Query 011992
Match_columns 473
No_of_seqs 379 out of 2636
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 07:28:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011992.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011992hhsearch_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 1.9E-38 4.2E-43 331.4 25.4 219 254-472 59-414 (415)
2 TIGR02997 Sig70-cyanoRpoD RNA 100.0 6.8E-36 1.5E-40 300.9 24.0 202 256-457 2-298 (298)
3 PRK05949 RNA polymerase sigma 100.0 1.4E-35 3E-40 302.9 25.3 215 254-470 17-326 (327)
4 PRK07405 RNA polymerase sigma 100.0 2.6E-35 5.6E-40 299.6 25.0 215 254-470 7-316 (317)
5 PRK07406 RNA polymerase sigma 100.0 1.8E-35 3.9E-40 306.4 24.1 215 255-469 63-372 (373)
6 PRK07921 RNA polymerase sigma 100.0 4.8E-31 1E-35 269.2 21.1 203 254-469 25-323 (324)
7 PRK05901 RNA polymerase sigma 100.0 3.9E-31 8.5E-36 282.6 20.2 209 246-470 205-509 (509)
8 COG0568 RpoD DNA-directed RNA 100.0 2.9E-28 6.2E-33 248.4 21.5 216 255-470 9-342 (342)
9 PRK09210 RNA polymerase sigma 100.0 2E-28 4.4E-33 253.7 19.1 177 254-470 95-367 (367)
10 PRK05658 RNA polymerase sigma 99.9 2.7E-24 5.8E-29 236.4 20.9 165 306-470 351-618 (619)
11 TIGR02393 RpoD_Cterm RNA polym 99.9 1.3E-24 2.7E-29 212.1 12.8 192 223-470 43-238 (238)
12 COG1191 FliA DNA-directed RNA 99.9 1.7E-24 3.6E-29 213.1 12.8 178 223-462 67-246 (247)
13 PRK05657 RNA polymerase sigma 99.9 1.7E-23 3.8E-28 213.8 19.6 171 256-466 54-320 (325)
14 TIGR02392 rpoH_proteo alternat 99.9 3.9E-23 8.5E-28 205.6 19.3 165 256-461 2-269 (270)
15 PRK06596 RNA polymerase factor 99.9 5.6E-23 1.2E-27 206.2 19.6 169 253-462 12-282 (284)
16 PRK07500 rpoH2 RNA polymerase 99.9 8.5E-23 1.8E-27 205.5 20.0 168 256-464 7-281 (289)
17 TIGR02394 rpoS_proteo RNA poly 99.9 7.8E-23 1.7E-27 204.8 19.2 171 255-465 13-279 (285)
18 PRK05803 sporulation sigma fac 99.9 2.1E-21 4.5E-26 188.8 19.3 167 256-462 17-229 (233)
19 PRK07122 RNA polymerase sigma 99.9 5.8E-22 1.3E-26 197.0 14.1 178 224-461 84-264 (264)
20 PRK05911 RNA polymerase sigma 99.9 9.3E-22 2E-26 194.6 13.0 184 223-462 69-255 (257)
21 PRK08215 sporulation sigma fac 99.9 9.4E-21 2E-25 187.0 18.4 154 263-460 12-257 (258)
22 TIGR02850 spore_sigG RNA polym 99.9 1.1E-20 2.4E-25 186.2 17.9 153 264-460 10-254 (254)
23 TIGR02941 Sigma_B RNA polymera 99.9 3E-20 6.5E-25 182.8 19.1 131 326-460 27-253 (255)
24 PRK07408 RNA polymerase sigma 99.9 1.8E-20 3.9E-25 185.3 17.6 133 327-463 24-254 (256)
25 PRK08583 RNA polymerase sigma 99.8 3.9E-20 8.6E-25 182.2 19.0 133 326-462 27-255 (257)
26 PRK06288 RNA polymerase sigma 99.8 5.5E-20 1.2E-24 182.6 18.6 158 263-463 5-263 (268)
27 PRK05602 RNA polymerase sigma 99.8 7.7E-20 1.7E-24 170.8 16.8 147 314-465 5-181 (186)
28 TIGR02846 spore_sigmaK RNA pol 99.8 1.4E-19 3E-24 175.5 18.9 136 325-460 45-226 (227)
29 PRK07670 RNA polymerase sigma 99.8 2.7E-19 5.9E-24 175.9 17.3 143 315-461 7-250 (251)
30 PRK09646 RNA polymerase sigma 99.8 3.6E-19 7.8E-24 167.9 16.7 143 316-462 17-192 (194)
31 PRK08301 sporulation sigma fac 99.8 6E-19 1.3E-23 171.2 16.9 147 316-462 39-232 (234)
32 TIGR02835 spore_sigmaE RNA pol 99.8 1E-18 2.2E-23 170.2 17.9 147 316-462 39-232 (234)
33 PRK09648 RNA polymerase sigma 99.8 1.1E-18 2.4E-23 163.4 17.4 139 318-461 13-188 (189)
34 PRK06986 fliA flagellar biosyn 99.8 7.8E-19 1.7E-23 170.9 16.3 134 325-462 5-234 (236)
35 PRK12513 RNA polymerase sigma 99.8 7E-19 1.5E-23 165.4 15.0 145 315-465 12-192 (194)
36 TIGR02952 Sig70_famx2 RNA poly 99.8 1.3E-18 2.9E-23 158.8 16.3 132 324-460 7-170 (170)
37 TIGR02980 SigBFG RNA polymeras 99.8 1E-18 2.2E-23 168.7 16.2 130 327-460 2-226 (227)
38 PRK12514 RNA polymerase sigma 99.8 1.3E-18 2.8E-23 161.3 16.2 142 315-461 5-178 (179)
39 PRK05572 sporulation sigma fac 99.8 1.8E-18 3.9E-23 170.2 17.8 132 326-461 30-251 (252)
40 PRK12427 flagellar biosynthesi 99.8 3.5E-19 7.5E-24 173.8 12.5 169 224-459 62-230 (231)
41 TIGR02885 spore_sigF RNA polym 99.8 1.2E-18 2.5E-23 168.8 15.9 133 324-460 7-231 (231)
42 PRK12538 RNA polymerase sigma 99.8 1.5E-18 3.3E-23 169.6 16.8 146 314-464 48-223 (233)
43 PRK12524 RNA polymerase sigma 99.8 1.9E-18 4.1E-23 163.2 16.7 146 314-464 11-188 (196)
44 PRK09641 RNA polymerase sigma 99.8 2.2E-18 4.7E-23 160.0 16.7 143 313-461 2-185 (187)
45 PRK06811 RNA polymerase factor 99.8 2.4E-18 5.2E-23 161.7 17.0 145 313-462 2-181 (189)
46 TIGR02948 SigW_bacill RNA poly 99.8 2.2E-18 4.8E-23 159.9 16.3 140 317-462 6-186 (187)
47 TIGR02939 RpoE_Sigma70 RNA pol 99.8 3.1E-18 6.8E-23 159.3 16.8 141 315-461 6-187 (190)
48 PRK12537 RNA polymerase sigma 99.8 2.6E-18 5.6E-23 160.3 16.0 141 315-460 9-181 (182)
49 PRK08295 RNA polymerase factor 99.8 4E-18 8.6E-23 161.3 17.5 149 311-464 6-206 (208)
50 PRK06759 RNA polymerase factor 99.8 2E-18 4.4E-23 155.7 14.7 127 327-459 3-153 (154)
51 PRK13919 putative RNA polymera 99.8 3.4E-18 7.4E-23 159.3 16.3 143 315-462 9-185 (186)
52 PRK12542 RNA polymerase sigma 99.8 1.5E-18 3.3E-23 162.1 13.6 141 325-469 6-179 (185)
53 PRK12534 RNA polymerase sigma 99.8 3.6E-18 7.8E-23 159.4 15.4 140 317-461 13-186 (187)
54 PRK12515 RNA polymerase sigma 99.8 4.7E-18 1E-22 159.3 15.5 146 314-465 7-184 (189)
55 TIGR02479 FliA_WhiG RNA polyme 99.8 2.3E-18 4.9E-23 166.3 13.4 181 224-460 43-223 (224)
56 PRK09652 RNA polymerase sigma 99.8 4.9E-18 1.1E-22 155.7 15.0 132 324-461 6-177 (182)
57 PRK11923 algU RNA polymerase s 99.8 1E-17 2.2E-22 157.1 17.1 141 316-462 7-188 (193)
58 PRK12519 RNA polymerase sigma 99.8 6.5E-18 1.4E-22 158.6 15.5 140 316-461 16-190 (194)
59 PRK09638 RNA polymerase sigma 99.8 6.4E-18 1.4E-22 155.9 14.8 144 312-461 1-175 (176)
60 PRK09643 RNA polymerase sigma 99.8 1.5E-17 3.4E-22 156.9 17.2 145 313-463 11-185 (192)
61 TIGR02954 Sig70_famx3 RNA poly 99.8 1.3E-17 2.8E-22 153.3 16.1 141 314-461 1-168 (169)
62 TIGR02859 spore_sigH RNA polym 99.8 2E-17 4.3E-22 155.2 17.0 142 314-460 4-197 (198)
63 PRK12543 RNA polymerase sigma 99.8 1E-17 2.2E-22 156.0 14.8 132 325-463 4-168 (179)
64 PRK11924 RNA polymerase sigma 99.8 1.6E-17 3.4E-22 151.9 15.6 134 324-463 9-176 (179)
65 PRK09415 RNA polymerase factor 99.8 1.7E-17 3.6E-22 154.7 15.7 130 327-462 15-177 (179)
66 PRK09640 RNA polymerase sigma 99.8 9.6E-18 2.1E-22 157.3 13.3 144 313-462 7-184 (188)
67 PRK11922 RNA polymerase sigma 99.8 2E-17 4.3E-22 160.7 16.0 142 315-462 16-199 (231)
68 PRK12531 RNA polymerase sigma 99.7 2E-17 4.4E-22 156.0 15.2 141 319-464 17-193 (194)
69 TIGR02985 Sig70_bacteroi1 RNA 99.7 2.3E-17 5E-22 148.1 14.8 127 328-460 1-161 (161)
70 PRK09645 RNA polymerase sigma 99.7 2.2E-17 4.8E-22 152.1 14.9 134 326-464 7-170 (173)
71 TIGR03001 Sig-70_gmx1 RNA poly 99.7 3.1E-17 6.7E-22 161.6 16.7 148 311-464 21-213 (244)
72 PRK12526 RNA polymerase sigma 99.7 6.4E-17 1.4E-21 154.4 17.4 134 325-463 35-204 (206)
73 PRK12529 RNA polymerase sigma 99.7 4.3E-17 9.2E-22 152.0 14.9 134 324-461 9-176 (178)
74 PRK12520 RNA polymerase sigma 99.7 3.7E-17 7.9E-22 153.5 14.0 130 329-464 3-183 (191)
75 TIGR02989 Sig-70_gvs1 RNA poly 99.7 5.1E-17 1.1E-21 147.1 14.2 127 328-460 1-159 (159)
76 PRK12539 RNA polymerase sigma 99.7 1.1E-16 2.3E-21 149.7 16.5 142 316-463 8-182 (184)
77 PRK12522 RNA polymerase sigma 99.7 8.4E-17 1.8E-21 148.6 15.4 129 328-462 3-169 (173)
78 PRK09642 RNA polymerase sigma 99.7 4.2E-17 9.1E-22 148.4 12.8 123 335-464 2-158 (160)
79 TIGR02984 Sig-70_plancto1 RNA 99.7 1.2E-16 2.5E-21 148.4 15.9 133 325-461 4-189 (189)
80 TIGR02999 Sig-70_X6 RNA polyme 99.7 1.3E-16 2.9E-21 148.0 15.7 139 316-460 4-182 (183)
81 PRK12512 RNA polymerase sigma 99.7 1.7E-16 3.6E-21 147.8 16.4 139 319-463 12-182 (184)
82 PRK12518 RNA polymerase sigma 99.7 7.3E-17 1.6E-21 148.7 13.6 135 323-464 6-172 (175)
83 PRK09649 RNA polymerase sigma 99.7 1.2E-16 2.7E-21 149.9 14.9 139 319-464 14-182 (185)
84 COG1595 RpoE DNA-directed RNA 99.7 2E-16 4.3E-21 147.8 16.1 137 321-463 8-178 (182)
85 PRK12516 RNA polymerase sigma 99.7 1E-16 2.2E-21 151.1 14.3 133 326-464 8-168 (187)
86 PRK09644 RNA polymerase sigma 99.7 1.4E-16 3E-21 146.1 14.7 129 330-465 3-161 (165)
87 PRK12533 RNA polymerase sigma 99.7 1.9E-16 4E-21 153.3 16.1 131 326-463 16-185 (216)
88 PRK12523 RNA polymerase sigma 99.7 1.6E-16 3.4E-21 146.9 14.8 130 327-463 9-170 (172)
89 TIGR02983 SigE-fam_strep RNA p 99.7 1.2E-16 2.7E-21 145.4 13.9 132 325-462 3-160 (162)
90 PRK12536 RNA polymerase sigma 99.7 2.3E-16 4.9E-21 147.1 15.0 138 320-463 13-180 (181)
91 PRK09647 RNA polymerase sigma 99.7 2.9E-16 6.2E-21 150.3 15.6 131 328-465 28-191 (203)
92 TIGR02937 sigma70-ECF RNA poly 99.7 4.4E-16 9.5E-21 136.5 14.7 127 328-460 1-158 (158)
93 TIGR02947 SigH_actino RNA poly 99.7 1.5E-16 3.3E-21 149.6 12.3 130 327-462 10-181 (193)
94 PRK12547 RNA polymerase sigma 99.7 4.2E-16 9.2E-21 143.1 14.9 131 327-463 5-163 (164)
95 PRK12528 RNA polymerase sigma 99.7 6.8E-16 1.5E-20 140.8 14.8 125 328-459 4-160 (161)
96 PRK12541 RNA polymerase sigma 99.7 8.9E-16 1.9E-20 140.0 14.8 126 327-459 4-159 (161)
97 PRK09639 RNA polymerase sigma 99.7 1.3E-15 2.7E-20 139.1 15.1 128 327-463 2-162 (166)
98 PRK12517 RNA polymerase sigma 99.7 7.8E-16 1.7E-20 145.1 14.2 135 323-463 18-179 (188)
99 PRK12535 RNA polymerase sigma 99.7 1.5E-15 3.3E-20 144.3 16.1 139 319-465 15-186 (196)
100 PRK09651 RNA polymerase sigma 99.7 5.6E-16 1.2E-20 143.5 12.7 134 327-464 9-171 (172)
101 TIGR02950 SigM_subfam RNA poly 99.7 4.5E-16 9.7E-21 140.2 10.8 121 334-461 1-154 (154)
102 TIGR02960 SigX5 RNA polymerase 99.7 1.1E-15 2.4E-20 154.4 14.9 132 326-463 3-193 (324)
103 TIGR02943 Sig70_famx1 RNA poly 99.7 1.3E-15 2.8E-20 143.5 14.0 127 332-464 6-183 (188)
104 PRK12540 RNA polymerase sigma 99.7 1.5E-15 3.2E-20 142.6 14.2 129 328-464 5-163 (182)
105 PRK12530 RNA polymerase sigma 99.7 1.5E-15 3.3E-20 142.9 13.9 126 333-464 12-186 (189)
106 PRK12527 RNA polymerase sigma 99.7 1.6E-15 3.4E-20 138.2 13.5 122 335-463 2-156 (159)
107 PRK12545 RNA polymerase sigma 99.7 1.5E-15 3.3E-20 144.4 14.0 127 332-464 12-191 (201)
108 PRK07037 extracytoplasmic-func 99.7 1.6E-15 3.5E-20 138.2 13.5 125 332-463 2-160 (163)
109 PRK08241 RNA polymerase factor 99.6 2.1E-15 4.5E-20 153.9 15.7 136 318-459 8-200 (339)
110 PRK12532 RNA polymerase sigma 99.6 1.6E-15 3.5E-20 142.8 13.7 128 331-464 8-188 (195)
111 PRK09637 RNA polymerase sigma 99.6 2.8E-15 6.1E-20 140.5 15.3 128 330-463 3-157 (181)
112 PRK12544 RNA polymerase sigma 99.6 2.8E-15 6.1E-20 143.7 14.4 127 331-463 21-199 (206)
113 PRK12525 RNA polymerase sigma 99.6 5.8E-15 1.3E-19 136.1 14.6 127 328-461 9-167 (168)
114 TIGR02959 SigZ RNA polymerase 99.6 4.8E-15 1E-19 137.2 13.8 122 335-462 2-150 (170)
115 PRK12546 RNA polymerase sigma 99.6 7.6E-15 1.7E-19 138.7 13.9 129 328-463 8-164 (188)
116 PRK12511 RNA polymerase sigma 99.6 1E-14 2.2E-19 137.1 14.2 128 331-464 7-163 (182)
117 PRK06704 RNA polymerase factor 99.6 2.4E-14 5.2E-19 140.0 12.2 132 319-462 9-166 (228)
118 PRK09636 RNA polymerase sigma 99.5 5.3E-14 1.1E-18 141.3 13.8 127 328-462 4-165 (293)
119 PRK09191 two-component respons 99.5 1.8E-13 4E-18 132.4 12.9 124 329-463 2-139 (261)
120 PRK09635 sigI RNA polymerase s 99.5 2.5E-13 5.3E-18 137.2 12.8 126 328-461 5-167 (290)
121 TIGR02957 SigX4 RNA polymerase 99.5 3.2E-13 7E-18 135.2 13.4 122 332-461 1-157 (281)
122 PRK09047 RNA polymerase factor 99.5 3.8E-13 8.2E-18 122.0 11.9 108 350-464 2-158 (161)
123 PRK07122 RNA polymerase sigma 99.5 2.9E-13 6.3E-18 134.8 10.9 115 328-451 40-166 (264)
124 TIGR02393 RpoD_Cterm RNA polym 99.4 1.4E-12 3E-17 127.5 10.5 118 329-451 1-126 (238)
125 TIGR03209 P21_Cbot clostridium 99.3 1.7E-11 3.7E-16 109.7 10.8 106 330-446 1-141 (142)
126 PRK05911 RNA polymerase sigma 99.3 2.4E-11 5.1E-16 120.6 12.9 115 327-451 22-149 (257)
127 PF04545 Sigma70_r4: Sigma-70, 99.2 2.2E-11 4.9E-16 91.4 7.3 50 405-458 1-50 (50)
128 COG1191 FliA DNA-directed RNA 99.2 5.8E-11 1.3E-15 117.5 10.3 129 319-452 14-150 (247)
129 PF07638 Sigma70_ECF: ECF sigm 99.1 1.9E-09 4.1E-14 101.8 14.9 140 317-461 5-184 (185)
130 TIGR02479 FliA_WhiG RNA polyme 99.1 3.5E-10 7.6E-15 109.3 9.8 114 333-451 1-122 (224)
131 PF08281 Sigma70_r4_2: Sigma-7 99.0 1.2E-09 2.5E-14 83.0 7.2 54 399-456 1-54 (54)
132 PRK12427 flagellar biosynthesi 98.9 4.4E-09 9.5E-14 102.9 10.6 116 329-450 16-139 (231)
133 PRK06930 positive control sigm 98.9 7.8E-08 1.7E-12 90.4 16.2 71 389-463 95-165 (170)
134 TIGR02895 spore_sigI RNA polym 98.7 3.5E-08 7.6E-13 96.3 9.3 60 324-383 5-66 (218)
135 PRK07921 RNA polymerase sigma 98.7 3.8E-09 8.3E-14 108.5 2.4 80 223-324 129-211 (324)
136 PRK05901 RNA polymerase sigma 98.7 8.9E-09 1.9E-13 111.3 3.3 79 224-324 315-396 (509)
137 PRK08311 putative RNA polymera 98.6 2.4E-07 5.3E-12 91.4 10.6 69 315-383 4-75 (237)
138 PRK07406 RNA polymerase sigma 98.6 2.4E-08 5.2E-13 104.5 2.4 80 223-324 179-261 (373)
139 COG0568 RpoD DNA-directed RNA 98.6 2.9E-08 6.4E-13 102.3 2.8 82 224-324 146-227 (342)
140 PRK05658 RNA polymerase sigma 98.6 2.5E-08 5.5E-13 110.5 2.4 79 224-324 424-505 (619)
141 PRK07408 RNA polymerase sigma 98.5 5E-08 1.1E-12 96.8 3.8 79 223-323 69-150 (256)
142 PRK09210 RNA polymerase sigma 98.5 4.1E-08 8.9E-13 102.5 2.8 81 223-325 172-255 (367)
143 PRK00118 putative DNA-binding 98.5 5E-07 1.1E-11 78.7 8.8 64 398-465 7-70 (104)
144 cd06171 Sigma70_r4 Sigma70, re 98.4 8.7E-07 1.9E-11 64.8 6.9 54 400-457 2-55 (55)
145 PRK07598 RNA polymerase sigma 98.4 1.1E-07 2.4E-12 100.6 2.4 84 223-325 218-301 (415)
146 PRK05949 RNA polymerase sigma 98.4 1.5E-07 3.3E-12 96.9 3.2 84 222-324 133-216 (327)
147 PF04542 Sigma70_r2: Sigma-70 98.3 1.1E-06 2.3E-11 68.9 4.4 50 333-382 1-50 (71)
148 PRK04217 hypothetical protein; 98.2 3.8E-06 8.2E-11 73.9 6.7 55 407-465 41-95 (110)
149 PRK07405 RNA polymerase sigma 98.2 8.1E-07 1.8E-11 91.1 2.6 83 223-324 124-206 (317)
150 TIGR02997 Sig70-cyanoRpoD RNA 98.1 9.7E-07 2.1E-11 89.5 2.5 83 223-324 117-199 (298)
151 PF04297 UPF0122: Putative hel 98.1 1.3E-05 2.8E-10 69.5 8.6 57 400-460 8-65 (101)
152 TIGR00721 tfx DNA-binding prot 98.1 6.4E-06 1.4E-10 75.1 6.8 53 408-465 6-58 (137)
153 PRK03975 tfx putative transcri 98.1 7E-06 1.5E-10 75.2 7.0 51 407-462 5-55 (141)
154 PRK07500 rpoH2 RNA polymerase 98.0 3.1E-06 6.6E-11 85.7 3.9 87 222-322 82-168 (289)
155 PRK06596 RNA polymerase factor 98.0 4.1E-06 8.9E-11 84.5 4.3 81 223-324 91-173 (284)
156 TIGR01636 phage_rinA phage tra 98.0 5.2E-05 1.1E-09 68.6 10.7 62 397-460 71-132 (134)
157 TIGR02850 spore_sigG RNA polym 98.0 5.6E-06 1.2E-10 81.9 4.3 81 223-325 77-159 (254)
158 PRK06288 RNA polymerase sigma 98.0 4.6E-06 1E-10 83.1 3.7 80 223-324 77-156 (268)
159 smart00421 HTH_LUXR helix_turn 97.9 2.9E-05 6.2E-10 57.8 5.6 46 407-457 2-47 (58)
160 PF04539 Sigma70_r3: Sigma-70 97.9 2.6E-05 5.6E-10 63.3 5.6 42 284-325 2-43 (78)
161 TIGR03879 near_KaiC_dom probab 97.9 3.4E-05 7.4E-10 63.1 6.2 48 400-451 7-55 (73)
162 TIGR02885 spore_sigF RNA polym 97.8 2E-05 4.4E-10 76.4 4.2 79 224-324 55-135 (231)
163 PRK08215 sporulation sigma fac 97.7 2E-05 4.2E-10 78.2 3.4 79 224-324 81-161 (258)
164 PF07374 DUF1492: Protein of u 97.7 0.00019 4.1E-09 61.9 8.8 55 398-456 44-99 (100)
165 TIGR02980 SigBFG RNA polymeras 97.7 2.7E-05 6E-10 75.2 4.1 82 224-324 47-128 (227)
166 PF00196 GerE: Bacterial regul 97.7 9.6E-05 2.1E-09 57.0 6.0 47 407-458 2-48 (58)
167 TIGR02392 rpoH_proteo alternat 97.7 4.2E-05 9.1E-10 76.5 5.1 83 222-323 77-160 (270)
168 PRK07670 RNA polymerase sigma 97.7 2.9E-05 6.3E-10 76.6 3.9 81 222-324 67-147 (251)
169 cd06170 LuxR_C_like C-terminal 97.7 0.00011 2.4E-09 54.9 6.0 45 409-458 1-45 (57)
170 PRK05657 RNA polymerase sigma 97.6 3E-05 6.5E-10 79.9 2.2 82 224-324 130-211 (325)
171 PF04967 HTH_10: HTH DNA bindi 97.6 0.0003 6.4E-09 54.2 6.9 48 409-456 1-51 (53)
172 PRK15411 rcsA colanic acid cap 97.4 0.00027 5.9E-09 68.0 6.3 46 408-458 137-182 (207)
173 PRK05572 sporulation sigma fac 97.4 0.00012 2.7E-09 72.2 3.8 78 224-323 76-155 (252)
174 PRK10840 transcriptional regul 97.4 0.00036 7.7E-09 66.2 6.3 46 407-457 149-194 (216)
175 PRK11475 DNA-binding transcrip 97.3 0.00038 8.3E-09 67.3 6.4 47 406-457 132-178 (207)
176 TIGR03541 reg_near_HchA LuxR f 97.3 0.00036 7.8E-09 68.3 6.2 48 406-458 169-216 (232)
177 PRK06986 fliA flagellar biosyn 97.3 0.00019 4.2E-09 70.0 4.2 80 223-324 54-133 (236)
178 PRK13719 conjugal transfer tra 97.3 0.00039 8.4E-09 67.9 6.2 50 403-457 138-187 (217)
179 PRK15201 fimbriae regulatory p 97.3 0.00047 1E-08 65.4 6.5 47 407-458 132-178 (198)
180 TIGR03020 EpsA transcriptional 97.3 0.00043 9.4E-09 69.0 6.4 48 406-458 188-235 (247)
181 PRK13870 transcriptional regul 97.3 0.00043 9.4E-09 68.1 6.3 46 408-458 173-218 (234)
182 PRK10100 DNA-binding transcrip 97.3 0.0005 1.1E-08 66.9 6.3 47 407-458 154-200 (216)
183 COG2197 CitB Response regulato 97.3 0.00047 1E-08 66.7 6.0 47 407-458 147-193 (211)
184 PRK10188 DNA-binding transcrip 97.2 0.0006 1.3E-08 67.4 6.5 46 408-458 179-224 (240)
185 TIGR02941 Sigma_B RNA polymera 97.1 0.00043 9.2E-09 68.4 4.3 81 224-324 73-154 (255)
186 COG4566 TtrR Response regulato 97.1 0.0021 4.5E-08 61.7 8.3 59 396-459 130-188 (202)
187 TIGR01321 TrpR trp operon repr 97.1 0.00093 2E-08 57.3 5.4 49 400-448 23-75 (94)
188 PF02001 DUF134: Protein of un 97.1 0.0015 3.2E-08 57.3 6.6 52 408-463 41-92 (106)
189 PF13936 HTH_38: Helix-turn-he 97.1 0.00076 1.7E-08 49.7 4.0 41 407-451 3-43 (44)
190 PRK09483 response regulator; P 97.0 0.0014 3E-08 60.9 6.1 46 407-457 147-192 (217)
191 COG2771 CsgD DNA-binding HTH d 96.9 0.003 6.5E-08 48.6 6.6 48 407-459 3-50 (65)
192 PRK15369 two component system 96.9 0.002 4.3E-08 58.3 6.4 46 407-457 148-193 (211)
193 TIGR01637 phage_arpU phage tra 96.9 0.0068 1.5E-07 54.3 9.5 64 396-461 66-130 (132)
194 PF00140 Sigma70_r1_2: Sigma-7 96.8 0.0005 1.1E-08 49.0 1.3 33 255-287 2-34 (37)
195 COG3413 Predicted DNA binding 96.8 0.0032 6.9E-08 61.0 6.9 54 408-461 155-211 (215)
196 COG2739 Uncharacterized protei 96.8 0.0035 7.5E-08 54.2 6.0 48 407-458 16-63 (105)
197 PRK09390 fixJ response regulat 96.7 0.005 1.1E-07 55.4 7.2 54 400-458 133-186 (202)
198 TIGR02394 rpoS_proteo RNA poly 96.7 0.0011 2.4E-08 66.8 3.1 79 224-324 90-171 (285)
199 PRK10651 transcriptional regul 96.6 0.0037 8E-08 57.3 5.9 46 407-457 154-199 (216)
200 PRK08583 RNA polymerase sigma 96.4 0.0095 2.1E-07 58.9 7.3 81 224-324 73-154 (257)
201 COG1342 Predicted DNA-binding 96.2 0.013 2.8E-07 50.3 6.2 51 409-463 34-84 (99)
202 PRK01381 Trp operon repressor; 96.2 0.0066 1.4E-07 52.5 4.3 48 400-447 23-74 (99)
203 PRK10403 transcriptional regul 96.2 0.01 2.2E-07 54.2 5.9 46 407-457 152-197 (215)
204 PRK15320 transcriptional activ 96.0 0.012 2.7E-07 56.9 5.9 67 386-458 143-209 (251)
205 COG1356 tfx Transcriptional re 96.0 0.006 1.3E-07 54.8 3.1 47 409-460 9-55 (143)
206 PRK04841 transcriptional regul 95.8 0.014 3.1E-07 66.7 6.5 47 407-458 837-883 (903)
207 PRK09935 transcriptional regul 95.7 0.023 4.9E-07 52.1 6.2 45 408-457 149-193 (210)
208 PRK13558 bacterio-opsin activa 95.7 0.022 4.8E-07 63.3 7.0 55 406-460 605-662 (665)
209 PRK09958 DNA-binding transcrip 95.7 0.025 5.4E-07 51.9 6.1 47 406-457 141-187 (204)
210 PF13613 HTH_Tnp_4: Helix-turn 95.6 0.032 6.9E-07 42.5 5.6 50 408-460 2-51 (53)
211 TIGR02895 spore_sigI RNA polym 95.6 0.015 3.2E-07 57.1 4.8 73 223-311 54-126 (218)
212 PRK10360 DNA-binding transcrip 95.6 0.03 6.6E-07 51.0 6.5 46 407-457 136-181 (196)
213 COG4941 Predicted RNA polymera 95.5 0.14 3.1E-06 53.3 11.5 125 331-459 8-167 (415)
214 PF01726 LexA_DNA_bind: LexA D 95.5 0.024 5.2E-07 45.3 4.6 46 406-451 1-49 (65)
215 PF13412 HTH_24: Winged helix- 95.3 0.057 1.2E-06 39.8 5.8 42 409-453 1-42 (48)
216 PRK15418 transcriptional regul 95.2 0.026 5.7E-07 58.2 5.3 36 415-454 20-55 (318)
217 PF13384 HTH_23: Homeodomain-l 95.2 0.019 4E-07 42.6 2.9 32 416-452 10-41 (50)
218 TIGR02531 yecD_yerC TrpR-relat 94.6 0.082 1.8E-06 44.9 5.6 39 407-452 35-73 (88)
219 cd00569 HTH_Hin_like Helix-tur 94.5 0.092 2E-06 34.1 4.8 36 409-448 6-41 (42)
220 PF06530 Phage_antitermQ: Phag 94.3 0.26 5.6E-06 44.2 8.6 54 405-462 59-112 (125)
221 PF05263 DUF722: Protein of un 93.5 0.31 6.7E-06 44.3 7.5 56 399-456 72-127 (130)
222 PF10668 Phage_terminase: Phag 93.3 0.15 3.3E-06 40.4 4.5 38 412-451 8-45 (60)
223 PF13404 HTH_AsnC-type: AsnC-t 93.0 0.3 6.6E-06 35.7 5.4 40 409-451 1-40 (42)
224 PF02796 HTH_7: Helix-turn-hel 93.0 0.13 2.7E-06 37.9 3.5 33 413-450 11-43 (45)
225 TIGR02395 rpoN_sigma RNA polym 93.0 1.3 2.9E-05 47.7 12.6 24 427-450 317-340 (429)
226 PF06056 Terminase_5: Putative 92.8 0.23 5E-06 38.9 4.9 33 415-452 5-37 (58)
227 COG2390 DeoR Transcriptional r 92.8 0.15 3.3E-06 52.9 5.0 36 415-454 17-52 (321)
228 PHA00675 hypothetical protein 92.7 0.22 4.8E-06 41.2 4.9 41 407-451 21-62 (78)
229 PF09862 DUF2089: Protein of u 92.7 0.33 7.2E-06 43.1 6.3 50 405-458 30-79 (113)
230 PRK10430 DNA-binding transcrip 92.6 0.25 5.5E-06 47.7 6.1 48 408-455 158-205 (239)
231 PF13518 HTH_28: Helix-turn-he 92.6 0.23 4.9E-06 36.6 4.5 28 427-454 11-38 (52)
232 COG2909 MalT ATP-dependent tra 92.2 0.17 3.6E-06 58.2 4.8 47 408-459 831-877 (894)
233 PF04218 CENP-B_N: CENP-B N-te 92.2 0.19 4.2E-06 38.4 3.7 40 408-451 6-45 (53)
234 PF00325 Crp: Bacterial regula 92.2 0.18 3.8E-06 35.1 3.1 24 428-451 2-25 (32)
235 smart00351 PAX Paired Box doma 91.9 0.44 9.6E-06 42.6 6.3 42 409-454 18-59 (125)
236 PF12802 MarR_2: MarR family; 91.9 0.39 8.4E-06 36.6 5.1 45 408-453 2-46 (62)
237 PRK05932 RNA polymerase factor 91.2 2.6 5.5E-05 45.9 12.4 45 406-450 309-365 (455)
238 PF13730 HTH_36: Helix-turn-he 91.2 0.82 1.8E-05 34.3 6.2 43 408-450 2-47 (55)
239 PF12645 HTH_16: Helix-turn-he 90.5 0.98 2.1E-05 36.2 6.3 56 319-374 4-65 (65)
240 PF01022 HTH_5: Bacterial regu 90.2 0.78 1.7E-05 33.8 5.2 37 411-451 2-38 (47)
241 PRK11083 DNA-binding response 89.8 0.49 1.1E-05 43.8 4.8 50 408-458 154-208 (228)
242 PF02650 HTH_WhiA: WhiA C-term 89.5 0.81 1.8E-05 38.7 5.3 45 406-453 35-81 (85)
243 PF01325 Fe_dep_repress: Iron 89.2 0.66 1.4E-05 36.4 4.3 43 409-451 2-45 (60)
244 cd00131 PAX Paired Box domain 89.1 1.1 2.3E-05 40.4 6.3 42 409-454 18-59 (128)
245 COG3415 Transposase and inacti 89.1 0.75 1.6E-05 42.3 5.3 35 415-453 12-46 (138)
246 PF03444 HrcA_DNA-bdg: Winged 88.9 1.1 2.3E-05 37.4 5.5 43 408-450 1-45 (78)
247 PHA02591 hypothetical protein; 88.7 0.9 2E-05 37.8 4.9 24 427-450 58-81 (83)
248 PF12840 HTH_20: Helix-turn-he 88.5 1.6 3.4E-05 33.8 6.0 36 411-450 10-46 (61)
249 PF08279 HTH_11: HTH domain; 88.2 0.95 2.1E-05 34.0 4.5 39 412-452 1-39 (55)
250 PRK12469 RNA polymerase factor 88.0 8.7 0.00019 42.2 13.3 45 406-450 335-391 (481)
251 smart00550 Zalpha Z-DNA-bindin 87.9 1.5 3.2E-05 35.1 5.6 24 428-451 22-45 (68)
252 PF13542 HTH_Tnp_ISL3: Helix-t 87.7 1.4 3E-05 32.7 5.1 26 427-452 26-51 (52)
253 PF13744 HTH_37: Helix-turn-he 87.6 1.1 2.3E-05 36.9 4.8 37 427-463 30-71 (80)
254 PRK10336 DNA-binding transcrip 87.5 0.91 2E-05 41.8 4.9 49 408-457 149-202 (219)
255 PRK10046 dpiA two-component re 87.4 0.61 1.3E-05 44.7 3.8 40 408-451 161-200 (225)
256 smart00344 HTH_ASNC helix_turn 87.3 1.5 3.3E-05 37.3 5.8 42 409-453 1-42 (108)
257 PRK10710 DNA-binding transcrip 86.8 1 2.3E-05 42.1 4.9 50 408-458 160-214 (240)
258 PF04539 Sigma70_r3: Sigma-70 86.7 1.5 3.3E-05 35.2 5.2 25 427-451 19-43 (78)
259 PF00356 LacI: Bacterial regul 86.7 0.68 1.5E-05 34.6 2.9 22 430-451 1-22 (46)
260 PF13463 HTH_27: Winged helix 86.6 1.3 2.8E-05 34.3 4.5 43 409-453 1-43 (68)
261 PF09339 HTH_IclR: IclR helix- 86.5 1 2.2E-05 33.8 3.8 34 418-451 8-41 (52)
262 PRK15479 transcriptional regul 86.1 1.3 2.8E-05 40.7 5.1 49 408-457 148-201 (221)
263 PF01418 HTH_6: Helix-turn-hel 86.0 2.9 6.3E-05 34.0 6.5 54 398-451 3-57 (77)
264 TIGR02154 PhoB phosphate regul 85.9 0.61 1.3E-05 43.0 2.8 49 408-457 154-207 (226)
265 PRK12423 LexA repressor; Provi 85.9 1.5 3.4E-05 42.1 5.7 48 407-458 2-52 (202)
266 PF12728 HTH_17: Helix-turn-he 85.7 0.88 1.9E-05 33.7 3.1 24 429-452 2-25 (51)
267 PF13022 HTH_Tnp_1_2: Helix-tu 85.5 3.1 6.7E-05 38.4 7.0 64 402-465 4-73 (142)
268 PF01371 Trp_repressor: Trp re 85.5 1 2.2E-05 38.2 3.7 45 409-454 27-74 (87)
269 PF01047 MarR: MarR family; I 85.2 1.7 3.6E-05 33.0 4.4 42 409-453 1-42 (59)
270 PRK11179 DNA-binding transcrip 84.4 2.3 4.9E-05 39.1 5.8 41 408-451 6-46 (153)
271 PF01978 TrmB: Sugar-specific 84.2 1.1 2.4E-05 35.3 3.1 41 408-451 5-45 (68)
272 CHL00148 orf27 Ycf27; Reviewed 84.0 1.5 3.2E-05 41.1 4.5 50 408-458 161-217 (240)
273 TIGR00498 lexA SOS regulatory 83.6 2 4.3E-05 40.9 5.2 45 407-451 2-49 (199)
274 TIGR01764 excise DNA binding d 83.1 1.4 3.1E-05 31.4 3.2 24 429-452 2-25 (49)
275 PRK00215 LexA repressor; Valid 82.9 2.5 5.3E-05 40.4 5.6 45 409-453 2-49 (205)
276 PRK13413 mpi multiple promoter 82.1 2.6 5.7E-05 40.1 5.4 35 412-451 161-195 (200)
277 TIGR03787 marine_sort_RR prote 82.1 2.4 5.1E-05 39.6 5.0 50 408-458 156-207 (227)
278 COG2973 TrpR Trp operon repres 82.0 3.3 7.2E-05 36.0 5.3 45 400-446 31-78 (103)
279 PF01726 LexA_DNA_bind: LexA D 81.6 4.8 0.0001 32.1 5.9 34 288-321 11-45 (65)
280 cd04762 HTH_MerR-trunc Helix-T 81.5 1.8 4E-05 30.6 3.2 25 429-453 1-25 (49)
281 smart00345 HTH_GNTR helix_turn 81.5 2.6 5.7E-05 31.3 4.2 29 426-458 17-46 (60)
282 COG1522 Lrp Transcriptional re 81.4 3.3 7.3E-05 37.2 5.6 43 407-452 4-46 (154)
283 PRK11169 leucine-responsive tr 81.3 2.6 5.7E-05 39.1 5.0 41 408-451 11-51 (164)
284 COG3355 Predicted transcriptio 81.1 6.2 0.00013 35.8 7.0 53 399-457 15-67 (126)
285 PF13551 HTH_29: Winged helix- 80.9 2.5 5.5E-05 35.6 4.4 26 427-452 10-36 (112)
286 PHA01976 helix-turn-helix prot 80.8 3.1 6.7E-05 32.3 4.5 25 427-451 14-38 (67)
287 PRK11511 DNA-binding transcrip 79.8 8.6 0.00019 34.1 7.6 43 284-326 7-49 (127)
288 COG2522 Predicted transcriptio 79.8 3.2 7E-05 37.3 4.8 25 427-451 21-45 (119)
289 PF01381 HTH_3: Helix-turn-hel 79.1 2.7 5.9E-05 31.2 3.5 25 427-451 8-32 (55)
290 PF00046 Homeobox: Homeobox do 78.6 4.1 8.9E-05 30.6 4.4 51 408-458 6-57 (57)
291 PF01527 HTH_Tnp_1: Transposas 78.4 2.4 5.3E-05 33.6 3.3 35 415-453 14-48 (76)
292 PRK11564 stationary phase indu 78.3 5.9 0.00013 42.1 7.1 52 408-459 10-61 (426)
293 PF13560 HTH_31: Helix-turn-he 78.2 2.8 6.1E-05 32.5 3.5 25 427-451 13-37 (64)
294 cd00090 HTH_ARSR Arsenical Res 77.8 6.6 0.00014 29.7 5.5 37 411-451 7-43 (78)
295 cd06571 Bac_DnaA_C C-terminal 77.8 7.7 0.00017 32.5 6.3 31 427-457 43-74 (90)
296 COG1508 RpoN DNA-directed RNA 77.7 28 0.00062 37.9 11.9 44 406-450 296-352 (444)
297 TIGR01610 phage_O_Nterm phage 77.5 6.7 0.00015 33.3 5.9 45 406-450 20-69 (95)
298 cd04761 HTH_MerR-SF Helix-Turn 77.4 1.9 4.2E-05 31.2 2.2 26 429-454 1-26 (49)
299 smart00420 HTH_DEOR helix_turn 77.3 6.1 0.00013 28.4 4.9 25 427-451 13-37 (53)
300 smart00418 HTH_ARSR helix_turn 77.2 4.2 9.2E-05 30.0 4.2 27 427-453 9-35 (66)
301 PF08220 HTH_DeoR: DeoR-like h 77.2 4.1 8.9E-05 31.4 4.1 25 426-450 12-36 (57)
302 PRK10072 putative transcriptio 77.1 3.9 8.5E-05 35.2 4.4 32 416-451 38-69 (96)
303 PRK09413 IS2 repressor TnpA; R 76.9 5.6 0.00012 35.1 5.5 35 415-453 20-54 (121)
304 PHA00542 putative Cro-like pro 76.5 4.2 9.1E-05 33.7 4.3 26 427-452 30-55 (82)
305 TIGR03070 couple_hipB transcri 76.4 5 0.00011 29.5 4.3 25 427-451 14-38 (58)
306 PF13011 LZ_Tnp_IS481: leucine 76.1 6.9 0.00015 33.2 5.4 43 408-453 8-50 (85)
307 COG5484 Uncharacterized conser 76.1 3.5 7.5E-05 41.5 4.2 25 427-451 18-42 (279)
308 PRK15435 bifunctional DNA-bind 76.1 1.1E+02 0.0024 32.3 17.8 95 207-325 28-122 (353)
309 PF02954 HTH_8: Bacterial regu 75.9 4.7 0.0001 29.1 3.8 38 411-451 4-41 (42)
310 COG0856 Orotate phosphoribosyl 75.8 3.6 7.9E-05 39.5 4.1 39 414-457 9-47 (203)
311 PF08822 DUF1804: Protein of u 75.5 6.6 0.00014 37.2 5.7 41 411-454 5-45 (165)
312 smart00346 HTH_ICLR helix_turn 75.2 7.5 0.00016 31.7 5.5 26 427-452 19-44 (91)
313 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 75.1 8.1 0.00018 29.6 5.1 39 408-450 4-42 (50)
314 smart00419 HTH_CRP helix_turn_ 74.8 4.5 9.7E-05 28.9 3.6 24 427-450 7-30 (48)
315 PF08765 Mor: Mor transcriptio 74.6 6.5 0.00014 34.2 5.2 41 412-458 62-102 (108)
316 PRK11302 DNA-binding transcrip 74.5 5.5 0.00012 39.5 5.4 52 398-451 3-57 (284)
317 TIGR02612 mob_myst_A mobile my 74.0 7.8 0.00017 36.1 5.8 51 410-464 24-80 (150)
318 smart00347 HTH_MARR helix_turn 73.8 8.8 0.00019 31.2 5.6 41 408-451 7-47 (101)
319 PF07750 GcrA: GcrA cell cycle 73.8 4.4 9.6E-05 38.1 4.2 34 414-451 8-42 (162)
320 TIGR00122 birA_repr_reg BirA b 73.6 7.8 0.00017 30.5 5.0 25 427-451 12-36 (69)
321 PRK10219 DNA-binding transcrip 73.6 25 0.00055 29.7 8.5 39 288-326 7-45 (107)
322 TIGR02844 spore_III_D sporulat 73.3 7.6 0.00017 32.5 5.0 25 427-451 18-42 (80)
323 PF14493 HTH_40: Helix-turn-he 73.3 8.3 0.00018 32.3 5.3 29 427-455 12-40 (91)
324 PRK03573 transcriptional regul 72.7 11 0.00024 33.7 6.3 42 408-451 28-69 (144)
325 TIGR02337 HpaR homoprotocatech 72.7 8.8 0.00019 33.2 5.6 41 408-451 25-65 (118)
326 PRK10870 transcriptional repre 72.3 20 0.00043 33.8 8.2 52 400-452 42-95 (176)
327 PRK09954 putative kinase; Prov 72.0 7.9 0.00017 40.0 6.0 42 409-453 1-42 (362)
328 COG1476 Predicted transcriptio 71.9 6.4 0.00014 32.1 4.0 25 427-451 13-37 (68)
329 PF13545 HTH_Crp_2: Crp-like h 71.6 4.6 0.0001 31.9 3.3 28 427-458 27-54 (76)
330 KOG0484 Transcription factor P 71.4 6.3 0.00014 34.7 4.2 49 407-459 27-75 (125)
331 COG1510 Predicted transcriptio 71.1 4.7 0.0001 38.4 3.6 29 426-458 39-67 (177)
332 COG1654 BirA Biotin operon rep 70.9 12 0.00026 31.3 5.6 32 424-459 15-46 (79)
333 PF08280 HTH_Mga: M protein tr 70.9 4.8 0.0001 31.2 3.1 25 426-450 17-41 (59)
334 PF13556 HTH_30: PucR C-termin 70.7 13 0.00028 28.7 5.5 42 416-461 4-45 (59)
335 TIGR01884 cas_HTH CRISPR locus 70.6 12 0.00025 36.0 6.3 45 404-451 136-180 (203)
336 cd00092 HTH_CRP helix_turn_hel 70.3 6.9 0.00015 29.9 3.9 25 427-451 24-48 (67)
337 PRK11337 DNA-binding transcrip 70.2 12 0.00027 37.5 6.7 63 397-461 14-83 (292)
338 PRK09480 slmA division inhibit 70.1 39 0.00084 30.9 9.6 75 289-363 17-91 (194)
339 TIGR01889 Staph_reg_Sar staphy 69.7 32 0.00068 29.6 8.3 45 408-452 22-67 (109)
340 KOG1597 Transcription initiati 69.3 71 0.0015 33.1 11.8 128 298-459 160-291 (308)
341 PF08535 KorB: KorB domain; I 69.1 4.2 9.1E-05 34.2 2.6 24 427-450 2-25 (93)
342 PRK15482 transcriptional regul 69.0 8.6 0.00019 38.6 5.3 51 399-451 4-57 (285)
343 PRK11512 DNA-binding transcrip 68.5 13 0.00029 33.3 6.0 41 408-451 37-77 (144)
344 cd07377 WHTH_GntR Winged helix 68.4 9.2 0.0002 28.8 4.2 26 429-458 26-51 (66)
345 smart00354 HTH_LACI helix_turn 68.2 5.3 0.00011 31.8 2.9 23 429-451 1-23 (70)
346 TIGR03830 CxxCG_CxxCG_HTH puta 68.0 17 0.00036 31.7 6.3 46 401-452 57-102 (127)
347 PRK00135 scpB segregation and 67.6 70 0.0015 30.8 10.9 32 408-442 87-118 (188)
348 PRK06030 hypothetical protein; 67.5 16 0.00034 33.0 6.1 50 412-469 57-106 (124)
349 PF13411 MerR_1: MerR HTH fami 67.3 2.8 6E-05 32.7 1.1 25 429-453 1-25 (69)
350 cd00086 homeodomain Homeodomai 67.0 16 0.00034 27.2 5.2 51 408-458 6-57 (59)
351 PF04645 DUF603: Protein of un 67.0 7.5 0.00016 37.0 4.0 25 427-451 17-42 (181)
352 cd01104 HTH_MlrA-CarA Helix-Tu 66.8 7.4 0.00016 30.2 3.5 23 429-451 1-23 (68)
353 COG5625 Predicted transcriptio 66.6 9.6 0.00021 33.4 4.3 65 399-463 7-73 (113)
354 PF12116 SpoIIID: Stage III sp 66.2 9.8 0.00021 32.0 4.1 46 413-460 6-51 (82)
355 PF08784 RPA_C: Replication pr 66.1 9.6 0.00021 32.4 4.3 43 408-450 44-87 (102)
356 TIGR00647 MG103 conserved hypo 65.5 30 0.00064 35.5 8.3 45 406-453 225-275 (279)
357 TIGR02787 codY_Gpos GTP-sensin 65.4 31 0.00067 34.8 8.2 56 399-458 167-224 (251)
358 PF11662 DUF3263: Protein of u 65.2 24 0.00052 29.4 6.2 47 408-454 2-48 (77)
359 PF02082 Rrf2: Transcriptional 65.0 12 0.00027 30.6 4.6 24 428-451 25-48 (83)
360 PF01710 HTH_Tnp_IS630: Transp 64.9 7.7 0.00017 34.2 3.5 25 427-451 70-94 (119)
361 PF05043 Mga: Mga helix-turn-h 64.8 5.3 0.00011 32.8 2.4 31 427-457 29-59 (87)
362 COG1846 MarR Transcriptional r 64.7 15 0.00033 30.7 5.3 40 409-452 20-60 (126)
363 TIGR02607 antidote_HigA addict 64.6 16 0.00035 29.0 5.1 25 427-451 17-41 (78)
364 COG1318 Predicted transcriptio 64.2 7 0.00015 37.3 3.3 27 427-453 60-86 (182)
365 COG1405 SUA7 Transcription ini 63.9 40 0.00087 34.6 9.0 26 427-452 250-275 (285)
366 PRK09726 antitoxin HipB; Provi 63.9 12 0.00026 31.1 4.4 25 427-451 24-48 (88)
367 PRK10141 DNA-binding transcrip 63.8 20 0.00042 32.0 5.9 45 403-450 7-52 (117)
368 PF00376 MerR: MerR family reg 63.7 4.6 9.9E-05 28.9 1.5 24 430-453 1-24 (38)
369 PF00392 GntR: Bacterial regul 63.5 8.7 0.00019 29.8 3.3 28 426-457 21-49 (64)
370 PRK11050 manganese transport r 63.5 13 0.00028 34.3 4.9 28 426-453 49-76 (152)
371 COG4709 Predicted membrane pro 62.8 19 0.0004 35.0 5.9 60 395-454 3-66 (195)
372 COG3093 VapI Plasmid maintenan 62.7 12 0.00027 32.9 4.3 35 415-451 12-46 (104)
373 smart00342 HTH_ARAC helix_turn 62.6 11 0.00025 29.2 3.9 26 428-453 1-26 (84)
374 PRK11557 putative DNA-binding 62.6 17 0.00036 36.2 5.9 48 402-451 3-53 (278)
375 PF05225 HTH_psq: helix-turn-h 62.2 26 0.00055 25.9 5.4 23 429-451 17-39 (45)
376 cd04764 HTH_MlrA-like_sg1 Heli 62.2 10 0.00022 29.5 3.5 23 429-451 1-23 (67)
377 COG2512 Predicted membrane-ass 62.2 12 0.00025 37.9 4.7 43 407-451 191-233 (258)
378 PF01710 HTH_Tnp_IS630: Transp 62.2 11 0.00025 33.1 4.2 24 427-450 17-40 (119)
379 COG1737 RpiR Transcriptional r 62.2 12 0.00027 37.7 4.9 53 397-451 4-59 (281)
380 TIGR02702 SufR_cyano iron-sulf 62.0 17 0.00036 34.9 5.6 26 427-452 14-39 (203)
381 PF00165 HTH_AraC: Bacterial r 61.3 13 0.00027 26.5 3.5 26 427-452 7-32 (42)
382 COG2345 Predicted transcriptio 61.3 16 0.00034 36.2 5.2 25 427-451 24-48 (218)
383 PF12844 HTH_19: Helix-turn-he 61.2 15 0.00032 28.1 4.2 25 427-451 11-35 (64)
384 PHA00738 putative HTH transcri 61.1 20 0.00042 31.8 5.3 37 411-450 12-48 (108)
385 PF13022 HTH_Tnp_1_2: Helix-tu 61.1 29 0.00062 32.2 6.6 33 294-326 26-58 (142)
386 smart00422 HTH_MERR helix_turn 60.7 6.8 0.00015 30.4 2.2 25 429-453 1-25 (70)
387 PRK01905 DNA-binding protein F 60.4 40 0.00086 27.5 6.8 25 427-451 49-73 (77)
388 COG1321 TroR Mn-dependent tran 60.3 17 0.00037 33.9 5.1 43 409-451 4-47 (154)
389 PRK10161 transcriptional regul 59.9 11 0.00024 35.1 3.9 50 408-458 154-208 (229)
390 PRK15044 transcriptional regul 59.7 66 0.0014 33.3 9.7 72 286-360 192-264 (295)
391 PRK03902 manganese transport t 59.4 20 0.00043 32.3 5.3 27 425-451 19-45 (142)
392 PRK09863 putative frv operon r 59.3 1.2E+02 0.0025 33.9 12.4 32 427-458 91-122 (584)
393 TIGR03697 NtcA_cyano global ni 58.4 11 0.00024 34.6 3.6 27 428-458 143-169 (193)
394 smart00389 HOX Homeodomain. DN 58.2 18 0.00039 26.7 4.1 47 409-455 7-54 (56)
395 PRK00423 tfb transcription ini 57.6 1.7E+02 0.0036 30.2 12.3 31 426-456 274-304 (310)
396 PF04552 Sigma54_DBD: Sigma-54 57.6 3.4 7.4E-05 38.8 0.0 47 400-450 23-71 (160)
397 TIGR01387 cztR_silR_copR heavy 57.4 17 0.00037 33.2 4.6 49 408-457 147-200 (218)
398 PRK09706 transcriptional repre 56.9 17 0.00038 32.4 4.5 25 427-451 17-41 (135)
399 PRK10955 DNA-binding transcrip 56.9 8.2 0.00018 35.8 2.5 46 408-458 156-210 (232)
400 cd00093 HTH_XRE Helix-turn-hel 56.7 24 0.00051 24.4 4.4 25 427-451 11-35 (58)
401 PRK10411 DNA-binding transcrip 56.4 22 0.00048 35.2 5.5 41 411-454 4-44 (240)
402 PRK14101 bifunctional glucokin 56.4 22 0.00048 40.1 6.2 63 396-460 341-410 (638)
403 PRK11161 fumarate/nitrate redu 56.3 41 0.00089 32.1 7.3 27 428-458 184-210 (235)
404 COG3877 Uncharacterized protei 56.2 28 0.00061 30.8 5.4 46 407-456 40-85 (122)
405 cd04763 HTH_MlrA-like Helix-Tu 56.2 15 0.00032 28.8 3.4 23 429-451 1-23 (68)
406 TIGR00738 rrf2_super rrf2 fami 56.0 26 0.00057 30.7 5.4 25 427-451 24-48 (132)
407 PF13443 HTH_26: Cro/C1-type H 56.0 12 0.00025 28.6 2.8 26 427-452 9-34 (63)
408 TIGR02698 CopY_TcrY copper tra 55.7 31 0.00068 31.0 5.9 44 408-454 1-48 (130)
409 PRK11753 DNA-binding transcrip 55.7 55 0.0012 30.5 7.9 27 428-458 168-194 (211)
410 smart00530 HTH_XRE Helix-turn- 55.5 22 0.00047 24.4 4.0 25 427-451 9-33 (56)
411 cd01392 HTH_LacI Helix-turn-he 55.2 7.6 0.00017 28.4 1.6 21 432-452 1-21 (52)
412 PRK10643 DNA-binding transcrip 54.9 14 0.0003 33.9 3.6 49 408-457 149-202 (222)
413 PRK13918 CRP/FNR family transc 54.8 13 0.00029 34.5 3.5 28 427-458 148-175 (202)
414 PF00292 PAX: 'Paired box' dom 54.8 28 0.00062 31.5 5.4 39 409-452 18-57 (125)
415 COG2944 Predicted transcriptio 54.7 28 0.00062 30.6 5.2 43 403-451 38-80 (104)
416 smart00352 POU Found in Pit-Oc 54.5 26 0.00056 29.1 4.6 34 427-460 23-67 (75)
417 PF08006 DUF1700: Protein of u 54.2 31 0.00067 32.4 5.9 57 395-451 3-63 (181)
418 TIGR00180 parB_part ParB-like 53.9 28 0.0006 33.0 5.5 42 408-451 102-143 (187)
419 PRK09863 putative frv operon r 53.8 28 0.0006 38.8 6.3 46 409-458 2-47 (584)
420 COG1476 Predicted transcriptio 53.8 41 0.0009 27.4 5.6 50 303-362 15-64 (68)
421 TIGR02431 pcaR_pcaU beta-ketoa 53.5 24 0.00053 34.6 5.3 36 416-451 12-47 (248)
422 PF09012 FeoC: FeoC like trans 53.1 11 0.00024 29.9 2.2 28 424-451 10-37 (69)
423 PRK04984 fatty acid metabolism 52.7 21 0.00046 34.5 4.6 30 425-458 27-57 (239)
424 PRK06266 transcription initiat 52.6 49 0.0011 31.6 6.9 48 399-451 11-59 (178)
425 PRK11517 transcriptional regul 51.9 28 0.00061 32.0 5.2 49 408-457 147-200 (223)
426 PRK06424 transcription factor; 51.6 23 0.0005 32.8 4.4 25 427-451 96-120 (144)
427 PHA02943 hypothetical protein; 51.6 25 0.00054 33.1 4.6 24 427-450 23-46 (165)
428 TIGR02944 suf_reg_Xantho FeS a 51.6 26 0.00057 30.9 4.7 26 426-451 23-48 (130)
429 PRK09834 DNA-binding transcrip 51.6 26 0.00056 34.8 5.2 39 413-451 11-49 (263)
430 PRK13890 conjugal transfer pro 51.3 24 0.00053 31.3 4.4 25 427-451 17-41 (120)
431 PRK10219 DNA-binding transcrip 51.0 43 0.00093 28.3 5.8 26 427-452 20-45 (107)
432 PF04703 FaeA: FaeA-like prote 50.8 16 0.00035 29.1 2.8 25 427-451 14-38 (62)
433 PF12298 Bot1p: Eukaryotic mit 50.7 34 0.00074 32.6 5.5 47 409-460 17-63 (172)
434 PRK13777 transcriptional regul 50.6 36 0.00079 32.6 5.8 41 408-451 42-82 (185)
435 PRK11414 colanic acid/biofilm 50.4 21 0.00045 34.3 4.1 30 425-458 31-60 (221)
436 PF02042 RWP-RK: RWP-RK domain 50.1 37 0.00079 26.2 4.6 23 428-450 15-37 (52)
437 PF10078 DUF2316: Uncharacteri 50.0 37 0.00081 29.1 5.0 25 427-451 22-46 (89)
438 PF07037 DUF1323: Putative tra 49.8 18 0.0004 32.5 3.3 23 429-451 1-23 (122)
439 COG4367 Uncharacterized protei 49.2 44 0.00095 28.7 5.3 24 427-450 22-45 (97)
440 smart00342 HTH_ARAC helix_turn 49.1 79 0.0017 24.3 6.7 60 302-364 1-62 (84)
441 PRK11511 DNA-binding transcrip 48.7 37 0.0008 30.1 5.2 26 427-452 24-49 (127)
442 TIGR03338 phnR_burk phosphonat 48.7 23 0.00051 33.5 4.2 30 425-458 31-60 (212)
443 PRK09943 DNA-binding transcrip 48.6 27 0.00058 32.8 4.5 25 427-451 19-43 (185)
444 COG5606 Uncharacterized conser 48.4 15 0.00033 31.4 2.4 36 427-462 40-80 (91)
445 PRK13509 transcriptional repre 48.3 36 0.00078 33.8 5.6 26 426-451 17-42 (251)
446 PRK03837 transcriptional regul 48.3 28 0.00061 33.6 4.7 30 425-458 33-63 (241)
447 PRK11014 transcriptional repre 48.2 25 0.00054 31.7 4.0 30 425-458 22-51 (141)
448 PRK10163 DNA-binding transcrip 47.8 36 0.00077 34.1 5.5 26 426-451 38-63 (271)
449 PRK15121 right oriC-binding tr 47.5 1.1E+02 0.0023 30.7 8.9 41 286-326 5-45 (289)
450 TIGR02812 fadR_gamma fatty aci 47.5 29 0.00062 33.6 4.6 30 425-458 26-56 (235)
451 smart00862 Trans_reg_C Transcr 47.3 65 0.0014 25.0 5.9 50 408-458 5-60 (78)
452 cd00383 trans_reg_C Effector d 47.2 47 0.001 27.0 5.2 49 408-457 23-76 (95)
453 PF12324 HTH_15: Helix-turn-he 47.1 37 0.00079 28.4 4.4 52 400-451 7-61 (77)
454 PRK11534 DNA-binding transcrip 46.7 30 0.00065 33.2 4.6 30 425-458 27-56 (224)
455 PRK10434 srlR DNA-bindng trans 46.5 32 0.00069 34.3 4.9 38 411-451 5-42 (256)
456 PF12759 HTH_Tnp_IS1: InsA C-t 46.3 29 0.00062 26.2 3.4 37 410-451 8-44 (46)
457 PF05930 Phage_AlpA: Prophage 46.0 25 0.00053 26.3 3.1 24 429-452 4-27 (51)
458 TIGR03613 RutR pyrimidine util 46.0 2.4E+02 0.0053 25.9 11.4 81 287-368 12-93 (202)
459 TIGR03826 YvyF flagellar opero 45.5 54 0.0012 30.2 5.8 38 290-327 34-71 (137)
460 PF05331 DUF742: Protein of un 45.5 35 0.00075 30.5 4.4 40 407-451 39-78 (114)
461 TIGR03764 ICE_PFGI_1_parB inte 45.4 2.3E+02 0.005 28.8 10.7 20 295-314 129-148 (258)
462 COG2963 Transposase and inacti 45.2 49 0.0011 28.6 5.3 43 408-454 7-51 (116)
463 PRK09990 DNA-binding transcrip 45.1 33 0.00071 33.5 4.7 30 425-458 27-57 (251)
464 PRK11569 transcriptional repre 45.1 36 0.00077 34.1 5.0 26 426-451 41-66 (274)
465 PRK09464 pdhR transcriptional 44.9 33 0.00072 33.6 4.7 30 425-458 30-60 (254)
466 cd04768 HTH_BmrR-like Helix-Tu 44.8 17 0.00036 30.9 2.2 26 429-454 1-26 (96)
467 TIGR00270 conserved hypothetic 44.8 34 0.00073 32.0 4.4 25 427-451 81-105 (154)
468 TIGR00637 ModE_repress ModE mo 44.5 63 0.0014 27.7 5.8 44 410-458 3-46 (99)
469 PF01381 HTH_3: Helix-turn-hel 44.3 53 0.0012 24.1 4.7 25 303-327 10-34 (55)
470 PF13744 HTH_37: Helix-turn-he 44.0 1.6E+02 0.0034 24.0 7.8 51 270-326 5-55 (80)
471 PRK08359 transcription factor; 43.9 34 0.00073 32.8 4.3 25 427-451 97-121 (176)
472 PRK10225 DNA-binding transcrip 43.8 35 0.00075 33.5 4.6 30 425-458 29-59 (257)
473 cd04775 HTH_Cfa-like Helix-Tur 43.7 17 0.00037 31.1 2.2 26 429-454 2-27 (102)
474 PRK10421 DNA-binding transcrip 43.6 35 0.00076 33.5 4.7 30 425-458 22-52 (253)
475 PRK10402 DNA-binding transcrip 43.6 48 0.001 31.8 5.5 27 428-458 169-195 (226)
476 PF12085 DUF3562: Protein of u 43.3 51 0.0011 26.8 4.6 41 429-472 8-48 (66)
477 cd01105 HTH_GlnR-like Helix-Tu 42.7 20 0.00042 30.0 2.3 25 429-453 2-26 (88)
478 PF00440 TetR_N: Bacterial reg 42.5 61 0.0013 23.5 4.7 22 427-448 15-36 (47)
479 cd00592 HTH_MerR-like Helix-Tu 42.5 19 0.00041 30.2 2.2 25 429-453 1-25 (100)
480 cd04766 HTH_HspR Helix-Turn-He 42.5 18 0.0004 30.1 2.1 27 429-455 2-28 (91)
481 PRK09391 fixK transcriptional 42.3 1E+02 0.0022 29.7 7.6 27 428-458 179-205 (230)
482 cd04773 HTH_TioE_rpt2 Second H 42.2 19 0.00041 31.3 2.2 26 429-454 1-26 (108)
483 PRK10906 DNA-binding transcrip 42.2 42 0.0009 33.5 5.0 38 411-451 5-42 (252)
484 TIGR02684 dnstrm_HI1420 probab 42.2 74 0.0016 26.9 5.7 23 427-451 44-66 (89)
485 TIGR00373 conserved hypothetic 42.1 50 0.0011 30.8 5.2 39 410-451 13-51 (158)
486 PF04814 HNF-1_N: Hepatocyte n 41.7 21 0.00046 34.3 2.6 52 399-453 105-156 (180)
487 cd04765 HTH_MlrA-like_sg2 Heli 41.5 32 0.00069 29.5 3.5 23 429-451 1-23 (99)
488 PRK11886 bifunctional biotin-- 41.3 47 0.001 34.0 5.3 40 412-454 5-44 (319)
489 PRK09393 ftrA transcriptional 41.2 1.3E+02 0.0028 30.5 8.5 40 287-326 219-258 (322)
490 PRK00082 hrcA heat-inducible t 41.0 37 0.00081 35.5 4.6 49 407-456 2-54 (339)
491 COG1349 GlpR Transcriptional r 41.0 32 0.0007 34.3 4.0 38 410-450 4-41 (253)
492 cd04780 HTH_MerR-like_sg5 Heli 40.9 21 0.00045 30.4 2.2 25 429-453 1-25 (95)
493 PF13404 HTH_AsnC-type: AsnC-t 40.8 86 0.0019 22.8 5.1 28 296-324 12-39 (42)
494 PF01371 Trp_repressor: Trp re 40.3 1.2E+02 0.0025 25.9 6.6 51 269-329 26-79 (87)
495 cd01106 HTH_TipAL-Mta Helix-Tu 39.9 22 0.00047 30.3 2.2 25 429-453 1-25 (103)
496 PF00126 HTH_1: Bacterial regu 39.9 60 0.0013 24.8 4.5 31 427-457 12-42 (60)
497 TIGR02010 IscR iron-sulfur clu 39.9 61 0.0013 29.0 5.2 27 425-451 22-48 (135)
498 COG1481 Uncharacterized protei 39.5 60 0.0013 33.8 5.6 43 407-452 252-296 (308)
499 cd01107 HTH_BmrR Helix-Turn-He 39.5 23 0.00049 30.6 2.3 26 429-454 1-26 (108)
500 PRK10681 DNA-binding transcrip 39.3 60 0.0013 32.3 5.5 38 411-451 7-44 (252)
No 1
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=100.00 E-value=1.9e-38 Score=331.35 Aligned_cols=219 Identities=39% Similarity=0.664 Sum_probs=199.1
Q ss_pred ChhHHhhhcccCccCCCChHHHHHHHHHHHHHHH--------------------HHHHHHHHHHHhCCCCCHHHHHHHcC
Q 011992 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR--------------------LEKEKSKLQSQFGREPTLIEWAKAIG 313 (473)
Q Consensus 254 ~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~k--------------------le~a~~~L~~~lGRePT~eEiA~~lG 313 (473)
.|++|.|++.++++|+||++||++|++++|.+.+ |++++.+|..++|++||..|||+++|
T Consensus 59 ~d~v~~yl~~igr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~~~~ 138 (415)
T PRK07598 59 TDLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKTAD 138 (415)
T ss_pred CChHHHHHHhcccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHHHhC
Confidence 4589999999999999999999999999999998 89999999999999999999995555
Q ss_pred ----------------------CCHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhh
Q 011992 314 ----------------------LSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVE 371 (473)
Q Consensus 314 ----------------------ms~eeL~~~l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAie 371 (473)
|+.++|...+..|..|+++||..|+++|+++|++|.+++.+++||+|||++|||++++
T Consensus 139 ~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~rave 218 (415)
T PRK07598 139 ISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVE 218 (415)
T ss_pred CcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHH
Confidence 5566666667788899999999999999999999999999999999999999999999
Q ss_pred hhCccCCCccccC-------------------------------------------------------------------
Q 011992 372 KFKPQAGCRFANT------------------------------------------------------------------- 384 (473)
Q Consensus 372 kFDp~kg~~FsT~------------------------------------------------------------------- 384 (473)
+|||.+|++|+|+
T Consensus 219 kFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~ 298 (415)
T PRK07598 219 KFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREV 298 (415)
T ss_pred HcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 9999999999990
Q ss_pred ----------------------------CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHH
Q 011992 385 ----------------------------GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGN 436 (473)
Q Consensus 385 ----------------------------~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe 436 (473)
....|++.+....+...|..+|..||+++|.||.|+|+|+||+++|++|||+
T Consensus 299 l~~~~~~~SLd~~vg~~~d~~l~d~l~~~~~~pee~~~~~~l~~~L~~~L~~L~~reR~VI~LRygl~d~~~~Tl~EIA~ 378 (415)
T PRK07598 299 LLRVPRSVSLETKVGKDKDTELGDLLETDDISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEIGR 378 (415)
T ss_pred HHHccCCcccccccCCCccccHHHhccCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCCCHHHHHH
Confidence 0123455566677788899999999999999999999999999999999999
Q ss_pred HHCCCHHHHHHHHHHHHHHHHHHhccCchhhhhhhh
Q 011992 437 IFGLSKERVRQLESRALYRLKQSLGGKASYGYADLL 472 (473)
Q Consensus 437 ~LGIS~~rVrqi~~RAL~KLR~~L~~~~l~~yldll 472 (473)
.||||+++|++++++|++|||+.-....+++|++-|
T Consensus 379 ~LGvS~erVRqie~rAl~KLR~~~~~~~l~~y~~~~ 414 (415)
T PRK07598 379 ALDLSRERVRQIESKALQKLRQPKRRNRIRDYLELL 414 (415)
T ss_pred HHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHHHhc
Confidence 999999999999999999999988888899998754
No 2
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=100.00 E-value=6.8e-36 Score=300.93 Aligned_cols=202 Identities=47% Similarity=0.798 Sum_probs=188.7
Q ss_pred hHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHH
Q 011992 256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 335 (473)
Q Consensus 256 ~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~ 335 (473)
+++.|++.+.+.|+||+|||.+|+++++....++..+..|..++|++||..|||+++|++..++...+..|..|++.||.
T Consensus 2 ~~~~yl~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Lv~ 81 (298)
T TIGR02997 2 LVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMIK 81 (298)
T ss_pred cHHHHHHHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHHHH
Confidence 57789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccccCCC-----------------------------
Q 011992 336 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGV----------------------------- 386 (473)
Q Consensus 336 ~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~~~----------------------------- 386 (473)
.|+++|+++|++|.+++.+++||+|||++|||+++++|||.+|++|+|+..
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 999999999999999999999999999999999999999999999988110
Q ss_pred ------------------------------------------------------------------CCchHHHHHHHHHH
Q 011992 387 ------------------------------------------------------------------EIPDISVQKQLMRQ 400 (473)
Q Consensus 387 ------------------------------------------------------------------~~pee~le~~el~e 400 (473)
..|++.+...+...
T Consensus 162 ~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~~~~~pe~~~~~~~~~~ 241 (298)
T TIGR02997 162 KIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDDGESPEEQVERESLRQ 241 (298)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCcchHHHhccCCCCCHHHHHHHHHHHH
Confidence 12345556666777
Q ss_pred HHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992 401 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457 (473)
Q Consensus 401 ~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR 457 (473)
.|.++|+.||+++|.||.++|||++++++|++|||+.||||+++|+|++++|++|||
T Consensus 242 ~L~~~L~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr 298 (298)
T TIGR02997 242 DLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298 (298)
T ss_pred HHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 899999999999999999999998889999999999999999999999999999986
No 3
>PRK05949 RNA polymerase sigma factor; Validated
Probab=100.00 E-value=1.4e-35 Score=302.86 Aligned_cols=215 Identities=42% Similarity=0.685 Sum_probs=198.0
Q ss_pred ChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHH
Q 011992 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL 333 (473)
Q Consensus 254 ~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~L 333 (473)
.|+++.|++.+.+.|+||++||++|+++++.+..++..+..|..++|++|+..|||.+++++..+|...++.|+.|++.|
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 35799999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccccCC----------------------------
Q 011992 334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTG---------------------------- 385 (473)
Q Consensus 334 i~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~~---------------------------- 385 (473)
|..|+++|+++|++|.+++.+++||+|||++|||+++++||+.+|++|+|+.
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 9999999999999999999999999999999999999999999999999900
Q ss_pred -------------------------------------------------------------------CCCchHHHHHHHH
Q 011992 386 -------------------------------------------------------------------VEIPDISVQKQLM 398 (473)
Q Consensus 386 -------------------------------------------------------------------~~~pee~le~~el 398 (473)
...|++.+.....
T Consensus 177 ~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~l~d~~~~pe~~~~~~~~ 256 (327)
T PRK05949 177 LNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEGPSPDQYITQELL 256 (327)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCccHHhhcCCCCCCHHHHHHHHHH
Confidence 1234555666777
Q ss_pred HHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCchhhhhh
Q 011992 399 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD 470 (473)
Q Consensus 399 ~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~l~~yld 470 (473)
...|..+|+.||+++|.||.++|||++++++|++|||+.||||+++|+|++.+|++|||+.. ..+..|+.
T Consensus 257 ~~~L~~~L~~L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~~~--~~l~~~~~ 326 (327)
T PRK05949 257 RQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRRRR--ANVKEYLA 326 (327)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH--HHHHHHHh
Confidence 88899999999999999999999999999999999999999999999999999999999943 45566653
No 4
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=2.6e-35 Score=299.65 Aligned_cols=215 Identities=38% Similarity=0.639 Sum_probs=197.1
Q ss_pred ChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHH
Q 011992 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL 333 (473)
Q Consensus 254 ~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~L 333 (473)
.+++..|+..+++.|+||+|||.+|+++++.+..+++.+..|..++|++|+..|||.+++++..++...+..|..|++.|
T Consensus 7 ~~~~~~yl~~i~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~~L 86 (317)
T PRK07405 7 TDLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRKM 86 (317)
T ss_pred CcHHHHHHHHccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHHHH
Confidence 34789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccccCC----------------------------
Q 011992 334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTG---------------------------- 385 (473)
Q Consensus 334 i~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~~---------------------------- 385 (473)
|..|+++|+++|++|.+++.+++||+||||+|||+++++||+.+|++|+|+.
T Consensus 87 ~~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir~p~~~~~~ 166 (317)
T PRK07405 87 VEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEK 166 (317)
T ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCccCChHHHHH
Confidence 9999999999999999999999999999999999999999999999998810
Q ss_pred -------------------------------------------------------------------CCCchHHHHHHHH
Q 011992 386 -------------------------------------------------------------------VEIPDISVQKQLM 398 (473)
Q Consensus 386 -------------------------------------------------------------------~~~pee~le~~el 398 (473)
...|++.+...++
T Consensus 167 ~~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~~~d~~~~pe~~~~~~~~ 246 (317)
T PRK07405 167 LNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTGASPEDFATQSSL 246 (317)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCccHHHhhcCCCCCHHHHHHHHHH
Confidence 1134555666777
Q ss_pred HHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCchhhhhh
Q 011992 399 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD 470 (473)
Q Consensus 399 ~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~l~~yld 470 (473)
...|.++|+.||+++|.||.++|+|+|++++|++|||+.||||++||+|++.+|++|||+.. ..+..|+.
T Consensus 247 ~~~l~~al~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~~~--~~l~~~~~ 316 (317)
T PRK07405 247 QLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKRK--ANIQEYLA 316 (317)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH--HHHHHHHh
Confidence 88899999999999999999999999999999999999999999999999999999999863 45556653
No 5
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=1.8e-35 Score=306.43 Aligned_cols=215 Identities=39% Similarity=0.743 Sum_probs=202.0
Q ss_pred hhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHH
Q 011992 255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLI 334 (473)
Q Consensus 255 ~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li 334 (473)
++++.|+..+++.|+||+|||++|+++++.+..+++.+..|..++|++|+..+||.+.|++..+|.+.+..|..|++.||
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 47899999999999999999999999999999999999999999999999999999999999999999998899999999
Q ss_pred HHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-------------------------------
Q 011992 335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------------------------------- 383 (473)
Q Consensus 335 ~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------------------------------- 383 (473)
..|+++|+++|++|.+++.+++||+|||++|||+++++||+.+|++|+|
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 9999999999999999999999999999999999999999999999999
Q ss_pred ----------------------------------------------------------------CCCCCchHHHHHHHHH
Q 011992 384 ----------------------------------------------------------------TGVEIPDISVQKQLMR 399 (473)
Q Consensus 384 ----------------------------------------------------------------~~~~~pee~le~~el~ 399 (473)
+....|++.+....+.
T Consensus 223 ~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~~~l~d~l~d~~~~pee~~~~~~~~ 302 (373)
T PRK07406 223 SRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADGETPEDDVAKNLLR 302 (373)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCcccHHHhcCCCCCCHHHHHHHHHHH
Confidence 0123456667777788
Q ss_pred HHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCchhhhh
Q 011992 400 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYA 469 (473)
Q Consensus 400 e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~l~~yl 469 (473)
..|..+|..||++||.||.+||++++++++|++|||+.||||++||+|++.+|++|||.......+..|+
T Consensus 303 ~~L~~aL~~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~~~~~~~l~~~~ 372 (373)
T PRK07406 303 EDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI 372 (373)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHh
Confidence 8999999999999999999999998889999999999999999999999999999999998888887775
No 6
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=99.97 E-value=4.8e-31 Score=269.20 Aligned_cols=203 Identities=37% Similarity=0.658 Sum_probs=173.9
Q ss_pred ChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHH
Q 011992 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL 333 (473)
Q Consensus 254 ~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~L 333 (473)
.+.+..|+....+.|+||+|||.+|+++++....++.. .+....++.. ...++...+..|..|++.|
T Consensus 25 ~~~~~~Yl~~i~~~~lLt~eeE~~La~~~~~g~~~~~~----------~~~~~~~~~~---~~~~l~~~~~~~~~A~~~L 91 (324)
T PRK07921 25 ADLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHL----------LETRKRLSEA---RKRDLAAVVRDGEAARRHL 91 (324)
T ss_pred CChHHHHHHHhcccCCCCHHHHHHHHHHHHhhhhhhhh----------hccccccchh---HHHHHHHHHhcCHHHHHHH
Confidence 35789999999999999999999999999876555443 1111111111 3457888888889999999
Q ss_pred HHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc------------------------------
Q 011992 334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------------------------------ 383 (473)
Q Consensus 334 i~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------------------------------ 383 (473)
|..|+++|+++|++|.+++.+++||+|||++|||+++++|||++|++|+|
T Consensus 92 v~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~~~~~~ 171 (324)
T PRK07921 92 LEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ 171 (324)
T ss_pred HHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCHHHHHH
Confidence 99999999999999999999999999999999999999999999999999
Q ss_pred ------------------------------------------------------------------CCCCCchHHHHHHH
Q 011992 384 ------------------------------------------------------------------TGVEIPDISVQKQL 397 (473)
Q Consensus 384 ------------------------------------------------------------------~~~~~pee~le~~e 397 (473)
.....|++.+...+
T Consensus 172 ~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~~ 251 (324)
T PRK07921 172 VNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAGL 251 (324)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCchHHHHhcCCCCCCHHHHHHHHH
Confidence 00123455566677
Q ss_pred HHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCchhhhh
Q 011992 398 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYA 469 (473)
Q Consensus 398 l~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~l~~yl 469 (473)
+...|..+|..|+++|+.||.+||||++|+++|++|||+.||||++||+||+.+|++|||.......+..|+
T Consensus 252 ~~~~l~~~L~~L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~~~~~~~l~~~~ 323 (324)
T PRK07921 252 LHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSYA 323 (324)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHHHHHHHHhh
Confidence 888899999999999999999999999999999999999999999999999999999999998777777775
No 7
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=99.97 E-value=3.9e-31 Score=282.61 Aligned_cols=209 Identities=36% Similarity=0.607 Sum_probs=176.2
Q ss_pred cccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhh
Q 011992 246 KLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS 325 (473)
Q Consensus 246 ~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~ 325 (473)
+.++..| +++.|+..++++|+||++||++|+++++.....+. .+.. ..+|+. ....++...+..
T Consensus 205 ~~~~~~d---~l~~YL~~i~~~~lLt~eEE~~La~~i~~g~~~~~---~~~~-------~~~~~~---~~~~~l~~~~~~ 268 (509)
T PRK05901 205 KLTATAD---PVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEE---LLAE-------GEKLDP---ELRRDLQWIGRD 268 (509)
T ss_pred hcccccc---HHHHHHHHhccCCCCCHHHHHHHHHHHHhCCchhh---hhhh-------cccchh---hhhhhhhhhccc
Confidence 3456544 79999999999999999999999999987532222 1111 012221 234667778888
Q ss_pred cchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------------------
Q 011992 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------------------- 383 (473)
Q Consensus 326 g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT---------------------- 383 (473)
|..|++.||..|+++|+++|++|.+++++++||||||++||++|+++|||.+|++|+|
T Consensus 269 g~~Ar~~LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IR 348 (509)
T PRK05901 269 GKRAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIR 348 (509)
T ss_pred hHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCcee
Confidence 8899999999999999999999999999999999999999999999999999999999
Q ss_pred --------------------------------------------------------------------------CCCCCc
Q 011992 384 --------------------------------------------------------------------------TGVEIP 389 (473)
Q Consensus 384 --------------------------------------------------------------------------~~~~~p 389 (473)
.....|
T Consensus 349 vP~~~~e~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~~p 428 (509)
T PRK05901 349 IPVHMVETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSP 428 (509)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCcccHHHhccCCCCCCH
Confidence 001234
Q ss_pred hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCchhhhh
Q 011992 390 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYA 469 (473)
Q Consensus 390 ee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~l~~yl 469 (473)
++.+....++..|..+|..|+++||.||.+||||++++++|++|||+.||||++|||||+.+||.|||.......+..|+
T Consensus 429 ~~~~~~~~l~~~L~~aL~~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~~~~~~~l~~~l 508 (509)
T PRK05901 429 VDAVSFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRDFL 508 (509)
T ss_pred HHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 45566777888899999999999999999999999889999999999999999999999999999999998888888887
Q ss_pred h
Q 011992 470 D 470 (473)
Q Consensus 470 d 470 (473)
+
T Consensus 509 ~ 509 (509)
T PRK05901 509 D 509 (509)
T ss_pred C
Confidence 4
No 8
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=99.96 E-value=2.9e-28 Score=248.40 Aligned_cols=216 Identities=38% Similarity=0.659 Sum_probs=189.2
Q ss_pred hhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHH-HhCCCCCHH---------------HHHHHcCCCH-H
Q 011992 255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQS-QFGREPTLI---------------EWAKAIGLSC-R 317 (473)
Q Consensus 255 ~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~-~lGRePT~e---------------EiA~~lGms~-e 317 (473)
+.++.|+......+++++++|.++...++....+......+.. .+|+.|+.. +++..+..++ .
T Consensus 9 d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Ee~ 88 (342)
T COG0568 9 DAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEEEK 88 (342)
T ss_pred hHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHHHH
Confidence 3678888888899999999999999999887766667777777 688999987 6666666665 6
Q ss_pred HHHHHHhhcc---hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------
Q 011992 318 DLKSELHSGN---SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------- 383 (473)
Q Consensus 318 eL~~~l~~g~---~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------- 383 (473)
++...+..|. .|..+||.+|+++|++||++|.++|+++.||||||++||++|+++|||++|++|+|
T Consensus 89 ~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAVekFdp~rG~kFsTYA~wWIrqaI~ 168 (342)
T COG0568 89 ALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQAIT 168 (342)
T ss_pred HHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHHHHhcCcccCCcchhHHHHHHHHHHH
Confidence 6777787774 59999999999999999999999999999999999999999999999999999999
Q ss_pred --------------------------------------------------------------------------------
Q 011992 384 -------------------------------------------------------------------------------- 383 (473)
Q Consensus 384 -------------------------------------------------------------------------------- 383 (473)
T Consensus 169 raI~~q~rtIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd~~ig~ded~~l~ 248 (342)
T COG0568 169 RAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDDEDSELG 248 (342)
T ss_pred HHHHHhcchhhHhHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccCCcCCCCcccHHH
Confidence
Q ss_pred -----CCCCCchHHHHHHHHHHHHHHHHhh-CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992 384 -----TGVEIPDISVQKQLMRQHVRNLLTL-LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457 (473)
Q Consensus 384 -----~~~~~pee~le~~el~e~L~~aL~~-LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR 457 (473)
.....|++.+....+.+.+...|.. |+++|+.||.+||+++|+++.|++|||+.+|||++|||||+.+|++|||
T Consensus 249 d~leD~~~~~p~~~~~~~~~~~~~~~~L~~~Lt~rE~~Vi~~R~gl~~~~~~TLeevg~~~~isrERvRQIE~kAl~KLr 328 (342)
T COG0568 249 DFLEDDKSVSPEDAVERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEAKALRKLR 328 (342)
T ss_pred HHhhcCCcCCHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCcchHHHHHHHhCCcHHHHHHHHHHHHHHHH
Confidence 1133678888888999999999999 9999999999999999999999999999999999999999999999999
Q ss_pred HHhcc-Cchhhhhh
Q 011992 458 QSLGG-KASYGYAD 470 (473)
Q Consensus 458 ~~L~~-~~l~~yld 470 (473)
..... ..+.+|++
T Consensus 329 ~~~~~~~~~~~~l~ 342 (342)
T COG0568 329 RHPERSALLRSYLD 342 (342)
T ss_pred HhhhhhhHHHHhhC
Confidence 55444 34566763
No 9
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=99.96 E-value=2e-28 Score=253.73 Aligned_cols=177 Identities=40% Similarity=0.745 Sum_probs=159.7
Q ss_pred ChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHH
Q 011992 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL 333 (473)
Q Consensus 254 ~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~L 333 (473)
.+.++.|+..+.+.|+||++||.+|+++++. ++..|++.|
T Consensus 95 ~d~~~~yl~~i~~~~~l~~~ee~~L~~~~~~----------------------------------------Gd~~A~~~L 134 (367)
T PRK09210 95 NDPVRMYLKEIGRVPLLTAEEEIELAKRIEE----------------------------------------GDEEAKQRL 134 (367)
T ss_pred CcHHHHHHHHhhccCCCCHHHHHHHHHHHHh----------------------------------------hHHHHHHHH
Confidence 4579999999999999999999999887654 234789999
Q ss_pred HHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc------------------------------
Q 011992 334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------------------------------ 383 (473)
Q Consensus 334 i~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------------------------------ 383 (473)
|..|+++|+++|++|.+++.+++||+|||++|||+++++||+.+|++|+|
T Consensus 135 i~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~~~~~~ 214 (367)
T PRK09210 135 AEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 214 (367)
T ss_pred HHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccHHHHHH
Confidence 99999999999999999999999999999999999999999999999999
Q ss_pred ------------------------------------------------------------------CCCCCchHHHHHHH
Q 011992 384 ------------------------------------------------------------------TGVEIPDISVQKQL 397 (473)
Q Consensus 384 ------------------------------------------------------------------~~~~~pee~le~~e 397 (473)
.....|+..+....
T Consensus 215 ~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~i~d~~~~~p~~~~~~~~ 294 (367)
T PRK09210 215 INKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYEL 294 (367)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCCCcchhhhhccCCCCCCHHHHHHHHH
Confidence 00124555566777
Q ss_pred HHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCchhhhhh
Q 011992 398 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD 470 (473)
Q Consensus 398 l~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~l~~yld 470 (473)
++..|..+|..||++||.||.+||||+||+++|++|||+.||||++|||||+.+||.|||.......+..|++
T Consensus 295 ~~~~l~~~l~~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~~~~~~~l~~~~~ 367 (367)
T PRK09210 295 LKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 367 (367)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhChHHHhHHHHhhC
Confidence 8889999999999999999999999999999999999999999999999999999999999998888888863
No 10
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=99.92 E-value=2.7e-24 Score=236.42 Aligned_cols=165 Identities=34% Similarity=0.663 Sum_probs=144.9
Q ss_pred HHHHHHcCCCHHHHHHH---Hhhcc----hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCC
Q 011992 306 IEWAKAIGLSCRDLKSE---LHSGN----SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAG 378 (473)
Q Consensus 306 eEiA~~lGms~eeL~~~---l~~g~----~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg 378 (473)
.++....+++.+++..+ +..|+ .|+++||..|+++|+++|++|.+++++++||+|||++||++|+++|||.+|
T Consensus 351 ~~ie~~~~Ls~eElk~l~~~i~~g~~~~~~a~~~Li~~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G 430 (619)
T PRK05658 351 EAIEEETGLTIEELKEINRQISKGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 430 (619)
T ss_pred HHHHHHhCCCHHHHHHHHHHHhccchhhhHHHHHHHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCC
Confidence 45667777777665444 34443 688999999999999999999999999999999999999999999999999
Q ss_pred Ccccc---------------------------------------------------------------------------
Q 011992 379 CRFAN--------------------------------------------------------------------------- 383 (473)
Q Consensus 379 ~~FsT--------------------------------------------------------------------------- 383 (473)
++|+|
T Consensus 431 ~~FstYA~~wIr~aI~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~ 510 (619)
T PRK05658 431 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEP 510 (619)
T ss_pred CchHHHhHHHHHHHHHHHHHHcCCceecCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCC
Confidence 99999
Q ss_pred ---------------------CCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCH
Q 011992 384 ---------------------TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSK 442 (473)
Q Consensus 384 ---------------------~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~ 442 (473)
.....|...+....++..|..+|..||++|+.||.+||||++++++|++|||+.||||+
T Consensus 511 ~Sld~~i~~~~~~~l~d~i~d~~~~~p~~~~~~~~~~~~l~~~l~~L~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~ 590 (619)
T PRK05658 511 ISLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTR 590 (619)
T ss_pred CcCCCCCCCCCCCchhhhcCCCCCCChHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCH
Confidence 00123455566778888999999999999999999999998889999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhccCchhhhhh
Q 011992 443 ERVRQLESRALYRLKQSLGGKASYGYAD 470 (473)
Q Consensus 443 ~rVrqi~~RAL~KLR~~L~~~~l~~yld 470 (473)
+|||||+.+|++|||.......++.|++
T Consensus 591 eRVrQie~~al~kLr~~~~~~~l~~~~~ 618 (619)
T PRK05658 591 ERIRQIEAKALRKLRHPSRSRKLRSFLD 618 (619)
T ss_pred HHHHHHHHHHHHHHhchHHHHHHHHHhc
Confidence 9999999999999999998889999986
No 11
>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=99.92 E-value=1.3e-24 Score=212.09 Aligned_cols=192 Identities=28% Similarity=0.422 Sum_probs=152.8
Q ss_pred hccCCCCCCcccccccccccccccccccCCCChhHHhhhc---ccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 011992 223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLW---GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQF 299 (473)
Q Consensus 223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~---~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~l 299 (473)
.|..+.+|.+|+|||.|||+ |+|.++ ++...| .|++. .+...++.++..+|.+.+
T Consensus 43 ~~fd~~~g~~FstYA~~~Ir-----~~I~~~---l~~~~~~vrip~~~--------------~~~~~~~~~~~~~l~~~~ 100 (238)
T TIGR02393 43 EKFDYRKGYKFSTYATWWIR-----QAITRA---IADQARTIRIPVHM--------------VETINKLIKAERQLTQEL 100 (238)
T ss_pred HHhCCCCCCChHHHhHHHHH-----HHHHHH---HHHcCCcEEeCHHH--------------HHHHHHHHHHHHHHHHHh
Confidence 35678899999999999999 999874 665554 45444 456778889999999999
Q ss_pred CCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHH-HHHHHhhhhCccCC
Q 011992 300 GREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSM-GLMKSVEKFKPQAG 378 (473)
Q Consensus 300 GRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~l-gL~kAiekFDp~kg 378 (473)
|++||.+|+|+.+|++.+++....... ....++++.++++.- .+...+.
T Consensus 101 g~~pt~~eia~~l~~~~~~v~~~~~~~-----------------------~~~~SLd~~~~~~~~~~l~d~l~------- 150 (238)
T TIGR02393 101 GREPTDEELAERMGMPAEKVREIKKIA-----------------------QEPISLETPIGEEEDSFLGDFIE------- 150 (238)
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHh-----------------------ccCCCcCCCCCCCCcccHHHHhc-------
Confidence 999999999999999999987654321 123556655543211 1111111
Q ss_pred CccccCCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 379 CRFANTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 379 ~~FsT~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
......|+..+...+....|..+|+.||++||.||.++|+|++++++|++|||+.||||.++|+|++.+|++|||.
T Consensus 151 ----d~~~~~p~~~~~~~~~~~~l~~~l~~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~ 226 (238)
T TIGR02393 151 ----DTSIESPDDYAAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRH 226 (238)
T ss_pred ----CCCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 1123567788888889999999999999999999999998888899999999999999999999999999999999
Q ss_pred HhccCchhhhhh
Q 011992 459 SLGGKASYGYAD 470 (473)
Q Consensus 459 ~L~~~~l~~yld 470 (473)
.+....+..|+|
T Consensus 227 ~~~~~~~~~~~~ 238 (238)
T TIGR02393 227 PSRSKKLKSFLD 238 (238)
T ss_pred hHHHhHHHHhhC
Confidence 998888888875
No 12
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=99.91 E-value=1.7e-24 Score=213.11 Aligned_cols=178 Identities=24% Similarity=0.351 Sum_probs=149.6
Q ss_pred hccCCCCCCcccccccccccccccccccCCCChhHHhhh--cccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Q 011992 223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFL--WGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFG 300 (473)
Q Consensus 223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~--~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lG 300 (473)
.|+++.+|.+|+|||.++|+ |+|+| .||+-+ |.||+. .+..+++..+..+|++++|
T Consensus 67 eryd~~kg~kF~tyA~~~I~-----Gei~d---~LR~~~~v~vpR~~--------------~~~~~~i~~~~~~l~~el~ 124 (247)
T COG1191 67 ERYDPSKGTKFSTYAVRRIR-----GEILD---YLRKNDSVKVPRSL--------------RELGRRIEEAIDELEQELG 124 (247)
T ss_pred HHcCcccCcchHHHHHHHHH-----HHHHH---HHHhCCCccCcHHH--------------HHHHHHHHHHHHHHHHHhC
Confidence 36789999999999999999 99999 499999 999998 5888899999999999999
Q ss_pred CCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCc
Q 011992 301 REPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCR 380 (473)
Q Consensus 301 RePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~ 380 (473)
|+||++|||+.+|++.+++...+..+... ...++++.+....-+ .
T Consensus 125 r~pt~~EIA~~L~i~~ee~~~~~~~~~~~---------------------~~~sld~~~~~~~d~-----------~--- 169 (247)
T COG1191 125 REPTDEEIAEELGIDKEEYIEALLAINGS---------------------QLLSLDEDVLKDDDD-----------D--- 169 (247)
T ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHhccc---------------------cccchhhhhcccccc-----------c---
Confidence 99999999999999999999887765421 123333333211100 0
Q ss_pred cccCCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992 381 FANTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 460 (473)
Q Consensus 381 FsT~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L 460 (473)
..+....|...+++.+....|.+++..|+++||.|+.+||+ +++|++|||++||||+++|+|++++|+.|||..|
T Consensus 170 -~~~~~~~~~~~~~~~~~~~~l~~ai~~L~EREk~Vl~l~y~----eelt~kEI~~~LgISes~VSql~kkai~kLr~~l 244 (247)
T COG1191 170 -VDDQIENPDDGVEKEELLEILKEAIEPLPEREKLVLVLRYK----EELTQKEIAEVLGISESRVSRLHKKAIKKLRKEL 244 (247)
T ss_pred -hhhccccchhHHHHHHHHHHHHHHHHccCHHHHHHHHHHHH----hccCHHHHHHHhCccHHHHHHHHHHHHHHHHHHh
Confidence 11224567778888899999999999999999999999999 9999999999999999999999999999999987
Q ss_pred cc
Q 011992 461 GG 462 (473)
Q Consensus 461 ~~ 462 (473)
..
T Consensus 245 ~~ 246 (247)
T COG1191 245 NK 246 (247)
T ss_pred cc
Confidence 64
No 13
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=99.91 E-value=1.7e-23 Score=213.78 Aligned_cols=171 Identities=36% Similarity=0.574 Sum_probs=150.6
Q ss_pred hHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHH
Q 011992 256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 335 (473)
Q Consensus 256 ~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~ 335 (473)
.++.|+..++..|+||+++|.+|+++++. ++..|++.||.
T Consensus 54 ~~~~y~~~~~~~~~l~~~ee~~li~~~~~----------------------------------------Gd~~A~~~Li~ 93 (325)
T PRK05657 54 ATQLYLNEIGYSPLLTAEEEVYFARRALR----------------------------------------GDFAARQRMIE 93 (325)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHH
Confidence 57889999999999999999999877543 44589999999
Q ss_pred HHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccccCC------------------------------
Q 011992 336 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTG------------------------------ 385 (473)
Q Consensus 336 ~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~~------------------------------ 385 (473)
.|.++|+++|++|.+++.+++|++||||+|+|+++++|++.+|++|+|+.
T Consensus 94 ~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~~i~~~~r~ir~p~~~~~~l~ 173 (325)
T PRK05657 94 SNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVKELN 173 (325)
T ss_pred HhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHcCCccccCHHHHHHHH
Confidence 99999999999999999999999999999999999999999998886400
Q ss_pred ------------------------------------------------------------------CCCchHHHHHHHHH
Q 011992 386 ------------------------------------------------------------------VEIPDISVQKQLMR 399 (473)
Q Consensus 386 ------------------------------------------------------------------~~~pee~le~~el~ 399 (473)
...|+..+...+..
T Consensus 174 ~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~e~~ 253 (325)
T PRK05657 174 VYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDDDMK 253 (325)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCCCCCCCcchhhhccCCCCCCHHHHHHHHHHH
Confidence 01234445556667
Q ss_pred HHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCchh
Q 011992 400 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASY 466 (473)
Q Consensus 400 e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~l~ 466 (473)
..|..+|..||+++|.||.++|||.+.+++|++|||+.||||+++|++++++|+++||+.+...++.
T Consensus 254 ~~L~~aL~~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~~~~~~ 320 (325)
T PRK05657 254 QSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQTQGLS 320 (325)
T ss_pred HHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhCccc
Confidence 7899999999999999999999887779999999999999999999999999999999999887764
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=99.91 E-value=3.9e-23 Score=205.55 Aligned_cols=165 Identities=33% Similarity=0.622 Sum_probs=137.6
Q ss_pred hHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHH
Q 011992 256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 335 (473)
Q Consensus 256 ~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~ 335 (473)
++..|+......|+|++++|.+|+.++.. .++..|++.||.
T Consensus 2 ~~~~yl~~~~~~~~l~~~~e~~l~~~~~~---------------------------------------~gd~~a~~~Lv~ 42 (270)
T TIGR02392 2 SLDAYIRAVNRIPMLTPEEEYQLAKRLRE---------------------------------------HGDLDAAKKLVL 42 (270)
T ss_pred hHHHHHHHHhcCCCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHHHHH
Confidence 36678888889999999999998876422 134589999999
Q ss_pred HHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccccC-------------------------------
Q 011992 336 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANT------------------------------- 384 (473)
Q Consensus 336 ~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~------------------------------- 384 (473)
.|+++|+++|++|.+++.+++||+|+|++|||+++++||+.+|++|+|+
T Consensus 43 ~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA~~~Ir~~i~~~l~~~~~~ir~p~~~~~~~~ 122 (270)
T TIGR02392 43 SHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRKL 122 (270)
T ss_pred HhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhhHHHHHHHHHHHHHHcCCceecCchHHHHHH
Confidence 9999999999999999999999999999999999999999999999990
Q ss_pred ------------C--C------------------------------------------------------CCchHHHHH-
Q 011992 385 ------------G--V------------------------------------------------------EIPDISVQK- 395 (473)
Q Consensus 385 ------------~--~------------------------------------------------------~~pee~le~- 395 (473)
. . ..|+..+..
T Consensus 123 ~~~~~~~~~~~~~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~l~d~~~~pe~~~~~~ 202 (270)
T TIGR02392 123 FFNLRKMKKRLQGWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDDEDDGGAPIAYLVDKTSDPEDTLEEE 202 (270)
T ss_pred HHHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCCCCCccccHHHHhcCCCCChHHHHHHH
Confidence 0 0 001111111
Q ss_pred ---HHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Q 011992 396 ---QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 461 (473)
Q Consensus 396 ---~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~ 461 (473)
......|..+|..||++||.||.++|+ . ++++|++|||+.||||.++|+|++.+|++|||..+.
T Consensus 203 ~~~~~~~~~L~~al~~L~~rer~vl~l~y~-~-~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~l~ 269 (270)
T TIGR02392 203 QWEELQRQALANALGSLDARSRRIIEARWL-D-DDKLTLQELAAEYGVSAERIRQIEKNAMKKLKAALA 269 (270)
T ss_pred HHHHHHHHHHHHHHHcCCHHHHHHHHHHhc-C-CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 123467899999999999999999996 1 268999999999999999999999999999999775
No 15
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=99.90 E-value=5.6e-23 Score=206.25 Aligned_cols=169 Identities=31% Similarity=0.551 Sum_probs=141.8
Q ss_pred CChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHH
Q 011992 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 332 (473)
Q Consensus 253 ~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~ 332 (473)
+.+.+..|+....+.|+||.++|.+|+.+++. .++..|++.
T Consensus 12 ~~~~~~~y~~~~~~~~~l~~~~e~~l~~~~~~---------------------------------------~Gd~~a~~~ 52 (284)
T PRK06596 12 PEGNLDAYIQAVNKIPMLTAEEEYMLAKRLRE---------------------------------------HGDLEAAKQ 52 (284)
T ss_pred CccHHHHHHHHHhccCCCCHHHHHHHHHHHHH---------------------------------------cCCHHHHHH
Confidence 34578889999999999999999999886432 134489999
Q ss_pred HHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccccC----------------------------
Q 011992 333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANT---------------------------- 384 (473)
Q Consensus 333 Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~---------------------------- 384 (473)
||..|+++|+++|++|.+++.+++||+|+|++||++++++||+.+|++|+|+
T Consensus 53 Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~~~l~~~~~~vr~p~~~~~ 132 (284)
T PRK06596 53 LVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKAQ 132 (284)
T ss_pred HHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHcCCeeeccchHHH
Confidence 9999999999999999999999999999999999999999999999999980
Q ss_pred -----------------C--------------------------------------C---------------CCchHHHH
Q 011992 385 -----------------G--------------------------------------V---------------EIPDISVQ 394 (473)
Q Consensus 385 -----------------~--------------------------------------~---------------~~pee~le 394 (473)
. . ..|++.++
T Consensus 133 ~~~~~~~~~~~~~l~~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~~~l~d~~~~p~~~~~ 212 (284)
T PRK06596 133 RKLFFNLRKAKKRLGWLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLEDKSSDPADVLE 212 (284)
T ss_pred HHHHHHHHHHHHHhccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCCCCCcchHHHHcCCCCCCchHHHH
Confidence 0 0 01111222
Q ss_pred HH----HHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Q 011992 395 KQ----LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 462 (473)
Q Consensus 395 ~~----el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~ 462 (473)
.. +....|..+|+.||++||.||.+||+. + +++|++|||+.||||.++|+|++++|++|||..+..
T Consensus 213 ~~~~~~~~~~~L~~al~~L~~rEr~VL~lry~~-~-~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~l~~ 282 (284)
T PRK06596 213 EDNWEDQRRALLADALEGLDERSRDIIEARWLD-D-DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIEA 282 (284)
T ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcC-C-CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 22 246678999999999999999999962 2 689999999999999999999999999999998764
No 16
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=99.90 E-value=8.5e-23 Score=205.48 Aligned_cols=168 Identities=31% Similarity=0.517 Sum_probs=142.1
Q ss_pred hHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHH
Q 011992 256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 335 (473)
Q Consensus 256 ~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~ 335 (473)
..+.|+....+.|+||+++|.+|+++++. .++..|++.||.
T Consensus 7 ~~~~y~~~~~~~~~l~~~~e~~L~~~~~~---------------------------------------~gd~~A~~~Lv~ 47 (289)
T PRK07500 7 ADRSMIRSAMKAPYLEREEEHALAYRWKD---------------------------------------HRDEDALHRIIS 47 (289)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHHHHH
Confidence 46779999999999999999999887643 134589999999
Q ss_pred HHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccccC-------------------------------
Q 011992 336 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANT------------------------------- 384 (473)
Q Consensus 336 ~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~------------------------------- 384 (473)
.|.++|+++|++|.+++.+++||+|||++|||+++++||+.+|.+|+|+
T Consensus 48 ~~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I~~~lr~~~~~iR~p~~~~~~~~ 127 (289)
T PRK07500 48 AHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKAL 127 (289)
T ss_pred HhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHCCCceecCccHHHHHH
Confidence 9999999999999999999999999999999999999999999889880
Q ss_pred -----------------------------------------------------------CC-------------CCchHH
Q 011992 385 -----------------------------------------------------------GV-------------EIPDIS 392 (473)
Q Consensus 385 -----------------------------------------------------------~~-------------~~pee~ 392 (473)
.. ..|++.
T Consensus 128 ~~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~i~d~~~~pe~~ 207 (289)
T PRK07500 128 FFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDDSPLPDEQ 207 (289)
T ss_pred HHHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCCCCCCcccHHHhccCCCCCchHH
Confidence 00 011222
Q ss_pred HH----HHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCc
Q 011992 393 VQ----KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 464 (473)
Q Consensus 393 le----~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~ 464 (473)
+. ..+....|..+|+.||++||.||.++|+ +++++|++|||+.||||+++|+|++++|++|||..+....
T Consensus 208 ~~~~~~~~~~~~~l~~al~~L~~rer~vl~lr~~--~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l~~~~ 281 (289)
T PRK07500 208 VESSIDGERRRRWLTQALQTLNERELRIIRERRL--REDGATLEALGEELGISKERVRQIEARALEKLRRALLSQS 281 (289)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhc--CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 21 1234567889999999999999999985 2379999999999999999999999999999999998654
No 17
>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=99.90 E-value=7.8e-23 Score=204.77 Aligned_cols=171 Identities=37% Similarity=0.590 Sum_probs=148.6
Q ss_pred hhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHH
Q 011992 255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLI 334 (473)
Q Consensus 255 ~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li 334 (473)
+.++.|+..++..|.||.++|.+|+.+.+. ++..|++.||
T Consensus 13 ~~~~~~~~~~~~~~~~~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~ 52 (285)
T TIGR02394 13 DVTQLYLREIGFKPLLTAEEEIAYARRALA----------------------------------------GDFEARKVMI 52 (285)
T ss_pred hHHHHHHHHHhccCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHH
Confidence 357889999999999999999988877543 3458999999
Q ss_pred HHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccccCC-----------------------------
Q 011992 335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTG----------------------------- 385 (473)
Q Consensus 335 ~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~~----------------------------- 385 (473)
..|.++|+++|++|.+++.+++||+|||++|+|+++++||+..|++|.|+.
T Consensus 53 ~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ain~~i~~~~~~~~~p~~~~~~~ 132 (285)
T TIGR02394 53 ESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHVIKEL 132 (285)
T ss_pred HHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHHHHHHHHcCCceeCcHHHHHHH
Confidence 999999999999999999999999999999999999999999888876400
Q ss_pred -------------------------------------------------------------------CCCchHHHHHHHH
Q 011992 386 -------------------------------------------------------------------VEIPDISVQKQLM 398 (473)
Q Consensus 386 -------------------------------------------------------------------~~~pee~le~~el 398 (473)
...|+..+...+.
T Consensus 133 ~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~~~~~pe~~~~~~e~ 212 (285)
T TIGR02394 133 NVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESLVQNDDL 212 (285)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCCCCCCCcchhhhhcCCCCCCHHHHHHHHHH
Confidence 0124455566677
Q ss_pred HHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCch
Q 011992 399 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 465 (473)
Q Consensus 399 ~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~l 465 (473)
...|.++|..||+++|.||.++|||.+.+++|++|||+.||||.++|++++++|+++||+.|...+.
T Consensus 213 ~~~L~~al~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~~~~~ 279 (285)
T TIGR02394 213 KQLIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILERDGV 279 (285)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 7889999999999999999999966666999999999999999999999999999999999986544
No 18
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=99.88 E-value=2.1e-21 Score=188.82 Aligned_cols=167 Identities=26% Similarity=0.484 Sum_probs=140.4
Q ss_pred hHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHH
Q 011992 256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 335 (473)
Q Consensus 256 ~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~ 335 (473)
.+..|+-..+..|+||+++|..|+..++. ++..+++.|+.
T Consensus 17 ~~~~~~~~~~~~~~~~~~~e~~l~~~~~~----------------------------------------gd~~a~~~l~~ 56 (233)
T PRK05803 17 FLVSYVKNNSFPQPLSEEEERKYLELMKE----------------------------------------GDEEARNILIE 56 (233)
T ss_pred HHHHHHHHhcccCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHH
Confidence 37788888888888999888877655432 24478999999
Q ss_pred HHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc--------------------C---C---C---
Q 011992 336 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN--------------------T---G---V--- 386 (473)
Q Consensus 336 ~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT--------------------~---~---~--- 386 (473)
.|.++|+++|.++.+++.+++|++||+++++|+++++|++..+..|.+ . . .
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 999999999999999999999999999999999999999987878877 0 0 0
Q ss_pred -----------------CCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHH
Q 011992 387 -----------------EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE 449 (473)
Q Consensus 387 -----------------~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~ 449 (473)
..++..+...+..+.|.++|..||+++|+||.++|++.+.+++|++|||+.||+|.++|++++
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 012333445566678999999999999999999996555599999999999999999999999
Q ss_pred HHHHHHHHHHhcc
Q 011992 450 SRALYRLKQSLGG 462 (473)
Q Consensus 450 ~RAL~KLR~~L~~ 462 (473)
++|+++||+.+..
T Consensus 217 ~rA~~kLr~~l~~ 229 (233)
T PRK05803 217 KRALKKLFKELYR 229 (233)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999998864
No 19
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=99.87 E-value=5.8e-22 Score=197.00 Aligned_cols=178 Identities=21% Similarity=0.306 Sum_probs=140.9
Q ss_pred ccCCCCCCcccccccccccccccccccCCCChhHHhhhc---ccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Q 011992 224 KVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLW---GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFG 300 (473)
Q Consensus 224 ~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~---~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lG 300 (473)
|+++.+|++|+|||.|||+ |+|+++ +|...| .|++. .+...+++++..+|.+.+|
T Consensus 84 rFDp~~G~~FsTYA~~~Ir-----g~I~~~---lr~~~~~ir~Pr~~--------------~~~~~~i~~~~~~l~~~lg 141 (264)
T PRK07122 84 RFDVETGSDFVSFAVPTIM-----GEVRRH---FRDNSWSVKVPRRL--------------KELHLRLGRATAELSQRLG 141 (264)
T ss_pred HcCCCCCCChHHHHHHHHH-----HHHHHH---HHHcCCccccCHHH--------------HHHHHHHHHHHHHHHHHhC
Confidence 6789999999999999999 999994 888777 55544 4567788999999999999
Q ss_pred CCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCc
Q 011992 301 REPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCR 380 (473)
Q Consensus 301 RePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~ 380 (473)
++||.+|||+.+|++.+++...+.... .....++++.+.++.-+. .
T Consensus 142 ~~pt~~eiA~~lg~~~~~v~~~~~~~~---------------------~~~~~SLd~~~~~~~~~~-------------~ 187 (264)
T PRK07122 142 RAPTASELAAELGMDREEVVEGLVAGS---------------------AYNTLSIDSGGGSGDDDA-------------R 187 (264)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHhh---------------------cCCCCcccccccCCCCCc-------------c
Confidence 999999999999999999887654221 112455665543211000 0
Q ss_pred cccCCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992 381 FANTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 460 (473)
Q Consensus 381 FsT~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L 460 (473)
...+....++..++..+....|..+|..||+++|.||.++|+ +++|++|||+.||||.++|++++++|+.+||..+
T Consensus 188 ~~~d~~~~~~~~~e~~~~~~~l~~~l~~L~~rer~vl~l~y~----~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l 263 (264)
T PRK07122 188 AIADTLGDVDAGLDQIENREALRPLLAALPERERTVLVLRFF----ESMTQTQIAERVGISQMHVSRLLAKTLARLRDQL 263 (264)
T ss_pred cchhccCCcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHc
Confidence 000112345556677778889999999999999999999998 9999999999999999999999999999999976
Q ss_pred c
Q 011992 461 G 461 (473)
Q Consensus 461 ~ 461 (473)
+
T Consensus 264 ~ 264 (264)
T PRK07122 264 E 264 (264)
T ss_pred C
Confidence 3
No 20
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=99.87 E-value=9.3e-22 Score=194.64 Aligned_cols=184 Identities=25% Similarity=0.350 Sum_probs=144.0
Q ss_pred hccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Q 011992 223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGRE 302 (473)
Q Consensus 223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRe 302 (473)
.+.++.+|+.|+||+.+||+ |+|+| .+|+..|.|++. .+...++..+...|.+.+||+
T Consensus 69 ~~fd~~~g~~F~tya~~~Ir-----~~i~~---~lr~~~~~pr~~--------------~~~~~~l~~~~~~l~~~~gr~ 126 (257)
T PRK05911 69 ERFDPEKSRRFEGYALFLIK-----AAIID---DLRKQDWVPRSV--------------HQKANKLADAMDSLRQSLGKE 126 (257)
T ss_pred HhcCCccCCCHHHHHHHHHH-----HHHHH---HHHhcCCCCHHH--------------HHHHHHHHHHHHHHHHHHCcC
Confidence 46688999999999999999 99999 499999988877 567788999999999999999
Q ss_pred CCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhh---hhHHHHHHHhhhhCccCCC
Q 011992 303 PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ---EGSMGLMKSVEKFKPQAGC 379 (473)
Q Consensus 303 PT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQ---Eg~lgL~kAiekFDp~kg~ 379 (473)
||.+|+|+.+|++.+++...+.....+ ...++++.+. ++..+. .+..+
T Consensus 127 pt~~eiA~~l~i~~~~v~~~~~~~~~~---------------------~~~Sld~~~~~~~~~~~~~--~l~~~------ 177 (257)
T PRK05911 127 PTDGELCEYLNISQQELSGWFSSARPA---------------------LILSLNEEFPCQSDDEAGL--ALEER------ 177 (257)
T ss_pred CCHHHHHHHhCcCHHHHHHHHHHhhcc---------------------ceeeccccCCCCCCCcccc--chhhh------
Confidence 999999999999999987665432110 1233333221 110000 00011
Q ss_pred ccccCCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 011992 380 RFANTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 459 (473)
Q Consensus 380 ~FsT~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~ 459 (473)
+.......|+..+...+....|..+|+.||+++|.||.++|+ +++|++|||+.||+|.++|++++.+|+++||+.
T Consensus 178 -l~d~~~~~~~~~~~~~~~~~~l~~al~~L~~~er~vi~l~y~----e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 252 (257)
T PRK05911 178 -IADERAETGYDVVDKKEFSSILAEAILALEEKERKVMALYYY----EELVLKEIGKILGVSESRVSQIHSKALLKLRAT 252 (257)
T ss_pred -ccCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 011112356777788888899999999999999999999999 999999999999999999999999999999998
Q ss_pred hcc
Q 011992 460 LGG 462 (473)
Q Consensus 460 L~~ 462 (473)
+..
T Consensus 253 l~~ 255 (257)
T PRK05911 253 LSA 255 (257)
T ss_pred HHh
Confidence 864
No 21
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=99.86 E-value=9.4e-21 Score=186.97 Aligned_cols=154 Identities=31% Similarity=0.512 Sum_probs=128.8
Q ss_pred ccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHHHHHHHHH
Q 011992 263 GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVV 342 (473)
Q Consensus 263 ~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~~yl~lV~ 342 (473)
.+...|+|+++|+..|+.+++. ++..+++.||..|.++|+
T Consensus 12 ~~~~~~~l~~~~~~~l~~~~~~----------------------------------------gd~~a~~~l~~~~~~~v~ 51 (258)
T PRK08215 12 NTSKLPVLKNEEMRELFERMQN----------------------------------------GDKEAREKLINGNLRLVL 51 (258)
T ss_pred cCCCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHHHHHHH
Confidence 3667889999999888776442 345789999999999999
Q ss_pred HHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccccC--------------------------------------
Q 011992 343 HVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANT-------------------------------------- 384 (473)
Q Consensus 343 sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~-------------------------------------- 384 (473)
++|++|.+++.+++|++|||++|+|+++++||+.+|.+|.|.
T Consensus 52 ~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~~~lr~~~~vrip~~~~~~~~~~~~~~~~ 131 (258)
T PRK08215 52 SVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLRDIAYKALQVREK 131 (258)
T ss_pred HHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCCceEecHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999998889880
Q ss_pred ------------------------------------CCCCc------------------hHHHHHHHHHHHHHHHHhhCC
Q 011992 385 ------------------------------------GVEIP------------------DISVQKQLMRQHVRNLLTLLN 410 (473)
Q Consensus 385 ------------------------------------~~~~p------------------ee~le~~el~e~L~~aL~~Lp 410 (473)
....| +...+.......|..+|+.||
T Consensus 132 l~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~ 211 (258)
T PRK08215 132 LINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQISDEKNKDENWLEEIALKEAMKKLN 211 (258)
T ss_pred HHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCCCCcchhhhhhccCccccHHHHHhHHHHHHHHHcCC
Confidence 00000 000112223446888999999
Q ss_pred HHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992 411 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 460 (473)
Q Consensus 411 erER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L 460 (473)
++++.||.++|+ +++|++|||+.||+|.++|++++++|+++||+.|
T Consensus 212 ~~er~vi~~~~~----~~~t~~eIA~~lgis~~~V~~~~~~al~kLr~~l 257 (258)
T PRK08215 212 DREKLILNLRFF----QGKTQMEVAEEIGISQAQVSRLEKAALKHMRKYI 257 (258)
T ss_pred HHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 999999999998 8999999999999999999999999999999876
No 22
>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=99.86 E-value=1.1e-20 Score=186.18 Aligned_cols=153 Identities=32% Similarity=0.509 Sum_probs=127.5
Q ss_pred cCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHHHHHHHHHH
Q 011992 264 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH 343 (473)
Q Consensus 264 pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~~yl~lV~s 343 (473)
..+.|+||++||.+|+.+++. ++..+++.||..|+++|++
T Consensus 10 ~~~~~~l~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~~~~~~~v~~ 49 (254)
T TIGR02850 10 TSKLPVLKNQEMRELFIRMQS----------------------------------------GDTTAREKLINGNLRLVLS 49 (254)
T ss_pred ccCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHHHH
Confidence 356789999999888766442 2447899999999999999
Q ss_pred HHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------------------------------------
Q 011992 344 VAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------------------------------------- 383 (473)
Q Consensus 344 IA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT---------------------------------------- 383 (473)
+|++|.+++.+++||+|||++|||+++++|++.+|.+|.|
T Consensus 50 ~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~~lr~~~~ir~p~~~~~~~~~~~~~~~~l 129 (254)
T TIGR02850 50 VIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLRDIAYKALQVRDKL 129 (254)
T ss_pred HHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHhCCCccCchHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999989988
Q ss_pred ----------------------------------CCCCCc----------------h--HHHHHHHHHHHHHHHHhhCCH
Q 011992 384 ----------------------------------TGVEIP----------------D--ISVQKQLMRQHVRNLLTLLNP 411 (473)
Q Consensus 384 ----------------------------------~~~~~p----------------e--e~le~~el~e~L~~aL~~Lpe 411 (473)
.+...+ + ...........|..+|..||+
T Consensus 130 ~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~l~~~l~~L~~ 209 (254)
T TIGR02850 130 ISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDEKNKDSQWLEGIALKEAMKRLNE 209 (254)
T ss_pred HHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCCCCCcchhhhhcCCccccHHHHHhHHHHHHHHHcCCH
Confidence 000000 0 000122234568899999999
Q ss_pred HHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992 412 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 460 (473)
Q Consensus 412 rER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L 460 (473)
++|.||.++|+ +++|++|||+.||+|.++|++++++|++|||..+
T Consensus 210 rer~vi~~~~~----~~~t~~eIA~~lgis~~~V~~~~~ral~kLr~~~ 254 (254)
T TIGR02850 210 REKMILNMRFF----EGKTQMEVAEEIGISQAQVSRLEKAALKHMRKYV 254 (254)
T ss_pred HHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhC
Confidence 99999999998 8999999999999999999999999999999854
No 23
>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=99.85 E-value=3e-20 Score=182.81 Aligned_cols=131 Identities=24% Similarity=0.410 Sum_probs=114.6
Q ss_pred cchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccccC---------------CC----
Q 011992 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANT---------------GV---- 386 (473)
Q Consensus 326 g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~---------------~~---- 386 (473)
+..|++.||..|.++|+++|++|.+++.+++|++||||+++|+++++|++..|..|.++ ..
T Consensus 27 d~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~ir 106 (255)
T TIGR02941 27 NGEAQEKLVDHYQNLVYSIAYKYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEIKRYLRDKTWSVH 106 (255)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHHHHHHHHHcCCCcC
Confidence 34799999999999999999999999999999999999999999999999888888660 00
Q ss_pred -----------------------------------------------------------------------------CCc
Q 011992 387 -----------------------------------------------------------------------------EIP 389 (473)
Q Consensus 387 -----------------------------------------------------------------------------~~p 389 (473)
..|
T Consensus 107 i~~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~ 186 (255)
T TIGR02941 107 VPRRIKELGPKIKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSDGSTVARLDSVGEV 186 (255)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCCCCCcccccccccCCc
Confidence 012
Q ss_pred hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992 390 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 460 (473)
Q Consensus 390 ee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L 460 (473)
++.+...+....+..+|+.||+++|.||.++|+ +++|++|||+.||+|.++|++++++|+++||..+
T Consensus 187 ~~~~~~~e~~~~l~~~l~~L~~~~r~ii~l~~~----~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~~ 253 (255)
T TIGR02941 187 EDGYDQTERRMVLEKILPILSEREKSIIHCTFE----ENLSQKETGERLGISQMHVSRLQRQAISKLKEAA 253 (255)
T ss_pred chHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 333444556667899999999999999999998 9999999999999999999999999999999875
No 24
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=99.85 E-value=1.8e-20 Score=185.25 Aligned_cols=133 Identities=26% Similarity=0.381 Sum_probs=114.7
Q ss_pred chHHHHHHHHHHHHHHHHHHHhhcC-CcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------------------
Q 011992 327 NSSREKLINANLRLVVHVAKQYQGR-GISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------------------- 383 (473)
Q Consensus 327 ~~A~e~Li~~yl~lV~sIA~ry~~~-~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT---------------------- 383 (473)
..|+++||..|+++|+++|++|.+. +.+++||+|+|++|||+++++|||.+|++|+|
T Consensus 24 ~~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~~~vr 103 (256)
T PRK07408 24 IALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTVR 103 (256)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHHcCCeee
Confidence 3899999999999999999999775 66799999999999999999999999999999
Q ss_pred ----------------------------------------------------------CC------C---------CCch
Q 011992 384 ----------------------------------------------------------TG------V---------EIPD 390 (473)
Q Consensus 384 ----------------------------------------------------------~~------~---------~~pe 390 (473)
+. . ..++
T Consensus 104 ~pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~~~d~~ 183 (256)
T PRK07408 104 IPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQDEDGSTSLGDLLPDPR 183 (256)
T ss_pred eCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCCCCCCccccccccCCcc
Confidence 00 0 0111
Q ss_pred H--HHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccC
Q 011992 391 I--SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 463 (473)
Q Consensus 391 e--~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~ 463 (473)
. .....+....|..+|..||+++|.||.++|+ +++|++|||+.||+|.++|++++++|+++||..+..+
T Consensus 184 ~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~y~----~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l~~~ 254 (256)
T PRK07408 184 YRSFQLAQEDRIRLQQALAQLEERTREVLEFVFL----HDLTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQPE 254 (256)
T ss_pred cchhhhhHHHHHHHHHHHHcCCHHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhcc
Confidence 1 1123345667999999999999999999999 9999999999999999999999999999999998765
No 25
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=99.85 E-value=3.9e-20 Score=182.15 Aligned_cols=133 Identities=23% Similarity=0.366 Sum_probs=114.6
Q ss_pred cchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccccC---------------CC----
Q 011992 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANT---------------GV---- 386 (473)
Q Consensus 326 g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~---------------~~---- 386 (473)
+..|++.||..|.++|+++|++|.++..+++|++||||+++|+++++|++..|..|.|+ ..
T Consensus 27 d~~a~~~l~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~~~ 106 (257)
T PRK08583 27 DEEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVH 106 (257)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHHHHHHHhcCCCcC
Confidence 44899999999999999999999999999999999999999999999999877777540 00
Q ss_pred -----------------------------------------------------------------------------CCc
Q 011992 387 -----------------------------------------------------------------------------EIP 389 (473)
Q Consensus 387 -----------------------------------------------------------------------------~~p 389 (473)
..|
T Consensus 107 i~r~~~~~~~~~~~~~~~~~~~~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~~~~ 186 (257)
T PRK08583 107 VPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSDGSTVTLLDIVGQQ 186 (257)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCCCCCccchHhhhcCCc
Confidence 011
Q ss_pred hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Q 011992 390 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 462 (473)
Q Consensus 390 ee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~ 462 (473)
+..+...+....+..+|..||+++|.||.++|+ +|+|++|||+.||||+++|++++++|+++||..+..
T Consensus 187 e~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l~~ 255 (257)
T PRK08583 187 EDGYELTEQRMILEKILPVLSDREKSIIQCTFI----ENLSQKETGERLGISQMHVSRLQRQAIKKLREAAFL 255 (257)
T ss_pred chhHHHHHHHHHHHHHHHhCCHHHHHHHHHHHh----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Confidence 222333455667889999999999999999999 999999999999999999999999999999998864
No 26
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=99.84 E-value=5.5e-20 Score=182.62 Aligned_cols=158 Identities=23% Similarity=0.396 Sum_probs=133.0
Q ss_pred ccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHHHHHHHHH
Q 011992 263 GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVV 342 (473)
Q Consensus 263 ~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~~yl~lV~ 342 (473)
..+..|+||.++|.+|+.+++. .++..+++.|+..|.++|+
T Consensus 5 ~~~~~~~~~~~~e~~l~~~~~~---------------------------------------~~d~~a~~~l~~~y~~lv~ 45 (268)
T PRK06288 5 MSGKIPKYAQQDETELWREYKK---------------------------------------TGDPKIREYLILKYSPLVK 45 (268)
T ss_pred ccCCCccccchHHHHHHHHHHH---------------------------------------cCCHHHHHHHHHHHHHHHH
Confidence 3567899999999998887543 1344789999999999999
Q ss_pred HHHHHhh-c--CCcchhhHhhhhHHHHHHHhhhhCccCCCcccc---------------CC-------------------
Q 011992 343 HVAKQYQ-G--RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------------TG------------------- 385 (473)
Q Consensus 343 sIA~ry~-~--~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT---------------~~------------------- 385 (473)
.+|+++. + .+.+++|++|||++|||+++++||+.+|.+|.| ..
T Consensus 46 ~~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i~d~~R~~~~~p~~~~~~~~~i~~~~~ 125 (268)
T PRK06288 46 YVAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSIDWIPRSVRQKARQIERAIA 125 (268)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcCccCHHHHHHHHHHHHHHH
Confidence 9999986 3 467899999999999999999999988888888 00
Q ss_pred ----------------------------------------------------------------CCCchHHHHHHHHHHH
Q 011992 386 ----------------------------------------------------------------VEIPDISVQKQLMRQH 401 (473)
Q Consensus 386 ----------------------------------------------------------------~~~pee~le~~el~e~ 401 (473)
...|+..+...+....
T Consensus 126 ~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~l~~~~~~~~~~~pe~~~~~~e~~~~ 205 (268)
T PRK06288 126 MLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGDEVSLMDTLESPAALNPDEIAEREEIKRV 205 (268)
T ss_pred HHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhccCCCcccchhhhhccCCCCCCHHHHHHHHHHHHH
Confidence 0112333445566678
Q ss_pred HHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccC
Q 011992 402 VRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 463 (473)
Q Consensus 402 L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~ 463 (473)
|..+|..||+++|.||.++|+ +++|++|||+.||+|.++|++++.+|+++||..+...
T Consensus 206 l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l~~~ 263 (268)
T PRK06288 206 IVEAIKTLPEREKKVLILYYY----EDLTLKEIGKVLGVTESRISQLHTKAVLQLRAKLAEI 263 (268)
T ss_pred HHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999 9999999999999999999999999999999998643
No 27
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=99.84 E-value=7.7e-20 Score=170.75 Aligned_cols=147 Identities=18% Similarity=0.274 Sum_probs=126.0
Q ss_pred CCHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc---------
Q 011992 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN--------- 383 (473)
Q Consensus 314 ms~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT--------- 383 (473)
++.+.|...+..|+ .+++.||..|.++|+++|+++.++..+++|++||+|+++|+++.+|++. +..|.+
T Consensus 5 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n~ 83 (186)
T PRK05602 5 DPDEELLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLNL 83 (186)
T ss_pred ccHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHHH
Confidence 55666766666666 9999999999999999999999999999999999999999999999875 345666
Q ss_pred --------------------CCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHH
Q 011992 384 --------------------TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKE 443 (473)
Q Consensus 384 --------------------~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~ 443 (473)
.....++..+...+....+..+|..||+++|.||.|+|+ +|+|++|||+.||+|.+
T Consensus 84 ~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~ 159 (186)
T PRK05602 84 CYDRLRRRREVPVEDAPDVPDPAPGPDAGLEARQRARRVEQALAALPERQREAIVLQYY----QGLSNIEAAAVMDISVD 159 (186)
T ss_pred HHHHHHhcCCCCcccccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHh----cCCCHHHHHHHhCcCHH
Confidence 011234445555566778999999999999999999999 99999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhccCch
Q 011992 444 RVRQLESRALYRLKQSLGGKAS 465 (473)
Q Consensus 444 rVrqi~~RAL~KLR~~L~~~~l 465 (473)
+|+++++||+++||+.+...+.
T Consensus 160 tV~~~l~Rar~~Lr~~l~~~~~ 181 (186)
T PRK05602 160 ALESLLARGRRALRAQLADLPG 181 (186)
T ss_pred HHHHHHHHHHHHHHHHHHhccc
Confidence 9999999999999999987654
No 28
>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=99.84 E-value=1.4e-19 Score=175.50 Aligned_cols=136 Identities=33% Similarity=0.625 Sum_probs=114.8
Q ss_pred hcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-------------------C-
Q 011992 325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-------------------T- 384 (473)
Q Consensus 325 ~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-------------------~- 384 (473)
++..+++.||..|.+.|+++|.++.++..+++|++||+|+++|+++++|+++.+..|.+ .
T Consensus 45 gd~~af~~l~~~y~~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~~d~~Rk~~r~~ 124 (227)
T TIGR02846 45 GDEEARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEILMHLRALKKTK 124 (227)
T ss_pred CCHHHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHHHHHHHHHhccc
Confidence 34489999999999999999999999999999999999999999999999887777766 0
Q ss_pred -C-----C--------------------CCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHH
Q 011992 385 -G-----V--------------------EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIF 438 (473)
Q Consensus 385 -~-----~--------------------~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~L 438 (473)
. . ..++..+...+..+.|.++|+.||+++|+||.++|+++..+++|++|||++|
T Consensus 125 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~l 204 (227)
T TIGR02846 125 GEVSLQDPIGVDKEGNEISLIDILGSDGDSVIEQVELNLEIKKLYKKLSVLDGREREVIEMRYGLGDGRRKTQREIAKIL 204 (227)
T ss_pred cceeccccccCCcccCcccHHHHhcCCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHH
Confidence 0 0 0112223344455679999999999999999999965444899999999999
Q ss_pred CCCHHHHHHHHHHHHHHHHHHh
Q 011992 439 GLSKERVRQLESRALYRLKQSL 460 (473)
Q Consensus 439 GIS~~rVrqi~~RAL~KLR~~L 460 (473)
|+|.++|++++++|+++||+.|
T Consensus 205 gis~~tV~~~~~rAl~~Lr~~~ 226 (227)
T TIGR02846 205 GISRSYVSRIEKRALMKLYKEL 226 (227)
T ss_pred CCCHHHHHHHHHHHHHHHHHHh
Confidence 9999999999999999999875
No 29
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=99.82 E-value=2.7e-19 Score=175.93 Aligned_cols=143 Identities=24% Similarity=0.424 Sum_probs=120.4
Q ss_pred CHHHHHHH-Hhhcc-hHHHHHHHHHHHHHHHHHHHhhc---CCcchhhHhhhhHHHHHHHhhhhCccCCCcccc------
Q 011992 315 SCRDLKSE-LHSGN-SSREKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------ 383 (473)
Q Consensus 315 s~eeL~~~-l~~g~-~A~e~Li~~yl~lV~sIA~ry~~---~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------ 383 (473)
++..|... ..+|+ .|++.||..|.++|+++|++|.+ +..+++|++|||++|||+++++|++.+|.+|.|
T Consensus 7 ~e~~l~~~~~~~~d~~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~~~i 86 (251)
T PRK07670 7 EEQKLWDRWKEERDPDAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRI 86 (251)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHH
Confidence 34455555 34444 89999999999999999999965 688999999999999999999999999889988
Q ss_pred ---------CCC--------------------------------------------------------------------
Q 011992 384 ---------TGV-------------------------------------------------------------------- 386 (473)
Q Consensus 384 ---------~~~-------------------------------------------------------------------- 386 (473)
...
T Consensus 87 rn~~~d~lR~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~ 166 (251)
T PRK07670 87 RGAIIDGLRKEDWLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQDD 166 (251)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCccccCCCC
Confidence 000
Q ss_pred -------------CCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992 387 -------------EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 453 (473)
Q Consensus 387 -------------~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL 453 (473)
..++..+...+....|..+|..||+++|.||.++|+ +++|++|||++||+|.++|++++++|+
T Consensus 167 ~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~EIA~~lgis~~tV~~~~~ra~ 242 (251)
T PRK07670 167 GENVSVTIRDDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLVISLFYK----EELTLTEIGQVLNLSTSRISQIHSKAL 242 (251)
T ss_pred cchhhhhhcCcCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 012233344555667899999999999999999999 999999999999999999999999999
Q ss_pred HHHHHHhc
Q 011992 454 YRLKQSLG 461 (473)
Q Consensus 454 ~KLR~~L~ 461 (473)
++||..+.
T Consensus 243 ~~Lr~~l~ 250 (251)
T PRK07670 243 FKLKKLLE 250 (251)
T ss_pred HHHHHHhh
Confidence 99999875
No 30
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=99.82 E-value=3.6e-19 Score=167.89 Aligned_cols=143 Identities=20% Similarity=0.238 Sum_probs=118.6
Q ss_pred HHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------
Q 011992 316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------- 383 (473)
Q Consensus 316 ~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------- 383 (473)
.+++...+..|+ .+++.||..|.+.|+++|.++.++..+++|++||+|+++|+++++|++..+..+.+
T Consensus 17 ~~~li~~~~~g~~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi~l~~~~~~~~~~~~~~~~wl~~ia~n~~~d 96 (194)
T PRK09646 17 LDALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARGSALAWLLTLAHRRAVD 96 (194)
T ss_pred HHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCcccccHHHHHHHHHHHHHHH
Confidence 344555555555 99999999999999999999999999999999999999999999998765422222
Q ss_pred -----------C----------CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCH
Q 011992 384 -----------T----------GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSK 442 (473)
Q Consensus 384 -----------~----------~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~ 442 (473)
. ....+++.+...+..+.|..+|..||+++|.||.|+|+ ++++++|||+.||+|.
T Consensus 97 ~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~EIA~~Lgis~ 172 (194)
T PRK09646 97 RVRSEQAASQREVRYGARNVDPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAYY----GGLTYREVAERLAVPL 172 (194)
T ss_pred HHHhhccccccccccccccccccccchHHHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCh
Confidence 0 00122333444556678999999999999999999999 9999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhcc
Q 011992 443 ERVRQLESRALYRLKQSLGG 462 (473)
Q Consensus 443 ~rVrqi~~RAL~KLR~~L~~ 462 (473)
++|+++++||+++||+.+..
T Consensus 173 ~tVk~~l~ra~~~Lr~~l~~ 192 (194)
T PRK09646 173 GTVKTRMRDGLIRLRDCLGV 192 (194)
T ss_pred HhHHHHHHHHHHHHHHHhcc
Confidence 99999999999999998854
No 31
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=99.81 E-value=6e-19 Score=171.20 Aligned_cols=147 Identities=31% Similarity=0.593 Sum_probs=119.6
Q ss_pred HHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------
Q 011992 316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------- 383 (473)
Q Consensus 316 ~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------- 383 (473)
...+...+..|+ .+++.++..|.+.|+++|+++.+++.+++|++||+|+++|+++++|++..+++|.+
T Consensus 39 ~~~L~~~~~~gd~~af~~l~~~y~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~~ 118 (234)
T PRK08301 39 EEYLLNKLPKGDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEIL 118 (234)
T ss_pred HHHHHHHHHccCHHHHHHHHHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHH
Confidence 445555555555 99999999999999999999999999999999999999999999999877667766
Q ss_pred --------C----CCCC------------------c-----hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCC
Q 011992 384 --------T----GVEI------------------P-----DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKP 428 (473)
Q Consensus 384 --------~----~~~~------------------p-----ee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~ 428 (473)
. .... + ...+........|..+|+.||+++|.||.|+|++...+|
T Consensus 119 d~lRk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~v~~L~y~l~~~eg 198 (234)
T PRK08301 119 MYLRRNNKVKAEVSFDEPLNIDWDGNELLLSDVLGTDNDIIYKDIEDEVDRKLLKKALKKLSDREKQIMELRFGLNGGEE 198 (234)
T ss_pred HHHHHHhccccccccccccccccCCCcccHHHhccCcccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCC
Confidence 0 0000 0 011223334567999999999999999999994333389
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Q 011992 429 KSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 462 (473)
Q Consensus 429 lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~ 462 (473)
+|++|||+.||||+++|+++++||+++||+.+..
T Consensus 199 ~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l~~ 232 (234)
T PRK08301 199 KTQKEVADMLGISQSYISRLEKRIIKRLKKEINK 232 (234)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 9999999999999999999999999999998753
No 32
>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=99.81 E-value=1e-18 Score=170.21 Aligned_cols=147 Identities=34% Similarity=0.613 Sum_probs=120.9
Q ss_pred HHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------
Q 011992 316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------- 383 (473)
Q Consensus 316 ~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------- 383 (473)
++.+...+..|+ .+++.|+..|.+.|+++|++|.+++.+++|++||+|+++|+++++|++..++.|.+
T Consensus 39 ~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~~ 118 (234)
T TIGR02835 39 EEALLQKLTQGDESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEIL 118 (234)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHH
Confidence 344555555555 99999999999999999999999999999999999999999999999877667766
Q ss_pred ---------C-C--CCC------------------ch-----HHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCC
Q 011992 384 ---------T-G--VEI------------------PD-----ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKP 428 (473)
Q Consensus 384 ---------~-~--~~~------------------pe-----e~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~ 428 (473)
. . ... ++ ..+........|..+|+.||+++|.|+.|+|++.++++
T Consensus 119 d~~Rk~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~eg 198 (234)
T TIGR02835 119 MYLRRNNKTRSEVSFDEPLNVDWDGNELLLSDVLGTDSDIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGTE 198 (234)
T ss_pred HHHHHhccccCcccccccccCCCCCCcchHHHhcCCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCCC
Confidence 0 0 000 00 11233345567999999999999999999996554589
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Q 011992 429 KSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 462 (473)
Q Consensus 429 lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~ 462 (473)
+|++|||+.||+|+++|++++++|+++||+.+..
T Consensus 199 ~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~l~~ 232 (234)
T TIGR02835 199 KTQKEVADMLGISQSYISRLEKRILKRLKKEINR 232 (234)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhhc
Confidence 9999999999999999999999999999998764
No 33
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=99.81 E-value=1.1e-18 Score=163.37 Aligned_cols=139 Identities=25% Similarity=0.347 Sum_probs=117.0
Q ss_pred HHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcC----CcchhhHhhhhHHHHHHHhhhhCccCCCcccc---------
Q 011992 318 DLKSELHSGN-SSREKLINANLRLVVHVAKQYQGR----GISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN--------- 383 (473)
Q Consensus 318 eL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~----~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT--------- 383 (473)
.+...+..|+ .+++.|+..|.+.|+++|.++.++ ..+++|++||+|+++|+++.+|+.. +..|.+
T Consensus 13 ~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~~~~wl~~i~~n~ 91 (189)
T PRK09648 13 ALVAEAVAGDRRALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITALPRYRDQ-GRPFLAFVYGIAAHK 91 (189)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHHHHHHhcc-CCcHHHHHHHHHHHH
Confidence 3555555555 999999999999999999998765 3689999999999999999999753 345655
Q ss_pred -----------------------CCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCC
Q 011992 384 -----------------------TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGL 440 (473)
Q Consensus 384 -----------------------~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGI 440 (473)
.....|+..+...+..+.|..+|..||+++|+||.++|+ +|+|++|||+.||+
T Consensus 92 ~~d~~r~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgi 167 (189)
T PRK09648 92 VADAHRAAGRDKAVPTEEVPERPSDDAGPEERALRSESSNRMRELLDTLPEKQREILILRVV----VGLSAEETAEAVGS 167 (189)
T ss_pred HHHHHHHhCCCccccccccccccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCC
Confidence 011234555556667778999999999999999999999 99999999999999
Q ss_pred CHHHHHHHHHHHHHHHHHHhc
Q 011992 441 SKERVRQLESRALYRLKQSLG 461 (473)
Q Consensus 441 S~~rVrqi~~RAL~KLR~~L~ 461 (473)
|.++|++.++||+++||+.+.
T Consensus 168 s~~tV~~~l~Ra~~~Lr~~l~ 188 (189)
T PRK09648 168 TPGAVRVAQHRALARLRAEIE 188 (189)
T ss_pred CHHHHHHHHHHHHHHHHHHhc
Confidence 999999999999999999874
No 34
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=99.80 E-value=7.8e-19 Score=170.92 Aligned_cols=134 Identities=25% Similarity=0.494 Sum_probs=117.5
Q ss_pred hcchHHHHHHHHHHHHHHHHHHHhh---cCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc---------------CCC
Q 011992 325 SGNSSREKLINANLRLVVHVAKQYQ---GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------------TGV 386 (473)
Q Consensus 325 ~g~~A~e~Li~~yl~lV~sIA~ry~---~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT---------------~~~ 386 (473)
.|.-++++||..|.++|+++|++|. ++..+++|++||||+|+|+++++|++..|.+|.| ...
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 3556889999999999999999997 6789999999999999999999999988888988 000
Q ss_pred ------------------------------------------------------------------------------CC
Q 011992 387 ------------------------------------------------------------------------------EI 388 (473)
Q Consensus 387 ------------------------------------------------------------------------------~~ 388 (473)
..
T Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~ 164 (236)
T PRK06986 85 WVPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGDSILVTEDHQDED 164 (236)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccccCCCcccccccCCCCCC
Confidence 12
Q ss_pred chHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Q 011992 389 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 462 (473)
Q Consensus 389 pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~ 462 (473)
|+..+...+....|..+|..||+++|.||.++|+ +++|++|||+.||||.++|++++++|+++||+.+..
T Consensus 165 ~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~~ 234 (236)
T PRK06986 165 PLQQLEDEELREALVEAIESLPEREQLVLSLYYQ----EELNLKEIGAVLGVSESRVSQIHSQAIKRLRARLGE 234 (236)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHhc----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 2344455566778999999999999999999999 999999999999999999999999999999998864
No 35
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=7e-19 Score=165.35 Aligned_cols=145 Identities=19% Similarity=0.268 Sum_probs=122.6
Q ss_pred CHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------
Q 011992 315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------- 383 (473)
Q Consensus 315 s~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT---------- 383 (473)
+.+.+...+..|+ .+++.|+..|.+.|+++|.++.++..+++|++||+|+++|+++++|++.. .|.+
T Consensus 12 ~~~~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~~~~~~~~~--~f~~wl~~i~~n~~ 89 (194)
T PRK12513 12 SDEALMLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRA--RFRTWLYQIARNLL 89 (194)
T ss_pred CHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCCC--chHHHHHHHHHHHH
Confidence 4555666666565 99999999999999999999999999999999999999999999998643 4554
Q ss_pred -------------C------------CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHH
Q 011992 384 -------------T------------GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIF 438 (473)
Q Consensus 384 -------------~------------~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~L 438 (473)
. ....|+..++..+....+..+|+.||+++|.||.|+|+ +|+|++|||+.|
T Consensus 90 ~~~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~l 165 (194)
T PRK12513 90 IDHWRRHGARQAPSLDADEQLHALADDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREH----GDLELEEIAELT 165 (194)
T ss_pred HHHHHHhccccccccccchhhhhcCCCCCCHHHHHHHHHHHHHHHHHHHhCCHhHhhheeeehc----cCCCHHHHHHHH
Confidence 0 01123344455667788999999999999999999998 999999999999
Q ss_pred CCCHHHHHHHHHHHHHHHHHHhccCch
Q 011992 439 GLSKERVRQLESRALYRLKQSLGGKAS 465 (473)
Q Consensus 439 GIS~~rVrqi~~RAL~KLR~~L~~~~l 465 (473)
|+|.++|+++++||+++||+.+...+.
T Consensus 166 gis~~tV~~~l~ra~~~Lr~~l~~~~~ 192 (194)
T PRK12513 166 GVPEETVKSRLRYALQKLRELLAEEVA 192 (194)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 999999999999999999999876543
No 36
>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=99.80 E-value=1.3e-18 Score=158.81 Aligned_cols=132 Identities=21% Similarity=0.357 Sum_probs=114.7
Q ss_pred hhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc--------------------
Q 011992 324 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-------------------- 383 (473)
Q Consensus 324 ~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-------------------- 383 (473)
.++..+++.|+..|.+.+++++.++.++..+++|++||+|+++|+++++|+...+ .|.+
T Consensus 7 ~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~~R~~~~~ 85 (170)
T TIGR02952 7 DREEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVNDYFRGSKRH 85 (170)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHHHHHhcCCC
Confidence 3455999999999999999999999999999999999999999999999986433 5655
Q ss_pred ------------CCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 384 ------------TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 384 ------------~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.....|++.+...+..+.+..+|..||+++|.||.++|+ +|+|++|||+.||+|+++|++.++|
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~eIA~~l~is~~tv~~~l~r 161 (170)
T TIGR02952 86 PLFSLDVFKELLSNEPNPEEAILKEEANEKLLKALKILTPKQQHVIALRFG----QNLPIAEVARILGKTEGAVKILQFR 161 (170)
T ss_pred CCCcHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 011244555566667788999999999999999999999 9999999999999999999999999
Q ss_pred HHHHHHHHh
Q 011992 452 ALYRLKQSL 460 (473)
Q Consensus 452 AL~KLR~~L 460 (473)
|+++||+.|
T Consensus 162 a~~~Lr~~l 170 (170)
T TIGR02952 162 AIKKLARQM 170 (170)
T ss_pred HHHHHHHhC
Confidence 999999864
No 37
>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=99.80 E-value=1e-18 Score=168.68 Aligned_cols=130 Identities=35% Similarity=0.565 Sum_probs=114.2
Q ss_pred chHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccccCC---------------C-----
Q 011992 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTG---------------V----- 386 (473)
Q Consensus 327 ~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~~---------------~----- 386 (473)
..|++.|+..|.++|+++|++|.+++.+++||+|||++|+|+++++|++.+|.+|.|+. .
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 36899999999999999999999999999999999999999999999999888888800 0
Q ss_pred ---------------------------------------------------------------------------CCchH
Q 011992 387 ---------------------------------------------------------------------------EIPDI 391 (473)
Q Consensus 387 ---------------------------------------------------------------------------~~pee 391 (473)
..++.
T Consensus 82 ~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~d~~~~~~~ 161 (227)
T TIGR02980 82 PRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIEDDDGDPIALLDTLGDEDD 161 (227)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCCCCCCCcccccccCCcch
Confidence 01123
Q ss_pred HHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992 392 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 460 (473)
Q Consensus 392 ~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L 460 (473)
.++..+....|..+|..||++++.||.++|+ +++|++|||+.||+|.++|++++++|+++||+.+
T Consensus 162 ~~~~~~~~~~l~~~l~~L~~~~r~vl~l~y~----~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~l 226 (227)
T TIGR02980 162 ALETVEDRLALKPLLAALPERERRILLLRFF----EDKTQSEIAERLGISQMHVSRLLRRALKKLREQL 226 (227)
T ss_pred HHHhHHHHHHHHHHHHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 3344456678999999999999999999998 9999999999999999999999999999999865
No 38
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=1.3e-18 Score=161.32 Aligned_cols=142 Identities=15% Similarity=0.149 Sum_probs=118.6
Q ss_pred CHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------
Q 011992 315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------- 383 (473)
Q Consensus 315 s~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT---------- 383 (473)
+...+...+..|+ .++..|+..|.+.|+++|.++.++..+++|++||+|+++|+++++|++..+ .|.+
T Consensus 5 ~~~~li~~~~~g~~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~~~-~~~~wl~~ia~n~~ 83 (179)
T PRK12514 5 DIEKLIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGL-SPMTWLITIARNHA 83 (179)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCcccc-cHHHHHHHHHHHHH
Confidence 3445555555555 899999999999999999999999999999999999999999999985432 3433
Q ss_pred ---------------------CCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCH
Q 011992 384 ---------------------TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSK 442 (473)
Q Consensus 384 ---------------------~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~ 442 (473)
.....|+..+...+....|..+|..||++++.||.++|+ +|+|++|||+.||+|+
T Consensus 84 ~d~~R~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~ 159 (179)
T PRK12514 84 IDRLRARKAVAVDIDEAHDLADPSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYL----EGLSYKELAERHDVPL 159 (179)
T ss_pred HHHHHhcCCcccccccchhccccCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCh
Confidence 001234445555555567899999999999999999999 9999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhc
Q 011992 443 ERVRQLESRALYRLKQSLG 461 (473)
Q Consensus 443 ~rVrqi~~RAL~KLR~~L~ 461 (473)
++|++.++||+++||+++.
T Consensus 160 ~tV~~~l~Rar~~Lr~~l~ 178 (179)
T PRK12514 160 NTMRTWLRRSLLKLRECLS 178 (179)
T ss_pred HHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999875
No 39
>PRK05572 sporulation sigma factor SigF; Validated
Probab=99.80 E-value=1.8e-18 Score=170.18 Aligned_cols=132 Identities=33% Similarity=0.535 Sum_probs=111.7
Q ss_pred cchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccccCCC-----------------C-
Q 011992 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGV-----------------E- 387 (473)
Q Consensus 326 g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~~~-----------------~- 387 (473)
+..+++.||..|.++|+++|++|.++..+++|++|||++++|+++++|++..+.+|.|... .
T Consensus 30 d~~a~~~L~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~~lr~~~~~r~ 109 (252)
T PRK05572 30 DQEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDGTVKV 109 (252)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHhCCCCCC
Confidence 4489999999999999999999999999999999999999999999999987778877000 0
Q ss_pred ------------------------Cch------------------------------------------------HHHHH
Q 011992 388 ------------------------IPD------------------------------------------------ISVQK 395 (473)
Q Consensus 388 ------------------------~pe------------------------------------------------e~le~ 395 (473)
.|. .....
T Consensus 110 ~~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~~~~~~ 189 (252)
T PRK05572 110 SRSLKETANKIRKDKDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGDPITLLDQIADQSEED 189 (252)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCcccCCCCcchhhhhcCCCchhh
Confidence 000 00011
Q ss_pred HHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Q 011992 396 QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 461 (473)
Q Consensus 396 ~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~ 461 (473)
......|..+|+.||++++.||.++|+ +++|++|||+.+|+|.++|++++++|+++||..+.
T Consensus 190 ~~~~~~l~~~l~~L~~~~~~v~~l~~~----~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~l~ 251 (252)
T PRK05572 190 WFDKIALKEAIRELDERERLIVYLRYF----KDKTQSEVAKRLGISQVQVSRLEKKILKQMKEKLD 251 (252)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHh----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhc
Confidence 123456889999999999999999998 99999999999999999999999999999998875
No 40
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=99.80 E-value=3.5e-19 Score=173.85 Aligned_cols=169 Identities=20% Similarity=0.338 Sum_probs=130.0
Q ss_pred ccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCC
Q 011992 224 KVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREP 303 (473)
Q Consensus 224 ~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGReP 303 (473)
+..+..+ .|++|+.+||+ |+|+| .+|+.+|.|++. .....+++++...|.+++|++|
T Consensus 62 ~fd~~~~-~F~tYa~~~Ir-----~~il~---~lr~~~~~~r~v--------------r~~~~~i~~~~~~l~~~~g~~p 118 (231)
T PRK12427 62 RYGHPDE-QFAAYAVHRIR-----GAILD---ELRELDWRPRRL--------------RQKTHKTNDAIREIAKRLGHEP 118 (231)
T ss_pred hcCCCCC-ChHHHHHHHHH-----HHHHH---HHHhcCCCCHHH--------------HHHHHHHHHHHHHHHHHHCCCC
Confidence 4444344 79999999999 99998 599999998877 3556788899999999999999
Q ss_pred CHHHHHHHcCCCHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc
Q 011992 304 TLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN 383 (473)
Q Consensus 304 T~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT 383 (473)
|.+|+|+.||++.+++...+.... .....++++.+.+.-.+ + +
T Consensus 119 t~~eiA~~lg~~~~~v~~~~~~~~---------------------~~~~~SLd~~~~~~~~~-----~---------~-- 161 (231)
T PRK12427 119 NFEEISAELNLTAEEYQEYLLLEN---------------------AGTLESLDELLALEAHN-----D---------I-- 161 (231)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHhc---------------------cCCceeccCcccCCCcc-----c---------c--
Confidence 999999999999999876554211 11235555554221100 0 0
Q ss_pred CCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 011992 384 TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 459 (473)
Q Consensus 384 ~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~ 459 (473)
.....+++ .......|..+|..||+++|.||.++|+ +++|++|||+.||||.++|+|++++|+++||..
T Consensus 162 ~~~~~~~~---~~~~~~~l~~~l~~L~~~er~vi~l~~~----~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr~~ 230 (231)
T PRK12427 162 LQSRDLEE---NIIIEDNLKQALSQLDEREQLILHLYYQ----HEMSLKEIALVLDLTEARICQLNKKIAQKIKSF 230 (231)
T ss_pred cCCCCHHH---HHHHHHHHHHHHHcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence 00112222 2235667999999999999999999998 999999999999999999999999999999964
No 41
>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=99.80 E-value=1.2e-18 Score=168.84 Aligned_cols=133 Identities=32% Similarity=0.544 Sum_probs=112.4
Q ss_pred hhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------------CC-
Q 011992 324 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------------TG- 385 (473)
Q Consensus 324 ~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------------~~- 385 (473)
.++..+++.||..|.++|+++|++|.+++.+++|++|||++|+|+++++|++..|.+|.| ..
T Consensus 7 ~gd~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~lr~~~~i 86 (231)
T TIGR02885 7 NGDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDDGII 86 (231)
T ss_pred cCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCCCe
Confidence 344589999999999999999999999999999999999999999999999988888988 00
Q ss_pred ------------------------CCCc--hH------------------------------------------------
Q 011992 386 ------------------------VEIP--DI------------------------------------------------ 391 (473)
Q Consensus 386 ------------------------~~~p--ee------------------------------------------------ 391 (473)
...| ++
T Consensus 87 ~~p~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~~~~ 166 (231)
T TIGR02885 87 KVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPIYLLDQIADKGS 166 (231)
T ss_pred ECCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCCCCCcchhhhhcCCCCc
Confidence 0001 00
Q ss_pred HHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992 392 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 460 (473)
Q Consensus 392 ~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L 460 (473)
..........+.++|+.||++++.||.++|+ +++|++|||+.||+|+++|++++++|+++||..|
T Consensus 167 ~~~~~~~~~~l~~~l~~L~~~e~~i~~~~~~----~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr~~l 231 (231)
T TIGR02885 167 EDSDWLEKIALKEAISKLDERERQIIMLRYF----KDKTQTEVANMLGISQVQVSRLEKKVLKKMKEKL 231 (231)
T ss_pred cHHhHHHHHHHHHHHHcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHhC
Confidence 0011123456888999999999999999998 8999999999999999999999999999999864
No 42
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=1.5e-18 Score=169.56 Aligned_cols=146 Identities=14% Similarity=0.212 Sum_probs=122.2
Q ss_pred CCHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc---------
Q 011992 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN--------- 383 (473)
Q Consensus 314 ms~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT--------- 383 (473)
.+.++|...+..|+ .+++.||..|.+.|+++++++.++..+++|++||+|+++|+++++|++..+ .|.+
T Consensus 48 ~~d~~Li~~~~~gd~~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN~ 126 (233)
T PRK12538 48 DEDEELLDRLATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSNR 126 (233)
T ss_pred ccHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHHH
Confidence 34556666666665 899999999999999999999999999999999999999999999975332 4544
Q ss_pred -----------C---------CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHH
Q 011992 384 -----------T---------GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKE 443 (473)
Q Consensus 384 -----------~---------~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~ 443 (473)
. ....++..+...+....|..+|..||+++|+||.|+|+ +|+|++|||+.||+|.+
T Consensus 127 ~id~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~L~~Lp~~~R~v~~L~~~----eg~s~~EIA~~Lgis~~ 202 (233)
T PRK12538 127 CIDLRRKPRTENVDAVPEVADGKPDAVSVIERNELSDLLEAAMQRLPEQQRIAVILSYH----ENMSNGEIAEVMDTTVA 202 (233)
T ss_pred HHHHHHhhcccccccccccccCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHh----cCCCHHHHHHHHCcCHH
Confidence 0 01123344555666678999999999999999999999 99999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhccCc
Q 011992 444 RVRQLESRALYRLKQSLGGKA 464 (473)
Q Consensus 444 rVrqi~~RAL~KLR~~L~~~~ 464 (473)
+|+++++||+++||+.+...+
T Consensus 203 tVk~~l~RAr~kLr~~l~~~~ 223 (233)
T PRK12538 203 AVESLLKRGRQQLRDLLRRHE 223 (233)
T ss_pred HHHHHHHHHHHHHHHHHHHhh
Confidence 999999999999999997554
No 43
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=99.79 E-value=1.9e-18 Score=163.25 Aligned_cols=146 Identities=18% Similarity=0.195 Sum_probs=122.7
Q ss_pred CCHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc---------
Q 011992 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN--------- 383 (473)
Q Consensus 314 ms~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT--------- 383 (473)
++...++..+..|+ .+++.||..|.+.|+++|.++.++..+++|++||+++++|+++.+|++.. ..|.+
T Consensus 11 ~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~-~~~~~wl~~ia~n~ 89 (196)
T PRK12524 11 VSDEALLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGE-ARVSTWLYRVVCNL 89 (196)
T ss_pred cCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhcccccc-chHHHHHHHHHHHH
Confidence 45566666666665 99999999999999999999999999999999999999999999997422 23444
Q ss_pred ---------------C-------CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCC
Q 011992 384 ---------------T-------GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLS 441 (473)
Q Consensus 384 ---------------~-------~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS 441 (473)
. ....+++.+...+....|..+|+.||+++|.||.|+|+ ++++++|||+.||||
T Consensus 90 ~~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~L~~~----~g~s~~eIA~~lgis 165 (196)
T PRK12524 90 CTDRLRRRRRASVDLDDAPEPADAAPGAEEALIEGDRMRALDAALAALPERQRQAVVLRHI----EGLSNPEIAEVMEIG 165 (196)
T ss_pred HHHHHHhhcCCCCCccccccccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcC
Confidence 0 01123344555666778999999999999999999999 999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhccCc
Q 011992 442 KERVRQLESRALYRLKQSLGGKA 464 (473)
Q Consensus 442 ~~rVrqi~~RAL~KLR~~L~~~~ 464 (473)
.++|+++++||+++||..+....
T Consensus 166 ~~tV~~~l~Ra~~~Lr~~l~~~~ 188 (196)
T PRK12524 166 VEAVESLTARGKRALAALLAGQR 188 (196)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcc
Confidence 99999999999999999987543
No 44
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=99.79 E-value=2.2e-18 Score=160.04 Aligned_cols=143 Identities=17% Similarity=0.296 Sum_probs=121.1
Q ss_pred CCCHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc--------
Q 011992 313 GLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-------- 383 (473)
Q Consensus 313 Gms~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-------- 383 (473)
.+..+.+...+..|+ .+++.++..|.+.|+++|+++.++..+++|++||+++++|+++++|++.. .|.+
T Consensus 2 ~~~~~~li~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn 79 (187)
T PRK09641 2 DLLIKRLIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATN 79 (187)
T ss_pred chHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHH
Confidence 344556666666666 99999999999999999999999999999999999999999999998743 4555
Q ss_pred ----------------C---C-------------CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCH
Q 011992 384 ----------------T---G-------------VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSL 431 (473)
Q Consensus 384 ----------------~---~-------------~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTl 431 (473)
. . ...|+..+...+....+..+|+.||+++++||.++|+ +|+++
T Consensus 80 ~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~~----~~~s~ 155 (187)
T PRK09641 80 LTIDRLRKRKPDYYLDAEVAGTEGLTMYSQLAADDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYI----EDLSL 155 (187)
T ss_pred HHHHHHHhcCccccccccccCCcchhhhcccccCcCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHh----hCCCH
Confidence 0 0 0123344455666678999999999999999999998 99999
Q ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Q 011992 432 SEVGNIFGLSKERVRQLESRALYRLKQSLG 461 (473)
Q Consensus 432 kEIAe~LGIS~~rVrqi~~RAL~KLR~~L~ 461 (473)
+|||+.||||.++|++.++||+++||+.+.
T Consensus 156 ~eIA~~lgis~~~v~~~l~Rar~~Lr~~l~ 185 (187)
T PRK09641 156 KEISEILDLPVGTVKTRIHRGREALRKQLR 185 (187)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999999999999999875
No 45
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=99.79 E-value=2.4e-18 Score=161.66 Aligned_cols=145 Identities=16% Similarity=0.254 Sum_probs=122.4
Q ss_pred CCCHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcC---CcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----
Q 011992 313 GLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGR---GISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----- 383 (473)
Q Consensus 313 Gms~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~---~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----- 383 (473)
.++++.|...+..|+ .+++.|+..|.+.|++++.++.++ ..+++|++||+++++|+++++|++..+ .|.+
T Consensus 2 ~~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~-~~~~wl~~i 80 (189)
T PRK06811 2 KINEDNFIKELKKKNEKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKG-SFKKWIAAI 80 (189)
T ss_pred CCcHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccc-cHHHHHHHH
Confidence 466777777777777 899999999999999999999875 357999999999999999999986433 4655
Q ss_pred --------------------------CCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHH
Q 011992 384 --------------------------TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNI 437 (473)
Q Consensus 384 --------------------------~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~ 437 (473)
.....+++.+...+....|..+|..||+++|.||.|+|+ +|+|++|||+.
T Consensus 81 arn~~~d~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIAe~ 156 (189)
T PRK06811 81 SKYKAIDYKRKLTKNNEIDSIDEFILISEESIENEIILKENKEEILKLINDLEKLDREIFIRRYL----LGEKIEEIAKK 156 (189)
T ss_pred HHHHHHHHHHHhccccccccchhhhhcccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----ccCCHHHHHHH
Confidence 011244455566667778999999999999999999998 99999999999
Q ss_pred HCCCHHHHHHHHHHHHHHHHHHhcc
Q 011992 438 FGLSKERVRQLESRALYRLKQSLGG 462 (473)
Q Consensus 438 LGIS~~rVrqi~~RAL~KLR~~L~~ 462 (473)
||+|.++|++.++||+++||...-.
T Consensus 157 lgis~~~V~~~l~Ra~~~Lr~~~~~ 181 (189)
T PRK06811 157 LGLTRSAIDNRLSRGRKKLQKNKLN 181 (189)
T ss_pred HCCCHHHHHHHHHHHHHHHHHcccC
Confidence 9999999999999999999986543
No 46
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=99.79 E-value=2.2e-18 Score=159.93 Aligned_cols=140 Identities=19% Similarity=0.293 Sum_probs=117.7
Q ss_pred HHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc------------
Q 011992 317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------------ 383 (473)
Q Consensus 317 eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------------ 383 (473)
+++...+..|+ .++..|+..|.+.|+++|.++.++..+++|++||+|+++|+++..|++.. .|.+
T Consensus 6 ~~li~~~~~gd~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~~ 83 (187)
T TIGR02948 6 KKRIKEVRKGDENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQR--KFSTWLYRIATNLTID 83 (187)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHHHH
Confidence 34555555555 99999999999999999999999999999999999999999999998754 4655
Q ss_pred -----------CC-----------------CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHH
Q 011992 384 -----------TG-----------------VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVG 435 (473)
Q Consensus 384 -----------~~-----------------~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIA 435 (473)
.. ...++..+...+....+.++|..||+++|.||.++|+ +|+|++|||
T Consensus 84 ~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA 159 (187)
T TIGR02948 84 RLRKRKPDFYLDDEVQGTDGLTMESQLAADEAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKYM----EDLSLKEIS 159 (187)
T ss_pred HHHhhcccccccccccCccccccccccccCcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhHHh----cCCCHHHHH
Confidence 00 0122334444555677999999999999999999998 999999999
Q ss_pred HHHCCCHHHHHHHHHHHHHHHHHHhcc
Q 011992 436 NIFGLSKERVRQLESRALYRLKQSLGG 462 (473)
Q Consensus 436 e~LGIS~~rVrqi~~RAL~KLR~~L~~ 462 (473)
+.||+|.++|++.++||+++||..+..
T Consensus 160 ~~lgis~~~v~~~l~Rar~~Lr~~l~~ 186 (187)
T TIGR02948 160 EILDLPVGTVKTRIHRGREALRKQLRH 186 (187)
T ss_pred HHHCCCHHHHHHHHHHHHHHHHHHhhc
Confidence 999999999999999999999998763
No 47
>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=99.79 E-value=3.1e-18 Score=159.32 Aligned_cols=141 Identities=18% Similarity=0.215 Sum_probs=119.8
Q ss_pred CHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------
Q 011992 315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------- 383 (473)
Q Consensus 315 s~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT---------- 383 (473)
+.+.+...+..|+ .+++.||..|.+.|+++|+++.++..+++|++||+|+++|+++++|++.. .|.+
T Consensus 6 ~d~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~~--~~~~wl~~iarn~~ 83 (190)
T TIGR02939 6 LDLELVERVQRGEKQAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGDS--AFYTWLYRIAVNTA 83 (190)
T ss_pred cHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCCC--ccHhHHHHHHHHHH
Confidence 3455666666655 89999999999999999999999999999999999999999999998642 3544
Q ss_pred ----------C-----C---------------CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHH
Q 011992 384 ----------T-----G---------------VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSE 433 (473)
Q Consensus 384 ----------~-----~---------------~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkE 433 (473)
. . ...|+..+...+....|..+|..||+++|.||.++|+ ++++++|
T Consensus 84 ~~~~r~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~E 159 (190)
T TIGR02939 84 KNHLVAQGRRPPTSDVEIEDAEHFEGADRLREIDTPERLLLSRELEQTVMRAVEALPEDLRTAITLREL----EGLSYED 159 (190)
T ss_pred HHHHHHhccCCCcccccccchhhhcccccccccCChHHHHHHHHHHHHHHHHHHcCCHHHhhhhhhhhh----cCCCHHH
Confidence 0 0 0123444555666778999999999999999999999 9999999
Q ss_pred HHHHHCCCHHHHHHHHHHHHHHHHHHhc
Q 011992 434 VGNIFGLSKERVRQLESRALYRLKQSLG 461 (473)
Q Consensus 434 IAe~LGIS~~rVrqi~~RAL~KLR~~L~ 461 (473)
||+.||+|.++|++.++||+++||+.+.
T Consensus 160 IA~~lgis~~tv~~~l~rar~~Lr~~l~ 187 (190)
T TIGR02939 160 IARIMDCPVGTVRSRIFRAREAIAIRLR 187 (190)
T ss_pred HHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 9999999999999999999999999986
No 48
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=99.79 E-value=2.6e-18 Score=160.34 Aligned_cols=141 Identities=13% Similarity=0.142 Sum_probs=116.7
Q ss_pred CHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------
Q 011992 315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------- 383 (473)
Q Consensus 315 s~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT---------- 383 (473)
+.+.+...+..|+ .+++.||..|.+.+++++.++.++..+++|++||+|+.+|+.+++|++.. ..|.+
T Consensus 9 ~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~-~~~~~wL~~iarn~~ 87 (182)
T PRK12537 9 DYEACLLACARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPAR-GSARGWIYSVTRHLA 87 (182)
T ss_pred hHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCccc-ccHHHHHHHHHHHHH
Confidence 3345566665555 99999999999999999999999999999999999999999999997532 24544
Q ss_pred -------------C-C-------CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCH
Q 011992 384 -------------T-G-------VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSK 442 (473)
Q Consensus 384 -------------~-~-------~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~ 442 (473)
. . ...++...+..+....+.++|+.||+++|+||.++|+ +|++++|||+.||||.
T Consensus 88 ~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~~~s~~eIA~~lgis~ 163 (182)
T PRK12537 88 LNVLRDTRREVVLDDDAEETAQTLHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAYV----DGCSHAEIAQRLGAPL 163 (182)
T ss_pred HHHHHhccccCccccchhhhcccccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCh
Confidence 0 0 0112233334445667999999999999999999999 9999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHh
Q 011992 443 ERVRQLESRALYRLKQSL 460 (473)
Q Consensus 443 ~rVrqi~~RAL~KLR~~L 460 (473)
++|+..++||+++||.++
T Consensus 164 ~tV~~~l~ra~~~Lr~~l 181 (182)
T PRK12537 164 GTVKAWIKRSLKALRECM 181 (182)
T ss_pred hhHHHHHHHHHHHHHHHh
Confidence 999999999999999986
No 49
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=99.79 E-value=4e-18 Score=161.29 Aligned_cols=149 Identities=20% Similarity=0.271 Sum_probs=121.5
Q ss_pred HcCCCHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc------
Q 011992 311 AIGLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------ 383 (473)
Q Consensus 311 ~lGms~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------ 383 (473)
...++.+.+...+..|+ .+++.|+..|.+.|+++|.++.++..+++|++||+|+++|+++.+|++.++.+|.|
T Consensus 6 ~~~~~~~~l~~~~~~~d~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~ 85 (208)
T PRK08295 6 YDELEDEELVELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCI 85 (208)
T ss_pred ccCCChHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHH
Confidence 44566667766666665 99999999999999999999999999999999999999999999999887667776
Q ss_pred -------------C-C--------C----------------------CCchHHHHHHHHHHHH-HHHHhhCCHHHHHHHH
Q 011992 384 -------------T-G--------V----------------------EIPDISVQKQLMRQHV-RNLLTLLNPKERCIVR 418 (473)
Q Consensus 384 -------------~-~--------~----------------------~~pee~le~~el~e~L-~~aL~~LperER~VL~ 418 (473)
. . . ..|+..+...+....+ ..++..||+++|.||.
T Consensus 86 ~n~~~d~~r~~~r~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~~r~vl~ 165 (208)
T PRK08295 86 TRQIITAIKTANRQKHIPLNSYVSLDKPIYDEESDRTLLDVISEAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLE 165 (208)
T ss_pred HHHHHHHHHHhhhhccccccceeecCCcccCCccchhHHHHhcCcccCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHH
Confidence 0 0 0 1222222223333444 4567999999999999
Q ss_pred HHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCc
Q 011992 419 LRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 464 (473)
Q Consensus 419 LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~ 464 (473)
+ |+ +++|++|||+.||+|.++|+..++||+++||+++....
T Consensus 166 l-~~----e~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l~~~~ 206 (208)
T PRK08295 166 L-YL----DGKSYQEIAEELNRHVKSIDNALQRVKRKLEKYLENRE 206 (208)
T ss_pred H-HH----ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhc
Confidence 9 77 89999999999999999999999999999999987653
No 50
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=99.79 E-value=2e-18 Score=155.67 Aligned_cols=127 Identities=20% Similarity=0.282 Sum_probs=109.9
Q ss_pred chHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------------------
Q 011992 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------------------- 383 (473)
Q Consensus 327 ~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------------------- 383 (473)
..+|+.|+..|.++|+++++++ ++..++||++||+++++|+++++|++..+ .|.+
T Consensus 3 ~~af~~l~~~y~~~l~~~~~~~-~~~~~aeDi~Qe~~l~l~~~~~~~~~~~~-~f~~wl~~i~~n~~ld~~rk~~~~~~~ 80 (154)
T PRK06759 3 PATFTEAVVLYEGLIVNQIKKL-GIYQDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYILERLKKEFAVQEK 80 (154)
T ss_pred cccHHHHHHHHHHHHHHHHHHh-CCcccHHHHHHHHHHHHHHHHHHhCccCC-chHHHHHHHHHHHHHHHHHHHHhhccc
Confidence 4689999999999999999886 56779999999999999999999987555 4655
Q ss_pred -CCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 011992 384 -TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 459 (473)
Q Consensus 384 -~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~ 459 (473)
...+.|++.+...+....|..+|..||+++|.||.++|+ +|+|++|||+.||+|.++|+++++||+++||+.
T Consensus 81 ~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~ii~l~~~----~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~ 153 (154)
T PRK06759 81 CVCVGEYEDHFHFEDVEMKVKDFMSVLDEKEKYIIFERFF----VGKTMGEIALETEMTYYQVRWIYRQALEKMRNS 153 (154)
T ss_pred ccccCCCcccccHHHHHHHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence 112344555555666788999999999999999999999 999999999999999999999999999999974
No 51
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=99.79 E-value=3.4e-18 Score=159.26 Aligned_cols=143 Identities=22% Similarity=0.308 Sum_probs=116.3
Q ss_pred CHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------
Q 011992 315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------- 383 (473)
Q Consensus 315 s~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT---------- 383 (473)
+..++...+..|+ .+++.|+..|.+.|+++++++.++..+++|++||+|+++|+++++|++..+ .|.+
T Consensus 9 ~~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~~-~~~~wl~~ia~n~~ 87 (186)
T PRK13919 9 SDEALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRG-SARAWLLALAHHAA 87 (186)
T ss_pred CHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCcccc-chHHHHHHHHHHHH
Confidence 4455656555555 999999999999999999999999999999999999999999999986432 3433
Q ss_pred ----------C-C------C------CCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCC
Q 011992 384 ----------T-G------V------EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGL 440 (473)
Q Consensus 384 ----------~-~------~------~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGI 440 (473)
. . . ..+............|.++|..||+++|.||.++|+ ++++++|||+.||+
T Consensus 88 ~d~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgi 163 (186)
T PRK13919 88 VDHVRRRAARPQPLEPDEREPEAFDLPGPGLDEEGHLDRTRLGRALKALSPEERRVIEVLYY----QGYTHREAAQLLGL 163 (186)
T ss_pred HHHHHhhhcccccccccccccccccCCCccccHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCc
Confidence 0 0 0 011112222334567999999999999999999999 99999999999999
Q ss_pred CHHHHHHHHHHHHHHHHHHhcc
Q 011992 441 SKERVRQLESRALYRLKQSLGG 462 (473)
Q Consensus 441 S~~rVrqi~~RAL~KLR~~L~~ 462 (473)
|.++|+..++||+++||..+..
T Consensus 164 s~~~V~~~l~ra~~~Lr~~l~~ 185 (186)
T PRK13919 164 PLGTLKTRARRALSRLKEVLRE 185 (186)
T ss_pred CHHHHHHHHHHHHHHHHHHhcC
Confidence 9999999999999999998864
No 52
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=1.5e-18 Score=162.09 Aligned_cols=141 Identities=19% Similarity=0.223 Sum_probs=117.7
Q ss_pred hcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc---------------------
Q 011992 325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN--------------------- 383 (473)
Q Consensus 325 ~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT--------------------- 383 (473)
++..+++.||..|.+.++++|.++.++..+++|++||+|+.+|+++++|+...+..|.+
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 44589999999999999999999999999999999999999999999997543345655
Q ss_pred ---CCC---------CCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 384 ---TGV---------EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 384 ---~~~---------~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
... ..++......+....|..+|..||+++|+||.|+|+ +|+|++|||+.||+|.++|+..+.|
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tVk~~l~R 161 (185)
T PRK12542 86 TFLEEYERESIEAVDENIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVF----YNLTYQEISSVMGITEANVRKQFER 161 (185)
T ss_pred hhhhhccccchhhhhccHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 000 011111222334467999999999999999999999 9999999999999999999999999
Q ss_pred HHHHHHHHhccCchhhhh
Q 011992 452 ALYRLKQSLGGKASYGYA 469 (473)
Q Consensus 452 AL~KLR~~L~~~~l~~yl 469 (473)
|+++||+.+.......|+
T Consensus 162 ar~~Lr~~l~~~~~~~~~ 179 (185)
T PRK12542 162 ARKRVQNMIGGIQHDEFK 179 (185)
T ss_pred HHHHHHHHHcccchHHHH
Confidence 999999999888777775
No 53
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=3.6e-18 Score=159.44 Aligned_cols=140 Identities=17% Similarity=0.183 Sum_probs=116.3
Q ss_pred HHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc------------
Q 011992 317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------------ 383 (473)
Q Consensus 317 eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------------ 383 (473)
..+...+..|+ .+++.|+..|.+.|+++|+++.++..+++|++||+|+++|+++++|++..+ .|.+
T Consensus 13 ~~l~~~~~~~~~~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~~n~~~d 91 (187)
T PRK12534 13 GRLLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIARNKAID 91 (187)
T ss_pred HHHHHHHHcCCHHHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHHH
Confidence 33444444454 999999999999999999999999999999999999999999999987543 2323
Q ss_pred -------C--------------CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCH
Q 011992 384 -------T--------------GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSK 442 (473)
Q Consensus 384 -------~--------------~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~ 442 (473)
. ....++......+....|..+|..||++++.|+.++|+ +|++++|||+.||+|+
T Consensus 92 ~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~ 167 (187)
T PRK12534 92 HLRANAPQRRNVALDDAGELRAADASPLERTERASTRRRIDHCLAELEPPRSELIRTAFF----EGITYEELAARTDTPI 167 (187)
T ss_pred HHHhcccccccccccchhhhccccCChhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCh
Confidence 0 00122333444566778999999999999999999999 9999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhc
Q 011992 443 ERVRQLESRALYRLKQSLG 461 (473)
Q Consensus 443 ~rVrqi~~RAL~KLR~~L~ 461 (473)
++|+++++||+++||..+.
T Consensus 168 ~~v~~~l~Rar~~Lr~~l~ 186 (187)
T PRK12534 168 GTVKSWIRRGLAKLKACLE 186 (187)
T ss_pred hHHHHHHHHHHHHHHHHHc
Confidence 9999999999999999875
No 54
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=4.7e-18 Score=159.28 Aligned_cols=146 Identities=21% Similarity=0.304 Sum_probs=122.8
Q ss_pred CCHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc---------
Q 011992 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN--------- 383 (473)
Q Consensus 314 ms~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT--------- 383 (473)
++.+++...+..|+ .+++.|+..|.+.++.++.++.++..+++|++||+|+.+|+++++|++. ..|.+
T Consensus 7 ~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~~~~~~~--~~~~~wl~~i~~n~ 84 (189)
T PRK12515 7 TTDEMLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIARFK 84 (189)
T ss_pred cCHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CChHHHHHHHHHHH
Confidence 45556666666555 8999999999999999999999999999999999999999999999863 24544
Q ss_pred ----------------------CCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCC
Q 011992 384 ----------------------TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLS 441 (473)
Q Consensus 384 ----------------------~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS 441 (473)
.....++..+...+....+..+|+.||+++|.||.++|+ ++++++|||+.||+|
T Consensus 85 ~~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis 160 (189)
T PRK12515 85 ALSALRRRKHEEIDDEAAAAIEDGADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVYY----HEKSVEEVGEIVGIP 160 (189)
T ss_pred HHHHHHccCCCCCccccccccCCCCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcC
Confidence 001123444455566778999999999999999999999 999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhccCch
Q 011992 442 KERVRQLESRALYRLKQSLGGKAS 465 (473)
Q Consensus 442 ~~rVrqi~~RAL~KLR~~L~~~~l 465 (473)
.++|+.++.||+++||+.+...+.
T Consensus 161 ~~tV~~~l~Rar~~Lr~~l~~~~~ 184 (189)
T PRK12515 161 ESTVKTRMFYARKKLAELLKAAGV 184 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcc
Confidence 999999999999999999886543
No 55
>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=99.77 E-value=2.3e-18 Score=166.28 Aligned_cols=181 Identities=27% Similarity=0.449 Sum_probs=141.4
Q ss_pred ccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCC
Q 011992 224 KVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREP 303 (473)
Q Consensus 224 ~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGReP 303 (473)
+..+..|..|.||+.++|+ +.++| .+|+..|.|++. .+...++..+..+|.+.+|++|
T Consensus 43 ~fd~~~~~~f~t~~~~~i~-----~~~~~---~lr~~~~~p~~~--------------~~~~~~l~~~~~~l~~~~~~~~ 100 (224)
T TIGR02479 43 RYDPSRGAKFETYAVQRIR-----GAMLD---ELRRLDWVPRSL--------------RQKARKLERAIRELEARLGREP 100 (224)
T ss_pred hcCCccCCCHHHHHHHHHH-----HHHHH---HHHHcCccCHHH--------------HHHHHHHHHHHHHHHHHHCcCC
Confidence 4567788899999999999 99988 588887877765 4667789999999999999999
Q ss_pred CHHHHHHHcCCCHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc
Q 011992 304 TLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN 383 (473)
Q Consensus 304 T~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT 383 (473)
+.+|+|+.+|++.+.+..++.... .+...++++.+.++--+. .+..+ +.+
T Consensus 101 ~~~ela~~l~~~~~~v~~~~~~~~---------------------~~~~~sl~~~~~~~~~~~--~~~~~-------~~~ 150 (224)
T TIGR02479 101 TEEEIAEELGMDLKEYRQALNEIN---------------------ALSLVSLDELLESGDDGG--SLIDR-------IED 150 (224)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHh---------------------cCCccccCCcccCCCccc--hhhhh-------ccc
Confidence 999999999999998877654211 112334555443211000 00000 111
Q ss_pred CCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992 384 TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 460 (473)
Q Consensus 384 ~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L 460 (473)
+....|+..+...+....|.++|+.||+++|.||.++|+ +++|++|||+.||+|.++|++++++|+++||+.+
T Consensus 151 ~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~y~----~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 223 (224)
T TIGR02479 151 DKSEDPEEELEREELREALAEAIESLSEREQLVLSLYYY----EELNLKEIGEVLGLTESRVSQIHSQALKKLRAKL 223 (224)
T ss_pred cccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHh----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHc
Confidence 224467778888888899999999999999999999999 9999999999999999999999999999999876
No 56
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=99.77 E-value=4.9e-18 Score=155.71 Aligned_cols=132 Identities=20% Similarity=0.251 Sum_probs=114.5
Q ss_pred hhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc--------------------
Q 011992 324 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-------------------- 383 (473)
Q Consensus 324 ~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-------------------- 383 (473)
.++..|++.|+..|.+.|+++++++.+++.+++|++||+++++|++++.|+ .+..|.+
T Consensus 6 ~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~r~~~~~ 83 (182)
T PRK09652 6 RGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR--GGAAFYTWLYRIARNTAINYLRKQGRR 83 (182)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHHHHHHHHcccCC
Confidence 445589999999999999999999999999999999999999999999998 3445655
Q ss_pred ---C-----------------CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHH
Q 011992 384 ---T-----------------GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKE 443 (473)
Q Consensus 384 ---~-----------------~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~ 443 (473)
. ....|+..+...+....+..+|..||++++.||.++|+ +++|++|||+.||+|++
T Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~ 159 (182)
T PRK09652 84 PPASDVDAEEAEDFDLADALRDISTPENELLSAELEQRVRAAIESLPEELRTAITLREI----EGLSYEEIAEIMGCPIG 159 (182)
T ss_pred CCccccccccccccccccccccccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHH
Confidence 0 00124445555566788999999999999999999998 99999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhc
Q 011992 444 RVRQLESRALYRLKQSLG 461 (473)
Q Consensus 444 rVrqi~~RAL~KLR~~L~ 461 (473)
+|++.+++|+++||+.+.
T Consensus 160 tV~~~l~ra~~~Lr~~l~ 177 (182)
T PRK09652 160 TVRSRIFRAREALRAKLQ 177 (182)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 999999999999999876
No 57
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=99.77 E-value=1e-17 Score=157.09 Aligned_cols=141 Identities=15% Similarity=0.210 Sum_probs=118.8
Q ss_pred HHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------
Q 011992 316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------- 383 (473)
Q Consensus 316 ~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------- 383 (473)
.+.+...+..|+ .+++.||..|.+.|+++++++.++..+++|++||+|+++|+++.+|++..+ |.+
T Consensus 7 ~~~ll~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~l~~~~~~~~~~~~--~~~wl~~ia~n~~~ 84 (193)
T PRK11923 7 DQQLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDSA--FYTWLYRIAINTAK 84 (193)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHhCcCCCCc--cHhHHHHHHHHHHH
Confidence 344555555555 899999999999999999999999999999999999999999999987542 333
Q ss_pred ---------C--------------------CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHH
Q 011992 384 ---------T--------------------GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEV 434 (473)
Q Consensus 384 ---------~--------------------~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEI 434 (473)
. ....|+..+...+....+..+|..||+++|.||.++|+ +|++++||
T Consensus 85 d~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eI 160 (193)
T PRK11923 85 NHLVSRGRRPPDSDVSSEDAEFYDGDHALKDIESPERALLRDEIEGTVHRTIQQLPEDLRTALTLREF----DGLSYEDI 160 (193)
T ss_pred HHHHHhcCCCccccccccchhhhcccccccCcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHHhhHHh----cCCCHHHH
Confidence 0 01223444555666788999999999999999999998 99999999
Q ss_pred HHHHCCCHHHHHHHHHHHHHHHHHHhcc
Q 011992 435 GNIFGLSKERVRQLESRALYRLKQSLGG 462 (473)
Q Consensus 435 Ae~LGIS~~rVrqi~~RAL~KLR~~L~~ 462 (473)
|+.||+|.++|++.++||+++||++++.
T Consensus 161 A~~lgis~~tv~~~l~Rar~~Lr~~l~~ 188 (193)
T PRK11923 161 ASVMQCPVGTVRSRIFRAREAIDKALQP 188 (193)
T ss_pred HHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999998863
No 58
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=99.77 E-value=6.5e-18 Score=158.59 Aligned_cols=140 Identities=22% Similarity=0.300 Sum_probs=115.7
Q ss_pred HHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------
Q 011992 316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------- 383 (473)
Q Consensus 316 ~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------- 383 (473)
..++...+..|+ .+++.|+..|.+.|+++++++.++..+++|++||+|+++|.. ..|++..+ .|.+
T Consensus 16 ~~~l~~~~~~gd~~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn~~~ 93 (194)
T PRK12519 16 DAELFSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRSRAI 93 (194)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHHHHH
Confidence 445555555555 999999999999999999999999999999999999999975 56775443 5655
Q ss_pred -------------C----------CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCC
Q 011992 384 -------------T----------GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGL 440 (473)
Q Consensus 384 -------------~----------~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGI 440 (473)
. ....++..+...+....|..+|..||+++++||.|+|+ +|+|++|||+.||+
T Consensus 94 d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~~----~g~s~~EIA~~lgi 169 (194)
T PRK12519 94 DRLRSRRSRQRLLERWQQELLGEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYY----EGLSQSEIAKRLGI 169 (194)
T ss_pred HHHHhcccccchhhhhhhhhcccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhhh----cCCCHHHHHHHhCC
Confidence 0 00123344445555677899999999999999999998 99999999999999
Q ss_pred CHHHHHHHHHHHHHHHHHHhc
Q 011992 441 SKERVRQLESRALYRLKQSLG 461 (473)
Q Consensus 441 S~~rVrqi~~RAL~KLR~~L~ 461 (473)
|.++|+++++||+++||+.+.
T Consensus 170 s~~tV~~~l~Ra~~~Lr~~l~ 190 (194)
T PRK12519 170 PLGTVKARARQGLLKLRELLQ 190 (194)
T ss_pred CHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999875
No 59
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=99.77 E-value=6.4e-18 Score=155.87 Aligned_cols=144 Identities=14% Similarity=0.228 Sum_probs=119.0
Q ss_pred cCCCHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-------
Q 011992 312 IGLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------- 383 (473)
Q Consensus 312 lGms~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------- 383 (473)
|.|+...+......|+ .+++.|+..|.+.|+++|+++.++..+++|++||+|+++|++++.|++. ..|.+
T Consensus 1 ~~~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~--~~~~~wl~~i~~ 78 (176)
T PRK09638 1 MQMDEKELIQKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGR--SKFSTWLISIAS 78 (176)
T ss_pred CCccHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHH
Confidence 3455666666666666 9999999999999999999999999999999999999999999999764 35555
Q ss_pred -----------------C----CCCCch--HHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCC
Q 011992 384 -----------------T----GVEIPD--ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGL 440 (473)
Q Consensus 384 -----------------~----~~~~pe--e~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGI 440 (473)
. ....++ ...........|..+|..||+++|+||.++|+ +|++++|||+.||+
T Consensus 79 n~~~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~l~i 154 (176)
T PRK09638 79 RLYKDHLRKQKREKLRLQRAKEETLRKEKWEAAIKGAEWSEMLDALSKLDPEFRAPVILKHY----YGYTYEEIAKMLNI 154 (176)
T ss_pred HHHHHHHHHhccccchhhhcccccCCccchHHHHHhhhHHHHHHHHHcCCHHHhheeeehhh----cCCCHHHHHHHHCC
Confidence 0 001111 22233345567899999999999999999998 99999999999999
Q ss_pred CHHHHHHHHHHHHHHHHHHhc
Q 011992 441 SKERVRQLESRALYRLKQSLG 461 (473)
Q Consensus 441 S~~rVrqi~~RAL~KLR~~L~ 461 (473)
|.++|++.+.||+++||+.+.
T Consensus 155 s~~~V~~~l~ra~~~l~~~l~ 175 (176)
T PRK09638 155 PEGTVKSRVHHGIKQLRKEWG 175 (176)
T ss_pred ChhHHHHHHHHHHHHHHHHhc
Confidence 999999999999999999874
No 60
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=99.77 E-value=1.5e-17 Score=156.88 Aligned_cols=145 Identities=17% Similarity=0.183 Sum_probs=122.4
Q ss_pred CCCHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc--------
Q 011992 313 GLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-------- 383 (473)
Q Consensus 313 Gms~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-------- 383 (473)
.++.+.+...+..|+ .+++.|+..|.+.|++++.++.++..+++|++||+|+.+|+++++|++.. .|.+
T Consensus 11 ~~~~~~l~~~~~~gd~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~~--~f~~wL~~i~rn 88 (192)
T PRK09643 11 ERSDAELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDA--AVSSWLHRIVVN 88 (192)
T ss_pred CcCHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCCC--ccHHHHHHHHHH
Confidence 355666666666665 99999999999999999999999999999999999999999999998643 3555
Q ss_pred ------------C--C-------CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCH
Q 011992 384 ------------T--G-------VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSK 442 (473)
Q Consensus 384 ------------~--~-------~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~ 442 (473)
. . ...+++.+...+....|..+|..||+++|.||.|+|+ ++++++|||+.||+|.
T Consensus 89 ~~~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~i~~l~~~----~g~s~~EIA~~lg~s~ 164 (192)
T PRK09643 89 ACLDRLRRAKARPTVPLDDVYPVAQLERDPTARVETALAVQRALMRLPVEQRAALVAVDM----QGYSVADAARMLGVAE 164 (192)
T ss_pred HHHHHHHccccCCCCCccccccccCCcccHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCH
Confidence 0 0 0112334455566778999999999999999999999 9999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhccC
Q 011992 443 ERVRQLESRALYRLKQSLGGK 463 (473)
Q Consensus 443 ~rVrqi~~RAL~KLR~~L~~~ 463 (473)
++|+..+.||+++||+.+...
T Consensus 165 ~tV~~rl~rar~~Lr~~l~~~ 185 (192)
T PRK09643 165 GTVKSRCARGRARLAELLGYL 185 (192)
T ss_pred HHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999998754
No 61
>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=99.76 E-value=1.3e-17 Score=153.34 Aligned_cols=141 Identities=21% Similarity=0.269 Sum_probs=115.5
Q ss_pred CCHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc---------
Q 011992 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN--------- 383 (473)
Q Consensus 314 ms~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT--------- 383 (473)
|+++++...+..|+ .+++.++..|.+.|++++.++.++..+++|++||+|+.+|+++++|++.. .|.+
T Consensus 1 ~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~~--~~~~wl~~i~~n~ 78 (169)
T TIGR02954 1 MNDEELVKKAKRGNKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPK--YFNTWLTRILINE 78 (169)
T ss_pred CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCcc--ccHHHHHHHHHHH
Confidence 34555655555555 99999999999999999999999999999999999999999999998643 4555
Q ss_pred -----------C---C---CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHH
Q 011992 384 -----------T---G---VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVR 446 (473)
Q Consensus 384 -----------~---~---~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVr 446 (473)
. . ...++.... .+....+..+|..||+++|+||.++|+ +|+|++|||+.||||.++|+
T Consensus 79 ~~d~~R~~~~~~~~~~~~~~~~~~~~~~-~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eiA~~lgis~~tv~ 153 (169)
T TIGR02954 79 CIDLLKKKKKVIPFDPNTSIEKGECETH-ADSRLDLYKAIDTLNDKYQTAIILRYY----HDLTIKEIAEVMNKPEGTVK 153 (169)
T ss_pred HHHHHHhcCCcCccccccccccchhhhc-hHHHHHHHHHHHhCCHHHhHHHHHHHH----cCCCHHHHHHHHCCCHHHHH
Confidence 0 0 001111111 122347899999999999999999999 99999999999999999999
Q ss_pred HHHHHHHHHHHHHhc
Q 011992 447 QLESRALYRLKQSLG 461 (473)
Q Consensus 447 qi~~RAL~KLR~~L~ 461 (473)
.+++||+++||+.+.
T Consensus 154 ~~l~Ra~~~Lr~~l~ 168 (169)
T TIGR02954 154 TYLHRALKKLKKRLE 168 (169)
T ss_pred HHHHHHHHHHHHHhc
Confidence 999999999999875
No 62
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=99.76 E-value=2e-17 Score=155.15 Aligned_cols=142 Identities=23% Similarity=0.287 Sum_probs=115.9
Q ss_pred CCHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc---------
Q 011992 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN--------- 383 (473)
Q Consensus 314 ms~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT--------- 383 (473)
|+..++...+..|+ .|++.||..|.+.|+++|+++.++..+++|++||+|+++|+++++|++..+..|.|
T Consensus 4 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~a~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~~~f~~wl~~~~~~~ 83 (198)
T TIGR02859 4 LEDEEIVELARQGNTHALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELCVTRQ 83 (198)
T ss_pred cchHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHccccCcHHHHHHHHHHHHHHHHHHhCcccCCChHHHHHHHHHHH
Confidence 45666777776766 99999999999999999999999999999999999999999999999876556655
Q ss_pred -----------CC------------------------------CCCchHHHHHHHHHHHHHHHHhhC-CHHHHHHHHHHh
Q 011992 384 -----------TG------------------------------VEIPDISVQKQLMRQHVRNLLTLL-NPKERCIVRLRF 421 (473)
Q Consensus 384 -----------~~------------------------------~~~pee~le~~el~e~L~~aL~~L-perER~VL~LrY 421 (473)
.. ...|+..+...+..+.|.++|+.| ++.++.|+. +|
T Consensus 84 ~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~~-~~ 162 (198)
T TIGR02859 84 IITAIKTATRQKHIPLNSYVSLNKPIYDEESDRTLLDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVLQ-SY 162 (198)
T ss_pred HHHHHHHHHHhcccchhhhcCcccccccccccchHHHHhhccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHH-HH
Confidence 00 012333344455566788999995 566666664 57
Q ss_pred hccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992 422 GIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 460 (473)
Q Consensus 422 ~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L 460 (473)
+ +++|++|||+.||+|.++|+..++||+++||+.+
T Consensus 163 ~----~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~~l 197 (198)
T TIGR02859 163 L----DGKSYQEIACDLNRHVKSIDNALQRVKRKLEKYL 197 (198)
T ss_pred H----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhc
Confidence 7 8999999999999999999999999999999876
No 63
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=99.76 E-value=1e-17 Score=155.99 Aligned_cols=132 Identities=17% Similarity=0.212 Sum_probs=114.9
Q ss_pred hcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc---------------------
Q 011992 325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN--------------------- 383 (473)
Q Consensus 325 ~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT--------------------- 383 (473)
++..+++.||..|.+.|+++++.+.++..+++|++||+|+.+|+++.+|++.. .|.+
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 34489999999999999999999999999999999999999999999998764 3443
Q ss_pred -------C-----CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 384 -------T-----GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 384 -------~-----~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
. ....|+. +...+....|..+|..||+++|.||.|+|+ +++|++|||+.||||.++|+..++|
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~l~~~l~~Lp~~~r~i~~l~~~----e~~s~~EIA~~lgis~~tV~~~l~r 156 (179)
T PRK12543 82 RIFEKAEEQRKPVSIDFSED-VLSKESNQELIELIHKLPYKLRQVIILRYL----HDYSQEEIAQLLQIPIGTVKSRIHA 156 (179)
T ss_pred ccccccccccccccccChHH-HHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----ccCCHHHHHHHHCCCHHHHHHHHHH
Confidence 0 0112333 556667788999999999999999999999 9999999999999999999999999
Q ss_pred HHHHHHHHhccC
Q 011992 452 ALYRLKQSLGGK 463 (473)
Q Consensus 452 AL~KLR~~L~~~ 463 (473)
|+++||+.+...
T Consensus 157 a~~~Lr~~l~~~ 168 (179)
T PRK12543 157 ALKKLRQKEQIE 168 (179)
T ss_pred HHHHHHHHHHHH
Confidence 999999998754
No 64
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=99.76 E-value=1.6e-17 Score=151.94 Aligned_cols=134 Identities=18% Similarity=0.217 Sum_probs=118.4
Q ss_pred hhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc--------------------
Q 011992 324 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-------------------- 383 (473)
Q Consensus 324 ~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-------------------- 383 (473)
.++..+++.|+..|++.|+++|+++.++..+++|++||+++++|.+++.|+ .+..|.+
T Consensus 9 ~~~~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~~~d~~r~~~~~ 86 (179)
T PRK11924 9 TGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNVCYDLLRRRRRE 86 (179)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHHHHHHHHhcccc
Confidence 344499999999999999999999999999999999999999999999997 2334554
Q ss_pred ------------C--CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHH
Q 011992 384 ------------T--GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE 449 (473)
Q Consensus 384 ------------~--~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~ 449 (473)
. ....|+..+...+....+..+|+.||++++.||.++|+ ++++++|||+.||+|+++|++++
T Consensus 87 ~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~~~~~~eIA~~lgis~~tv~~~~ 162 (179)
T PRK11924 87 KAVLSDDALEPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYV----EGLSYREIAEILGVPVGTVKSRL 162 (179)
T ss_pred cccCcccccccccCCccCCHHHHHhhHHHHHHHHHHHHhCCHHHHHHhhHHHH----cCCCHHHHHHHHCCCHHHHHHHH
Confidence 0 23456667777888889999999999999999999998 99999999999999999999999
Q ss_pred HHHHHHHHHHhccC
Q 011992 450 SRALYRLKQSLGGK 463 (473)
Q Consensus 450 ~RAL~KLR~~L~~~ 463 (473)
++|+++||+.+...
T Consensus 163 ~ra~~~lr~~l~~~ 176 (179)
T PRK11924 163 RRARQLLRECLEAQ 176 (179)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999988754
No 65
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=99.76 E-value=1.7e-17 Score=154.68 Aligned_cols=130 Identities=18% Similarity=0.199 Sum_probs=114.2
Q ss_pred chHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------------------
Q 011992 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------------------- 383 (473)
Q Consensus 327 ~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------------------- 383 (473)
..|++.||..|.+.|++++.++.++..+++|++||+|+.+|+++++|+... .|.+
T Consensus 15 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~~--~~~awl~~ia~n~~~d~~Rk~~~~~~~ 92 (179)
T PRK09415 15 EDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKS--SLKTWLYRIAINHCKDYLKSWHNKKVI 92 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCCc--ccHHHHHHHHHHHHHHHHHhhcccccc
Confidence 389999999999999999999999999999999999999999999997642 4554
Q ss_pred --C--------CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992 384 --T--------GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 453 (473)
Q Consensus 384 --~--------~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL 453 (473)
. ....++..+...+....|..+|+.||+++|+||.|+|+ +|+|++|||+.||||.++|++++.||+
T Consensus 93 ~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~l~is~~tv~~~l~Ra~ 168 (179)
T PRK09415 93 VTEDIFTYMESQKESVEEEVIQNAEDERLASAVMSLPIKYREVIYLFYY----EELSIKEIAEVTGVNENTVKTRLKKAK 168 (179)
T ss_pred ccccccccccccccCcHHHHHHHHHHHHHHHHHHhCCHHHhhHhHhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 0 11234555566667788999999999999999999999 999999999999999999999999999
Q ss_pred HHHHHHhcc
Q 011992 454 YRLKQSLGG 462 (473)
Q Consensus 454 ~KLR~~L~~ 462 (473)
++||+.+..
T Consensus 169 ~~Lr~~l~~ 177 (179)
T PRK09415 169 ELLKKGLEE 177 (179)
T ss_pred HHHHHHHhc
Confidence 999998864
No 66
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=99.75 E-value=9.6e-18 Score=157.26 Aligned_cols=144 Identities=22% Similarity=0.345 Sum_probs=118.4
Q ss_pred CCCHHHHHHHHhh----cchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----
Q 011992 313 GLSCRDLKSELHS----GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----- 383 (473)
Q Consensus 313 Gms~eeL~~~l~~----g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----- 383 (473)
+++.+++...++. +..|++.||..|.+.|+++|.++.++..+++|++||+|+++|+++++|++. ..|.+
T Consensus 7 ~~~~~~li~~~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~~~~~~~~~--~~~~~wl~~i 84 (188)
T PRK09640 7 ELNDEELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGK--SKFKTWLYSI 84 (188)
T ss_pred CCCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHHHhcCC--CcchHHHHHH
Confidence 4566666666653 348999999999999999999999999999999999999999999999853 35655
Q ss_pred --------------C-CC---------CCch-HHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHH
Q 011992 384 --------------T-GV---------EIPD-ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIF 438 (473)
Q Consensus 384 --------------~-~~---------~~pe-e~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~L 438 (473)
. .. ..+. ......+....|..+|+.||+++|.||.|+|+ +|++++|||+.|
T Consensus 85 a~n~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~l 160 (188)
T PRK09640 85 TYNECITQYRKERRKRRLMDALSLDPLEEASEEKAPKPEERGGLDRWLVHVNPIDREILVLRFV----AELEFQEIADIM 160 (188)
T ss_pred HHHHHHHHHHHhcccccCcchhhhcccccccccccccHHHHHHHHHHHHhcChhheeeeeeHHh----cCCCHHHHHHHH
Confidence 0 00 0111 11123345577999999999999999999999 999999999999
Q ss_pred CCCHHHHHHHHHHHHHHHHHHhcc
Q 011992 439 GLSKERVRQLESRALYRLKQSLGG 462 (473)
Q Consensus 439 GIS~~rVrqi~~RAL~KLR~~L~~ 462 (473)
|||.++|+..+.||+++||+.+..
T Consensus 161 gis~~tV~~~l~Ra~~~Lr~~l~~ 184 (188)
T PRK09640 161 HMGLSATKMRYKRALDKLREKFAG 184 (188)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999998753
No 67
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=99.75 E-value=2e-17 Score=160.69 Aligned_cols=142 Identities=22% Similarity=0.309 Sum_probs=120.4
Q ss_pred CHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------
Q 011992 315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------- 383 (473)
Q Consensus 315 s~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT---------- 383 (473)
+.+.+...+..|+ .+++.|+..|.+.|++++.++.++..+++|++||+|+++|+++++|++.. .|.+
T Consensus 16 ~~~~l~~~~~~gd~~a~~~l~~~y~~~l~~~a~~~~~~~~~AEDlvQE~fi~l~~~~~~~~~~~--~~~~wL~~iarn~~ 93 (231)
T PRK11922 16 SDRELVARVLAGDEAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGDA--SLSTWLSRIVLNEA 93 (231)
T ss_pred cHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHhcCCCc--hhHHHHHHHHHHHH
Confidence 3445555555455 99999999999999999999999999999999999999999999998753 4444
Q ss_pred --------------C--C---------------CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHH
Q 011992 384 --------------T--G---------------VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLS 432 (473)
Q Consensus 384 --------------~--~---------------~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlk 432 (473)
. . ...|+..+...+..+.|..+|..||+++|+||.++|+ +++|++
T Consensus 94 ~d~~Rk~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~ 169 (231)
T PRK11922 94 LGRLRRRRRLVNLAEMVMASTIAGGERTPLADPAEDPERAAARREIRALLERAIDALPDAFRAVFVLRVV----EELSVE 169 (231)
T ss_pred HHHHHhhcccccchhcccccccccccccccCcccCChHHHHHHHHHHHHHHHHHHhCCHHHhhhheeehh----cCCCHH
Confidence 0 0 0134455566677788999999999999999999998 999999
Q ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Q 011992 433 EVGNIFGLSKERVRQLESRALYRLKQSLGG 462 (473)
Q Consensus 433 EIAe~LGIS~~rVrqi~~RAL~KLR~~L~~ 462 (473)
|||+.||+|.++|++++.||+++||+.+..
T Consensus 170 EIAe~lgis~~tVk~~l~Rar~kLr~~l~~ 199 (231)
T PRK11922 170 ETAQALGLPEETVKTRLHRARRLLRESLAR 199 (231)
T ss_pred HHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999875
No 68
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=99.75 E-value=2e-17 Score=155.97 Aligned_cols=141 Identities=13% Similarity=0.195 Sum_probs=114.8
Q ss_pred HHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc--------------
Q 011992 319 LKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-------------- 383 (473)
Q Consensus 319 L~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-------------- 383 (473)
+...+..|+ .+++.||..|.+.|+.+|.++.++..+++|++||+|+.+|+.+++|++..+ .|.+
T Consensus 17 li~~~~~~d~~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l~l~~~~~~~~~~~~-~~~~wL~~iarn~~ld~~ 95 (194)
T PRK12531 17 CMEKVKSRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYTIIRNLCFDLL 95 (194)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-hHHHHHHHHHHHHHHHHH
Confidence 444455555 899999999999999999999999999999999999999999999986432 4555
Q ss_pred ---C--C------CCCch----------HHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCH
Q 011992 384 ---T--G------VEIPD----------ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSK 442 (473)
Q Consensus 384 ---~--~------~~~pe----------e~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~ 442 (473)
. . ...++ ...+.......+..+|..||+++|.||.|+|+ ++++++|||+.||||.
T Consensus 96 Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~l~~~l~~Lp~~~r~v~~l~~~----eg~s~~EIA~~lgis~ 171 (194)
T PRK12531 96 RKQKGKDLHIHADDIWPSDYYPPDLVDHYSPEQDMLKEQVMKFLDRLPKAQRDVLQAVYL----EELPHQQVAEMFDIPL 171 (194)
T ss_pred HHhcccccccchhhcccccccccccccccCHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCcCH
Confidence 0 0 00000 01112234467899999999999999999999 9999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhccCc
Q 011992 443 ERVRQLESRALYRLKQSLGGKA 464 (473)
Q Consensus 443 ~rVrqi~~RAL~KLR~~L~~~~ 464 (473)
++|+..+++|+++||..+..+.
T Consensus 172 ~tVk~rl~ra~~~Lr~~l~~~~ 193 (194)
T PRK12531 172 GTVKSRLRLAVEKLRHSMDAES 193 (194)
T ss_pred HHHHHHHHHHHHHHHHHhhhcc
Confidence 9999999999999999987654
No 69
>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=99.75 E-value=2.3e-17 Score=148.09 Aligned_cols=127 Identities=20% Similarity=0.205 Sum_probs=111.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc------------------------
Q 011992 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------------------------ 383 (473)
Q Consensus 328 ~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------------------------ 383 (473)
.|++.|+..|.+.|+++++++.++..+++|++||+++++|+++.+|++.. .|.+
T Consensus 1 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~~--~~~~wl~~i~r~~~~d~~r~~~~~~~~~ 78 (161)
T TIGR02985 1 KAFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEVE--SFKAYLFTIVKNRSLNYLRHKQVEEKYQ 78 (161)
T ss_pred ChHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhccccc--cHHHHHHHHHHHHHHHHHHHHHhHhHHH
Confidence 37899999999999999999999999999999999999999999997643 5655
Q ss_pred ----------CCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992 384 ----------TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 453 (473)
Q Consensus 384 ----------~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL 453 (473)
.....++..+...+....|..++..||++++.||.++|. +|+|.+|||+.||+|+++|++++.+|+
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~il~l~~~----~~~~~~eIA~~lgis~~tv~~~~~ra~ 154 (161)
T TIGR02985 79 EEILEIEVDELSENDPEEELEAKELQLIIYKAIEKLPEQCRKIFILSRF----EGKSYKEIAEELGISVKTVEYHISKAL 154 (161)
T ss_pred HHHHhhcccccCCCCcHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 011234555666777788999999999999999999998 999999999999999999999999999
Q ss_pred HHHHHHh
Q 011992 454 YRLKQSL 460 (473)
Q Consensus 454 ~KLR~~L 460 (473)
++||+.|
T Consensus 155 ~~Lr~~l 161 (161)
T TIGR02985 155 KELRKEL 161 (161)
T ss_pred HHHHhhC
Confidence 9999864
No 70
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=99.75 E-value=2.2e-17 Score=152.09 Aligned_cols=134 Identities=16% Similarity=0.171 Sum_probs=112.4
Q ss_pred cchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------------------
Q 011992 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------------------- 383 (473)
Q Consensus 326 g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT---------------------- 383 (473)
+..+++.||..|.+.++++|.++.++..+++|++||.|+.+|+..++|++.. ..|.+
T Consensus 7 ~~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~~~~~~~~~~-~~~~~wL~~iarn~~~d~~Rk~~~~~~ 85 (173)
T PRK09645 7 EAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTG-RSARAWLFTVARNLVIDERRSARARPV 85 (173)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHHHHHHHhhccccc
Confidence 4589999999999999999999999999999999999999999999996422 23444
Q ss_pred ----C----CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 011992 384 ----T----GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR 455 (473)
Q Consensus 384 ----~----~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~K 455 (473)
. ....++..+...+....|..+|+.||+++|+||.|+|+ +|+|++|||+.||+|+++|+.+++||+++
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~L~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~ 161 (173)
T PRK09645 86 EGGDDVLGVPEQSAPDEVDRALDRLLVADALAQLSPEHRAVLVRSYY----RGWSTAQIAADLGIPEGTVKSRLHYALRA 161 (173)
T ss_pred ccccccccCCCCCCchHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 0 01122333444445567999999999999999999999 99999999999999999999999999999
Q ss_pred HHHHhccCc
Q 011992 456 LKQSLGGKA 464 (473)
Q Consensus 456 LR~~L~~~~ 464 (473)
||+.+...+
T Consensus 162 Lr~~l~~~~ 170 (173)
T PRK09645 162 LRLALQERG 170 (173)
T ss_pred HHHHhhccc
Confidence 999987543
No 71
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=99.75 E-value=3.1e-17 Score=161.61 Aligned_cols=148 Identities=18% Similarity=0.233 Sum_probs=121.9
Q ss_pred HcCCCHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHH-------HhhhhCccCCCccc
Q 011992 311 AIGLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMK-------SVEKFKPQAGCRFA 382 (473)
Q Consensus 311 ~lGms~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~k-------AiekFDp~kg~~Fs 382 (473)
.|+.++..+...+..|+ .||..|+..|.+.|+.++.++.++..+++|++||+|+.+|. ++.+|++.. .|.
T Consensus 21 ~~~~~d~~Li~~~~~gd~~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~~--~~~ 98 (244)
T TIGR03001 21 QLHAADLYLACACAQGEPAALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGRG--PLL 98 (244)
T ss_pred cccccHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccchhhhhhccCCCC--chH
Confidence 35567777888777777 89999999999999999999999999999999999999995 677787532 454
Q ss_pred c------------------------CC---------CCCchHHHHH----HHHHHHHHHHHhhCCHHHHHHHHHHhhccC
Q 011992 383 N------------------------TG---------VEIPDISVQK----QLMRQHVRNLLTLLNPKERCIVRLRFGIED 425 (473)
Q Consensus 383 T------------------------~~---------~~~pee~le~----~el~e~L~~aL~~LperER~VL~LrY~L~~ 425 (473)
+ .. ...|+..+.. .+..+.|.++|+.||+++|+||.|+|+
T Consensus 99 tWL~~Ia~N~~id~lRk~~r~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~e~~~~l~~aL~~Lp~~~R~v~~L~~~--- 175 (244)
T TIGR03001 99 SWVRIVATRIALELQAQERRHSPVEEPTELAALPAPGSDPELDLLRERYRQDFRQALREALAALSERERHLLRLHFV--- 175 (244)
T ss_pred hHHHHHHHHHHHHHHHHhcccCccccccccccccCCCCCHHHHHHHHhhHHHHHHHHHHHHHhCCHHHHHHHHHHHH---
Confidence 4 00 0122333322 235567999999999999999999999
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCc
Q 011992 426 GKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 464 (473)
Q Consensus 426 ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~ 464 (473)
+|+|++|||++||||.++|+..++||+++||+.+....
T Consensus 176 -eg~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~~~ 213 (244)
T TIGR03001 176 -DGLSMDRIGAMYQVHRSTVSRWVAQARERLLERTRRRL 213 (244)
T ss_pred -cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999987653
No 72
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=99.74 E-value=6.4e-17 Score=154.45 Aligned_cols=134 Identities=13% Similarity=0.154 Sum_probs=110.7
Q ss_pred hcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-------------------C-
Q 011992 325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-------------------T- 384 (473)
Q Consensus 325 ~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-------------------~- 384 (473)
++..+++.|+..|.+.|++++.++.++..+++|++||+|+.+|+++..|++.++ .|.+ .
T Consensus 35 ~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wl~~I~rn~~~d~~Rk~~~~~ 113 (206)
T PRK12526 35 RDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYTVMRNAAFDMLRKIKAKK 113 (206)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCccc-chhHHHHHHHHHHHHHHHHHhcccc
Confidence 444999999999999999999999999999999999999999999999986544 2443 0
Q ss_pred -CC----C-----------CchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHH
Q 011992 385 -GV----E-----------IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL 448 (473)
Q Consensus 385 -~~----~-----------~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi 448 (473)
.. . .+............|..+|..||+++|.||.++|+ +++|++|||+.||+|.++|+.+
T Consensus 114 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~EIA~~lgis~~tV~~~ 189 (206)
T PRK12526 114 EQNLGDDIWPIEQALAESQSESEEFSDHLMDKQILSYIEKLPEAQQTVVKGVYF----QELSQEQLAQQLNVPLGTVKSR 189 (206)
T ss_pred ccccccccchhhhhcccccCchHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHH
Confidence 00 0 00111112223457899999999999999999999 9999999999999999999999
Q ss_pred HHHHHHHHHHHhccC
Q 011992 449 ESRALYRLKQSLGGK 463 (473)
Q Consensus 449 ~~RAL~KLR~~L~~~ 463 (473)
++||+++||+.+...
T Consensus 190 l~Ra~~~Lr~~l~~~ 204 (206)
T PRK12526 190 LRLALAKLKVQMGEQ 204 (206)
T ss_pred HHHHHHHHHHHHhhc
Confidence 999999999998653
No 73
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=99.74 E-value=4.3e-17 Score=151.97 Aligned_cols=134 Identities=10% Similarity=0.008 Sum_probs=111.8
Q ss_pred hhcchHHHHHHHHHHHHHHHHHHHhhc--CCcchhhHhhhhHHHHHHHhhhhCccCCCcccc------------------
Q 011992 324 HSGNSSREKLINANLRLVVHVAKQYQG--RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------------------ 383 (473)
Q Consensus 324 ~~g~~A~e~Li~~yl~lV~sIA~ry~~--~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------------------ 383 (473)
.++..+|+.||..|.+.|++++..+.+ +..+++|++||+|+.+|+.++.|+......|.+
T Consensus 9 ~~d~~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~~Rk~~ 88 (178)
T PRK12529 9 SADRDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSWRRRQS 88 (178)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHHHHHHH
Confidence 445589999999999999998766665 467899999999999999999886433334554
Q ss_pred --------------CCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHH
Q 011992 384 --------------TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE 449 (473)
Q Consensus 384 --------------~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~ 449 (473)
.....|++.+...+....|..+|..||+++|.||.|+|+ +|+|++|||+.||+|+++|+.++
T Consensus 89 ~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tVk~~l 164 (178)
T PRK12529 89 LELAWLEALATLPEPLHPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMATL----DGMKQKDIAQALDIALPTVKKYI 164 (178)
T ss_pred HHhhhhhHhhhccCcCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHH
Confidence 011245555555666778999999999999999999999 99999999999999999999999
Q ss_pred HHHHHHHHHHhc
Q 011992 450 SRALYRLKQSLG 461 (473)
Q Consensus 450 ~RAL~KLR~~L~ 461 (473)
++|+.+|++.+.
T Consensus 165 ~rAl~~~~~~~~ 176 (178)
T PRK12529 165 HQAYVTCLSLMP 176 (178)
T ss_pred HHHHHHHHHhCC
Confidence 999999998764
No 74
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=99.73 E-value=3.7e-17 Score=153.53 Aligned_cols=130 Identities=15% Similarity=0.131 Sum_probs=111.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------------------CC
Q 011992 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------------------TG 385 (473)
Q Consensus 329 A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------------------~~ 385 (473)
+|+.|+..|.+.|+++|++++++..+++|++||.|+.+|+++++|+... .|.+ ..
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 6889999999999999999999999999999999999999999997543 3544 00
Q ss_pred C----------------------------CCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHH
Q 011992 386 V----------------------------EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNI 437 (473)
Q Consensus 386 ~----------------------------~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~ 437 (473)
. ..|+..+...+....|..+|..||+++|.||.|+|+ +|+|++|||+.
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~ 156 (191)
T PRK12520 81 DDADEQSDDDLFDALFAADGHYREPPSDWGDPDAALSRREFFEVLQACVDRLPPRTGRVFMMREW----LELETEEICQE 156 (191)
T ss_pred cccccchhhhhhhhhcccccccccCccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHH
Confidence 0 123333445556677999999999999999999999 99999999999
Q ss_pred HCCCHHHHHHHHHHHHHHHHHHhccCc
Q 011992 438 FGLSKERVRQLESRALYRLKQSLGGKA 464 (473)
Q Consensus 438 LGIS~~rVrqi~~RAL~KLR~~L~~~~ 464 (473)
||+|+++|++.+.||+++||+.+....
T Consensus 157 lgis~~tV~~~l~Rar~~Lr~~l~~~~ 183 (191)
T PRK12520 157 LQITATNAWVLLYRARMRLRECLDLHW 183 (191)
T ss_pred HCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999998765
No 75
>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=99.73 E-value=5.1e-17 Score=147.08 Aligned_cols=127 Identities=19% Similarity=0.247 Sum_probs=107.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-------------------CC-C-
Q 011992 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-------------------TG-V- 386 (473)
Q Consensus 328 ~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-------------------~~-~- 386 (473)
++++.++..|.+.|+++|+++.++..++||++||+++.+|+++++|++.. .|.+ .. .
T Consensus 1 ~~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~~~ 78 (159)
T TIGR02989 1 EAFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRDRLVF 78 (159)
T ss_pred CHHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhccccccc
Confidence 37899999999999999999999999999999999999999999998653 4555 00 0
Q ss_pred -----------CCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 011992 387 -----------EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR 455 (473)
Q Consensus 387 -----------~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~K 455 (473)
..+.......+....|..+|+.||++++.||.++|+ +|++++|||+.||||.++|+..++||+++
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~v~~l~~~----~g~~~~eIA~~l~is~~tv~~~l~Rar~~ 154 (159)
T TIGR02989 79 DDELLEALAAEAEATEADRSEDELQALEGCLEKLPERQRELLQLRYQ----RGVSLTALAEQLGRTVNAVYKALSRLRVR 154 (159)
T ss_pred CHHHHHHHHhhcccchHhhHHHHHHHHHHHHHHCCHHHHHHHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 011122223444567899999999999999999998 99999999999999999999999999999
Q ss_pred HHHHh
Q 011992 456 LKQSL 460 (473)
Q Consensus 456 LR~~L 460 (473)
||+++
T Consensus 155 Lr~~~ 159 (159)
T TIGR02989 155 LRDCV 159 (159)
T ss_pred HHhcC
Confidence 99864
No 76
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=99.73 E-value=1.1e-16 Score=149.68 Aligned_cols=142 Identities=17% Similarity=0.171 Sum_probs=114.8
Q ss_pred HHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHH----HhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-------
Q 011992 316 CRDLKSELHSGN-SSREKLINANLRLVVHVAK----QYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------- 383 (473)
Q Consensus 316 ~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~----ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------- 383 (473)
...+...+..|+ .+|+.||..|.+.|+++++ ++.++..+++|++||+++.+|++++.|++.. .|.+
T Consensus 8 ~~~l~~~~~~gd~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~--~f~~wl~~i~~ 85 (184)
T PRK12539 8 LKALMLASLDGDAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTPWVYAIAR 85 (184)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCCC--ChHHHHHHHHH
Confidence 344555555555 9999999999999999986 4557889999999999999999999998753 4555
Q ss_pred -----------C---C-----CC--CchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCH
Q 011992 384 -----------T---G-----VE--IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSK 442 (473)
Q Consensus 384 -----------~---~-----~~--~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~ 442 (473)
. . .. .+.......+....|..+|..||+++|.||.|+|+ +|++++|||+.||+|.
T Consensus 86 n~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~ 161 (184)
T PRK12539 86 YKLIDHLRRTRASLADVPIDDADELVAHDDHAAVESTLDLGRLLARLPEKMRLAIQAVKL----EGLSVAEAATRSGMSE 161 (184)
T ss_pred HHHHHHHHHHhccccccChhhhccccCCcHHhhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCcHHHHHHHHCcCH
Confidence 0 0 00 01122233445677999999999999999999999 9999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhccC
Q 011992 443 ERVRQLESRALYRLKQSLGGK 463 (473)
Q Consensus 443 ~rVrqi~~RAL~KLR~~L~~~ 463 (473)
++|+.+++||+++||+.+...
T Consensus 162 ~tV~~~l~ra~~~Lr~~l~~~ 182 (184)
T PRK12539 162 SAVKVSVHRGLKALAALIGRE 182 (184)
T ss_pred HHHHHHHHHHHHHHHHHHhhc
Confidence 999999999999999988654
No 77
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=99.73 E-value=8.4e-17 Score=148.62 Aligned_cols=129 Identities=16% Similarity=0.196 Sum_probs=110.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-------------------C--C-
Q 011992 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-------------------T--G- 385 (473)
Q Consensus 328 ~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-------------------~--~- 385 (473)
..+++|+..|.++|+++|++|.++..+++|++||+++.+|+++++|++.. +|.+ . .
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 45889999999999999999999999999999999999999999998743 4555 0 0
Q ss_pred ----------------CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHH
Q 011992 386 ----------------VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE 449 (473)
Q Consensus 386 ----------------~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~ 449 (473)
...+.+.....+..+.|..+|..||++++.|+.|+|. +|++++|||+.||+|.++|+..+
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~~~s~~EIA~~lgis~~tV~~~l 156 (173)
T PRK12522 81 LDLFHKEDGGEIEFADDVNISEEFIQKVEAEMIREVIQLLNEKYKTVLVLYYY----EQYSYKEMSEILNIPIGTVKYRL 156 (173)
T ss_pred ccccchhhhhhhccccCCCChHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHH
Confidence 0011122444556678999999999999999999999 99999999999999999999999
Q ss_pred HHHHHHHHHHhcc
Q 011992 450 SRALYRLKQSLGG 462 (473)
Q Consensus 450 ~RAL~KLR~~L~~ 462 (473)
+||+++||+.+..
T Consensus 157 ~Ra~~~Lr~~l~~ 169 (173)
T PRK12522 157 NYAKKQMREHLEG 169 (173)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999998864
No 78
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=99.72 E-value=4.2e-17 Score=148.40 Aligned_cols=123 Identities=13% Similarity=0.050 Sum_probs=106.0
Q ss_pred HHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------------------C-------
Q 011992 335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------------------T------- 384 (473)
Q Consensus 335 ~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------------------~------- 384 (473)
..|.+.++++|.+++++..+++|++||+|+.+|+++++|++. .|.+ .
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 468999999999999999999999999999999999999853 3655 0
Q ss_pred ----CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992 385 ----GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 460 (473)
Q Consensus 385 ----~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L 460 (473)
....+++.+...+....|..+|+.||+++|.||.|+|+ +|+|++|||+.||+|.++|+++++||+++||+.+
T Consensus 79 ~~~~~~~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 79 ENIKSSHNIEDLLLTKEQKLLIAQKLRELPENYRDVVLAHYL----EEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred hhccCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 00123445555666778999999999999999999999 9999999999999999999999999999999999
Q ss_pred ccCc
Q 011992 461 GGKA 464 (473)
Q Consensus 461 ~~~~ 464 (473)
...+
T Consensus 155 ~~~~ 158 (160)
T PRK09642 155 KEEE 158 (160)
T ss_pred hhhc
Confidence 7654
No 79
>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=99.72 E-value=1.2e-16 Score=148.41 Aligned_cols=133 Identities=21% Similarity=0.235 Sum_probs=110.1
Q ss_pred hcchHHHHHHHHHHHHHHHHHHHhh----cCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------------C
Q 011992 325 SGNSSREKLINANLRLVVHVAKQYQ----GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------------T 384 (473)
Q Consensus 325 ~g~~A~e~Li~~yl~lV~sIA~ry~----~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------------~ 384 (473)
++..+++.|+..|.+.|+.+|+++. ++..+++|++||+++.+|+++.+|+...+..|.+ .
T Consensus 4 ~~~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r~~ 83 (189)
T TIGR02984 4 GDQEALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNVLADALRRH 83 (189)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHHHHHHHH
Confidence 3448999999999999999999875 3677899999999999999999997654444554 0
Q ss_pred ------------C---------------------CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCH
Q 011992 385 ------------G---------------------VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSL 431 (473)
Q Consensus 385 ------------~---------------------~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTl 431 (473)
. ...|++.+...+....|..+|..||+++|.||.++|+ +|+++
T Consensus 84 ~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vi~l~~~----~g~s~ 159 (189)
T TIGR02984 84 LGAQKRDIRREQSLDAGGRLDESSVRLAAQLAADGPSPSQVAARREAAVRLAQALAKLPEDYREVILLRHL----EGLSF 159 (189)
T ss_pred HHHHhhhcccccCCCcccccCCcchhHHHHccCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh----cCCCH
Confidence 0 0012333444555678999999999999999999998 99999
Q ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Q 011992 432 SEVGNIFGLSKERVRQLESRALYRLKQSLG 461 (473)
Q Consensus 432 kEIAe~LGIS~~rVrqi~~RAL~KLR~~L~ 461 (473)
+|||+.||||.++|++.++||+++||+.++
T Consensus 160 ~eIA~~lgis~~~v~~~l~Ra~~~Lr~~l~ 189 (189)
T TIGR02984 160 AEVAERMDRSEGAVSMLWVRGLARLRQILE 189 (189)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHHHHHHhC
Confidence 999999999999999999999999998763
No 80
>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=99.72 E-value=1.3e-16 Score=148.00 Aligned_cols=139 Identities=19% Similarity=0.283 Sum_probs=107.0
Q ss_pred HHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCc-----chhhHhhhhHHHHHH-HhhhhCccCCCcccc-----
Q 011992 316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGI-----SLHDLLQEGSMGLMK-SVEKFKPQAGCRFAN----- 383 (473)
Q Consensus 316 ~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~-----saEDLiQEg~lgL~k-AiekFDp~kg~~FsT----- 383 (473)
...+...+..|+ .+++.|+..|.+.++++|+++.++.. +++|++||+|+.+|+ ...+|++.. .|.+
T Consensus 4 ~~~li~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~~--~~~~wl~~i 81 (183)
T TIGR02999 4 VTELLQQWQNGDAAARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWDDRA--HFFAAAAKA 81 (183)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCCchH--HHHHHHHHH
Confidence 345556666666 89999999999999999999999887 899999999999998 777786542 2322
Q ss_pred ---------------CC-----CC-----CchHHHHHHHHH---HHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHH
Q 011992 384 ---------------TG-----VE-----IPDISVQKQLMR---QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVG 435 (473)
Q Consensus 384 ---------------~~-----~~-----~pee~le~~el~---e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIA 435 (473)
.. .. .+.......+.. +.+...|+.||+++|.||.|+|+ +|+|++|||
T Consensus 82 ~~n~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA 157 (183)
T TIGR02999 82 MRRILVDHARRRRAQKRGGGAVRVPLDEVLPDAEADLDEELLDLDDALDKLAQVDPRQAEVVELRFF----AGLTVEEIA 157 (183)
T ss_pred HHHHHHHHHHHHHHHhccCCccccccccccCCCCccHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHH----cCCCHHHHH
Confidence 00 00 011111111222 23334456699999999999999 999999999
Q ss_pred HHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992 436 NIFGLSKERVRQLESRALYRLKQSL 460 (473)
Q Consensus 436 e~LGIS~~rVrqi~~RAL~KLR~~L 460 (473)
++||+|+++|+.+++||+++||+.+
T Consensus 158 ~~lgis~~tVk~~l~Rar~~Lr~~l 182 (183)
T TIGR02999 158 ELLGVSVRTVERDWRFARAWLADEL 182 (183)
T ss_pred HHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 9999999999999999999999876
No 81
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=99.72 E-value=1.7e-16 Score=147.82 Aligned_cols=139 Identities=19% Similarity=0.223 Sum_probs=111.8
Q ss_pred HHHHHhhc-chHHHHHHHHHHHHHHHHHHHhhc----CCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------
Q 011992 319 LKSELHSG-NSSREKLINANLRLVVHVAKQYQG----RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------- 383 (473)
Q Consensus 319 L~~~l~~g-~~A~e~Li~~yl~lV~sIA~ry~~----~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT---------- 383 (473)
+...+..| ..+++.||..|.+.|+++|.++++ +..+++|++||+++.+|...+.|+.. ..|.+
T Consensus 12 l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~--~~~~~wl~~i~rn~~ 89 (184)
T PRK12512 12 LMRSANAGDAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWLFAIARNKL 89 (184)
T ss_pred HHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCcc--ccHHHHHHHHHHHHH
Confidence 34444444 499999999999999999998875 35689999999999999999999763 34554
Q ss_pred ---------C-C-------CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHH
Q 011992 384 ---------T-G-------VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVR 446 (473)
Q Consensus 384 ---------~-~-------~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVr 446 (473)
. . ...+............+..+|+.||+++|+||.++|+ +|+|++|||+.||+|.++|+
T Consensus 90 ~d~~Rr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~l~is~~tV~ 165 (184)
T PRK12512 90 IDALRRRGRRVFVDIDDFAETLPAEPATETLPAGDVGRHLETLPPRQRDVVQSISV----EGASIKETAAKLSMSEGAVR 165 (184)
T ss_pred HHHHHhhcccccCCchhccccccccchhhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHH
Confidence 0 0 0011111122334567899999999999999999999 99999999999999999999
Q ss_pred HHHHHHHHHHHHHhccC
Q 011992 447 QLESRALYRLKQSLGGK 463 (473)
Q Consensus 447 qi~~RAL~KLR~~L~~~ 463 (473)
..+++|+++||+.+..+
T Consensus 166 ~~l~ra~~~Lr~~l~~~ 182 (184)
T PRK12512 166 VALHRGLAALAAKFRSE 182 (184)
T ss_pred HHHHHHHHHHHHHhhcC
Confidence 99999999999998765
No 82
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=99.72 E-value=7.3e-17 Score=148.68 Aligned_cols=135 Identities=18% Similarity=0.147 Sum_probs=110.7
Q ss_pred HhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-------------------
Q 011992 323 LHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------------------- 383 (473)
Q Consensus 323 l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------------------- 383 (473)
..++..+++.||..|.+.|+++++++.+ ..+++|++||+|+.+|+.++.|++. ..|.+
T Consensus 6 ~~gd~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~~~~ 82 (175)
T PRK12518 6 QRGDRQSFRQLYRRYQQKVRSTLYQLCG-RELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATDARRQFAQ 82 (175)
T ss_pred HcCCHHHHHHHHHHHHHHHHHHHHHHcC-HhHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHHHHHHhhc
Confidence 3444599999999999999999999875 5789999999999999999999864 24554
Q ss_pred -------CC------CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011992 384 -------TG------VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 450 (473)
Q Consensus 384 -------~~------~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~ 450 (473)
.. ...++......+....+.++|+.||+++|.||.|+|+ +|+|++|||+.||+|.++|++.++
T Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~eIA~~lg~s~~tv~~~l~ 158 (175)
T PRK12518 83 RPSRIQDDSLNDQPSRPSDTPDLMQLHYQDLVQQGLQTLSLEHRAVLVLHDL----EDLPQKEIAEILNIPVGTVKSRLF 158 (175)
T ss_pred cccchhcccccccccCCCCcHHHHHHHHHHHHHHHHHhCCHHHeeeeeehHh----cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 00 0111222333344467899999999999999999999 999999999999999999999999
Q ss_pred HHHHHHHHHhccCc
Q 011992 451 RALYRLKQSLGGKA 464 (473)
Q Consensus 451 RAL~KLR~~L~~~~ 464 (473)
||+++||+.+...+
T Consensus 159 Rar~~L~~~l~~~~ 172 (175)
T PRK12518 159 YARRQLRKFLQQQG 172 (175)
T ss_pred HHHHHHHHHHHhcc
Confidence 99999999987643
No 83
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=99.71 E-value=1.2e-16 Score=149.86 Aligned_cols=139 Identities=19% Similarity=0.123 Sum_probs=110.6
Q ss_pred HHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc--------------
Q 011992 319 LKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-------------- 383 (473)
Q Consensus 319 L~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-------------- 383 (473)
+...+..|+ .+++.||..|.+.+++++. +.++..+++|++||+|+.+|+.+++|++.. .|.+
T Consensus 14 l~~~~~~gd~~af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~flkl~~~~~~~~~~~--~~~~Wl~~Iarn~~~d~~ 90 (185)
T PRK09649 14 LALSAAKGNGRALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSARS--SARTWLLAIARHVVADHI 90 (185)
T ss_pred HHHHHHccCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHhccccCccc--hHHHHHHHHHHHHHHHHH
Confidence 444444444 8999999999999999995 688889999999999999999999998642 4544
Q ss_pred --------CC-CCC------chHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHH
Q 011992 384 --------TG-VEI------PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL 448 (473)
Q Consensus 384 --------~~-~~~------pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi 448 (473)
.. ... ++......+....|..+|..||+++|.||.|+|+ +++|++|||+.||+|+++|+..
T Consensus 91 Rk~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~L~~~----~g~s~~EIA~~lgis~~tVk~~ 166 (185)
T PRK09649 91 RHVRSRPRTTRGARPEHLIDGDRHARGFEDLVEVTTMIADLTTDQREALLLTQL----LGLSYADAAAVCGCPVGTIRSR 166 (185)
T ss_pred HHhccccccccccchhhccChhhhhhhHHHHHHHHHHHHhCCHHHhHHhhhHHH----cCCCHHHHHHHHCCCHHHHHHH
Confidence 00 000 1111112233456889999999999999999999 9999999999999999999999
Q ss_pred HHHHHHHHHHHhccCc
Q 011992 449 ESRALYRLKQSLGGKA 464 (473)
Q Consensus 449 ~~RAL~KLR~~L~~~~ 464 (473)
++||+++||+.+...+
T Consensus 167 l~Rar~~Lr~~~~~~~ 182 (185)
T PRK09649 167 VARARDALLADAEPDD 182 (185)
T ss_pred HHHHHHHHHhhCCccc
Confidence 9999999999766544
No 84
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=99.71 E-value=2e-16 Score=147.83 Aligned_cols=137 Identities=22% Similarity=0.316 Sum_probs=116.1
Q ss_pred HHHhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------------
Q 011992 321 SELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------------- 383 (473)
Q Consensus 321 ~~l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------------- 383 (473)
....++..++..++..+.+.++++++++.++..+++|++||+|+.+|+++..|. .+..|.+
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~~--~~~~~~~wl~~Ia~n~~iD~~R~~ 85 (182)
T COG1595 8 EALRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSFR--GRSSFKAWLYRIARNLAIDRLRKR 85 (182)
T ss_pred HHHhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcC--CCCchHHHHHHHHHHHHHHHHHHh
Confidence 334555689999999999999999999999999999999999999999999992 2335655
Q ss_pred ---------------CCCCCch--HHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHH
Q 011992 384 ---------------TGVEIPD--ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVR 446 (473)
Q Consensus 384 ---------------~~~~~pe--e~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVr 446 (473)
.....++ ..+...+....|.++|..||+++|.+|.|+|+ +|+|++|||+.||||.++|+
T Consensus 86 ~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~~----~gls~~EIA~~l~i~~~tVk 161 (182)
T COG1595 86 KRRRARVEEADLLPEEADPAPDLAELLLAEEELERLRRALARLPPRQREAFLLRYL----EGLSYEEIAEILGISVGTVK 161 (182)
T ss_pred cccccccccccccccccCcccccchHHHHHHHHHHHHHHHHhCCHHHhHHhhhHhh----cCCCHHHHHHHHCCCHHHHH
Confidence 0111111 13455677889999999999999999999999 99999999999999999999
Q ss_pred HHHHHHHHHHHHHhccC
Q 011992 447 QLESRALYRLKQSLGGK 463 (473)
Q Consensus 447 qi~~RAL~KLR~~L~~~ 463 (473)
..+++|+.+||+.+...
T Consensus 162 s~l~ra~~~l~~~l~~~ 178 (182)
T COG1595 162 SRLHRARKKLREQLEEA 178 (182)
T ss_pred HHHHHHHHHHHHHHhhc
Confidence 99999999999998764
No 85
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=99.71 E-value=1e-16 Score=151.12 Aligned_cols=133 Identities=21% Similarity=0.160 Sum_probs=110.3
Q ss_pred cchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------------------
Q 011992 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------------------- 383 (473)
Q Consensus 326 g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT---------------------- 383 (473)
+..+|..|+..|.+.++++|++++++..+++|++||+|+.+|+.+++|+... .|.+
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 3478999999999999999999999999999999999999999999997542 3544
Q ss_pred CCC----C--CchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992 384 TGV----E--IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457 (473)
Q Consensus 384 ~~~----~--~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR 457 (473)
... . ..............|..+|+.||+++|+||.|+|+ +|++++|||+.||+|+++|+.+++||+++||
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~i~~L~~~----~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr 161 (187)
T PRK12516 86 DTDGMFTEQLAVHPSQYGTLDLQDFRAALDQLPDDQREAIILVGA----SGFAYEEAAEICGCAVGTIKSRVNRARQRLQ 161 (187)
T ss_pred ccccccccccCCCcchhhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 000 0 00111112233467899999999999999999999 9999999999999999999999999999999
Q ss_pred HHhccCc
Q 011992 458 QSLGGKA 464 (473)
Q Consensus 458 ~~L~~~~ 464 (473)
+.+....
T Consensus 162 ~~l~~~~ 168 (187)
T PRK12516 162 EILQIEG 168 (187)
T ss_pred HHHHhhc
Confidence 9997653
No 86
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=99.71 E-value=1.4e-16 Score=146.08 Aligned_cols=129 Identities=17% Similarity=0.097 Sum_probs=112.2
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc--------------------------
Q 011992 330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-------------------------- 383 (473)
Q Consensus 330 ~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-------------------------- 383 (473)
|+.||..|.+.|+++|+++.++..+++|++||+|+.+|++++.|++. .|.+
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 67899999999999999999999999999999999999999999753 3544
Q ss_pred ----CCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 011992 384 ----TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 459 (473)
Q Consensus 384 ----~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~ 459 (473)
.....+++.+...+....+.++|..||+++|+||.|+|+ +|++++|||+.||+|.++|+.+++||+++||+.
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~ 155 (165)
T PRK09644 80 EIEAIQAESTEEYVVAKNSYEKLIQIIHTLPVIEAQAILLCDV----HELTYEEAASVLDLKLNTYKSHLFRGRKRLKAL 155 (165)
T ss_pred HHhhhcccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHHH----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 011234555555666788999999999999999999999 999999999999999999999999999999999
Q ss_pred hccCch
Q 011992 460 LGGKAS 465 (473)
Q Consensus 460 L~~~~l 465 (473)
+.....
T Consensus 156 l~~~~~ 161 (165)
T PRK09644 156 LKEEKS 161 (165)
T ss_pred HHhhhh
Confidence 876543
No 87
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=99.71 E-value=1.9e-16 Score=153.31 Aligned_cols=131 Identities=21% Similarity=0.195 Sum_probs=113.8
Q ss_pred cchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------------------
Q 011992 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------------------- 383 (473)
Q Consensus 326 g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT---------------------- 383 (473)
...+|..||..|.+.++++++++.++..+++|++||+|+.+|+.+++|++. .|.+
T Consensus 16 ~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~~---~~~aWL~~IarN~~~d~~Rk~~~~~~ 92 (216)
T PRK12533 16 RGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRGD---NARPWLLAIVRHTWYSEWRRRANAHE 92 (216)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCcc---chHhHHHHHHHHHHHHHHHhhccccc
Confidence 347899999999999999999999999999999999999999999999753 2444
Q ss_pred -C---C-------------CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHH
Q 011992 384 -T---G-------------VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVR 446 (473)
Q Consensus 384 -~---~-------------~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVr 446 (473)
. . ...|+..+...+....|..+|..||+++|+||.|+|+ +++|++|||+.||||+++|+
T Consensus 93 ~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y~----eg~s~~EIAe~LgiS~~tVk 168 (216)
T PRK12533 93 VAAPDTLDDADSLDDWQPAGEDPLALLLRAEDVRLVNAALAKLPVEYREVLVLREL----EDMSYREIAAIADVPVGTVM 168 (216)
T ss_pred ccccccccccccccccccCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHhHhhhHHh----cCCCHHHHHHHHCCCHHHHH
Confidence 0 0 0123444556667788999999999999999999999 99999999999999999999
Q ss_pred HHHHHHHHHHHHHhccC
Q 011992 447 QLESRALYRLKQSLGGK 463 (473)
Q Consensus 447 qi~~RAL~KLR~~L~~~ 463 (473)
++++||+++||+.+...
T Consensus 169 ~~L~RAr~~Lr~~l~~~ 185 (216)
T PRK12533 169 SRLARARRRLAALLGGA 185 (216)
T ss_pred HHHHHHHHHHHHHHccc
Confidence 99999999999999754
No 88
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=99.71 E-value=1.6e-16 Score=146.87 Aligned_cols=130 Identities=16% Similarity=0.097 Sum_probs=108.8
Q ss_pred chHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------------------
Q 011992 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------------------- 383 (473)
Q Consensus 327 ~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------------------- 383 (473)
..++..||..|.+.|+++|.++.++..+++|++||+|+.+|+.. .|... ..|.+
T Consensus 9 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~~-~~~~~--~~~~~wL~~Iarn~~~d~~Rk~~~~~~~ 85 (172)
T PRK12523 9 SELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGRP-ELPTP--REPRAFLAAVAKGLMFDHFRRAALEQAY 85 (172)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHccc-ccCcc--hhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 38999999999999999999999999999999999999999863 45432 23544
Q ss_pred ----C-----CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011992 384 ----T-----GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 454 (473)
Q Consensus 384 ----~-----~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~ 454 (473)
. ....++......+....+..+|..||+++|.||.|+|+ +|++++|||++||+|.++|++++++|++
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~L~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~ 161 (172)
T PRK12523 86 LAELALVPEAEQPSPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRL----DGMGHAEIAERLGVSVSRVRQYLAQGLR 161 (172)
T ss_pred HHHHhhcccccCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 0 11233444444455567999999999999999999999 9999999999999999999999999999
Q ss_pred HHHHHhccC
Q 011992 455 RLKQSLGGK 463 (473)
Q Consensus 455 KLR~~L~~~ 463 (473)
+||..|..+
T Consensus 162 ~~~~~l~~~ 170 (172)
T PRK12523 162 QCYIALYGE 170 (172)
T ss_pred HHHHHhcCC
Confidence 999988754
No 89
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=99.71 E-value=1.2e-16 Score=145.39 Aligned_cols=132 Identities=20% Similarity=0.209 Sum_probs=111.5
Q ss_pred hcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------------C---
Q 011992 325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------------T--- 384 (473)
Q Consensus 325 ~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------------~--- 384 (473)
++..+++.|+..|.+.|++++..+.++..+++|++||+|+.+|.++++|+.. ..|.+ .
T Consensus 3 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~rk~~~~~ 80 (162)
T TIGR02983 3 ATEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRDP--DAPDAYVRRVLVNLARSRWRRRRLLE 80 (162)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCCc--ccHHHHHHHHHHHHHHHHHHhhcccc
Confidence 4458999999999999999999999999999999999999999999999542 34544 0
Q ss_pred ------CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 385 ------GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 385 ------~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
....+.......+..+.|..+|..||+++|.||.|+|+ +|+|++|||+.||+|.++|++++.||+++||+
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 81 LPTRELPDAAAPDPAPDVALRAALARALRRLPARQRAVVVLRYY----EDLSEAQVAEALGISVGTVKSRLSRALARLRE 156 (162)
T ss_pred ccccccCcccCCccchhHHHHHHHHHHHHhCCHHHHHHhhhHHH----hcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 00112222334556678999999999999999999999 99999999999999999999999999999999
Q ss_pred Hhcc
Q 011992 459 SLGG 462 (473)
Q Consensus 459 ~L~~ 462 (473)
.+..
T Consensus 157 ~l~~ 160 (162)
T TIGR02983 157 LLEE 160 (162)
T ss_pred HhcC
Confidence 8764
No 90
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=99.70 E-value=2.3e-16 Score=147.11 Aligned_cols=138 Identities=14% Similarity=0.142 Sum_probs=111.3
Q ss_pred HHHHhhcchHHHHHHHHHHHHHHHHHHHhhc-CCcchhhHhhhhHHHHHHHhhhhCccCCCcccc---------------
Q 011992 320 KSELHSGNSSREKLINANLRLVVHVAKQYQG-RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN--------------- 383 (473)
Q Consensus 320 ~~~l~~g~~A~e~Li~~yl~lV~sIA~ry~~-~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT--------------- 383 (473)
.....++..+++.||..|.+.|+.++.++.+ +..+++|++||+|+.+|++++.|++.. .|.+
T Consensus 13 ~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~~--~~~~wl~~iarN~~~d~~R 90 (181)
T PRK12536 13 LRGLAGDAAAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRADQ--PLTAWVHAIARYKLMDFLR 90 (181)
T ss_pred HHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHHHHHHH
Confidence 3344445599999999999999999988764 578999999999999999999998643 4544
Q ss_pred -----C--CCCCc-------hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHH
Q 011992 384 -----T--GVEIP-------DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE 449 (473)
Q Consensus 384 -----~--~~~~p-------ee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~ 449 (473)
. ..... .......+....+.++|+.||++++.||.++|. +|++++|||+.||+|+++|+..+
T Consensus 91 k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~l~is~~tV~~~l 166 (181)
T PRK12536 91 SRARREALHDPLDDESELFATSDDEAAEARRDLGKLLEQLPDRQRLPIVHVKL----EGLSVAETAQLTGLSESAVKVGI 166 (181)
T ss_pred HHhccccccCCccchhhhcCCCCcchHHHHHHHHHHHHHCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHH
Confidence 0 00000 000112345567999999999999999999999 99999999999999999999999
Q ss_pred HHHHHHHHHHhccC
Q 011992 450 SRALYRLKQSLGGK 463 (473)
Q Consensus 450 ~RAL~KLR~~L~~~ 463 (473)
++|+++||+.+..+
T Consensus 167 ~rar~~Lr~~l~~~ 180 (181)
T PRK12536 167 HRGLKALAAKIRGE 180 (181)
T ss_pred HHHHHHHHHHhcCC
Confidence 99999999988754
No 91
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=99.70 E-value=2.9e-16 Score=150.27 Aligned_cols=131 Identities=22% Similarity=0.287 Sum_probs=114.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc------------------------
Q 011992 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------------------------ 383 (473)
Q Consensus 328 ~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------------------------ 383 (473)
.+++.|+..|++.+++++.++.++..+++|++||+|+.+|++..+|++. .|.+
T Consensus 28 ~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~~---~~~~wL~~iarn~~~d~~Rk~~~~~~~~ 104 (203)
T PRK09647 28 PSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQPG---TFEGWLHRITTNLFLDMVRRRARIRMEA 104 (203)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc---ccHHHHHHHHHHHHHHHHHhcccCcccc
Confidence 8999999999999999999999999999999999999999999999752 3544
Q ss_pred ---------CCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011992 384 ---------TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 454 (473)
Q Consensus 384 ---------~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~ 454 (473)
.....|+..+...+....|..+|..||++++.||.|+|+ +|++++|||+.||+|.++|++.++||++
T Consensus 105 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~L~~~~r~v~~L~~~----~g~s~~EIA~~Lgis~~tV~~~l~RArk 180 (203)
T PRK09647 105 LPEDYDRVPGDEPNPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDI----EGLSYEEIAATLGVKLGTVRSRIHRGRQ 180 (203)
T ss_pred ccccccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 001233445556667788999999999999999999999 9999999999999999999999999999
Q ss_pred HHHHHhccCch
Q 011992 455 RLKQSLGGKAS 465 (473)
Q Consensus 455 KLR~~L~~~~l 465 (473)
+||+.+....-
T Consensus 181 ~Lr~~l~~~~~ 191 (203)
T PRK09647 181 QLRAALAAHAP 191 (203)
T ss_pred HHHHHHHHhch
Confidence 99999976543
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=99.69 E-value=4.4e-16 Score=136.53 Aligned_cols=127 Identities=27% Similarity=0.438 Sum_probs=110.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------------C------
Q 011992 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------------T------ 384 (473)
Q Consensus 328 ~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------------~------ 384 (473)
.+++.++..|.++|+++++++.++..+++|++||+++++|++++.|++. ..|.+ .
T Consensus 1 ~a~~~l~~~~~~~v~~~~~~~~~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~rk~~~~~~~~ 78 (158)
T TIGR02937 1 EAFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRRLRREL 78 (158)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHHHHHHHHhccCCcch
Confidence 3688999999999999999999999999999999999999999999887 45655 1
Q ss_pred --------CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 011992 385 --------GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 456 (473)
Q Consensus 385 --------~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KL 456 (473)
....++...........|.++|+.||++++.||.++|+ .|++..|||+.+|+|+++|+++..+++++|
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~ii~~~~~----~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl 154 (158)
T TIGR02937 79 DLLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYL----EGLSYKEIAEILGISVGTVKRRLKRARKKL 154 (158)
T ss_pred hhhhhcccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 01234444555667778999999999999999999988 899999999999999999999999999999
Q ss_pred HHHh
Q 011992 457 KQSL 460 (473)
Q Consensus 457 R~~L 460 (473)
|+.+
T Consensus 155 ~~~l 158 (158)
T TIGR02937 155 RELL 158 (158)
T ss_pred HhhC
Confidence 9864
No 93
>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=99.69 E-value=1.5e-16 Score=149.60 Aligned_cols=130 Identities=19% Similarity=0.169 Sum_probs=108.6
Q ss_pred chHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc--------------------C-C
Q 011992 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN--------------------T-G 385 (473)
Q Consensus 327 ~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT--------------------~-~ 385 (473)
..+|+.|+..|.+.|+++|.++.++..+++|++||+|+.+|+++.+|++.. .|.+ . .
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 478999999999999999999999999999999999999999999997542 4554 0 0
Q ss_pred C--C-------------------CchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHH
Q 011992 386 V--E-------------------IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKER 444 (473)
Q Consensus 386 ~--~-------------------~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~r 444 (473)
. . .++......+....|..+|..||+++|.||.|+|+ +|+|++|||+.||+|.++
T Consensus 88 ~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~r~i~~L~~~----~g~s~~EIA~~lgis~~t 163 (193)
T TIGR02947 88 SDDDDIEDWQLAKAASHTSNGLRSAELEALDGLPDQDIKDALQGLPEEFRQAVYLADV----EGFAYKEIAEIMGTPIGT 163 (193)
T ss_pred ccchhhhhhhhccccccccccccchhHHHHhhhhHHHHHHHHHhCCHHHhhheeehhh----cCCCHHHHHHHHCCCHHH
Confidence 0 0 00011111223467899999999999999999999 999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhcc
Q 011992 445 VRQLESRALYRLKQSLGG 462 (473)
Q Consensus 445 Vrqi~~RAL~KLR~~L~~ 462 (473)
|+.+++||+++||+.+..
T Consensus 164 Vk~~l~Rar~~Lr~~l~~ 181 (193)
T TIGR02947 164 VMSRLHRGRKQLRKQLVD 181 (193)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 999999999999999864
No 94
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=99.69 E-value=4.2e-16 Score=143.10 Aligned_cols=131 Identities=18% Similarity=0.130 Sum_probs=108.6
Q ss_pred chHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------------------C
Q 011992 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------------------T 384 (473)
Q Consensus 327 ~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------------------~ 384 (473)
...|..+|..|.+.|+++|+++.++..++||++||+|+.+|+.++.|+... .|.+ .
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 357889999999999999999999999999999999999999999997533 3544 0
Q ss_pred C------CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 385 G------VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 385 ~------~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
. ...+............+..+|..||+++|+||.|+|+ +|++++|||+.||+|.++|++.++||+++||.
T Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 158 (164)
T PRK12547 83 SDGVFTARVAVHPAQYGSLDLQDFKKALNLLSADQREAIILIGA----SGFSYEDAAAICGCAVGTIKSRVSRARNRLQE 158 (164)
T ss_pred ccccccccCCCCchhhhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 0 0001111122334567899999999999999999999 99999999999999999999999999999999
Q ss_pred HhccC
Q 011992 459 SLGGK 463 (473)
Q Consensus 459 ~L~~~ 463 (473)
.+...
T Consensus 159 ~l~~~ 163 (164)
T PRK12547 159 LLKVD 163 (164)
T ss_pred HHhcc
Confidence 88643
No 95
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=99.68 E-value=6.8e-16 Score=140.81 Aligned_cols=125 Identities=16% Similarity=0.077 Sum_probs=104.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc------------------------
Q 011992 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------------------------ 383 (473)
Q Consensus 328 ~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------------------------ 383 (473)
.+++.|+..|.+.|+++|.++.++..+++|++||+|+.+|+..+.|++. .|.+
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 5889999999999999999999999999999999999999998877542 2433
Q ss_pred ---CC-----CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 011992 384 ---TG-----VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR 455 (473)
Q Consensus 384 ---~~-----~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~K 455 (473)
.. ...++......+....|..+|..||+++|.||.|+|+ +|++++|||+.||+|.++|+..+++|+++
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~----~g~s~~EIA~~l~is~~tV~~~l~ra~~~ 156 (161)
T PRK12528 81 EALAQLPERVAPSEEERAIILETLVELDQLLDGLPPLVKRAFLLAQV----DGLGYGEIATELGISLATVKRYLNKAAMR 156 (161)
T ss_pred HHhhccccccCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 00 0112222333344568899999999999999999999 99999999999999999999999999999
Q ss_pred HHHH
Q 011992 456 LKQS 459 (473)
Q Consensus 456 LR~~ 459 (473)
|+..
T Consensus 157 ~~~~ 160 (161)
T PRK12528 157 CYFA 160 (161)
T ss_pred HHhc
Confidence 9975
No 96
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=99.67 E-value=8.9e-16 Score=140.01 Aligned_cols=126 Identities=17% Similarity=0.139 Sum_probs=105.4
Q ss_pred chHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------------------
Q 011992 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------------------- 383 (473)
Q Consensus 327 ~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------------------- 383 (473)
..+++.++..|.+.|+++|.++.++..+++|++||+|+.+|+.+++|++. .|.+
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 36899999999999999999999999999999999999999999999753 3655
Q ss_pred --CC-----CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 011992 384 --TG-----VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 456 (473)
Q Consensus 384 --~~-----~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KL 456 (473)
.. ...++...........+..+|..||+++|.||.|+|. ++++++|||+.||+|.++|++.++||+++|
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~~~r~v~~l~~~----~~~s~~eIA~~lgis~~tv~~~l~Rar~~L 156 (161)
T PRK12541 81 TIEEFHLPNVPSTEHEYFIKHEIASWLDSLSSLPLERRNVLLLRDY----YGFSYKEIAEMTGLSLAKVKIELHRGRKET 156 (161)
T ss_pred chhhhhccCCCCcHHHHHHHhHHHHHHHHHHHCCHHHHHHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 00 0112222222233345668999999999999999999 999999999999999999999999999999
Q ss_pred HHH
Q 011992 457 KQS 459 (473)
Q Consensus 457 R~~ 459 (473)
|+.
T Consensus 157 ~~~ 159 (161)
T PRK12541 157 KSI 159 (161)
T ss_pred Hhh
Confidence 975
No 97
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=99.67 E-value=1.3e-15 Score=139.12 Aligned_cols=128 Identities=20% Similarity=0.200 Sum_probs=108.7
Q ss_pred chHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------------------
Q 011992 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------------------- 383 (473)
Q Consensus 327 ~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------------------- 383 (473)
..+++.|+..|.+.|+++|+++.++..+++|++||+|+.+|++ .|+. +..|.+
T Consensus 2 ~~~f~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fi~~~~~--~~~~--~~~~~~wl~~i~rn~~~d~~rk~~~~~~~ 77 (166)
T PRK09639 2 DETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKG--IENEKGWLIKSARNVAYNYLRSEKRRRAR 77 (166)
T ss_pred chHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH--hccc--ccchHHHHHHHHHHHHHHHHHHhcccccc
Confidence 3579999999999999999999999999999999999999998 5653 234554
Q ss_pred ----------CCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992 384 ----------TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 453 (473)
Q Consensus 384 ----------~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL 453 (473)
.....|++.....+....+..+|..||+++|.||.++| +|++++|||+.||+|.++|+..+.||+
T Consensus 78 ~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~-----~g~s~~eIA~~lgis~~tV~~~i~ra~ 152 (166)
T PRK09639 78 ILGEFQWQEVDNEPSPEEIWIRKEEITKVQEVLAKMTERDRTVLLLRF-----SGYSYKEIAEALGIKESSVGTTLARAK 152 (166)
T ss_pred ccchhhhhhccCCCChHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 01123455555566677899999999999999999998 599999999999999999999999999
Q ss_pred HHHHHHhccC
Q 011992 454 YRLKQSLGGK 463 (473)
Q Consensus 454 ~KLR~~L~~~ 463 (473)
++||+.+...
T Consensus 153 ~~Lr~~l~~~ 162 (166)
T PRK09639 153 KKFRKIYEQM 162 (166)
T ss_pred HHHHHHHHHh
Confidence 9999988743
No 98
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=99.67 E-value=7.8e-16 Score=145.10 Aligned_cols=135 Identities=21% Similarity=0.181 Sum_probs=111.9
Q ss_pred HhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-------------------
Q 011992 323 LHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------------------- 383 (473)
Q Consensus 323 l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------------------- 383 (473)
+..+..+|+.+|..|.+.|+++|+++.++..+++|++||+|+.+|+.++.|.+.. .|.+
T Consensus 18 ~~~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~~--~~~~wL~~Iarn~~~~~~r~~~~ 95 (188)
T PRK12517 18 MLSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEK--AAKAWLITILRRENARRFERKQF 95 (188)
T ss_pred hhccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCcc--chHHHHHHHHHHHHHHHHHHhcc
Confidence 3445689999999999999999999999999999999999999999999997542 3433
Q ss_pred --CCC-----C-CchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 011992 384 --TGV-----E-IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR 455 (473)
Q Consensus 384 --~~~-----~-~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~K 455 (473)
... . .+....+.....+.|..+|..||+++|.||.++|+ +|++++|||+.||||+++|+.+++||+++
T Consensus 96 ~~~~~~~~~~~~~~~~~~e~~~~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~ 171 (188)
T PRK12517 96 DLVDIEDDSIEDDASHSSEEEMEQEWLRRQIAKLDPEYREPLLLQVI----GGFSGEEIAEILDLNKNTVMTRLFRARNQ 171 (188)
T ss_pred CccCcccccccCccccChhHHHHHHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 000 0 01111223334567999999999999999999999 99999999999999999999999999999
Q ss_pred HHHHhccC
Q 011992 456 LKQSLGGK 463 (473)
Q Consensus 456 LR~~L~~~ 463 (473)
||+.+...
T Consensus 172 Lr~~l~~~ 179 (188)
T PRK12517 172 LKEALEKP 179 (188)
T ss_pred HHHHHHHH
Confidence 99998754
No 99
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=99.67 E-value=1.5e-15 Score=144.31 Aligned_cols=139 Identities=17% Similarity=0.145 Sum_probs=111.4
Q ss_pred HHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc--------------
Q 011992 319 LKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-------------- 383 (473)
Q Consensus 319 L~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-------------- 383 (473)
+...+..++ .+++.||..|.+.++.++. +.++..+++|++||.|+.+|+..++|++.. .|.+
T Consensus 15 l~~~~~~~d~~a~~~l~~~y~~~l~~~~~-~~~~~~~AEDivQevflkl~~~~~~~~~~~--~~~~WL~~Iarn~~id~~ 91 (196)
T PRK12535 15 LALAAGRGDRAALTEFIRETQDDVWRLLA-HLGGHDIADDLTQETYLRVMSALPRFAARS--SARTWLLSLARRVWVDNI 91 (196)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHHhhhcCCcc--cHHHHHHHHHHHHHHHHH
Confidence 433444444 8999999999999999975 578888999999999999999999997632 3444
Q ss_pred ------CC------------CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHH
Q 011992 384 ------TG------------VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERV 445 (473)
Q Consensus 384 ------~~------------~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rV 445 (473)
.. ...++.. ...+....+..+|+.||+++|+||.|+|+ +|+|++|||+.||+|.++|
T Consensus 92 Rk~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIAe~lgis~~tV 166 (196)
T PRK12535 92 RHDMARPRKSATEYEDAAATTASNETT-GSWSEWIDVRTLIDALPPERREALILTQV----LGYTYEEAAKIADVRVGTI 166 (196)
T ss_pred HhhccCCCcccccccccccccCCcchh-HHHHHHHHHHHHHHcCCHHHHHHhhhHHH----hCCCHHHHHHHhCCCHHHH
Confidence 00 0111211 12223457899999999999999999999 9999999999999999999
Q ss_pred HHHHHHHHHHHHHHhccCch
Q 011992 446 RQLESRALYRLKQSLGGKAS 465 (473)
Q Consensus 446 rqi~~RAL~KLR~~L~~~~l 465 (473)
++.++||+++||+.+.....
T Consensus 167 ~~~l~Rar~~Lr~~l~~~~~ 186 (196)
T PRK12535 167 RSRVARARADLIAATATGQA 186 (196)
T ss_pred HHHHHHHHHHHHHHhccccc
Confidence 99999999999999987643
No 100
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=99.67 E-value=5.6e-16 Score=143.52 Aligned_cols=134 Identities=16% Similarity=0.088 Sum_probs=107.5
Q ss_pred chHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHH--hhhhCccCCCcccc---------------------
Q 011992 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKS--VEKFKPQAGCRFAN--------------------- 383 (473)
Q Consensus 327 ~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kA--iekFDp~kg~~FsT--------------------- 383 (473)
..+++.++..|.+.+++++.++.++..+++|++||.|+.+|+. +..+++.+++-|..
T Consensus 9 ~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~~~~~~~~~~~~wL~~iarn~~~d~~R~~~~~~~~~~~ 88 (172)
T PRK09651 9 SLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVSETLSTIRDPRSFLCTIAKRVMVDLFRRNALEKAYLEM 88 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhhcccccccCHHHHHHHHHHHHHHHHHHHHHHHhhhhhH
Confidence 4789999999999999999999999999999999999999987 33332212111111
Q ss_pred ------CCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992 384 ------TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457 (473)
Q Consensus 384 ------~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR 457 (473)
.....|+......+....+..+|+.||+++|.||.|+|+ +|+|++|||+.||+|.++|+..++||+.+|+
T Consensus 89 ~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~ 164 (172)
T PRK09651 89 LALMPEGGAPSPEERESQLETLQLLDSMLDGLNGKTREAFLLSQL----DGLTYSEIAHKLGVSVSSVKKYVAKATEHCL 164 (172)
T ss_pred HhhccccCCCChHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhhhc----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 001233334444455678999999999999999999999 9999999999999999999999999999999
Q ss_pred HHhccCc
Q 011992 458 QSLGGKA 464 (473)
Q Consensus 458 ~~L~~~~ 464 (473)
...-..+
T Consensus 165 ~~~~~~~ 171 (172)
T PRK09651 165 LFRLEYG 171 (172)
T ss_pred HHHHHcC
Confidence 8765543
No 101
>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=99.66 E-value=4.5e-16 Score=140.17 Aligned_cols=121 Identities=22% Similarity=0.212 Sum_probs=103.4
Q ss_pred HHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc--------------------C---------
Q 011992 334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN--------------------T--------- 384 (473)
Q Consensus 334 i~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT--------------------~--------- 384 (473)
|..|.+.|+++++++.++..+++|++||+|+.+|+++++|++ ..|.+ .
T Consensus 1 y~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~~~d~~r~~~~~~~~~~~~~~~ 77 (154)
T TIGR02950 1 YREYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNAFIDWYRKDKKIQTIDDDAIGD 77 (154)
T ss_pred CchHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHHHHHHHHHhhhhccccHhhhhh
Confidence 357899999999999999999999999999999999999986 35655 0
Q ss_pred ----CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992 385 ----GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 460 (473)
Q Consensus 385 ----~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L 460 (473)
....|+..+...+....|..+|+.||++++.||.++|+ +|++++|||+.||+|+++|++.++||+++||+.+
T Consensus 78 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~l 153 (154)
T TIGR02950 78 LEQHPVESPEHHLLIKIEQEEITHHLSRLPENYRTVLILREF----KEFSYKEIAELLNLSLAKVKSNLFRARKELKKLL 153 (154)
T ss_pred ccccccCChhHHHHHHHHHHHHHHHHHhCCHhheeeeeehhh----ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 01123444444555678999999999999999999998 9999999999999999999999999999999876
Q ss_pred c
Q 011992 461 G 461 (473)
Q Consensus 461 ~ 461 (473)
+
T Consensus 154 ~ 154 (154)
T TIGR02950 154 E 154 (154)
T ss_pred C
Confidence 3
No 102
>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=99.66 E-value=1.1e-15 Score=154.44 Aligned_cols=132 Identities=17% Similarity=0.213 Sum_probs=110.3
Q ss_pred cchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc--------------------C-
Q 011992 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN--------------------T- 384 (473)
Q Consensus 326 g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT--------------------~- 384 (473)
+..+++.||..|.+.|+++|++++++..+++|++||.|+.+|+++++|+... .|.+ .
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 4489999999999999999999999999999999999999999999997532 3444 0
Q ss_pred --C--C---------------------------------CCchHHHHHHH-HHHHHHHHHhhCCHHHHHHHHHHhhccCC
Q 011992 385 --G--V---------------------------------EIPDISVQKQL-MRQHVRNLLTLLNPKERCIVRLRFGIEDG 426 (473)
Q Consensus 385 --~--~---------------------------------~~pee~le~~e-l~e~L~~aL~~LperER~VL~LrY~L~~g 426 (473)
. . ..|+..+...+ ....+..+|..||+++|.||.|+|+
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~---- 156 (324)
T TIGR02960 81 PVGLGAPSADGTAAASEAAEVTWLEPLPDLTLDLDDPAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRDV---- 156 (324)
T ss_pred ccccCCCCCcccccccccccccccCCCCccccccccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHH----
Confidence 0 0 01222222233 3456889999999999999999999
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccC
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 463 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~ 463 (473)
++++++|||++||+|+++|+++++||+++||+.+...
T Consensus 157 ~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 193 (324)
T TIGR02960 157 LGWRAAETAELLGTSTASVNSALQRARATLDEVGPSA 193 (324)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcccc
Confidence 9999999999999999999999999999999998743
No 103
>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=99.66 E-value=1.3e-15 Score=143.48 Aligned_cols=127 Identities=13% Similarity=0.097 Sum_probs=107.8
Q ss_pred HHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------------------C---C
Q 011992 332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------------------T---G 385 (473)
Q Consensus 332 ~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------------------~---~ 385 (473)
+.+..|.+.|+++|+++.++..+++|++||+|+.+|+..++|++. ..|.+ . .
T Consensus 6 ~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R~~~r~~~~~~~~~ 83 (188)
T TIGR02943 6 QELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKNKIIDALRAKGREVKVSDLDD 83 (188)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHHHHHHHHHhhcccCCcccccc
Confidence 567789999999999999999999999999999999999999754 24443 0 0
Q ss_pred C-------------------------CCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCC
Q 011992 386 V-------------------------EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGL 440 (473)
Q Consensus 386 ~-------------------------~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGI 440 (473)
. ..|+..+...+....+..+|..||+++|+||.|+|+ ++++++|||+.||+
T Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~lgi 159 (188)
T TIGR02943 84 ELDDEAFNALFTQNGHWAQHGQPQHWNTPEKQLENKEFWEVFEACLYHLPEQTARVFMMREV----LGFESDEICQELEI 159 (188)
T ss_pred ccccchhhhhhccccchhccccccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHhCC
Confidence 0 122344555566678999999999999999999999 99999999999999
Q ss_pred CHHHHHHHHHHHHHHHHHHhccCc
Q 011992 441 SKERVRQLESRALYRLKQSLGGKA 464 (473)
Q Consensus 441 S~~rVrqi~~RAL~KLR~~L~~~~ 464 (473)
|.++|++++.||+++||+++....
T Consensus 160 s~~tvk~rl~Rar~~Lr~~l~~~~ 183 (188)
T TIGR02943 160 STSNCHVLLYRARLSLRACLSINW 183 (188)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999999987543
No 104
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=99.66 E-value=1.5e-15 Score=142.63 Aligned_cols=129 Identities=21% Similarity=0.219 Sum_probs=107.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc---------------------C--
Q 011992 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------------------T-- 384 (473)
Q Consensus 328 ~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT---------------------~-- 384 (473)
.++..++..|++.|+++|.++.++..+++|++||+|+.+|+++++|++.. .|.+ .
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 46778999999999999999999999999999999999999999997543 3444 0
Q ss_pred -C------CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992 385 -G------VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457 (473)
Q Consensus 385 -~------~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR 457 (473)
. ...++. ........|..+|+.||+++|+||.|+|+ +|+|++|||+.||+|.++|++.++||+++||
T Consensus 83 ~~~~~~~~~~~~~~--~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr 156 (182)
T PRK12540 83 DGSYAKTLKSQPGQ--NAHLEFEEFRAALDKLPQDQREALILVGA----SGFSYEDAAAICGCAVGTIKSRVNRARSKLS 156 (182)
T ss_pred cccccccccCCCch--HHHHHHHHHHHHHHhCCHHHHHHhhHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 0 011111 11223456899999999999999999999 9999999999999999999999999999999
Q ss_pred HHhccCc
Q 011992 458 QSLGGKA 464 (473)
Q Consensus 458 ~~L~~~~ 464 (473)
+.+....
T Consensus 157 ~~l~~~~ 163 (182)
T PRK12540 157 ALLYVDG 163 (182)
T ss_pred HHHHhcc
Confidence 9998654
No 105
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=99.65 E-value=1.5e-15 Score=142.95 Aligned_cols=126 Identities=17% Similarity=0.104 Sum_probs=104.4
Q ss_pred HHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc---------------------CC-----C
Q 011992 333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------------------TG-----V 386 (473)
Q Consensus 333 Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT---------------------~~-----~ 386 (473)
-|..|.+.++++|.++.++..+++|++||+|+.+|++++.|++.. .|.+ .. .
T Consensus 12 ~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~~--~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~~~~~~ 89 (189)
T PRK12530 12 EIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQS--ALKTWIFAILKNKIIDLIRYRKRFVNESELIEE 89 (189)
T ss_pred HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCCc--cHHHHHHHHHHHHHHHHHHhhccCCCccccccc
Confidence 356788899999999999999999999999999999999997643 3443 00 0
Q ss_pred -----------------------CCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHH
Q 011992 387 -----------------------EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKE 443 (473)
Q Consensus 387 -----------------------~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~ 443 (473)
..++..+...+....|..+|+.||+++|+||.|+|+ +|+|++|||+.||+|++
T Consensus 90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~ 165 (189)
T PRK12530 90 DSPNSFFDEKGHWKPEYYEPSEWQEVENTVYKEEFWLIFEACLNHLPAQQARVFMMREY----LELSSEQICQECDISTS 165 (189)
T ss_pred ccchhhhcccccccccccCCccccCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHhHHHH----cCCCHHHHHHHHCCCHH
Confidence 011223334455667899999999999999999999 99999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhccCc
Q 011992 444 RVRQLESRALYRLKQSLGGKA 464 (473)
Q Consensus 444 rVrqi~~RAL~KLR~~L~~~~ 464 (473)
+|+.+++||+++||+++....
T Consensus 166 tVk~~l~RAr~~Lr~~l~~~~ 186 (189)
T PRK12530 166 NLHVLLYRARLQLQACLSKNW 186 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999987543
No 106
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=99.65 E-value=1.6e-15 Score=138.16 Aligned_cols=122 Identities=13% Similarity=0.104 Sum_probs=104.9
Q ss_pred HHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------------------------C--
Q 011992 335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------------------------T-- 384 (473)
Q Consensus 335 ~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------------------------~-- 384 (473)
..|++.++.++.+++++..+++|++||+|+.+|+..+.|++. .|.+ .
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~~---~~~~wL~~ia~n~~~d~~R~~~~~~~~~~~~~~~~ 78 (159)
T PRK12527 2 ENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQIE---HPRAFLYRTALNLVVDRHRRHRVRQAEPLEVLDEE 78 (159)
T ss_pred hhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhcccccccc---chHHHHHHHHHHHHHHHHHHHhcccccchhhhhcc
Confidence 568889999999999999999999999999999999888642 4444 0
Q ss_pred ---CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Q 011992 385 ---GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 461 (473)
Q Consensus 385 ---~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~ 461 (473)
....|+..+..++....|..+|..||++++.||.|+|+ +++|++|||+.||+|+++|+..+.||+++||+.+.
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~ 154 (159)
T PRK12527 79 ERLHSPSPQTRLDLGQRLALLQRALAELPPACRDSFLLRKL----EGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMR 154 (159)
T ss_pred ccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 01234555566666778999999999999999999999 99999999999999999999999999999999987
Q ss_pred cC
Q 011992 462 GK 463 (473)
Q Consensus 462 ~~ 463 (473)
..
T Consensus 155 ~~ 156 (159)
T PRK12527 155 QW 156 (159)
T ss_pred hc
Confidence 54
No 107
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=99.65 E-value=1.5e-15 Score=144.41 Aligned_cols=127 Identities=17% Similarity=0.140 Sum_probs=105.3
Q ss_pred HHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-------------------C-CC-----
Q 011992 332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-------------------T-GV----- 386 (473)
Q Consensus 332 ~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-------------------~-~~----- 386 (473)
.++..|.+.++++|++++++..+++|++||+|+.+|+++++|++.. .|.+ . ..
T Consensus 12 ~~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~~--~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~~~ 89 (201)
T PRK12545 12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQS--AHKTWVFGILRNKLIDTLRARQRTVNLSALDA 89 (201)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhccccc--hHHHHHHHHHHHHHHHHHHhhccccccccccc
Confidence 3588899999999999999999999999999999999999998653 3444 0 00
Q ss_pred ----------------------------CCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHH
Q 011992 387 ----------------------------EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIF 438 (473)
Q Consensus 387 ----------------------------~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~L 438 (473)
..++......+....+..+|..||+++|.||.|+|+ +|++++|||+.|
T Consensus 90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~v~~L~~~----eg~s~~EIA~~l 165 (201)
T PRK12545 90 ELDGEALLDRELFKDNGHWAAHAKPRPWPKPETILQQQQFWTLFETCLDHLPEQIGRVFMMREF----LDFEIDDICTEL 165 (201)
T ss_pred ccchhhhhhhhhhcccccccccccCcCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHH
Confidence 011222233344457889999999999999999999 999999999999
Q ss_pred CCCHHHHHHHHHHHHHHHHHHhccCc
Q 011992 439 GLSKERVRQLESRALYRLKQSLGGKA 464 (473)
Q Consensus 439 GIS~~rVrqi~~RAL~KLR~~L~~~~ 464 (473)
|+|+++|+..+.||+++||+.+...+
T Consensus 166 gis~~tVk~~l~RAr~~Lr~~l~~~~ 191 (201)
T PRK12545 166 TLTANHCSVLLYRARTRLRTCLSEKG 191 (201)
T ss_pred CcCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999999999996543
No 108
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=99.65 E-value=1.6e-15 Score=138.21 Aligned_cols=125 Identities=15% Similarity=0.185 Sum_probs=104.7
Q ss_pred HHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc------------------------C---
Q 011992 332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------------------------T--- 384 (473)
Q Consensus 332 ~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------------------------~--- 384 (473)
.++..|.+.++++|.++.++..+++|++||+++++|+....|++.. |.+ .
T Consensus 2 ~~~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~---~~~wl~~iarn~~~d~~R~~~~~~~~~~~~~ 78 (163)
T PRK07037 2 DVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVKQ---PVAYLFRIVRNLAIDHYRRQALENKYHGDEE 78 (163)
T ss_pred hHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhccccCCccc---HHHHHHHHHHHHHHHHHHhhccccccccccc
Confidence 3677899999999999999999999999999999999887775432 222 0
Q ss_pred -------CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992 385 -------GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457 (473)
Q Consensus 385 -------~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR 457 (473)
....++..+...+..+.+..+|..||+++|.||.++|+ +++|++|||+.||+|.++|+..+.||+++||
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~EIA~~lgis~~tV~~~l~ra~~~lr 154 (163)
T PRK07037 79 DGLDVPSPEASPEAALINRDTLRHVADALSELPARTRYAFEMYRL----HGETQKDIARELGVSPTLVNFMIRDALVHCR 154 (163)
T ss_pred cccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 01233444455566678899999999999999999999 9999999999999999999999999999999
Q ss_pred HHhccC
Q 011992 458 QSLGGK 463 (473)
Q Consensus 458 ~~L~~~ 463 (473)
+.+...
T Consensus 155 ~~l~~~ 160 (163)
T PRK07037 155 KCLDAC 160 (163)
T ss_pred HHHhcc
Confidence 998654
No 109
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=99.65 E-value=2.1e-15 Score=153.93 Aligned_cols=136 Identities=19% Similarity=0.192 Sum_probs=110.8
Q ss_pred HHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-------------
Q 011992 318 DLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------------- 383 (473)
Q Consensus 318 eL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------------- 383 (473)
+|...+..|+ .+++.||..|.+.|+++|+++.++..+++|++||+|+.+|+.+++|++. ..|.+
T Consensus 8 ~l~~~~~~gd~~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~ 85 (339)
T PRK08241 8 ALLARAAAGDRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGR--SSLRTWLYRIATNVCLDA 85 (339)
T ss_pred HHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhhhccccc--cchHHHHHHHHHHHHHHH
Confidence 3444444444 9999999999999999999999999999999999999999999999743 23443
Q ss_pred --------C---CC-------------------------------CCchHHHHHHH-HHHHHHHHHhhCCHHHHHHHHHH
Q 011992 384 --------T---GV-------------------------------EIPDISVQKQL-MRQHVRNLLTLLNPKERCIVRLR 420 (473)
Q Consensus 384 --------~---~~-------------------------------~~pee~le~~e-l~e~L~~aL~~LperER~VL~Lr 420 (473)
. .. ..|+..+...+ ....|..+|..||+++|.||.|+
T Consensus 86 ~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~ 165 (339)
T PRK08241 86 LEGRARRPLPTDLGAPAADPVDELVERPEVPWLEPYPDALLDPAAADPAARVVARESVRLAFVAALQHLPPRQRAVLILR 165 (339)
T ss_pred HHhhccccCccccCCCcCcccccccccccccccCCCCcccccccCCChHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhH
Confidence 0 00 01222223223 34568899999999999999999
Q ss_pred hhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 011992 421 FGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 459 (473)
Q Consensus 421 Y~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~ 459 (473)
|+ +++|++|||++||+|.++|+++++||+++||+.
T Consensus 166 ~~----~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 200 (339)
T PRK08241 166 DV----LGWSAAEVAELLDTSVAAVNSALQRARATLAER 200 (339)
T ss_pred Hh----hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhhc
Confidence 99 999999999999999999999999999999994
No 110
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=99.65 E-value=1.6e-15 Score=142.83 Aligned_cols=128 Identities=18% Similarity=0.178 Sum_probs=107.5
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCcc-hhhHhhhhHHHHHHHhhhhCccCCCcccc---------------------CC---
Q 011992 331 EKLINANLRLVVHVAKQYQGRGIS-LHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------------------TG--- 385 (473)
Q Consensus 331 e~Li~~yl~lV~sIA~ry~~~~~s-aEDLiQEg~lgL~kAiekFDp~kg~~FsT---------------------~~--- 385 (473)
+..+..|.+.|+++|+++.++..+ ++|++||+|+.+|+++++|+.. ..|.+ ..
T Consensus 8 ~~~~~~~~~~l~~~a~~~~~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~~~ 85 (195)
T PRK12532 8 DAELIESRKLLLHFARLQLPDHPDLAEDLVQETLLSAYSAGDSFQGR--ALVNSWLFAILKNKIIDALRQIGRQRKVFTL 85 (195)
T ss_pred hhhHHHHHHHHHHHHHHHcCChhhhHHHHHHHHHHHHHHhccccccc--chHHHHHHHHHHHHHHHHHHHhccccccccc
Confidence 355678899999999999999888 9999999999999999999753 24544 00
Q ss_pred ----------------------------CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHH
Q 011992 386 ----------------------------VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNI 437 (473)
Q Consensus 386 ----------------------------~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~ 437 (473)
...|+..+...+....+..+|..||+++|+||.|+|+ +|+|++|||+.
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~L~~~----~g~s~~EIA~~ 161 (195)
T PRK12532 86 LDDELLDEAFESHFSQNGHWTPEGQPQHWNTPEKSLNNNEFQKILQSCLYNLPENTARVFTLKEI----LGFSSDEIQQM 161 (195)
T ss_pred ccccccchhhhhhhccccccccccCccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHH----hCCCHHHHHHH
Confidence 0123344445566678999999999999999999999 99999999999
Q ss_pred HCCCHHHHHHHHHHHHHHHHHHhccCc
Q 011992 438 FGLSKERVRQLESRALYRLKQSLGGKA 464 (473)
Q Consensus 438 LGIS~~rVrqi~~RAL~KLR~~L~~~~ 464 (473)
||+|.++|+++++||+++||+++....
T Consensus 162 lgis~~tVk~~l~Rar~~Lr~~l~~~~ 188 (195)
T PRK12532 162 CGISTSNYHTIMHRARESLRQCLQIKW 188 (195)
T ss_pred HCCCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 999999999999999999999997554
No 111
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=99.65 E-value=2.8e-15 Score=140.54 Aligned_cols=128 Identities=18% Similarity=0.127 Sum_probs=109.7
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc--------------------------
Q 011992 330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-------------------------- 383 (473)
Q Consensus 330 ~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-------------------------- 383 (473)
++.|+..|.+.|++++.++.++..+++|++||+++.+|+.+..|+.. ..|.+
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~aeDi~QEvflkl~~~~~~~~~~--~~~~~wL~~i~~n~~~d~~Rk~~~~~~~~~~ 80 (181)
T PRK09637 3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDG--SSIKSWLYQIANNTIIDFYRKKNRSEELPDD 80 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHhHHHhccc--cchHHHHHHHHHHHHHHHHHhccccCCcchh
Confidence 67899999999999999999999999999999999999999999753 35655
Q ss_pred C-CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Q 011992 384 T-GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 462 (473)
Q Consensus 384 ~-~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~ 462 (473)
. ....++......+....+..+|+.||+++|.||.|+|+ +|+++.|||++||+|.++|+.++.||+++||+.+..
T Consensus 81 ~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 156 (181)
T PRK09637 81 LLFEDEEREENAKKELAPCLRPFIDALPEKYAEALRLTEL----EGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG 156 (181)
T ss_pred hhccCCChhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 0 01122333444556678999999999999999999999 999999999999999999999999999999998875
Q ss_pred C
Q 011992 463 K 463 (473)
Q Consensus 463 ~ 463 (473)
.
T Consensus 157 ~ 157 (181)
T PRK09637 157 C 157 (181)
T ss_pred c
Confidence 3
No 112
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=99.64 E-value=2.8e-15 Score=143.73 Aligned_cols=127 Identities=19% Similarity=0.202 Sum_probs=108.1
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc--------------------CC----C
Q 011992 331 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN--------------------TG----V 386 (473)
Q Consensus 331 e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT--------------------~~----~ 386 (473)
..++..|.+.|+++|+++.++...++|++||+|+.+|+.+.+|+.. ..|.+ .. .
T Consensus 21 ~~~~~~~~~~l~~~~~~~~~d~~~AEDivQEvfikl~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~~~~~~~~~~ 98 (206)
T PRK12544 21 PVFLEDLRKQMIKFATLQLSDLHLAEDAVQEALIGALKNADSFAGR--AAFKTWVFAILKNKIIDLLRQKKRHVSASSLL 98 (206)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhhcccccccccc
Confidence 4688899999999999999999999999999999999999999754 23544 00 0
Q ss_pred ----------------------------CCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHH
Q 011992 387 ----------------------------EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIF 438 (473)
Q Consensus 387 ----------------------------~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~L 438 (473)
..|+..+...+....+..+|..||+++|+||.|+|+ ++++++|||+.|
T Consensus 99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~L~~L~~~~r~v~~L~~~----~g~s~~EIAe~l 174 (206)
T PRK12544 99 RDEEEEEDFEELFDESGHWQKDERPQAWGNPEESLEQEQFWRIFEACLDGLPAKYARVFMMREF----IELETNEICHAV 174 (206)
T ss_pred cccchhhHHHHhhcccccccccccccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHH
Confidence 123334445555567899999999999999999999 999999999999
Q ss_pred CCCHHHHHHHHHHHHHHHHHHhccC
Q 011992 439 GLSKERVRQLESRALYRLKQSLGGK 463 (473)
Q Consensus 439 GIS~~rVrqi~~RAL~KLR~~L~~~ 463 (473)
|+|.++|++.++||+++||+.+...
T Consensus 175 gis~~tV~~~l~RAr~~Lr~~l~~~ 199 (206)
T PRK12544 175 DLSVSNLNVLLYRARLRLRECLENK 199 (206)
T ss_pred CcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999998753
No 113
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=99.63 E-value=5.8e-15 Score=136.08 Aligned_cols=127 Identities=14% Similarity=0.078 Sum_probs=107.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc------------------------
Q 011992 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------------------------ 383 (473)
Q Consensus 328 ~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------------------------ 383 (473)
..+..++..|++.++++|.++.++..+++|++||+|+.+|+....++. ..|.+
T Consensus 9 ~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~~---~~~~~wl~~Iarn~~~d~~Rr~~~~~~~~ 85 (168)
T PRK12525 9 TLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEGWRRQDLERAYL 85 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCcccc---cCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 678899999999999999999999999999999999999986554432 13433
Q ss_pred ---C-----CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 011992 384 ---T-----GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR 455 (473)
Q Consensus 384 ---~-----~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~K 455 (473)
. ....|+..+...+....|..+|..||+++|.||.|+|+ +|+|++|||+.||+|+++|+..+.+|+++
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~----eg~s~~EIA~~l~is~~tV~~~l~ra~~~ 161 (168)
T PRK12525 86 QSLAEAPEAVQPSPEEQWMVIETLLAIDRLLDGLSGKARAAFLMSQL----EGLTYVEIGERLGVSLSRIHQYMVEAFKC 161 (168)
T ss_pred HHHhcccccccCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 0 01244444555566778999999999999999999999 99999999999999999999999999999
Q ss_pred HHHHhc
Q 011992 456 LKQSLG 461 (473)
Q Consensus 456 LR~~L~ 461 (473)
||..+.
T Consensus 162 ~~~~~~ 167 (168)
T PRK12525 162 CYQGFQ 167 (168)
T ss_pred HHHhhc
Confidence 998764
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=99.62 E-value=4.8e-15 Score=137.18 Aligned_cols=122 Identities=17% Similarity=0.152 Sum_probs=103.8
Q ss_pred HHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc------------------------C---CCC
Q 011992 335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------------------------T---GVE 387 (473)
Q Consensus 335 ~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------------------------~---~~~ 387 (473)
..|.+.++.+++++.++..+++|++||+|+.+|+++++|+.. ..|.+ . ...
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~l~~~~~~~~~~--~~f~~wl~~iarn~~~d~~Rk~~~~~~~~~~~~~~~ 79 (170)
T TIGR02959 2 DEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDG--QKIQSWLYQIARNTIIDFYRSKSRSVELPESLLAAD 79 (170)
T ss_pred chHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhccCccccchhhcccC
Confidence 468889999999999999999999999999999999999853 35655 0 011
Q ss_pred CchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Q 011992 388 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 462 (473)
Q Consensus 388 ~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~ 462 (473)
.+++.....+....|..+|..||+++|.||.|+|+ ++++++|||+.||+|.++|++.++||+++||..+..
T Consensus 80 ~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 150 (170)
T TIGR02959 80 SAREETFVKELSQCIPPMIKELPDEYREAIRLTEL----EGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLET 150 (170)
T ss_pred CccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 23333444556678999999999999999999999 999999999999999999999999999999999864
No 115
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=99.61 E-value=7.6e-15 Score=138.74 Aligned_cols=129 Identities=18% Similarity=0.176 Sum_probs=103.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------------------CC
Q 011992 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------------------TG 385 (473)
Q Consensus 328 ~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------------------~~ 385 (473)
..++.|+. |.+.|+++|+.++++..+++|++||+|+.+|+++..|+.. ..|.+ ..
T Consensus 8 ~~~~~l~~-~~~~l~~~a~~~l~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n~~~d~~Rk~~r~~~~~ 84 (188)
T PRK12546 8 DPRDELVE-HLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSDRRKHKREVPDP 84 (188)
T ss_pred hHHHHHHH-HHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHHHHHHHHHHhcccccCc
Confidence 34555544 7799999999999999999999999999999999999753 24544 00
Q ss_pred CC------CchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 011992 386 VE------IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 459 (473)
Q Consensus 386 ~~------~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~ 459 (473)
.. ..............+..+|..||+++|.||.|+|+ +|++++|||+.||||.++|++++.||+++||+.
T Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~v~~L~~~----~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~ 160 (188)
T PRK12546 85 EGVHAASLAVKPAHDGRLAMSDFRAAFAQLPDEQREALILVGA----SGFSYEEAAEMCGVAVGTVKSRANRARARLAEL 160 (188)
T ss_pred ccccccccccCCcchhHHHHHHHHHHHHhCCHHHhHHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 00 00001112233457899999999999999999999 999999999999999999999999999999999
Q ss_pred hccC
Q 011992 460 LGGK 463 (473)
Q Consensus 460 L~~~ 463 (473)
+...
T Consensus 161 l~~~ 164 (188)
T PRK12546 161 LQLE 164 (188)
T ss_pred Hhcc
Confidence 8753
No 116
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=99.61 E-value=1e-14 Score=137.13 Aligned_cols=128 Identities=13% Similarity=0.124 Sum_probs=104.7
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------------------CC---
Q 011992 331 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------------------TG--- 385 (473)
Q Consensus 331 e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------------------~~--- 385 (473)
...+..+++.|+.+|.++.++..+++|++||+|+.+|+++..|+... .|.+ ..
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 44577899999999999999999999999999999999999997532 4544 00
Q ss_pred ----CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Q 011992 386 ----VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 461 (473)
Q Consensus 386 ----~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~ 461 (473)
...+............|..+|..||+++|.||.|+|+ +|+|++|||+.||||.++|++.++||+++||+.+.
T Consensus 85 ~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~----eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~ 160 (182)
T PRK12511 85 AVLADASLPAAQEHAVRLAQIRDAFFDLPEEQRAALHLVAI----EGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFEE 160 (182)
T ss_pred hhccccCCCcchHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 0011111222334567889999999999999999999 99999999999999999999999999999999987
Q ss_pred cCc
Q 011992 462 GKA 464 (473)
Q Consensus 462 ~~~ 464 (473)
..+
T Consensus 161 ~~~ 163 (182)
T PRK12511 161 GTG 163 (182)
T ss_pred hcC
Confidence 543
No 117
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=99.56 E-value=2.4e-14 Score=140.05 Aligned_cols=132 Identities=18% Similarity=0.157 Sum_probs=103.2
Q ss_pred HHHHHhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc---------------
Q 011992 319 LKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN--------------- 383 (473)
Q Consensus 319 L~~~l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT--------------- 383 (473)
+.+.+..+..+++.++..| +.++++|.++.++..++||++||+|+.+|+..+..+ .|.+
T Consensus 9 ~~~~~~~~~~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~~~~~~~-----~~~~WL~~IarN~~id~~R 82 (228)
T PRK06704 9 LKNHIDMNHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQKYSNKD-----ICMTLVYKIARNRWLDQIK 82 (228)
T ss_pred HhcccCCCHHHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCccc-----cHHHHHHHHHHHHHHHHHh
Confidence 3444444556777777766 789999999999999999999999999998643322 2333
Q ss_pred --C---------CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992 384 --T---------GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 452 (473)
Q Consensus 384 --~---------~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA 452 (473)
. ....+.. ...+..+.+..+|+.||+++|.||.|+|+ +++|++|||+.||+|+++|+.++.||
T Consensus 83 k~k~~~~~~~~~~~~~~~~--~~~~~~~~l~~~L~~Lp~~~R~v~lL~~~----eg~S~~EIAe~LgiS~~tVksrL~Ra 156 (228)
T PRK06704 83 SKSVHEKIRDQITFEEPHE--KIADLHEMVGKVLSSLNVQQSAILLLKDV----FQYSIADIAKVCSVSEGAVKASLFRS 156 (228)
T ss_pred ccccccccccccccCChHH--HHHHHHHHHHHHHHhCCHHHhhHhhhHHh----hCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 0 0011111 12234567899999999999999999999 99999999999999999999999999
Q ss_pred HHHHHHHhcc
Q 011992 453 LYRLKQSLGG 462 (473)
Q Consensus 453 L~KLR~~L~~ 462 (473)
+++||+.+..
T Consensus 157 rk~Lr~~l~~ 166 (228)
T PRK06704 157 RNRLKTVSEE 166 (228)
T ss_pred HHHHHHHHHh
Confidence 9999999865
No 118
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=99.55 E-value=5.3e-14 Score=141.34 Aligned_cols=127 Identities=19% Similarity=0.156 Sum_probs=103.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------------------C
Q 011992 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------------------T 384 (473)
Q Consensus 328 ~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------------------~ 384 (473)
..+..++..|.+.++++|++++++..++||++||+|+. |.....|+. ..|.+ .
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 34678999999999999999999999999999999999 666666642 23444 0
Q ss_pred -C----------CCCchHHH-HHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992 385 -G----------VEIPDISV-QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 452 (473)
Q Consensus 385 -~----------~~~pee~l-e~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA 452 (473)
. ...|++.. ...+....+..+|+.||+++|.||.|+|+ ++++++|||++||+|+++|+++++||
T Consensus 80 ~~~~~~e~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~R~v~~L~~~----~g~s~~EIA~~lg~s~~tVk~~l~RA 155 (293)
T PRK09636 80 VGPWLPEPVVEELDDPLEAVVAAEDLSLALMLALERLSPLERAAFLLHDV----FGVPFDEIASTLGRSPAACRQLASRA 155 (293)
T ss_pred cCCcCCcCCCCCCCChHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 0 01122222 23444567899999999999999999999 99999999999999999999999999
Q ss_pred HHHHHHHhcc
Q 011992 453 LYRLKQSLGG 462 (473)
Q Consensus 453 L~KLR~~L~~ 462 (473)
+++||+.+..
T Consensus 156 r~~Lr~~~~~ 165 (293)
T PRK09636 156 RKHVRAARPR 165 (293)
T ss_pred HHHHHhhCCC
Confidence 9999998753
No 119
>PRK09191 two-component response regulator; Provisional
Probab=99.50 E-value=1.8e-13 Score=132.39 Aligned_cols=124 Identities=16% Similarity=0.130 Sum_probs=103.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc------------C--CCCCchHHHH
Q 011992 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------------T--GVEIPDISVQ 394 (473)
Q Consensus 329 A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------------~--~~~~pee~le 394 (473)
++..+|..|.+.++++|.++.++..+++|++||+|+.+|+....|++.. .|.+ . ....+..
T Consensus 2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~~--~~~~wl~~~~~~~~~~~~~~~~~~~~--- 76 (261)
T PRK09191 2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEAS--SPRVGLYRLFHRLWSSAGANDPEPGS--- 76 (261)
T ss_pred chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCCc--chhhHHHHHHHHHhccccccCCCCCC---
Confidence 5788999999999999999999999999999999999999999997632 2333 0 0000110
Q ss_pred HHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccC
Q 011992 395 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 463 (473)
Q Consensus 395 ~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~ 463 (473)
.....+..+|..||+++|.||.|+|+ +++|++|||+.||+|+++|+.++.+|+++||..+...
T Consensus 77 --~~~~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~~~ 139 (261)
T PRK09191 77 --PFEARAERRLAGLTPLPRQAFLLTAL----EGFSVEEAAEILGVDPAEAEALLDDARAEIARQVATR 139 (261)
T ss_pred --CchHHHHHHHHhCCHHHhHHHHHHHH----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHhccCCCe
Confidence 01127899999999999999999999 9999999999999999999999999999999877643
No 120
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=99.48 E-value=2.5e-13 Score=137.17 Aligned_cols=126 Identities=18% Similarity=0.095 Sum_probs=103.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------------------C
Q 011992 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------------------T 384 (473)
Q Consensus 328 ~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------------------~ 384 (473)
..+..+|..|.+.++++|++++++..++||++||+|+.+|++...+. ..|.+ .
T Consensus 5 ~~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~~----~~~~aWL~~Ia~n~~id~lRk~~~rr~~~ 80 (290)
T PRK09635 5 DPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGDI----DDERGWLIVVTSRLCLDHIKSASTRRERP 80 (290)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCcccc----ccHHHHHHHHHHHHHHHHHhhhhccCcCc
Confidence 56788999999999999999999999999999999999998765421 12222 0
Q ss_pred --C-C----------CCchH-HHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011992 385 --G-V----------EIPDI-SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 450 (473)
Q Consensus 385 --~-~----------~~pee-~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~ 450 (473)
. . ..|++ .....+....+..+|+.|||++|.||.|+|+ .+++++|||++||+|+++|+++++
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~al~~~L~~L~p~~R~vf~L~~~----~g~s~~EIA~~Lgis~~tVr~~l~ 156 (290)
T PRK09635 81 QDIAAWHDGDASVSSVDPADRVTLDDEVRLALLIMLERLGPAERVVFVLHEI----FGLPYQQIATTIGSQASTCRQLAH 156 (290)
T ss_pred ccccccCccccCCCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHH----hCCCHHHHHHHHCcCHHHHHHHHH
Confidence 0 0 11222 2334555678999999999999999999999 999999999999999999999999
Q ss_pred HHHHHHHHHhc
Q 011992 451 RALYRLKQSLG 461 (473)
Q Consensus 451 RAL~KLR~~L~ 461 (473)
||+++||....
T Consensus 157 RAr~~Lr~~~~ 167 (290)
T PRK09635 157 RARRKINESRI 167 (290)
T ss_pred HHHHHHHhhCC
Confidence 99999998654
No 121
>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=99.48 E-value=3.2e-13 Score=135.21 Aligned_cols=122 Identities=25% Similarity=0.193 Sum_probs=97.9
Q ss_pred HHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------------------C-C--
Q 011992 332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------------------T-G-- 385 (473)
Q Consensus 332 ~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------------------~-~-- 385 (473)
++|..|.+.++++|+++.++..++||++||+|+.+++. .|+.. ..|.+ . .
T Consensus 1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~~--~~~~awL~~Ia~n~~ld~lR~~~~~~~~~~~~~ 76 (281)
T TIGR02957 1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQI--ENPKAYLTKVVTRRCIDVLRSARARREVYVGPW 76 (281)
T ss_pred ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Ccccc--cCHHHHHHHHHHHHHHHHHHHhhhcccccCCCC
Confidence 36889999999999999999999999999999997764 34321 23433 0 0
Q ss_pred --------CCCchHHHHH-HHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 011992 386 --------VEIPDISVQK-QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 456 (473)
Q Consensus 386 --------~~~pee~le~-~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KL 456 (473)
...|++.+.. +.+...+..+|+.||+++|.||.|+|+ ++++++|||+.||+|+++|+++++||+++|
T Consensus 77 ~~e~~~~~~~~~~~~~~~~e~~~~~l~~~l~~L~~~~R~v~~L~~~----~g~s~~EIA~~lg~s~~tVr~~l~RAr~~L 152 (281)
T TIGR02957 77 LPEPLLTTSADPAESVELAESLSMAYLLLLERLSPLERAVFVLREV----FDYPYEEIASIVGKSEANCRQLVSRARRHL 152 (281)
T ss_pred CCcccCCCCCChHHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 0123333332 334557888999999999999999999 999999999999999999999999999999
Q ss_pred HHHhc
Q 011992 457 KQSLG 461 (473)
Q Consensus 457 R~~L~ 461 (473)
|+...
T Consensus 153 r~~~~ 157 (281)
T TIGR02957 153 DARRP 157 (281)
T ss_pred HhhCC
Confidence 99765
No 122
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=99.47 E-value=3.8e-13 Score=121.97 Aligned_cols=108 Identities=19% Similarity=0.235 Sum_probs=86.3
Q ss_pred cCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------------------CC---------C------------
Q 011992 350 GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------------------TG---------V------------ 386 (473)
Q Consensus 350 ~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------------------~~---------~------------ 386 (473)
++..+++|++||+|+.+|+.+..+ + +..|.+ .. .
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 345678999999999999987763 2 233443 00 0
Q ss_pred ------CCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992 387 ------EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 460 (473)
Q Consensus 387 ------~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L 460 (473)
..|+..+...+....|..+|..||+++|.||.|+|+ +|+|++|||+.||+|.++|+.++.||+++||+.+
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 154 (161)
T PRK09047 79 SADEGAESPADKLERAQVLQLIEEAIQKLPARQREAFLLRYW----EDMDVAETAAAMGCSEGSVKTHCSRATHALAKAL 154 (161)
T ss_pred cccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 122333444556678999999999999999999999 9999999999999999999999999999999999
Q ss_pred ccCc
Q 011992 461 GGKA 464 (473)
Q Consensus 461 ~~~~ 464 (473)
...+
T Consensus 155 ~~~~ 158 (161)
T PRK09047 155 EAKG 158 (161)
T ss_pred HhcC
Confidence 7654
No 123
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=99.46 E-value=2.9e-13 Score=134.80 Aligned_cols=115 Identities=25% Similarity=0.434 Sum_probs=88.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccccCCCCCchHHHHHHHHHHHHHHH--
Q 011992 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQHVRNL-- 405 (473)
Q Consensus 328 ~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~~~~~pee~le~~el~e~L~~a-- 405 (473)
.++++||..|+++|.++|++|.+++++++||+|+|++||++|+++|||.+|++|+|+..++....+ ...|.+.
T Consensus 40 ~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~iGLi~AierFDp~~G~~FsTYA~~~Irg~I-----~~~lr~~~~ 114 (264)
T PRK07122 40 RQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEV-----RRHFRDNSW 114 (264)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHH-----HHHHHHcCC
Confidence 478999999999999999999999999999999999999999999999999999997766533332 2222221
Q ss_pred HhhCCHHHHHHH----------HHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 406 LTLLNPKERCIV----------RLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 406 L~~LperER~VL----------~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
+=.+|-+-+..+ .-.+ |...|..|||+.||++...|.+++..
T Consensus 115 ~ir~Pr~~~~~~~~i~~~~~~l~~~l----g~~pt~~eiA~~lg~~~~~v~~~~~~ 166 (264)
T PRK07122 115 SVKVPRRLKELHLRLGRATAELSQRL----GRAPTASELAAELGMDREEVVEGLVA 166 (264)
T ss_pred ccccCHHHHHHHHHHHHHHHHHHHHh----CCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 011443332221 1123 48899999999999999999987654
No 124
>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=99.39 E-value=1.4e-12 Score=127.50 Aligned_cols=118 Identities=30% Similarity=0.514 Sum_probs=87.0
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccccCCCCCchHHHHHHHHHHHHHHHHh-
Q 011992 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQHVRNLLT- 407 (473)
Q Consensus 329 A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~~~~~pee~le~~el~e~L~~aL~- 407 (473)
|+++||..|+++|+++|++|.+++.+++||+|||++||++|+++|||.+|++|+|+..++....+. ..+.+...
T Consensus 1 a~~~Li~~~~~lv~~ia~~~~~~~~~~eDLiQeG~igL~~A~~~fd~~~g~~FstYA~~~Ir~~I~-----~~l~~~~~~ 75 (238)
T TIGR02393 1 AKKQLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAIT-----RAIADQART 75 (238)
T ss_pred CHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCChHHHhHHHHHHHHH-----HHHHHcCCc
Confidence 578999999999999999999999999999999999999999999999999999977665433322 22211111
Q ss_pred -hCCHHHHHH----HHHH--hhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 408 -LLNPKERCI----VRLR--FGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 408 -~LperER~V----L~Lr--Y~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.+|..-+.. .... +.-..|.++|.+|||+.||++...|.++...
T Consensus 76 vrip~~~~~~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~ 126 (238)
T TIGR02393 76 IRIPVHMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKI 126 (238)
T ss_pred EEeCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 133332211 1110 0011248999999999999999999987553
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=99.30 E-value=1.7e-11 Score=109.68 Aligned_cols=106 Identities=12% Similarity=0.135 Sum_probs=80.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhh-----hCccCCCcccc-------------------C-
Q 011992 330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEK-----FKPQAGCRFAN-------------------T- 384 (473)
Q Consensus 330 ~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiek-----FDp~kg~~FsT-------------------~- 384 (473)
|+.||..|.+.++++|+++... ++ +||.++.+|..+.+ |++. ..|.+ .
T Consensus 1 f~~~~~~y~~~l~~~~~~~~~~----~~-~qdvf~~~w~~~~~~~~~~~~~~--~~~~~wL~~iarN~~id~~Rk~~~~~ 73 (142)
T TIGR03209 1 FEEIYMNFKNTIDIFTRKYNLY----YD-YNDILYHLWIILKKIDLNKFNTE--NDLEKYISTSLKRYCLDICNKKNRDK 73 (142)
T ss_pred ChHHHHHHHHHHHHHHHHhcch----hh-HHHHHHHHHHHHHHhhhhhcCch--hHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 4679999999999999998652 23 49999999998865 4332 24544 0
Q ss_pred CC----------CCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHH
Q 011992 385 GV----------EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVR 446 (473)
Q Consensus 385 ~~----------~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVr 446 (473)
.. ..+.+.+...+....+.++|+.||+++|+||.|+|+ +|+|++|||++||+|.++|+
T Consensus 74 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~----~~~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 74 KIIYNSEITDIKLSLINVYSSNDLEFEFNDLISILPNKQKKIIYMKFF----EDMKEIDIAKKLHISRQSVY 141 (142)
T ss_pred hhhhhhhhhccccchhHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHhhc
Confidence 00 011223334445567899999999999999999999 99999999999999999996
No 126
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=99.30 E-value=2.4e-11 Score=120.56 Aligned_cols=115 Identities=23% Similarity=0.344 Sum_probs=85.3
Q ss_pred chHHHHHHHHHHHHHHHHHHHhhc---CCcchhhHhhhhHHHHHHHhhhhCccCCCccccCCCCCchHHHHHHHHHHHHH
Q 011992 327 NSSREKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQHVR 403 (473)
Q Consensus 327 ~~A~e~Li~~yl~lV~sIA~ry~~---~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~~~~~pee~le~~el~e~L~ 403 (473)
..|++.||..|+++|+++|++|.+ .+++++||+|+|++|||+++++|||++|++|.|+...+....+. ..++
T Consensus 22 ~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i~-----~~lr 96 (257)
T PRK05911 22 IEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAII-----DDLR 96 (257)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHH-----HHHH
Confidence 389999999999999999999852 35679999999999999999999999999999865544333222 2222
Q ss_pred HHHhhCCHHHHH----H------HHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 404 NLLTLLNPKERC----I------VRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 404 ~aL~~LperER~----V------L~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
+. ..+|..-+. + +.-.++ ..+|..|||+.||++.+.|..+...
T Consensus 97 ~~-~~~pr~~~~~~~~l~~~~~~l~~~~g----r~pt~~eiA~~l~i~~~~v~~~~~~ 149 (257)
T PRK05911 97 KQ-DWVPRSVHQKANKLADAMDSLRQSLG----KEPTDGELCEYLNISQQELSGWFSS 149 (257)
T ss_pred hc-CCCCHHHHHHHHHHHHHHHHHHHHHC----cCCCHHHHHHHhCcCHHHHHHHHHH
Confidence 11 123332211 1 222344 8899999999999999999887654
No 127
>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=99.24 E-value=2.2e-11 Score=91.38 Aligned_cols=50 Identities=36% Similarity=0.628 Sum_probs=46.5
Q ss_pred HHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 405 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 405 aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
||+.||++|+.||.++|+ +++|+.|||+.||+|.++|++++.+|++|||+
T Consensus 1 Al~~L~~~er~vi~~~y~----~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 1 ALDQLPPREREVIRLRYF----EGLTLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp HHCTS-HHHHHHHHHHHT----ST-SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred ChhhCCHHHHHHHHHHhc----CCCCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 688999999999999999 99999999999999999999999999999995
No 128
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=99.21 E-value=5.8e-11 Score=117.51 Aligned_cols=129 Identities=25% Similarity=0.408 Sum_probs=89.3
Q ss_pred HHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCc-chhhHhhhhHHHHHHHhhhhCccCCCccccCCCCCchHHHHHH
Q 011992 319 LKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGI-SLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQ 396 (473)
Q Consensus 319 L~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~-saEDLiQEg~lgL~kAiekFDp~kg~~FsT~~~~~pee~le~~ 396 (473)
+......|+ .++ .||.+|+|+|.++|++|.+.+. ..|||+|-|++||++|+++||+.+|.+|+|+........+.+.
T Consensus 14 ~~~~~~~g~~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d~ 92 (247)
T COG1191 14 LLEYYAEGDEEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILDY 92 (247)
T ss_pred HHHHHHhcCHHHH-HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHHH
Confidence 444444555 777 9999999999999999987766 9999999999999999999999999999996543322222111
Q ss_pred HHHH---HHHHHHhhCCHHHH---HHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992 397 LMRQ---HVRNLLTLLNPKER---CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 452 (473)
Q Consensus 397 el~e---~L~~aL~~LperER---~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA 452 (473)
.... ++-.-+..+..+-. .-+...++ .+.|..|||+.|||+..-|.+.+...
T Consensus 93 LR~~~~v~vpR~~~~~~~~i~~~~~~l~~el~----r~pt~~EIA~~L~i~~ee~~~~~~~~ 150 (247)
T COG1191 93 LRKNDSVKVPRSLRELGRRIEEAIDELEQELG----REPTDEEIAEELGIDKEEYIEALLAI 150 (247)
T ss_pred HHhCCCccCcHHHHHHHHHHHHHHHHHHHHhC----CCCcHHHHHHHhCCCHHHHHHHHHHh
Confidence 1110 11111111111111 12334555 99999999999999999888765443
No 129
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=99.10 E-value=1.9e-09 Score=101.81 Aligned_cols=140 Identities=22% Similarity=0.302 Sum_probs=94.7
Q ss_pred HHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcC---Ccchhh--HhhhhHHHHHHHhhhhCccCCCcccc-------
Q 011992 317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGR---GISLHD--LLQEGSMGLMKSVEKFKPQAGCRFAN------- 383 (473)
Q Consensus 317 eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~---~~saED--LiQEg~lgL~kAiekFDp~kg~~FsT------- 383 (473)
.++...++.|+ .|++.|+..|++.+..+|++++.. ..+.+| +++|+|+.++......+......|..
T Consensus 5 t~ll~~~~~GD~~A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~~lv~ea~lrl~~~~~~~~~~~~~~f~~~~~~~~r 84 (185)
T PF07638_consen 5 TELLDRWRQGDEAALDQLFERYYPELRRLARRRLRRERRGHDLQDTALVHEAFLRLARRGRFVQFSDRRHFWALLARIMR 84 (185)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHhccccCCchhHHHHHHHHHHHHhccccccCCCCHHHHHHHHHHHHH
Confidence 34555566666 999999999999999999887643 234554 46777777665222111111111221
Q ss_pred ---------------C------C---C--C-CchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHH
Q 011992 384 ---------------T------G---V--E-IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGN 436 (473)
Q Consensus 384 ---------------~------~---~--~-~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe 436 (473)
. . . . .........++.+.+..... |+|+++++|.++|+ +|+|.+|||+
T Consensus 85 r~lid~~R~~~a~KRg~~~~~~~l~~~~~~~~~~~~~~~~~l~e~l~~L~~-l~~~~~~~v~l~~~----~Gls~~EIA~ 159 (185)
T PF07638_consen 85 RKLIDHARRRQAQKRGGDQVRVELDERADSGDEPSPEELLELEEALERLLA-LDPRQRRVVELRFF----EGLSVEEIAE 159 (185)
T ss_pred HHHHHHHHHHHHHhcCCCCcccchhhhhccccCCCHHHHHHHHHHHHHHHc-cCHHHHHHHHHHHH----CCCCHHHHHH
Confidence 0 0 0 0 00111122234444554444 99999999999999 9999999999
Q ss_pred HHCCCHHHHHHHHHHHHHHHHHHhc
Q 011992 437 IFGLSKERVRQLESRALYRLKQSLG 461 (473)
Q Consensus 437 ~LGIS~~rVrqi~~RAL~KLR~~L~ 461 (473)
.||||+.+|+..+..|..+|+..|.
T Consensus 160 ~lgiS~~tV~r~l~~aR~~l~~~l~ 184 (185)
T PF07638_consen 160 RLGISERTVRRRLRRARAWLRRELR 184 (185)
T ss_pred HHCcCHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999999998875
No 130
>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=99.10 E-value=3.5e-10 Score=109.33 Aligned_cols=114 Identities=25% Similarity=0.421 Sum_probs=79.5
Q ss_pred HHHHHHHHHHHHHHHhhc---CCcchhhHhhhhHHHHHHHhhhhCccCCCccccCCCCCchHHHHHHHHHH-----HHHH
Q 011992 333 LINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQ-----HVRN 404 (473)
Q Consensus 333 Li~~yl~lV~sIA~ry~~---~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~~~~~pee~le~~el~e-----~L~~ 404 (473)
|+..|.++|+++|++|.+ ++.+++|++|||++|+|+++++||+.+|.+|+|+........+.....+. .+.+
T Consensus 1 L~~~~~~lv~~~a~~~~~~~~~~~~~eDl~Qe~~~~l~~a~~~fd~~~~~~f~t~~~~~i~~~~~~~lr~~~~~p~~~~~ 80 (224)
T TIGR02479 1 LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLDWVPRSLRQ 80 (224)
T ss_pred CHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHHcCccCHHHHH
Confidence 578999999999999986 78999999999999999999999999999998854433222221111100 1111
Q ss_pred HHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 405 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 405 aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.+..|....+. +.-.++ ...+.+|||+.||++...|+++...
T Consensus 81 ~~~~l~~~~~~-l~~~~~----~~~~~~ela~~l~~~~~~v~~~~~~ 122 (224)
T TIGR02479 81 KARKLERAIRE-LEARLG----REPTEEEIAEELGMDLKEYRQALNE 122 (224)
T ss_pred HHHHHHHHHHH-HHHHHC----cCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 11122111111 222344 7889999999999999999998753
No 131
>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=99.00 E-value=1.2e-09 Score=83.00 Aligned_cols=54 Identities=30% Similarity=0.440 Sum_probs=46.6
Q ss_pred HHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 011992 399 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 456 (473)
Q Consensus 399 ~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KL 456 (473)
++.|.++|..||+++|.||.++|+ +|+|++|||+.+|+|.++|++.+.+|+++|
T Consensus 1 r~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIa~~l~~s~~~v~~~l~ra~~~L 54 (54)
T PF08281_consen 1 REALQQALAQLPERQREIFLLRYF----QGMSYAEIAEILGISESTVKRRLRRARKKL 54 (54)
T ss_dssp HHHHHHHHHCS-HHHHHHHHHHHT----S---HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHH----HCcCHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence 367899999999999999999999 999999999999999999999999999987
No 132
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=98.94 E-value=4.4e-09 Score=102.94 Aligned_cols=116 Identities=22% Similarity=0.264 Sum_probs=77.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhhc---CCcchhhHhhhhHHHHHHHhhhhCccCCCccccCCCCCchHHHHHHHHH-----H
Q 011992 329 SREKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMR-----Q 400 (473)
Q Consensus 329 A~e~Li~~yl~lV~sIA~ry~~---~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~~~~~pee~le~~el~-----e 400 (473)
....|+..|.++|.++|++|.. .+.+++||+|||++|||+++++||+..+ .|+|+........+...... .
T Consensus 16 ~~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~il~~lr~~~~~~r 94 (231)
T PRK12427 16 EEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELRELDWRPR 94 (231)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHHHHhcCCCCH
Confidence 3457899999999999999874 4679999999999999999999997555 78875444322222111000 0
Q ss_pred HHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011992 401 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 450 (473)
Q Consensus 401 ~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~ 450 (473)
.+...+..+. +-..-+.-.++ ...|..|||+.||++.+.|.++..
T Consensus 95 ~vr~~~~~i~-~~~~~l~~~~g----~~pt~~eiA~~lg~~~~~v~~~~~ 139 (231)
T PRK12427 95 RLRQKTHKTN-DAIREIAKRLG----HEPNFEEISAELNLTAEEYQEYLL 139 (231)
T ss_pred HHHHHHHHHH-HHHHHHHHHHC----CCCCHHHHHHHhCCCHHHHHHHHH
Confidence 0111111111 11112222334 889999999999999999988764
No 133
>PRK06930 positive control sigma-like factor; Validated
Probab=98.88 E-value=7.8e-08 Score=90.43 Aligned_cols=71 Identities=18% Similarity=0.285 Sum_probs=63.8
Q ss_pred chHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccC
Q 011992 389 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 463 (473)
Q Consensus 389 pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~ 463 (473)
+.......+....|..+|..||+++|.||.|+|+ +|+|++|||+.||+|.++|++++.||+++|+..+...
T Consensus 95 ~~~~~~~~e~~~~l~~al~~L~~rer~V~~L~~~----eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~~ 165 (170)
T PRK06930 95 EPESVISEWDKIRIEDALSVLTEREKEVYLMHRG----YGLSYSEIADYLNIKKSTVQSMIERAEKKIARQINES 165 (170)
T ss_pred ChhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence 4444555667788999999999999999999998 9999999999999999999999999999999988754
No 134
>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=98.74 E-value=3.5e-08 Score=96.28 Aligned_cols=60 Identities=23% Similarity=0.406 Sum_probs=54.3
Q ss_pred hhcchHHHHHHHHHHHHHHHHHHHhhcCC--cchhhHhhhhHHHHHHHhhhhCccCCCcccc
Q 011992 324 HSGNSSREKLINANLRLVVHVAKQYQGRG--ISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN 383 (473)
Q Consensus 324 ~~g~~A~e~Li~~yl~lV~sIA~ry~~~~--~saEDLiQEg~lgL~kAiekFDp~kg~~FsT 383 (473)
+.|+..+++||..|.++|.++|.++.++. .+.||++|+|++|+|+|+++||+++|..|.+
T Consensus 5 ~~gd~~~e~LI~~Y~plI~~~a~~~~~~~~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~s 66 (218)
T TIGR02895 5 QPGNEEREELIRQYKPFIAKIVSSVCGRYIDTKSDDELSIGLIAFNEAIESYDSNKGKSFLS 66 (218)
T ss_pred hcCChHHHHHHHHhHHHHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHH
Confidence 45665599999999999999999998764 5799999999999999999999999999988
No 135
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=98.74 E-value=3.8e-09 Score=108.54 Aligned_cols=80 Identities=20% Similarity=0.173 Sum_probs=67.5
Q ss_pred hccCCCCCCcccccccccccccccccccCCCChhHHhhh---cccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 011992 223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFL---WGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQF 299 (473)
Q Consensus 223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~---~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~l 299 (473)
.+..+.+|++|+|||.|||+ |+|.++ ++... |.|++. .+.+.++.++..+|.+.+
T Consensus 129 ~~fdp~~G~rFsTYA~~wIr-----~aI~~~---i~~~~r~vrlP~~~--------------~~~~~~l~~~~~~l~~~l 186 (324)
T PRK07921 129 EKFDYTKGFKFSTYATWWIR-----QAITRG---MADQSRTIRLPVHL--------------VEQVNKLARIKRELHQQL 186 (324)
T ss_pred HHcCCccCCCHHHHHHHHHH-----HHHHHH---HHHcCCCccCCHHH--------------HHHHHHHHHHHHHHHHHh
Confidence 46688999999999999999 999985 66544 455544 466778999999999999
Q ss_pred CCCCCHHHHHHHcCCCHHHHHHHHh
Q 011992 300 GREPTLIEWAKAIGLSCRDLKSELH 324 (473)
Q Consensus 300 GRePT~eEiA~~lGms~eeL~~~l~ 324 (473)
||+||.+|||+.+|++.+++...+.
T Consensus 187 gr~pt~~EiA~~lgi~~~~v~~~~~ 211 (324)
T PRK07921 187 GREATDEELAEESGIPEEKIADLLE 211 (324)
T ss_pred CCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 9999999999999999999887653
No 136
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=98.68 E-value=8.9e-09 Score=111.34 Aligned_cols=79 Identities=19% Similarity=0.205 Sum_probs=66.0
Q ss_pred ccCCCCCCcccccccccccccccccccCCCChhHHhhh---cccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Q 011992 224 KVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFL---WGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFG 300 (473)
Q Consensus 224 ~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~---~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lG 300 (473)
|+.+.+|++|+|||.|||| |+|.++ ++... |.|++. .+.+.+|.+++.+|.+.+|
T Consensus 315 kFDp~rG~rFSTYA~wWIR-----qaI~ra---I~d~~r~IRvP~~~--------------~e~i~kl~~~~~~L~~~lg 372 (509)
T PRK05901 315 KFDYTKGYKFSTYATWWIR-----QAITRA---MADQARTIRIPVHM--------------VETINKLGRIERELLQELG 372 (509)
T ss_pred HhCcccCCCchhhhHHHHH-----HHHHHH---HHHcCCceecCHHH--------------HHHHHHHHHHHHHHHHHhC
Confidence 5688999999999999999 999874 44433 455544 4567788899999999999
Q ss_pred CCCCHHHHHHHcCCCHHHHHHHHh
Q 011992 301 REPTLIEWAKAIGLSCRDLKSELH 324 (473)
Q Consensus 301 RePT~eEiA~~lGms~eeL~~~l~ 324 (473)
|+||.+|||+.||++.+.+..++.
T Consensus 373 r~PT~eELAe~Lgis~e~V~~~~~ 396 (509)
T PRK05901 373 REPTPEELAKEMGFTPEKVREIQK 396 (509)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Confidence 999999999999999999887654
No 137
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=98.60 E-value=2.4e-07 Score=91.42 Aligned_cols=69 Identities=23% Similarity=0.406 Sum_probs=59.1
Q ss_pred CHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCc--chhhHhhhhHHHHHHHhhhhCccCCCcccc
Q 011992 315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGI--SLHDLLQEGSMGLMKSVEKFKPQAGCRFAN 383 (473)
Q Consensus 315 s~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~--saEDLiQEg~lgL~kAiekFDp~kg~~FsT 383 (473)
+.+++...+..|+ .|++.|+..|.++|+++|.++.++.. .++|++|++++++|+++++|++.+|..|.+
T Consensus 4 ~~~~Li~~~~~gD~~AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~a 75 (237)
T PRK08311 4 SLEDILEKIKNGDEELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLS 75 (237)
T ss_pred cHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHH
Confidence 3445555556565 89999999999999999999988775 589999999999999999999988877877
No 138
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=98.56 E-value=2.4e-08 Score=104.51 Aligned_cols=80 Identities=19% Similarity=0.192 Sum_probs=66.9
Q ss_pred hccCCCCCCcccccccccccccccccccCCCChhHHhhhc---ccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 011992 223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLW---GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQF 299 (473)
Q Consensus 223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~---~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~l 299 (473)
.+..+.+|.+|+|||.|||+ |+|.++ ++...| .|++. .+.+.++.++...|.+.+
T Consensus 179 ~kFd~~kg~~FsTYA~wWIR-----qaI~~~---I~~~~r~IRlP~~~--------------~~~~~~i~~a~~~l~~~l 236 (373)
T PRK07406 179 EKFDHEKGYKFSTYATWWIR-----QAITRA---IADQSRTIRLPVHL--------------YETISRIKKTTKVLSQEF 236 (373)
T ss_pred HhcCCccCCCHHHHHHHHHH-----HHHHHH---HHhcCCceeCCHHH--------------HHHHHHHHHHHHHHHHHh
Confidence 35688899999999999999 999885 655444 55544 466778999999999999
Q ss_pred CCCCCHHHHHHHcCCCHHHHHHHHh
Q 011992 300 GREPTLIEWAKAIGLSCRDLKSELH 324 (473)
Q Consensus 300 GRePT~eEiA~~lGms~eeL~~~l~ 324 (473)
||+||.+|||+.+|++.+++.....
T Consensus 237 gr~Pt~~EIA~~lg~~~e~v~~~~~ 261 (373)
T PRK07406 237 GRKPTEEEIAESMEMTIEKLRFIAK 261 (373)
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 9999999999999999999876543
No 139
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=98.56 E-value=2.9e-08 Score=102.27 Aligned_cols=82 Identities=21% Similarity=0.218 Sum_probs=63.4
Q ss_pred ccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCC
Q 011992 224 KVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREP 303 (473)
Q Consensus 224 ~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGReP 303 (473)
|+++.+|++|+|||+|||+ ++|.++...--++.+.|-+. ++.+.+|.+++.+|.+.+|++|
T Consensus 146 kFdp~rG~kFsTYA~wWIr-----qaI~raI~~q~rtIRipvh~--------------~e~~nkl~r~~r~l~q~~~r~p 206 (342)
T COG0568 146 KFDPEKGFKFSTYATWWIR-----QAITRAIADQARTIRIPVHQ--------------VELINKLRRVKRELLQELGREP 206 (342)
T ss_pred hcCcccCCcchhHHHHHHH-----HHHHHHHHHhcchhhHhHHH--------------HHHHHHHHHHHHHHHHHhcCCC
Confidence 5689999999999999999 77776411122233333322 5567778889999999999999
Q ss_pred CHHHHHHHcCCCHHHHHHHHh
Q 011992 304 TLIEWAKAIGLSCRDLKSELH 324 (473)
Q Consensus 304 T~eEiA~~lGms~eeL~~~l~ 324 (473)
+.+|||+.+|++.+++.....
T Consensus 207 ~~eeia~~l~~~~~~V~~m~~ 227 (342)
T COG0568 207 TPEEIAEELGVSPDKVREMLK 227 (342)
T ss_pred CHHHHHHHhCCCHHHHHHHHH
Confidence 999999999999988877654
No 140
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=98.55 E-value=2.5e-08 Score=110.54 Aligned_cols=79 Identities=19% Similarity=0.212 Sum_probs=67.4
Q ss_pred ccCCCCCCcccccccccccccccccccCCCChhHHhhhc---ccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Q 011992 224 KVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLW---GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFG 300 (473)
Q Consensus 224 ~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~---~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lG 300 (473)
|+.+.+|++|+|||.|||+ |+|.++ ++...| .|++. ++...++.++...|.+.+|
T Consensus 424 kfd~~~G~~FstYA~~wIr-----~aI~~~---i~~~~r~irip~~~--------------~~~~~k~~~~~~~~~~~~g 481 (619)
T PRK05658 424 KFEYRRGYKFSTYATWWIR-----QAITRS---IADQARTIRIPVHM--------------IETINKLNRISRQMLQEIG 481 (619)
T ss_pred hcCccCCCchHHHhHHHHH-----HHHHHH---HHHcCCceecCHHH--------------HHHHHHHHHHHHHHHHHhC
Confidence 4688999999999999999 999984 766555 45444 4567788999999999999
Q ss_pred CCCCHHHHHHHcCCCHHHHHHHHh
Q 011992 301 REPTLIEWAKAIGLSCRDLKSELH 324 (473)
Q Consensus 301 RePT~eEiA~~lGms~eeL~~~l~ 324 (473)
|+||.+|||+.||++.+++...+.
T Consensus 482 r~pt~~eiA~~l~~~~~~v~~~~~ 505 (619)
T PRK05658 482 REPTPEELAERLGMPEDKVRKVLK 505 (619)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Confidence 999999999999999999887654
No 141
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=98.54 E-value=5e-08 Score=96.78 Aligned_cols=79 Identities=18% Similarity=0.138 Sum_probs=68.2
Q ss_pred hccCCCCCCcccccccccccccccccccCCCChhHHhhhc---ccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 011992 223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLW---GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQF 299 (473)
Q Consensus 223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~---~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~l 299 (473)
.+..+.+|.+|+||+++||+ |+|+|+ +|...| .|++. .+...+++++..+|.+.+
T Consensus 69 ~~fd~~~g~~F~tya~~~Ir-----~~i~~~---lr~~~~~vr~pr~~--------------~~~~~~~~~~~~~l~~~l 126 (256)
T PRK07408 69 ERFDPSKGHAFSSFAIPYIR-----GEIQHY---LRDKSPTVRIPRRW--------------QELQRQAKKVRQELRQEL 126 (256)
T ss_pred HhcCCCCCCCcHHHHHHHHH-----HHHHHH---HHHcCCeeeeCHHH--------------HHHHHHHHHHHHHHHHHh
Confidence 35688999999999999999 999994 887555 56555 466778999999999999
Q ss_pred CCCCCHHHHHHHcCCCHHHHHHHH
Q 011992 300 GREPTLIEWAKAIGLSCRDLKSEL 323 (473)
Q Consensus 300 GRePT~eEiA~~lGms~eeL~~~l 323 (473)
||+||.+|||+.+|++.+++....
T Consensus 127 gr~pt~~elA~~lgi~~~~v~~~~ 150 (256)
T PRK07408 127 GRQPTDQEIAQALDISLEEWQEIK 150 (256)
T ss_pred CCCCCHHHHHHHcCCCHHHHHHHH
Confidence 999999999999999999987754
No 142
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=98.52 E-value=4.1e-08 Score=102.49 Aligned_cols=81 Identities=17% Similarity=0.169 Sum_probs=66.7
Q ss_pred hccCCCCCCcccccccccccccccccccCCCChhHHhhh---cccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 011992 223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFL---WGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQF 299 (473)
Q Consensus 223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~---~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~l 299 (473)
.+..+.+|.+|+|||.|||+ |+|.++ ++... |.|++. ...+.++.++..+|.+.+
T Consensus 172 ~~fd~~~g~~FsTyA~~wIr-----~aI~~~---i~~~~r~irip~~~--------------~~~~~~~~~~~~~l~~~l 229 (367)
T PRK09210 172 EKFDYRKGFKFSTYATWWIR-----QAITRA---IADQARTIRIPVHM--------------VETINKLIRVQRQLLQEL 229 (367)
T ss_pred HhcCCCCCCchHHHHHHHHH-----HHHHHH---HHHcCCceeccHHH--------------HHHHHHHHHHHHHHHHHh
Confidence 35678899999999999999 998874 54444 445444 456778899999999999
Q ss_pred CCCCCHHHHHHHcCCCHHHHHHHHhh
Q 011992 300 GREPTLIEWAKAIGLSCRDLKSELHS 325 (473)
Q Consensus 300 GRePT~eEiA~~lGms~eeL~~~l~~ 325 (473)
||+||.+|||+.||++.+++..++..
T Consensus 230 gr~pt~~EiA~~l~~~~~~v~~~~~~ 255 (367)
T PRK09210 230 GREPTPEEIAEEMDMPPEKVREILKI 255 (367)
T ss_pred CCCCCHHHHHHHhCcCHHHHHHHHHH
Confidence 99999999999999999998876543
No 143
>PRK00118 putative DNA-binding protein; Validated
Probab=98.51 E-value=5e-07 Score=78.65 Aligned_cols=64 Identities=22% Similarity=0.155 Sum_probs=57.1
Q ss_pred HHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCch
Q 011992 398 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 465 (473)
Q Consensus 398 l~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~l 465 (473)
+...+.-+...||++++.|+.++|+ +++|++|||+.+|+|+++|+.++.+|+++||+++..-++
T Consensus 7 ~~~l~d~~~~~L~ekqRevl~L~y~----eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~~ 70 (104)
T PRK00118 7 MNLLFDFYGSLLTEKQRNYMELYYL----DDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHL 70 (104)
T ss_pred HHHHHHHHhccCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHCh
Confidence 3445566778999999999999999 999999999999999999999999999999999876543
No 144
>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=98.42 E-value=8.7e-07 Score=64.80 Aligned_cols=54 Identities=37% Similarity=0.589 Sum_probs=50.1
Q ss_pred HHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992 400 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457 (473)
Q Consensus 400 e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR 457 (473)
..+..++..|++.++.++.++|. ++++..+||+.+|+|.++|+.++.++..+||
T Consensus 2 ~~~~~~~~~l~~~~~~~~~~~~~----~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 2 ERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 35788899999999999999998 8999999999999999999999999988874
No 145
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=98.40 E-value=1.1e-07 Score=100.58 Aligned_cols=84 Identities=15% Similarity=0.154 Sum_probs=67.2
Q ss_pred hccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Q 011992 223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGRE 302 (473)
Q Consensus 223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRe 302 (473)
.|+.+.+|.+|+||++|||| |+|.+......+.++.|.+. ...+.+|.+++..|.+.+||.
T Consensus 218 ekFDp~rG~rFSTYa~wwIR-----qaI~r~i~~~srtIrlP~~i--------------~e~l~~lrk~~r~L~~~lgR~ 278 (415)
T PRK07598 218 EKFDPTKGYRFSTYAYWWIR-----QGITRAIATQSRTIRLPVHI--------------TEKLNKIKKAQRKISQEKGRT 278 (415)
T ss_pred HHcCcccCCCHHHHHHHHHH-----HHHHHHHHHcCCceehhHHH--------------HHHHHHHHHHHHHHHHHhCCC
Confidence 46788999999999999999 99887411122234455555 355778889999999999999
Q ss_pred CCHHHHHHHcCCCHHHHHHHHhh
Q 011992 303 PTLIEWAKAIGLSCRDLKSELHS 325 (473)
Q Consensus 303 PT~eEiA~~lGms~eeL~~~l~~ 325 (473)
||.+|||+.+||+.+.+..++..
T Consensus 279 pt~~EiA~~l~is~~~vr~~l~~ 301 (415)
T PRK07598 279 PTIEDIAQELEMTPTQVREVLLR 301 (415)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Confidence 99999999999999999887653
No 146
>PRK05949 RNA polymerase sigma factor; Validated
Probab=98.40 E-value=1.5e-07 Score=96.93 Aligned_cols=84 Identities=18% Similarity=0.141 Sum_probs=65.8
Q ss_pred hhccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Q 011992 222 KRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGR 301 (473)
Q Consensus 222 ~~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGR 301 (473)
..+..+.+|.+|+|||.|||| ++|.++.....+.++.|.+. .+.+.++.++...+...+||
T Consensus 133 ~~kfd~~~G~rFsTYa~wwIr-----q~I~r~i~~~~r~iRlP~~~--------------~~~~~~l~k~~~~l~~~lgr 193 (327)
T PRK05949 133 VEKFDPTRGYKFSTYAYWWIR-----QAITRAIAQQARTIRLPIHI--------------TEKLNKIKKTQRELSQKLGR 193 (327)
T ss_pred HHhcCCcCCCChhhhhHHHHH-----HHHHHHHHHcCCceeCCHHH--------------HHHHHHHHHHHHHHHHHhCC
Confidence 345688999999999999999 99887422223334455444 35566788888899999999
Q ss_pred CCCHHHHHHHcCCCHHHHHHHHh
Q 011992 302 EPTLIEWAKAIGLSCRDLKSELH 324 (473)
Q Consensus 302 ePT~eEiA~~lGms~eeL~~~l~ 324 (473)
+||.+|+|+.+|++.+++...+.
T Consensus 194 ~pt~~eiA~~l~i~~~~v~~~~~ 216 (327)
T PRK05949 194 SATPAEIAKELELEPSQIREYLS 216 (327)
T ss_pred CCCHHHHHHHhCcCHHHHHHHHH
Confidence 99999999999999999887653
No 147
>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=98.26 E-value=1.1e-06 Score=68.88 Aligned_cols=50 Identities=26% Similarity=0.490 Sum_probs=45.7
Q ss_pred HHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccc
Q 011992 333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFA 382 (473)
Q Consensus 333 Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~Fs 382 (473)
||+.|.++|++++.++.++..+++|++||+++++|+++++|++..+..|.
T Consensus 1 L~~~~~~~l~~~~~~~~~~~~~~eD~~qe~~~~l~~~~~~~~~~~~~~~~ 50 (71)
T PF04542_consen 1 LYERYYPLLYRYARRYTGDPEDAEDLVQEAFIKLWRAIDSYDPDRGDSFR 50 (71)
T ss_dssp HHHHTHHHHHHHHHTCTTCSSHHHHHHHHHHHHHHHHHHHTSTTSSSHHH
T ss_pred CHHHHHHHHHHHHHHHhCCHhhHHHHhhHHHHHHHhhhhcccccccCCHH
Confidence 68899999999999999999999999999999999999999987764444
No 148
>PRK04217 hypothetical protein; Provisional
Probab=98.19 E-value=3.8e-06 Score=73.88 Aligned_cols=55 Identities=20% Similarity=0.136 Sum_probs=51.0
Q ss_pred hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCch
Q 011992 407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 465 (473)
Q Consensus 407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~l 465 (473)
..|++.+++++.++|+ +++|++|||+.||||.++|++++.+|+++|++.+.....
T Consensus 41 ~~Lt~eereai~l~~~----eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~~~ 95 (110)
T PRK04217 41 IFMTYEEFEALRLVDY----EGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGRE 95 (110)
T ss_pred ccCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhccc
Confidence 4699999999999998 999999999999999999999999999999999876543
No 149
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=98.17 E-value=8.1e-07 Score=91.10 Aligned_cols=83 Identities=18% Similarity=0.169 Sum_probs=65.4
Q ss_pred hccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Q 011992 223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGRE 302 (473)
Q Consensus 223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRe 302 (473)
.+..+.+|.+|.||+.|||| ++|.++.....+.++.|.+. .+.+.++.++...+...+|++
T Consensus 124 ~~fd~~~g~rf~tYa~~wIR-----~~I~~~i~~~~~~ir~p~~~--------------~~~~~~l~~~~~~l~~~~gr~ 184 (317)
T PRK07405 124 EKFDPTKGYRFSTYAYWWIR-----QAITRAIAEKSRTIRLPIHI--------------TEKLNKIKKAQRQLSQQLGRA 184 (317)
T ss_pred HHhCcCCCCChHHHHHHHHH-----HHHHHHHHhcCCCccCChHH--------------HHHHHHHHHHHHHHHHHhCCC
Confidence 35677789999999999999 99877422222344455544 456678888999999999999
Q ss_pred CCHHHHHHHcCCCHHHHHHHHh
Q 011992 303 PTLIEWAKAIGLSCRDLKSELH 324 (473)
Q Consensus 303 PT~eEiA~~lGms~eeL~~~l~ 324 (473)
||.+|||+.+|++.+.+...+.
T Consensus 185 pt~~eiA~~~~~~~~~v~~~~~ 206 (317)
T PRK07405 185 ATIGELAEELELTPKQVREYLE 206 (317)
T ss_pred CCHHHHHHHhCcCHHHHHHHHH
Confidence 9999999999999998887754
No 150
>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=98.14 E-value=9.7e-07 Score=89.47 Aligned_cols=83 Identities=18% Similarity=0.165 Sum_probs=64.1
Q ss_pred hccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Q 011992 223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGRE 302 (473)
Q Consensus 223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRe 302 (473)
.+..+.+|.+|+||+.|||+ ++|.++...-.+..+.|.+. .+.+.++.++...+.+.+|++
T Consensus 117 ~kfd~~~g~rFsTya~~wIr-----~~I~r~i~~~~r~vr~p~~~--------------~~~~~~~rk~~~~l~~~~~~~ 177 (298)
T TIGR02997 117 EKFDPTRGYKFSTYAYWWIR-----QGITRAIANQSRTIRLPIHI--------------TEKLNKIKKVQRELSQKLGRT 177 (298)
T ss_pred HHhCccCCCChHHHHHHHHH-----HHHHHHHHhcCCCeeCcHHH--------------HHHHHHHHHHHHHHHHHhCCC
Confidence 35678899999999999999 88876422222333444433 345667888888999999999
Q ss_pred CCHHHHHHHcCCCHHHHHHHHh
Q 011992 303 PTLIEWAKAIGLSCRDLKSELH 324 (473)
Q Consensus 303 PT~eEiA~~lGms~eeL~~~l~ 324 (473)
||.+|+|+.+|++.+++.....
T Consensus 178 pt~~eia~~l~~~~~~v~~~~~ 199 (298)
T TIGR02997 178 PSEAEIAEALELEPEQVRELLQ 199 (298)
T ss_pred CCHHHHHHHhCCCHHHHHHHHH
Confidence 9999999999999999887654
No 151
>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=98.13 E-value=1.3e-05 Score=69.48 Aligned_cols=57 Identities=26% Similarity=0.326 Sum_probs=45.0
Q ss_pred HHHHHHHhh-CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992 400 QHVRNLLTL-LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 460 (473)
Q Consensus 400 e~L~~aL~~-LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L 460 (473)
..|.+.... |+++++.++.+||. +++|+.|||+.+|||+..|...++||..+|...=
T Consensus 8 ~~L~d~Yg~LLT~kQ~~~l~lyy~----eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~yE 65 (101)
T PF04297_consen 8 NLLFDFYGELLTEKQREILELYYE----EDLSLSEIAEELGISRQAVYDSIKRAEKKLEEYE 65 (101)
T ss_dssp HHHHHHHGGGS-HHHHHHHHHHCT----S---HHHHHHHCTS-HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHCCHHHHHHHHHHHc----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 344555544 99999999999999 9999999999999999999999999999997653
No 152
>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=98.11 E-value=6.4e-06 Score=75.09 Aligned_cols=53 Identities=19% Similarity=0.256 Sum_probs=47.1
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCch
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 465 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~l 465 (473)
.|+++|++|+.|++ +|+|++|||+.||+|+++|+.++++|+++|+.......+
T Consensus 6 ~Lte~qr~VL~Lr~-----~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~a~~~~~l 58 (137)
T TIGR00721 6 FLTERQIKVLELRE-----KGLSQKEIAKELKTTRANVSAIEKRAMENIEKARNTLDF 58 (137)
T ss_pred CCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHhHHHHHHHHhhHHHH
Confidence 59999999999964 799999999999999999999999999999986544333
No 153
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=98.11 E-value=7e-06 Score=75.18 Aligned_cols=51 Identities=24% Similarity=0.399 Sum_probs=46.8
Q ss_pred hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Q 011992 407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 462 (473)
Q Consensus 407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~ 462 (473)
..|+++|++||.+++ +|+|++|||+.||+|+++|++++++|+++||+.+..
T Consensus 5 ~~Lt~rqreVL~lr~-----~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~t 55 (141)
T PRK03975 5 SFLTERQIEVLRLRE-----RGLTQQEIADILGTSRANVSSIEKRARENIEKARET 55 (141)
T ss_pred cCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 469999999999954 799999999999999999999999999999987654
No 154
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=98.05 E-value=3.1e-06 Score=85.72 Aligned_cols=87 Identities=16% Similarity=0.104 Sum_probs=60.1
Q ss_pred hhccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Q 011992 222 KRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGR 301 (473)
Q Consensus 222 ~~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGR 301 (473)
-.+..+.+|..|+|||.|||+ |+|.+ .++...|.++.- +...+..+..+ +++++.....+...+|+
T Consensus 82 ~~~fd~~~~~~f~tya~~~Ir-----~~I~~---~lr~~~~~iR~p---~~~~~~~~~~~---~~~~~~~~~~~~~~l~~ 147 (289)
T PRK07500 82 AARFEPDREVRFSTYATWWIR-----ASIQD---YILRNWSIVRGG---TSSAQKALFFN---LRRLRARLAQADEELTK 147 (289)
T ss_pred HHHcCCCCCCChHHHHHHHHH-----HHHHH---HHHHCCCceecC---ccHHHHHHHHH---HHHHHHHHHhhhcccCC
Confidence 345677889999999999999 99998 488766666532 11222222222 22333333334446899
Q ss_pred CCCHHHHHHHcCCCHHHHHHH
Q 011992 302 EPTLIEWAKAIGLSCRDLKSE 322 (473)
Q Consensus 302 ePT~eEiA~~lGms~eeL~~~ 322 (473)
+||.+|||+.+|++.+++...
T Consensus 148 ~pt~~eiA~~l~~~~~~v~~~ 168 (289)
T PRK07500 148 QEIHREIATALGVSLSDVEMM 168 (289)
T ss_pred CCCHHHHHHHhCcCHHHHHHH
Confidence 999999999999999988654
No 155
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=98.03 E-value=4.1e-06 Score=84.54 Aligned_cols=81 Identities=10% Similarity=0.054 Sum_probs=55.5
Q ss_pred hccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHh--C
Q 011992 223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQF--G 300 (473)
Q Consensus 223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~l--G 300 (473)
.+..+.+|.+|+|||.|||+ |+|.|+ +++. |...+.| ++ +..+++..+...+.+++ +
T Consensus 91 ~~fd~~~~~~FstYA~~~Ir-----~~i~~~---l~~~-~~~vr~p--~~----------~~~~~~~~~~~~~~~~l~~~ 149 (284)
T PRK06596 91 KRFDPEVGVRLVSFAVHWIK-----AEIHEY---ILRN-WRIVKVA--TT----------KAQRKLFFNLRKAKKRLGWL 149 (284)
T ss_pred HHhCcccCCCHHHHHHHHHH-----HHHHHH---HHHc-CCeeecc--ch----------HHHHHHHHHHHHHHHHhccC
Confidence 35678999999999999999 999984 7765 4222222 11 11122222333333444 4
Q ss_pred CCCCHHHHHHHcCCCHHHHHHHHh
Q 011992 301 REPTLIEWAKAIGLSCRDLKSELH 324 (473)
Q Consensus 301 RePT~eEiA~~lGms~eeL~~~l~ 324 (473)
++||.+|||+.+|++.+++.....
T Consensus 150 ~~~t~~eiA~~l~~~~~~v~~~~~ 173 (284)
T PRK06596 150 NPEEVEMVAEELGVSEEEVREMES 173 (284)
T ss_pred CCCCHHHHHHHhCcCHHHHHHHHH
Confidence 999999999999999999887643
No 156
>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=98.01 E-value=5.2e-05 Score=68.61 Aligned_cols=62 Identities=18% Similarity=0.264 Sum_probs=54.9
Q ss_pred HHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992 397 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 460 (473)
Q Consensus 397 el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L 460 (473)
...+.|..+|+.|++.+|.||.++|+ .+..+|..+||..||+|+.+|.++..+++.+|...+
T Consensus 71 ~~~~~I~~~l~~Ld~~er~II~~rY~--~~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~l 132 (134)
T TIGR01636 71 RNRDAIENCLNEADEQTRVIIQELYM--KKRPLTLVGLAQQLFISKSTAYRLRNHIIEAVAEEL 132 (134)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHc--cCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 45678999999999999999999997 112359999999999999999999999999999875
No 157
>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=97.99 E-value=5.6e-06 Score=81.92 Aligned_cols=81 Identities=20% Similarity=0.091 Sum_probs=64.9
Q ss_pred hccCCCCCCcccccccccccccccccccCCCChhHHhhhc--ccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Q 011992 223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLW--GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFG 300 (473)
Q Consensus 223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~--~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lG 300 (473)
.+..+..|..|.||+.++|+ ++++|+ +|+..+ .|++. .+...++.++..++.+++|
T Consensus 77 ~~fd~~~~~~f~tyl~~~ir-----n~~~~~---lr~~~~ir~p~~~--------------~~~~~~~~~~~~~l~~~l~ 134 (254)
T TIGR02850 77 DNFDLSQNVKFSTYAVPMII-----GEIRRY---LRDNNPIRVSRSL--------------RDIAYKALQVRDKLISENS 134 (254)
T ss_pred HhcCCCCCCChHHHHHHHHH-----HHHHHH---HHhCCCccCchHH--------------HHHHHHHHHHHHHHHHHhC
Confidence 45677788899999999999 999884 776442 33333 3445678888899999999
Q ss_pred CCCCHHHHHHHcCCCHHHHHHHHhh
Q 011992 301 REPTLIEWAKAIGLSCRDLKSELHS 325 (473)
Q Consensus 301 RePT~eEiA~~lGms~eeL~~~l~~ 325 (473)
++||.+|+|+.+|++.+++...+..
T Consensus 135 ~~pt~~elA~~l~~~~e~v~~~~~~ 159 (254)
T TIGR02850 135 KEPTVSEIAKELKVPQEEVVFALDA 159 (254)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHh
Confidence 9999999999999999998776554
No 158
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=97.98 E-value=4.6e-06 Score=83.12 Aligned_cols=80 Identities=26% Similarity=0.403 Sum_probs=68.8
Q ss_pred hccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Q 011992 223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGRE 302 (473)
Q Consensus 223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRe 302 (473)
.+..+.+|..|.||+.+||+ ++++| .+|+..|.|++. .+...++.++...|++.+|++
T Consensus 77 ~~fd~~~~~~f~ty~~~~ir-----~~i~d---~~R~~~~~p~~~--------------~~~~~~i~~~~~~l~~~~~~~ 134 (268)
T PRK06288 77 EKFDPEREIKFKTYAVTRIR-----GAIFD---ELRSIDWIPRSV--------------RQKARQIERAIAMLEARLGRT 134 (268)
T ss_pred HHcCcccCCCHHHHHHHHHH-----HHHHH---HHHhcCccCHHH--------------HHHHHHHHHHHHHHHHHHCCC
Confidence 34566777899999999999 99998 499988988877 355678889999999999999
Q ss_pred CCHHHHHHHcCCCHHHHHHHHh
Q 011992 303 PTLIEWAKAIGLSCRDLKSELH 324 (473)
Q Consensus 303 PT~eEiA~~lGms~eeL~~~l~ 324 (473)
||.+|||+.+|++.+.+...+.
T Consensus 135 pt~~eia~~lg~~~~~v~~~~~ 156 (268)
T PRK06288 135 PSDEEIADELGISLEEYNSLLS 156 (268)
T ss_pred CCHHHHHHHcCCCHHHHHHHHH
Confidence 9999999999999998877654
No 159
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=97.88 E-value=2.9e-05 Score=57.78 Aligned_cols=46 Identities=26% Similarity=0.420 Sum_probs=41.2
Q ss_pred hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992 407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457 (473)
Q Consensus 407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR 457 (473)
..|+++++.++.+. . .+++.+|||+.+|+|+++|+.++.+++.+|+
T Consensus 2 ~~l~~~e~~i~~~~-~----~g~s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 2 ASLTPREREVLRLL-A----EGLTNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCCCHHHHHHHHHH-H----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 46899999998774 4 7899999999999999999999999988875
No 160
>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=97.87 E-value=2.6e-05 Score=63.31 Aligned_cols=42 Identities=31% Similarity=0.608 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhh
Q 011992 284 DLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS 325 (473)
Q Consensus 284 ~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~ 325 (473)
++++|.+++.+|.+++||+||.+|||+.||++.+++..++..
T Consensus 2 ~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~ 43 (78)
T PF04539_consen 2 KLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQA 43 (78)
T ss_dssp HHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHh
Confidence 467899999999999999999999999999999999877653
No 161
>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=97.87 E-value=3.4e-05 Score=63.10 Aligned_cols=48 Identities=19% Similarity=0.219 Sum_probs=42.9
Q ss_pred HHHHHHHhhCCHHHHHHHHHH-hhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 400 QHVRNLLTLLNPKERCIVRLR-FGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 400 e~L~~aL~~LperER~VL~Lr-Y~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
..+.+.|+.||++++.++.|+ |. +++|++|||+.||+|+++|+.++++
T Consensus 7 ~~~~~~l~~l~~~~r~af~L~R~~----eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 7 KKLAERLTWVDSLAEAAAALAREE----AGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred hhHHHHHhcCCHHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 346778899999999999995 56 8999999999999999999999875
No 162
>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=97.78 E-value=2e-05 Score=76.45 Aligned_cols=79 Identities=24% Similarity=0.181 Sum_probs=63.7
Q ss_pred ccCCCCCCcccccccccccccccccccCCCChhHHhhh--cccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Q 011992 224 KVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFL--WGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGR 301 (473)
Q Consensus 224 ~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~--~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGR 301 (473)
+..+..|..|.||+.++|+ ++|+|+ +|... +.|++. .+...++..+...|...+|+
T Consensus 55 ~f~~~~~~~f~tyl~~~i~-----~~i~~~---lr~~~~i~~p~~~--------------~~~~~~~~~~~~~l~~~~~r 112 (231)
T TIGR02885 55 KFDLSYDVKFSTYAVPMIM-----GEIKRF---LRDDGIIKVSRSL--------------KELARKIRYMKEELSKELGR 112 (231)
T ss_pred hcCCCCCCCcHHHHHHHHH-----HHHHHH---HHhCCCeECCHHH--------------HHHHHHHHHHHHHHHHHHCc
Confidence 4456677899999999999 999984 77644 355544 34566788888999999999
Q ss_pred CCCHHHHHHHcCCCHHHHHHHHh
Q 011992 302 EPTLIEWAKAIGLSCRDLKSELH 324 (473)
Q Consensus 302 ePT~eEiA~~lGms~eeL~~~l~ 324 (473)
.||.+|+|+.+|++.+++...+.
T Consensus 113 ~pt~~ela~~l~~~~~~v~~~~~ 135 (231)
T TIGR02885 113 EPTINELAEALGVSPEEIVMALE 135 (231)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHH
Confidence 99999999999999998876654
No 163
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=97.74 E-value=2e-05 Score=78.15 Aligned_cols=79 Identities=19% Similarity=0.081 Sum_probs=63.4
Q ss_pred ccCCCCCCcccccccccccccccccccCCCChhHHhhhc--ccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Q 011992 224 KVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLW--GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGR 301 (473)
Q Consensus 224 ~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~--~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGR 301 (473)
+..+.+|..|.||+.++|+ ++++|+ +|+..+ .|++. .+...++.++..++.+++|+
T Consensus 81 ~fd~~~~~~f~t~l~~~ir-----~~i~~~---lr~~~~vrip~~~--------------~~~~~~~~~~~~~l~~~~~r 138 (258)
T PRK08215 81 NFDLSQNVKFSTYAVPMII-----GEIRRY---LRDNNPIRVSRSL--------------RDIAYKALQVREKLINENSK 138 (258)
T ss_pred hcCCCCCCCcHHHHHHHHH-----HHHHHH---HHhCCceEecHHH--------------HHHHHHHHHHHHHHHHHhCC
Confidence 4566778899999999999 999984 776542 33333 34456778888999999999
Q ss_pred CCCHHHHHHHcCCCHHHHHHHHh
Q 011992 302 EPTLIEWAKAIGLSCRDLKSELH 324 (473)
Q Consensus 302 ePT~eEiA~~lGms~eeL~~~l~ 324 (473)
+|+..|+|+.+|++.+++...+.
T Consensus 139 ~p~~~eia~~l~v~~~~v~~~~~ 161 (258)
T PRK08215 139 EPTVEEIAKELEVPREEVVFALD 161 (258)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHH
Confidence 99999999999999999877553
No 164
>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=97.72 E-value=0.00019 Score=61.87 Aligned_cols=55 Identities=22% Similarity=0.439 Sum_probs=50.0
Q ss_pred HHHHHHHHHhhCC-HHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 011992 398 MRQHVRNLLTLLN-PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 456 (473)
Q Consensus 398 l~e~L~~aL~~Lp-erER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KL 456 (473)
.+..+..+|+.|+ +.+|.||.++|. .+++..+||+.||+|+.++..++.+|++.|
T Consensus 44 ~k~ei~~~I~~l~d~~~r~iL~~~Yi----~~~~~~~I~~~l~~S~~t~yr~~~~Al~~L 99 (100)
T PF07374_consen 44 EKLEIRRAINKLEDPDERLILRMRYI----NKLTWEQIAEELNISRRTYYRIHKKALKEL 99 (100)
T ss_pred HHHHHHHHHHHccChhHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHhc
Confidence 4556888998886 789999999999 899999999999999999999999999876
No 165
>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=97.72 E-value=2.7e-05 Score=75.25 Aligned_cols=82 Identities=18% Similarity=0.235 Sum_probs=64.7
Q ss_pred ccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCC
Q 011992 224 KVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREP 303 (473)
Q Consensus 224 ~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGReP 303 (473)
+..+.+|..|.||+.++|+ ++|+| .+|+..|..+ .| -.......++..+...+.+.+|++|
T Consensus 47 ~f~~~~~~~F~ty~~~~i~-----~~~~~---~~r~~~~~~r-i~----------~~~~~~~~~~~~~~~~l~~~~~~~p 107 (227)
T TIGR02980 47 RFDPSYGVKFSTFAVPTIM-----GEIKR---FFRDDTWAVR-VP----------RRLKELGLKINKATEELTQRLGRSP 107 (227)
T ss_pred hcCcccCCCcHHHHHHHHH-----HHHHH---HHHHcCCcee-cC----------HHHHHHHHHHHHHHHHHHHHHCCCC
Confidence 4456678899999999999 99998 4888777443 22 0013445677888999999999999
Q ss_pred CHHHHHHHcCCCHHHHHHHHh
Q 011992 304 TLIEWAKAIGLSCRDLKSELH 324 (473)
Q Consensus 304 T~eEiA~~lGms~eeL~~~l~ 324 (473)
+.+|+|+.+|++.+++...+.
T Consensus 108 ~~~ela~~l~~~~~~v~~~~~ 128 (227)
T TIGR02980 108 TIAEIAEELGVSEEEVVEALE 128 (227)
T ss_pred CHHHHHHHhCCCHHHHHHHHH
Confidence 999999999999998876554
No 166
>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=97.70 E-value=9.6e-05 Score=56.99 Aligned_cols=47 Identities=23% Similarity=0.317 Sum_probs=40.8
Q ss_pred hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
..|+++|.+|+.+.. .|++.+|||+.||||..+|+....++++||.-
T Consensus 2 ~~LT~~E~~vl~~l~-----~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~ 48 (58)
T PF00196_consen 2 PSLTERELEVLRLLA-----QGMSNKEIAEELGISEKTVKSHRRRIMKKLGV 48 (58)
T ss_dssp GSS-HHHHHHHHHHH-----TTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred CccCHHHHHHHHHHH-----hcCCcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence 469999999998887 69999999999999999999999999999863
No 167
>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=97.69 E-value=4.2e-05 Score=76.49 Aligned_cols=83 Identities=17% Similarity=0.191 Sum_probs=53.3
Q ss_pred hhccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Q 011992 222 KRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGR 301 (473)
Q Consensus 222 ~~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGR 301 (473)
-.+..+.+|.+|+|||.|||+ |+|+++ ++.. |...+.| ++....++ ..++..+...+. .++
T Consensus 77 ~~~fd~~~~~~FsTYA~~~Ir-----~~i~~~---l~~~-~~~ir~p--~~~~~~~~------~~~~~~~~~~~~--~~~ 137 (270)
T TIGR02392 77 VKRFDPERGVRLVSFAVHWIK-----AEIHEY---ILRN-WRLVKVA--TTKAQRKL------FFNLRKMKKRLQ--GWL 137 (270)
T ss_pred HHHhCcccCCChHHhhHHHHH-----HHHHHH---HHHc-CCceecC--chHHHHHH------HHHHHHHHHHHh--cCC
Confidence 345678999999999999999 999984 7764 5433333 11111111 122333333332 125
Q ss_pred CC-CHHHHHHHcCCCHHHHHHHH
Q 011992 302 EP-TLIEWAKAIGLSCRDLKSEL 323 (473)
Q Consensus 302 eP-T~eEiA~~lGms~eeL~~~l 323 (473)
.| +.+|||+.+|++.+++....
T Consensus 138 ~~~~~~eiA~~l~~~~~~v~~~~ 160 (270)
T TIGR02392 138 NPEEVEAIAEELGVSEREVREME 160 (270)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHH
Confidence 56 69999999999999987753
No 168
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=97.69 E-value=2.9e-05 Score=76.62 Aligned_cols=81 Identities=21% Similarity=0.295 Sum_probs=68.8
Q ss_pred hhccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Q 011992 222 KRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGR 301 (473)
Q Consensus 222 ~~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGR 301 (473)
..+..+.+|..|.+|+.++|+ +.++|+ +|+..|.|++. .+...+++++...+.+.+|+
T Consensus 67 ~~~f~~~~~~~f~tyl~~~ir-----n~~~d~---lR~~~~~p~~~--------------~~~~~~~~~~~~~~~~~~~~ 124 (251)
T PRK07670 67 LEKFDPSRDLKFDTYASFRIR-----GAIIDG---LRKEDWLPRSM--------------REKTKKVEAAIEKLEQRYMR 124 (251)
T ss_pred HHHcCcccCCCHHHHHHHHHH-----HHHHHH---HHhcCCCCHHH--------------HHHHHHHHHHHHHHHHHHCC
Confidence 345577778899999999999 999984 88877777665 45677788888999999999
Q ss_pred CCCHHHHHHHcCCCHHHHHHHHh
Q 011992 302 EPTLIEWAKAIGLSCRDLKSELH 324 (473)
Q Consensus 302 ePT~eEiA~~lGms~eeL~~~l~ 324 (473)
+|+.+|||+.+|++.+++..++.
T Consensus 125 ~~~~~eia~~l~~~~~~v~~~~~ 147 (251)
T PRK07670 125 NVTPKEVAAELGMTEEEVEATMN 147 (251)
T ss_pred CCCHHHHHHHhCcCHHHHHHHHH
Confidence 99999999999999999887764
No 169
>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=97.68 E-value=0.00011 Score=54.86 Aligned_cols=45 Identities=29% Similarity=0.507 Sum_probs=39.8
Q ss_pred CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
|+++++.++.++ . .+++.+|||+.+|+|..+|+..+.+++++|+.
T Consensus 1 l~~~e~~i~~~~-~----~~~s~~eia~~l~~s~~tv~~~~~~~~~~l~~ 45 (57)
T cd06170 1 LTPREREVLRLL-A----EGKTNKEIADILGISEKTVKTHLRNIMRKLGV 45 (57)
T ss_pred CCHHHHHHHHHH-H----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence 689999999875 4 68999999999999999999999998877764
No 170
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=97.59 E-value=3e-05 Score=79.93 Aligned_cols=82 Identities=15% Similarity=0.087 Sum_probs=62.7
Q ss_pred ccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCC
Q 011992 224 KVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREP 303 (473)
Q Consensus 224 ~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGReP 303 (473)
+..+.+|..|+||+.|||+ ++|.++.....+..+.|++. ++++.++.++...|+..+|++|
T Consensus 130 ~fd~~rg~~Fstyatw~iR-----~ai~~~i~~~~r~ir~p~~~--------------~~~l~~~~R~~~~l~~~l~r~~ 190 (325)
T PRK05657 130 KFDPERGFRFSTYATWWIR-----QTIERAIMNQTRTIRLPVHV--------------VKELNVYLRAARELEHKLDHEP 190 (325)
T ss_pred HhCCccCCCHHHHHHHHHH-----HHHHHHHHHcCCccccCHHH--------------HHHHHHHHHHHHHHHHHhCCCC
Confidence 5567889999999999999 88876411112234455443 4555667778888999999999
Q ss_pred CHHHHHHHcCCCHHHHHHHHh
Q 011992 304 TLIEWAKAIGLSCRDLKSELH 324 (473)
Q Consensus 304 T~eEiA~~lGms~eeL~~~l~ 324 (473)
+.+|+|..+|++.+++.+.+.
T Consensus 191 t~~eiA~~l~~~~~~v~~~l~ 211 (325)
T PRK05657 191 SAEEIAELLDKPVDDVSRMLA 211 (325)
T ss_pred CHHHHHHHhCcCHHHHHHHHH
Confidence 999999999999999887764
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=97.57 E-value=0.0003 Score=54.22 Aligned_cols=48 Identities=25% Similarity=0.376 Sum_probs=42.3
Q ss_pred CCHHHHHHHHHHhhccC---CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 011992 409 LNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQLESRALYRL 456 (473)
Q Consensus 409 LperER~VL~LrY~L~~---ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KL 456 (473)
|+++|+++|..-|..+. -++-|+.|||+.||||.+++..++.+|.+||
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRrae~kl 51 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRRAERKL 51 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 78999999988775432 3788999999999999999999999999987
No 172
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=97.42 E-value=0.00027 Score=68.00 Aligned_cols=46 Identities=11% Similarity=0.237 Sum_probs=43.3
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
.|+++|++|+.+.- +|+|.+|||+.||+|+.||+...++.++||.-
T Consensus 137 ~LT~RE~eVL~lla-----~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~v 182 (207)
T PRK15411 137 SLSRTESSMLRMWM-----AGQGTIQISDQMNIKAKTVSSHKGNIKRKIKT 182 (207)
T ss_pred cCCHHHHHHHHHHH-----cCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCC
Confidence 49999999999887 79999999999999999999999999999963
No 173
>PRK05572 sporulation sigma factor SigF; Validated
Probab=97.40 E-value=0.00012 Score=72.22 Aligned_cols=78 Identities=22% Similarity=0.189 Sum_probs=63.4
Q ss_pred ccCCCCCCcccccccccccccccccccCCCChhHHhhh--cccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Q 011992 224 KVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFL--WGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGR 301 (473)
Q Consensus 224 ~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~--~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGR 301 (473)
+..+..+..|.+|+.++|+ ++|+|+ +|... |.|++. .+...+++++...+..++||
T Consensus 76 ~f~~~~~~~f~twl~~~i~-----~~i~~~---lr~~~~~r~~~~~--------------~~~~~~~~~~~~~l~~~~~r 133 (252)
T PRK05572 76 KFDLSYDVKFSTYAVPMII-----GEIQRF---LRDDGTVKVSRSL--------------KETANKIRKDKDELSKELGR 133 (252)
T ss_pred HcCCCCCCChHHHHHHHHH-----HHHHHH---HHhCCCCCCCHHH--------------HHHHHHHHHHHHHHHHHHCc
Confidence 4455566789999999999 999984 77654 566655 35667888899999999999
Q ss_pred CCCHHHHHHHcCCCHHHHHHHH
Q 011992 302 EPTLIEWAKAIGLSCRDLKSEL 323 (473)
Q Consensus 302 ePT~eEiA~~lGms~eeL~~~l 323 (473)
+|+..|+|+.+|++.+++....
T Consensus 134 ~p~~~eia~~l~~~~~~v~~~~ 155 (252)
T PRK05572 134 EPTIEELAEYLGVTPEEVVLAQ 155 (252)
T ss_pred CCCHHHHHHHhCcCHHHHHHHH
Confidence 9999999999999998876543
No 174
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=97.36 E-value=0.00036 Score=66.21 Aligned_cols=46 Identities=22% Similarity=0.291 Sum_probs=43.0
Q ss_pred hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992 407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457 (473)
Q Consensus 407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR 457 (473)
..|++||++|+.+.- +|+|.+|||+.||+|..||+.+.++.++||-
T Consensus 149 ~~Lt~rE~evl~~~~-----~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~ 194 (216)
T PRK10840 149 KRLSPKESEVLRLFA-----EGFLVTEIAKKLNRSIKTISSQKKSAMMKLG 194 (216)
T ss_pred ccCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 359999999999887 6999999999999999999999999999984
No 175
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=97.35 E-value=0.00038 Score=67.31 Aligned_cols=47 Identities=19% Similarity=0.320 Sum_probs=43.7
Q ss_pred HhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992 406 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457 (473)
Q Consensus 406 L~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR 457 (473)
+..|++||++|+.+.- +|+|.+|||+.|+||+.||+....+.++||.
T Consensus 132 ~~~LT~RE~eVL~ll~-----~G~snkeIA~~L~iS~~TV~~h~~~I~~KLg 178 (207)
T PRK11475 132 SRMLSPTEREILRFMS-----RGYSMPQIAEQLERNIKTIRAHKFNVMSKLG 178 (207)
T ss_pred cCCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 3469999999999887 6999999999999999999999999999985
No 176
>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=97.34 E-value=0.00036 Score=68.35 Aligned_cols=48 Identities=19% Similarity=0.267 Sum_probs=44.3
Q ss_pred HhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 406 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 406 L~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
...|+++|++||.+.. +|+|.+|||++||||+.+|+..+.++++||+.
T Consensus 169 ~~~Lt~re~evl~~~a-----~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~ 216 (232)
T TIGR03541 169 AGVLSEREREVLAWTA-----LGRRQADIAAILGISERTVENHLRSARRKLGV 216 (232)
T ss_pred hccCCHHHHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence 3579999999999964 79999999999999999999999999999974
No 177
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=97.34 E-value=0.00019 Score=70.04 Aligned_cols=80 Identities=28% Similarity=0.436 Sum_probs=64.3
Q ss_pred hccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Q 011992 223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGRE 302 (473)
Q Consensus 223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRe 302 (473)
.+..+..|..|.+|+.++++ +.++| .+|+..|.|+.. .+...++..+...+.+.+|++
T Consensus 54 ~~f~~~~~~~f~tyl~~~ir-----n~~~~---~lR~~~~~~~~~--------------~~~~~~~~~~~~~~~~~~~~~ 111 (236)
T PRK06986 54 RRYDGEQGASFETYAGQRIR-----GAMLD---ELRSLDWVPRSV--------------RRNAREVAQAIRQLEQELGRE 111 (236)
T ss_pred HhcCcccCCChHHHHHHHHH-----HHHHH---HHHHcCCCCHHH--------------HHHHHHHHHHHHHHHHHHCCC
Confidence 34566678899999999999 99998 488876655433 234456777888999999999
Q ss_pred CCHHHHHHHcCCCHHHHHHHHh
Q 011992 303 PTLIEWAKAIGLSCRDLKSELH 324 (473)
Q Consensus 303 PT~eEiA~~lGms~eeL~~~l~ 324 (473)
|+.+|||+.+|++.+++..++.
T Consensus 112 ~~~~ela~~l~i~~~~v~~~~~ 133 (236)
T PRK06986 112 PTDTEVAEKLGLSLEEYREMLL 133 (236)
T ss_pred CCHHHHHHHcCCCHHHHHHHHH
Confidence 9999999999999998876554
No 178
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=97.33 E-value=0.00039 Score=67.93 Aligned_cols=50 Identities=8% Similarity=-0.050 Sum_probs=46.6
Q ss_pred HHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992 403 RNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457 (473)
Q Consensus 403 ~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR 457 (473)
.+++..|+++|++|+.+.- +|+|.+|||+.|++|+.||+...++.++||.
T Consensus 138 ~~~~~~LS~RE~eVL~Lia-----~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLg 187 (217)
T PRK13719 138 LEAKNKVTKYQNDVFILYS-----FGFSHEYIAQLLNITVGSSKNKISEILKFFG 187 (217)
T ss_pred hhccCCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 5667889999999999987 6999999999999999999999999999985
No 179
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=97.33 E-value=0.00047 Score=65.44 Aligned_cols=47 Identities=23% Similarity=0.352 Sum_probs=43.6
Q ss_pred hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
..|+++|++|+.+.- +|+|.+|||+.||+|..||+....++++||.-
T Consensus 132 ~~LSpRErEVLrLLA-----qGkTnKEIAe~L~IS~rTVkth~srImkKLgV 178 (198)
T PRK15201 132 RHFSVTERHLLKLIA-----SGYHLSETAALLSLSEEQTKSLRRSIMRKLHV 178 (198)
T ss_pred CCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 359999999999887 79999999999999999999999999999864
No 180
>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=97.31 E-value=0.00043 Score=68.96 Aligned_cols=48 Identities=21% Similarity=0.261 Sum_probs=44.3
Q ss_pred HhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 406 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 406 L~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
+..|+++|++|+.+.. +|+|.+|||++||||+.||+..+.++++||.-
T Consensus 188 ~~~LT~RE~evl~l~a-----~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v 235 (247)
T TIGR03020 188 AGLITAREAEILAWVR-----DGKTNEEIAAILGISSLTVKNHLQHIFKKLDV 235 (247)
T ss_pred ccCCCHHHHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence 4579999999999865 79999999999999999999999999999864
No 181
>PRK13870 transcriptional regulator TraR; Provisional
Probab=97.30 E-value=0.00043 Score=68.14 Aligned_cols=46 Identities=26% Similarity=0.364 Sum_probs=42.9
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
.|++||++||.+.= +|+|..|||.+||||+.||..+++.|++||-.
T Consensus 173 ~LT~RE~E~L~W~A-----~GKT~~EIa~ILgISe~TV~~Hl~na~~KLga 218 (234)
T PRK13870 173 WLDPKEATYLRWIA-----VGKTMEEIADVEGVKYNSVRVKLREAMKRFDV 218 (234)
T ss_pred CCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 59999999998877 79999999999999999999999999999853
No 182
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=97.27 E-value=0.0005 Score=66.87 Aligned_cols=47 Identities=17% Similarity=0.145 Sum_probs=43.9
Q ss_pred hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
..|+++|++|+.+.+ .|+|.+|||+.|++|+.||+...+++++||.-
T Consensus 154 ~~Lt~rE~~Vl~l~~-----~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v 200 (216)
T PRK10100 154 ALLTHREKEILNKLR-----IGASNNEIARSLFISENTVKTHLYNLFKKIAV 200 (216)
T ss_pred CCCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 459999999999998 59999999999999999999999999999864
No 183
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=97.27 E-value=0.00047 Score=66.73 Aligned_cols=47 Identities=30% Similarity=0.352 Sum_probs=43.6
Q ss_pred hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
..|++||++|+.+.- +|+|.+|||+.|++|+.||+.+.++.++||.-
T Consensus 147 ~~LT~RE~eVL~lla-----~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~v 193 (211)
T COG2197 147 ELLTPRELEVLRLLA-----EGLSNKEIAEELNLSEKTVKTHVSNILRKLGV 193 (211)
T ss_pred CCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHhHHHHHHHHHHHHcCC
Confidence 469999999999877 79999999999999999999999999999853
No 184
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=97.23 E-value=0.0006 Score=67.38 Aligned_cols=46 Identities=15% Similarity=0.251 Sum_probs=43.2
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
.|+++|++||.+.. +|+|.+|||++||||+.||+.++.++++||--
T Consensus 179 ~LT~rE~evl~~~a-----~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~~ 224 (240)
T PRK10188 179 NFSKREKEILKWTA-----EGKTSAEIAMILSISENTVNFHQKNMQKKFNA 224 (240)
T ss_pred CCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 59999999999986 79999999999999999999999999999863
No 185
>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=97.13 E-value=0.00043 Score=68.39 Aligned_cols=81 Identities=19% Similarity=0.196 Sum_probs=64.4
Q ss_pred ccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHH-HHHHHHHHHHHHHHHHHhCCC
Q 011992 224 KVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQ-IQDLIRLEKEKSKLQSQFGRE 302 (473)
Q Consensus 224 ~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~-iq~l~kle~a~~~L~~~lGRe 302 (473)
+..+..+..|.+|+.++|+ ++++| .+|+..|..+ .| +. .....++..+...+...+|+.
T Consensus 73 ~~~~~~~~~f~tyl~~~i~-----n~~~~---~lr~~~~~ir-i~-----------~~~~~~~~~~~~~~~~l~~~~~r~ 132 (255)
T TIGR02941 73 RYDYSIGNAFEPFAIPTII-----GEIKR---YLRDKTWSVH-VP-----------RRIKELGPKIKKAIDELTDHLQRS 132 (255)
T ss_pred HcCCcCCCCcHhHHHHHHH-----HHHHH---HHHHcCCCcC-CC-----------HHHHHHHHHHHHHHHHHHHHhCCC
Confidence 4456677899999999999 99998 4888877443 32 11 233457888899999999999
Q ss_pred CCHHHHHHHcCCCHHHHHHHHh
Q 011992 303 PTLIEWAKAIGLSCRDLKSELH 324 (473)
Q Consensus 303 PT~eEiA~~lGms~eeL~~~l~ 324 (473)
|+.+|+|+.+|++.+++...+.
T Consensus 133 p~~~eia~~l~i~~~~~~~~~~ 154 (255)
T TIGR02941 133 PKIIEIADHLGLSEEEVLEIME 154 (255)
T ss_pred CCHHHHHHHhCCCHHHHHHHHH
Confidence 9999999999999998876554
No 186
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=97.10 E-value=0.0021 Score=61.73 Aligned_cols=59 Identities=17% Similarity=0.271 Sum_probs=53.2
Q ss_pred HHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 011992 396 QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 459 (473)
Q Consensus 396 ~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~ 459 (473)
......+...+.+|++|||+|+...- .|+..++||..||||+.||.-+..+.+.|++..
T Consensus 130 ~~~~~~~~~~l~tLT~RERqVl~~vV-----~G~~NKqIA~dLgiS~rTVe~HRanvM~Km~a~ 188 (202)
T COG4566 130 ADRQAAIRARLATLTPRERQVLDLVV-----RGLMNKQIAFDLGISERTVELHRANVMEKMQAR 188 (202)
T ss_pred HHHHHHHHHHHHhcCHHHHHHHHHHH-----cCcccHHHHHHcCCchhhHHHHHHHHHHHHhhc
Confidence 34567888999999999999999887 699999999999999999999999999998764
No 187
>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=97.10 E-value=0.00093 Score=57.27 Aligned_cols=49 Identities=22% Similarity=0.244 Sum_probs=41.9
Q ss_pred HHHHHHH-hhCCHHHHHHHHHHhhccC---CCCCCHHHHHHHHCCCHHHHHHH
Q 011992 400 QHVRNLL-TLLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQL 448 (473)
Q Consensus 400 e~L~~aL-~~LperER~VL~LrY~L~~---ge~lTlkEIAe~LGIS~~rVrqi 448 (473)
+.+...| ..|+|+|+.+|..||+|.+ ..++|++|||+.+|||..+|...
T Consensus 23 ~~l~~~l~~lLTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~ 75 (94)
T TIGR01321 23 DDMQLLLELILTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRG 75 (94)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHH
Confidence 3455566 3499999999999999987 67999999999999999999764
No 188
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=97.08 E-value=0.0015 Score=57.26 Aligned_cols=52 Identities=19% Similarity=0.170 Sum_probs=48.4
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccC
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 463 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~ 463 (473)
.|+..|-+.|+|.++ +++|++|.|+.||||+.|+..++..|.+|+-..|-..
T Consensus 41 ~L~~dElEAiRL~D~----egl~QeeaA~~MgVSR~T~~ril~~ARkKiA~ALv~G 92 (106)
T PF02001_consen 41 VLTVDELEAIRLVDY----EGLSQEEAAERMGVSRPTFQRILESARKKIADALVEG 92 (106)
T ss_pred EeeHHHHHHHHHHHH----cCCCHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHCC
Confidence 488899999999999 9999999999999999999999999999999887654
No 189
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=97.06 E-value=0.00076 Score=49.67 Aligned_cols=41 Identities=24% Similarity=0.339 Sum_probs=24.8
Q ss_pred hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
..|++.||..|...+- +|+|..|||+.||++.+||+..++|
T Consensus 3 ~~Lt~~eR~~I~~l~~----~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 3 KHLTPEERNQIEALLE----QGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ---------HHHHHHC----S---HHHHHHHTT--HHHHHHHHHH
T ss_pred cchhhhHHHHHHHHHH----cCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 3589999999988887 8999999999999999999998876
No 190
>PRK09483 response regulator; Provisional
Probab=96.99 E-value=0.0014 Score=60.91 Aligned_cols=46 Identities=22% Similarity=0.300 Sum_probs=42.1
Q ss_pred hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992 407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457 (473)
Q Consensus 407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR 457 (473)
..|+++|++|+.+.. +|++.+|||+.|++|..||+.+.++.++||-
T Consensus 147 ~~Lt~rE~~vl~~~~-----~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~ 192 (217)
T PRK09483 147 ASLSERELQIMLMIT-----KGQKVNEISEQLNLSPKTVNSYRYRMFSKLN 192 (217)
T ss_pred cccCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 469999999998764 7999999999999999999999999999984
No 191
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=96.94 E-value=0.003 Score=48.56 Aligned_cols=48 Identities=33% Similarity=0.432 Sum_probs=43.0
Q ss_pred hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 011992 407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 459 (473)
Q Consensus 407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~ 459 (473)
..|+++|.+++.+.- .|++.+|||..+|+|..+|+....++..||.-.
T Consensus 3 ~~Lt~rE~~v~~l~~-----~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~~~ 50 (65)
T COG2771 3 ADLTPREREILRLVA-----QGKSNKEIARILGISEETVKTHLRNIYRKLGVK 50 (65)
T ss_pred ccCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence 358999999998877 579999999999999999999999999998643
No 192
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=96.93 E-value=0.002 Score=58.33 Aligned_cols=46 Identities=22% Similarity=0.382 Sum_probs=42.3
Q ss_pred hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992 407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457 (473)
Q Consensus 407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR 457 (473)
..|+++|++|+.+ +. ++++.+|||+.|++|..||+....++++||.
T Consensus 148 ~~lt~~e~~vl~l-~~----~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 148 PLLTPRERQILKL-IT----EGYTNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred cCCCHHHHHHHHH-HH----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 4599999999998 44 8999999999999999999999999999985
No 193
>TIGR01637 phage_arpU phage transcriptional regulator, ArpU family. This model represents a family of phage proteins, including ArpU, called a putative autolysin regulatory protein. ArpU was described as a regulator of cellular muramidase-2 of Enterococcus hirae but appears to have been cloned from a prophage. This family appears related to the RinA family of bacteriophage transcriptional activators and to some sporulation-specific sigma factors. We propose that this is a phage transcriptional activator family.
Probab=96.90 E-value=0.0068 Score=54.25 Aligned_cols=64 Identities=20% Similarity=0.237 Sum_probs=54.8
Q ss_pred HHHHHHHHHHH-hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Q 011992 396 QLMRQHVRNLL-TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 461 (473)
Q Consensus 396 ~el~e~L~~aL-~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~ 461 (473)
......+..++ +.|++.+|.||..+|. + .++++..+|+..||+|+.+...+..+|+.++-..+.
T Consensus 66 ~~~~~~i~~ai~~~l~~~~r~Il~~~Yl-~-~~~~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~~l~ 130 (132)
T TIGR01637 66 EQEARAIVNAIVNQLDEISRQILYDKYL-E-PDQKYDYQIMMELGYSHRQYYRIKKRALLRFATLYG 130 (132)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHc-C-ccccchHHHHHHhCCcHHHHHHHHHHHHHHHHHHhC
Confidence 34456777888 9999999999999998 1 128899999999999999999999999999877664
No 194
>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=96.84 E-value=0.0005 Score=49.01 Aligned_cols=33 Identities=42% Similarity=0.469 Sum_probs=29.2
Q ss_pred hhHHhhhcccCccCCCChHHHHHHHHHHHHHHH
Q 011992 255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIR 287 (473)
Q Consensus 255 ~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~k 287 (473)
|+++.|+..+++.|+||++||++|+++|+....
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 579999999999999999999999999998654
No 195
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=96.79 E-value=0.0032 Score=61.02 Aligned_cols=54 Identities=20% Similarity=0.265 Sum_probs=47.0
Q ss_pred hCCHHHHHHHHHHhhccC---CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Q 011992 408 LLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 461 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~---ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~ 461 (473)
.|+++|++||..-|-.+. -+.-+++|||+.||||.+++.+++++|.+||=..+.
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~~~~ 211 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLIEAYF 211 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Confidence 699999999998776432 478899999999999999999999999999866543
No 196
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=96.75 E-value=0.0035 Score=54.24 Aligned_cols=48 Identities=25% Similarity=0.328 Sum_probs=43.9
Q ss_pred hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
.-|+.+++..+.+||. .++|+.|||+.++||++.|...++|+-..|-.
T Consensus 16 sLLT~KQ~~Y~~lyy~----dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~~ 63 (105)
T COG2739 16 SLLTKKQKNYLELYYL----DDLSLSEIAEEFNVSRQAIYDNIKRTEKILED 63 (105)
T ss_pred HHHhHHHHHHHHHHHH----hhccHHHHHHHhCccHHHHHHHHHHHHHHHHH
Confidence 3489999999999999 99999999999999999999999998877654
No 197
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=96.71 E-value=0.005 Score=55.45 Aligned_cols=54 Identities=13% Similarity=0.185 Sum_probs=47.4
Q ss_pred HHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 400 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 400 e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
..+...+..|++++++|+.+.+ .+++.++||+.+|+|..+|+....++++||+.
T Consensus 133 ~~~~~~~~~l~~~e~~vl~~~~-----~~~~~~~ia~~l~~s~~tv~~~~~~~~~kl~~ 186 (202)
T PRK09390 133 ADIRARIASLSERERQVMDGLV-----AGLSNKVIARDLDISPRTVEVYRANVMTKMQA 186 (202)
T ss_pred HHHHHHHHhhhhhHHHHHHHHH-----ccCchHHHHHHcCCCHHHHHHHHHHHHHHHcc
Confidence 3456677889999999999744 68999999999999999999999999999864
No 198
>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=96.69 E-value=0.0011 Score=66.78 Aligned_cols=79 Identities=19% Similarity=0.192 Sum_probs=60.2
Q ss_pred ccCCCCCCcccccccccccccccccccCCCChhHHhh---hcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Q 011992 224 KVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLF---LWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFG 300 (473)
Q Consensus 224 ~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~---~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lG 300 (473)
+..+..|..|.||+.|+++ +++.++ ++.. .|.|++. ++.++.+.+....+...+|
T Consensus 90 ~fd~~~g~~f~tya~w~i~-----~ain~~---i~~~~~~~~~p~~~--------------~~~~~~~~r~~~~l~~~~~ 147 (285)
T TIGR02394 90 KFDPERGFRFSTYATWWIR-----QTIERA---IMNQARTIRLPVHV--------------IKELNVYLRAARQLEKKLG 147 (285)
T ss_pred HhCCCCCCCcHhhhHHHHH-----HHHHHH---HHHcCCceeCcHHH--------------HHHHHHHHHHHHHHHHHhC
Confidence 4567788899999999999 888663 4333 3445544 3455556666677788899
Q ss_pred CCCCHHHHHHHcCCCHHHHHHHHh
Q 011992 301 REPTLIEWAKAIGLSCRDLKSELH 324 (473)
Q Consensus 301 RePT~eEiA~~lGms~eeL~~~l~ 324 (473)
++|+..|+|..+|++.+++..++.
T Consensus 148 r~~~~~e~a~~l~~~~~~~~~~~~ 171 (285)
T TIGR02394 148 REPSVEEIAELLDKPVEDVSRVLA 171 (285)
T ss_pred CCCCHHHHHHHhCcCHHHHHHHHH
Confidence 999999999999999988887654
No 199
>PRK10651 transcriptional regulator NarL; Provisional
Probab=96.64 E-value=0.0037 Score=57.34 Aligned_cols=46 Identities=20% Similarity=0.294 Sum_probs=42.2
Q ss_pred hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992 407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457 (473)
Q Consensus 407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR 457 (473)
..|+++|++|+.+.. ++++.+|||+.|++|..||+...++.++||.
T Consensus 154 ~~Lt~rE~~vl~~l~-----~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl~ 199 (216)
T PRK10651 154 NQLTPRERDILKLIA-----QGLPNKMIARRLDITESTVKVHVKHMLKKMK 199 (216)
T ss_pred ccCCHHHHHHHHHHH-----cCCCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 359999999999865 7899999999999999999999999999985
No 200
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=96.36 E-value=0.0095 Score=58.91 Aligned_cols=81 Identities=17% Similarity=0.219 Sum_probs=63.2
Q ss_pred ccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHH-HHHHHHHHHHHHHHHHhCCC
Q 011992 224 KVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQI-QDLIRLEKEKSKLQSQFGRE 302 (473)
Q Consensus 224 ~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~i-q~l~kle~a~~~L~~~lGRe 302 (473)
+..+..+..|.+|+.++|+ +.++| .+|+..|..+ +| +.+ ....++..+...+...+|+.
T Consensus 73 ~f~~~~~~~f~tyl~~~i~-----n~~~~---~lr~~~~~~~-i~-----------r~~~~~~~~~~~~~~~~~~~~~r~ 132 (257)
T PRK08583 73 RYDPSFGRSFEAFAVPTII-----GEIKR---YLRDKTWSVH-VP-----------RRIKELGPKIKKAVDELTTELQRS 132 (257)
T ss_pred HcCccCCCChHHHHHHHHH-----HHHHH---HHHhcCCCcC-CC-----------HHHHHHHHHHHHHHHHHHHHhCCC
Confidence 4556677789999999999 99998 4888888443 22 222 33457778888899999999
Q ss_pred CCHHHHHHHcCCCHHHHHHHHh
Q 011992 303 PTLIEWAKAIGLSCRDLKSELH 324 (473)
Q Consensus 303 PT~eEiA~~lGms~eeL~~~l~ 324 (473)
|+.+|+|+.+|++.+++.....
T Consensus 133 ~~~~e~a~~~~~~~~~~~~~~~ 154 (257)
T PRK08583 133 PKISEIADRLGVSEEEVLEAME 154 (257)
T ss_pred CCHHHHHHHhCCCHHHHHHHHH
Confidence 9999999999999988766543
No 201
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=96.21 E-value=0.013 Score=50.26 Aligned_cols=51 Identities=20% Similarity=0.133 Sum_probs=47.3
Q ss_pred CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccC
Q 011992 409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 463 (473)
Q Consensus 409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~ 463 (473)
|+..|-++|+|..+ ++++++|-|..||||+.|+...+..|++|+-..|-+.
T Consensus 34 lt~eElEAlRLvD~----~~l~QeeAA~rMgISr~Tfwr~l~sAR~KvA~aLveG 84 (99)
T COG1342 34 LTIEELEALRLVDY----EGLTQEEAALRMGISRQTFWRLLTSARKKVADALVEG 84 (99)
T ss_pred ecHHHHHHHHHHhH----hhccHHHHHHHhcccHHHHHHHHHHHHHHHHHHHhcC
Confidence 77888999999999 9999999999999999999999999999999887654
No 202
>PRK01381 Trp operon repressor; Provisional
Probab=96.17 E-value=0.0066 Score=52.54 Aligned_cols=48 Identities=27% Similarity=0.320 Sum_probs=39.5
Q ss_pred HHHHHHHhh-CCHHHHHHHHHHhhccC---CCCCCHHHHHHHHCCCHHHHHH
Q 011992 400 QHVRNLLTL-LNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQ 447 (473)
Q Consensus 400 e~L~~aL~~-LperER~VL~LrY~L~~---ge~lTlkEIAe~LGIS~~rVrq 447 (473)
+.+...|.. |+|+|+.+|..||.|.. ..++|++|||+.+|||..+|..
T Consensus 23 ~~~~~~l~~llTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITR 74 (99)
T PRK01381 23 DLHLPLLTLLLTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATITR 74 (99)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeehh
Confidence 445555655 99999999999998876 4579999999999999887754
No 203
>PRK10403 transcriptional regulator NarP; Provisional
Probab=96.16 E-value=0.01 Score=54.17 Aligned_cols=46 Identities=15% Similarity=0.230 Sum_probs=41.8
Q ss_pred hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992 407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457 (473)
Q Consensus 407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR 457 (473)
..|+++|.+|+.+.. ++.|.+|||+.+|+|+.||+..+.+.++||.
T Consensus 152 ~~Lt~~e~~vl~~~~-----~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~ 197 (215)
T PRK10403 152 SVLTERELDVLHELA-----QGLSNKQIASVLNISEQTVKVHIRNLLRKLN 197 (215)
T ss_pred ccCCHHHHHHHHHHH-----CCCCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 359999999998765 6899999999999999999999999999884
No 204
>PRK15320 transcriptional activator SprB; Provisional
Probab=96.04 E-value=0.012 Score=56.92 Aligned_cols=67 Identities=19% Similarity=0.212 Sum_probs=50.6
Q ss_pred CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 386 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 386 ~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
.+.|++.+..-. .-.....--.|+++|.+|+.+-- .|+|.+|||+.|++|.++|+...++.+.||.-
T Consensus 143 ~~~~~~~~~~~~-~~~~~~~~~~LSdREIEVL~LLA-----kG~SNKEIAekL~LS~KTVSTYKnRLLeKLgA 209 (251)
T PRK15320 143 GETPEEVLFNIN-QYAWWNLPPGVTQAKYALLILLS-----SGHPAIELAKKFGLGTKTVSIYRKKVMYRLGM 209 (251)
T ss_pred CCChHHHhhhcc-ceeeecCCCCCCHHHHHHHHHHH-----cCCCHHHHHHHhccchhhHHHHHHHHHHHcCC
Confidence 455665443211 11233344679999999998876 69999999999999999999999999988863
No 205
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=95.96 E-value=0.006 Score=54.84 Aligned_cols=47 Identities=26% Similarity=0.352 Sum_probs=43.7
Q ss_pred CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992 409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 460 (473)
Q Consensus 409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L 460 (473)
|++++-+|+.||- .|+|.+|||++||-|+..|+-|+++|+.++.+..
T Consensus 9 lte~qikvl~lRe-----kG~tQ~eIA~~L~TTraNvSaIEkrA~enIekar 55 (143)
T COG1356 9 LTEQQIKVLVLRE-----KGLTQSEIARILKTTRANVSAIEKRALENIEKAR 55 (143)
T ss_pred eehhheeeeehhh-----ccccHHHHHHHHccchhhHHHHHHHHHHHHHHHH
Confidence 8899999999998 6999999999999999999999999999987753
No 206
>PRK04841 transcriptional regulator MalT; Provisional
Probab=95.84 E-value=0.014 Score=66.69 Aligned_cols=47 Identities=11% Similarity=0.155 Sum_probs=43.4
Q ss_pred hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
..|+++|++|+.+.. +|+|.+|||+.|+||.+||+.++++...||.-
T Consensus 837 ~~lt~~e~~v~~~~~-----~g~~~~~ia~~l~~s~~tv~~h~~~~~~kl~v 883 (903)
T PRK04841 837 SPLTQREWQVLGLIY-----SGYSNEQIAGELDVAATTIKTHIRNLYQKLGI 883 (903)
T ss_pred CCCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 349999999999977 79999999999999999999999999999863
No 207
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=95.73 E-value=0.023 Score=52.10 Aligned_cols=45 Identities=24% Similarity=0.242 Sum_probs=40.1
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR 457 (473)
.|+++|..|+.+.. ++++.+|||+.|++|..+|+....++++||.
T Consensus 149 ~lt~re~~vl~~l~-----~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl~ 193 (210)
T PRK09935 149 VLSNREVTILRYLV-----SGLSNKEIADQLLLSNKTVSAHKSNIYGKLG 193 (210)
T ss_pred cCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 38899998887643 6899999999999999999999999999985
No 208
>PRK13558 bacterio-opsin activator; Provisional
Probab=95.68 E-value=0.022 Score=63.26 Aligned_cols=55 Identities=13% Similarity=0.085 Sum_probs=46.3
Q ss_pred HhhCCHHHHHHHHHHhhccC---CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992 406 LTLLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 460 (473)
Q Consensus 406 L~~LperER~VL~LrY~L~~---ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L 460 (473)
...|+++|+++|..-|..+. -++-|..|||+.||||.+++++++++|.+||=..+
T Consensus 605 ~~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~~~~lr~a~~~l~~~~ 662 (665)
T PRK13558 605 ENDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFHQHLRAAERKLVGAF 662 (665)
T ss_pred hhhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 46799999999999887221 13449999999999999999999999999986654
No 209
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=95.65 E-value=0.025 Score=51.93 Aligned_cols=47 Identities=21% Similarity=0.320 Sum_probs=42.3
Q ss_pred HhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992 406 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457 (473)
Q Consensus 406 L~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR 457 (473)
+..|+++|.+|+.+.. .+.+.+|||+.+++|..+|+...++.++||.
T Consensus 141 ~~~lt~~E~~vl~~l~-----~g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl~ 187 (204)
T PRK09958 141 LDSLSKQEISVMRYIL-----DGKDNNDIAEKMFISNKTVSTYKSRLMEKLE 187 (204)
T ss_pred cccCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 3569999999998877 6889999999999999999999999998884
No 210
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=95.63 E-value=0.032 Score=42.48 Aligned_cols=50 Identities=18% Similarity=0.242 Sum_probs=43.2
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 460 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L 460 (473)
+|+..++.++.|.|. -.+.+++.||..+|||+++|+++.+..+.-|...+
T Consensus 2 kLs~~d~lll~L~~L---R~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~l 51 (53)
T PF13613_consen 2 KLSLEDQLLLTLMYL---RLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQVL 51 (53)
T ss_pred CCCHHHHHHHHHHHH---HcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHhc
Confidence 588889988887665 38899999999999999999999999988877654
No 211
>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=95.63 E-value=0.015 Score=57.05 Aligned_cols=73 Identities=10% Similarity=0.024 Sum_probs=50.7
Q ss_pred hccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Q 011992 223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGRE 302 (473)
Q Consensus 223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRe 302 (473)
.+.++.+|..|.+|+.++|+ |+++|+ +|+.......+++-...+| ....+..+..++..++++.
T Consensus 54 ~~yd~~kg~~F~sya~~~Ir-----~~i~dy---lRk~~k~~~~v~~~~~~~e--------~~~~~~~~~~~~~~~~~~~ 117 (218)
T TIGR02895 54 ESYDSNKGKSFLSFAKLIIK-----RRLIDY---IRKNQKYQNLLYLDEDYDE--------NPLEFNKSMEEYRNEIENE 117 (218)
T ss_pred HHCCCCCCCCHHHHHHHHHH-----HHHHHH---HHhcccccCeeeCCchHHH--------HHHHHHHHHHHHHHHHccc
Confidence 45678999999999999999 999994 8876522112221111111 2335556677888899999
Q ss_pred CCHHHHHHH
Q 011992 303 PTLIEWAKA 311 (473)
Q Consensus 303 PT~eEiA~~ 311 (473)
|+.+||+..
T Consensus 118 ~~~eEI~~~ 126 (218)
T TIGR02895 118 NRRLEILEY 126 (218)
T ss_pred cHHHHHHHH
Confidence 999999873
No 212
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=95.61 E-value=0.03 Score=51.02 Aligned_cols=46 Identities=20% Similarity=0.255 Sum_probs=41.8
Q ss_pred hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992 407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457 (473)
Q Consensus 407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR 457 (473)
..|+++|.+|+.+.. ++++.++||+.|++|..+|+.+.++.++||.
T Consensus 136 ~~Lt~~E~~il~~l~-----~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~ 181 (196)
T PRK10360 136 DPLTKRERQVAEKLA-----QGMAVKEIAAELGLSPKTVHVHRANLMEKLG 181 (196)
T ss_pred cCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 359999999999866 5899999999999999999999999998885
No 213
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=95.53 E-value=0.14 Score=53.31 Aligned_cols=125 Identities=16% Similarity=0.149 Sum_probs=80.1
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCC-C-------cccc------------------C
Q 011992 331 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAG-C-------RFAN------------------T 384 (473)
Q Consensus 331 e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg-~-------~FsT------------------~ 384 (473)
+..+..-.+.+..-.-+|.++-.-+||.+||+|+...+...+--+... . +|.. .
T Consensus 8 e~~~r~~~~r~~a~L~r~~rd~dlAEEa~~dA~~~Ale~WPr~G~P~~PaAWL~~v~R~~aiD~~Rr~~~~~~~~~el~~ 87 (415)
T COG4941 8 EAAARIERPRAMAALARYLRDLDLAEEALQDAFAAALERWPRAGPPRNPAAWLIAVGRNRAIDRVRRRARRDAAPPELLL 87 (415)
T ss_pred HHHHHHhhhHHHHHHHHHhcccchHHHHHHHHHHHHHHhCcccCCCCChHHHHHHHHhhhHHHHHHHHHHhccCChhhcc
Confidence 334444555566666677788888999999999865544332211110 0 0000 0
Q ss_pred CCCCchHH---------HHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 011992 385 GVEIPDIS---------VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR 455 (473)
Q Consensus 385 ~~~~pee~---------le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~K 455 (473)
..++.+.. +.++.++-.+.-|=-.||+.+|-.+.|+.. .|+|..|||..+=|++.++-|.+.||..+
T Consensus 88 ~~e~~e~~~a~~~~d~~i~Dd~LRLiFvccHPal~~~~riALtLR~v----~GLs~~eIArAFLv~e~am~QRivRAK~r 163 (415)
T COG4941 88 SDEDEEMEEAEALDDEHIRDDRLRLIFVCCHPALPPEQRIALTLRLV----GGLSTAEIARAFLVPEAAMAQRIVRAKAR 163 (415)
T ss_pred cccchhhhccccccccccchhhHHhhhhhcCCCCChhhHHHHHHHHH----cCCcHHHHHHHHcCCcHHHHHHHHHHHHH
Confidence 00111111 111112222222225699999999999999 89999999999999999999999999999
Q ss_pred HHHH
Q 011992 456 LKQS 459 (473)
Q Consensus 456 LR~~ 459 (473)
++..
T Consensus 164 i~~a 167 (415)
T COG4941 164 IREA 167 (415)
T ss_pred HHhc
Confidence 9974
No 214
>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=95.47 E-value=0.024 Score=45.34 Aligned_cols=46 Identities=17% Similarity=0.403 Sum_probs=30.3
Q ss_pred HhhCCHHHHHHHHH--HhhccCCCCCCHHHHHHHHCCC-HHHHHHHHHH
Q 011992 406 LTLLNPKERCIVRL--RFGIEDGKPKSLSEVGNIFGLS-KERVRQLESR 451 (473)
Q Consensus 406 L~~LperER~VL~L--rY~L~~ge~lTlkEIAe~LGIS-~~rVrqi~~R 451 (473)
+..|+++|++||.. .|.-..|..+|+.|||+.+|++ .++|.+.+..
T Consensus 1 M~~LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~ 49 (65)
T PF01726_consen 1 MKELTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKA 49 (65)
T ss_dssp -----HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence 35799999999865 3333457899999999999996 9999886543
No 215
>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=95.26 E-value=0.057 Score=39.76 Aligned_cols=42 Identities=17% Similarity=0.226 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992 409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 453 (473)
Q Consensus 409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL 453 (473)
|++.++.||..-+. +.+.|..|||+.+|+|.++|++++++-.
T Consensus 1 l~~~~~~Il~~l~~---~~~~t~~ela~~~~is~~tv~~~l~~L~ 42 (48)
T PF13412_consen 1 LDETQRKILNYLRE---NPRITQKELAEKLGISRSTVNRYLKKLE 42 (48)
T ss_dssp --HHHHHHHHHHHH---CTTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH---cCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 56778888866554 3569999999999999999999776543
No 216
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=95.24 E-value=0.026 Score=58.22 Aligned_cols=36 Identities=22% Similarity=0.344 Sum_probs=33.2
Q ss_pred HHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011992 415 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 454 (473)
Q Consensus 415 ~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~ 454 (473)
.|-.|||. +++|..|||+.||||+.+|++++.+|++
T Consensus 20 ~vA~lYY~----~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~ 55 (318)
T PRK15418 20 RIAWFYYH----DGLTQSEIGERLGLTRLKVSRLLEKGRQ 55 (318)
T ss_pred HHHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 46678998 9999999999999999999999999985
No 217
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=95.17 E-value=0.019 Score=42.56 Aligned_cols=32 Identities=28% Similarity=0.361 Sum_probs=22.9
Q ss_pred HHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992 416 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 452 (473)
Q Consensus 416 VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA 452 (473)
+|.++. +|.|..+||+.+|||+.+|+.+.++-
T Consensus 10 ii~l~~-----~G~s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 10 IIRLLR-----EGWSIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp HHHHHH-----HT--HHHHHHHHTS-HHHHHHHHT--
T ss_pred HHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHc
Confidence 455555 59999999999999999999998764
No 218
>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=94.56 E-value=0.082 Score=44.86 Aligned_cols=39 Identities=15% Similarity=0.244 Sum_probs=31.3
Q ss_pred hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992 407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 452 (473)
Q Consensus 407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA 452 (473)
..|++| ..|+.+.- .|+|..|||+.+|||+.||..+ .++
T Consensus 35 ~~Ls~R-~~I~~ll~-----~G~S~~eIA~~LgISrsTIyRi-~R~ 73 (88)
T TIGR02531 35 QSLAQR-LQVAKMLK-----QGKTYSDIEAETGASTATISRV-KRC 73 (88)
T ss_pred HhhhHH-HHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHH-HHh
Confidence 458888 77766644 6899999999999999999984 444
No 219
>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=94.51 E-value=0.092 Score=34.10 Aligned_cols=36 Identities=19% Similarity=0.335 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHH
Q 011992 409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL 448 (473)
Q Consensus 409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi 448 (473)
+++.++..+...|. .+.+..+||+.+|++..+|+.+
T Consensus 6 ~~~~~~~~i~~~~~----~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 6 LTPEQIEEARRLLA----AGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHh
Confidence 55666666666665 6789999999999999999875
No 220
>PF06530 Phage_antitermQ: Phage antitermination protein Q; InterPro: IPR010534 This entry is represented by Bacteriophage 933W, GpQ. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage antitermination protein Q and related bacterial sequences. Phage 993W gene Q encodes a phage-specific positive regulator of late gene expression, thought, by analogy to the corresponding gene of phage lambda, to be a transcription antiterminator. GpQ positively regulates expression of the phage late gene operons. Bacterial host RNA polymerase modified by antitermination proteins transcribes through termination sites that otherwise prevent expression of the regulated genes [, ].; GO: 0003677 DNA binding, 0060567 negative regulation of transcription termination, DNA-dependent
Probab=94.32 E-value=0.26 Score=44.21 Aligned_cols=54 Identities=19% Similarity=0.121 Sum_probs=48.3
Q ss_pred HHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Q 011992 405 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 462 (473)
Q Consensus 405 aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~ 462 (473)
.|..-.+.+-.+|.+||. .+.|...||..+++|...|++.+.+|-.-+..+|.-
T Consensus 59 ~L~~~~~~~~~ll~~~Yv----~g~s~r~IA~~~~~s~~~ir~~l~~ae~~i~g~l~~ 112 (125)
T PF06530_consen 59 RLKKRDPEEYDLLILYYV----YGWSKRQIARKLKCSEGKIRKRLQRAEGFIDGCLSM 112 (125)
T ss_pred HHHccCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHhhhhHhhhhHH
Confidence 345578889999999999 999999999999999999999999999998887643
No 221
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=93.48 E-value=0.31 Score=44.32 Aligned_cols=56 Identities=16% Similarity=0.337 Sum_probs=46.4
Q ss_pred HHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 011992 399 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 456 (473)
Q Consensus 399 ~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KL 456 (473)
...|...++.|.+.++.||.|+|. ...++|-.+||..|++++.+++.+...-...+
T Consensus 72 k~~id~~~~~l~de~k~Ii~lry~--~r~~~TW~~IA~~l~i~erta~r~~~~fK~~i 127 (130)
T PF05263_consen 72 KEAIDRWLETLIDEEKRIIKLRYD--RRSRRTWYQIAQKLHISERTARRWRDRFKNDI 127 (130)
T ss_pred HHHHHHHHHhhCHHHHHHHHHHHc--ccccchHHHHHHHhCccHHHHHHHHHHHHHHh
Confidence 456778889999999999999998 22459999999999999999998776654433
No 222
>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=93.30 E-value=0.15 Score=40.37 Aligned_cols=38 Identities=16% Similarity=0.279 Sum_probs=29.0
Q ss_pred HHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 412 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 412 rER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
+--..+.+|.. .+..+++++||+.||||.++|+...++
T Consensus 8 ~rdkA~e~y~~--~~g~i~lkdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 8 NRDKAFEIYKE--SNGKIKLKDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred CHHHHHHHHHH--hCCCccHHHHHHHHCCCHHHHHHHhhh
Confidence 33445555543 346899999999999999999987654
No 223
>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=92.98 E-value=0.3 Score=35.68 Aligned_cols=40 Identities=33% Similarity=0.422 Sum_probs=27.6
Q ss_pred CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
|++-.+.||...-. +...++.+||+.+|+|+.+|...+.+
T Consensus 1 lD~~D~~Il~~Lq~---d~r~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 1 LDELDRKILRLLQE---DGRRSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp --HHHHHHHHHHHH----TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH---cCCccHHHHHHHHCcCHHHHHHHHHH
Confidence 34556677665443 25789999999999999999987764
No 224
>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=92.97 E-value=0.13 Score=37.90 Aligned_cols=33 Identities=24% Similarity=0.296 Sum_probs=24.2
Q ss_pred HHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011992 413 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 450 (473)
Q Consensus 413 ER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~ 450 (473)
..+|+.|+- +|+|..+||+.+|||+.||..++.
T Consensus 11 ~~~i~~l~~-----~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 11 IEEIKELYA-----EGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHHHH-----TT--HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHh
Confidence 455666665 679999999999999999998753
No 225
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=92.96 E-value=1.3 Score=47.67 Aligned_cols=24 Identities=29% Similarity=0.483 Sum_probs=22.2
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLES 450 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~ 450 (473)
.++|+++||+.+|++++||+...+
T Consensus 317 kPLtlkdiA~~lglheSTVSRav~ 340 (429)
T TIGR02395 317 KPLTLREVAEELGLHESTISRAIN 340 (429)
T ss_pred cCCcHHHHHHHhCCCccchhhhhc
Confidence 789999999999999999998765
No 226
>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=92.80 E-value=0.23 Score=38.90 Aligned_cols=33 Identities=18% Similarity=0.249 Sum_probs=27.4
Q ss_pred HHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992 415 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 452 (473)
Q Consensus 415 ~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA 452 (473)
.+..||. .|++.+|||+.||++..+|.....+-
T Consensus 5 ~A~~LY~-----~G~~~~eIA~~Lg~~~~TV~~W~~r~ 37 (58)
T PF06056_consen 5 QARSLYL-----QGWSIKEIAEELGVPRSTVYSWKDRY 37 (58)
T ss_pred HHHHHHH-----cCCCHHHHHHHHCCChHHHHHHHHhh
Confidence 3445554 79999999999999999999988763
No 227
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=92.77 E-value=0.15 Score=52.90 Aligned_cols=36 Identities=22% Similarity=0.262 Sum_probs=32.3
Q ss_pred HHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011992 415 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 454 (473)
Q Consensus 415 ~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~ 454 (473)
.+-.|||. +++|..|||+.||||+.+|+..+.+|++
T Consensus 17 ~~A~lYY~----~gltQ~eIA~~LgiSR~~v~rlL~~Ar~ 52 (321)
T COG2390 17 RAAWLYYV----EGLTQSEIAERLGISRATVSRLLAKARE 52 (321)
T ss_pred HHHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 34578998 9999999999999999999999999875
No 228
>PHA00675 hypothetical protein
Probab=92.73 E-value=0.22 Score=41.22 Aligned_cols=41 Identities=17% Similarity=0.072 Sum_probs=33.2
Q ss_pred hhCCHHHHHHHHHHh-hccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 407 TLLNPKERCIVRLRF-GIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 407 ~~LperER~VL~LrY-~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
..|++.+-+.|+..+ . .+.|+.+||+.||||+++|.+|...
T Consensus 21 AKLt~~qV~~IR~l~~r----~G~s~~~IA~~fGVsrstV~~I~~g 62 (78)
T PHA00675 21 AKLTDAEVERIRELHEV----EGMSYAVLAEKFEQSKGAIAKICRY 62 (78)
T ss_pred cccCHHHHHHHHHHHHh----cCccHHHHHHHhCCCHHHHHHHHcc
Confidence 357777777666555 5 7889999999999999999998754
No 229
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=92.70 E-value=0.33 Score=43.13 Aligned_cols=50 Identities=20% Similarity=0.299 Sum_probs=43.3
Q ss_pred HHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 405 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 405 aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
.+..|++.+..-|..... ..=+++|+++.||||..|||..+.+.+.+|.-
T Consensus 30 ~~~~L~~E~~~Fi~~Fi~----~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 30 WFARLSPEQLEFIKLFIK----NRGNLKEMEKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred hhhcCCHHHHHHHHHHHH----hcCCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence 456799888887776665 56699999999999999999999999999976
No 230
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=92.63 E-value=0.25 Score=47.69 Aligned_cols=48 Identities=15% Similarity=0.070 Sum_probs=36.8
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR 455 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~K 455 (473)
.|++++.+++.....=..++|+|.+|||+.||+|+.||+....++...
T Consensus 158 ~Lt~re~~~l~~~i~~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~ 205 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAHQDYEFSTDELANAVNISRVSCRKYLIWLVNC 205 (239)
T ss_pred CCCHHHHHHHHHHHHhCCCCCcCHHHHHHHhCchHHHHHHHHHHHHhC
Confidence 488888777654431112389999999999999999999999887543
No 231
>PF13518 HTH_28: Helix-turn-helix domain
Probab=92.62 E-value=0.23 Score=36.62 Aligned_cols=28 Identities=25% Similarity=0.336 Sum_probs=24.1
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESRALY 454 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~RAL~ 454 (473)
++.|+.+||+.+|||..+|+.++.+-..
T Consensus 11 ~g~s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 11 EGESVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred cCCCHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 5669999999999999999998876543
No 232
>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]
Probab=92.20 E-value=0.17 Score=58.15 Aligned_cols=47 Identities=17% Similarity=0.093 Sum_probs=43.6
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 459 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~ 459 (473)
.|+.||++|+.+.| .|+|.+|||+.|.||..||+.++...-.||.-.
T Consensus 831 ~Ls~RE~eVL~Lia-----~G~SN~eIa~~L~isl~TVKtH~rniy~KLgV~ 877 (894)
T COG2909 831 PLSQRELEVLGLIA-----QGLSNEEIAQELFISLTTVKTHIRNIYQKLGVA 877 (894)
T ss_pred CccHHHHHHHHHHH-----ccCCHHHHHHHHHHHHHHHHHHHHHHHHHhCcc
Confidence 49999999999999 699999999999999999999999999998643
No 233
>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=92.19 E-value=0.19 Score=38.45 Aligned_cols=40 Identities=20% Similarity=0.305 Sum_probs=28.3
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.|+-.++.=+.-+|. .|.+..+||..+||+.+||+.|+..
T Consensus 6 ~LTl~eK~~iI~~~e----~g~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 6 SLTLEEKLEIIKRLE----EGESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp S--HHHHHHHHHHHH----CTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred cCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 466667665555566 7889999999999999999999875
No 234
>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=92.17 E-value=0.18 Score=35.07 Aligned_cols=24 Identities=21% Similarity=0.573 Sum_probs=17.7
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 428 PKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 428 ~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
++|.+|||+.+|+++++|+.++++
T Consensus 2 ~mtr~diA~~lG~t~ETVSR~l~~ 25 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVSRILKK 25 (32)
T ss_dssp E--HHHHHHHHTS-HHHHHHHHHH
T ss_pred CcCHHHHHHHhCCcHHHHHHHHHH
Confidence 478999999999999999875543
No 235
>smart00351 PAX Paired Box domain.
Probab=91.91 E-value=0.44 Score=42.57 Aligned_cols=42 Identities=14% Similarity=0.051 Sum_probs=34.3
Q ss_pred CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011992 409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 454 (473)
Q Consensus 409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~ 454 (473)
++..+|.-|.+.|. ++.+..+||+.+|||..+|..++.+...
T Consensus 18 ~s~~~R~riv~~~~----~G~s~~~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 18 LPDEERQRIVELAQ----NGVRPCDISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred CCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 56666665556666 7899999999999999999999998653
No 236
>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=91.86 E-value=0.39 Score=36.64 Aligned_cols=45 Identities=22% Similarity=0.262 Sum_probs=32.8
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 453 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL 453 (473)
.|++.+..||...+. .++.++|..|||+.+|++.++|+.++.+-.
T Consensus 2 glt~~q~~vL~~l~~-~~~~~~t~~~la~~l~~~~~~vs~~v~~L~ 46 (62)
T PF12802_consen 2 GLTPSQFRVLMALAR-HPGEELTQSELAERLGISKSTVSRIVKRLE 46 (62)
T ss_dssp TSTHHHHHHHHHHHH-STTSGEEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHH-CCCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 477788888776555 122338999999999999999998766543
No 237
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=91.25 E-value=2.6 Score=45.89 Aligned_cols=45 Identities=13% Similarity=0.373 Sum_probs=32.0
Q ss_pred HhhCCHHHHHHHHH---------HhhccCC---CCCCHHHHHHHHCCCHHHHHHHHH
Q 011992 406 LTLLNPKERCIVRL---------RFGIEDG---KPKSLSEVGNIFGLSKERVRQLES 450 (473)
Q Consensus 406 L~~LperER~VL~L---------rY~L~~g---e~lTlkEIAe~LGIS~~rVrqi~~ 450 (473)
+..|.-|.+.++.. -|+..|. .++|+++||+.+|+.++||+...+
T Consensus 309 i~~i~~R~~TL~~v~~~Iv~~Q~~Ff~~G~~~LkPLtlkdvAe~lglheSTVSRav~ 365 (455)
T PRK05932 309 IKSLEQRKETLLKVARCIVEQQRDFFEHGEEALKPLVLKDIAEELGMHESTISRATT 365 (455)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCcCccHHHHHHHhCCCccchhhhhc
Confidence 34566666655433 3433332 789999999999999999998764
No 238
>PF13730 HTH_36: Helix-turn-helix domain
Probab=91.16 E-value=0.82 Score=34.34 Aligned_cols=43 Identities=16% Similarity=0.200 Sum_probs=31.0
Q ss_pred hCCHHHHHHHHHHhhccC---CCCCCHHHHHHHHCCCHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQLES 450 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~---ge~lTlkEIAe~LGIS~~rVrqi~~ 450 (473)
.|++.++.|+..-....+ +--+|.+.||+.+|+|+.+|...+.
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~ 47 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAIK 47 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 588888888754333322 2334999999999999999987443
No 239
>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=90.49 E-value=0.98 Score=36.15 Aligned_cols=56 Identities=18% Similarity=0.287 Sum_probs=43.9
Q ss_pred HHHHHhhcchHHHHHHHHHHHHHHHHHHHhh----c--CCcchhhHhhhhHHHHHHHhhhhC
Q 011992 319 LKSELHSGNSSREKLINANLRLVVHVAKQYQ----G--RGISLHDLLQEGSMGLMKSVEKFK 374 (473)
Q Consensus 319 L~~~l~~g~~A~e~Li~~yl~lV~sIA~ry~----~--~~~saEDLiQEg~lgL~kAiekFD 374 (473)
+.++..|+..|.++++..|.+++.+++.+-. + ++.-=+|+-|+--..|+.++-+|+
T Consensus 4 I~~A~~GD~~A~~~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kLi~~I~~F~ 65 (65)
T PF12645_consen 4 IKAAKQGDPEAMEEILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKLIEAILKFE 65 (65)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHHHHHHHccC
Confidence 4455556669999999999999999997732 2 123347999999999999999885
No 240
>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=90.19 E-value=0.78 Score=33.81 Aligned_cols=37 Identities=27% Similarity=0.390 Sum_probs=27.6
Q ss_pred HHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 411 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 411 erER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
|.-..|+.+-.. .+++..||++.+|+|+++|++.+..
T Consensus 2 ~~R~~Il~~L~~----~~~~~~el~~~l~~s~~~vs~hL~~ 38 (47)
T PF01022_consen 2 PTRLRILKLLSE----GPLTVSELAEELGLSQSTVSHHLKK 38 (47)
T ss_dssp HHHHHHHHHHTT----SSEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHh----CCCchhhHHHhccccchHHHHHHHH
Confidence 344455555544 7899999999999999999997654
No 241
>PRK11083 DNA-binding response regulator CreB; Provisional
Probab=89.84 E-value=0.49 Score=43.78 Aligned_cols=50 Identities=14% Similarity=0.050 Sum_probs=42.9
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCC-----HHHHHHHHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLS-----KERVRQLESRALYRLKQ 458 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS-----~~rVrqi~~RAL~KLR~ 458 (473)
.|+++|.+|+.+... +.|+.+|.+||++.++.+ ..+|+.++++.++||..
T Consensus 154 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~l~~Kl~~ 208 (228)
T PRK11083 154 TLTRYEFLLLKTLLL-SPGRVFSRQQLMDIVWEDAQDSYDRTVDTHIKTLRAKLRA 208 (228)
T ss_pred ecCHHHHHHHHHHHh-CCCceECHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhcc
Confidence 499999999987764 445679999999999986 78999999999999974
No 242
>PF02650 HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IPR023054 This domain is found at the C terminus of the sporulation regulator WhiA. It is predicted to form a DNA binding helix-turn-helix structure []. ; PDB: 3HYI_A.
Probab=89.45 E-value=0.81 Score=38.66 Aligned_cols=45 Identities=29% Similarity=0.339 Sum_probs=34.7
Q ss_pred HhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHH--CCCHHHHHHHHHHHH
Q 011992 406 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIF--GLSKERVRQLESRAL 453 (473)
Q Consensus 406 L~~LperER~VL~LrY~L~~ge~lTlkEIAe~L--GIS~~rVrqi~~RAL 453 (473)
++.||+..+++..+|.. ..+.|+.|+|+.| .||.+.|..++.+..
T Consensus 35 ~~~l~~~l~~~a~lRl~---~Pd~SL~EL~~~~~~~iSKSgvnhrlrKl~ 81 (85)
T PF02650_consen 35 LDKLPEKLREFAELRLE---NPDASLKELGELLEPPISKSGVNHRLRKLK 81 (85)
T ss_dssp GGGS-HHHHHHHHHHHH----TTS-HHHHHHTT--T--HHHHHHHHHHHH
T ss_pred cccCCHHHHHHHHHHHH---CccccHHHHHHHHcCcCcHHHHHHHHHHHH
Confidence 47899999999988875 4789999999999 999999998876643
No 243
>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=89.17 E-value=0.66 Score=36.38 Aligned_cols=43 Identities=19% Similarity=0.396 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHHhhcc-CCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 409 LNPKERCIVRLRFGIE-DGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 409 LperER~VL~LrY~L~-~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
|++....-|...|.|. +++..+..+||+.||+|..+|...+++
T Consensus 2 Lt~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~ 45 (60)
T PF01325_consen 2 LTESEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKR 45 (60)
T ss_dssp CSCHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHH
Confidence 4555555555555554 468899999999999999999985443
No 244
>cd00131 PAX Paired Box domain
Probab=89.15 E-value=1.1 Score=40.37 Aligned_cols=42 Identities=12% Similarity=-0.005 Sum_probs=33.1
Q ss_pred CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011992 409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 454 (473)
Q Consensus 409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~ 454 (473)
|+...|.-|.+.|. +|++..+||+.+|||.++|..++++-..
T Consensus 18 lS~d~R~rIv~~~~----~G~s~~~iA~~~~Vs~~tV~r~i~r~~e 59 (128)
T cd00131 18 LPDSIRQRIVELAQ----SGIRPCDISRQLRVSHGCVSKILNRYYE 59 (128)
T ss_pred CCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 55555554445566 8999999999999999999999887553
No 245
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=89.14 E-value=0.75 Score=42.26 Aligned_cols=35 Identities=26% Similarity=0.232 Sum_probs=29.2
Q ss_pred HHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992 415 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 453 (473)
Q Consensus 415 ~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL 453 (473)
.++..+++ +|+|.+|||+++|||.++|..++.+-.
T Consensus 12 ~~~~~~~~----~G~S~re~Ak~~gvs~sTvy~wv~r~~ 46 (138)
T COG3415 12 RVVDAVVG----EGLSCREAAKRFGVSISTVYRWVRRYR 46 (138)
T ss_pred HHHHHHHH----cCccHHHHHHHhCccHHHHHHHHHHhc
Confidence 34455555 899999999999999999999988754
No 246
>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=88.90 E-value=1.1 Score=37.43 Aligned_cols=43 Identities=23% Similarity=0.409 Sum_probs=35.2
Q ss_pred hCCHHHHHHHHH--HhhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011992 408 LLNPKERCIVRL--RFGIEDGKPKSLSEVGNIFGLSKERVRQLES 450 (473)
Q Consensus 408 ~LperER~VL~L--rY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~ 450 (473)
.|++++++||.. .-++..|++-.-++||+.+|+|..+||+.+.
T Consensus 1 ~Lt~rq~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~ 45 (78)
T PF03444_consen 1 MLTERQREILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMA 45 (78)
T ss_pred CCCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHH
Confidence 388999999864 2234567999999999999999999999654
No 247
>PHA02591 hypothetical protein; Provisional
Probab=88.68 E-value=0.9 Score=37.84 Aligned_cols=24 Identities=21% Similarity=0.436 Sum_probs=22.5
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLES 450 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~ 450 (473)
.|+|.++||+.||++.++|++.+.
T Consensus 58 qGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 58 KGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHh
Confidence 799999999999999999999865
No 248
>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=88.50 E-value=1.6 Score=33.76 Aligned_cols=36 Identities=28% Similarity=0.374 Sum_probs=27.4
Q ss_pred HHHHHHHHHH-hhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011992 411 PKERCIVRLR-FGIEDGKPKSLSEVGNIFGLSKERVRQLES 450 (473)
Q Consensus 411 erER~VL~Lr-Y~L~~ge~lTlkEIAe~LGIS~~rVrqi~~ 450 (473)
|.-+.|+.+- -. +++|..|||+.+|++.++|+..+.
T Consensus 10 p~R~~Il~~L~~~----~~~t~~ela~~l~~~~~t~s~hL~ 46 (61)
T PF12840_consen 10 PTRLRILRLLASN----GPMTVSELAEELGISQSTVSYHLK 46 (61)
T ss_dssp HHHHHHHHHHHHC----STBEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHhcC----CCCCHHHHHHHHCCCHHHHHHHHH
Confidence 5555565554 33 899999999999999999988654
No 249
>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=88.21 E-value=0.95 Score=33.97 Aligned_cols=39 Identities=21% Similarity=0.417 Sum_probs=26.9
Q ss_pred HHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992 412 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 452 (473)
Q Consensus 412 rER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA 452 (473)
|++.|+.+-+ ..++..|.+|||+.||||+.+|+..+...
T Consensus 1 R~~~il~~L~--~~~~~it~~eLa~~l~vS~rTi~~~i~~L 39 (55)
T PF08279_consen 1 RQKQILKLLL--ESKEPITAKELAEELGVSRRTIRRDIKEL 39 (55)
T ss_dssp HHHHHHHHHH--HTTTSBEHHHHHHHCTS-HHHHHHHHHHH
T ss_pred CHHHHHHHHH--HcCCCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 3455555432 23355999999999999999999865543
No 250
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=87.97 E-value=8.7 Score=42.21 Aligned_cols=45 Identities=20% Similarity=0.261 Sum_probs=32.6
Q ss_pred HhhCCHHHHHHHHH---------HhhccCC---CCCCHHHHHHHHCCCHHHHHHHHH
Q 011992 406 LTLLNPKERCIVRL---------RFGIEDG---KPKSLSEVGNIFGLSKERVRQLES 450 (473)
Q Consensus 406 L~~LperER~VL~L---------rY~L~~g---e~lTlkEIAe~LGIS~~rVrqi~~ 450 (473)
+..|..|.+.++.. -|+..|. .++++++||+.+|+.++||+...+
T Consensus 335 i~si~qR~~TllkV~~~Iv~~Q~~Ff~~G~~~LkPLtlkdVAe~lglHeSTVSRa~~ 391 (481)
T PRK12469 335 IRNAQQRFDTIQRVAECIVARQRDFFRYGEIALKPLVLRDVAEELGLHESTISRATG 391 (481)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCcCCcHHHHHHHhCCCcchhhHHhc
Confidence 35566666666543 3333332 789999999999999999998765
No 251
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=87.92 E-value=1.5 Score=35.11 Aligned_cols=24 Identities=17% Similarity=0.284 Sum_probs=21.1
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 428 PKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 428 ~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
+.+..|||+.+||+..+|++++.+
T Consensus 22 ~~ta~eLa~~lgl~~~~v~r~L~~ 45 (68)
T smart00550 22 TSTALQLAKNLGLPKKEVNRVLYS 45 (68)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHH
Confidence 599999999999999999886553
No 252
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=87.65 E-value=1.4 Score=32.68 Aligned_cols=26 Identities=27% Similarity=0.429 Sum_probs=23.1
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESRA 452 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~RA 452 (473)
+..|+++||+.+|||..+|..++.+.
T Consensus 26 ~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 26 ESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 34799999999999999999998764
No 253
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=87.64 E-value=1.1 Score=36.91 Aligned_cols=37 Identities=27% Similarity=0.352 Sum_probs=26.6
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHH-----HHHHHHHHHhccC
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLES-----RALYRLKQSLGGK 463 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~-----RAL~KLR~~L~~~ 463 (473)
.++|..|+|+.||++.++|+.+++ -.+.+|...+..-
T Consensus 30 ~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~aL 71 (80)
T PF13744_consen 30 RGLTQAELAERLGISQPRVSRLENGKIDDFSLDTLLRYLEAL 71 (80)
T ss_dssp CT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHHHT
T ss_pred cCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHHHc
Confidence 899999999999999999999985 2466666665543
No 254
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional
Probab=87.54 E-value=0.91 Score=41.83 Aligned_cols=49 Identities=16% Similarity=0.180 Sum_probs=41.6
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLK 457 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LG-----IS~~rVrqi~~RAL~KLR 457 (473)
.|+++|.+|+.+... +.|..+|.+||++.+. ++..+|+..+++.++||.
T Consensus 149 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~lr~Kl~ 202 (219)
T PRK10336 149 TLKPKEFALLELLMR-NAGRVLPRKLIEEKLYTWDEEVTSNAVEVHVHHLRRKLG 202 (219)
T ss_pred ecCHHHHHHHHHHHh-CCCccCcHHHHHHHhcCCCCCCCccCHHHHHHHHHHhcC
Confidence 499999999986663 3345699999999996 999999999999888885
No 255
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=87.40 E-value=0.61 Score=44.68 Aligned_cols=40 Identities=15% Similarity=0.174 Sum_probs=29.4
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.|+++ +|+.+.-. +..|+|.+|||+.||||+.||+.....
T Consensus 161 ~Lt~r--~Vl~~~~~--g~~g~s~~eIa~~l~iS~~Tv~~~~~~ 200 (225)
T PRK10046 161 PLTLN--AVRKLFKE--PGVQHTAETVAQALTISRTTARRYLEY 200 (225)
T ss_pred HHHHH--HHHHHHHc--CCCCcCHHHHHHHhCccHHHHHHHHHH
Confidence 35554 56655432 223799999999999999999998753
No 256
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=87.29 E-value=1.5 Score=37.28 Aligned_cols=42 Identities=26% Similarity=0.224 Sum_probs=32.5
Q ss_pred CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992 409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 453 (473)
Q Consensus 409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL 453 (473)
|++.++.|+..... +...|..|||+.+|+|+.+|+..+.+-.
T Consensus 1 ld~~D~~il~~L~~---~~~~~~~~la~~l~~s~~tv~~~l~~L~ 42 (108)
T smart00344 1 LDEIDRKILEELQK---DARISLAELAKKVGLSPSTVHNRVKRLE 42 (108)
T ss_pred CCHHHHHHHHHHHH---hCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 46677888765543 2468999999999999999998766543
No 257
>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional
Probab=86.76 E-value=1 Score=42.13 Aligned_cols=50 Identities=18% Similarity=0.120 Sum_probs=44.0
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LG-----IS~~rVrqi~~RAL~KLR~ 458 (473)
.|+++|++|+.+... +.|++.+.++|++.+. ++..+|...+++.++||..
T Consensus 160 ~Lt~~e~~il~~l~~-~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~lr~kl~~ 214 (240)
T PRK10710 160 DLTPAEFRLLKTLSH-EPGKVFSREQLLNHLYDDYRVVTDRTIDSHIKNLRRKLES 214 (240)
T ss_pred ecCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCcCcCCCccCHHHHHHHHHHHhhc
Confidence 499999999987765 4457899999999998 9999999999999999963
No 258
>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=86.75 E-value=1.5 Score=35.15 Aligned_cols=25 Identities=28% Similarity=0.417 Sum_probs=20.3
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
+..|..|||+.||||...|+.++..
T Consensus 19 r~Pt~eEiA~~lgis~~~v~~~l~~ 43 (78)
T PF04539_consen 19 REPTDEEIAEELGISVEEVRELLQA 43 (78)
T ss_dssp S--BHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCHHHHHHHHcccHHHHHHHHHh
Confidence 8999999999999999999987764
No 259
>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=86.73 E-value=0.68 Score=34.58 Aligned_cols=22 Identities=18% Similarity=0.356 Sum_probs=20.1
Q ss_pred CHHHHHHHHCCCHHHHHHHHHH
Q 011992 430 SLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 430 TlkEIAe~LGIS~~rVrqi~~R 451 (473)
|++|||+..|||..+|+..++.
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~ 22 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNG 22 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTT
T ss_pred CHHHHHHHHCcCHHHHHHHHhC
Confidence 6899999999999999998764
No 260
>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=86.59 E-value=1.3 Score=34.31 Aligned_cols=43 Identities=19% Similarity=0.286 Sum_probs=27.3
Q ss_pred CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992 409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 453 (473)
Q Consensus 409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL 453 (473)
|+..+..||.... ..+++++..+||+.+|++..+|+.++++..
T Consensus 1 lt~~q~~vL~~l~--~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~ 43 (68)
T PF13463_consen 1 LTRPQWQVLRALA--HSDGPMTQSDLAERLGISKSTVSRIIKKLE 43 (68)
T ss_dssp --HHHHHHHHHHT----TS-BEHHHHHHHTT--HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHH--ccCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4556666655444 234899999999999999999997655544
No 261
>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=86.48 E-value=1 Score=33.81 Aligned_cols=34 Identities=35% Similarity=0.461 Sum_probs=25.6
Q ss_pred HHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 418 RLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 418 ~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.|.++-..+.++++.|||+.+|+++++|..++..
T Consensus 8 iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~t 41 (52)
T PF09339_consen 8 ILEALAESGGPLTLSEIARALGLPKSTVHRLLQT 41 (52)
T ss_dssp HHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 4444445557789999999999999999887653
No 262
>PRK15479 transcriptional regulatory protein TctD; Provisional
Probab=86.08 E-value=1.3 Score=40.73 Aligned_cols=49 Identities=18% Similarity=0.233 Sum_probs=41.3
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLK 457 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LG-----IS~~rVrqi~~RAL~KLR 457 (473)
.|+++|.+|+.+... +.|...+.++|++.+. +|..+|...+++.++||.
T Consensus 148 ~Lt~~E~~il~~l~~-~~~~~~~~~~i~~~l~~~~~~~~~~tv~~~i~~ir~kl~ 201 (221)
T PRK15479 148 ALTPREQALLTVLMY-RRTRPVSRQQLFEQVFSLNDEVSPESIELYIHRLRKKLQ 201 (221)
T ss_pred ecCHHHHHHHHHHHh-CCCCcCcHHHHHHHhcCCCCCCCcccHHHHHHHHHHhcC
Confidence 499999999977653 3346679999999986 999999999999999885
No 263
>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=85.99 E-value=2.9 Score=34.04 Aligned_cols=54 Identities=19% Similarity=0.272 Sum_probs=36.4
Q ss_pred HHHHHHHHHhhCCHHHHHHHHHHhh-ccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 398 MRQHVRNLLTLLNPKERCIVRLRFG-IEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 398 l~e~L~~aL~~LperER~VL~LrY~-L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
+...|......|++.|+.|.....- .+.-..+|..|||+..|||.++|....++
T Consensus 3 l~~~i~~~~~~ls~~e~~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~kk 57 (77)
T PF01418_consen 3 LLEKIRSQYNSLSPTEKKIADYILENPDEIAFMSISELAEKAGVSPSTIVRFCKK 57 (77)
T ss_dssp HHHHHHHHGGGS-HHHHHHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHHHH
T ss_pred HHHHHHHHHhhCCHHHHHHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHHHH
Confidence 3456777888999999998754221 00116899999999999999999876554
No 264
>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB. PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself. It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well.
Probab=85.95 E-value=0.61 Score=42.98 Aligned_cols=49 Identities=16% Similarity=0.117 Sum_probs=41.6
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHH-----HHHHCCCHHHHHHHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEV-----GNIFGLSKERVRQLESRALYRLK 457 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEI-----Ae~LGIS~~rVrqi~~RAL~KLR 457 (473)
.|+++|.+|+.+... +.|+++|.++| |+.++++..+|+..+++.++||.
T Consensus 154 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~l~~Kl~ 207 (226)
T TIGR02154 154 SLGPTEFRLLHFFMT-HPERVYSREQLLDRVWGRDVYVEERTVDVHIRRLRKALN 207 (226)
T ss_pred EcCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCCCCCCCCccHHHHHHHHHHhhc
Confidence 499999999887764 33467888888 77899999999999999999986
No 265
>PRK12423 LexA repressor; Provisional
Probab=85.90 E-value=1.5 Score=42.09 Aligned_cols=48 Identities=29% Similarity=0.468 Sum_probs=35.7
Q ss_pred hhCCHHHHHHHHHHh--hccCCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHHHHH
Q 011992 407 TLLNPKERCIVRLRF--GIEDGKPKSLSEVGNIFG-LSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 407 ~~LperER~VL~LrY--~L~~ge~lTlkEIAe~LG-IS~~rVrqi~~RAL~KLR~ 458 (473)
..|++++++|+..-- ....|-.+|..|||+.+| +|+++|+. +++.|++
T Consensus 2 ~~lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~----~l~~L~~ 52 (202)
T PRK12423 2 DTLTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARK----HVQALAE 52 (202)
T ss_pred CcCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHH----HHHHHHH
Confidence 348999999986422 223345789999999999 59999995 6666665
No 266
>PF12728 HTH_17: Helix-turn-helix domain
Probab=85.74 E-value=0.88 Score=33.72 Aligned_cols=24 Identities=17% Similarity=0.376 Sum_probs=21.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Q 011992 429 KSLSEVGNIFGLSKERVRQLESRA 452 (473)
Q Consensus 429 lTlkEIAe~LGIS~~rVrqi~~RA 452 (473)
+|.+|+|+.||||..+|.++..+.
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcC
Confidence 689999999999999999998654
No 267
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=85.53 E-value=3.1 Score=38.39 Aligned_cols=64 Identities=19% Similarity=0.326 Sum_probs=37.0
Q ss_pred HHHHHhhCCHHHHHHHHHH----hhccCCCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHhccCch
Q 011992 402 VRNLLTLLNPKERCIVRLR----FGIEDGKPKSLSEVGNIFGLSKERVRQLES--RALYRLKQSLGGKAS 465 (473)
Q Consensus 402 L~~aL~~LperER~VL~Lr----Y~L~~ge~lTlkEIAe~LGIS~~rVrqi~~--RAL~KLR~~L~~~~l 465 (473)
+.+.=..|++.++....+- |..++|+.+|+.|||+.+||++.++..+.+ ++.....+.+....+
T Consensus 4 ~~~le~~L~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis~~tLYrWr~~~~~Fiey~n~la~~~~ 73 (142)
T PF13022_consen 4 LKELEAKLTLQQRKAAQLLVENELMPENGERRTQAEIAEEVGISRSTLYRWRQQNKAFIEYKNELADRFL 73 (142)
T ss_dssp HHHHHTTS-HHHHHHHHHHHHHHHS------S-HHHHHHHHTS-HHHHHHHHHH-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHcCHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCCHHHHHHHHhcCHHHHHHHHHHHHHHH
Confidence 3344467898888854432 222345789999999999999999999985 344444444444433
No 268
>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=85.49 E-value=1 Score=38.23 Aligned_cols=45 Identities=24% Similarity=0.323 Sum_probs=31.9
Q ss_pred CCHHHHHHHHHHhhccC---CCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011992 409 LNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQLESRALY 454 (473)
Q Consensus 409 LperER~VL~LrY~L~~---ge~lTlkEIAe~LGIS~~rVrqi~~RAL~ 454 (473)
+++.|+.-+..|+.+-. .+++|+.||++.+|+|..+|.. .+|+|+
T Consensus 27 ~T~~E~~~l~~R~~va~~lL~~g~syreIa~~tgvS~aTItR-vsr~Lk 74 (87)
T PF01371_consen 27 CTPDELEALAQRWQVAKELLDEGKSYREIAEETGVSIATITR-VSRCLK 74 (87)
T ss_dssp SSHHHHHHHHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHH-HHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHH-HHHHHH
Confidence 67777766655544322 2689999999999999999875 344443
No 269
>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=85.16 E-value=1.7 Score=32.95 Aligned_cols=42 Identities=24% Similarity=0.384 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992 409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 453 (473)
Q Consensus 409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL 453 (473)
|+..|-.+|...+. ..+.+..|||+.+|++.++|..+..+-.
T Consensus 1 lt~~q~~iL~~l~~---~~~~~~~~la~~~~~~~~~~t~~i~~L~ 42 (59)
T PF01047_consen 1 LTPSQFRILRILYE---NGGITQSELAEKLGISRSTVTRIIKRLE 42 (59)
T ss_dssp STHHHHHHHHHHHH---HSSEEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH---cCCCCHHHHHHHHCCChhHHHHHHHHHH
Confidence 45556666655443 2679999999999999999998766543
No 270
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=84.44 E-value=2.3 Score=39.06 Aligned_cols=41 Identities=15% Similarity=0.261 Sum_probs=33.1
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.|++.++.||.+--. +...++.|||+.+|+|+++|+.++.+
T Consensus 6 ~lD~~D~~Il~~Lq~---d~R~s~~eiA~~lglS~~tV~~Ri~r 46 (153)
T PRK11179 6 QIDNLDRGILEALME---NARTPYAELAKQFGVSPGTIHVRVEK 46 (153)
T ss_pred ccCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 378888888875543 25789999999999999999987655
No 271
>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=84.21 E-value=1.1 Score=35.29 Aligned_cols=41 Identities=17% Similarity=0.213 Sum_probs=31.0
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.|++.|..|+..-.. ..+.|..|||+.+|+++.+|+..+.+
T Consensus 5 gLs~~E~~vy~~Ll~---~~~~t~~eIa~~l~i~~~~v~~~L~~ 45 (68)
T PF01978_consen 5 GLSENEAKVYLALLK---NGPATAEEIAEELGISRSTVYRALKS 45 (68)
T ss_dssp CHHHHHHHHHHHHHH---HCHEEHHHHHHHHTSSHHHHHHHHHH
T ss_pred CcCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 467778887643321 16899999999999999999885543
No 272
>CHL00148 orf27 Ycf27; Reviewed
Probab=83.98 E-value=1.5 Score=41.09 Aligned_cols=50 Identities=18% Similarity=0.115 Sum_probs=42.4
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHH-------CCCHHHHHHHHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-------GLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~L-------GIS~~rVrqi~~RAL~KLR~ 458 (473)
.|+++|.+|+.+... +.|+++|.+||++.+ +++..+|..++++.++||..
T Consensus 161 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~l~~~~~~~~~~~~tv~~~i~~lr~KL~~ 217 (240)
T CHL00148 161 RLTGMEFSLLELLIS-KSGEIFSRATILKEVWGYTPERHIDTRVVDVHISRLRAKLED 217 (240)
T ss_pred EcCHHHHHHHHHHHH-CCCEEEcHHHHHHHhcCCCcccCCCcccHHHHHHHHHHHhcc
Confidence 399999999986653 345789999999999 48999999999999999974
No 273
>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=83.57 E-value=2 Score=40.87 Aligned_cols=45 Identities=18% Similarity=0.268 Sum_probs=34.6
Q ss_pred hhCCHHHHHHHHHHhh--ccCCCCCCHHHHHHHHCCC-HHHHHHHHHH
Q 011992 407 TLLNPKERCIVRLRFG--IEDGKPKSLSEVGNIFGLS-KERVRQLESR 451 (473)
Q Consensus 407 ~~LperER~VL~LrY~--L~~ge~lTlkEIAe~LGIS-~~rVrqi~~R 451 (473)
..|+++|+.||..... ..+|.+.|..|||+.+|++ .++|..++.+
T Consensus 2 ~~lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~ 49 (199)
T TIGR00498 2 KPLTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKA 49 (199)
T ss_pred CccCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHH
Confidence 3589999999876442 2345679999999999998 9999875443
No 274
>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=83.12 E-value=1.4 Score=31.41 Aligned_cols=24 Identities=25% Similarity=0.407 Sum_probs=21.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Q 011992 429 KSLSEVGNIFGLSKERVRQLESRA 452 (473)
Q Consensus 429 lTlkEIAe~LGIS~~rVrqi~~RA 452 (473)
+|.+|+|+.||||+.+|.++.+..
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g 25 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEG 25 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcC
Confidence 689999999999999999998765
No 275
>PRK00215 LexA repressor; Validated
Probab=82.95 E-value=2.5 Score=40.40 Aligned_cols=45 Identities=24% Similarity=0.263 Sum_probs=34.9
Q ss_pred CCHHHHHHHHHHh--hccCCCCCCHHHHHHHHCC-CHHHHHHHHHHHH
Q 011992 409 LNPKERCIVRLRF--GIEDGKPKSLSEVGNIFGL-SKERVRQLESRAL 453 (473)
Q Consensus 409 LperER~VL~LrY--~L~~ge~lTlkEIAe~LGI-S~~rVrqi~~RAL 453 (473)
|+++|+.||.+.. ....+.++|+.|||+.+|+ +.++|..++.+-.
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~ 49 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALE 49 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 7888999886543 2344578899999999999 9999998765533
No 276
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=82.13 E-value=2.6 Score=40.14 Aligned_cols=35 Identities=29% Similarity=0.358 Sum_probs=28.0
Q ss_pred HHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 412 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 412 rER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.++.|..++ . +|+|+.+||+.||||.++|..+.+.
T Consensus 161 ~~~~i~~~~-~----~g~s~~~iak~lgis~~Tv~r~~k~ 195 (200)
T PRK13413 161 KEEKIKKLL-D----KGTSKSEIARKLGVSRTTLARFLKT 195 (200)
T ss_pred hHHHHHHHH-H----CCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 345566554 3 6899999999999999999998863
No 277
>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator. This model describes a family of DNA-binding response regulator proteins, associated with an adjacent histidine kinase (TIGR03785) to form a two-component system. This system co-occurs with, and often is adjacent to, a proteobacterial variant form of the protein sorting transpeptidase called sortase (TIGR03784), and a single target protein for the sortase. We give this protein the gene symbol pdsR, for Proteobacterial Dedicated Sortase system Response regulator.
Probab=82.07 E-value=2.4 Score=39.56 Aligned_cols=50 Identities=14% Similarity=0.087 Sum_probs=41.2
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHH--HHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEV--GNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEI--Ae~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
.|+++|.+||.+... +.|.-+|.++| |..++++..+|+.+.++.++||..
T Consensus 156 ~Lt~~E~~il~~l~~-~~g~v~s~~~i~~~~~~~~~~~tv~~~v~rlr~Kl~~ 207 (227)
T TIGR03787 156 DLTVTEFWMVHALAK-HPGHVKSRQQLMDAAKIVVDDSTITSHIKRIRKKFQA 207 (227)
T ss_pred cCCHHHHHHHHHHHh-CCCccccHHHHHHHhhhcCCccCHHHHHHHHHHHhcc
Confidence 399999999887663 12344699999 888999999999999999999863
No 278
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=82.05 E-value=3.3 Score=35.96 Aligned_cols=45 Identities=29% Similarity=0.369 Sum_probs=33.1
Q ss_pred HHHHHHHhhCCHHHHHHHHHHhhccC---CCCCCHHHHHHHHCCCHHHHH
Q 011992 400 QHVRNLLTLLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVR 446 (473)
Q Consensus 400 e~L~~aL~~LperER~VL~LrY~L~~---ge~lTlkEIAe~LGIS~~rVr 446 (473)
+.|..++ |++.||+.+-.|+.|-. ..+++.+||+..||+|..+|-
T Consensus 31 ~~lL~ll--LTpdEReal~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtIT 78 (103)
T COG2973 31 QPLLTLL--LTPDEREALGTRVRIVEELLRGELSQREIAQKLGVSIATIT 78 (103)
T ss_pred HHHHHHH--cCHhHHHHHHHHHHHHHHHHhccccHHHHHHHhCcchhhhc
Confidence 3444444 78888887766665432 268999999999999999874
No 279
>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=81.58 E-value=4.8 Score=32.15 Aligned_cols=34 Identities=24% Similarity=0.292 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHcCCC-HHHHHH
Q 011992 288 LEKEKSKLQSQFGREPTLIEWAKAIGLS-CRDLKS 321 (473)
Q Consensus 288 le~a~~~L~~~lGRePT~eEiA~~lGms-~eeL~~ 321 (473)
+-....+.....|.+||..|||+.+|+. ...+..
T Consensus 11 vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~ 45 (65)
T PF01726_consen 11 VLEFIREYIEENGYPPTVREIAEALGLKSTSTVQR 45 (65)
T ss_dssp HHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHH
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHH
Confidence 3344556677899999999999999996 544443
No 280
>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=81.53 E-value=1.8 Score=30.61 Aligned_cols=25 Identities=16% Similarity=0.300 Sum_probs=22.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992 429 KSLSEVGNIFGLSKERVRQLESRAL 453 (473)
Q Consensus 429 lTlkEIAe~LGIS~~rVrqi~~RAL 453 (473)
+|..|+|+.+|||..+|+.+.....
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 5789999999999999999988764
No 281
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=81.50 E-value=2.6 Score=31.25 Aligned_cols=29 Identities=38% Similarity=0.533 Sum_probs=23.2
Q ss_pred CCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 426 GKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 426 ge~l-TlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
|+.+ |..|||+.+|+|+.+|++ ++++|.+
T Consensus 17 ~~~l~s~~~la~~~~vs~~tv~~----~l~~L~~ 46 (60)
T smart00345 17 GDKLPSERELAAQLGVSRTTVRE----ALSRLEA 46 (60)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHH----HHHHHHH
Confidence 4556 899999999999999988 5555554
No 282
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=81.38 E-value=3.3 Score=37.19 Aligned_cols=43 Identities=30% Similarity=0.269 Sum_probs=33.8
Q ss_pred hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992 407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 452 (473)
Q Consensus 407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA 452 (473)
..|++.++.||.+--. | -..++.|||+.+|+|..+|+.++.+-
T Consensus 4 ~~lD~~D~~IL~~L~~--d-~r~~~~eia~~lglS~~~v~~Ri~~L 46 (154)
T COG1522 4 MKLDDIDRRILRLLQE--D-ARISNAELAERVGLSPSTVLRRIKRL 46 (154)
T ss_pred ccccHHHHHHHHHHHH--h-CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 3578888888875443 2 45999999999999999999876653
No 283
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=81.31 E-value=2.6 Score=39.12 Aligned_cols=41 Identities=22% Similarity=0.098 Sum_probs=32.3
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.|++.++.||.+--. +...|+.|||+.+|+|+++|+.++.+
T Consensus 11 ~lD~~D~~IL~~Lq~---d~R~s~~eiA~~lglS~~tv~~Ri~r 51 (164)
T PRK11169 11 DLDRIDRNILNELQK---DGRISNVELSKRVGLSPTPCLERVRR 51 (164)
T ss_pred hHHHHHHHHHHHhcc---CCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 367778888764332 36789999999999999999987665
No 284
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=81.07 E-value=6.2 Score=35.80 Aligned_cols=53 Identities=17% Similarity=0.217 Sum_probs=41.0
Q ss_pred HHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992 399 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457 (473)
Q Consensus 399 ~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR 457 (473)
...+..++-.|++.+-+|+..-.. .+.++|..|||+.||+++++|.. |+++|-
T Consensus 15 ~~dvl~c~~GLs~~Dv~v~~~LL~--~~~~~tvdelae~lnr~rStv~r----sl~~L~ 67 (126)
T COG3355 15 CEDVLKCVYGLSELDVEVYKALLE--ENGPLTVDELAEILNRSRSTVYR----SLQNLL 67 (126)
T ss_pred HHHHHHHHhCCcHHHHHHHHHHHh--hcCCcCHHHHHHHHCccHHHHHH----HHHHHH
Confidence 345677778899999998765541 23799999999999999999976 555553
No 285
>PF13551 HTH_29: Winged helix-turn helix
Probab=80.94 E-value=2.5 Score=35.56 Aligned_cols=26 Identities=19% Similarity=0.349 Sum_probs=23.5
Q ss_pred CCC-CHHHHHHHHCCCHHHHHHHHHHH
Q 011992 427 KPK-SLSEVGNIFGLSKERVRQLESRA 452 (473)
Q Consensus 427 e~l-TlkEIAe~LGIS~~rVrqi~~RA 452 (473)
++. |..+||+.+|+|+.+|..++++-
T Consensus 10 ~g~~~~~~ia~~lg~s~~Tv~r~~~~~ 36 (112)
T PF13551_consen 10 EGVSTIAEIARRLGISRRTVYRWLKRY 36 (112)
T ss_pred cCCCcHHHHHHHHCcCHHHHHHHHHHH
Confidence 677 59999999999999999998873
No 286
>PHA01976 helix-turn-helix protein
Probab=80.82 E-value=3.1 Score=32.30 Aligned_cols=25 Identities=16% Similarity=0.238 Sum_probs=23.4
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.++|..|+|+.+|+|.++|+++++.
T Consensus 14 ~glt~~~lA~~~gvs~~~v~~~e~g 38 (67)
T PHA01976 14 RAWSAPELSRRAGVRHSLIYDFEAD 38 (67)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 7899999999999999999999864
No 287
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=79.84 E-value=8.6 Score=34.13 Aligned_cols=43 Identities=14% Similarity=0.142 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhc
Q 011992 284 DLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSG 326 (473)
Q Consensus 284 ~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g 326 (473)
+...++++..-+.+.+...++.+++|+.+|++...+.+.++..
T Consensus 7 ~~~~i~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 7 DAITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred cHHHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3445677777888889999999999999999999998887754
No 288
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=79.83 E-value=3.2 Score=37.26 Aligned_cols=25 Identities=24% Similarity=0.309 Sum_probs=23.2
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
+|+|..+||+.||+|+..|+|.++.
T Consensus 21 eG~Sq~~iA~LLGltqaAVS~Yls~ 45 (119)
T COG2522 21 EGLSQYRIAKLLGLTQAAVSQYLSG 45 (119)
T ss_pred cCCcHHHHHHHhCCCHHHHHHHHcc
Confidence 7999999999999999999998764
No 289
>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=79.09 E-value=2.7 Score=31.21 Aligned_cols=25 Identities=24% Similarity=0.426 Sum_probs=21.5
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.++|.+|+|+.+|+|+++|+.+++.
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 7899999999999999999999876
No 290
>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=78.57 E-value=4.1 Score=30.64 Aligned_cols=51 Identities=12% Similarity=0.137 Sum_probs=38.7
Q ss_pred hCCHHHHHHHHHHhhccCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDG-KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~g-e~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
.+++.+..+|.-+|..+.. ......+||..+||+...|..+...-..+.|+
T Consensus 6 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 6 RFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 4677888888888874221 23346789999999999999999887777663
No 291
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=78.36 E-value=2.4 Score=33.61 Aligned_cols=35 Identities=23% Similarity=0.251 Sum_probs=28.7
Q ss_pred HHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992 415 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 453 (473)
Q Consensus 415 ~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL 453 (473)
.||..+.. .|.|..+||..+||+.++++.+.....
T Consensus 14 ~~v~~~~~----~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 14 QAVREYLE----SGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp HHHHHHHH----HHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHH----CCCceEeeecccccccccccHHHHHHh
Confidence 35555545 789999999999999999999998876
No 292
>PRK11564 stationary phase inducible protein CsiE; Provisional
Probab=78.27 E-value=5.9 Score=42.06 Aligned_cols=52 Identities=15% Similarity=0.187 Sum_probs=43.6
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 459 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~ 459 (473)
.+++.||..+.+.+.|...+..++.++|+.|+||++||.+-+.+....|.+.
T Consensus 10 ~~s~~ER~~~il~~LL~~~~~v~l~~Lae~l~VSrsTi~~DLk~l~~~L~~y 61 (426)
T PRK11564 10 VLSAPQRRCQILLMLFQPGLTVTLETFSQLNGVDDDTARQDIAETGREIQRY 61 (426)
T ss_pred CCCHHHHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHHHh
Confidence 4788898887777767667899999999999999999999888777777663
No 293
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=78.16 E-value=2.8 Score=32.53 Aligned_cols=25 Identities=20% Similarity=0.340 Sum_probs=21.2
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.++|..++|+.+|+|.++|+++++.
T Consensus 13 ~gls~~~lA~~~g~s~s~v~~iE~G 37 (64)
T PF13560_consen 13 AGLSQAQLADRLGVSQSTVSRIERG 37 (64)
T ss_dssp HTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 6899999999999999999999864
No 294
>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=77.83 E-value=6.6 Score=29.74 Aligned_cols=37 Identities=30% Similarity=0.457 Sum_probs=26.6
Q ss_pred HHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 411 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 411 erER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
..+..|+...+. .+.+..||++.+|++..+|+..+.+
T Consensus 7 ~~~~~il~~l~~----~~~~~~ei~~~~~i~~~~i~~~l~~ 43 (78)
T cd00090 7 PTRLRILRLLLE----GPLTVSELAERLGLSQSTVSRHLKK 43 (78)
T ss_pred hHHHHHHHHHHH----CCcCHHHHHHHHCcCHhHHHHHHHH
Confidence 344555554343 3399999999999999999776554
No 295
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.
Probab=77.76 E-value=7.7 Score=32.49 Aligned_cols=31 Identities=26% Similarity=0.290 Sum_probs=25.2
Q ss_pred CCCCHHHHHHHHC-CCHHHHHHHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFG-LSKERVRQLESRALYRLK 457 (473)
Q Consensus 427 e~lTlkEIAe~LG-IS~~rVrqi~~RAL~KLR 457 (473)
-++|+.|||+.|| .+.++|.....+.-++++
T Consensus 43 ~~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~ 74 (90)
T cd06571 43 TGLSLPEIGRAFGGRDHSTVLHAVRKIEELLE 74 (90)
T ss_pred hCCCHHHHHHHhCCCCHhHHHHHHHHHHHHHH
Confidence 5899999999999 999999995555554444
No 296
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=77.65 E-value=28 Score=37.87 Aligned_cols=44 Identities=23% Similarity=0.480 Sum_probs=31.9
Q ss_pred HhhCCHHHHHHHHH---------HhhccCC----CCCCHHHHHHHHCCCHHHHHHHHH
Q 011992 406 LTLLNPKERCIVRL---------RFGIEDG----KPKSLSEVGNIFGLSKERVRQLES 450 (473)
Q Consensus 406 L~~LperER~VL~L---------rY~L~~g----e~lTlkEIAe~LGIS~~rVrqi~~ 450 (473)
+..|.-|++.++.. -|+ .+| .++++++||+.+|+.++||+....
T Consensus 296 iksL~qR~~TLlkV~~~Iv~~Q~~Ff-~~g~~~l~PL~LrdvA~~i~~HESTISRai~ 352 (444)
T COG1508 296 IKSLEQREETLLKVAEEIVEYQKAFF-EGGEEALKPLVLRDVADEIGMHESTISRAIT 352 (444)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH-hCCcccCCcccHHHHHHHhCccHHHHHHHHh
Confidence 45677777766532 222 333 678999999999999999998765
No 297
>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=77.50 E-value=6.7 Score=33.29 Aligned_cols=45 Identities=16% Similarity=0.187 Sum_probs=32.8
Q ss_pred HhhCCHHHHHHHHHH----hhcc-CCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011992 406 LTLLNPKERCIVRLR----FGIE-DGKPKSLSEVGNIFGLSKERVRQLES 450 (473)
Q Consensus 406 L~~LperER~VL~Lr----Y~L~-~ge~lTlkEIAe~LGIS~~rVrqi~~ 450 (473)
...+++++..+|... |+.. ....+|..|||+.+|+++++|+..++
T Consensus 20 ~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~ 69 (95)
T TIGR01610 20 GADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIK 69 (95)
T ss_pred hCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHH
Confidence 356888888877632 2211 13789999999999999999887443
No 298
>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=77.36 E-value=1.9 Score=31.17 Aligned_cols=26 Identities=23% Similarity=0.388 Sum_probs=23.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011992 429 KSLSEVGNIFGLSKERVRQLESRALY 454 (473)
Q Consensus 429 lTlkEIAe~LGIS~~rVrqi~~RAL~ 454 (473)
+|..|+|+.+||+..+|+....+.+-
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~~~g~l 26 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERIGLL 26 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999999887763
No 299
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=77.27 E-value=6.1 Score=28.42 Aligned_cols=25 Identities=20% Similarity=0.376 Sum_probs=22.0
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.+.+..+|++.+|++..+|+..+..
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~ 37 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNK 37 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 5699999999999999999886644
No 300
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=77.21 E-value=4.2 Score=29.98 Aligned_cols=27 Identities=22% Similarity=0.304 Sum_probs=23.4
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESRAL 453 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~RAL 453 (473)
+..+..+|++.+|+|..+|+.++.+-.
T Consensus 9 ~~~~~~~i~~~l~is~~~v~~~l~~L~ 35 (66)
T smart00418 9 GELCVCELAEILGLSQSTVSHHLKKLR 35 (66)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHHH
Confidence 789999999999999999988776533
No 301
>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=77.19 E-value=4.1 Score=31.36 Aligned_cols=25 Identities=24% Similarity=0.318 Sum_probs=22.0
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Q 011992 426 GKPKSLSEVGNIFGLSKERVRQLES 450 (473)
Q Consensus 426 ge~lTlkEIAe~LGIS~~rVrqi~~ 450 (473)
....+.+|+|+.||||..||+.-+.
T Consensus 12 ~~~~s~~ela~~~~VS~~TiRRDl~ 36 (57)
T PF08220_consen 12 KGKVSVKELAEEFGVSEMTIRRDLN 36 (57)
T ss_pred cCCEEHHHHHHHHCcCHHHHHHHHH
Confidence 3688999999999999999998654
No 302
>PRK10072 putative transcriptional regulator; Provisional
Probab=77.10 E-value=3.9 Score=35.24 Aligned_cols=32 Identities=28% Similarity=0.479 Sum_probs=27.0
Q ss_pred HHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 416 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 416 VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
|-.+|.. .++|..|+|+.+|||.++|+++++.
T Consensus 38 ik~LR~~----~glTQ~elA~~lGvS~~TVs~WE~G 69 (96)
T PRK10072 38 FEQLRKG----TGLKIDDFARVLGVSVAMVKEWESR 69 (96)
T ss_pred HHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 4445665 7899999999999999999999863
No 303
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=76.91 E-value=5.6 Score=35.15 Aligned_cols=35 Identities=17% Similarity=0.196 Sum_probs=28.9
Q ss_pred HHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992 415 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 453 (473)
Q Consensus 415 ~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL 453 (473)
.++.+.+. .+.|..+||+.+|||.++|+.+.++..
T Consensus 20 ~aV~~~~~----~g~sv~evA~e~gIs~~tl~~W~r~y~ 54 (121)
T PRK09413 20 AIVQQSFE----PGMTVSLVARQHGVAASQLFLWRKQYQ 54 (121)
T ss_pred HHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHh
Confidence 35555555 789999999999999999999988753
No 304
>PHA00542 putative Cro-like protein
Probab=76.49 E-value=4.2 Score=33.69 Aligned_cols=26 Identities=12% Similarity=0.102 Sum_probs=23.7
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESRA 452 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~RA 452 (473)
.++|..|+|+.+|||.++|+.++...
T Consensus 30 ~glTq~elA~~lgIs~~tIsr~e~g~ 55 (82)
T PHA00542 30 AGWSQEQIADATDVSQPTICRIYSGR 55 (82)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHcCC
Confidence 68999999999999999999998653
No 305
>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=76.45 E-value=5 Score=29.53 Aligned_cols=25 Identities=12% Similarity=0.279 Sum_probs=23.1
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.++|..++|+.+|+|.++|+.+++.
T Consensus 14 ~gltq~~lA~~~gvs~~~vs~~e~g 38 (58)
T TIGR03070 14 LGLTQADLADLAGVGLRFIRDVENG 38 (58)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 6899999999999999999999864
No 306
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=76.10 E-value=6.9 Score=33.16 Aligned_cols=43 Identities=19% Similarity=0.210 Sum_probs=35.9
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 453 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL 453 (473)
.|++.-|..|..+.. .++.+..++|+.+|||..+++.+..|-.
T Consensus 8 ~Lt~~gR~~lv~~vv---~~g~~~a~aA~~~gVS~~Ta~kW~~Ryr 50 (85)
T PF13011_consen 8 RLTPRGRLRLVRRVV---EQGWPVAHAAAEFGVSRRTAYKWLARYR 50 (85)
T ss_pred CCCHHHHHHHHHHHH---HcCCcHHHHHHHhCCCHHHHHHHHHHHH
Confidence 588888887776663 2689999999999999999999988754
No 307
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=76.09 E-value=3.5 Score=41.55 Aligned_cols=25 Identities=20% Similarity=0.444 Sum_probs=23.8
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
++|.+++||+.||||..+|+.+.+|
T Consensus 18 ~gmk~~dIAeklGvspntiksWKrr 42 (279)
T COG5484 18 KGMKLKDIAEKLGVSPNTIKSWKRR 42 (279)
T ss_pred hhccHHHHHHHhCCChHHHHHHHHh
Confidence 7899999999999999999999876
No 308
>PRK15435 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional
Probab=76.07 E-value=1.1e+02 Score=32.26 Aligned_cols=95 Identities=17% Similarity=0.234 Sum_probs=59.8
Q ss_pred ceEeecchhhHHHhhhhccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHH
Q 011992 207 VKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLI 286 (473)
Q Consensus 207 ~~~v~s~r~~er~~~~~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~ 286 (473)
.+-|++|+--=|-+-+.|.++..++.| |.....- ..+.+. +..+-. |...+ +.+ ....
T Consensus 28 ~~~V~tTgi~CRp~C~ar~p~~eNv~f--f~~~~~A----~~aGfR---pC~rCr--P~~~~---~~~--------~~~~ 85 (353)
T PRK15435 28 VFAVRTTGIFCRPSCRARHALRENVRF--YANASEA----LAAGFR---PCKRCQ--PDKAN---PQQ--------HRLD 85 (353)
T ss_pred EEEEeecceEEcccccccCCCcCCccc--cCCHHHH----HHcCCC---chhccC--Ccccc---hhh--------hHHH
Confidence 567899998888888888899999998 5555333 123333 222111 11110 000 1122
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhh
Q 011992 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS 325 (473)
Q Consensus 287 kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~ 325 (473)
.++++..-+.+ +..++.+++|+.+|++...+.+..+.
T Consensus 86 ~i~~a~~~I~~--~~~lsl~eLA~~lG~S~~~L~R~Fkk 122 (353)
T PRK15435 86 KITHACRLLEQ--ETPVTLEALADQVAMSPFHLHRLFKA 122 (353)
T ss_pred HHHHHHHHHHh--CCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 44555554544 56789999999999999999888866
No 309
>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=75.87 E-value=4.7 Score=29.13 Aligned_cols=38 Identities=13% Similarity=0.255 Sum_probs=25.0
Q ss_pred HHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 411 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 411 erER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
+-|+.+|.-... ..+-+..+.|+.||||+.++...+.+
T Consensus 4 ~~E~~~i~~aL~---~~~gn~~~aA~~Lgisr~tL~~klkk 41 (42)
T PF02954_consen 4 EFEKQLIRQALE---RCGGNVSKAARLLGISRRTLYRKLKK 41 (42)
T ss_dssp HHHHHHHHHHHH---HTTT-HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHH---HhCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 445666544332 03568999999999999999876653
No 310
>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]
Probab=75.81 E-value=3.6 Score=39.46 Aligned_cols=39 Identities=21% Similarity=0.238 Sum_probs=32.2
Q ss_pred HHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992 414 RCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457 (473)
Q Consensus 414 R~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR 457 (473)
+..+.|.- .|+|..|||+.|++|++|++.++.|+..+..
T Consensus 9 ~kA~eLk~-----~Glt~gEIAdELNvSreTa~WL~~r~~~~~~ 47 (203)
T COG0856 9 KKARELKS-----KGLTTGEIADELNVSRETATWLLTRAFKKES 47 (203)
T ss_pred HHHHHHHH-----CCCcHHHhhhhhhhhHHHHHHHHhhhhhccC
Confidence 33445554 7999999999999999999999999877654
No 311
>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=75.51 E-value=6.6 Score=37.21 Aligned_cols=41 Identities=22% Similarity=0.214 Sum_probs=31.7
Q ss_pred HHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011992 411 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 454 (473)
Q Consensus 411 erER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~ 454 (473)
+.-|.-++-.|.. +++++..||...|||.+|++.+..+|..
T Consensus 5 ~e~R~~~R~~YV~---~~~sLe~aA~~~gVs~~TarrWK~~Ak~ 45 (165)
T PF08822_consen 5 QETRDAVRRAYVF---DRLSLEQAAAKCGVSYATARRWKREAKA 45 (165)
T ss_pred HHHHHHHHHHHHh---CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3344444444431 7899999999999999999999998854
No 312
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=75.17 E-value=7.5 Score=31.68 Aligned_cols=26 Identities=27% Similarity=0.349 Sum_probs=23.2
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESRA 452 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~RA 452 (473)
.+++..|||+.+|++..+|+.++..-
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l~~L 44 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLNTL 44 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 57999999999999999999877654
No 313
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=75.08 E-value=8.1 Score=29.56 Aligned_cols=39 Identities=21% Similarity=0.242 Sum_probs=26.2
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 450 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~ 450 (473)
.|++.||--|..... .|+++.|||..+|-|+..|+..++
T Consensus 4 ~Lt~~Eqaqid~m~q----lG~s~~~isr~i~RSr~~Ir~yl~ 42 (50)
T PF11427_consen 4 TLTDAEQAQIDVMHQ----LGMSLREISRRIGRSRTCIRRYLK 42 (50)
T ss_dssp ---HHHHHHHHHHHH----TT--HHHHHHHHT--HHHHHHHHH
T ss_pred cCCHHHHHHHHHHHH----hchhHHHHHHHhCccHHHHHHHhc
Confidence 477778777776666 799999999999999999987653
No 314
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=74.82 E-value=4.5 Score=28.85 Aligned_cols=24 Identities=25% Similarity=0.483 Sum_probs=20.0
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLES 450 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~ 450 (473)
-+.+..|||+.+|+|..+|++.+.
T Consensus 7 ~~~s~~~la~~l~~s~~tv~~~l~ 30 (48)
T smart00419 7 LPLTRQEIAELLGLTRETVSRTLK 30 (48)
T ss_pred eccCHHHHHHHHCCCHHHHHHHHH
Confidence 368999999999999999966443
No 315
>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=74.64 E-value=6.5 Score=34.18 Aligned_cols=41 Identities=22% Similarity=0.337 Sum_probs=26.7
Q ss_pred HHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 412 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 412 rER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
+.+.|...+ .|.+..|+|..+|+|..+|++|+++...+-+.
T Consensus 62 R~~~I~~~f------~G~n~~eLA~kyglS~r~I~~Ii~~~~~~~~~ 102 (108)
T PF08765_consen 62 RNREIRREF------NGMNVRELARKYGLSERQIYRIIKRVRRRERR 102 (108)
T ss_dssp HHHHHHHH--------SS-HHHHHHHHT--HHHHHHHHHHHHH----
T ss_pred HHHHHHHHh------CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 445555533 47899999999999999999999988776554
No 316
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=74.55 E-value=5.5 Score=39.54 Aligned_cols=52 Identities=15% Similarity=0.240 Sum_probs=41.7
Q ss_pred HHHHHHHHHhhCCHHHHHHHHHHhhccCC---CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 398 MRQHVRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 398 l~e~L~~aL~~LperER~VL~LrY~L~~g---e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
+.+.|...+..|++.|+.|... .+++. ..+|..|||+..|+|..+|....++
T Consensus 3 i~~~i~~~~~~Lt~~e~~Ia~y--il~n~~~v~~~si~~lA~~~~vS~aTv~Rf~kk 57 (284)
T PRK11302 3 MLEKIQSRLEHLSKSERKVAEV--ILASPQTAIHSSIATLAKMANVSEPTVNRFCRS 57 (284)
T ss_pred HHHHHHHHHhhCCHHHHHHHHH--HHhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHH
Confidence 3466888889999999999754 33332 4589999999999999999887765
No 317
>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=74.02 E-value=7.8 Score=36.06 Aligned_cols=51 Identities=24% Similarity=0.320 Sum_probs=36.9
Q ss_pred CHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH------HHHHHHHHhccCc
Q 011992 410 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR------ALYRLKQSLGGKA 464 (473)
Q Consensus 410 perER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R------AL~KLR~~L~~~~ 464 (473)
+|..-.|-.+|-. .|+|..|+|+.+|||.++|+++++. .+..|.+.....+
T Consensus 24 ~p~~~~Ir~~R~~----lGmTq~eLAerlGVS~~tIs~iE~G~~~~~psl~~L~kIA~aLg 80 (150)
T TIGR02612 24 TPKEGWVRAIRKA----LGMSGAQLAGRLGVTPQRVEALEKSELSGTVTLKTLRAAAEALD 80 (150)
T ss_pred cCcHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHcCCCCCCCCHHHHHHHHHHcC
Confidence 4444445556666 8999999999999999999999985 3445555444333
No 318
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=73.83 E-value=8.8 Score=31.19 Aligned_cols=41 Identities=27% Similarity=0.442 Sum_probs=32.1
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.|+..+..||.+-+. ..+.+..+||+.++++..+|+..+++
T Consensus 7 ~l~~~~~~il~~l~~---~~~~~~~~la~~~~~s~~~i~~~l~~ 47 (101)
T smart00347 7 GLTPTQFLVLRILYE---EGPLSVSELAKRLGVSPSTVTRVLDR 47 (101)
T ss_pred CCCHHHHHHHHHHHH---cCCcCHHHHHHHHCCCchhHHHHHHH
Confidence 477778888777664 24689999999999999998875544
No 319
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=73.76 E-value=4.4 Score=38.09 Aligned_cols=34 Identities=21% Similarity=0.211 Sum_probs=27.4
Q ss_pred HHHHHHHhhccCCCCCCHHHHHHHHC-CCHHHHHHHHHH
Q 011992 414 RCIVRLRFGIEDGKPKSLSEVGNIFG-LSKERVRQLESR 451 (473)
Q Consensus 414 R~VL~LrY~L~~ge~lTlkEIAe~LG-IS~~rVrqi~~R 451 (473)
-+.|.-.+. +|+|..|||+.|| ||++.|--..+|
T Consensus 8 ~~~L~~lw~----~G~SasqIA~~lg~vsRnAViGk~hR 42 (162)
T PF07750_consen 8 VERLRKLWA----EGLSASQIARQLGGVSRNAVIGKAHR 42 (162)
T ss_pred HHHHHHHHH----cCCCHHHHHHHhCCcchhhhhhhhhc
Confidence 334444455 8999999999999 999999887776
No 320
>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=73.64 E-value=7.8 Score=30.52 Aligned_cols=25 Identities=24% Similarity=0.388 Sum_probs=21.6
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
...+..|||+.+|+|..+|++.+.+
T Consensus 12 ~~~~~~eLa~~l~vS~~tv~~~l~~ 36 (69)
T TIGR00122 12 NPFSGEKLGEALGMSRTAVNKHIQT 36 (69)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4678999999999999999986554
No 321
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=73.60 E-value=25 Score=29.73 Aligned_cols=39 Identities=13% Similarity=0.056 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhc
Q 011992 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSG 326 (473)
Q Consensus 288 le~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g 326 (473)
++.+..-+...+...++.+++|+.+|++...+.+.++..
T Consensus 7 ~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 7 IQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 555666777788999999999999999999998887653
No 322
>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=73.31 E-value=7.6 Score=32.46 Aligned_cols=25 Identities=24% Similarity=0.434 Sum_probs=22.1
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
...|+++||+.+|||..||+..+..
T Consensus 18 ~~~ti~dvA~~~gvS~~TVsr~L~~ 42 (80)
T TIGR02844 18 TKATVRETAKVFGVSKSTVHKDVTE 42 (80)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHhcC
Confidence 5789999999999999999997653
No 323
>PF14493 HTH_40: Helix-turn-helix domain
Probab=73.28 E-value=8.3 Score=32.28 Aligned_cols=29 Identities=21% Similarity=0.245 Sum_probs=26.8
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESRALYR 455 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~RAL~K 455 (473)
+|+|+.|||+.-|++.+||..++.++...
T Consensus 12 ~G~si~eIA~~R~L~~sTI~~HL~~~~~~ 40 (91)
T PF14493_consen 12 KGLSIEEIAKIRGLKESTIYGHLAELIES 40 (91)
T ss_pred cCCCHHHHHHHcCCCHHHHHHHHHHHHHh
Confidence 79999999999999999999999888754
No 324
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=72.71 E-value=11 Score=33.74 Aligned_cols=42 Identities=7% Similarity=0.033 Sum_probs=32.3
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.|++.+-.||...+. .+++.|..|||+.+|++.++|..++.+
T Consensus 28 glt~~q~~vL~~l~~--~~~~~t~~eLa~~l~~~~~tvt~~v~~ 69 (144)
T PRK03573 28 ELTQTHWVTLHNIHQ--LPPEQSQIQLAKAIGIEQPSLVRTLDQ 69 (144)
T ss_pred CCCHHHHHHHHHHHH--cCCCCCHHHHHHHhCCChhhHHHHHHH
Confidence 588888777765542 125689999999999999999976554
No 325
>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=72.70 E-value=8.8 Score=33.24 Aligned_cols=41 Identities=12% Similarity=0.151 Sum_probs=32.1
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.|+..+..||...+. +.+.+..|||+.+|++.++|..++.+
T Consensus 25 ~lt~~q~~iL~~l~~---~~~~t~~ela~~~~~~~~tvs~~l~~ 65 (118)
T TIGR02337 25 GLTEQQWRILRILAE---QGSMEFTQLANQACILRPSLTGILAR 65 (118)
T ss_pred CCCHHHHHHHHHHHH---cCCcCHHHHHHHhCCCchhHHHHHHH
Confidence 588888887765443 36799999999999999999765444
No 326
>PRK10870 transcriptional repressor MprA; Provisional
Probab=72.32 E-value=20 Score=33.77 Aligned_cols=52 Identities=12% Similarity=0.117 Sum_probs=36.8
Q ss_pred HHHHHHHh--hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992 400 QHVRNLLT--LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 452 (473)
Q Consensus 400 e~L~~aL~--~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA 452 (473)
..+.+.+. .|++.+-.||...+. .++.+.+..|||+.+|++.++|.+++.+-
T Consensus 42 ~~~~~~l~~~gLt~~q~~iL~~L~~-~~~~~it~~eLa~~l~l~~~tvsr~v~rL 95 (176)
T PRK10870 42 ENRNKMLKAQGINETLFMALITLES-QENHSIQPSELSCALGSSRTNATRIADEL 95 (176)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHhc-CCCCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 34455553 488877777766553 22356899999999999999998766553
No 327
>PRK09954 putative kinase; Provisional
Probab=71.99 E-value=7.9 Score=40.02 Aligned_cols=42 Identities=19% Similarity=0.279 Sum_probs=32.9
Q ss_pred CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992 409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 453 (473)
Q Consensus 409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL 453 (473)
|+++++.||.+... + ...|..|||+.||||+.+|+.++.+-.
T Consensus 1 ~~~~~~~il~~l~~--~-~~~s~~~la~~l~~s~~~v~~~i~~L~ 42 (362)
T PRK09954 1 MNNREKEILAILRR--N-PLIQQNEIADILQISRSRVAAHIMDLM 42 (362)
T ss_pred CChHHHHHHHHHHH--C-CCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 46677777766553 2 479999999999999999999877544
No 328
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=71.87 E-value=6.4 Score=32.05 Aligned_cols=25 Identities=16% Similarity=0.331 Sum_probs=23.1
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.++|..|.|+.+|||+.||..|++.
T Consensus 13 ~~ltQ~elA~~vgVsRQTi~~iEkg 37 (68)
T COG1476 13 LGLTQEELAKLVGVSRQTIIAIEKG 37 (68)
T ss_pred hCcCHHHHHHHcCcCHHHHHHHHcC
Confidence 6899999999999999999998864
No 329
>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=71.59 E-value=4.6 Score=31.91 Aligned_cols=28 Identities=36% Similarity=0.671 Sum_probs=22.6
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
-++|.++||..+|+|+.+|.+. +++|++
T Consensus 27 ~~lt~~~iA~~~g~sr~tv~r~----l~~l~~ 54 (76)
T PF13545_consen 27 LPLTQEEIADMLGVSRETVSRI----LKRLKD 54 (76)
T ss_dssp EESSHHHHHHHHTSCHHHHHHH----HHHHHH
T ss_pred ecCCHHHHHHHHCCCHHHHHHH----HHHHHH
Confidence 4689999999999999998874 445544
No 330
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=71.43 E-value=6.3 Score=34.75 Aligned_cols=49 Identities=14% Similarity=0.186 Sum_probs=43.6
Q ss_pred hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 011992 407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 459 (473)
Q Consensus 407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~ 459 (473)
.+|.+-||....-+|- .-+|-+|||-.+++++.+|..+...-..|.|+.
T Consensus 27 ~QLkELErvF~ETHYP----DIYTREEiA~kidLTEARVQVWFQNRRAKfRKQ 75 (125)
T KOG0484|consen 27 AQLKELERVFAETHYP----DIYTREEIALKIDLTEARVQVWFQNRRAKFRKQ 75 (125)
T ss_pred HHHHHHHHHHHhhcCC----cchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHH
Confidence 4688888888888887 889999999999999999999999888888764
No 331
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=71.07 E-value=4.7 Score=38.45 Aligned_cols=29 Identities=34% Similarity=0.598 Sum_probs=24.9
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 426 GKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 426 ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
.+++|+.||++.+|+|+++|++ ++++|..
T Consensus 39 ~~Pmtl~Ei~E~lg~Sks~vS~----~lkkL~~ 67 (177)
T COG1510 39 RKPLTLDEIAEALGMSKSNVSM----GLKKLQD 67 (177)
T ss_pred CCCccHHHHHHHHCCCcchHHH----HHHHHHh
Confidence 3899999999999999999998 6666654
No 332
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=70.92 E-value=12 Score=31.27 Aligned_cols=32 Identities=19% Similarity=0.294 Sum_probs=26.2
Q ss_pred cCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 011992 424 EDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 459 (473)
Q Consensus 424 ~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~ 459 (473)
.++...|-++||+.||+|+.+|.. .+++||+.
T Consensus 15 ~~~~~~SGe~La~~LgiSRtaVwK----~Iq~Lr~~ 46 (79)
T COG1654 15 LTGNFVSGEKLAEELGISRTAVWK----HIQQLREE 46 (79)
T ss_pred cCCCcccHHHHHHHHCccHHHHHH----HHHHHHHh
Confidence 344789999999999999999976 66777753
No 333
>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=70.86 E-value=4.8 Score=31.18 Aligned_cols=25 Identities=16% Similarity=0.218 Sum_probs=21.0
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Q 011992 426 GKPKSLSEVGNIFGLSKERVRQLES 450 (473)
Q Consensus 426 ge~lTlkEIAe~LGIS~~rVrqi~~ 450 (473)
...+++.|||+.+|+|..+|+.-+.
T Consensus 17 ~~~~~~~ela~~l~~S~rti~~~i~ 41 (59)
T PF08280_consen 17 NKWITLKELAKKLNISERTIKNDIN 41 (59)
T ss_dssp HTSBBHHHHHHHCTS-HHHHHHHHH
T ss_pred CCCCcHHHHHHHHCCCHHHHHHHHH
Confidence 4789999999999999999988544
No 334
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=70.67 E-value=13 Score=28.71 Aligned_cols=42 Identities=12% Similarity=0.134 Sum_probs=31.0
Q ss_pred HHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Q 011992 416 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 461 (473)
Q Consensus 416 VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~ 461 (473)
.+..++. .+.+..+.|+.|+|.++||+.++.|+-..+.--+.
T Consensus 4 TL~~yl~----~~~n~~~tA~~L~iHrNTl~yRl~ki~~l~g~dl~ 45 (59)
T PF13556_consen 4 TLRAYLE----NNGNISKTARALHIHRNTLRYRLKKIEELLGLDLD 45 (59)
T ss_dssp HHHHHHH----TTT-HHHHHHHHTS-HHHHHHHHHHHHHHHS--TT
T ss_pred HHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCcCCC
Confidence 3455555 78999999999999999999999888777655444
No 335
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=70.57 E-value=12 Score=35.98 Aligned_cols=45 Identities=18% Similarity=0.178 Sum_probs=35.2
Q ss_pred HHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 404 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 404 ~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.....|++++..|+.+... ..+.+..|||+.+|+|.++|++++.+
T Consensus 136 ~~~~~ls~~~~~IL~~l~~---~g~~s~~eia~~l~is~stv~r~L~~ 180 (203)
T TIGR01884 136 PLLAGLSREELKVLEVLKA---EGEKSVKNIAKKLGKSLSTISRHLRE 180 (203)
T ss_pred hhhcCCCHHHHHHHHHHHH---cCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 3456799999888765543 13679999999999999999876665
No 336
>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=70.26 E-value=6.9 Score=29.88 Aligned_cols=25 Identities=24% Similarity=0.440 Sum_probs=21.2
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
..+|..|||+.+|+|..+|+.++.+
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~ 48 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKE 48 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 5799999999999999999765443
No 337
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=70.22 E-value=12 Score=37.45 Aligned_cols=63 Identities=16% Similarity=0.298 Sum_probs=47.9
Q ss_pred HHHHHHHHHHhhCCHHHHHHHHHHhhccCC---CCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHhc
Q 011992 397 LMRQHVRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLESR----ALYRLKQSLG 461 (473)
Q Consensus 397 el~e~L~~aL~~LperER~VL~LrY~L~~g---e~lTlkEIAe~LGIS~~rVrqi~~R----AL~KLR~~L~ 461 (473)
.+...|...+..|++.|+.|.... +++. ..+|..|||+..|+|..+|-...++ +..-||..+.
T Consensus 14 ~i~~~i~~~~~~Lt~~e~~Ia~yi--l~~~~~v~~~si~~lA~~~~vS~aTi~Rf~kkLGf~gf~efk~~l~ 83 (292)
T PRK11337 14 GLGPYIRMKQEGLTPLESRVVEWL--LKPGDLSEATALKDIAEALAVSEAMIVKVAKKLGFSGFRNLRSALE 83 (292)
T ss_pred hHHHHHHHHHhhcCHHHHHHHHHH--HhCHHHHHhcCHHHHHHHhCCChHHHHHHHHHcCCCCHHHHHHHHH
Confidence 456688889999999999997543 3332 5689999999999999999887765 4455554443
No 338
>PRK09480 slmA division inhibitor protein; Provisional
Probab=70.07 E-value=39 Score=30.94 Aligned_cols=75 Identities=17% Similarity=0.003 Sum_probs=47.8
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhH
Q 011992 289 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGS 363 (473)
Q Consensus 289 e~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~ 363 (473)
+.+..-+..+-|...|..+||+..|++...+.....+.+.-+..++..+..-+............+..+.+...+
T Consensus 17 ~aa~~l~~~~~G~~~ti~~Ia~~agvs~gt~Y~~F~~K~~L~~~v~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ 91 (194)
T PRK09480 17 QALAQMLESPPGERITTAKLAARVGVSEAALYRHFPSKARMFEGLIEFIEESLFSRINQILKDEKDTLARARLIL 91 (194)
T ss_pred HHHHHHHHhcCCCccCHHHHHHHhCCCHhHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHccCCCHHHHHHHHH
Confidence 333444445547889999999999999999999888777666666666655444443333322233444444433
No 339
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=69.68 E-value=32 Score=29.61 Aligned_cols=45 Identities=11% Similarity=0.054 Sum_probs=35.0
Q ss_pred hCCHHHHHHHHHHhhc-cCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGI-EDGKPKSLSEVGNIFGLSKERVRQLESRA 452 (473)
Q Consensus 408 ~LperER~VL~LrY~L-~~ge~lTlkEIAe~LGIS~~rVrqi~~RA 452 (473)
.|+..+-.||..-+.+ ..+.+.+..|||+.++++.++|+.++.+-
T Consensus 22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~L 67 (109)
T TIGR01889 22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKL 67 (109)
T ss_pred CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHH
Confidence 6899988888665511 12367999999999999999999866553
No 340
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=69.33 E-value=71 Score=33.10 Aligned_cols=128 Identities=14% Similarity=0.160 Sum_probs=72.2
Q ss_pred HhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHHHH----HHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhh
Q 011992 298 QFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINAN----LRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKF 373 (473)
Q Consensus 298 ~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~~y----l~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekF 373 (473)
+.+.+-|..||+...+++..++-+.++---++.+..+..+ ..++.+++.. +.+.--+|++-.-+.+.++.|
T Consensus 160 q~~~pRT~kEI~~~anv~kKEIgr~~K~i~~~l~~s~~~~s~~t~~~m~RFCs~-----L~L~~~~q~aA~e~a~ka~~~ 234 (308)
T KOG1597|consen 160 QEDVPRTFKEISAVANVSKKEIGRCVKLIGEALETSVDLISISTGDFMPRFCSN-----LGLPKSAQEAATEIAEKAEEM 234 (308)
T ss_pred hcCCCchHHHHHHHHcCCHHHHHHHHHHHHHHHhccchhhhhhHHHHHHHHHHh-----cCCCHHHHHHHHHHHHHHHHh
Confidence 4577788999999999998888775554334433333332 2233333332 233333455555555555555
Q ss_pred CccCCCccccCCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992 374 KPQAGCRFANTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 453 (473)
Q Consensus 374 Dp~kg~~FsT~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL 453 (473)
+.-.| ..|.... - -+|.|.-.|.+ +..+.+||+++.||++.||++-.+--.
T Consensus 235 ~~~~g--------RsPiSIA------A--------------a~IYmisqls~-~kkt~keI~~vtgVaE~TIr~sYK~Ly 285 (308)
T KOG1597|consen 235 DIRAG--------RSPISIA------A--------------AAIYMISQLSD-EKKTQKEIGEVTGVAEVTIRNSYKDLY 285 (308)
T ss_pred ccccC--------CCchhHH------H--------------HHHHHHHHhcc-CcccHHHHHHHhhhhHHHHHHHHHHHh
Confidence 54322 1221110 0 01111111112 799999999999999999999776655
Q ss_pred HHHHHH
Q 011992 454 YRLKQS 459 (473)
Q Consensus 454 ~KLR~~ 459 (473)
-.+-+.
T Consensus 286 p~~~~l 291 (308)
T KOG1597|consen 286 PHADKL 291 (308)
T ss_pred hchhhh
Confidence 554443
No 341
>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=69.09 E-value=4.2 Score=34.22 Aligned_cols=24 Identities=17% Similarity=0.108 Sum_probs=18.1
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLES 450 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~ 450 (473)
.|+|..|||+.+|.|++.|++++.
T Consensus 2 ~G~tq~eIA~~lGks~s~Vs~~l~ 25 (93)
T PF08535_consen 2 FGWTQEEIAKRLGKSRSWVSNHLA 25 (93)
T ss_dssp TT--HHHHHHHTT--HHHHHHHHG
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Confidence 479999999999999999999875
No 342
>PRK15482 transcriptional regulator MurR; Provisional
Probab=68.97 E-value=8.6 Score=38.55 Aligned_cols=51 Identities=16% Similarity=0.240 Sum_probs=40.8
Q ss_pred HHHHHHHHhhCCHHHHHHHHHHhhccCC---CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 399 RQHVRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 399 ~e~L~~aL~~LperER~VL~LrY~L~~g---e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
...|......|++.|+.|.... +++. ..+|..|||+..|+|..+|-..-++
T Consensus 4 l~~i~~~~~~Lt~~e~~Ia~yI--l~n~~~v~~~si~elA~~~~vS~aTv~Rf~kk 57 (285)
T PRK15482 4 LTKIRNAESEFTENEQKIADFL--RANVSELKSVSSRKMAKQLGISQSSIVKFAQK 57 (285)
T ss_pred HHHHHHHHhhcCHHHHHHHHHH--HhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHH
Confidence 3567778889999999997543 3332 4699999999999999999887765
No 343
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=68.45 E-value=13 Score=33.31 Aligned_cols=41 Identities=5% Similarity=-0.008 Sum_probs=33.4
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.|+..+-.||...+. ..+.|..|||+.+|++.++|..++.+
T Consensus 37 glt~~q~~vL~~l~~---~~~~t~~eLa~~l~i~~~tvsr~l~~ 77 (144)
T PRK11512 37 DITAAQFKVLCSIRC---AACITPVELKKVLSVDLGALTRMLDR 77 (144)
T ss_pred CCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 588888888876543 26799999999999999999886655
No 344
>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=68.41 E-value=9.2 Score=28.81 Aligned_cols=26 Identities=35% Similarity=0.482 Sum_probs=21.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 429 KSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 429 lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
.+..+||+.+|+|+++|++ ++.+|.+
T Consensus 26 ~~~~~la~~~~is~~~v~~----~l~~L~~ 51 (66)
T cd07377 26 PSERELAEELGVSRTTVRE----ALRELEA 51 (66)
T ss_pred CCHHHHHHHHCCCHHHHHH----HHHHHHH
Confidence 4599999999999999986 5555544
No 345
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=68.24 E-value=5.3 Score=31.85 Aligned_cols=23 Identities=22% Similarity=0.416 Sum_probs=20.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 011992 429 KSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 429 lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.|++|||+.+|||.++|+.+++.
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln~ 23 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLNG 23 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCC
Confidence 37899999999999999988754
No 346
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=67.99 E-value=17 Score=31.68 Aligned_cols=46 Identities=22% Similarity=0.226 Sum_probs=33.1
Q ss_pred HHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992 401 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 452 (473)
Q Consensus 401 ~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA 452 (473)
.....-..+.+.+-.-++.. .++|..++|+.+|++..+|+.+++..
T Consensus 57 ~~~~~~~~~~~~~i~~~r~~------~gltq~~lA~~lg~~~~tis~~e~g~ 102 (127)
T TIGR03830 57 FYRKVDGLLTPPEIRRIRKK------LGLSQREAAELLGGGVNAFSRYERGE 102 (127)
T ss_pred HHHHccCCcCHHHHHHHHHH------cCCCHHHHHHHhCCCHHHHHHHHCCC
Confidence 33444455666654444444 46999999999999999999988743
No 347
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=67.59 E-value=70 Score=30.83 Aligned_cols=32 Identities=16% Similarity=0.176 Sum_probs=26.8
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSK 442 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~ 442 (473)
.|+.-.-++|...++ ..+.|..||+++.|++.
T Consensus 87 ~LS~aaLEtLaiIay---~qPiTr~eI~~irGv~~ 118 (188)
T PRK00135 87 SLSQAALEVLAIIAY---KQPITRIEIDEIRGVNS 118 (188)
T ss_pred CCCHHHHHHHHHHHH---cCCcCHHHHHHHHCCCH
Confidence 588888888876544 27999999999999986
No 348
>PRK06030 hypothetical protein; Provisional
Probab=67.53 E-value=16 Score=33.05 Aligned_cols=50 Identities=12% Similarity=0.074 Sum_probs=32.5
Q ss_pred HHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCchhhhh
Q 011992 412 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYA 469 (473)
Q Consensus 412 rER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~l~~yl 469 (473)
|+--+...+-. -++|+.+||+.+|-+.+||..-.+ ++++.+.+..++..+
T Consensus 57 RqIAMYL~r~~----~~~sl~~IG~~FGRDHSTV~haik----kIe~~~~d~~lk~~v 106 (124)
T PRK06030 57 RQIAMYVAHVS----LGWPMNEVALAFGRDRTTVGHACH----TVEDLRDDAAFDARV 106 (124)
T ss_pred HHHHHHHHHHH----cCCCHHHHHHHHCCChhHHHHHHH----HHHHHhhCHHHHHHH
Confidence 33334344444 689999999999999999998665 333333444444333
No 349
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=67.26 E-value=2.8 Score=32.68 Aligned_cols=25 Identities=28% Similarity=0.514 Sum_probs=22.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992 429 KSLSEVGNIFGLSKERVRQLESRAL 453 (473)
Q Consensus 429 lTlkEIAe~LGIS~~rVrqi~~RAL 453 (473)
+|..|+|+.+|||..+|+....+.+
T Consensus 1 yti~eva~~~gvs~~tlr~y~~~gl 25 (69)
T PF13411_consen 1 YTIKEVAKLLGVSPSTLRYYEREGL 25 (69)
T ss_dssp EEHHHHHHHTTTTHHHHHHHHHTTS
T ss_pred CcHHHHHHHHCcCHHHHHHHHHhcC
Confidence 4789999999999999999988766
No 350
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=67.02 E-value=16 Score=27.17 Aligned_cols=51 Identities=16% Similarity=0.198 Sum_probs=38.0
Q ss_pred hCCHHHHHHHHHHhhccCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDG-KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~g-e~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
.+++.+..+|.-.|..+.. ......+||..+|++...|..+...-..+.+.
T Consensus 6 ~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 6 RFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 3667778888877764222 33347889999999999999998887776653
No 351
>PF04645 DUF603: Protein of unknown function, DUF603; InterPro: IPR006739 This family includes several uncharacterised proteins from Borrelia species.
Probab=67.00 E-value=7.5 Score=36.98 Aligned_cols=25 Identities=20% Similarity=0.337 Sum_probs=22.0
Q ss_pred CC-CCHHHHHHHHCCCHHHHHHHHHH
Q 011992 427 KP-KSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 427 e~-lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
+| ++..|||++||||+..|..+..+
T Consensus 17 eg~L~d~~Ia~~lgvs~~nV~kmR~K 42 (181)
T PF04645_consen 17 EGRLSDAEIAKELGVSRVNVWKMRQK 42 (181)
T ss_pred cCCccHHHHHHHHCchHHHHHHHHHH
Confidence 66 99999999999999999876654
No 352
>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=66.80 E-value=7.4 Score=30.15 Aligned_cols=23 Identities=26% Similarity=0.488 Sum_probs=20.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 011992 429 KSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 429 lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
+|..|+|+.+|||..+++.+..+
T Consensus 1 ~s~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 47899999999999999998865
No 353
>COG5625 Predicted transcription regulator containing HTH domain [Transcription]
Probab=66.62 E-value=9.6 Score=33.43 Aligned_cols=65 Identities=22% Similarity=0.235 Sum_probs=43.1
Q ss_pred HHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH--HHHHHHhccC
Q 011992 399 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL--YRLKQSLGGK 463 (473)
Q Consensus 399 ~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL--~KLR~~L~~~ 463 (473)
...+..+|..+.=+--+|+...+.+..+.++...||+..||||+-+|+....--+ --|+..+-..
T Consensus 7 l~~l~~~L~~~glk~~eI~IY~lLve~~~~mri~ei~rEl~is~rtvr~~v~~l~rrGll~relvqk 73 (113)
T COG5625 7 LRKLGKALEAIGLKKNEIRIYSLLVEKGRGMRIREIQRELGISERTVRAAVAVLLRRGLLARELVQK 73 (113)
T ss_pred HHHHHHHHHHcCCCcchhhhhhHHHHhcCCchHHHHHHHHhHHHHHHHHHHHHHHHhhHHHHHHHhc
Confidence 3456666665554444455555555556899999999999999999988776655 2344444333
No 354
>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent 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. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.
Probab=66.25 E-value=9.8 Score=31.99 Aligned_cols=46 Identities=26% Similarity=0.411 Sum_probs=28.9
Q ss_pred HHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992 413 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 460 (473)
Q Consensus 413 ER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L 460 (473)
+|-+-.-.|.++ ...|..+.|+.+|||.+||..-+..=|.++-..|
T Consensus 6 eR~i~i~~yIi~--~~aTVR~~Ak~FGvSKSTVHkDvteRL~~in~~L 51 (82)
T PF12116_consen 6 ERVIEIANYIIE--TKATVRQAAKVFGVSKSTVHKDVTERLPKINPEL 51 (82)
T ss_dssp HHHHHHHHHHHH--H---HHHHHHHHTS-HHHHHHHHTTHHHHH-HHH
T ss_pred HHHHHHHHHHHH--cccHHHHHHHHHCCcHHHHHHHHHHHHHhcCHHH
Confidence 444444455544 5799999999999999999987766555554433
No 355
>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=66.10 E-value=9.6 Score=32.40 Aligned_cols=43 Identities=16% Similarity=0.244 Sum_probs=31.0
Q ss_pred hCCHHHHHHHHHHhh-ccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFG-IEDGKPKSLSEVGNIFGLSKERVRQLES 450 (473)
Q Consensus 408 ~LperER~VL~LrY~-L~~ge~lTlkEIAe~LGIS~~rVrqi~~ 450 (473)
.|++..++|+.+.-. -...+|.+..+|++.||++...|++.+.
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~ 87 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALD 87 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHH
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHH
Confidence 688888888876554 3345899999999999999999988543
No 356
>TIGR00647 MG103 conserved hypothetical protein.
Probab=65.49 E-value=30 Score=35.52 Aligned_cols=45 Identities=16% Similarity=0.211 Sum_probs=38.7
Q ss_pred HhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHC------CCHHHHHHHHHHHH
Q 011992 406 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG------LSKERVRQLESRAL 453 (473)
Q Consensus 406 L~~LperER~VL~LrY~L~~ge~lTlkEIAe~LG------IS~~rVrqi~~RAL 453 (473)
++.||+.-+++..+|.. ..+.|++|+|+.|+ ||++.|..+++|..
T Consensus 225 l~~Lp~~L~~~a~lRl~---~Pd~SL~ELgell~~~~~~~isKSgvnhRlrKl~ 275 (279)
T TIGR00647 225 FEKLPLNFQRICLLKID---HPDWSLEQIAEFFASKYKVKISRSGIQHRLRKLK 275 (279)
T ss_pred cccCCHHHHHHHHHHHh---CcccCHHHHHHHhccCCCCCcCHHHHHHHHHHHH
Confidence 46899999999998875 47899999999994 99999998877654
No 357
>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=65.38 E-value=31 Score=34.80 Aligned_cols=56 Identities=18% Similarity=0.211 Sum_probs=42.6
Q ss_pred HHHHHHHHhhCCHHHHHHHHHHhhc-cC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 399 RQHVRNLLTLLNPKERCIVRLRFGI-ED-GKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 399 ~e~L~~aL~~LperER~VL~LrY~L-~~-ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
+..+.-||+.|+=-|.+.+...+.. ++ ..-.+..+||+.+|||++.|+. |+++|..
T Consensus 167 ka~Vq~Ai~tLSySEleAv~~IL~~L~~~egrlse~eLAerlGVSRs~ire----AlrkLE~ 224 (251)
T TIGR02787 167 KAAVQMAINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIVN----ALRKLES 224 (251)
T ss_pred HHHHHHHHHhccHhHHHHHHHHHHHhccccccccHHHHHHHHCCCHHHHHH----HHHHHHH
Confidence 3467778999999998888665543 33 2468999999999999999887 5666654
No 358
>PF11662 DUF3263: Protein of unknown function (DUF3263); InterPro: IPR021678 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=65.22 E-value=24 Score=29.44 Aligned_cols=47 Identities=19% Similarity=0.135 Sum_probs=37.1
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 454 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~ 454 (473)
.|+++++.||.+--..-...|-+-+.|-+.+|+|.-+..|+++..+.
T Consensus 2 ~Ls~~d~~iL~fE~~ww~~~GaKe~aIre~fGls~~rYyq~Ln~LiD 48 (77)
T PF11662_consen 2 GLSDRDRAILDFERRWWRHGGAKEEAIREEFGLSPTRYYQRLNALID 48 (77)
T ss_pred CCCHHHHHHHHHHHHhCcCCCCcHHHHHHHHCCCHHHHHHHHHHHhC
Confidence 68999999997632222235778999999999999999999988653
No 359
>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=64.98 E-value=12 Score=30.58 Aligned_cols=24 Identities=25% Similarity=0.474 Sum_probs=19.6
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 428 PKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 428 ~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
..|.+|||+.+|+++..|++++.+
T Consensus 25 ~~s~~eiA~~~~i~~~~l~kil~~ 48 (83)
T PF02082_consen 25 PVSSKEIAERLGISPSYLRKILQK 48 (83)
T ss_dssp -BEHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 489999999999999999986543
No 360
>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=64.88 E-value=7.7 Score=34.24 Aligned_cols=25 Identities=20% Similarity=0.319 Sum_probs=21.9
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.+.|+.|||+.||||.++|...+.+
T Consensus 70 pd~tl~Ela~~l~Vs~~ti~~~Lkr 94 (119)
T PF01710_consen 70 PDATLRELAERLGVSPSTIWRALKR 94 (119)
T ss_pred CCcCHHHHHHHcCCCHHHHHHHHHH
Confidence 7899999999999999999875544
No 361
>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=64.76 E-value=5.3 Score=32.83 Aligned_cols=31 Identities=13% Similarity=0.081 Sum_probs=24.5
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESRALYRLK 457 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR 457 (473)
+..++.++|+.++||+++|...+.+.-+.|+
T Consensus 29 ~~~s~~~la~~~~iS~sti~~~i~~l~~~l~ 59 (87)
T PF05043_consen 29 EYVSIEDLAEELFISRSTIYRDIKKLNKYLK 59 (87)
T ss_dssp SEEEHHHHHHHHT--HHHHHHHHHHHHHHHH
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 8899999999999999999987666655555
No 362
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=64.74 E-value=15 Score=30.72 Aligned_cols=40 Identities=20% Similarity=0.303 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHHhhccCCCCCCH-HHHHHHHCCCHHHHHHHHHHH
Q 011992 409 LNPKERCIVRLRFGIEDGKPKSL-SEVGNIFGLSKERVRQLESRA 452 (473)
Q Consensus 409 LperER~VL~LrY~L~~ge~lTl-kEIAe~LGIS~~rVrqi~~RA 452 (473)
|++.+..|+...+. .+... .+||+.++++.++|..++.+-
T Consensus 20 lt~~q~~~L~~l~~----~~~~~~~~la~~l~i~~~~vt~~l~~L 60 (126)
T COG1846 20 LTPPQYQVLLALYE----AGGITVKELAERLGLDRSTVTRLLKRL 60 (126)
T ss_pred CCHHHHHHHHHHHH----hCCCcHHHHHHHHCCCHHHHHHHHHHH
Confidence 99999999987776 34433 999999999999999876653
No 363
>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=64.59 E-value=16 Score=28.97 Aligned_cols=25 Identities=12% Similarity=0.275 Sum_probs=23.2
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.++|..++|+.+|+|..+|+.+++.
T Consensus 17 ~~~t~~~lA~~~gis~~tis~~~~g 41 (78)
T TIGR02607 17 LGLSIRALAKALGVSRSTLSRIVNG 41 (78)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 7899999999999999999999864
No 364
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=64.15 E-value=7 Score=37.32 Aligned_cols=27 Identities=19% Similarity=0.261 Sum_probs=24.0
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESRAL 453 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~RAL 453 (473)
-++|..|||+.+|.|+.+|+.++.-.-
T Consensus 60 ag~Ti~EIAeelG~TeqTir~hlkget 86 (182)
T COG1318 60 AGMTISEIAEELGRTEQTVRNHLKGET 86 (182)
T ss_pred ccCcHHHHHHHhCCCHHHHHHHHhcch
Confidence 579999999999999999999887543
No 365
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=63.95 E-value=40 Score=34.60 Aligned_cols=26 Identities=15% Similarity=0.309 Sum_probs=23.2
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESRA 452 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~RA 452 (473)
...|.+|||++.||++.||++..+.-
T Consensus 250 ~~~tq~eva~v~~vtevTIrnrykel 275 (285)
T COG1405 250 ERRTQKEVAKVAGVTEVTIRNRYKEL 275 (285)
T ss_pred CchHHHHHHHHhCCeeeHHHHHHHHH
Confidence 68999999999999999999988443
No 366
>PRK09726 antitoxin HipB; Provisional
Probab=63.86 E-value=12 Score=31.09 Aligned_cols=25 Identities=16% Similarity=0.330 Sum_probs=23.5
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.++|..|+|+.+|||.++|+++++.
T Consensus 24 ~gltq~elA~~~gvs~~tis~~e~g 48 (88)
T PRK09726 24 NGWTQSELAKKIGIKQATISNFENN 48 (88)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 6899999999999999999999884
No 367
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=63.75 E-value=20 Score=32.03 Aligned_cols=45 Identities=16% Similarity=0.224 Sum_probs=31.9
Q ss_pred HHHHhhCCHHHH-HHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011992 403 RNLLTLLNPKER-CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 450 (473)
Q Consensus 403 ~~aL~~LperER-~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~ 450 (473)
.+.+..|.+.-| .||.+-. ++.+++..||++.+|+++++|+++++
T Consensus 7 ~~~fkaLadptRl~IL~~L~---~~~~~~v~ela~~l~lsqstvS~HL~ 52 (117)
T PRK10141 7 LQLFKILSDETRLGIVLLLR---ESGELCVCDLCTALDQSQPKISRHLA 52 (117)
T ss_pred HHHHHHhCCHHHHHHHHHHH---HcCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 455566766655 4554332 12579999999999999999998654
No 368
>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=63.73 E-value=4.6 Score=28.87 Aligned_cols=24 Identities=29% Similarity=0.571 Sum_probs=19.7
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHH
Q 011992 430 SLSEVGNIFGLSKERVRQLESRAL 453 (473)
Q Consensus 430 TlkEIAe~LGIS~~rVrqi~~RAL 453 (473)
|..|+|+.+|||..+|+......+
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~Gl 24 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYEREGL 24 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHTTS
T ss_pred CHHHHHHHHCCCHHHHHHHHHCCC
Confidence 467999999999999999887653
No 369
>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=63.54 E-value=8.7 Score=29.84 Aligned_cols=28 Identities=39% Similarity=0.597 Sum_probs=21.3
Q ss_pred CCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992 426 GKPK-SLSEVGNIFGLSKERVRQLESRALYRLK 457 (473)
Q Consensus 426 ge~l-TlkEIAe~LGIS~~rVrqi~~RAL~KLR 457 (473)
|+.+ +..+||+.+|+|+.+|+. |+..|.
T Consensus 21 g~~lps~~~la~~~~vsr~tvr~----al~~L~ 49 (64)
T PF00392_consen 21 GDRLPSERELAERYGVSRTTVRE----ALRRLE 49 (64)
T ss_dssp TSBE--HHHHHHHHTS-HHHHHH----HHHHHH
T ss_pred CCEeCCHHHHHHHhccCCcHHHH----HHHHHH
Confidence 4777 999999999999999988 555554
No 370
>PRK11050 manganese transport regulator MntR; Provisional
Probab=63.48 E-value=13 Score=34.28 Aligned_cols=28 Identities=14% Similarity=0.188 Sum_probs=23.7
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992 426 GKPKSLSEVGNIFGLSKERVRQLESRAL 453 (473)
Q Consensus 426 ge~lTlkEIAe~LGIS~~rVrqi~~RAL 453 (473)
+++.+..|||+.+||+.++|+.++.+-.
T Consensus 49 ~~~~t~~eLA~~l~is~stVsr~l~~Le 76 (152)
T PRK11050 49 VGEARQVDIAARLGVSQPTVAKMLKRLA 76 (152)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4689999999999999999998665543
No 371
>COG4709 Predicted membrane protein [Function unknown]
Probab=62.78 E-value=19 Score=34.95 Aligned_cols=60 Identities=20% Similarity=0.176 Sum_probs=47.6
Q ss_pred HHHHHHHHHHHHhhCCHHHHHHHHHHhh--ccC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011992 395 KQLMRQHVRNLLTLLNPKERCIVRLRFG--IED--GKPKSLSEVGNIFGLSKERVRQLESRALY 454 (473)
Q Consensus 395 ~~el~e~L~~aL~~LperER~VL~LrY~--L~~--ge~lTlkEIAe~LGIS~~rVrqi~~RAL~ 454 (473)
+.+....|++.|+.||+.+|.=+..+|. +++ ..+.|-.||++.||=+.+-.+++.++..-
T Consensus 3 k~efL~eL~~yL~~Lp~~~r~e~m~dyeehF~~a~~~GksE~EI~~~LG~P~eiA~ei~s~~~~ 66 (195)
T COG4709 3 KTEFLNELEQYLEGLPREERREIMYDYEEHFREAQEAGKSEEEIAKDLGDPKEIAAEILSERGI 66 (195)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhhhhcCCCHHHHHHHhCCHHHHHHHHHHHccc
Confidence 4567788999999999999987655442 122 37889999999999999999998877553
No 372
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=62.66 E-value=12 Score=32.86 Aligned_cols=35 Identities=17% Similarity=0.302 Sum_probs=27.4
Q ss_pred HHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 415 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 415 ~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
+||.-.|. ...++|..+.|+.|||++.+|+.+++.
T Consensus 12 EiL~eefl--ep~glt~~~lA~~lgV~r~~is~ling 46 (104)
T COG3093 12 EILREEFL--EPLGLTQTELAEALGVTRNTISELING 46 (104)
T ss_pred HHHHHHHh--ccccCCHHHHHHHhCCCHHHHHHHHcC
Confidence 45555555 113799999999999999999998864
No 373
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=62.61 E-value=11 Score=29.15 Aligned_cols=26 Identities=19% Similarity=0.471 Sum_probs=22.7
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992 428 PKSLSEVGNIFGLSKERVRQLESRAL 453 (473)
Q Consensus 428 ~lTlkEIAe~LGIS~~rVrqi~~RAL 453 (473)
+.|+.+||+.+|+|...+.++..+..
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~~ 26 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKET 26 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHh
Confidence 36899999999999999999887755
No 374
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=62.60 E-value=17 Score=36.20 Aligned_cols=48 Identities=17% Similarity=0.227 Sum_probs=38.5
Q ss_pred HHHHHhhCCHHHHHHHHHHhhccCC---CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 402 VRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 402 L~~aL~~LperER~VL~LrY~L~~g---e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
|.+....|++.|+.|.... +++. ..+|..|+|+..|+|..+|....++
T Consensus 3 i~~~~~~Lt~~e~~ia~yi--l~n~~~v~~~si~elA~~~~vS~aTv~Rf~kk 53 (278)
T PRK11557 3 IRQRYPGLAQSDRKLADYL--LLQPDTARHLSSQQLANEAGVSQSSVVKFAQK 53 (278)
T ss_pred hhHhhhhCCHHHHHHHHHH--HhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHH
Confidence 5567788999999997543 3332 4699999999999999999887765
No 375
>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=62.22 E-value=26 Score=25.89 Aligned_cols=23 Identities=13% Similarity=0.325 Sum_probs=17.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 011992 429 KSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 429 lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
+|+.+.|+.+||+.+|++..++.
T Consensus 17 ~S~r~AA~~ygVp~sTL~~r~~g 39 (45)
T PF05225_consen 17 MSIRKAAKKYGVPRSTLRRRLRG 39 (45)
T ss_dssp S-HHHHHHHHT--HHHHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHcC
Confidence 99999999999999999966554
No 376
>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=62.21 E-value=10 Score=29.54 Aligned_cols=23 Identities=26% Similarity=0.473 Sum_probs=20.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 011992 429 KSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 429 lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
++..|+|+.+|||..+++.+..+
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 47899999999999999999876
No 377
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=62.17 E-value=12 Score=37.93 Aligned_cols=43 Identities=30% Similarity=0.329 Sum_probs=35.0
Q ss_pred hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
..|++.|+.||.+--. .|...++.||-+.+|+|+.+|+.++++
T Consensus 191 ~~L~~~e~~il~~i~~--~GGri~Q~eL~r~lglsktTvsR~L~~ 233 (258)
T COG2512 191 YDLNEDEKEILDLIRE--RGGRITQAELRRALGLSKTTVSRILRR 233 (258)
T ss_pred CCCCHHHHHHHHHHHH--hCCEEeHHHHHHhhCCChHHHHHHHHH
Confidence 3599999999876554 345689999999999999999876554
No 378
>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=62.16 E-value=11 Score=33.12 Aligned_cols=24 Identities=33% Similarity=0.458 Sum_probs=22.7
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLES 450 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~ 450 (473)
.|.|..|+|..+|||..+|..++.
T Consensus 17 ~g~s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 17 KGKSIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred ccchHHHHHHHhCcHHHHHHHHHH
Confidence 788999999999999999999977
No 379
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=62.15 E-value=12 Score=37.70 Aligned_cols=53 Identities=19% Similarity=0.248 Sum_probs=42.0
Q ss_pred HHHHHHHHHHhhCCHHHHHHHHHHhhccCC---CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 397 LMRQHVRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 397 el~e~L~~aL~~LperER~VL~LrY~L~~g---e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.+...|......|++.||.|-... |++. -.+|..|||+..|||+.+|-...++
T Consensus 4 ~l~~~I~~~~~~Lt~~er~iA~yi--l~~~~~~~~~si~elA~~a~VS~aTv~Rf~~k 59 (281)
T COG1737 4 NLLERIRERYDSLTKSERKIADYI--LANPDEVALLSIAELAERAGVSPATVVRFARK 59 (281)
T ss_pred hHHHHHHHHHhcCCHHHHHHHHHH--HhCHHHHHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence 356778889999999999996543 3332 4679999999999999999876655
No 380
>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=62.01 E-value=17 Score=34.85 Aligned_cols=26 Identities=12% Similarity=0.176 Sum_probs=23.9
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESRA 452 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~RA 452 (473)
.++|..|||+.+||+..+|++++.+-
T Consensus 14 ~~~t~~eLA~~lgis~~tV~~~L~~L 39 (203)
T TIGR02702 14 GQATAAALAEALAISPQAVRRHLKDL 39 (203)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 56999999999999999999998874
No 381
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=61.35 E-value=13 Score=26.46 Aligned_cols=26 Identities=15% Similarity=0.263 Sum_probs=19.8
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESRA 452 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~RA 452 (473)
.+.++.+||+.+|+|+...+.+.++.
T Consensus 7 ~~~~l~~iA~~~g~S~~~f~r~Fk~~ 32 (42)
T PF00165_consen 7 QKLTLEDIAEQAGFSPSYFSRLFKKE 32 (42)
T ss_dssp SS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 78999999999999999988776654
No 382
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=61.28 E-value=16 Score=36.23 Aligned_cols=25 Identities=28% Similarity=0.347 Sum_probs=22.9
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.+.|..|||++||||...|++++..
T Consensus 24 g~~sa~elA~~Lgis~~avR~HL~~ 48 (218)
T COG2345 24 GPVSADELAEELGISPMAVRRHLDD 48 (218)
T ss_pred CCccHHHHHHHhCCCHHHHHHHHHH
Confidence 6899999999999999999997754
No 383
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=61.20 E-value=15 Score=28.14 Aligned_cols=25 Identities=16% Similarity=0.405 Sum_probs=20.4
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.++|..++|+.+|++.++++.+++.
T Consensus 11 ~~lt~~~~a~~~~i~~~~i~~~e~g 35 (64)
T PF12844_consen 11 KGLTQKDLAEKLGISRSTISKIENG 35 (64)
T ss_dssp CT--HHHHHHHHTS-HHHHHHHHTT
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 6899999999999999999999865
No 384
>PHA00738 putative HTH transcription regulator
Probab=61.15 E-value=20 Score=31.81 Aligned_cols=37 Identities=22% Similarity=0.002 Sum_probs=27.6
Q ss_pred HHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011992 411 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 450 (473)
Q Consensus 411 erER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~ 450 (473)
|.-+.||.+-.. |++++..||++.+++|..+|+++++
T Consensus 12 ptRr~IL~lL~~---~e~~~V~eLae~l~lSQptVS~HLK 48 (108)
T PHA00738 12 ILRRKILELIAE---NYILSASLISHTLLLSYTTVLRHLK 48 (108)
T ss_pred HHHHHHHHHHHH---cCCccHHHHHHhhCCCHHHHHHHHH
Confidence 444555554332 3579999999999999999999654
No 385
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=61.14 E-value=29 Score=32.18 Aligned_cols=33 Identities=24% Similarity=0.249 Sum_probs=21.3
Q ss_pred HHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhc
Q 011992 294 KLQSQFGREPTLIEWAKAIGLSCRDLKSELHSG 326 (473)
Q Consensus 294 ~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g 326 (473)
++....|..+|.+|||+++|++...|.++....
T Consensus 26 e~~~~~~~r~T~~eiAee~Gis~~tLYrWr~~~ 58 (142)
T PF13022_consen 26 ELMPENGERRTQAEIAEEVGISRSTLYRWRQQN 58 (142)
T ss_dssp HHS------S-HHHHHHHHTS-HHHHHHHHHH-
T ss_pred HHhhhccccchHHHHHHHhCCCHHHHHHHHhcC
Confidence 454555678999999999999999999998754
No 386
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=60.72 E-value=6.8 Score=30.41 Aligned_cols=25 Identities=28% Similarity=0.412 Sum_probs=22.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992 429 KSLSEVGNIFGLSKERVRQLESRAL 453 (473)
Q Consensus 429 lTlkEIAe~LGIS~~rVrqi~~RAL 453 (473)
+|..|+|+.+|||..+|+.+....+
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~~~gl 25 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYERIGL 25 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999977555
No 387
>PRK01905 DNA-binding protein Fis; Provisional
Probab=60.43 E-value=40 Score=27.54 Aligned_cols=25 Identities=12% Similarity=0.227 Sum_probs=20.5
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.+-+..+.|+.|||++.+++..+++
T Consensus 49 ~~gn~s~aAr~LGIsrstL~rklkk 73 (77)
T PRK01905 49 AGGNQSLAAEYLGINRNTLRKKLQQ 73 (77)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3567999999999999998776654
No 388
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=60.27 E-value=17 Score=33.85 Aligned_cols=43 Identities=14% Similarity=0.210 Sum_probs=30.0
Q ss_pred CCHHHHHHHHHHhhc-cCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 409 LNPKERCIVRLRFGI-EDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 409 LperER~VL~LrY~L-~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
+++....-+...|.+ .++......+||+.|||+..+|.+++++
T Consensus 4 ~s~~~edYL~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~r 47 (154)
T COG1321 4 LSETEEDYLETIYELLEEKGFARTKDIAERLKVSPPSVTEMLKR 47 (154)
T ss_pred cchHHHHHHHHHHHHHhccCcccHHHHHHHhCCCcHHHHHHHHH
Confidence 444444444444422 3456789999999999999999886554
No 389
>PRK10161 transcriptional regulator PhoB; Provisional
Probab=59.95 E-value=11 Score=35.13 Aligned_cols=50 Identities=14% Similarity=0.052 Sum_probs=39.4
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHH-----HHCCCHHHHHHHHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGN-----IFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe-----~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
.|+++|.+|+.+... +.|+..|.++|.. .++++..+|+..+++.++||..
T Consensus 154 ~Lt~~E~~ll~~l~~-~~~~~~s~~~l~~~~~~~~~~~~~~tv~~~i~rlr~Kl~~ 208 (229)
T PRK10161 154 EMGPTEFKLLHFFMT-HPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEP 208 (229)
T ss_pred EcCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhcc
Confidence 499999998866553 4457888777754 5678999999999999999863
No 390
>PRK15044 transcriptional regulator SirC; Provisional
Probab=59.70 E-value=66 Score=33.28 Aligned_cols=72 Identities=19% Similarity=0.107 Sum_probs=48.1
Q ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHhh-cCCcchhhHhh
Q 011992 286 IRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQ-GRGISLHDLLQ 360 (473)
Q Consensus 286 ~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~~yl~lV~sIA~ry~-~~~~saEDLiQ 360 (473)
..++++..-+.+.++++++.++||+.+|++...+.+.++.....+.+.+.. .+ ...|.+.. ....++.++..
T Consensus 192 s~~~kV~~~I~~nl~~~~SLeeLA~~lgmS~~tL~R~Fk~eg~T~~~y~~~-~R--L~~A~~LL~~t~~sIseIA~ 264 (295)
T PRK15044 192 TTKEKVYNIIISDLTRKWSQAEVAGKLFMSVSSLKRKLAAEEVSFSKIYLD-AR--MNQAIKLLRMGAGNISQVAT 264 (295)
T ss_pred hHHHHHHHHHHhCcccCCCHHHHHHHhCCCHHHHHHHHHHcCCCHHHHHHH-HH--HHHHHHHHHcCCCCHHHHHH
Confidence 346667778888899999999999999999999998887543334444432 22 23444443 33456555554
No 391
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=59.44 E-value=20 Score=32.32 Aligned_cols=27 Identities=7% Similarity=0.238 Sum_probs=22.9
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 425 DGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 425 ~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.+...+..+||+.||||.++|+..+.+
T Consensus 19 ~~~~~~~~ela~~l~vs~~svs~~l~~ 45 (142)
T PRK03902 19 EKGYARVSDIAEALSVHPSSVTKMVQK 45 (142)
T ss_pred cCCCcCHHHHHHHhCCChhHHHHHHHH
Confidence 346789999999999999999986644
No 392
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=59.30 E-value=1.2e+02 Score=33.86 Aligned_cols=32 Identities=16% Similarity=0.215 Sum_probs=28.3
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
++.++.++|+.|.||++||.+-+.+....+..
T Consensus 91 ~~~~~~~La~~l~vS~sTi~~dl~~v~~~l~~ 122 (584)
T PRK09863 91 TFTPMAQLASALNLSRTWVAERLPRLNQRYER 122 (584)
T ss_pred CCccHHHHHHHhCCCHHHHHHHHHHHHHhhhc
Confidence 68999999999999999999988887776663
No 393
>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=58.43 E-value=11 Score=34.63 Aligned_cols=27 Identities=15% Similarity=0.247 Sum_probs=22.8
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 428 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 428 ~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
.+|.+|||..+|+|+++|+. ++++|++
T Consensus 143 ~~t~~~iA~~lG~tretvsR----~l~~l~~ 169 (193)
T TIGR03697 143 RLSHQAIAEAIGSTRVTITR----LLGDLRK 169 (193)
T ss_pred CCCHHHHHHHhCCcHHHHHH----HHHHHHH
Confidence 58999999999999999987 5566655
No 394
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=58.20 E-value=18 Score=26.70 Aligned_cols=47 Identities=15% Similarity=0.171 Sum_probs=35.4
Q ss_pred CCHHHHHHHHHHhhccCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 011992 409 LNPKERCIVRLRFGIEDG-KPKSLSEVGNIFGLSKERVRQLESRALYR 455 (473)
Q Consensus 409 LperER~VL~LrY~L~~g-e~lTlkEIAe~LGIS~~rVrqi~~RAL~K 455 (473)
+++.+..+|.-.|..+.. ......+||+.+|++...|..+......+
T Consensus 7 ~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~ 54 (56)
T smart00389 7 FTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAK 54 (56)
T ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhc
Confidence 677888888888863322 23357889999999999999988776554
No 395
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=57.64 E-value=1.7e+02 Score=30.20 Aligned_cols=31 Identities=23% Similarity=0.362 Sum_probs=26.3
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 011992 426 GKPKSLSEVGNIFGLSKERVRQLESRALYRL 456 (473)
Q Consensus 426 ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KL 456 (473)
|.+.|++|||...||++.+|++..+.-.+.|
T Consensus 274 g~~~t~keIa~v~~Vs~~tI~~~ykel~~~l 304 (310)
T PRK00423 274 GERRTQREVAEVAGVTEVTVRNRYKELAEKL 304 (310)
T ss_pred CCCCCHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence 4789999999999999999998776666544
No 396
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=57.61 E-value=3.4 Score=38.81 Aligned_cols=47 Identities=11% Similarity=0.184 Sum_probs=0.0
Q ss_pred HHHHHHHhhCCHHHHHHHHH--HhhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011992 400 QHVRNLLTLLNPKERCIVRL--RFGIEDGKPKSLSEVGNIFGLSKERVRQLES 450 (473)
Q Consensus 400 e~L~~aL~~LperER~VL~L--rY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~ 450 (473)
+.|......|=+.++.-|.- .+. .++|+++||+.||++++||+...+
T Consensus 23 ~TL~~v~~~iv~~Q~~ff~~g~~~l----~PLt~~~iA~~lgl~~STVSRav~ 71 (160)
T PF04552_consen 23 ETLLRVAQAIVERQKDFFLGGPGAL----KPLTMKDIADELGLHESTVSRAVK 71 (160)
T ss_dssp -----------------------------------------------------
T ss_pred HHHHHHHHHHHHHHHHHHhcCcccC----cCCCHHHHHHHhCCCHhHHHHHHc
Confidence 34444444555555554431 122 789999999999999999998665
No 397
>TIGR01387 cztR_silR_copR heavy metal response regulator. Members of this family contain a response regulator receiver domain (Pfam:PF00072) and an associated transcriptional regulatory region (Pfam:PF00486). This group is separated phylogenetically from related proteins with similar architecture and contains a number of proteins associated with heavy metal resistance efflux systems for copper, silver, cadmium, and/or zinc. Most members encoded by genes adjacent to genes for encoding a member of the heavy metal sensor histidine kinase family (TIGRFAMs:TIGR01386), its partner in the two-component response regulator system.
Probab=57.36 E-value=17 Score=33.19 Aligned_cols=49 Identities=14% Similarity=0.121 Sum_probs=40.2
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-----GLSKERVRQLESRALYRLK 457 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~L-----GIS~~rVrqi~~RAL~KLR 457 (473)
.|+++|.+|+.+... +.|+-.|.++|++.+ ..+..+|..++++.++||.
T Consensus 147 ~Lt~~E~~il~~l~~-~~~~~~sr~~i~~~~~~~~~~~~~~~~~~~i~~lr~kl~ 200 (218)
T TIGR01387 147 TLTRKEFQLLWLLMR-RTGEVLPRTVIASLVWGMNFDSDTNVVDVAIRRLRAKVD 200 (218)
T ss_pred eCCHHHHHHHHHHHh-CCCeeEcHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhhc
Confidence 499999999987764 345669999999999 4567889998888888885
No 398
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=56.90 E-value=17 Score=32.42 Aligned_cols=25 Identities=16% Similarity=0.104 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.++|..++|+.+|||.++|+++++.
T Consensus 17 ~gltq~~lA~~~gvs~~~is~~E~g 41 (135)
T PRK09706 17 LKLSQRSLAKAVKVSHVSISQWERD 41 (135)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 6899999999999999999999865
No 399
>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional
Probab=56.87 E-value=8.2 Score=35.83 Aligned_cols=46 Identities=13% Similarity=0.000 Sum_probs=37.9
Q ss_pred hCCHHHHHHHHHHhhccCCCCCC---------HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKS---------LSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lT---------lkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
.|+++|.+|+.+... +++ ..+||..++++..+|+.++++.++||..
T Consensus 156 ~Lt~~E~~~l~~l~~-----~~~~v~sr~~l~~~~~~~~~~~~~~tv~~~i~~lr~Kl~~ 210 (232)
T PRK10955 156 ELTGTEFTLLYLLAQ-----HLGQVVSREHLSQEVLGKRLTPFDRAIDMHISNLRRKLPD 210 (232)
T ss_pred cCCHHHHHHHHHHHh-----CCCceEcHHHHHHHHhCCCCCCCCcCHHHHHHHHHHhccc
Confidence 499999999887763 444 4778888899999999999999999863
No 400
>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=56.67 E-value=24 Score=24.41 Aligned_cols=25 Identities=20% Similarity=0.405 Sum_probs=22.5
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.++|..++|+.+|++..+|++++..
T Consensus 11 ~~~s~~~~a~~~~~~~~~v~~~~~g 35 (58)
T cd00093 11 KGLTQEELAEKLGVSRSTISRIENG 35 (58)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHcC
Confidence 5799999999999999999987764
No 401
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=56.43 E-value=22 Score=35.21 Aligned_cols=41 Identities=17% Similarity=0.236 Sum_probs=31.3
Q ss_pred HHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011992 411 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 454 (473)
Q Consensus 411 erER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~ 454 (473)
+|++.|+.+-.. ....+..|||+.||||+.|||.-+..-..
T Consensus 4 ~R~~~Il~~l~~---~~~~~~~eLa~~l~VS~~TiRRdL~~L~~ 44 (240)
T PRK10411 4 ARQQAIVDLLLN---HTSLTTEALAEQLNVSKETIRRDLNELQT 44 (240)
T ss_pred HHHHHHHHHHHH---cCCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 455566554332 36899999999999999999999887544
No 402
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=56.40 E-value=22 Score=40.06 Aligned_cols=63 Identities=17% Similarity=0.277 Sum_probs=47.2
Q ss_pred HHHHHHHHHHHhhCCHHHHHHHHHHhhccCC---CCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHh
Q 011992 396 QLMRQHVRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLESR----ALYRLKQSL 460 (473)
Q Consensus 396 ~el~e~L~~aL~~LperER~VL~LrY~L~~g---e~lTlkEIAe~LGIS~~rVrqi~~R----AL~KLR~~L 460 (473)
..+.+.|.+....|++.||.|.... +++. ..+|..|||+..|+|..+|....++ ...-||..+
T Consensus 341 ~~l~~~I~~~~~~Lt~~E~~IA~yI--l~n~~~v~~~si~eLA~~~~vS~aTV~Rf~kkLGf~Gf~efK~~L 410 (638)
T PRK14101 341 SAVFERIRQMRDALTPAERRVADLA--LNHPRSIINDPIVDIARKADVSQPTVIRFCRSLGCQGLSDFKLKL 410 (638)
T ss_pred HHHHHHHHHHHhhcCHHHHHHHHHH--HhCHHHHHhccHHHHHHHhCCCHHHHHHHHHHhCCCCHHHHHHHH
Confidence 3456778888999999999997543 3332 4679999999999999999887766 344444444
No 403
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=56.28 E-value=41 Score=32.15 Aligned_cols=27 Identities=26% Similarity=0.507 Sum_probs=22.2
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 428 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 428 ~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
.+|.++||..+|+|+.+|+.++ ++|++
T Consensus 184 ~lt~~~iA~~lG~sr~tvsR~l----~~l~~ 210 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETISRLL----GRFQK 210 (235)
T ss_pred cccHHHHHHHhCCcHHHHHHHH----HHHHH
Confidence 5899999999999999998754 45554
No 404
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=56.24 E-value=28 Score=30.84 Aligned_cols=46 Identities=24% Similarity=0.232 Sum_probs=38.6
Q ss_pred hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 011992 407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 456 (473)
Q Consensus 407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KL 456 (473)
+-|++.+-+-+.+++- --=+++||-..+|+|.-+||..+...+++|
T Consensus 40 ~~Lt~d~LeFv~lf~r----~RGnlKEvEr~lg~sYptvR~kld~vlram 85 (122)
T COG3877 40 EYLTSDQLEFVELFLR----CRGNLKEVERELGISYPTVRTKLDEVLRAM 85 (122)
T ss_pred cccCHhHhHHHHHHHH----HccCHHHHHHHHCCccHHHHHHHHHHHHHc
Confidence 4588888888888876 456899999999999999999888877765
No 405
>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=56.19 E-value=15 Score=28.80 Aligned_cols=23 Identities=22% Similarity=0.355 Sum_probs=20.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 011992 429 KSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 429 lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
++..|+|+.+|||..+++.....
T Consensus 1 ~~i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 47899999999999999998765
No 406
>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=56.00 E-value=26 Score=30.70 Aligned_cols=25 Identities=20% Similarity=0.375 Sum_probs=22.0
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
...+..|||+.+|++...|++++..
T Consensus 24 ~~~s~~eia~~~~i~~~~v~~il~~ 48 (132)
T TIGR00738 24 GPVSVKEIAERQGISRSYLEKILRT 48 (132)
T ss_pred CcCcHHHHHHHHCcCHHHHHHHHHH
Confidence 4899999999999999999986654
No 407
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=55.95 E-value=12 Score=28.62 Aligned_cols=26 Identities=8% Similarity=0.218 Sum_probs=20.0
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESRA 452 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~RA 452 (473)
.++|..++|+.+||++++|+.+.+.-
T Consensus 9 ~~it~~~La~~~gis~~tl~~~~~~~ 34 (63)
T PF13443_consen 9 RGITQKDLARKTGISRSTLSRILNGK 34 (63)
T ss_dssp TT--HHHHHHHHT--HHHHHHHHTTT
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcc
Confidence 67899999999999999999998865
No 408
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=55.72 E-value=31 Score=30.99 Aligned_cols=44 Identities=14% Similarity=0.185 Sum_probs=34.6
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHH----CCCHHHHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF----GLSKERVRQLESRALY 454 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~L----GIS~~rVrqi~~RAL~ 454 (473)
.|++.|..|+...+. .++.|..||.+.| |++..||...+.|-.+
T Consensus 1 ~Lt~~E~~VM~vlW~---~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~ 48 (130)
T TIGR02698 1 SISDAEWEVMRVVWT---LGETTSRDIIRILAEKKDWSDSTIKTLLGRLVD 48 (130)
T ss_pred CCCHHHHHHHHHHHc---CCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHH
Confidence 378889998876653 2578999988887 7999999998877655
No 409
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=55.70 E-value=55 Score=30.49 Aligned_cols=27 Identities=33% Similarity=0.475 Sum_probs=22.2
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 428 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 428 ~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
..|.+|||..+|+++++|+++ +++|++
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR~----l~~l~~ 194 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRV----LKMLED 194 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHHH----HHHHHH
Confidence 688999999999999999875 445554
No 410
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=55.54 E-value=22 Score=24.39 Aligned_cols=25 Identities=20% Similarity=0.388 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.++|..++|+.+|++..+|++++..
T Consensus 9 ~~~s~~~la~~~~i~~~~i~~~~~~ 33 (56)
T smart00530 9 KGLTQEELAEKLGVSRSTLSRIENG 33 (56)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 6799999999999999999987654
No 411
>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=55.24 E-value=7.6 Score=28.44 Aligned_cols=21 Identities=14% Similarity=0.248 Sum_probs=18.3
Q ss_pred HHHHHHHCCCHHHHHHHHHHH
Q 011992 432 SEVGNIFGLSKERVRQLESRA 452 (473)
Q Consensus 432 kEIAe~LGIS~~rVrqi~~RA 452 (473)
++||+.+|||.++|+.+++.-
T Consensus 1 ~~lA~~~gvs~~tvs~~l~g~ 21 (52)
T cd01392 1 KDIARAAGVSVATVSRVLNGK 21 (52)
T ss_pred CcHHHHHCcCHHHHHHHHcCC
Confidence 379999999999999998753
No 412
>PRK10643 DNA-binding transcriptional regulator BasR; Provisional
Probab=54.89 E-value=14 Score=33.86 Aligned_cols=49 Identities=14% Similarity=0.059 Sum_probs=35.0
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHH-----HHCCCHHHHHHHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGN-----IFGLSKERVRQLESRALYRLK 457 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe-----~LGIS~~rVrqi~~RAL~KLR 457 (473)
.|+++|.+|+.+... ..|...+.++|.+ .++++..+|+.+.++.++||.
T Consensus 149 ~Lt~~E~~il~~l~~-~~g~~~~~~~~~~~~~~~~~~~~~~tv~~~i~~lr~Kl~ 202 (222)
T PRK10643 149 ILTPKEFALLSRLML-KAGSPVHREILYQDIYNWDDEPSSNTLEVHIHNLRDKVG 202 (222)
T ss_pred ecCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhCC
Confidence 499999999986552 1223334444444 268999999999999999885
No 413
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=54.83 E-value=13 Score=34.53 Aligned_cols=28 Identities=18% Similarity=0.223 Sum_probs=22.6
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
-..|.++||..+|+|+++|+. ++++|++
T Consensus 148 ~~~t~~~iA~~lG~tretvsR----~l~~l~~ 175 (202)
T PRK13918 148 IYATHDELAAAVGSVRETVTK----VIGELSR 175 (202)
T ss_pred ecCCHHHHHHHhCccHHHHHH----HHHHHHH
Confidence 357999999999999999987 4555554
No 414
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=54.82 E-value=28 Score=31.55 Aligned_cols=39 Identities=23% Similarity=0.198 Sum_probs=26.9
Q ss_pred CCHHHHH-HHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992 409 LNPKERC-IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 452 (473)
Q Consensus 409 LperER~-VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA 452 (473)
||...|+ ||.|.. ++.+..+||..|+||.+.|+.|+.|=
T Consensus 18 Lp~~~R~rIvela~-----~G~rp~~Isr~l~Vs~gcVsKIl~Ry 57 (125)
T PF00292_consen 18 LPNELRQRIVELAK-----EGVRPCDISRQLRVSHGCVSKILSRY 57 (125)
T ss_dssp S-HHHHHHHHHHHH-----TT--HHHHHHHHT--HHHHHHHHHHH
T ss_pred CcHHHHHHHHHHhh-----hcCCHHHHHHHHccchhHHHHHHHHH
Confidence 4544444 666776 69999999999999999999998863
No 415
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=54.67 E-value=28 Score=30.60 Aligned_cols=43 Identities=23% Similarity=0.245 Sum_probs=36.2
Q ss_pred HHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 403 RNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 403 ~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
......|++.|-..|+-.+ ++|..+-|..||+|.++|+.++..
T Consensus 38 l~~~~~ls~~eIk~iRe~~------~lSQ~vFA~~L~vs~~Tv~~WEqG 80 (104)
T COG2944 38 LLKVKTLSPTEIKAIREKL------GLSQPVFARYLGVSVSTVRKWEQG 80 (104)
T ss_pred hccCCCCCHHHHHHHHHHh------CCCHHHHHHHHCCCHHHHHHHHcC
Confidence 3344668988888887776 599999999999999999999975
No 416
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=54.48 E-value=26 Score=29.12 Aligned_cols=34 Identities=24% Similarity=0.368 Sum_probs=27.0
Q ss_pred CCCCHHHHHHHHC------CCHHHHHHHHHH-----HHHHHHHHh
Q 011992 427 KPKSLSEVGNIFG------LSKERVRQLESR-----ALYRLKQSL 460 (473)
Q Consensus 427 e~lTlkEIAe~LG------IS~~rVrqi~~R-----AL~KLR~~L 460 (473)
-|+|..++|+.+| +|..+|+++++. ...||+-.|
T Consensus 23 lGLTQ~dvA~~lg~~~g~i~SQstISR~Es~~ls~~n~~kl~p~l 67 (75)
T smart00352 23 LGFTQADVGLALGALYGPDFSQTTICRFEALQLSFKNMCKLKPLL 67 (75)
T ss_pred cCCCHHHHHHHhcccccCcCCHHHHHHHHhcCccHHHHHHHHHHH
Confidence 6899999999999 599999998863 444555444
No 417
>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=54.17 E-value=31 Score=32.40 Aligned_cols=57 Identities=23% Similarity=0.248 Sum_probs=45.4
Q ss_pred HHHHHHHHHHHHhhCCHHHHHHHHHHhh--ccC--CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 395 KQLMRQHVRNLLTLLNPKERCIVRLRFG--IED--GKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 395 ~~el~e~L~~aL~~LperER~VL~LrY~--L~~--ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
+++..+.|++.|+.||+.|++=+.-+|. +++ .+|.|-+||.+.||=++.-++++...
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 KNEFLNELEKYLKKLPEEEREEILEYYEEYFDDAGEEGKSEEEIIAELGSPKEIAREILAE 63 (181)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhCCCCHHHHHHHcCCHHHHHHHHHHh
Confidence 5667788999999999999886655543 233 26799999999999999999888755
No 418
>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=53.91 E-value=28 Score=32.99 Aligned_cols=42 Identities=19% Similarity=0.196 Sum_probs=30.7
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.|++-|+-....... +. .++|.+|||+.+|+|..+|++.+.-
T Consensus 102 ~lt~~e~a~~~~~l~-~~-~g~s~~~iA~~lg~s~~~V~r~l~l 143 (187)
T TIGR00180 102 DLSPIEEAQAYKRLL-EK-FSMTQEDLAKKIGKSRAHITNLLRL 143 (187)
T ss_pred CCCHHHHHHHHHHHH-HH-hCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 577777655443321 11 4799999999999999999998764
No 419
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=53.80 E-value=28 Score=38.75 Aligned_cols=46 Identities=24% Similarity=0.252 Sum_probs=36.2
Q ss_pred CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
|++|+.+++.+--. +..|..++|+.||||..||+.-+...=..|++
T Consensus 2 l~~R~~~iL~~L~~----~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~ 47 (584)
T PRK09863 2 LNERELKIVDLLEQ----QDRSGGELAQQLGVSRRTIVRDIAYINFTLNG 47 (584)
T ss_pred hHHHHHHHHHHHHc----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 56788888765422 68999999999999999999877766555555
No 420
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=53.76 E-value=41 Score=27.39 Aligned_cols=50 Identities=24% Similarity=0.359 Sum_probs=38.7
Q ss_pred CCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhh
Q 011992 303 PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEG 362 (473)
Q Consensus 303 PT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg 362 (473)
-|-+|+|+.+|++.+.+..+-++... -.+.+.++||+.+ +..++|+++..
T Consensus 15 ltQ~elA~~vgVsRQTi~~iEkgky~-------Psl~La~kia~~f---~~~iedIF~~~ 64 (68)
T COG1476 15 LTQEELAKLVGVSRQTIIAIEKGKYN-------PSLELALKIARVF---GKTIEDIFQLE 64 (68)
T ss_pred cCHHHHHHHcCcCHHHHHHHHcCCCC-------chHHHHHHHHHHh---CCCHHHHHhhh
Confidence 58899999999999999988776542 2456777888777 47888888743
No 421
>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=53.54 E-value=24 Score=34.58 Aligned_cols=36 Identities=14% Similarity=0.179 Sum_probs=27.0
Q ss_pred HHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 416 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 416 VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
+-.|.++-..+.++++.|||+.+|+++++|..++.-
T Consensus 12 l~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~t 47 (248)
T TIGR02431 12 LAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLT 47 (248)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 333444323347899999999999999999987654
No 422
>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=53.06 E-value=11 Score=29.93 Aligned_cols=28 Identities=29% Similarity=0.424 Sum_probs=21.0
Q ss_pred cCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 424 EDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 424 ~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
..+...|+.|||..||+++..|..++..
T Consensus 10 ~~~~~~S~~eLa~~~~~s~~~ve~mL~~ 37 (69)
T PF09012_consen 10 RERGRVSLAELAREFGISPEAVEAMLEQ 37 (69)
T ss_dssp HHS-SEEHHHHHHHTT--HHHHHHHHHH
T ss_pred HHcCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 3347799999999999999999987654
No 423
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=52.66 E-value=21 Score=34.53 Aligned_cols=30 Identities=23% Similarity=0.474 Sum_probs=25.3
Q ss_pred CCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 425 DGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 425 ~ge~l-TlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
.|+.+ |-.|+|+.+|||+.+||. |+..|..
T Consensus 27 pG~~LPsE~eLae~~gVSRt~VRe----AL~~L~~ 57 (239)
T PRK04984 27 PGSILPAERELSELIGVTRTTLRE----VLQRLAR 57 (239)
T ss_pred CCCcCCCHHHHHHHHCCCHHHHHH----HHHHHHH
Confidence 35777 799999999999999998 7777764
No 424
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=52.62 E-value=49 Score=31.57 Aligned_cols=48 Identities=8% Similarity=0.099 Sum_probs=32.4
Q ss_pred HHHHHHHHhhCCHHHHHHHHH-HhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 399 RQHVRNLLTLLNPKERCIVRL-RFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 399 ~e~L~~aL~~LperER~VL~L-rY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
+..+...+.. ++....|+.. ... ..+|..|||+.|||+...||+++.+
T Consensus 11 ~~~l~~~~~~-~~~~~~Vl~~L~~~----g~~tdeeLA~~Lgi~~~~VRk~L~~ 59 (178)
T PRK06266 11 QKVLFEIMEG-DEEGFEVLKALIKK----GEVTDEEIAEQTGIKLNTVRKILYK 59 (178)
T ss_pred HHHHHHHhcC-CccHhHHHHHHHHc----CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 3444444442 5555555553 332 4799999999999999999996654
No 425
>PRK11517 transcriptional regulatory protein YedW; Provisional
Probab=51.89 E-value=28 Score=31.99 Aligned_cols=49 Identities=14% Similarity=0.078 Sum_probs=39.3
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-----GLSKERVRQLESRALYRLK 457 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~L-----GIS~~rVrqi~~RAL~KLR 457 (473)
.|+++|..|+.+-.. +.|+-.|..+|.+.+ ..+..+|..+++|.++||.
T Consensus 147 ~Lt~~E~~il~~l~~-~~g~~~s~~~i~~~~w~~~~~~~~~tv~~~i~rlr~Kl~ 200 (223)
T PRK11517 147 TLTRKEFQLLWLLAS-RAGEIIPRTVIASEIWGINFDSDTNTVDVAIRRLRAKVD 200 (223)
T ss_pred eCCHHHHHHHHHHHh-CCCccCCHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhhc
Confidence 599999999877654 445778999999997 4467899998888888885
No 426
>PRK06424 transcription factor; Provisional
Probab=51.65 E-value=23 Score=32.77 Aligned_cols=25 Identities=12% Similarity=0.056 Sum_probs=23.5
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.++|..|+|+.+|++.++|++|++.
T Consensus 96 ~GLSQ~eLA~~iGvs~stIskiE~G 120 (144)
T PRK06424 96 LSMSQADLAAKIFERKNVIASIERG 120 (144)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 7899999999999999999999874
No 427
>PHA02943 hypothetical protein; Provisional
Probab=51.63 E-value=25 Score=33.12 Aligned_cols=24 Identities=25% Similarity=0.257 Sum_probs=21.2
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLES 450 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~ 450 (473)
...|..|||+.||+|-+.|+.++.
T Consensus 23 G~~TtseIAkaLGlS~~qa~~~Ly 46 (165)
T PHA02943 23 GCKTTSRIANKLGVSHSMARNALY 46 (165)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHH
Confidence 468899999999999999998764
No 428
>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=51.58 E-value=26 Score=30.90 Aligned_cols=26 Identities=23% Similarity=0.388 Sum_probs=22.5
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 426 GKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 426 ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
+...+..|||+.+|+|...|++++.+
T Consensus 23 ~~~~s~~eia~~l~is~~~v~~~l~~ 48 (130)
T TIGR02944 23 SQPYSAAEIAEQTGLNAPTVSKILKQ 48 (130)
T ss_pred CCCccHHHHHHHHCcCHHHHHHHHHH
Confidence 46789999999999999999986554
No 429
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=51.56 E-value=26 Score=34.84 Aligned_cols=39 Identities=21% Similarity=0.226 Sum_probs=27.6
Q ss_pred HHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 413 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 413 ER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
+|-+-.|.++-+.+.++++.|||+.+|+++++|..++..
T Consensus 11 ~ral~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~t 49 (263)
T PRK09834 11 SRGLMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLET 49 (263)
T ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 344444444333345699999999999999999886554
No 430
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=51.31 E-value=24 Score=31.32 Aligned_cols=25 Identities=16% Similarity=0.183 Sum_probs=23.2
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.++|.+|+|+.+|||.++|+++++.
T Consensus 17 ~Glsq~eLA~~~Gis~~~is~iE~g 41 (120)
T PRK13890 17 RHMTKKELSERSGVSISFLSDLTTG 41 (120)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 6899999999999999999999864
No 431
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=51.05 E-value=43 Score=28.31 Aligned_cols=26 Identities=19% Similarity=0.238 Sum_probs=24.2
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESRA 452 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~RA 452 (473)
++.++++||+.+|+|+.++..+.++.
T Consensus 20 ~~~~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 20 QPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 78999999999999999999988886
No 432
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=50.78 E-value=16 Score=29.09 Aligned_cols=25 Identities=24% Similarity=0.352 Sum_probs=20.4
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.+++-.|||+.+|+|..+|+.++..
T Consensus 14 ~p~~T~eiA~~~gls~~~aR~yL~~ 38 (62)
T PF04703_consen 14 GPLKTREIADALGLSIYQARYYLEK 38 (62)
T ss_dssp S-EEHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 6899999999999999999987643
No 433
>PF12298 Bot1p: Eukaryotic mitochondrial regulator protein ; InterPro: IPR021036 This entry represents Ribosomal protein S35, which localises to the mitochondria in live cells and co-fractionates with purified mitochondrial ribosomes. This group of proteins have a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery and a role in mitochondrial integrity. Observations also indicate that in Schizosaccharomyces pombe (Fission yeast), alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms [].
Probab=50.68 E-value=34 Score=32.60 Aligned_cols=47 Identities=21% Similarity=0.274 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992 409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 460 (473)
Q Consensus 409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L 460 (473)
|++.-|.-|.-.+. .++++.++||..+||...||.-|++ |+.+.+.+
T Consensus 17 lse~~r~~Iy~~~~---~~~~sv~~vS~~ygi~~~RV~AIvr--LkeiE~~~ 63 (172)
T PF12298_consen 17 LSEELREQIYEDVM---QDGKSVREVSQKYGIKIQRVEAIVR--LKEIEKRW 63 (172)
T ss_pred CCHHHHHHHHHHHH---hCCCCHHHHHHHhCCCHHHHHHHHH--HHHHHHHH
Confidence 55555554444443 1678999999999999999987664 34444444
No 434
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=50.57 E-value=36 Score=32.65 Aligned_cols=41 Identities=20% Similarity=0.189 Sum_probs=33.1
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.|+..+-.||...+. ..+.|.+|||+.++++.++|..++.+
T Consensus 42 gLt~~q~~iL~~L~~---~~~itq~eLa~~l~l~~sTvtr~l~r 82 (185)
T PRK13777 42 DLNINEHHILWIAYH---LKGASISEIAKFGVMHVSTAFNFSKK 82 (185)
T ss_pred CCCHHHHHHHHHHHh---CCCcCHHHHHHHHCCCHhhHHHHHHH
Confidence 689898888866554 36899999999999999998775543
No 435
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=50.39 E-value=21 Score=34.28 Aligned_cols=30 Identities=30% Similarity=0.397 Sum_probs=25.8
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 425 DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 425 ~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
.|+.++-.+||+.||||+..||. |+..|..
T Consensus 31 pG~~L~e~~La~~lgVSRtpVRE----AL~~L~~ 60 (221)
T PRK11414 31 PGARLITKNLAEQLGMSITPVRE----ALLRLVS 60 (221)
T ss_pred CCCccCHHHHHHHHCCCchhHHH----HHHHHHH
Confidence 46888999999999999999998 7777754
No 436
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=50.11 E-value=37 Score=26.25 Aligned_cols=23 Identities=13% Similarity=0.199 Sum_probs=19.1
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Q 011992 428 PKSLSEVGNIFGLSKERVRQLES 450 (473)
Q Consensus 428 ~lTlkEIAe~LGIS~~rVrqi~~ 450 (473)
.++.+|.|+.|||+...++.+-.
T Consensus 15 hlp~~eAA~~Lgv~~T~LKr~CR 37 (52)
T PF02042_consen 15 HLPIKEAAKELGVSVTTLKRRCR 37 (52)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Confidence 59999999999999887776543
No 437
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=49.97 E-value=37 Score=29.06 Aligned_cols=25 Identities=24% Similarity=0.264 Sum_probs=22.6
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
-++|.++||..||+|.+.|.+++.-
T Consensus 22 ~~ls~~~ia~dL~~s~~~le~vL~l 46 (89)
T PF10078_consen 22 SGLSLEQIAADLGTSPEHLEQVLNL 46 (89)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 6899999999999999999998753
No 438
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=49.83 E-value=18 Score=32.55 Aligned_cols=23 Identities=13% Similarity=0.338 Sum_probs=21.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 011992 429 KSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 429 lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
||-+|+|+.+|+++.||..+..+
T Consensus 1 MT~eELA~~tG~srQTINrWvRk 23 (122)
T PF07037_consen 1 MTPEELAELTGYSRQTINRWVRK 23 (122)
T ss_pred CCHHHHHHHhCccHHHHHHHHHh
Confidence 68899999999999999998765
No 439
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.21 E-value=44 Score=28.70 Aligned_cols=24 Identities=13% Similarity=0.239 Sum_probs=21.6
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLES 450 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~ 450 (473)
-.+|.+|||..||+|+..|..++.
T Consensus 22 ~~LS~~~iA~~Ln~t~~~lekil~ 45 (97)
T COG4367 22 CPLSDEEIATALNWTEVKLEKILQ 45 (97)
T ss_pred ccccHHHHHHHhCCCHHHHHHHHH
Confidence 579999999999999999988774
No 440
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=49.11 E-value=79 Score=24.26 Aligned_cols=60 Identities=17% Similarity=0.264 Sum_probs=34.8
Q ss_pred CCCHHHHHHHcCCCHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhh-cCCcchhhHhhhhHH
Q 011992 302 EPTLIEWAKAIGLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQ-GRGISLHDLLQEGSM 364 (473)
Q Consensus 302 ePT~eEiA~~lGms~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~-~~~~saEDLiQEg~l 364 (473)
+++..+||+.+|++...+.+.+.... ......+... .+. .|..+. .+..+++|+.++..+
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~~~~s~~~~~~~~--r~~-~a~~~l~~~~~~~~~ia~~~g~ 62 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKETGTTPKQYLRDR--RLE-RARRLLRDTDLSVTEIALRVGF 62 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHhCcCHHHHHHHH--HHH-HHHHHHHcCCCCHHHHHHHhCC
Confidence 47889999999999999888776432 1122222111 122 233333 335777777765433
No 441
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=48.74 E-value=37 Score=30.05 Aligned_cols=26 Identities=27% Similarity=0.354 Sum_probs=24.2
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESRA 452 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~RA 452 (473)
+..++.+||+.+|+|+.++..+.++.
T Consensus 24 ~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 24 SPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 78999999999999999999988876
No 442
>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=48.66 E-value=23 Score=33.52 Aligned_cols=30 Identities=27% Similarity=0.434 Sum_probs=25.7
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 425 DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 425 ~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
.|+.++-.++|+.||||+..||. |+..|..
T Consensus 31 pG~~L~e~~La~~lgVSRtpVRe----AL~~L~~ 60 (212)
T TIGR03338 31 PGAKLNESDIAARLGVSRGPVRE----AFRALEE 60 (212)
T ss_pred CCCEecHHHHHHHhCCChHHHHH----HHHHHHH
Confidence 45889999999999999999998 6766654
No 443
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=48.62 E-value=27 Score=32.82 Aligned_cols=25 Identities=16% Similarity=0.290 Sum_probs=23.5
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.++|..|+|+.+|+|.++|+++++.
T Consensus 19 ~glt~~elA~~~gis~~~is~~E~g 43 (185)
T PRK09943 19 QGLSQRRAAELSGLTHSAISTIEQD 43 (185)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHcC
Confidence 7899999999999999999999975
No 444
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=48.45 E-value=15 Score=31.38 Aligned_cols=36 Identities=19% Similarity=0.369 Sum_probs=28.0
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH-----HHHHHHHhcc
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESRA-----LYRLKQSLGG 462 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~RA-----L~KLR~~L~~ 462 (473)
.+++.++||+.+||++++|+.....- +.||...|..
T Consensus 40 ~~l~Q~qiae~lgV~qprvS~l~~gk~~~fs~dkLvtml~~ 80 (91)
T COG5606 40 AALSQAQIAELLGVTQPRVSDLARGKIQDFSIDKLVTMLAR 80 (91)
T ss_pred HHHHHHHHHHHhCCCCchHHHHHhcchhHhhHHHHHHHHHH
Confidence 68999999999999999999876653 4455555543
No 445
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=48.34 E-value=36 Score=33.83 Aligned_cols=26 Identities=15% Similarity=0.093 Sum_probs=23.0
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 426 GKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 426 ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
+...+.+|||+.||||+.||+.-+..
T Consensus 17 ~~~~~~~ela~~l~vS~~TirRdL~~ 42 (251)
T PRK13509 17 LGFVTVEKVIERLGISPATARRDINK 42 (251)
T ss_pred cCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 36799999999999999999987665
No 446
>PRK03837 transcriptional regulator NanR; Provisional
Probab=48.33 E-value=28 Score=33.62 Aligned_cols=30 Identities=37% Similarity=0.511 Sum_probs=25.3
Q ss_pred CCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 425 DGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 425 ~ge~l-TlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
.|+-+ +..+||+.+|||+..||. |+..|..
T Consensus 33 pG~~Lp~E~~Lae~~gVSRt~VRE----AL~~L~~ 63 (241)
T PRK03837 33 PGDQLPSERELMAFFGVGRPAVRE----ALQALKR 63 (241)
T ss_pred CCCCCCCHHHHHHHhCCCHHHHHH----HHHHHHH
Confidence 35778 899999999999999998 6766664
No 447
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=48.19 E-value=25 Score=31.72 Aligned_cols=30 Identities=27% Similarity=0.617 Sum_probs=24.3
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 425 DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 425 ~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
+|+..+..|||+.+|||+..|++ ++.+|++
T Consensus 22 ~g~~~s~~~ia~~~~is~~~vrk----~l~~L~~ 51 (141)
T PRK11014 22 EGRMTSISEVTEVYGVSRNHMVK----IINQLSR 51 (141)
T ss_pred CCCccCHHHHHHHHCcCHHHHHH----HHHHHHh
Confidence 35668999999999999999988 5555654
No 448
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=47.76 E-value=36 Score=34.12 Aligned_cols=26 Identities=19% Similarity=0.189 Sum_probs=22.7
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 426 GKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 426 ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
+.++++.|||+.+|+++++|..+++-
T Consensus 38 ~~~~tl~eIa~~lglpkStv~RlL~t 63 (271)
T PRK10163 38 GGSSSVSDISLNLDLPLSTTFRLLKV 63 (271)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 36799999999999999999887654
No 449
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=47.51 E-value=1.1e+02 Score=30.71 Aligned_cols=41 Identities=15% Similarity=0.030 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhc
Q 011992 286 IRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSG 326 (473)
Q Consensus 286 ~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g 326 (473)
..|+++..-++..+...++.++||+.+|++...+.+..+.-
T Consensus 5 ~~i~~~~~~i~~~~~~~~~l~~lA~~~~~S~~~l~r~F~~~ 45 (289)
T PRK15121 5 GIIRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDV 45 (289)
T ss_pred HHHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 45677777788889999999999999999999999888763
No 450
>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=47.48 E-value=29 Score=33.59 Aligned_cols=30 Identities=23% Similarity=0.474 Sum_probs=25.7
Q ss_pred CCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 425 DGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 425 ~ge~l-TlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
.|+.+ +-.++|+.||||+..||. |+.+|..
T Consensus 26 pG~~LpsE~~La~~lgVSRtpVRE----AL~~Le~ 56 (235)
T TIGR02812 26 PGSILPAERELSELIGVTRTTLRE----VLQRLAR 56 (235)
T ss_pred CCCcCcCHHHHHHHHCcCHHHHHH----HHHHHHH
Confidence 45888 899999999999999998 7777765
No 451
>smart00862 Trans_reg_C Transcriptional regulatory protein, C terminal. This domain is almost always found associated with the response regulator receiver domain. It may play a role in DNA binding.
Probab=47.33 E-value=65 Score=25.03 Aligned_cols=50 Identities=22% Similarity=0.231 Sum_probs=34.0
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHH------CCCHHHHHHHHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF------GLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~L------GIS~~rVrqi~~RAL~KLR~ 458 (473)
.|++++..+|.+-. ...|+..|.++|.+.+ +.+..+|++.+++.+++|..
T Consensus 5 ~Lt~~e~~lL~~L~-~~~~~~vs~~~l~~~lw~~~~~~~~~~~l~~~i~~LR~~l~~ 60 (78)
T smart00862 5 KLTPKEFRLLELLL-RNPGRVVSREELLEAVWGDDDDDVDDNTLDVHISRLRKKLED 60 (78)
T ss_pred ecCHHHHHHHHHHH-hCCCCccCHHHHHHHHcCCCCCCCccchHHHHHHHHHHHHhc
Confidence 47888888665433 3445789999999986 35666777766666666553
No 452
>cd00383 trans_reg_C Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and a response regulator. The former autophosphorylates in a histidine residue on detecting an external stimulus. The phosphate is then transferred to an invariant aspartate residue in a highly conserved receiver domain of the response regulator. Phosphorylation activates a variable effector domain of the response regulator, which triggers the cellular response. The C-terminal effector domain contains DNA and RNA polymerase binding sites. Several dimers or monomers bind head to tail to small tandem repeats upstream of the genes. The RNA polymerase binding sites interact with the alpha or sigma subunite of RNA polymerase.
Probab=47.16 E-value=47 Score=26.95 Aligned_cols=49 Identities=22% Similarity=0.164 Sum_probs=34.2
Q ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHH
Q 011992 408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLK 457 (473)
Q Consensus 408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LG-----IS~~rVrqi~~RAL~KLR 457 (473)
.|+++|..+|.+-.. ..|+..|.++|.+.+. .+...+.+.+++.+++|.
T Consensus 23 ~Lt~~e~~lL~~L~~-~~~~~vs~~~l~~~lw~~~~~~~~~~l~~~I~rLRkkl~ 76 (95)
T cd00383 23 ELTPKEFELLELLAR-NPGRVLSREQLLEAVWGDDYDVDDRTVDVHISRLRKKLE 76 (95)
T ss_pred EeCHHHHHHHHHHHh-CCCCcCCHHHHHHHhcCCCCCCCcccHHHHHHHHHHHhc
Confidence 488899998876553 5568999999999884 455666665555444443
No 453
>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=47.09 E-value=37 Score=28.37 Aligned_cols=52 Identities=17% Similarity=0.181 Sum_probs=30.3
Q ss_pred HHHHHHHhhC--CHHHHHHH-HHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 400 QHVRNLLTLL--NPKERCIV-RLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 400 e~L~~aL~~L--perER~VL-~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
..|.+.|... +.....++ -+...|-.|++.|..++|..+|.+.+.|++.+..
T Consensus 7 ~~l~~~L~~~~~~~~~~~L~r~LLr~LA~G~PVt~~~LA~a~g~~~e~v~~~L~~ 61 (77)
T PF12324_consen 7 TRLAERLTSGNRPGGFAWLLRPLLRLLAKGQPVTVEQLAAALGWPVEEVRAALAA 61 (77)
T ss_dssp HHHHHHHHHHHSSTTHHHHHHHHHHHHTTTS-B-HHHHHHHHT--HHHHHHHHHH
T ss_pred HHHHHHhcCCCCCCccHHHHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHh
Confidence 3444555444 33333222 2333355679999999999999999999987654
No 454
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=46.65 E-value=30 Score=33.19 Aligned_cols=30 Identities=20% Similarity=0.246 Sum_probs=25.5
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 425 DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 425 ~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
.|+.++..|+|+.||||+..||. |+.+|..
T Consensus 27 pG~~L~e~eLae~lgVSRtpVRE----AL~~L~~ 56 (224)
T PRK11534 27 PDEKLRMSLLTSRYALGVGPLRE----ALSQLVA 56 (224)
T ss_pred CCCcCCHHHHHHHHCCChHHHHH----HHHHHHH
Confidence 45889999999999999999988 7777654
No 455
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=46.49 E-value=32 Score=34.31 Aligned_cols=38 Identities=13% Similarity=0.150 Sum_probs=28.6
Q ss_pred HHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 411 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 411 erER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
+|.+.|+.+--- ....+..|+|+.||||+.|||+-+..
T Consensus 5 eR~~~Il~~L~~---~~~v~v~eLa~~l~VS~~TIRRDL~~ 42 (256)
T PRK10434 5 QRQAAILEYLQK---QGKTSVEELAQYFDTTGTTIRKDLVI 42 (256)
T ss_pred HHHHHHHHHHHH---cCCEEHHHHHHHHCCCHHHHHHHHHH
Confidence 455556554332 25689999999999999999997665
No 456
>PF12759 HTH_Tnp_IS1: InsA C-terminal domain; InterPro: IPR024431 This entry represents the helix-turn-helix domain found at the C-terminal of InsA.
Probab=46.34 E-value=29 Score=26.24 Aligned_cols=37 Identities=14% Similarity=0.218 Sum_probs=29.7
Q ss_pred CHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 410 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 410 perER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
|.-..+|+.|-+ .+.-..++|..|+|+.++|-..++.
T Consensus 8 pgikeqIvema~-----nG~GiRdtaRvL~I~~nTVlrtLK~ 44 (46)
T PF12759_consen 8 PGIKEQIVEMAF-----NGSGIRDTARVLKISINTVLRTLKN 44 (46)
T ss_pred ccHHHHHHHHHh-----cCCcchhhHhHhcchHHHHHHHHhc
Confidence 444567888888 6899999999999999999765543
No 457
>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=46.05 E-value=25 Score=26.34 Aligned_cols=24 Identities=21% Similarity=0.439 Sum_probs=19.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Q 011992 429 KSLSEVGNIFGLSKERVRQLESRA 452 (473)
Q Consensus 429 lTlkEIAe~LGIS~~rVrqi~~RA 452 (473)
++.+|+++.+|+|..++....+..
T Consensus 4 l~~~ev~~~~g~s~~ti~~~~k~g 27 (51)
T PF05930_consen 4 LRIKEVAELLGVSRSTIYRLIKDG 27 (51)
T ss_dssp E-HHHHHHHHSS-HHHHHHHHHHH
T ss_pred ccHHHHHHHHCCCHHHHHHHHhcc
Confidence 578999999999999999988754
No 458
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=45.96 E-value=2.4e+02 Score=25.94 Aligned_cols=81 Identities=14% Similarity=0.106 Sum_probs=50.6
Q ss_pred HHHHHHHHHHHHhCCC-CCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHH
Q 011992 287 RLEKEKSKLQSQFGRE-PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMG 365 (473)
Q Consensus 287 kle~a~~~L~~~lGRe-PT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lg 365 (473)
+|-.+-.++..+.|-. .|..+||+.+|++...+.....+.+.-+..++..+..........+.. ..+..+-+.+.+..
T Consensus 12 ~Il~aA~~lf~e~G~~~~s~~~IA~~agvs~~~lY~hF~sKe~L~~av~~~~~~~~~~~~~~~~~-~~~~~e~l~~~~~~ 90 (202)
T TIGR03613 12 AILSAALDTFSRFGFHGTSLEQIAELAGVSKTNLLYYFPSKDALYLAVLRQILDIWLSPLKAFTE-DFAPLAAIKAYIRA 90 (202)
T ss_pred HHHHHHHHHHHHhCcccCCHHHHHHHhCCCHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcc-CCCHHHHHHHHHHH
Confidence 4444445555566655 889999999999999999988776666666766665554444333322 23334444444444
Q ss_pred HHH
Q 011992 366 LMK 368 (473)
Q Consensus 366 L~k 368 (473)
.+.
T Consensus 91 ~~~ 93 (202)
T TIGR03613 91 KLE 93 (202)
T ss_pred HHH
Confidence 443
No 459
>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=45.52 E-value=54 Score=30.20 Aligned_cols=38 Identities=21% Similarity=0.219 Sum_probs=30.7
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcc
Q 011992 290 KEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGN 327 (473)
Q Consensus 290 ~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~ 327 (473)
.++.=|...-|+..|..||++++|++.+.|.++++.|.
T Consensus 34 kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~IreGR 71 (137)
T TIGR03826 34 KVYKFLRKHENRQATVSEIVEETGVSEKLILKFIREGR 71 (137)
T ss_pred HHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 33344455567778999999999999999999999886
No 460
>PF05331 DUF742: Protein of unknown function (DUF742); InterPro: IPR007995 This family consists of several uncharacterised Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown.
Probab=45.50 E-value=35 Score=30.45 Aligned_cols=40 Identities=35% Similarity=0.470 Sum_probs=35.6
Q ss_pred hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
..|.+.++.|+.+.- ...|..|||..|+++.+-|+-+..-
T Consensus 39 ~~l~pE~~~Il~lC~-----~~~SVAEiAA~L~lPlgVvrVLvsD 78 (114)
T PF05331_consen 39 AGLGPEHRAILELCR-----RPLSVAEIAARLGLPLGVVRVLVSD 78 (114)
T ss_pred CCCCHHHHHHHHHHC-----CCccHHHHHHhhCCCchhhhhhHHH
Confidence 469999999999987 5999999999999999999887764
No 461
>TIGR03764 ICE_PFGI_1_parB integrating conjugative element, PFGI_1 class, ParB family protein. Members of this protein family carry the ParB-type nuclease domain and are found in integrating conjugative elements (ICE) in the same class as PFGI-1 of Pseudomonas fluorescens Pf-5.
Probab=45.37 E-value=2.3e+02 Score=28.83 Aligned_cols=20 Identities=15% Similarity=0.290 Sum_probs=16.5
Q ss_pred HHHHhCCCCCHHHHHHHcCC
Q 011992 295 LQSQFGREPTLIEWAKAIGL 314 (473)
Q Consensus 295 L~~~lGRePT~eEiA~~lGm 314 (473)
+++.+|..-|.+|+|+.+|.
T Consensus 129 ~e~~~g~~ltq~ela~~lgk 148 (258)
T TIGR03764 129 YEKELGESLSQRELARRLSA 148 (258)
T ss_pred HHhhccCCCCHHHHHHHhcc
Confidence 34667889999999999986
No 462
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=45.22 E-value=49 Score=28.56 Aligned_cols=43 Identities=21% Similarity=0.254 Sum_probs=32.8
Q ss_pred hCCHHHH-HHHHHHhhccCCCCCCHHHHHHHHCC-CHHHHHHHHHHHHH
Q 011992 408 LLNPKER-CIVRLRFGIEDGKPKSLSEVGNIFGL-SKERVRQLESRALY 454 (473)
Q Consensus 408 ~LperER-~VL~LrY~L~~ge~lTlkEIAe~LGI-S~~rVrqi~~RAL~ 454 (473)
..++..+ +|+.++.. .+.|+.+||..+|| +.+.++++..+...
T Consensus 7 ~~s~EfK~~iv~~~~~----~g~sv~~vAr~~gv~~~~~l~~W~~~~~~ 51 (116)
T COG2963 7 KYSPEFKLEAVALYLR----GGDTVSEVAREFGIVSATQLYKWRIQLQK 51 (116)
T ss_pred cCCHHHHHHHHHHHHh----cCccHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 3455555 57777776 67899999999996 99999887776554
No 463
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=45.12 E-value=33 Score=33.55 Aligned_cols=30 Identities=23% Similarity=0.348 Sum_probs=25.6
Q ss_pred CCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 425 DGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 425 ~ge~l-TlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
.|+.+ +-.|||+.||||+..||. ||++|..
T Consensus 27 pG~~LPsE~eLa~~~gVSRtpVRE----AL~~L~~ 57 (251)
T PRK09990 27 VGQALPSERRLCEKLGFSRSALRE----GLTVLRG 57 (251)
T ss_pred CCCcCcCHHHHHHHHCCCHHHHHH----HHHHHHH
Confidence 46888 899999999999999998 7777764
No 464
>PRK11569 transcriptional repressor IclR; Provisional
Probab=45.05 E-value=36 Score=34.12 Aligned_cols=26 Identities=19% Similarity=0.302 Sum_probs=22.9
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 426 GKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 426 ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
+.++++.|||+.+|+++++|..++.-
T Consensus 41 ~~~~~lseia~~lglpksTv~RlL~t 66 (274)
T PRK11569 41 NGSVALTELAQQAGLPNSTTHRLLTT 66 (274)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 46799999999999999999887654
No 465
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=44.85 E-value=33 Score=33.56 Aligned_cols=30 Identities=27% Similarity=0.458 Sum_probs=25.2
Q ss_pred CCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 425 DGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 425 ~ge~l-TlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
.|+.+ +-.|+|+.||||+..||. |+..|..
T Consensus 30 pG~~LpsE~eLa~~lgVSRtpVRE----AL~~L~~ 60 (254)
T PRK09464 30 PGEKLPPERELAKQFDVSRPSLRE----AIQRLEA 60 (254)
T ss_pred CCCcCCCHHHHHHHhCCCHHHHHH----HHHHHHH
Confidence 35777 899999999999999998 6766654
No 466
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. 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.
Probab=44.84 E-value=17 Score=30.87 Aligned_cols=26 Identities=19% Similarity=0.448 Sum_probs=22.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011992 429 KSLSEVGNIFGLSKERVRQLESRALY 454 (473)
Q Consensus 429 lTlkEIAe~LGIS~~rVrqi~~RAL~ 454 (473)
+|..|+|+.+|||..+++.....++-
T Consensus 1 ~ti~eva~~~gvs~~tLRyye~~Gll 26 (96)
T cd04768 1 LTIGEFAKLAGVSIRTLRHYDDIGLF 26 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 47899999999999999999887653
No 467
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=44.77 E-value=34 Score=31.97 Aligned_cols=25 Identities=8% Similarity=0.157 Sum_probs=23.5
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.++|.+++|+.+|++.++|+++++.
T Consensus 81 ~glSqeeLA~~lgvs~s~IsriE~G 105 (154)
T TIGR00270 81 RGWSQEQLAKKIQEKESLIKKIENA 105 (154)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 7899999999999999999999864
No 468
>TIGR00637 ModE_repress ModE molybdate transport repressor domain. ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.
Probab=44.50 E-value=63 Score=27.74 Aligned_cols=44 Identities=11% Similarity=0.107 Sum_probs=32.0
Q ss_pred CHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 410 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 410 perER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
+.++-.+|.... +.-|+...|+.||||.++|++.+++.-..|..
T Consensus 3 ~~~~l~~~~av~-----~~gSis~AA~~L~iS~stvs~~I~~LE~~lg~ 46 (99)
T TIGR00637 3 DPRRVALLKAIA-----RMGSISQAAKDAGISYKSAWDYIRAMNNLSGE 46 (99)
T ss_pred CHHHHHHHHHHH-----HhCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence 344555555555 57899999999999999999866655544443
No 469
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=44.30 E-value=53 Score=24.07 Aligned_cols=25 Identities=16% Similarity=0.157 Sum_probs=20.0
Q ss_pred CCHHHHHHHcCCCHHHHHHHHhhcc
Q 011992 303 PTLIEWAKAIGLSCRDLKSELHSGN 327 (473)
Q Consensus 303 PT~eEiA~~lGms~eeL~~~l~~g~ 327 (473)
-|..|+|+.+|++...+.++..+..
T Consensus 10 ls~~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 10 LSQKELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp S-HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred CCHHHHHHHhCCCcchhHHHhcCCC
Confidence 4678999999999999999988854
No 470
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=44.02 E-value=1.6e+02 Score=23.98 Aligned_cols=51 Identities=24% Similarity=0.197 Sum_probs=28.6
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhc
Q 011992 270 LTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSG 326 (473)
Q Consensus 270 LT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g 326 (473)
|++++..++-.+.+-+..|.... . .+.-|..|+|+.+|++...+-+..++.
T Consensus 5 l~~~~~~~~~~k~~l~~~i~~~~----~--~~~ltQ~e~A~~lgisq~~vS~l~~g~ 55 (80)
T PF13744_consen 5 LGFEEAEELEAKAQLMAAIRELR----E--ERGLTQAELAERLGISQPRVSRLENGK 55 (80)
T ss_dssp ----HHHHHHHHHHHHHHHHHHH----H--CCT--HHHHHHHHTS-HHHHHHHHTT-
T ss_pred CCHhHHHHHHHHHHHHHHHHHHH----H--HcCCCHHHHHHHHCCChhHHHHHHcCc
Confidence 44555555554444444443332 2 355789999999999999998887643
No 471
>PRK08359 transcription factor; Validated
Probab=43.91 E-value=34 Score=32.81 Aligned_cols=25 Identities=24% Similarity=0.328 Sum_probs=23.0
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.++|++|+|+.+|+++++|+.|++.
T Consensus 97 kglSQeeLA~~lgvs~stI~~iE~G 121 (176)
T PRK08359 97 SGLSYEELSHEVGLSVNDLRRIAHG 121 (176)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 7899999999999999999998654
No 472
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=43.81 E-value=35 Score=33.54 Aligned_cols=30 Identities=23% Similarity=0.392 Sum_probs=25.4
Q ss_pred CCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 425 DGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 425 ~ge~l-TlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
-|+.+ +-.++|+.||||+..||. |+..|..
T Consensus 29 pG~~LpsE~eLa~~~gVSRtpVRE----AL~~L~~ 59 (257)
T PRK10225 29 PGERLPPEREIAEMLDVTRTVVRE----ALIMLEI 59 (257)
T ss_pred CCCcCcCHHHHHHHhCCCHHHHHH----HHHHHHH
Confidence 35788 699999999999999998 7777765
No 473
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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 N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=43.71 E-value=17 Score=31.13 Aligned_cols=26 Identities=23% Similarity=0.384 Sum_probs=23.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011992 429 KSLSEVGNIFGLSKERVRQLESRALY 454 (473)
Q Consensus 429 lTlkEIAe~LGIS~~rVrqi~~RAL~ 454 (473)
++..|+|+.+|||..+++.....++-
T Consensus 2 ~~i~eva~~~gvs~~tLR~ye~~Gll 27 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYESIGLI 27 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 68899999999999999999988765
No 474
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=43.60 E-value=35 Score=33.45 Aligned_cols=30 Identities=23% Similarity=0.377 Sum_probs=25.2
Q ss_pred CCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 425 DGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 425 ~ge~l-TlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
.|+.+ +-.|+|+.||||+..||. ||+.|..
T Consensus 22 pG~~LpsE~eLae~~gVSRtpVRE----AL~~Le~ 52 (253)
T PRK10421 22 AGMKLPAERQLAMQLGVSRNSLRE----ALAKLVS 52 (253)
T ss_pred CCCcCCCHHHHHHHhCCCHHHHHH----HHHHHHH
Confidence 45788 799999999999999998 7776664
No 475
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=43.60 E-value=48 Score=31.80 Aligned_cols=27 Identities=15% Similarity=0.220 Sum_probs=22.3
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 428 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 428 ~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
..|.+|||..+|+|+++|+. ++++|++
T Consensus 169 ~~t~~~lA~~lG~sretvsR----~L~~L~~ 195 (226)
T PRK10402 169 HEKHTQAAEYLGVSYRHLLY----VLAQFIQ 195 (226)
T ss_pred cchHHHHHHHHCCcHHHHHH----HHHHHHH
Confidence 46899999999999999987 5566655
No 476
>PF12085 DUF3562: Protein of unknown function (DUF3562); InterPro: IPR021945 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 62 to 84 amino acids in length. This protein has two completely conserved residues (A and Y) that may be functionally important.
Probab=43.31 E-value=51 Score=26.77 Aligned_cols=41 Identities=20% Similarity=0.342 Sum_probs=31.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCchhhhhhhh
Q 011992 429 KSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLL 472 (473)
Q Consensus 429 lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~l~~yldll 472 (473)
-.+++||+..|++.+.|++.....+..|+. +-...+|+-+|
T Consensus 8 e~i~~iA~~t~~P~e~V~~my~dt~~~l~~---~ARV~DYl~lf 48 (66)
T PF12085_consen 8 EVIRSIAEETGTPAETVRRMYDDTMRELSS---GARVHDYLPLF 48 (66)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHHHHHc---CCchhhhHHHH
Confidence 357899999999999999999998887764 34455666544
No 477
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. 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 two 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=42.75 E-value=20 Score=29.96 Aligned_cols=25 Identities=28% Similarity=0.498 Sum_probs=22.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992 429 KSLSEVGNIFGLSKERVRQLESRAL 453 (473)
Q Consensus 429 lTlkEIAe~LGIS~~rVrqi~~RAL 453 (473)
+|..|+|+.+|||..+++.+..+.+
T Consensus 2 ~ti~evA~~~gvs~~tLR~ye~~Gl 26 (88)
T cd01105 2 IGIGEVSKLTGVSPRQLRYWEEKGL 26 (88)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 6899999999999999999987765
No 478
>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=42.52 E-value=61 Score=23.49 Aligned_cols=22 Identities=18% Similarity=0.291 Sum_probs=20.4
Q ss_pred CCCCHHHHHHHHCCCHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQL 448 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi 448 (473)
++.|+.+||+.+|+|++.+.+.
T Consensus 15 ~~~s~~~Ia~~~gvs~~~~y~~ 36 (47)
T PF00440_consen 15 EAVSIRDIARRAGVSKGSFYRY 36 (47)
T ss_dssp TTSSHHHHHHHHTSCHHHHHHH
T ss_pred HhCCHHHHHHHHccchhhHHHH
Confidence 7999999999999999999864
No 479
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, 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=42.51 E-value=19 Score=30.22 Aligned_cols=25 Identities=28% Similarity=0.542 Sum_probs=22.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992 429 KSLSEVGNIFGLSKERVRQLESRAL 453 (473)
Q Consensus 429 lTlkEIAe~LGIS~~rVrqi~~RAL 453 (473)
++..|+|+.+||+..+|+.+....+
T Consensus 1 ~~~~eva~~~gi~~~tlr~~~~~Gl 25 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEEKGL 25 (100)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999988765
No 480
>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=42.48 E-value=18 Score=30.12 Aligned_cols=27 Identities=19% Similarity=0.273 Sum_probs=23.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 011992 429 KSLSEVGNIFGLSKERVRQLESRALYR 455 (473)
Q Consensus 429 lTlkEIAe~LGIS~~rVrqi~~RAL~K 455 (473)
+|..|+|+.+|||..+|+.....++-.
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye~~Gli~ 28 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYERLGLLS 28 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCCCcC
Confidence 588999999999999999998765543
No 481
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=42.25 E-value=1e+02 Score=29.73 Aligned_cols=27 Identities=33% Similarity=0.572 Sum_probs=22.3
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992 428 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458 (473)
Q Consensus 428 ~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~ 458 (473)
.+|.++||..+|+++++|+. ++++|++
T Consensus 179 ~lt~~~IA~~lGisretlsR----~L~~L~~ 205 (230)
T PRK09391 179 PMSRRDIADYLGLTIETVSR----ALSQLQD 205 (230)
T ss_pred cCCHHHHHHHHCCCHHHHHH----HHHHHHH
Confidence 57999999999999999987 4555654
No 482
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. 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. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=42.25 E-value=19 Score=31.25 Aligned_cols=26 Identities=19% Similarity=0.501 Sum_probs=23.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011992 429 KSLSEVGNIFGLSKERVRQLESRALY 454 (473)
Q Consensus 429 lTlkEIAe~LGIS~~rVrqi~~RAL~ 454 (473)
+|..|+|+.+|||..+++.....++-
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~Gll 26 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEKEGLL 26 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999999887653
No 483
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=42.24 E-value=42 Score=33.49 Aligned_cols=38 Identities=18% Similarity=0.166 Sum_probs=27.8
Q ss_pred HHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 411 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 411 erER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
+|.+.|+.+..- ....+..|||+.||||+.|||.-+..
T Consensus 5 ~R~~~Il~~l~~---~~~~~~~ela~~l~vS~~TiRRdL~~ 42 (252)
T PRK10906 5 QRHDAIIELVKQ---QGYVSTEELVEHFSVSPQTIRRDLND 42 (252)
T ss_pred HHHHHHHHHHHH---cCCEeHHHHHHHhCCCHHHHHHHHHH
Confidence 455555554432 25689999999999999999985443
No 484
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein. gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.
Probab=42.19 E-value=74 Score=26.94 Aligned_cols=23 Identities=22% Similarity=0.274 Sum_probs=19.8
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.++| ++|+..|||+++|+++++.
T Consensus 44 ~glS--qLAe~~GIs~stLs~iE~g 66 (89)
T TIGR02684 44 RGMT--QLARKTGLSRESLYKALSG 66 (89)
T ss_pred CChH--HHHHHHCCCHHHHHHHHcC
Confidence 4555 6999999999999999865
No 485
>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=42.15 E-value=50 Score=30.78 Aligned_cols=39 Identities=10% Similarity=-0.038 Sum_probs=27.8
Q ss_pred CHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 410 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 410 perER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
.+....|+..-. .. ..+|.+|||+.|||+...||.++.+
T Consensus 13 g~~~v~Vl~aL~--~~-~~~tdEeLa~~Lgi~~~~VRk~L~~ 51 (158)
T TIGR00373 13 EEEVGLVLFSLG--IK-GEFTDEEISLELGIKLNEVRKALYA 51 (158)
T ss_pred ChhHHHHHHHHh--cc-CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 344555555322 12 5799999999999999999986544
No 486
>PF04814 HNF-1_N: Hepatocyte nuclear factor 1 (HNF-1), N terminus; InterPro: IPR006899 This domain consists of the N terminus of homeobox-containing transcription factor HNF-1. This region contains a dimerisation sequence [] and an acidic region that may be involved in transcription activation. Mutations and the common Ala/Val 98 polymorphism in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3) [].; GO: 0045893 positive regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2GYP_B 1IC8_B 2H8R_B 1G2Y_D 1F93_H 1G39_D 1G2Z_B 1JB6_B.
Probab=41.69 E-value=21 Score=34.32 Aligned_cols=52 Identities=19% Similarity=0.156 Sum_probs=36.8
Q ss_pred HHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992 399 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 453 (473)
Q Consensus 399 ~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL 453 (473)
...+...|..=|-.-++.|..|.. .+..+..||++..|||.+.|+|++.++.
T Consensus 105 ~~~Ve~llr~D~~~VkeeIK~fl~---~h~IsQ~~V~q~TGisQS~lSq~L~kGt 156 (180)
T PF04814_consen 105 RAEVEELLRRDPWRVKEEIKAFLQ---QHNISQREVVQVTGISQSHLSQHLNKGT 156 (180)
T ss_dssp HHHHHHCTTS-HHHHHHHHHHHHH---HCT--CHHHHHHHT--HHHHHHHHCTB-
T ss_pred HHHHHHHHhhCHHHHHHHHHHHHH---HcCCcHHHHHHHhhhhHHHHHHHHHcCC
Confidence 366667776667777778877765 3789999999999999999999987653
No 487
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), 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. 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.
Probab=41.47 E-value=32 Score=29.49 Aligned_cols=23 Identities=35% Similarity=0.507 Sum_probs=20.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 011992 429 KSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 429 lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
+|..|+|+.+|||..+++.+...
T Consensus 1 yti~EvA~~~gVs~~tLR~ye~~ 23 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRYWETE 23 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 47899999999999999998766
No 488
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=41.34 E-value=47 Score=34.01 Aligned_cols=40 Identities=18% Similarity=0.151 Sum_probs=30.3
Q ss_pred HHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011992 412 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 454 (473)
Q Consensus 412 rER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~ 454 (473)
+.+.|+.+.. ++...+..|||+.+|||+.+|++.+.+-..
T Consensus 5 r~~~il~~L~---~~~~~s~~~LA~~lgvsr~tV~~~l~~L~~ 44 (319)
T PRK11886 5 VMLQLLSLLA---DGDFHSGEQLGEELGISRAAIWKHIQTLEE 44 (319)
T ss_pred HHHHHHHHHH---cCCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4455555443 236789999999999999999998877553
No 489
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=41.16 E-value=1.3e+02 Score=30.51 Aligned_cols=40 Identities=15% Similarity=0.186 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhc
Q 011992 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSG 326 (473)
Q Consensus 287 kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g 326 (473)
.+.++..-+...+...++.+++|+.+||+...+.+.++..
T Consensus 219 ~~~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~ 258 (322)
T PRK09393 219 RLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAA 258 (322)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4556666777788899999999999999999999888764
No 490
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=41.03 E-value=37 Score=35.49 Aligned_cols=49 Identities=24% Similarity=0.378 Sum_probs=37.6
Q ss_pred hhCCHHHHHHHHH--HhhccCCCCCCHHHHHHH--HCCCHHHHHHHHHHHHHHH
Q 011992 407 TLLNPKERCIVRL--RFGIEDGKPKSLSEVGNI--FGLSKERVRQLESRALYRL 456 (473)
Q Consensus 407 ~~LperER~VL~L--rY~L~~ge~lTlkEIAe~--LGIS~~rVrqi~~RAL~KL 456 (473)
..|++|+++|+.. ..++..+++.+.++||+. +|+|..|||..+.. |.++
T Consensus 2 ~~l~~R~~~Il~~IV~~yi~~~~pv~s~~l~~~~~l~~S~aTIR~dm~~-Le~~ 54 (339)
T PRK00082 2 SMLDERQREILRAIVEDYIATGEPVGSKTLSKRYGLGVSSATIRNDMAD-LEEL 54 (339)
T ss_pred CccCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHhCCCCChHHHHHHHHH-HHhC
Confidence 3588999999862 223455699999999977 99999999997763 4443
No 491
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=40.95 E-value=32 Score=34.29 Aligned_cols=38 Identities=21% Similarity=0.312 Sum_probs=29.1
Q ss_pred CHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011992 410 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 450 (473)
Q Consensus 410 perER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~ 450 (473)
.+|.+.|+.+--. ....+.+|+|+.||||+.|||.=+.
T Consensus 4 ~eR~~~Il~~l~~---~g~v~v~eLa~~~~VS~~TIRRDL~ 41 (253)
T COG1349 4 EERHQKILELLKE---KGKVSVEELAELFGVSEMTIRRDLN 41 (253)
T ss_pred HHHHHHHHHHHHH---cCcEEHHHHHHHhCCCHHHHHHhHH
Confidence 3567777766443 2568999999999999999998543
No 492
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=40.90 E-value=21 Score=30.41 Aligned_cols=25 Identities=20% Similarity=0.262 Sum_probs=22.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992 429 KSLSEVGNIFGLSKERVRQLESRAL 453 (473)
Q Consensus 429 lTlkEIAe~LGIS~~rVrqi~~RAL 453 (473)
++..|+|+.+|||..+|+.....++
T Consensus 1 m~I~eva~~~gvs~~tlR~Ye~~GL 25 (95)
T cd04780 1 MRMSELSKRSGVSVATIKYYLREGL 25 (95)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999888765
No 493
>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=40.78 E-value=86 Score=22.75 Aligned_cols=28 Identities=25% Similarity=0.405 Sum_probs=19.6
Q ss_pred HHHhCCCCCHHHHHHHcCCCHHHHHHHHh
Q 011992 296 QSQFGREPTLIEWAKAIGLSCRDLKSELH 324 (473)
Q Consensus 296 ~~~lGRePT~eEiA~~lGms~eeL~~~l~ 324 (473)
.+..|| -+..+||+.+|++...+.+.++
T Consensus 12 Lq~d~r-~s~~~la~~lglS~~~v~~Ri~ 39 (42)
T PF13404_consen 12 LQEDGR-RSYAELAEELGLSESTVRRRIR 39 (42)
T ss_dssp HHH-TT-S-HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHcCC-ccHHHHHHHHCcCHHHHHHHHH
Confidence 344465 5688999999999999887664
No 494
>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=40.27 E-value=1.2e+02 Score=25.85 Aligned_cols=51 Identities=24% Similarity=0.204 Sum_probs=34.2
Q ss_pred CCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHH---HHhhcchH
Q 011992 269 LLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS---ELHSGNSS 329 (473)
Q Consensus 269 lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~---~l~~g~~A 329 (473)
++|+.|=..|..+++-.++ -+...-+-.|||+.+|++...+-+ .++.+...
T Consensus 26 L~T~~E~~~l~~R~~va~~----------lL~~g~syreIa~~tgvS~aTItRvsr~Lk~~~~~ 79 (87)
T PF01371_consen 26 LCTPDELEALAQRWQVAKE----------LLDEGKSYREIAEETGVSIATITRVSRCLKYGDDG 79 (87)
T ss_dssp HSSHHHHHHHHHHHHHHHH----------HHHTTSSHHHHHHHHTSTHHHHHHHHHHHHHSHCH
T ss_pred hCCHHHHHHHHHHHHHHHH----------HHHCCCCHHHHHHHhCCCHHHHHHHHHHHHcCCHH
Confidence 5788888888877765331 233446789999999999776543 44444433
No 495
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=39.89 E-value=22 Score=30.33 Aligned_cols=25 Identities=20% Similarity=0.339 Sum_probs=22.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992 429 KSLSEVGNIFGLSKERVRQLESRAL 453 (473)
Q Consensus 429 lTlkEIAe~LGIS~~rVrqi~~RAL 453 (473)
+|..|+|+.+|||..+++.....++
T Consensus 1 ~ti~eva~~~gvs~~tlR~ye~~Gl 25 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDEIGL 25 (103)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999888765
No 496
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 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, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=39.86 E-value=60 Score=24.79 Aligned_cols=31 Identities=19% Similarity=0.212 Sum_probs=24.1
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992 427 KPKSLSEVGNIFGLSKERVRQLESRALYRLK 457 (473)
Q Consensus 427 e~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR 457 (473)
+..++...|+.||||.++|++.+++.-..|-
T Consensus 12 ~~gs~~~AA~~l~is~~~vs~~i~~LE~~lg 42 (60)
T PF00126_consen 12 ETGSISAAAEELGISQSAVSRQIKQLEEELG 42 (60)
T ss_dssp HHSSHHHHHHHCTSSHHHHHHHHHHHHHHHT
T ss_pred HhCCHHHHHHHhhccchHHHHHHHHHHHHhC
Confidence 3569999999999999999986555444443
No 497
>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=39.85 E-value=61 Score=28.97 Aligned_cols=27 Identities=22% Similarity=0.394 Sum_probs=22.6
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 425 DGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 425 ~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
+++..+.+|||+.++++..-|++++.+
T Consensus 22 ~~~~~s~~~ia~~~~ip~~~l~kil~~ 48 (135)
T TIGR02010 22 ETGPVTLADISERQGISLSYLEQLFAK 48 (135)
T ss_pred CCCcCcHHHHHHHHCcCHHHHHHHHHH
Confidence 345789999999999999999886544
No 498
>COG1481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.49 E-value=60 Score=33.77 Aligned_cols=43 Identities=28% Similarity=0.259 Sum_probs=36.1
Q ss_pred hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCC--CHHHHHHHHHHH
Q 011992 407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGL--SKERVRQLESRA 452 (473)
Q Consensus 407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGI--S~~rVrqi~~RA 452 (473)
+.||++-+++-.+|.. ..+.|++|||+.+.. |++-|..++.|.
T Consensus 252 ~~lpe~l~e~a~LRl~---hpd~SLeeLg~~l~~~iSKSGvnHrlrkl 296 (308)
T COG1481 252 EKLPEKLREAALLRLE---HPDASLEELGELLEPPISKSGVNHRLRKL 296 (308)
T ss_pred hhCCHHHHHHHHHhhc---ChhhhHHHHHHHhcCcccHHHHHHHHHHH
Confidence 6899999999988875 478999999999997 888887766553
No 499
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares 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.
Probab=39.46 E-value=23 Score=30.63 Aligned_cols=26 Identities=19% Similarity=0.273 Sum_probs=23.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011992 429 KSLSEVGNIFGLSKERVRQLESRALY 454 (473)
Q Consensus 429 lTlkEIAe~LGIS~~rVrqi~~RAL~ 454 (473)
++..|+|+.+|||..+++.....++-
T Consensus 1 ~~i~eva~~~gis~~tlR~ye~~GLi 26 (108)
T cd01107 1 FTIGEFAKLSNLSIKALRYYDKIGLL 26 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCC
Confidence 57899999999999999999988764
No 500
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=39.30 E-value=60 Score=32.27 Aligned_cols=38 Identities=11% Similarity=0.156 Sum_probs=28.3
Q ss_pred HHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992 411 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451 (473)
Q Consensus 411 erER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R 451 (473)
+|+..|+.+-- .....+..|+|+.||||+.|||.-+..
T Consensus 7 eR~~~I~~~l~---~~~~v~v~eLa~~~~VS~~TIRRDL~~ 44 (252)
T PRK10681 7 ERIGQLLQALK---RSDKLHLKDAAALLGVSEMTIRRDLNA 44 (252)
T ss_pred HHHHHHHHHHH---HcCCCcHHHHHHHhCCCHHHHHHHHHH
Confidence 34555554322 236789999999999999999988775
Done!