=21.9
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHH
Q 014852 364 GVTPSVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~aL~r 389 (417)
.+..|++|+|+.+|++..+|.+....
T Consensus 13 ~~glt~~~lA~~~gvs~~~v~~~e~g 38 (67)
T PHA01976 13 ARAWSAPELSRRAGVRHSLIYDFEAD 38 (67)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 34569999999999999999987653
No 322
>PRK09480 slmA division inhibitor protein; Provisional
Probab=38.58 E-value=2.8e+02 Score=24.68 Aligned_cols=72 Identities=18% Similarity=0.028 Sum_probs=46.6
Q ss_pred HhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHH
Q 014852 233 ERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLR 304 (417)
Q Consensus 233 ~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLik 304 (417)
..-|...|..++|+.+|++...+..--..-++-+..+++.+..-+............+..+.++..+-.++.
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 333567899999999999999998877776666677777665544444333333333455555555444444
No 323
>PRK09480 slmA division inhibitor protein; Provisional
Probab=38.34 E-value=87 Score=27.99 Aligned_cols=37 Identities=19% Similarity=0.232 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHH-HHc-CCCccHHHHHHHcCCCHHHHHH
Q 014852 349 RLGLIRNAKLRL-EEK-GVTPSVDRIAEYLNMSQKKVRN 385 (417)
Q Consensus 349 ~~~kI~~a~~~L-~e~-gRepS~eEIAe~LGIS~etVr~ 385 (417)
...+|.++...| ... |...|+++||+..||+.+++..
T Consensus 11 ~r~~Il~aa~~l~~~~~G~~~ti~~Ia~~agvs~gt~Y~ 49 (194)
T PRK09480 11 RREQILQALAQMLESPPGERITTAKLAARVGVSEAALYR 49 (194)
T ss_pred HHHHHHHHHHHHHHhcCCCccCHHHHHHHhCCCHhHHHH
Confidence 334555554444 443 7788999999999999999854
No 324
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=38.15 E-value=36 Score=25.78 Aligned_cols=22 Identities=14% Similarity=0.282 Sum_probs=19.5
Q ss_pred cHHHHHHHcCCCHHHHHHHHHH
Q 014852 368 SVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 368 S~eEIAe~LGIS~etVr~aL~r 389 (417)
|..|+|+.+||+..+++.....
T Consensus 2 s~~eva~~~gvs~~tlr~~~~~ 23 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYERI 23 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHHHC
Confidence 5789999999999999988653
No 325
>PHA00675 hypothetical protein
Probab=37.95 E-value=75 Score=26.28 Aligned_cols=22 Identities=18% Similarity=0.150 Sum_probs=19.8
Q ss_pred cHHHHHHHcCCCHHHHHHHHHH
Q 014852 368 SVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 368 S~eEIAe~LGIS~etVr~aL~r 389 (417)
|+.+||+.+|+|..+|.++...
T Consensus 41 s~~~IA~~fGVsrstV~~I~~g 62 (78)
T PHA00675 41 SYAVLAEKFEQSKGAIAKICRY 62 (78)
T ss_pred cHHHHHHHhCCCHHHHHHHHcc
Confidence 8999999999999999988653
No 326
>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=37.92 E-value=50 Score=31.13 Aligned_cols=27 Identities=26% Similarity=0.402 Sum_probs=24.0
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 364 GVTPSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~aL~ra 390 (417)
.+-||..|+|+.+|+|..||++++...
T Consensus 30 ~~LPsE~eLa~~~~VSR~TvR~Al~~L 56 (238)
T TIGR02325 30 DYLPAEMQLAERFGVNRHTVRRAIAAL 56 (238)
T ss_pred CcCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 467899999999999999999998753
No 327
>PF13730 HTH_36: Helix-turn-helix domain
Probab=37.66 E-value=1.1e+02 Score=22.13 Aligned_cols=25 Identities=44% Similarity=0.627 Sum_probs=20.9
Q ss_pred hCCCCchHHHHHHhcCChHHHHHHh
Q 014852 235 LGCEPSMEQLAASLRISRPELQSIL 259 (417)
Q Consensus 235 lg~eps~~e~A~~~~~s~~eLr~~l 259 (417)
.++-||.+.+|..+|+++..+++.+
T Consensus 22 ~~~~pS~~~la~~~g~s~~Tv~~~i 46 (55)
T PF13730_consen 22 GGCFPSQETLAKDLGVSRRTVQRAI 46 (55)
T ss_pred CCCCcCHHHHHHHHCcCHHHHHHHH
Confidence 3567999999999999999888543
No 328
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=37.47 E-value=74 Score=31.04 Aligned_cols=36 Identities=17% Similarity=0.148 Sum_probs=27.0
Q ss_pred HHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 355 NAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 355 ~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
..+..|... ..+++.|+|+.+|+|+.|||+=+....
T Consensus 11 ~I~~~l~~~-~~v~v~eLa~~~~VS~~TIRRDL~~Le 46 (252)
T PRK10681 11 QLLQALKRS-DKLHLKDAAALLGVSEMTIRRDLNAHS 46 (252)
T ss_pred HHHHHHHHc-CCCcHHHHHHHhCCCHHHHHHHHHHhh
Confidence 334445543 447999999999999999988776543
No 329
>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=37.08 E-value=34 Score=30.75 Aligned_cols=25 Identities=16% Similarity=0.143 Sum_probs=22.8
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~rar 391 (417)
.|++|||..+|++.++|-.+++..+
T Consensus 144 ~t~~~iA~~lG~tretvsR~l~~l~ 168 (193)
T TIGR03697 144 LSHQAIAEAIGSTRVTITRLLGDLR 168 (193)
T ss_pred CCHHHHHHHhCCcHHHHHHHHHHHH
Confidence 4999999999999999999988765
No 330
>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=37.01 E-value=40 Score=25.66 Aligned_cols=23 Identities=9% Similarity=0.335 Sum_probs=19.8
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHh
Q 014852 368 SVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 368 S~eEIAe~LGIS~etVr~aL~ra 390 (417)
+..|+|+.+||+..+++......
T Consensus 2 ~i~evA~~~gvs~~tlR~~~~~g 24 (67)
T cd04764 2 TIKEVSEIIGVKPHTLRYYEKEF 24 (67)
T ss_pred CHHHHHHHHCcCHHHHHHHHHhc
Confidence 57899999999999999886553
No 331
>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=36.98 E-value=50 Score=23.64 Aligned_cols=41 Identities=17% Similarity=0.328 Sum_probs=27.9
Q ss_pred cCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhh
Q 014852 203 EELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (417)
Q Consensus 203 ~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~ 260 (417)
-+-+++++..++.+...+|. +..++|..+|+|...+.+.+.
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 34466665566777777774 478999999999998876553
No 332
>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=36.70 E-value=59 Score=26.13 Aligned_cols=38 Identities=16% Similarity=0.158 Sum_probs=28.0
Q ss_pred HHHHHHHHHHcCCCccHHHHHHHcCC--CHHHHHHHHHHhC
Q 014852 353 IRNAKLRLEEKGVTPSVDRIAEYLNM--SQKKVRNATEAIG 391 (417)
Q Consensus 353 I~~a~~~L~e~gRepS~eEIAe~LGI--S~etVr~aL~rar 391 (417)
+..++... +.|+..|+.+||+.+|. ....|-.++....
T Consensus 5 V~~~v~~I-P~G~v~TYg~iA~~~g~p~~~R~Vg~al~~np 44 (79)
T cd06445 5 VWEALRQI-PYGEVTTYGQIAKLAGTPKAARAVGSALARNP 44 (79)
T ss_pred HHHHHhcC-CCCCcCcHHHHHHHHCCCCcHHHHHHHHHhCC
Confidence 44444444 36899999999999999 5778877776554
No 333
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=36.63 E-value=2e+02 Score=25.17 Aligned_cols=26 Identities=4% Similarity=0.028 Sum_probs=22.7
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~rar 391 (417)
..++.|||+.+|++..+|-..+.+.-
T Consensus 54 ~~t~~eLa~~l~i~~~tvsr~l~~Le 79 (144)
T PRK11512 54 CITPVELKKVLSVDLGALTRMLDRLV 79 (144)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 46999999999999999988887653
No 334
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=36.30 E-value=1.7e+02 Score=25.51 Aligned_cols=28 Identities=11% Similarity=0.132 Sum_probs=23.2
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 364 GVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
+...++.|||+.+|++..+|-..+.+..
T Consensus 44 ~~~~t~~eLa~~l~~~~~tvt~~v~~Le 71 (144)
T PRK03573 44 PPEQSQIQLAKAIGIEQPSLVRTLDQLE 71 (144)
T ss_pred CCCCCHHHHHHHhCCChhhHHHHHHHHH
Confidence 3345899999999999999998887654
No 335
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=36.17 E-value=1e+02 Score=25.48 Aligned_cols=37 Identities=14% Similarity=0.115 Sum_probs=26.1
Q ss_pred HHHHHHHHHH-cCCCccHHHHHHHcCCCHHHHHHHHHH
Q 014852 353 IRNAKLRLEE-KGVTPSVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 353 I~~a~~~L~e-~gRepS~eEIAe~LGIS~etVr~aL~r 389 (417)
+.++..-+.. ....++.++||+.+|+|..++......
T Consensus 7 ~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~ 44 (107)
T PRK10219 7 IQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRT 44 (107)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3444444433 455679999999999999998776544
No 336
>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=36.05 E-value=44 Score=25.71 Aligned_cols=26 Identities=23% Similarity=0.317 Sum_probs=23.0
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~rar 391 (417)
..+..|||+.+|++..+|.+.+....
T Consensus 13 ~~~~~eLa~~l~vS~~tv~~~l~~L~ 38 (69)
T TIGR00122 13 PFSGEKLGEALGMSRTAVNKHIQTLR 38 (69)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 35799999999999999999988764
No 337
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=36.01 E-value=34 Score=30.10 Aligned_cols=30 Identities=23% Similarity=0.254 Sum_probs=26.6
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAIGKVFSL 396 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~rark~LSL 396 (417)
.+.++||+.|+++..+|+..+.+.++++..
T Consensus 153 ~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~~ 182 (196)
T PRK10360 153 MAVKEIAAELGLSPKTVHVHRANLMEKLGV 182 (196)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 589999999999999999999988877643
No 338
>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=35.88 E-value=35 Score=28.09 Aligned_cols=25 Identities=24% Similarity=0.186 Sum_probs=18.4
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~rar 391 (417)
.|+.|||+.||.|...|.+.+....
T Consensus 4 ~tq~eIA~~lGks~s~Vs~~l~Ll~ 28 (93)
T PF08535_consen 4 WTQEEIAKRLGKSRSWVSNHLALLD 28 (93)
T ss_dssp --HHHHHHHTT--HHHHHHHHGGGS
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHc
Confidence 4899999999999999999877553
No 339
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=35.77 E-value=64 Score=24.37 Aligned_cols=26 Identities=23% Similarity=0.204 Sum_probs=19.5
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~rar 391 (417)
..|+.++|+.+|++..+|.++..--.
T Consensus 14 gls~~~lA~~~g~s~s~v~~iE~G~~ 39 (64)
T PF13560_consen 14 GLSQAQLADRLGVSQSTVSRIERGRR 39 (64)
T ss_dssp TS-HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred CCCHHHHHHHHCcCHHHHHHHHCCCC
Confidence 46999999999999999998865433
No 340
>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=35.36 E-value=62 Score=30.61 Aligned_cols=27 Identities=19% Similarity=0.153 Sum_probs=23.9
Q ss_pred cCCCccHHHHHHHcCCCHHHHHHHHHH
Q 014852 363 KGVTPSVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 363 ~gRepS~eEIAe~LGIS~etVr~aL~r 389 (417)
-.+-||..|+|+.+|+|..||++++..
T Consensus 22 g~~LPsE~eLa~~~~VSR~TVR~Al~~ 48 (230)
T TIGR02018 22 GHRIPSEHELVAQYGCSRMTVNRALRE 48 (230)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 346789999999999999999999875
No 341
>PRK04841 transcriptional regulator MalT; Provisional
Probab=35.30 E-value=32 Score=38.78 Aligned_cols=30 Identities=13% Similarity=0.243 Sum_probs=26.3
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAIGKVFSL 396 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~rark~LSL 396 (417)
.|.+|||+.|+||+.||+..+..+..++.+
T Consensus 854 ~~~~~ia~~l~~s~~tv~~h~~~~~~kl~v 883 (903)
T PRK04841 854 YSNEQIAGELDVAATTIKTHIRNLYQKLGI 883 (903)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 499999999999999999999988766644
No 342
>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=35.09 E-value=47 Score=31.21 Aligned_cols=28 Identities=21% Similarity=0.348 Sum_probs=24.3
Q ss_pred cCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 363 KGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 363 ~gRepS~eEIAe~LGIS~etVr~aL~ra 390 (417)
-.+-|+..|+|+.+|++.-||++++...
T Consensus 22 g~~lPsE~eLa~~~~Vsr~Tvr~Al~~L 49 (231)
T TIGR03337 22 GDKLPSERDLGERFNTTRVTIREALQQL 49 (231)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 3457899999999999999999998754
No 343
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=34.65 E-value=63 Score=30.90 Aligned_cols=27 Identities=19% Similarity=0.308 Sum_probs=23.8
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 364 GVTPSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~aL~ra 390 (417)
.+-||..|+|+.+|+|..||++++...
T Consensus 27 ~~LPsE~eL~~~~~VSR~TvR~Al~~L 53 (240)
T PRK09764 27 DALPTESALQTEFGVSRVTVRQALRQL 53 (240)
T ss_pred CcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 466899999999999999999998753
No 344
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=34.64 E-value=42 Score=29.64 Aligned_cols=28 Identities=14% Similarity=0.317 Sum_probs=24.4
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 364 GVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
|..++..|||+.+|||...|++++....
T Consensus 23 g~~~s~~~ia~~~~is~~~vrk~l~~L~ 50 (141)
T PRK11014 23 GRMTSISEVTEVYGVSRNHMVKIINQLS 50 (141)
T ss_pred CCccCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4557999999999999999999987654
No 345
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=34.52 E-value=60 Score=31.82 Aligned_cols=35 Identities=23% Similarity=0.274 Sum_probs=26.0
Q ss_pred HHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHH
Q 014852 354 RNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 354 ~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~r 389 (417)
...+..|.+ ...++++|+|+.+|+|+.|||+=+..
T Consensus 8 ~~Il~~l~~-~g~v~v~eLa~~~~VS~~TIRRDL~~ 42 (253)
T COG1349 8 QKILELLKE-KGKVSVEELAELFGVSEMTIRRDLNE 42 (253)
T ss_pred HHHHHHHHH-cCcEEHHHHHHHhCCCHHHHHHhHHH
Confidence 334444544 34579999999999999999986654
No 346
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=34.24 E-value=63 Score=30.53 Aligned_cols=36 Identities=28% Similarity=0.268 Sum_probs=29.3
Q ss_pred HHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 355 NAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 355 ~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
.....+...| +.|.+|||+.|||...+|+.++.+..
T Consensus 22 ~v~~~l~~kg-e~tDeela~~l~i~~~~vrriL~~L~ 57 (176)
T COG1675 22 LVVDALLEKG-ELTDEELAELLGIKKNEVRRILYALY 57 (176)
T ss_pred HHHHHHHhcC-CcChHHHHHHhCccHHHHHHHHHHHH
Confidence 3444455555 78999999999999999999998765
No 347
>PRK09726 antitoxin HipB; Provisional
Probab=34.20 E-value=75 Score=25.85 Aligned_cols=24 Identities=13% Similarity=0.145 Sum_probs=20.6
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHH
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATE 388 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~ 388 (417)
+..|++|+|+.+||+..+|.+...
T Consensus 24 ~gltq~elA~~~gvs~~tis~~e~ 47 (88)
T PRK09726 24 NGWTQSELAKKIGIKQATISNFEN 47 (88)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHC
Confidence 356899999999999999988765
No 348
>PRK06424 transcription factor; Provisional
Probab=33.78 E-value=96 Score=28.23 Aligned_cols=39 Identities=5% Similarity=-0.024 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHH
Q 014852 350 LGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 350 ~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~r 389 (417)
...+...+..+. ..+..|++|+|+.+|++..+|..+..-
T Consensus 82 ~~~~g~~Ir~lR-e~~GLSQ~eLA~~iGvs~stIskiE~G 120 (144)
T PRK06424 82 VEDYAELVKNAR-ERLSMSQADLAAKIFERKNVIASIERG 120 (144)
T ss_pred HHHHHHHHHHHH-HHcCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 333444444442 245679999999999999999988654
No 349
>PRK11569 transcriptional repressor IclR; Provisional
Probab=33.55 E-value=83 Score=30.90 Aligned_cols=37 Identities=5% Similarity=0.080 Sum_probs=28.2
Q ss_pred HHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 355 NAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 355 ~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
..++.|.+.....+..|||+.+|++..+|..++....
T Consensus 32 ~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~ 68 (274)
T PRK11569 32 KLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQ 68 (274)
T ss_pred HHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3333344445567999999999999999999987653
No 350
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=33.45 E-value=90 Score=26.62 Aligned_cols=24 Identities=21% Similarity=0.171 Sum_probs=20.1
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHH
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATE 388 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~ 388 (417)
.+.|+.|||+.||||..+|-+.-+
T Consensus 54 ~~~tQrEIa~~lGiS~atIsR~sn 77 (94)
T TIGR01321 54 GNMSQREIASKLGVSIATITRGSN 77 (94)
T ss_pred CCCCHHHHHHHhCCChhhhhHHHh
Confidence 456999999999999999876543
No 351
>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=33.22 E-value=86 Score=24.55 Aligned_cols=26 Identities=23% Similarity=0.436 Sum_probs=17.9
Q ss_pred HHhhCCCCchHHHHHHhcCC-hHHHHH
Q 014852 232 KERLGCEPSMEQLAASLRIS-RPELQS 257 (417)
Q Consensus 232 ~~~lg~eps~~e~A~~~~~s-~~eLr~ 257 (417)
-...|.+||..|+|..+|++ ...+..
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 35789999999999999996 555443
No 352
>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=33.10 E-value=1.2e+02 Score=25.66 Aligned_cols=42 Identities=19% Similarity=0.164 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHHcCCCccHHHHHHHcC-CCHHHHHHHHHHhCc
Q 014852 351 GLIRNAKLRLEEKGVTPSVDRIAEYLN-MSQKKVRNATEAIGK 392 (417)
Q Consensus 351 ~kI~~a~~~L~e~gRepS~eEIAe~LG-IS~etVr~aL~rark 392 (417)
..|..+...|...|+.||+.-|-+.|| -|..+|...++.-+.
T Consensus 4 e~V~~Aa~~L~~~G~~pT~~~Vr~~lG~GS~~ti~~~l~~w~~ 46 (120)
T PF11740_consen 4 EDVIEAADELLAAGKKPTVRAVRERLGGGSMSTISKHLKEWRE 46 (120)
T ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHHCCCCHHHHHHHHHHHHH
Confidence 457888888988899999999999999 999999999887653
No 353
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=32.90 E-value=94 Score=23.34 Aligned_cols=58 Identities=17% Similarity=0.223 Sum_probs=33.6
Q ss_pred CCchHHHHHHhcCChHHHHHHhhhhH-HHHHHHHHHhHHHHHHHHHHcc-CCCCChhhhhhhH
Q 014852 238 EPSMEQLAASLRISRPELQSILMECS-LAREKLVMSNVRLVMSIAQRYD-NMGADMADLVQGG 298 (417)
Q Consensus 238 eps~~e~A~~~~~s~~eLr~~l~~~~-~Are~LIe~yl~LV~sIA~Ry~-~~g~e~EDLIQEG 298 (417)
+++.+++|..+|++...|.+.+.... ......+.. ..+. .|..+. ......+|+.++.
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~~~~s~~~~~~~--~r~~-~a~~~l~~~~~~~~~ia~~~ 60 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKETGTTPKQYLRD--RRLE-RARRLLRDTDLSVTEIALRV 60 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHhCcCHHHHHHH--HHHH-HHHHHHHcCCCCHHHHHHHh
Confidence 46889999999999999887776432 112222111 1122 233333 3346777777665
No 354
>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=32.86 E-value=80 Score=29.61 Aligned_cols=26 Identities=23% Similarity=0.336 Sum_probs=23.3
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~rar 391 (417)
.+|..|||+.|||+..+|...+....
T Consensus 15 ~~t~~eLA~~lgis~~tV~~~L~~Le 40 (203)
T TIGR02702 15 QATAAALAEALAISPQAVRRHLKDLE 40 (203)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 37999999999999999999988753
No 355
>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=32.48 E-value=55 Score=26.82 Aligned_cols=39 Identities=18% Similarity=0.167 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHcCCCccHHHHHHHcC--CCHHHHHHHHHHh
Q 014852 351 GLIRNAKLRLEEKGVTPSVDRIAEYLN--MSQKKVRNATEAI 390 (417)
Q Consensus 351 ~kI~~a~~~L~e~gRepS~eEIAe~LG--IS~etVr~aL~ra 390 (417)
.++.+++..++ .|+..|+.+||+.+| -....|-.++...
T Consensus 5 ~~V~~~v~~IP-~G~v~TYg~iA~~~g~p~~ar~Vg~al~~n 45 (85)
T PF01035_consen 5 RRVWEAVRQIP-YGKVTTYGEIARLLGRPKAARAVGSALARN 45 (85)
T ss_dssp HHHHHHHTTS--TT-BEEHHHHHHHTT-TTCHHHHHHHHHTS
T ss_pred HHHHHHHHcCC-CCceEeHHHHHHHHhhcccHHHHHHHhccc
Confidence 34555555554 588889999999999 7788888888764
No 356
>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=32.46 E-value=47 Score=26.98 Aligned_cols=21 Identities=33% Similarity=0.483 Sum_probs=19.5
Q ss_pred cHHHHHHHcCCCHHHHHHHHH
Q 014852 368 SVDRIAEYLNMSQKKVRNATE 388 (417)
Q Consensus 368 S~eEIAe~LGIS~etVr~aL~ 388 (417)
|.+|+++.||++..+|..++.
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 357
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=32.45 E-value=6.6e+02 Score=28.04 Aligned_cols=27 Identities=11% Similarity=0.011 Sum_probs=22.9
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
..|..+|+++.||++...+++.+...-
T Consensus 505 ~p~~~~~~~~~l~~~~~~~~~~l~~l~ 531 (614)
T PRK10512 505 EPWWVRDLAKETGTDEQAMRLTLRQAA 531 (614)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 457899999999999999888877653
No 358
>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=32.13 E-value=51 Score=25.22 Aligned_cols=22 Identities=9% Similarity=0.170 Sum_probs=19.3
Q ss_pred cHHHHHHHcCCCHHHHHHHHHH
Q 014852 368 SVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 368 S~eEIAe~LGIS~etVr~aL~r 389 (417)
+..|+|+.+||+..+++.....
T Consensus 2 ~i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 2 TIGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh
Confidence 5789999999999999988654
No 359
>PF11176 DUF2962: Protein of unknown function (DUF2962); InterPro: IPR021346 This eukaryotic family of proteins has no known function. ; PDB: 2KKM_A.
Probab=31.83 E-value=1.7e+02 Score=26.83 Aligned_cols=91 Identities=21% Similarity=0.307 Sum_probs=44.9
Q ss_pred hhHHHHHHhhc--ccCCCCHHHHHHHHHHHH--ccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHH
Q 014852 191 NRLKGYVKGVV--SEELLTHAEVVRLSKKIK--TGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAR 266 (417)
Q Consensus 191 ~~~~~yl~~i~--~~~lLt~~eE~eLirk~k--~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Ar 266 (417)
+.+.-|-+.|. ....+|.++-.+|+...- ..++|++. +.+.+-||+|+..|..
T Consensus 49 ~r~~wFq~~i~~~~~~~~t~~e~~~lI~~yl~R~DeEleql--~~~rR~gRp~s~re~~--------------------- 105 (155)
T PF11176_consen 49 ERLKWFQEAIDEKDKKPFTLEEIHELIERYLHRFDEELEQL--KKERRKGRPPSNREDL--------------------- 105 (155)
T ss_dssp HHHHHHHHHHHSTT-----HHHHHHHHHHHHHHHHHHHHHH--HHHGGGT---TTHHHH---------------------
T ss_pred HHHHHHHHHccccCCCCCCHHHHHHHHHHHHhcCHHHHHHH--HHhhcCCCCCchHHHH---------------------
Confidence 34443333343 367799999999997653 33333333 3446789999765532
Q ss_pred HHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCC
Q 014852 267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKG 314 (417)
Q Consensus 267 e~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG 314 (417)
++. .+-.-...|. .|++.-||..+.++.+++. ||++-+
T Consensus 106 ---L~~---~~~~E~~ey~-~G~~vPDLtd~~nv~~Lr~---W~G~~~ 143 (155)
T PF11176_consen 106 ---LEQ---KIEREEEEYK-TGFEVPDLTDEKNVKLLRE---WNGDWG 143 (155)
T ss_dssp ---HHH---HHHHHHHHHH-TTEEEE-S--HHHHHHHHT----SS-ST
T ss_pred ---HHH---HHHHHHHHHh-hCeeCCCCCCHHHHHHHHh---cCCChh
Confidence 111 1223334555 7999999999999888775 666544
No 360
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=31.76 E-value=64 Score=24.29 Aligned_cols=24 Identities=21% Similarity=0.311 Sum_probs=20.1
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~ra 390 (417)
+++++||+.+|++...+.......
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~ 25 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKE 25 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Confidence 578999999999999998876643
No 361
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=31.62 E-value=41 Score=30.55 Aligned_cols=25 Identities=12% Similarity=0.221 Sum_probs=22.5
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~rar 391 (417)
.|+++||..+|++.++|-..+...+
T Consensus 150 ~t~~~iA~~lG~tretvsR~l~~l~ 174 (202)
T PRK13918 150 ATHDELAAAVGSVRETVTKVIGELS 174 (202)
T ss_pred CCHHHHHHHhCccHHHHHHHHHHHH
Confidence 4899999999999999999887765
No 362
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=31.59 E-value=91 Score=26.34 Aligned_cols=25 Identities=20% Similarity=0.206 Sum_probs=21.6
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~ra 390 (417)
..|.++||+.||++.+.|.+++..-
T Consensus 23 ~ls~~~ia~dL~~s~~~le~vL~l~ 47 (89)
T PF10078_consen 23 GLSLEQIAADLGTSPEHLEQVLNLK 47 (89)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHcCC
Confidence 4699999999999999999986543
No 363
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=31.52 E-value=98 Score=30.20 Aligned_cols=34 Identities=18% Similarity=0.161 Sum_probs=26.3
Q ss_pred HHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 356 AKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 356 a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~ra 390 (417)
.+..|.+ ....+..|||+.+|+|..||++-+...
T Consensus 10 Il~~l~~-~~~~~~~ela~~l~vS~~TirRdL~~L 43 (251)
T PRK13509 10 LLELLAQ-LGFVTVEKVIERLGISPATARRDINKL 43 (251)
T ss_pred HHHHHHH-cCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3444443 445799999999999999999888754
No 364
>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=31.15 E-value=68 Score=26.84 Aligned_cols=26 Identities=19% Similarity=0.219 Sum_probs=20.0
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~rar 391 (417)
..+.++||+.+|++..+|+.++....
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 46899999999999999999988765
No 365
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=30.91 E-value=1.1e+02 Score=29.88 Aligned_cols=34 Identities=21% Similarity=0.230 Sum_probs=26.8
Q ss_pred HHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 358 LRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 358 ~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
..|...+...+..|||+.||++..+|..++....
T Consensus 18 ~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~ 51 (263)
T PRK09834 18 RALNRLDGGATVGLLAELTGLHRTTVRRLLETLQ 51 (263)
T ss_pred HHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3344445557999999999999999999987653
No 366
>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=30.84 E-value=1.2e+02 Score=21.69 Aligned_cols=23 Identities=22% Similarity=0.296 Sum_probs=17.9
Q ss_pred CchHHHHHHhcCChHHHHHHhhh
Q 014852 239 PSMEQLAASLRISRPELQSILME 261 (417)
Q Consensus 239 ps~~e~A~~~~~s~~eLr~~l~~ 261 (417)
.+..++|+.+|+|...+..++..
T Consensus 18 ~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 18 RSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp S-HHHHHHHHTS-HHHHHHHHHH
T ss_pred ccHHHHHHHHCcCHHHHHHHHHH
Confidence 57899999999999998877653
No 367
>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=30.79 E-value=64 Score=22.76 Aligned_cols=22 Identities=18% Similarity=0.339 Sum_probs=17.7
Q ss_pred cHHHHHHHcCCCHHHHHHHHHH
Q 014852 368 SVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 368 S~eEIAe~LGIS~etVr~aL~r 389 (417)
.+.+.|+.|||+..++...+..
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 5789999999999999887753
No 368
>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=30.72 E-value=1.2e+02 Score=28.23 Aligned_cols=25 Identities=12% Similarity=0.203 Sum_probs=22.6
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~rar 391 (417)
.+.+|||+.+|++..+|...+..+.
T Consensus 121 ~s~~~iA~~lg~s~~~V~r~l~l~~ 145 (187)
T TIGR00180 121 MTQEDLAKKIGKSRAHITNLLRLLK 145 (187)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHc
Confidence 4899999999999999999988765
No 369
>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=30.66 E-value=1.3e+02 Score=21.34 Aligned_cols=31 Identities=23% Similarity=0.073 Sum_probs=22.8
Q ss_pred HHHHHHHc-CCCccHHHHHHHcCCCHHHHHHH
Q 014852 356 AKLRLEEK-GVTPSVDRIAEYLNMSQKKVRNA 386 (417)
Q Consensus 356 a~~~L~e~-gRepS~eEIAe~LGIS~etVr~a 386 (417)
+...+.+. ....|.++||+.+|++...+...
T Consensus 5 a~~l~~~~G~~~~s~~~Ia~~~gvs~~~~y~~ 36 (47)
T PF00440_consen 5 ALELFAEKGYEAVSIRDIARRAGVSKGSFYRY 36 (47)
T ss_dssp HHHHHHHHHTTTSSHHHHHHHHTSCHHHHHHH
T ss_pred HHHHHHHhCHHhCCHHHHHHHHccchhhHHHH
Confidence 33444333 46679999999999999998653
No 370
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=30.26 E-value=57 Score=25.28 Aligned_cols=25 Identities=16% Similarity=0.260 Sum_probs=21.5
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHH
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~r 389 (417)
+..|..++|+.+|++..+|...+..
T Consensus 17 ~~~t~~~lA~~~gis~~tis~~~~g 41 (78)
T TIGR02607 17 LGLSIRALAKALGVSRSTLSRIVNG 41 (78)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 4468999999999999999998763
No 371
>smart00351 PAX Paired Box domain.
Probab=29.84 E-value=50 Score=28.91 Aligned_cols=26 Identities=15% Similarity=-0.038 Sum_probs=23.3
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhCc
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAIGK 392 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~rark 392 (417)
.+..+||+.+||+..+|...+.+.+.
T Consensus 34 ~s~~~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 34 VRPCDISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 48899999999999999999988754
No 372
>PRK09954 putative kinase; Provisional
Probab=29.54 E-value=90 Score=31.57 Aligned_cols=35 Identities=17% Similarity=0.146 Sum_probs=27.2
Q ss_pred HHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 356 AKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 356 a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
.+..|.+.+ ..|..|||+.||++..+|+.++.+..
T Consensus 8 il~~l~~~~-~~s~~~la~~l~~s~~~v~~~i~~L~ 42 (362)
T PRK09954 8 ILAILRRNP-LIQQNEIADILQISRSRVAAHIMDLM 42 (362)
T ss_pred HHHHHHHCC-CCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 344454444 46999999999999999999988654
No 373
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=29.37 E-value=60 Score=30.75 Aligned_cols=28 Identities=11% Similarity=0.420 Sum_probs=24.1
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 364 GVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
.+-|+..|||+.+|+|..+|++++....
T Consensus 29 ~~LPsE~eLae~~gVSRt~VReAL~~L~ 56 (239)
T PRK04984 29 SILPAERELSELIGVTRTTLREVLQRLA 56 (239)
T ss_pred CcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3456899999999999999999998753
No 374
>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=29.32 E-value=40 Score=24.10 Aligned_cols=19 Identities=21% Similarity=0.163 Sum_probs=16.7
Q ss_pred HHHHHcCCCHHHHHHHHHH
Q 014852 371 RIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 371 EIAe~LGIS~etVr~aL~r 389 (417)
|||+.+|++..+|..+++-
T Consensus 2 ~lA~~~gvs~~tvs~~l~g 20 (52)
T cd01392 2 DIARAAGVSVATVSRVLNG 20 (52)
T ss_pred cHHHHHCcCHHHHHHHHcC
Confidence 7999999999999988764
No 375
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=28.81 E-value=95 Score=29.83 Aligned_cols=27 Identities=30% Similarity=0.379 Sum_probs=23.4
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
+-|+..++|+.+|||...|+.++.+..
T Consensus 32 ~LpsE~eLa~~~gVSRtpVREAL~~L~ 58 (257)
T PRK10225 32 RLPPEREIAEMLDVTRTVVREALIMLE 58 (257)
T ss_pred cCcCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 445899999999999999999998753
No 376
>PRK00901 methylated-DNA--protein-cysteine methyltransferase; Provisional
Probab=28.66 E-value=1.1e+02 Score=28.22 Aligned_cols=66 Identities=17% Similarity=0.147 Sum_probs=39.6
Q ss_pred hHHHHHHhhccccccCccH--HHHHHHHHHHHHHHHHcCCCccHHHHHHHcCCCH--HHHHHHHHHhCccccc
Q 014852 328 GVSRALVENSRTLRLPNHL--HERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQ--KKVRNATEAIGKVFSL 396 (417)
Q Consensus 328 ~i~~~Ird~~r~irlp~~~--~e~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~--etVr~aL~rark~LSL 396 (417)
.+..|+........+|-.. .....++.+++...+ .|+..|+.|||+.+|.+. ..|-+++.+ +++.+
T Consensus 51 ~l~~Yf~G~~~~f~lpl~~~gt~fq~~Vw~~l~~Ip-~G~t~tY~~lA~~~g~p~a~RAVg~A~~~--NP~~i 120 (155)
T PRK00901 51 QLEEYFEGKRKKFDLPLAPQGTEFQKKVWKALQEIP-YGETRSYKEIAVNIGNPKACRAVGLANNK--NPIPI 120 (155)
T ss_pred HHHHHHcCCCcCCceeecCCCChHHHHHHHHHccCC-CCCcCCHHHHHHHHCCCchHHHHHHHHHh--CCCCC
Confidence 3444555544333344332 234456666665554 589999999999999875 455555443 45544
No 377
>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=28.51 E-value=1.1e+02 Score=22.82 Aligned_cols=29 Identities=17% Similarity=0.203 Sum_probs=22.0
Q ss_pred cCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 363 KGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 363 ~gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
....++..+||+.++++..+|...++...
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 35667999999999999999999888764
No 378
>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=28.50 E-value=1.2e+02 Score=28.64 Aligned_cols=43 Identities=28% Similarity=0.404 Sum_probs=31.7
Q ss_pred HHHHHHHccCcchhHHHHHHHhhC-CCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHH
Q 014852 213 RLSKKIKTGLSLDDHKLRLKERLG-CEPSMEQLAASLRISRPELQSILMECSLAREKLVMS 272 (417)
Q Consensus 213 eLirk~k~Gd~l~~~~~~l~~~lg-~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~ 272 (417)
.|.++|..|.. .-| +-||..++|+.+|+|+..+|+ |++.|...
T Consensus 16 ~l~~~I~~g~~----------~~G~~LPsE~eLa~~~~VSR~TvR~-------Al~~L~~e 59 (238)
T TIGR02325 16 KIEQEIAAGHL----------RAGDYLPAEMQLAERFGVNRHTVRR-------AIAALVER 59 (238)
T ss_pred HHHHHHHcCCC----------CCCCcCcCHHHHHHHHCCCHHHHHH-------HHHHHHHC
Confidence 46677777765 233 359999999999999999994 55665544
No 379
>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=28.47 E-value=1.1e+02 Score=26.21 Aligned_cols=26 Identities=23% Similarity=0.254 Sum_probs=23.0
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~rar 391 (417)
.++.+|||+.+|+|...|++++....
T Consensus 25 ~~s~~eia~~~~i~~~~v~~il~~L~ 50 (132)
T TIGR00738 25 PVSVKEIAERQGISRSYLEKILRTLR 50 (132)
T ss_pred cCcHHHHHHHHCcCHHHHHHHHHHHH
Confidence 56999999999999999999987654
No 380
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=28.45 E-value=40 Score=24.92 Aligned_cols=21 Identities=19% Similarity=0.256 Sum_probs=18.4
Q ss_pred ccHHHHHHHcCCCHHHHHHHH
Q 014852 367 PSVDRIAEYLNMSQKKVRNAT 387 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL 387 (417)
.++.|+|+.||++...|-..+
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 368899999999999999988
No 381
>PRK10072 putative transcriptional regulator; Provisional
Probab=28.43 E-value=62 Score=27.48 Aligned_cols=26 Identities=19% Similarity=0.118 Sum_probs=21.9
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~rar 391 (417)
..|+.|+|+.+|++..+|.+....-+
T Consensus 46 glTQ~elA~~lGvS~~TVs~WE~G~r 71 (96)
T PRK10072 46 GLKIDDFARVLGVSVAMVKEWESRRV 71 (96)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHcCCC
Confidence 45899999999999999999876443
No 382
>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=28.38 E-value=63 Score=27.92 Aligned_cols=28 Identities=18% Similarity=0.178 Sum_probs=24.2
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 364 GVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
+..++..|||+.+|+|...|.+++....
T Consensus 23 ~~~~s~~eia~~l~is~~~v~~~l~~L~ 50 (130)
T TIGR02944 23 SQPYSAAEIAEQTGLNAPTVSKILKQLS 50 (130)
T ss_pred CCCccHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3456999999999999999999988765
No 383
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=28.37 E-value=61 Score=30.90 Aligned_cols=27 Identities=19% Similarity=0.304 Sum_probs=23.9
Q ss_pred cCCCccHHHHHHHcCCCHHHHHHHHHH
Q 014852 363 KGVTPSVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 363 ~gRepS~eEIAe~LGIS~etVr~aL~r 389 (417)
-.+-||-.|+|+.+|+|..||++++..
T Consensus 30 g~kLPsE~eLa~~~~VSR~TvR~Al~~ 56 (241)
T PRK11402 30 GQQIPTENELCTQYNVSRITIRKAISD 56 (241)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 346789999999999999999999864
No 384
>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=28.23 E-value=69 Score=23.94 Aligned_cols=42 Identities=26% Similarity=0.389 Sum_probs=28.8
Q ss_pred CCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhh
Q 014852 204 ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMEC 262 (417)
Q Consensus 204 ~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~ 262 (417)
.-||.++-.++++.+..|. +..++|..+|++...+...+..-
T Consensus 5 ~~LTl~eK~~iI~~~e~g~-----------------s~~~ia~~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 5 KSLTLEEKLEIIKRLEEGE-----------------SKRDIAREFGVSRSTVSTILKNK 46 (53)
T ss_dssp SS--HHHHHHHHHHHHCTT------------------HHHHHHHHT--CCHHHHHHHCH
T ss_pred ccCCHHHHHHHHHHHHcCC-----------------CHHHHHHHhCCCHHHHHHHHHhH
Confidence 3488999999999988765 46788888888888887766643
No 385
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=28.22 E-value=1.4e+02 Score=27.36 Aligned_cols=38 Identities=11% Similarity=0.166 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHHH-HHcC-CCccHHHHHHHcCCCHHHHHH
Q 014852 348 ERLGLIRNAKLRL-EEKG-VTPSVDRIAEYLNMSQKKVRN 385 (417)
Q Consensus 348 e~~~kI~~a~~~L-~e~g-RepS~eEIAe~LGIS~etVr~ 385 (417)
+...+|.++...| .+.| ...|.++||+..|++.+++..
T Consensus 11 ~~r~~Il~aa~~lf~~~G~~~~ti~~Ia~~agvsk~t~Y~ 50 (213)
T PRK09975 11 KTRQELIETAIAQFALRGVSNTTLNDIADAANVTRGAIYW 50 (213)
T ss_pred HHHHHHHHHHHHHHHHcCcccCCHHHHHHHcCCCHHHHHH
Confidence 3344555554444 5666 457999999999999999955
No 386
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=28.18 E-value=79 Score=20.97 Aligned_cols=24 Identities=17% Similarity=0.231 Sum_probs=20.3
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHH
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATE 388 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~ 388 (417)
+..|..++|+.+|++..+|.....
T Consensus 9 ~~~s~~~la~~~~i~~~~i~~~~~ 32 (56)
T smart00530 9 KGLTQEELAEKLGVSRSTLSRIEN 32 (56)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHC
Confidence 346899999999999999987654
No 387
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=27.78 E-value=56 Score=29.83 Aligned_cols=25 Identities=12% Similarity=0.151 Sum_probs=22.6
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~rar 391 (417)
.|.+|||+.+|++.++|.++++..+
T Consensus 169 ~t~~~lA~~lG~tr~tvsR~l~~l~ 193 (211)
T PRK11753 169 ITRQEIGRIVGCSREMVGRVLKMLE 193 (211)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 5899999999999999999987765
No 388
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=27.50 E-value=61 Score=31.05 Aligned_cols=27 Identities=19% Similarity=0.362 Sum_probs=23.6
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
+-|+..|||+.+|||...|+.++....
T Consensus 33 ~LpsE~eLa~~lgVSRtpVREAL~~L~ 59 (254)
T PRK09464 33 KLPPERELAKQFDVSRPSLREAIQRLE 59 (254)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 446999999999999999999998753
No 389
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=27.43 E-value=1.6e+02 Score=26.23 Aligned_cols=26 Identities=27% Similarity=0.199 Sum_probs=22.1
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~rar 391 (417)
..|+.+||+.||++...|.+.+.--+
T Consensus 22 G~Sq~~iA~LLGltqaAVS~Yls~kr 47 (119)
T COG2522 22 GLSQYRIAKLLGLTQAAVSQYLSGKR 47 (119)
T ss_pred CCcHHHHHHHhCCCHHHHHHHHccCC
Confidence 56999999999999999998875433
No 390
>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=27.40 E-value=1.2e+02 Score=30.33 Aligned_cols=41 Identities=17% Similarity=0.303 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHH-cCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 350 LGLIRNAKLRLEE-KGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 350 ~~kI~~a~~~L~e-~gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
+..+.+.+..|.. .|| .+..+||+.+|+|...|++++++..
T Consensus 182 leAv~~IL~~L~~~egr-lse~eLAerlGVSRs~ireAlrkLE 223 (251)
T TIGR02787 182 LEAVEHIFEELDGNEGL-LVASKIADRVGITRSVIVNALRKLE 223 (251)
T ss_pred HHHHHHHHHHhcccccc-ccHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3445666666654 344 5889999999999999999988753
No 391
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=27.34 E-value=66 Score=30.93 Aligned_cols=27 Identities=22% Similarity=0.306 Sum_probs=23.5
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
+-|+..|||+.+|||...|+.++....
T Consensus 25 ~LpsE~eLae~~gVSRtpVREAL~~Le 51 (253)
T PRK10421 25 KLPAERQLAMQLGVSRNSLREALAKLV 51 (253)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 445899999999999999999998754
No 392
>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=27.27 E-value=1.6e+02 Score=23.41 Aligned_cols=36 Identities=19% Similarity=0.221 Sum_probs=27.6
Q ss_pred HHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 355 NAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 355 ~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~ra 390 (417)
..+..+.......+..+||+.++++.++|...+..+
T Consensus 49 ~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~l~~~ 84 (105)
T PF01399_consen 49 RNLRQLSKPYSSISISEIAKALQLSEEEVESILIDL 84 (105)
T ss_dssp HHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred HHHHHHHHHhcccchHHHHHHhccchHHHHHHHHHH
Confidence 334444446777899999999999999999987665
No 393
>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=27.24 E-value=1.5e+02 Score=23.51 Aligned_cols=26 Identities=15% Similarity=0.083 Sum_probs=18.9
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHH
Q 014852 364 GVTPSVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~aL~r 389 (417)
-...|..|||+.+|+|..+|-+..+.
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 34569999999999999999876554
No 394
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=27.17 E-value=1e+02 Score=30.22 Aligned_cols=34 Identities=12% Similarity=0.133 Sum_probs=25.5
Q ss_pred HHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHH
Q 014852 355 NAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 355 ~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~r 389 (417)
..+..|.+ ...+++.|||+.||+|+.||++-+..
T Consensus 9 ~Il~~l~~-~~~~~~~ela~~l~vS~~TiRRdL~~ 42 (252)
T PRK10906 9 AIIELVKQ-QGYVSTEELVEHFSVSPQTIRRDLND 42 (252)
T ss_pred HHHHHHHH-cCCEeHHHHHHHhCCCHHHHHHHHHH
Confidence 33344544 44589999999999999999986654
No 395
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=27.13 E-value=3.8e+02 Score=22.52 Aligned_cols=23 Identities=17% Similarity=0.244 Sum_probs=20.1
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHh
Q 014852 368 SVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 368 S~eEIAe~LGIS~etVr~aL~ra 390 (417)
...+.|+.|||+..+++..+++.
T Consensus 70 n~s~AAr~LGIsRsTL~rKLkr~ 92 (95)
T PRK00430 70 NQTRAALMLGINRGTLRKKLKKY 92 (95)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHh
Confidence 58899999999999998887753
No 396
>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=26.83 E-value=1.4e+02 Score=21.83 Aligned_cols=25 Identities=20% Similarity=0.275 Sum_probs=21.2
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~rar 391 (417)
.+..|||+.++++..++-..+...-
T Consensus 18 ~~~~~la~~~~~~~~~~t~~i~~L~ 42 (59)
T PF01047_consen 18 ITQSELAEKLGISRSTVTRIIKRLE 42 (59)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHCCChhHHHHHHHHHH
Confidence 7999999999999999988877653
No 397
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=26.77 E-value=1e+02 Score=30.74 Aligned_cols=31 Identities=13% Similarity=0.200 Sum_probs=24.1
Q ss_pred HHHcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 360 LEEKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 360 L~e~gRepS~eEIAe~LGIS~etVr~aL~ra 390 (417)
+...+-.+.+.|||+.|||+++.|...+.-.
T Consensus 19 i~~~qp~v~q~eIA~~lgiT~QaVsehiK~L 49 (260)
T COG1497 19 IAVRQPRVKQKEIAKKLGITLQAVSEHIKEL 49 (260)
T ss_pred HHHhCCCCCHHHHHHHcCCCHHHHHHHHHHH
Confidence 3333445689999999999999998877654
No 398
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=26.76 E-value=90 Score=32.31 Aligned_cols=30 Identities=20% Similarity=0.296 Sum_probs=25.2
Q ss_pred HHcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 361 EEKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 361 ~e~gRepS~eEIAe~LGIS~etVr~aL~ra 390 (417)
++-.+-|+..++|+.+|+|..+|++++...
T Consensus 24 ~~g~~lps~r~la~~~~vsr~tv~~a~~~L 53 (431)
T PRK15481 24 RPGDSLPPVRELASELGVNRNTVAAAYKRL 53 (431)
T ss_pred CCCCcCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 344566899999999999999999997654
No 399
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=26.72 E-value=93 Score=21.53 Aligned_cols=27 Identities=15% Similarity=0.064 Sum_probs=19.7
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 364 GVTPSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~aL~ra 390 (417)
....++++||+.+|++........+..
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 445699999999999999998887665
No 400
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=26.64 E-value=2.9e+02 Score=23.82 Aligned_cols=35 Identities=17% Similarity=0.163 Sum_probs=27.9
Q ss_pred HHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhh
Q 014852 228 KLRLKERLGCEPSMEQLAASLRISRPELQSILMEC 262 (417)
Q Consensus 228 ~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~ 262 (417)
..-+.+.+..+++.+++|..+|+|...|.+..++.
T Consensus 15 ~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 15 LDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 34456677778999999999999999888776643
No 401
>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=26.44 E-value=1.4e+02 Score=29.62 Aligned_cols=106 Identities=21% Similarity=0.140 Sum_probs=59.6
Q ss_pred CHHHHHHHHHHH-HccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHcc
Q 014852 207 THAEVVRLSKKI-KTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYD 285 (417)
Q Consensus 207 t~~eE~eLirk~-k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~ 285 (417)
+++....|++.+ .-||.-.-.-.++.+-.|+-|+.++-...+++.-+++ .|-++++.++..+.
T Consensus 11 ~~~~~~~L~~~l~~laD~elil~~r~~ew~~~AP~LeediAl~~ia~Del----------------GHAr~ly~ll~el~ 74 (263)
T PF05138_consen 11 PEEYREALIRYLLRLADDELILGQRLSEWCGHAPSLEEDIALANIAQDEL----------------GHARLLYRLLEELE 74 (263)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHHHHHHTGGGGSSSHHHHHHHHHHHHHHH----------------HHHHHHHHHHHHCH
T ss_pred hhhhHHHHHHHHHHHhChHHHhhhHHhHHHhhCCCHHHHHHHHHHHHHHH----------------HHHHHHHHHHHHHh
Confidence 344444455433 2334333333456667899999888665555544443 35678899999987
Q ss_pred CCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHH
Q 014852 286 NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRA 332 (417)
Q Consensus 286 ~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~ 332 (417)
+.|.+.++|...-.-+=++.+.-|+ .++..|+..++++-+.+.
T Consensus 75 g~G~~~d~la~~R~~~~~rn~~l~e----~p~~dwa~~v~r~~l~d~ 117 (263)
T PF05138_consen 75 GEGRDEDDLAFLRDAREFRNLLLFE----QPNGDWADTVARQFLFDR 117 (263)
T ss_dssp CCCHHHHHHHHHHHTTCS-SSGGGG----S---SHHHHHHHHHHHHH
T ss_pred ccCCChhHHHhhcccchhhhhhhhc----cCCCCHHHHHHHHHHHHH
Confidence 7776766665443222222222222 266789998888866653
No 402
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=26.24 E-value=1.3e+02 Score=28.91 Aligned_cols=44 Identities=27% Similarity=0.355 Sum_probs=33.5
Q ss_pred HHHHHHHHccCcchhHHHHHHHhhC-CCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHH
Q 014852 212 VRLSKKIKTGLSLDDHKLRLKERLG-CEPSMEQLAASLRISRPELQSILMECSLAREKLVMS 272 (417)
Q Consensus 212 ~eLirk~k~Gd~l~~~~~~l~~~lg-~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~ 272 (417)
..|..+|..|.. ..| .-|+..++|+.+|+|+..++ .|.+.|++.
T Consensus 14 ~~i~~~I~~G~~----------~~G~~LPsE~eLa~~f~VSR~TvR-------kAL~~L~~e 58 (236)
T COG2188 14 EDIRQRIESGEL----------PPGDKLPSERELAEQFGVSRMTVR-------KALDELVEE 58 (236)
T ss_pred HHHHHHHHhCCC----------CCCCCCCCHHHHHHHHCCcHHHHH-------HHHHHHHHC
Confidence 356777887776 334 45999999999999999999 456666554
No 403
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=26.17 E-value=1.4e+02 Score=29.11 Aligned_cols=35 Identities=20% Similarity=0.135 Sum_probs=26.4
Q ss_pred HHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 357 KLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 357 ~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
+..|.+.....+..|||+.+|+|..+|...+....
T Consensus 10 L~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~ 44 (246)
T COG1414 10 LDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLV 44 (246)
T ss_pred HHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHH
Confidence 33344433445899999999999999999987654
No 404
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=26.11 E-value=1.3e+02 Score=30.53 Aligned_cols=27 Identities=11% Similarity=0.243 Sum_probs=22.7
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
-..|+.|||+.+|+++.||++.....-
T Consensus 250 ~~~tq~eva~v~~vtevTIrnrykel~ 276 (285)
T COG1405 250 ERRTQKEVAKVAGVTEVTIRNRYKELA 276 (285)
T ss_pred CchHHHHHHHHhCCeeeHHHHHHHHHH
Confidence 344999999999999999999985543
No 405
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=26.11 E-value=1.2e+02 Score=27.76 Aligned_cols=26 Identities=19% Similarity=0.240 Sum_probs=17.8
Q ss_pred cCCCccHHHHHHHcCCCHHHHHHHHH
Q 014852 363 KGVTPSVDRIAEYLNMSQKKVRNATE 388 (417)
Q Consensus 363 ~gRepS~eEIAe~LGIS~etVr~aL~ 388 (417)
.+...|.+|||+.+||+..++-...+
T Consensus 31 ~~~r~T~~eiAee~Gis~~tLYrWr~ 56 (142)
T PF13022_consen 31 NGERRTQAEIAEEVGISRSTLYRWRQ 56 (142)
T ss_dssp ----S-HHHHHHHHTS-HHHHHHHHH
T ss_pred ccccchHHHHHHHhCCCHHHHHHHHh
Confidence 34567999999999999999977664
No 406
>PRK03837 transcriptional regulator NanR; Provisional
Probab=25.95 E-value=69 Score=30.27 Aligned_cols=27 Identities=22% Similarity=0.411 Sum_probs=23.8
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
+-|+..+||+.+|||...|++++....
T Consensus 36 ~Lp~E~~Lae~~gVSRt~VREAL~~L~ 62 (241)
T PRK03837 36 QLPSERELMAFFGVGRPAVREALQALK 62 (241)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 445999999999999999999998754
No 407
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=25.94 E-value=56 Score=24.72 Aligned_cols=30 Identities=20% Similarity=0.428 Sum_probs=24.0
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHhCcccccc
Q 014852 368 SVDRIAEYLNMSQKKVRNATEAIGKVFSLD 397 (417)
Q Consensus 368 S~eEIAe~LGIS~etVr~aL~rark~LSLD 397 (417)
+..+.|+.|+|...||+.++.++.+.+.+|
T Consensus 14 n~~~tA~~L~iHrNTl~yRl~ki~~l~g~d 43 (59)
T PF13556_consen 14 NISKTARALHIHRNTLRYRLKKIEELLGLD 43 (59)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHHHHHHS--
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHCcC
Confidence 789999999999999999999998776554
No 408
>PHA00542 putative Cro-like protein
Probab=25.85 E-value=72 Score=25.86 Aligned_cols=26 Identities=19% Similarity=0.124 Sum_probs=22.2
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~ra 390 (417)
+..|+.|+|+.+||+..+|..++...
T Consensus 30 ~glTq~elA~~lgIs~~tIsr~e~g~ 55 (82)
T PHA00542 30 AGWSQEQIADATDVSQPTICRIYSGR 55 (82)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHcCC
Confidence 34699999999999999999987544
No 409
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=25.85 E-value=2.1e+02 Score=26.79 Aligned_cols=25 Identities=20% Similarity=0.204 Sum_probs=22.2
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~rar 391 (417)
.+.+|||+.+|++.++|-+.+....
T Consensus 170 ~t~~~lA~~lG~sretvsR~L~~L~ 194 (226)
T PRK10402 170 EKHTQAAEYLGVSYRHLLYVLAQFI 194 (226)
T ss_pred chHHHHHHHHCCcHHHHHHHHHHHH
Confidence 3899999999999999999887755
No 410
>PRK15044 transcriptional regulator SirC; Provisional
Probab=25.80 E-value=2.8e+02 Score=28.39 Aligned_cols=60 Identities=17% Similarity=0.119 Sum_probs=40.7
Q ss_pred HHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhh
Q 014852 193 LKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (417)
Q Consensus 193 ~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~ 261 (417)
+..|++.....+.|........ .+.+..-+.+.+..+++.+++|..+|+|+..|.+....
T Consensus 172 Ls~~l~~~~~~~~L~~~~~is~---------~~kV~~~I~~nl~~~~SLeeLA~~lgmS~~tL~R~Fk~ 231 (295)
T PRK15044 172 ISAFVRKPGGFDFLERAIKITT---------KEKVYNIIISDLTRKWSQAEVAGKLFMSVSSLKRKLAA 231 (295)
T ss_pred HHHHHhcccchhhHHHHhhhhH---------HHHHHHHHHhCcccCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 4455665444444444433222 22344556778889999999999999999999987765
No 411
>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=25.56 E-value=2e+02 Score=21.63 Aligned_cols=35 Identities=29% Similarity=0.374 Sum_probs=22.7
Q ss_pred HHHHHHHccCcchhHHHHHHHhhC-CCCchHHHHHHhcCChHHHHH
Q 014852 213 RLSKKIKTGLSLDDHKLRLKERLG-CEPSMEQLAASLRISRPELQS 257 (417)
Q Consensus 213 eLirk~k~Gd~l~~~~~~l~~~lg-~eps~~e~A~~~~~s~~eLr~ 257 (417)
.|...+..|.. ..| .-|+..++|..+++|...+++
T Consensus 8 ~l~~~I~~g~~----------~~g~~lps~~~la~~~~vsr~tvr~ 43 (64)
T PF00392_consen 8 QLRQAILSGRL----------PPGDRLPSERELAERYGVSRTTVRE 43 (64)
T ss_dssp HHHHHHHTTSS-----------TTSBE--HHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHcCCC----------CCCCEeCCHHHHHHHhccCCcHHHH
Confidence 45566666654 233 348999999999999999884
No 412
>PF14493 HTH_40: Helix-turn-helix domain
Probab=25.43 E-value=1.2e+02 Score=24.87 Aligned_cols=26 Identities=12% Similarity=0.166 Sum_probs=22.4
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~rar 391 (417)
..|++|||+.-|+++.||...+..+-
T Consensus 13 G~si~eIA~~R~L~~sTI~~HL~~~~ 38 (91)
T PF14493_consen 13 GLSIEEIAKIRGLKESTIYGHLAELI 38 (91)
T ss_pred CCCHHHHHHHcCCCHHHHHHHHHHHH
Confidence 45999999999999999999876553
No 413
>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=25.16 E-value=1.4e+02 Score=28.17 Aligned_cols=43 Identities=28% Similarity=0.309 Sum_probs=30.9
Q ss_pred HHHHHHHccCcchhHHHHHHHhhC-CCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHH
Q 014852 213 RLSKKIKTGLSLDDHKLRLKERLG-CEPSMEQLAASLRISRPELQSILMECSLAREKLVMS 272 (417)
Q Consensus 213 eLirk~k~Gd~l~~~~~~l~~~lg-~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~ 272 (417)
.|.++|..|.. ..| +-|+..|+|+.+|+|+..++ .|.+.|+..
T Consensus 8 ~l~~~I~~g~~----------~~G~~LPsE~eLa~~~gVSR~TVR-------~Al~~L~~e 51 (233)
T TIGR02404 8 DLEQKITHGQY----------KEGDYLPSEHELMDQYGASRETVR-------KALNLLTEA 51 (233)
T ss_pred HHHHHHHhCCC----------CCCCCCcCHHHHHHHHCCCHHHHH-------HHHHHHHHC
Confidence 35556666554 233 45999999999999999999 466666554
No 414
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=25.14 E-value=1.3e+02 Score=29.12 Aligned_cols=27 Identities=11% Similarity=0.160 Sum_probs=23.7
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
...+..|||+.+|+|..+|..++....
T Consensus 27 ~~l~l~eia~~lgl~kstv~Rll~tL~ 53 (257)
T PRK15090 27 REIGITELSQRVMMSKSTVYRFLQTMK 53 (257)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 457999999999999999999988654
No 415
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=24.94 E-value=1e+02 Score=29.51 Aligned_cols=28 Identities=25% Similarity=0.391 Sum_probs=24.1
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 364 GVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
.+-|+..|||+.+|||...|+.++.+..
T Consensus 29 ~~LPsE~eLa~~~gVSRtpVREAL~~L~ 56 (251)
T PRK09990 29 QALPSERRLCEKLGFSRSALREGLTVLR 56 (251)
T ss_pred CcCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4456999999999999999999998753
No 416
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=24.91 E-value=2.2e+02 Score=26.80 Aligned_cols=25 Identities=28% Similarity=0.383 Sum_probs=22.5
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~rar 391 (417)
+|+++||..||++.++|-++++..+
T Consensus 180 lt~~~IA~~lGisretlsR~L~~L~ 204 (230)
T PRK09391 180 MSRRDIADYLGLTIETVSRALSQLQ 204 (230)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4899999999999999999887765
No 417
>COG0350 Ada Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=24.86 E-value=1.9e+02 Score=26.87 Aligned_cols=47 Identities=21% Similarity=0.152 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHHHHcCCCccHHHHHHHcCCCH--HHHHHHHHHhCcccccc
Q 014852 348 ERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQ--KKVRNATEAIGKVFSLD 397 (417)
Q Consensus 348 e~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~--etVr~aL~rark~LSLD 397 (417)
....++.+++...+ .|...|+.|||+.+|-+. ..|-.+ ..++++++=
T Consensus 88 ~Fq~~Vw~aL~~IP-~Get~TY~eiA~~ig~p~a~rAVG~A--~~~NPl~Ii 136 (168)
T COG0350 88 GFQGRVWQALREIP-YGETVTYGEIARRLGRPTAVRAVGNA--NGANPLPII 136 (168)
T ss_pred hHHHHHHHHHhcCC-CCCcEeHHHHHHHhCCCcHHHHHHHH--hccCCceEE
Confidence 34455666655554 688899999999999932 223333 334666653
No 418
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=24.68 E-value=1.5e+02 Score=28.26 Aligned_cols=36 Identities=25% Similarity=0.424 Sum_probs=27.5
Q ss_pred HHHHHHHccCcchhHHHHHHHhhC-CCCchHHHHHHhcCChHHHHHH
Q 014852 213 RLSKKIKTGLSLDDHKLRLKERLG-CEPSMEQLAASLRISRPELQSI 258 (417)
Q Consensus 213 eLirk~k~Gd~l~~~~~~l~~~lg-~eps~~e~A~~~~~s~~eLr~~ 258 (417)
.|.++|..|.. .-| .-|+..++|+.+|+|+..+++.
T Consensus 17 ~i~~~I~~G~~----------~~g~kLPsE~eLa~~~~VSR~TvR~A 53 (241)
T PRK11402 17 RLLDDIAQGVY----------QAGQQIPTENELCTQYNVSRITIRKA 53 (241)
T ss_pred HHHHHHHcCCC----------CCCCcCcCHHHHHHHHCCCHHHHHHH
Confidence 46677777765 222 4599999999999999999953
No 419
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=24.63 E-value=1.1e+02 Score=26.69 Aligned_cols=26 Identities=27% Similarity=0.220 Sum_probs=22.4
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~rar 391 (417)
.+|+.+-|..||+|+.+|++..+..+
T Consensus 57 ~lSQ~vFA~~L~vs~~Tv~~WEqGr~ 82 (104)
T COG2944 57 GLSQPVFARYLGVSVSTVRKWEQGRK 82 (104)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHcCCc
Confidence 46999999999999999999876544
No 420
>smart00753 PAM PCI/PINT associated module.
Probab=24.56 E-value=2e+02 Score=22.71 Aligned_cols=37 Identities=22% Similarity=0.218 Sum_probs=28.0
Q ss_pred HHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 354 RNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 354 ~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~ra 390 (417)
...+..+.......+..+||+.++++.+.|...+..+
T Consensus 12 ~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~ 48 (88)
T smart00753 12 LTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKA 48 (88)
T ss_pred HHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHH
Confidence 3344455445677899999999999999988876654
No 421
>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=24.56 E-value=2e+02 Score=22.71 Aligned_cols=37 Identities=22% Similarity=0.218 Sum_probs=28.0
Q ss_pred HHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 354 RNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 354 ~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~ra 390 (417)
...+..+.......+..+||+.++++.+.|...+..+
T Consensus 12 ~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~ 48 (88)
T smart00088 12 LTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKA 48 (88)
T ss_pred HHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHH
Confidence 3344455445677899999999999999988876654
No 422
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=24.47 E-value=2.9e+02 Score=24.12 Aligned_cols=35 Identities=17% Similarity=0.185 Sum_probs=27.4
Q ss_pred CCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHH
Q 014852 238 EPSMEQLAASLRISRPELQSILMECSLAREKLVMS 272 (417)
Q Consensus 238 eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~ 272 (417)
.-+.+++|..+|++...++..+..+...+..++..
T Consensus 127 g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~~ 161 (166)
T PRK09639 127 GYSYKEIAEALGIKESSVGTTLARAKKKFRKIYEQ 161 (166)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 34689999999999999999888777665555543
No 423
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=24.36 E-value=77 Score=30.75 Aligned_cols=29 Identities=28% Similarity=0.344 Sum_probs=25.3
Q ss_pred HcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 362 EKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 362 e~gRepS~eEIAe~LGIS~etVr~aL~ra 390 (417)
.-.+-|+..|+|+.+|+|...|+.++...
T Consensus 30 ~G~~LP~EreLae~fgVSR~~vREAl~~L 58 (241)
T COG2186 30 PGDRLPSERELAERFGVSRTVVREALKRL 58 (241)
T ss_pred CCCCCCCHHHHHHHHCCCcHHHHHHHHHH
Confidence 34577899999999999999999998764
No 424
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=24.29 E-value=1.9e+02 Score=23.87 Aligned_cols=36 Identities=17% Similarity=0.197 Sum_probs=27.8
Q ss_pred HHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 354 RNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 354 ~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~ra 390 (417)
..+++.|...|| .+..+||..++.|+..|+..+.+-
T Consensus 5 ~qlRd~l~~~gr-~s~~~Ls~~~~~p~~~VeaMLe~l 40 (78)
T PRK15431 5 IQVRDLLALRGR-MEAAQISQTLNTPQPMINAMLQQL 40 (78)
T ss_pred HHHHHHHHHcCc-ccHHHHHHHHCcCHHHHHHHHHHH
Confidence 344455555555 689999999999999999988753
No 425
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=24.20 E-value=1.2e+02 Score=24.34 Aligned_cols=50 Identities=24% Similarity=0.322 Sum_probs=35.4
Q ss_pred CchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhH
Q 014852 239 PSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGG 298 (417)
Q Consensus 239 ps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG 298 (417)
-+-+++|..+|+|+..+...-.+. +.-.+.+.+.+|+-| +...||+++..
T Consensus 15 ltQ~elA~~vgVsRQTi~~iEkgk-------y~Psl~La~kia~~f---~~~iedIF~~~ 64 (68)
T COG1476 15 LTQEELAKLVGVSRQTIIAIEKGK-------YNPSLELALKIARVF---GKTIEDIFQLE 64 (68)
T ss_pred cCHHHHHHHcCcCHHHHHHHHcCC-------CCchHHHHHHHHHHh---CCCHHHHHhhh
Confidence 456888999999988876544432 223466677888877 58899998854
No 426
>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=24.11 E-value=1.8e+02 Score=24.72 Aligned_cols=26 Identities=12% Similarity=0.289 Sum_probs=20.3
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhCc
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAIGK 392 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~rark 392 (417)
-++.|||...|+|+..|.+++...+.
T Consensus 73 ~n~~eLA~kyglS~r~I~~Ii~~~~~ 98 (108)
T PF08765_consen 73 MNVRELARKYGLSERQIYRIIKRVRR 98 (108)
T ss_dssp S-HHHHHHHHT--HHHHHHHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 37999999999999999999987653
No 427
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=24.05 E-value=1.2e+02 Score=28.55 Aligned_cols=28 Identities=7% Similarity=0.064 Sum_probs=23.2
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 364 GVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
|...+..|+|+.+|||...|+.++.+..
T Consensus 28 G~~L~e~eLae~lgVSRtpVREAL~~L~ 55 (224)
T PRK11534 28 DEKLRMSLLTSRYALGVGPLREALSQLV 55 (224)
T ss_pred CCcCCHHHHHHHHCCChHHHHHHHHHHH
Confidence 4445678999999999999999988753
No 428
>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=23.82 E-value=2.8e+02 Score=25.34 Aligned_cols=24 Identities=17% Similarity=0.213 Sum_probs=20.3
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHH
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~r 389 (417)
..|+.|+|+.+||+..+|..+...
T Consensus 38 GmTq~eLAerlGVS~~tIs~iE~G 61 (150)
T TIGR02612 38 GMSGAQLAGRLGVTPQRVEALEKS 61 (150)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHcC
Confidence 458999999999999999888764
No 429
>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=23.67 E-value=80 Score=29.89 Aligned_cols=27 Identities=11% Similarity=0.431 Sum_probs=23.7
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
+-|+..+||+.+|||...|+.++.+..
T Consensus 29 ~LpsE~~La~~lgVSRtpVREAL~~Le 55 (235)
T TIGR02812 29 ILPAERELSELIGVTRTTLREVLQRLA 55 (235)
T ss_pred cCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 445899999999999999999998754
No 430
>PF09824 ArsR: ArsR transcriptional regulator; InterPro: IPR014517 Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family.
Probab=23.66 E-value=34 Score=31.80 Aligned_cols=30 Identities=33% Similarity=0.673 Sum_probs=21.9
Q ss_pred ccccccccccchhHHHHHHhhHh-HHHhhhccc
Q 014852 95 NSIEEESSELDYSVEALLLLQKS-MLEKQWNLS 126 (417)
Q Consensus 95 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~ 126 (417)
++|++.-.+ ...++|.+|.|. |+|-||..|
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 445544422 338999999885 999999988
No 431
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=23.66 E-value=1.3e+02 Score=22.15 Aligned_cols=34 Identities=15% Similarity=0.031 Sum_probs=26.5
Q ss_pred HHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhCc
Q 014852 359 RLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGK 392 (417)
Q Consensus 359 ~L~e~gRepS~eEIAe~LGIS~etVr~aL~rark 392 (417)
.|..+...++.+.||...||+..+|.++.+....
T Consensus 12 ~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~ 45 (53)
T PF13613_consen 12 TLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIP 45 (53)
T ss_pred HHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHH
Confidence 3444445679999999999999999998776543
No 432
>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=23.60 E-value=1.8e+02 Score=22.42 Aligned_cols=52 Identities=33% Similarity=0.353 Sum_probs=29.2
Q ss_pred HHHHHhhCCCCchHHHHHHhcCChHHHH-HHhhhhHHHHHHHHHHhHHHHHHHH
Q 014852 229 LRLKERLGCEPSMEQLAASLRISRPELQ-SILMECSLAREKLVMSNVRLVMSIA 281 (417)
Q Consensus 229 ~~l~~~lg~eps~~e~A~~~~~s~~eLr-~~l~~~~~Are~LIe~yl~LV~sIA 281 (417)
.+|.+.+|.. +..++|+.+|++...+. .....+.--.+.|+.-...+=+++-
T Consensus 4 ~rl~~~~g~~-~~~~lA~~lgis~st~s~~~~~r~~~P~~~l~~ia~~~gvsl~ 56 (66)
T PF07022_consen 4 ERLKEALGVK-SDKELAERLGISKSTLSNNWKKRGSIPAEWLIKIALETGVSLD 56 (66)
T ss_dssp HHHHHHHT-S-SCHHHHCCTT--HHHHH-HHHHSSS--HHHHHHHHHHH---HH
T ss_pred HHHHHHhCCC-CHHHHHHHhCcCHHHhhHHHHhCCCCCHHHHHHHHHHHCcCHH
Confidence 4566666655 66899999999999988 6666654445555544443333333
No 433
>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=23.55 E-value=48 Score=26.59 Aligned_cols=31 Identities=19% Similarity=0.267 Sum_probs=24.3
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
...++.+++|+.+++|..++.+.+..+++.+
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 5567999999999999999999998877544
No 434
>PRK04217 hypothetical protein; Provisional
Probab=23.40 E-value=3.7e+02 Score=23.40 Aligned_cols=49 Identities=16% Similarity=0.247 Sum_probs=34.2
Q ss_pred CCCCHHHHHHHHHHHH-ccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHH
Q 014852 204 ELLTHAEVVRLSKKIK-TGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (417)
Q Consensus 204 ~lLt~~eE~eLirk~k-~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LI 270 (417)
..|+.++ .+++.... .|. +.+|+|+.+|+|...+...+......+.+.+
T Consensus 41 ~~Lt~ee-reai~l~~~eGl-----------------S~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 41 IFMTYEE-FEALRLVDYEGL-----------------TQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred ccCCHHH-HHHHHHHHHcCC-----------------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4466666 46665554 332 6889999999999999998887655444433
No 435
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=23.38 E-value=3.3e+02 Score=23.81 Aligned_cols=31 Identities=16% Similarity=0.142 Sum_probs=24.0
Q ss_pred chHHHHHHhcCChHHHHHHhhhhHHHHHHHH
Q 014852 240 SMEQLAASLRISRPELQSILMECSLAREKLV 270 (417)
Q Consensus 240 s~~e~A~~~~~s~~eLr~~l~~~~~Are~LI 270 (417)
+.+++|..+|++...+...+.....-+.+.+
T Consensus 146 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 146 SYEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5789999999999999888876555444443
No 436
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.00 E-value=93 Score=27.05 Aligned_cols=27 Identities=26% Similarity=0.336 Sum_probs=23.4
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhCc
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATEAIGK 392 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~rark 392 (417)
..|..|||+..+||.+.|...+.++-.
T Consensus 33 DlSl~EIAee~~VSRqAIyDnIKr~~~ 59 (105)
T COG2739 33 DLSLSEIAEEFNVSRQAIYDNIKRTEK 59 (105)
T ss_pred hccHHHHHHHhCccHHHHHHHHHHHHH
Confidence 359999999999999999998887654
No 437
>PF06784 UPF0240: Uncharacterised protein family (UPF0240); InterPro: IPR009622 This is a group of proteins of unknown function.
Probab=22.82 E-value=1.5e+02 Score=27.88 Aligned_cols=39 Identities=23% Similarity=0.402 Sum_probs=32.9
Q ss_pred HHHHHHHHHHcCCCc---cHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 353 IRNAKLRLEEKGVTP---SVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 353 I~~a~~~L~e~gRep---S~eEIAe~LGIS~etVr~aL~rar 391 (417)
+..|+.-|...+..| |.+-||+..++.++.|++++..-.
T Consensus 120 l~qal~lL~~Hq~~P~~WtaekIA~eY~L~~~dv~~iL~yF~ 161 (179)
T PF06784_consen 120 LRQALELLNNHQLDPETWTAEKIAQEYKLDEKDVKNILKYFK 161 (179)
T ss_pred HHHHHHHHHHhccCccccCHHHHHHHhCCCHHHHHHHHHhcC
Confidence 567777777767777 799999999999999999998764
No 438
>PRK11050 manganese transport regulator MntR; Provisional
Probab=22.69 E-value=2.2e+02 Score=25.61 Aligned_cols=29 Identities=21% Similarity=0.139 Sum_probs=24.3
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCc
Q 014852 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGK 392 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~aL~rark 392 (417)
+-..+..|||+.||++..+|..++.....
T Consensus 49 ~~~~t~~eLA~~l~is~stVsr~l~~Le~ 77 (152)
T PRK11050 49 VGEARQVDIAARLGVSQPTVAKMLKRLAR 77 (152)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 33568999999999999999999877653
No 439
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=22.56 E-value=3.4e+02 Score=23.64 Aligned_cols=35 Identities=20% Similarity=0.128 Sum_probs=28.0
Q ss_pred CchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHh
Q 014852 239 PSMEQLAASLRISRPELQSILMECSLAREKLVMSN 273 (417)
Q Consensus 239 ps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~y 273 (417)
-+.+|+|..+|+|...++..+.....+....+..+
T Consensus 122 ~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~~~ 156 (159)
T PRK12527 122 LSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQW 156 (159)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 35899999999999999999888777666655543
No 440
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=22.52 E-value=7.1e+02 Score=24.06 Aligned_cols=33 Identities=12% Similarity=0.051 Sum_probs=19.1
Q ss_pred CCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHH
Q 014852 288 GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYV 321 (417)
Q Consensus 288 g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA 321 (417)
....+++-+.-.|..-.-..-|... |..|..|+
T Consensus 214 ~ls~~~lA~~~giS~r~L~r~Fk~~-G~T~~~yi 246 (302)
T PRK09685 214 ILRPEWIAGELGISVRSLYRLFAEQ-GLVVAQYI 246 (302)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHc-CCCHHHHH
Confidence 4677777777666554444455443 55555553
No 441
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=22.51 E-value=3.2e+02 Score=23.80 Aligned_cols=34 Identities=15% Similarity=0.101 Sum_probs=26.6
Q ss_pred CchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHH
Q 014852 239 PSMEQLAASLRISRPELQSILMECSLAREKLVMS 272 (417)
Q Consensus 239 ps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~ 272 (417)
-+.+++|..+|+|...++..+......+.+.+..
T Consensus 142 ~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~~ 175 (179)
T PRK11924 142 LSYREIAEILGVPVGTVKSRLRRARQLLRECLEA 175 (179)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 3578999999999999999888776655555543
No 442
>PRK14999 histidine utilization repressor; Provisional
Probab=22.49 E-value=1.8e+02 Score=27.66 Aligned_cols=44 Identities=27% Similarity=0.251 Sum_probs=32.5
Q ss_pred HHHHHHHHccCcchhHHHHHHHhhC-CCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHH
Q 014852 212 VRLSKKIKTGLSLDDHKLRLKERLG-CEPSMEQLAASLRISRPELQSILMECSLAREKLVMS 272 (417)
Q Consensus 212 ~eLirk~k~Gd~l~~~~~~l~~~lg-~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~ 272 (417)
..|..+|..|.. .-| +-|+..++|+.+|+|+..++ .|.+.|...
T Consensus 19 ~~i~~~I~~g~~----------~~G~~LPsE~eLa~~~gVSR~TVR-------~Al~~L~~e 63 (241)
T PRK14999 19 QDICKKIAGGVW----------QPHDRIPSEAELVAQYGFSRMTIN-------RALRELTDE 63 (241)
T ss_pred HHHHHHHHcCCC----------CCCCcCCCHHHHHHHHCCCHHHHH-------HHHHHHHHC
Confidence 356677777765 334 46999999999999999999 455555544
No 443
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=22.49 E-value=94 Score=27.27 Aligned_cols=27 Identities=11% Similarity=0.069 Sum_probs=23.6
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
..++.+|||+.+++|...+++++....
T Consensus 24 ~~~s~~~ia~~~~ip~~~l~kil~~L~ 50 (135)
T TIGR02010 24 GPVTLADISERQGISLSYLEQLFAKLR 50 (135)
T ss_pred CcCcHHHHHHHHCcCHHHHHHHHHHHH
Confidence 346999999999999999999987654
No 444
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=22.33 E-value=3e+02 Score=25.70 Aligned_cols=36 Identities=17% Similarity=0.177 Sum_probs=29.0
Q ss_pred chHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHH
Q 014852 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVR 275 (417)
Q Consensus 240 s~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~ 275 (417)
+.+|+|..+|++...++..+......+.+.+..+.|
T Consensus 156 s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~~~~~ 191 (203)
T PRK09647 156 SYEEIAATLGVKLGTVRSRIHRGRQQLRAALAAHAP 191 (203)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhch
Confidence 579999999999999999888887766666655444
No 445
>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=22.29 E-value=99 Score=20.65 Aligned_cols=24 Identities=17% Similarity=0.279 Sum_probs=20.4
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHH
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~r 389 (417)
..+..++|+.+|++..+|...+..
T Consensus 12 ~~s~~~~a~~~~~~~~~v~~~~~g 35 (58)
T cd00093 12 GLTQEELAEKLGVSRSTISRIENG 35 (58)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHcC
Confidence 458999999999999999887653
No 446
>PRK01381 Trp operon repressor; Provisional
Probab=22.28 E-value=81 Score=27.18 Aligned_cols=21 Identities=14% Similarity=0.143 Sum_probs=17.7
Q ss_pred CccHHHHHHHcCCCHHHHHHH
Q 014852 366 TPSVDRIAEYLNMSQKKVRNA 386 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~a 386 (417)
+.|+.|||+.||++.-+|-.-
T Consensus 55 ~~sQREIa~~lGvSiaTITRg 75 (99)
T PRK01381 55 ELSQREIKQELGVGIATITRG 75 (99)
T ss_pred CcCHHHHHHHhCCceeeehhh
Confidence 469999999999998887543
No 447
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=22.21 E-value=1.5e+02 Score=25.84 Aligned_cols=26 Identities=23% Similarity=0.355 Sum_probs=23.2
Q ss_pred CccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 366 epS~eEIAe~LGIS~etVr~aL~rar 391 (417)
.+|+.|||+.|.+|...++.+++...
T Consensus 19 ~vtl~elA~~l~cS~Rn~r~lLkkm~ 44 (115)
T PF12793_consen 19 EVTLDELAELLFCSRRNARTLLKKMQ 44 (115)
T ss_pred ceeHHHHHHHhCCCHHHHHHHHHHHH
Confidence 45999999999999999999988754
No 448
>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=22.08 E-value=1.8e+02 Score=27.52 Aligned_cols=43 Identities=26% Similarity=0.270 Sum_probs=31.3
Q ss_pred HHHHHHHccCcchhHHHHHHHhhC-CCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHH
Q 014852 213 RLSKKIKTGLSLDDHKLRLKERLG-CEPSMEQLAASLRISRPELQSILMECSLAREKLVMS 272 (417)
Q Consensus 213 eLirk~k~Gd~l~~~~~~l~~~lg-~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~ 272 (417)
.|.++|..|.. .-| +-|+..++|+.+|+|+..++ .|++.|...
T Consensus 9 ~l~~~I~~g~~----------~~g~~LPsE~eLa~~~~VSR~TVR-------~Al~~L~~e 52 (230)
T TIGR02018 9 DILERIRSGEW----------PPGHRIPSEHELVAQYGCSRMTVN-------RALRELTDA 52 (230)
T ss_pred HHHHHHHhCCC----------CCCCcCcCHHHHHHHHCCCHHHHH-------HHHHHHHHC
Confidence 35566666654 223 35999999999999999999 566666655
No 449
>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=22.08 E-value=2e+02 Score=20.87 Aligned_cols=21 Identities=19% Similarity=0.404 Sum_probs=18.3
Q ss_pred cHHHHHHHcCCCHHHHHHHHH
Q 014852 368 SVDRIAEYLNMSQKKVRNATE 388 (417)
Q Consensus 368 S~eEIAe~LGIS~etVr~aL~ 388 (417)
..++||+.|||+...|.....
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 578999999999999988654
No 450
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=22.03 E-value=1.4e+02 Score=28.66 Aligned_cols=27 Identities=30% Similarity=0.267 Sum_probs=23.2
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
+-|+..+||+.+|||...|+.++....
T Consensus 31 ~LpsE~eLae~~gVSRtpVREAL~~L~ 57 (253)
T PRK11523 31 KLPAERFIADEKNVSRTVVREAIIMLE 57 (253)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 445799999999999999999998743
No 451
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=22.00 E-value=62 Score=29.26 Aligned_cols=27 Identities=15% Similarity=0.087 Sum_probs=21.2
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
+..|++|||++||-+...|.-+.++|+
T Consensus 22 kG~tQ~eIA~~L~TTraNvSaIEkrA~ 48 (143)
T COG1356 22 KGLTQSEIARILKTTRANVSAIEKRAL 48 (143)
T ss_pred ccccHHHHHHHHccchhhHHHHHHHHH
Confidence 445999999999999888866655543
No 452
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=21.98 E-value=1e+02 Score=25.29 Aligned_cols=29 Identities=24% Similarity=0.297 Sum_probs=24.8
Q ss_pred cCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 363 KGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 363 ~gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
.+.-.|-++||+.||||...|-..++..+
T Consensus 16 ~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr 44 (79)
T COG1654 16 TGNFVSGEKLAEELGISRTAVWKHIQQLR 44 (79)
T ss_pred CCCcccHHHHHHHHCccHHHHHHHHHHHH
Confidence 35557999999999999999988887766
No 453
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=21.96 E-value=1.7e+02 Score=24.19 Aligned_cols=34 Identities=15% Similarity=0.114 Sum_probs=27.1
Q ss_pred HHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhh
Q 014852 228 KLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (417)
Q Consensus 228 ~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~ 261 (417)
..-+.+.+..+++.+++|..+++|...|.+...+
T Consensus 11 ~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~ 44 (107)
T PRK10219 11 IAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRT 44 (107)
T ss_pred HHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3445667778899999999999999888776654
No 454
>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=21.96 E-value=3e+02 Score=19.56 Aligned_cols=24 Identities=33% Similarity=0.498 Sum_probs=19.3
Q ss_pred CCchHHHHHHhcCChHHHHHHhhh
Q 014852 238 EPSMEQLAASLRISRPELQSILME 261 (417)
Q Consensus 238 eps~~e~A~~~~~s~~eLr~~l~~ 261 (417)
+-+..|+|..+|+|...++.....
T Consensus 20 ~~t~~eIa~~lg~s~~~V~~~~~~ 43 (50)
T PF04545_consen 20 GLTLEEIAERLGISRSTVRRILKR 43 (50)
T ss_dssp T-SHHHHHHHHTSCHHHHHHHHHH
T ss_pred CCCHHHHHHHHCCcHHHHHHHHHH
Confidence 346899999999999998876554
No 455
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=21.73 E-value=97 Score=28.12 Aligned_cols=31 Identities=16% Similarity=0.019 Sum_probs=26.8
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVF 394 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~aL~rark~L 394 (417)
+...|..|||+++|++..||...+.+.+..=
T Consensus 19 ~~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G 49 (138)
T COG3415 19 GEGLSCREAAKRFGVSISTVYRWVRRYRETG 49 (138)
T ss_pred HcCccHHHHHHHhCccHHHHHHHHHHhcccc
Confidence 4456999999999999999999999987543
No 456
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=21.69 E-value=2.5e+02 Score=26.51 Aligned_cols=35 Identities=20% Similarity=0.205 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHHH
Q 014852 351 GLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRN 385 (417)
Q Consensus 351 ~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~ 385 (417)
.-+..+...+.+.|-..|.++||+..|++..+|..
T Consensus 17 ~Il~aA~~lF~~~Gy~~s~~~IA~~AGvsk~tiy~ 51 (225)
T PRK11552 17 QLIAAALAQFGEYGLHATTRDIAAQAGQNIAAITY 51 (225)
T ss_pred HHHHHHHHHHHHhCccCCHHHHHHHhCCCHHHHHH
Confidence 34555555566666448999999999999999954
No 457
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=21.66 E-value=1.6e+02 Score=27.54 Aligned_cols=33 Identities=18% Similarity=0.158 Sum_probs=24.5
Q ss_pred HHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHH
Q 014852 355 NAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATE 388 (417)
Q Consensus 355 ~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~ 388 (417)
..+..|.. ....+..++|+.+|+|..||+.-+.
T Consensus 11 ~Il~~l~~-~~~~~~~~La~~~~vS~~TiRRDl~ 43 (185)
T PRK04424 11 ALQELIEE-NPFITDEELAEKFGVSIQTIRLDRM 43 (185)
T ss_pred HHHHHHHH-CCCEEHHHHHHHHCcCHHHHHHHHH
Confidence 33344444 4457999999999999999987553
No 458
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=21.62 E-value=97 Score=25.28 Aligned_cols=22 Identities=18% Similarity=0.154 Sum_probs=19.8
Q ss_pred cHHHHHHHcCCCHHHHHHHHHH
Q 014852 368 SVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 368 S~eEIAe~LGIS~etVr~aL~r 389 (417)
++.|+|+.+||++.+++.....
T Consensus 3 ~i~e~A~~~gvs~~tLr~ye~~ 24 (91)
T cd04766 3 VISVAAELSGMHPQTLRLYERL 24 (91)
T ss_pred CHHHHHHHHCcCHHHHHHHHHC
Confidence 6889999999999999998764
No 459
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=21.55 E-value=2.8e+02 Score=25.05 Aligned_cols=35 Identities=17% Similarity=0.106 Sum_probs=27.7
Q ss_pred CchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHh
Q 014852 239 PSMEQLAASLRISRPELQSILMECSLAREKLVMSN 273 (417)
Q Consensus 239 ps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~y 273 (417)
-+..|+|..+|+|...++..+......+...+..|
T Consensus 158 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~ 192 (194)
T PRK12519 158 LSQSEIAKRLGIPLGTVKARARQGLLKLRELLQDL 192 (194)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 46899999999999999998887766655555443
No 460
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=21.47 E-value=2.8e+02 Score=25.45 Aligned_cols=60 Identities=15% Similarity=0.231 Sum_probs=33.9
Q ss_pred HhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHHHcCC-CccHHHHHHHcCCCHHHHHHHHHH
Q 014852 326 RQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGV-TPSVDRIAEYLNMSQKKVRNATEA 389 (417)
Q Consensus 326 R~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~e~gR-epS~eEIAe~LGIS~etVr~aL~r 389 (417)
|+...+.++++.+ .+|....+. -+........+.+. ..|.+||.+.||-|.+-.++.+..
T Consensus 3 k~efL~~L~~~L~--~lp~~e~~e--~l~~Y~e~f~d~~~~G~sEeeii~~LG~P~~iA~~i~~~ 63 (181)
T PF08006_consen 3 KNEFLNELEKYLK--KLPEEEREE--ILEYYEEYFDDAGEEGKSEEEIIAELGSPKEIAREILAE 63 (181)
T ss_pred HHHHHHHHHHHHH--cCCHHHHHH--HHHHHHHHHHHhhhCCCCHHHHHHHcCCHHHHHHHHHHh
Confidence 3445555555543 356553322 23333333332221 238999999999998888887643
No 461
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=21.25 E-value=1.7e+02 Score=28.57 Aligned_cols=26 Identities=31% Similarity=0.349 Sum_probs=22.7
Q ss_pred CCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852 365 VTPSVDRIAEYLNMSQKKVRNATEAI 390 (417)
Q Consensus 365 RepS~eEIAe~LGIS~etVr~aL~ra 390 (417)
-..|..|||+.|||+...|+..|...
T Consensus 24 g~~sa~elA~~Lgis~~avR~HL~~L 49 (218)
T COG2345 24 GPVSADELAEELGISPMAVRRHLDDL 49 (218)
T ss_pred CCccHHHHHHHhCCCHHHHHHHHHHH
Confidence 34599999999999999999998764
No 462
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=21.19 E-value=1.7e+02 Score=28.83 Aligned_cols=38 Identities=18% Similarity=0.239 Sum_probs=29.0
Q ss_pred HHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 354 RNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 354 ~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
+.....+...+...|-+|+|+.+|+|.-+++..+..+-
T Consensus 161 ~~i~~~~~~~~~~~Taeela~~~giSRvTaRRYLeyl~ 198 (224)
T COG4565 161 QKVREALKEPDQELTAEELAQALGISRVTARRYLEYLV 198 (224)
T ss_pred HHHHHHHhCcCCccCHHHHHHHhCccHHHHHHHHHHHH
Confidence 33333444445667999999999999999999998764
No 463
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=21.16 E-value=2.5e+02 Score=25.71 Aligned_cols=25 Identities=8% Similarity=0.108 Sum_probs=21.1
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHH
Q 014852 364 GVTPSVDRIAEYLNMSQKKVRNATE 388 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~aL~ 388 (417)
.+..|++++|+.+|++..+|.++.+
T Consensus 80 ~~glSqeeLA~~lgvs~s~IsriE~ 104 (154)
T TIGR00270 80 KRGWSQEQLAKKIQEKESLIKKIEN 104 (154)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 4567999999999999999988753
No 464
>cd00131 PAX Paired Box domain
Probab=21.07 E-value=2.2e+02 Score=25.10 Aligned_cols=30 Identities=17% Similarity=-0.002 Sum_probs=25.7
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAIGKVFSL 396 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~rark~LSL 396 (417)
.+..+||+.+||+..+|...+.+.+..=++
T Consensus 34 ~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v 63 (128)
T cd00131 34 IRPCDISRQLRVSHGCVSKILNRYYETGSI 63 (128)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHcCCc
Confidence 489999999999999999999987754444
No 465
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=21.01 E-value=1e+02 Score=22.57 Aligned_cols=25 Identities=16% Similarity=0.210 Sum_probs=20.2
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 367 PSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 367 pS~eEIAe~LGIS~etVr~aL~rar 391 (417)
.+.+|+++.+|++..++...+....
T Consensus 4 l~~~ev~~~~g~s~~ti~~~~k~g~ 28 (51)
T PF05930_consen 4 LRIKEVAELLGVSRSTIYRLIKDGK 28 (51)
T ss_dssp E-HHHHHHHHSS-HHHHHHHHHHHH
T ss_pred ccHHHHHHHHCCCHHHHHHHHhccc
Confidence 4689999999999999999988654
No 466
>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=20.96 E-value=97 Score=28.67 Aligned_cols=28 Identities=32% Similarity=0.362 Sum_probs=24.1
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 364 GVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
|...+..++|+.+|||...|+.++.+..
T Consensus 32 G~~L~e~~La~~lgVSRtpVReAL~~L~ 59 (212)
T TIGR03338 32 GAKLNESDIAARLGVSRGPVREAFRALE 59 (212)
T ss_pred CCEecHHHHHHHhCCChHHHHHHHHHHH
Confidence 4455889999999999999999998754
No 467
>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=20.89 E-value=5.2e+02 Score=22.25 Aligned_cols=41 Identities=20% Similarity=0.210 Sum_probs=26.9
Q ss_pred CCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHH
Q 014852 238 EPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMS 279 (417)
Q Consensus 238 eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~s 279 (417)
.-|..|+|..+|+|+..+...+..+...+ .=++.-+.++..
T Consensus 33 DlSlsEIAe~~~iSRqaV~d~ikr~~~~L-~~yE~kL~l~~k 73 (101)
T PF04297_consen 33 DLSLSEIAEELGISRQAVYDSIKRAEKKL-EEYEEKLGLVEK 73 (101)
T ss_dssp ---HHHHHHHCTS-HHHHHHHHHHHHHHH-HHHHHHH-HHHH
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHH-HHHHHHHhhHHH
Confidence 35899999999999999999998877655 233444444443
No 468
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=20.78 E-value=2.2e+02 Score=27.91 Aligned_cols=39 Identities=13% Similarity=0.158 Sum_probs=28.8
Q ss_pred HHHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 353 IRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 353 I~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
|.+...+-.+.|-.+|..++|-.||+|..||++.+..-.
T Consensus 92 IvRl~~EAy~QgglLT~~Dla~LL~~S~~TI~~~i~~yq 130 (220)
T PF07900_consen 92 IVRLTNEAYDQGGLLTQEDLAMLLGISPRTISKDIKEYQ 130 (220)
T ss_pred HHHHHHHHHHcCCcccHHHHHHHHCCCHHHHHHHHHHHH
Confidence 333333333456678999999999999999998876554
No 469
>PRK08359 transcription factor; Validated
Probab=20.75 E-value=2.2e+02 Score=26.93 Aligned_cols=24 Identities=13% Similarity=0.195 Sum_probs=20.6
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHH
Q 014852 364 GVTPSVDRIAEYLNMSQKKVRNAT 387 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~aL 387 (417)
.+..|++|+|+.+|++..+|..+.
T Consensus 96 ~kglSQeeLA~~lgvs~stI~~iE 119 (176)
T PRK08359 96 KSGLSYEELSHEVGLSVNDLRRIA 119 (176)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHH
Confidence 456799999999999999998763
No 470
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=20.34 E-value=88 Score=29.30 Aligned_cols=24 Identities=25% Similarity=0.407 Sum_probs=21.2
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 368 SVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 368 S~eEIAe~LGIS~etVr~aL~rar 391 (417)
+.++||..||++.++|..+++..+
T Consensus 175 t~~~iA~~lG~tretvsR~l~~L~ 198 (236)
T PRK09392 175 EKRVLASYLGMTPENLSRAFAALA 198 (236)
T ss_pred CHHHHHHHhCCChhHHHHHHHHHH
Confidence 689999999999999999887654
No 471
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=20.26 E-value=1.4e+02 Score=28.03 Aligned_cols=28 Identities=32% Similarity=0.299 Sum_probs=22.8
Q ss_pred CCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852 364 GVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (417)
Q Consensus 364 gRepS~eEIAe~LGIS~etVr~aL~rar 391 (417)
|-..+..+||+.+|||...|+.++.+..
T Consensus 32 G~~L~e~~La~~lgVSRtpVREAL~~L~ 59 (221)
T PRK11414 32 GARLITKNLAEQLGMSITPVREALLRLV 59 (221)
T ss_pred CCccCHHHHHHHHCCCchhHHHHHHHHH
Confidence 3334568999999999999999998764
Done!