Query 012638
Match_columns 459
No_of_seqs 335 out of 1727
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 04:45:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012638.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012638hhsearch_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 6.4E-48 1.4E-52 401.0 27.1 233 217-452 58-332 (415)
2 PRK05949 RNA polymerase sigma 100.0 8.6E-45 1.9E-49 368.8 26.8 232 218-452 17-248 (327)
3 TIGR02997 Sig70-cyanoRpoD RNA 100.0 1.1E-44 2.4E-49 362.7 26.8 229 221-452 3-231 (298)
4 PRK07406 RNA polymerase sigma 100.0 1.2E-44 2.6E-49 373.1 26.5 231 219-452 63-293 (373)
5 PRK07405 RNA polymerase sigma 100.0 1.6E-43 3.4E-48 358.0 26.7 231 219-452 8-238 (317)
6 COG0568 RpoD DNA-directed RNA 100.0 3E-41 6.4E-46 342.2 20.3 224 230-453 17-261 (342)
7 PRK05901 RNA polymerase sigma 100.0 4.8E-40 1E-44 349.5 20.9 215 218-448 210-424 (509)
8 PRK07921 RNA polymerase sigma 100.0 1.5E-39 3.3E-44 330.0 22.9 215 218-448 25-239 (324)
9 PRK09210 RNA polymerase sigma 100.0 3.1E-34 6.8E-39 295.5 21.7 187 219-448 96-282 (367)
10 PRK05658 RNA polymerase sigma 100.0 8.1E-34 1.8E-38 309.8 23.5 173 276-448 354-533 (619)
11 PRK07122 RNA polymerase sigma 100.0 4.4E-32 9.5E-37 268.0 17.0 154 295-448 40-197 (264)
12 TIGR02393 RpoD_Cterm RNA polym 100.0 1.1E-31 2.4E-36 260.2 17.1 153 296-448 1-153 (238)
13 PRK07408 RNA polymerase sigma 100.0 1.5E-30 3.2E-35 255.7 19.8 160 291-450 20-185 (256)
14 PRK07500 rpoH2 RNA polymerase 100.0 3.5E-30 7.6E-35 257.6 21.3 183 230-452 14-205 (289)
15 TIGR02850 spore_sigG RNA polym 100.0 3.5E-29 7.7E-34 245.1 20.9 154 295-449 34-189 (254)
16 PRK06596 RNA polymerase factor 100.0 6.2E-29 1.4E-33 247.9 20.9 159 292-452 44-208 (284)
17 TIGR02392 rpoH_proteo alternat 100.0 2.6E-28 5.7E-33 241.3 20.7 160 292-453 31-197 (270)
18 PRK08215 sporulation sigma fac 100.0 8.2E-28 1.8E-32 235.8 20.7 156 295-451 37-194 (258)
19 PRK05657 RNA polymerase sigma 100.0 1.5E-27 3.2E-32 242.5 21.2 185 223-448 53-239 (325)
20 PRK05911 RNA polymerase sigma 100.0 3.7E-27 8E-32 231.9 19.3 157 291-450 18-184 (257)
21 TIGR02885 spore_sigF RNA polym 99.9 5.1E-27 1.1E-31 225.8 18.4 160 288-448 3-165 (231)
22 COG1191 FliA DNA-directed RNA 99.9 4.1E-27 8.9E-32 230.7 17.2 170 284-455 12-185 (247)
23 TIGR02980 SigBFG RNA polymeras 99.9 1.2E-25 2.6E-30 215.5 17.7 154 295-448 3-160 (227)
24 PRK06288 RNA polymerase sigma 99.9 1.2E-24 2.5E-29 214.8 20.2 149 296-447 32-188 (268)
25 TIGR02941 Sigma_B RNA polymera 99.9 1.2E-24 2.7E-29 212.6 19.5 156 283-438 15-174 (255)
26 PRK07670 RNA polymerase sigma 99.9 3.4E-24 7.5E-29 209.4 18.8 162 282-446 7-176 (251)
27 TIGR02394 rpoS_proteo RNA poly 99.9 9.2E-24 2E-28 210.3 19.2 166 283-448 33-199 (285)
28 PRK05572 sporulation sigma fac 99.9 1.3E-23 2.8E-28 205.4 19.2 164 284-448 20-186 (252)
29 PRK12427 flagellar biosynthesi 99.9 3.7E-23 8.1E-28 200.7 17.4 138 296-437 16-158 (231)
30 TIGR02479 FliA_WhiG RNA polyme 99.9 3.7E-23 8.1E-28 198.4 16.5 145 300-447 1-151 (224)
31 PRK08583 RNA polymerase sigma 99.9 9.1E-23 2E-27 199.7 18.9 167 283-449 15-188 (257)
32 PRK06986 fliA flagellar biosyn 99.9 6.1E-22 1.3E-26 191.6 17.6 143 292-437 5-152 (236)
33 PRK05803 sporulation sigma fac 99.8 8.1E-18 1.8E-22 162.7 20.3 170 245-424 8-221 (233)
34 TIGR02895 spore_sigI RNA polym 99.8 3.1E-18 6.7E-23 165.7 15.1 129 289-417 3-142 (218)
35 TIGR02846 spore_sigmaK RNA pol 99.8 3.7E-17 8.1E-22 157.7 19.4 142 283-424 35-220 (227)
36 PRK08301 sporulation sigma fac 99.8 1.5E-17 3.4E-22 160.4 15.2 143 282-424 38-224 (234)
37 TIGR02859 spore_sigH RNA polym 99.7 4.6E-17 1E-21 151.7 15.7 144 281-424 4-191 (198)
38 PRK08295 RNA polymerase factor 99.7 6.4E-17 1.4E-21 152.0 16.4 145 280-424 8-196 (208)
39 PRK05602 RNA polymerase sigma 99.7 5.7E-17 1.2E-21 150.5 15.4 143 281-424 5-170 (186)
40 TIGR02835 spore_sigmaE RNA pol 99.7 6.7E-17 1.4E-21 156.6 16.4 142 283-424 39-224 (234)
41 PRK12513 RNA polymerase sigma 99.7 1.3E-16 2.7E-21 149.1 15.4 142 281-424 11-181 (194)
42 PRK06811 RNA polymerase factor 99.7 1.4E-16 3.1E-21 148.7 15.2 144 280-424 2-173 (189)
43 PRK09646 RNA polymerase sigma 99.7 1.4E-16 3E-21 149.4 14.8 142 282-424 16-184 (194)
44 PRK09648 RNA polymerase sigma 99.7 4.6E-16 9.9E-21 144.8 15.8 141 283-424 11-181 (189)
45 PRK13919 putative RNA polymera 99.7 3.6E-16 7.8E-21 144.7 14.9 143 281-424 8-177 (186)
46 TIGR02954 Sig70_famx3 RNA poly 99.7 4.2E-16 9.1E-21 142.4 15.0 142 281-424 1-161 (169)
47 PRK12514 RNA polymerase sigma 99.7 3.7E-16 8E-21 144.0 14.5 142 282-424 5-171 (179)
48 PRK09640 RNA polymerase sigma 99.7 6.7E-16 1.4E-20 144.0 15.9 143 280-424 7-176 (188)
49 PRK12537 RNA polymerase sigma 99.7 3.9E-16 8.4E-21 144.8 14.2 143 281-424 8-175 (182)
50 PRK12524 RNA polymerase sigma 99.7 3.8E-16 8.2E-21 146.7 14.0 145 280-425 10-179 (196)
51 PRK06759 RNA polymerase factor 99.7 4.9E-16 1.1E-20 139.3 13.1 128 295-424 4-148 (154)
52 TIGR02948 SigW_bacill RNA poly 99.7 6.6E-16 1.4E-20 142.5 14.2 140 283-424 5-178 (187)
53 PRK09638 RNA polymerase sigma 99.7 8.3E-16 1.8E-20 140.9 14.7 143 280-424 2-168 (176)
54 PRK09643 RNA polymerase sigma 99.7 1E-15 2.3E-20 143.6 15.2 142 281-424 12-176 (192)
55 TIGR02952 Sig70_famx2 RNA poly 99.7 9.3E-16 2E-20 139.1 14.1 137 287-424 2-164 (170)
56 PRK09641 RNA polymerase sigma 99.7 9.3E-16 2E-20 141.4 14.1 142 281-424 3-178 (187)
57 PRK12531 RNA polymerase sigma 99.7 7.9E-16 1.7E-20 144.3 13.7 141 283-424 14-183 (194)
58 PRK12534 RNA polymerase sigma 99.7 9.7E-16 2.1E-20 142.2 13.9 141 283-424 12-179 (187)
59 PRK12538 RNA polymerase sigma 99.7 1.5E-15 3.1E-20 147.9 15.3 143 281-424 48-213 (233)
60 TIGR02939 RpoE_Sigma70 RNA pol 99.7 2.7E-15 5.9E-20 138.7 15.6 142 281-424 5-180 (190)
61 PRK12519 RNA polymerase sigma 99.7 1.9E-15 4.1E-20 141.0 14.4 141 282-424 15-183 (194)
62 PRK12536 RNA polymerase sigma 99.6 3.4E-15 7.4E-20 138.4 15.2 140 283-424 8-171 (181)
63 PRK12526 RNA polymerase sigma 99.6 2.7E-15 5.9E-20 142.4 14.7 140 284-424 26-195 (206)
64 PRK11922 RNA polymerase sigma 99.6 4.1E-15 8.9E-20 143.7 15.9 142 281-424 15-191 (231)
65 PRK11923 algU RNA polymerase s 99.6 4.3E-15 9.3E-20 138.5 15.3 141 282-424 6-180 (193)
66 PRK09652 RNA polymerase sigma 99.6 2E-15 4.4E-20 137.4 12.8 134 289-424 3-170 (182)
67 PRK12539 RNA polymerase sigma 99.6 4.3E-15 9.3E-20 138.1 15.0 140 283-424 8-173 (184)
68 PRK12542 RNA polymerase sigma 99.6 1.7E-15 3.6E-20 140.7 11.3 134 291-424 4-164 (185)
69 PRK12515 RNA polymerase sigma 99.6 5.1E-15 1.1E-19 137.9 14.6 143 280-424 6-173 (189)
70 TIGR02999 Sig-70_X6 RNA polyme 99.6 5.8E-15 1.2E-19 136.1 14.0 140 283-424 4-176 (183)
71 COG1595 RpoE DNA-directed RNA 99.6 9.8E-15 2.1E-19 135.6 15.0 135 288-424 7-169 (182)
72 PRK09649 RNA polymerase sigma 99.6 7.4E-15 1.6E-19 137.1 14.1 141 283-426 11-174 (185)
73 TIGR03001 Sig-70_gmx1 RNA poly 99.6 9.1E-15 2E-19 143.5 15.2 144 279-424 22-203 (244)
74 TIGR02989 Sig-70_gvs1 RNA poly 99.6 8.9E-15 1.9E-19 131.6 12.6 128 296-425 2-154 (159)
75 PRK12512 RNA polymerase sigma 99.6 2.4E-14 5.2E-19 132.5 15.5 138 285-424 11-173 (184)
76 PRK11924 RNA polymerase sigma 99.6 3.8E-14 8.3E-19 128.7 15.0 137 286-424 3-167 (179)
77 PRK12522 RNA polymerase sigma 99.6 2.6E-14 5.7E-19 131.2 13.6 127 296-424 4-161 (173)
78 PRK12520 RNA polymerase sigma 99.6 1.8E-14 4E-19 134.4 12.6 127 296-424 3-173 (191)
79 PRK12543 RNA polymerase sigma 99.6 2.4E-14 5.2E-19 132.5 13.1 131 292-424 3-159 (179)
80 TIGR02947 SigH_actino RNA poly 99.6 3.4E-14 7.4E-19 132.8 13.3 131 292-424 7-173 (193)
81 PRK12518 RNA polymerase sigma 99.6 5.6E-14 1.2E-18 128.7 13.8 135 287-424 2-162 (175)
82 PRK09415 RNA polymerase factor 99.6 5.6E-14 1.2E-18 130.2 13.9 128 295-424 16-169 (179)
83 PRK12516 RNA polymerase sigma 99.6 5.4E-14 1.2E-18 131.9 13.7 128 295-424 10-158 (187)
84 PRK09645 RNA polymerase sigma 99.6 5.3E-14 1.1E-18 128.8 13.3 130 294-424 8-160 (173)
85 TIGR02937 sigma70-ECF RNA poly 99.6 5.5E-14 1.2E-18 122.2 12.7 126 296-424 2-152 (158)
86 TIGR02983 SigE-fam_strep RNA p 99.5 5.6E-14 1.2E-18 127.2 13.0 131 292-424 2-152 (162)
87 PRK08241 RNA polymerase factor 99.5 7.6E-14 1.6E-18 141.6 14.4 139 284-424 7-195 (339)
88 PRK12529 RNA polymerase sigma 99.5 6E-14 1.3E-18 130.1 12.3 135 290-424 7-169 (178)
89 PRK12547 RNA polymerase sigma 99.5 1.1E-13 2.4E-18 126.3 13.7 128 295-424 6-154 (164)
90 TIGR02984 Sig-70_plancto1 RNA 99.5 1.1E-13 2.5E-18 127.5 13.3 133 292-424 3-182 (189)
91 PRK12541 RNA polymerase sigma 99.5 1.3E-13 2.8E-18 125.1 13.4 127 295-424 5-154 (161)
92 PRK12535 RNA polymerase sigma 99.5 1.7E-13 3.6E-18 129.7 14.5 138 284-424 13-175 (196)
93 PRK12523 RNA polymerase sigma 99.5 6.7E-14 1.5E-18 128.6 10.5 132 291-425 5-162 (172)
94 TIGR02985 Sig70_bacteroi1 RNA 99.5 1.2E-13 2.6E-18 123.1 11.7 127 296-424 2-155 (161)
95 PRK09644 RNA polymerase sigma 99.5 1.5E-13 3.3E-18 125.2 12.1 125 297-424 3-150 (165)
96 PRK12533 RNA polymerase sigma 99.5 2E-13 4.3E-18 131.6 13.3 131 291-424 14-176 (216)
97 TIGR02960 SigX5 RNA polymerase 99.5 2.1E-13 4.6E-18 137.0 13.2 130 293-424 2-184 (324)
98 PRK08311 putative RNA polymera 99.5 4.8E-13 1E-17 131.1 15.0 91 282-372 4-97 (237)
99 PRK12528 RNA polymerase sigma 99.5 3E-13 6.5E-18 122.6 12.2 127 295-424 4-155 (161)
100 PRK09642 RNA polymerase sigma 99.5 2E-13 4.4E-18 123.4 10.8 121 301-424 1-148 (160)
101 PRK12540 RNA polymerase sigma 99.5 6.5E-13 1.4E-17 124.1 13.4 127 296-424 6-153 (182)
102 PRK09639 RNA polymerase sigma 99.5 6.4E-13 1.4E-17 120.5 12.6 125 295-424 3-153 (166)
103 PRK09647 RNA polymerase sigma 99.5 9.2E-13 2E-17 125.5 13.6 130 292-424 24-180 (203)
104 PRK12532 RNA polymerase sigma 99.5 7.3E-13 1.6E-17 124.1 12.6 125 298-424 8-178 (195)
105 PRK12545 RNA polymerase sigma 99.5 5.5E-13 1.2E-17 126.2 11.9 124 299-424 12-181 (201)
106 PRK09637 RNA polymerase sigma 99.4 1.4E-12 3E-17 121.7 13.7 126 297-424 3-148 (181)
107 PRK12530 RNA polymerase sigma 99.4 9.2E-13 2E-17 123.4 12.5 125 298-424 10-176 (189)
108 TIGR02950 SigM_subfam RNA poly 99.4 7.7E-13 1.7E-17 118.4 11.1 121 301-424 1-147 (154)
109 PRK12544 RNA polymerase sigma 99.4 1.2E-12 2.6E-17 125.0 12.8 126 297-424 20-190 (206)
110 PRK12517 RNA polymerase sigma 99.4 2E-12 4.4E-17 121.3 13.9 130 293-424 21-170 (188)
111 TIGR02959 SigZ RNA polymerase 99.4 1.3E-12 2.9E-17 120.2 11.9 121 302-424 2-142 (170)
112 PF04542 Sigma70_r2: Sigma-70 99.4 6.4E-13 1.4E-17 103.8 8.2 70 300-369 1-70 (71)
113 TIGR02943 Sig70_famx1 RNA poly 99.4 1.5E-12 3.2E-17 122.0 11.9 125 298-424 5-173 (188)
114 PRK12546 RNA polymerase sigma 99.4 2.9E-12 6.2E-17 120.6 13.4 126 296-424 9-155 (188)
115 PRK09651 RNA polymerase sigma 99.4 4.5E-12 9.8E-17 116.7 12.5 127 295-424 10-161 (172)
116 PRK12511 RNA polymerase sigma 99.4 4.5E-12 9.7E-17 118.6 12.6 127 296-424 5-153 (182)
117 PRK06704 RNA polymerase factor 99.3 1.1E-11 2.3E-16 121.0 12.6 133 287-425 9-159 (228)
118 PRK07037 extracytoplasmic-func 99.3 1.2E-11 2.7E-16 111.9 12.0 123 299-424 2-151 (163)
119 PRK12527 RNA polymerase sigma 99.3 1.2E-11 2.5E-16 112.0 11.3 121 301-424 1-147 (159)
120 PRK12525 RNA polymerase sigma 99.3 2.3E-11 5E-16 111.5 13.0 127 295-424 9-160 (168)
121 PRK09636 RNA polymerase sigma 99.3 5.1E-11 1.1E-15 119.1 12.6 125 296-424 5-157 (293)
122 PF04539 Sigma70_r3: Sigma-70 99.2 3.5E-11 7.5E-16 97.5 6.9 74 379-452 1-75 (78)
123 PRK09191 two-component respons 99.2 9.7E-11 2.1E-15 112.6 10.1 121 296-424 2-130 (261)
124 TIGR02957 SigX4 RNA polymerase 99.2 1.7E-10 3.7E-15 115.0 12.1 122 299-424 1-150 (281)
125 TIGR03209 P21_Cbot clostridium 99.2 1.3E-10 2.9E-15 103.3 9.7 113 297-416 1-141 (142)
126 PRK09635 sigI RNA polymerase s 99.2 2.6E-10 5.6E-15 114.7 12.9 127 295-425 5-161 (290)
127 PRK09047 RNA polymerase factor 99.1 6.8E-10 1.5E-14 100.0 9.7 105 317-424 2-148 (161)
128 PF07638 Sigma70_ECF: ECF sigm 98.9 7.3E-08 1.6E-12 90.6 14.9 141 284-424 5-177 (185)
129 TIGR02393 RpoD_Cterm RNA polym 96.5 0.062 1.4E-06 52.4 13.5 35 254-288 88-122 (238)
130 PF00140 Sigma70_r1_2: Sigma-7 96.3 0.0011 2.4E-08 47.1 0.2 34 220-256 3-36 (37)
131 PRK07670 RNA polymerase sigma 96.1 0.088 1.9E-06 51.7 12.4 36 254-289 110-145 (251)
132 PRK09210 RNA polymerase sigma 96.0 0.12 2.5E-06 54.2 13.2 128 254-422 217-349 (367)
133 PRK07408 RNA polymerase sigma 95.8 0.047 1E-06 54.1 9.2 35 254-288 114-148 (256)
134 PF12645 HTH_16: Helix-turn-he 95.8 0.035 7.6E-07 44.4 6.7 57 285-341 2-65 (65)
135 PRK06288 RNA polymerase sigma 95.8 0.26 5.6E-06 48.9 14.2 35 254-288 119-153 (268)
136 PRK05949 RNA polymerase sigma 95.7 0.14 3E-06 52.9 12.4 35 254-288 179-213 (327)
137 PRK07122 RNA polymerase sigma 95.4 0.27 5.9E-06 49.0 12.8 35 254-288 128-162 (264)
138 PRK05911 RNA polymerase sigma 95.4 0.23 4.9E-06 49.3 12.2 29 396-424 219-247 (257)
139 COG1191 FliA DNA-directed RNA 95.3 0.36 7.8E-06 48.3 13.3 126 254-422 111-236 (247)
140 TIGR02479 FliA_WhiG RNA polyme 95.2 0.41 8.8E-06 46.0 12.9 35 254-288 84-118 (224)
141 TIGR02394 rpoS_proteo RNA poly 95.1 0.32 6.9E-06 48.8 12.5 28 397-424 241-268 (285)
142 PRK05901 RNA polymerase sigma 95.0 0.43 9.4E-06 52.3 14.0 128 254-422 359-491 (509)
143 PRK07598 RNA polymerase sigma 95.0 0.41 8.8E-06 51.2 13.5 37 253-289 262-298 (415)
144 PRK07921 RNA polymerase sigma 94.9 0.49 1.1E-05 48.9 13.3 35 254-288 174-208 (324)
145 TIGR02885 spore_sigF RNA polym 94.7 0.23 4.9E-06 47.9 9.8 34 255-288 99-132 (231)
146 TIGR02997 Sig70-cyanoRpoD RNA 94.6 0.54 1.2E-05 47.6 12.8 35 254-288 162-196 (298)
147 TIGR02850 spore_sigG RNA polym 94.3 0.43 9.2E-06 47.1 10.8 36 254-289 121-156 (254)
148 PF04539 Sigma70_r3: Sigma-70 94.0 0.14 3.1E-06 41.1 5.8 38 253-290 4-41 (78)
149 PRK07500 rpoH2 RNA polymerase 93.9 0.62 1.4E-05 47.1 11.4 28 397-424 244-271 (289)
150 PRK07405 RNA polymerase sigma 93.9 0.74 1.6E-05 47.3 12.0 36 253-288 168-203 (317)
151 PRK06986 fliA flagellar biosyn 93.9 1.1 2.5E-05 43.4 12.8 29 396-424 198-226 (236)
152 PRK07406 RNA polymerase sigma 93.6 1.1 2.5E-05 47.2 13.1 35 254-288 224-258 (373)
153 TIGR02941 Sigma_B RNA polymera 93.4 0.51 1.1E-05 46.4 9.5 30 395-424 218-247 (255)
154 PF08281 Sigma70_r4_2: Sigma-7 92.8 0.11 2.3E-06 39.0 3.0 31 394-424 22-52 (54)
155 PRK05572 sporulation sigma fac 92.8 1.7 3.7E-05 42.7 12.2 34 254-287 119-152 (252)
156 PRK08215 sporulation sigma fac 92.7 1.8 3.9E-05 42.7 12.3 34 255-288 125-158 (258)
157 PRK12427 flagellar biosynthesi 91.9 2.7 5.9E-05 41.0 12.3 34 255-288 103-136 (231)
158 TIGR02980 SigBFG RNA polymeras 91.6 0.79 1.7E-05 44.0 8.2 29 396-424 192-220 (227)
159 PF01726 LexA_DNA_bind: LexA D 91.6 0.59 1.3E-05 37.3 6.0 44 379-422 6-50 (65)
160 PHA02547 55 RNA polymerase sig 91.1 0.66 1.4E-05 43.9 6.6 64 305-368 47-113 (179)
161 PRK05658 RNA polymerase sigma 90.8 2.1 4.6E-05 47.9 11.6 35 254-288 468-502 (619)
162 PF04545 Sigma70_r4: Sigma-70, 90.8 0.68 1.5E-05 34.2 5.3 31 393-423 15-45 (50)
163 PRK05657 RNA polymerase sigma 89.2 4.5 9.8E-05 41.7 11.7 29 396-424 280-308 (325)
164 PRK08583 RNA polymerase sigma 88.5 2.9 6.2E-05 41.1 9.4 30 395-424 218-247 (257)
165 PRK06596 RNA polymerase factor 86.3 10 0.00023 38.2 12.1 27 397-423 247-273 (284)
166 COG4941 Predicted RNA polymera 83.0 6.1 0.00013 41.5 8.7 125 298-424 8-162 (415)
167 TIGR03879 near_KaiC_dom probab 80.8 2 4.3E-05 35.4 3.4 25 397-421 31-55 (73)
168 cd06171 Sigma70_r4 Sigma70, re 79.4 4.4 9.6E-05 28.6 4.7 29 396-424 24-52 (55)
169 PHA02591 hypothetical protein; 78.6 4.5 9.8E-05 33.8 4.9 25 397-421 58-82 (83)
170 PF13404 HTH_AsnC-type: AsnC-t 78.5 6.5 0.00014 28.7 5.2 24 398-421 17-40 (42)
171 PRK00118 putative DNA-binding 77.9 4 8.6E-05 35.7 4.7 30 395-424 30-59 (104)
172 COG0568 RpoD DNA-directed RNA 77.4 44 0.00095 35.2 12.9 36 252-287 188-223 (342)
173 PF02796 HTH_7: Helix-turn-hel 75.7 3.6 7.8E-05 30.1 3.3 23 398-420 21-43 (45)
174 smart00421 HTH_LUXR helix_turn 75.5 4 8.7E-05 29.5 3.5 28 397-424 17-44 (58)
175 PRK04217 hypothetical protein; 74.7 4 8.7E-05 36.1 3.9 28 397-424 57-84 (110)
176 PF13936 HTH_38: Helix-turn-he 74.7 5.6 0.00012 29.1 4.0 27 395-421 17-43 (44)
177 PRK06930 positive control sigm 74.5 4.7 0.0001 38.0 4.5 30 395-424 127-156 (170)
178 PF00325 Crp: Bacterial regula 74.3 3.4 7.4E-05 28.8 2.6 25 399-423 3-27 (32)
179 PF13542 HTH_Tnp_ISL3: Helix-t 73.8 8.5 0.00019 28.3 4.9 26 396-421 25-50 (52)
180 PF08279 HTH_11: HTH domain; 72.3 8 0.00017 28.8 4.5 27 398-424 15-41 (55)
181 cd06170 LuxR_C_like C-terminal 71.8 5.7 0.00012 28.8 3.6 28 397-424 14-41 (57)
182 PF04967 HTH_10: HTH DNA bindi 71.7 5.8 0.00013 30.6 3.6 27 397-423 22-48 (53)
183 PF00196 GerE: Bacterial regul 71.0 4.5 9.7E-05 30.8 2.9 32 393-424 13-44 (58)
184 COG4367 Uncharacterized protei 70.7 11 0.00023 32.3 5.3 40 385-424 9-49 (97)
185 PF10668 Phage_terminase: Phag 70.5 9.6 0.00021 30.3 4.7 29 390-418 14-42 (60)
186 PF13412 HTH_24: Winged helix- 70.2 14 0.00031 26.8 5.4 26 397-422 16-41 (48)
187 PF14502 HTH_41: Helix-turn-he 69.2 6.5 0.00014 29.9 3.3 35 396-430 4-40 (48)
188 TIGR00721 tfx DNA-binding prot 67.0 6.8 0.00015 35.9 3.7 28 396-423 19-46 (137)
189 PF06971 Put_DNA-bind_N: Putat 66.9 11 0.00024 28.7 4.2 46 373-418 3-48 (50)
190 cd00092 HTH_CRP helix_turn_hel 66.7 19 0.00042 27.2 5.8 27 397-423 24-50 (67)
191 PF13730 HTH_36: Helix-turn-he 65.2 7.8 0.00017 28.8 3.2 27 396-422 23-49 (55)
192 PF13384 HTH_23: Homeodomain-l 64.9 6.9 0.00015 28.5 2.8 26 398-423 17-42 (50)
193 PF00356 LacI: Bacterial regul 63.0 8.5 0.00018 28.7 2.9 23 400-422 1-23 (46)
194 PF12728 HTH_17: Helix-turn-he 62.3 11 0.00023 27.7 3.4 25 399-423 2-26 (51)
195 PRK03975 tfx putative transcri 62.0 9.7 0.00021 35.1 3.7 28 396-423 19-46 (141)
196 TIGR02392 rpoH_proteo alternat 61.6 13 0.00027 37.1 4.8 26 397-422 235-260 (270)
197 TIGR01764 excise DNA binding d 61.5 12 0.00026 26.4 3.5 25 399-423 2-26 (49)
198 PF06056 Terminase_5: Putative 60.9 22 0.00048 27.8 5.0 27 397-423 12-38 (58)
199 PF04297 UPF0122: Putative hel 60.4 18 0.0004 31.5 5.0 33 392-424 27-59 (101)
200 COG2197 CitB Response regulato 60.2 12 0.00027 35.9 4.3 33 391-423 156-188 (211)
201 PRK15411 rcsA colanic acid cap 60.2 13 0.00027 35.6 4.4 38 386-423 140-177 (207)
202 PF13744 HTH_37: Helix-turn-he 59.4 24 0.00052 28.8 5.3 36 396-431 29-64 (80)
203 smart00345 HTH_GNTR helix_turn 59.1 13 0.00028 27.3 3.4 26 398-423 20-45 (60)
204 PRK14082 hypothetical protein; 59.0 29 0.00063 28.0 5.4 54 296-351 10-63 (65)
205 PRK11511 DNA-binding transcrip 58.2 29 0.00063 30.6 6.0 41 382-422 9-49 (127)
206 TIGR03020 EpsA transcriptional 57.1 22 0.00048 35.5 5.7 29 396-424 203-231 (247)
207 PRK10840 transcriptional regul 56.9 16 0.00036 34.1 4.5 34 390-423 157-190 (216)
208 COG0856 Orotate phosphoribosyl 56.5 19 0.00041 34.7 4.7 35 396-430 16-50 (203)
209 PRK13719 conjugal transfer tra 56.1 17 0.00038 35.8 4.6 38 386-423 146-183 (217)
210 PRK10430 DNA-binding transcrip 55.8 21 0.00047 34.1 5.2 31 394-424 174-204 (239)
211 PF01325 Fe_dep_repress: Iron 55.7 25 0.00054 27.4 4.6 38 385-423 10-47 (60)
212 cd04762 HTH_MerR-trunc Helix-T 55.0 18 0.0004 25.2 3.5 24 400-423 2-25 (49)
213 PRK15201 fimbriae regulatory p 54.0 20 0.00044 34.6 4.5 35 389-423 139-173 (198)
214 PF12324 HTH_15: Helix-turn-he 53.5 28 0.00061 29.0 4.7 28 396-423 36-63 (77)
215 PRK11475 DNA-binding transcrip 53.5 20 0.00042 34.6 4.5 34 390-423 141-174 (207)
216 COG2771 CsgD DNA-binding HTH d 53.1 32 0.0007 25.7 4.8 29 395-423 16-44 (65)
217 PRK13870 transcriptional regul 52.1 13 0.00027 36.6 2.9 29 396-424 186-214 (234)
218 TIGR03826 YvyF flagellar opero 52.0 50 0.0011 30.3 6.6 44 383-426 31-74 (137)
219 PRK10219 DNA-binding transcrip 51.5 44 0.00096 28.1 5.9 38 384-421 7-44 (107)
220 PF08784 RPA_C: Replication pr 50.3 25 0.00055 29.7 4.2 28 396-423 63-90 (102)
221 COG1522 Lrp Transcriptional re 50.0 33 0.00073 30.5 5.2 32 390-422 15-46 (154)
222 smart00550 Zalpha Z-DNA-bindin 49.7 52 0.0011 26.1 5.6 30 394-423 17-47 (68)
223 PRK12423 LexA repressor; Provi 49.1 44 0.00096 31.9 6.1 41 382-422 9-50 (202)
224 PRK10100 DNA-binding transcrip 48.8 28 0.00061 33.7 4.8 30 394-423 166-195 (216)
225 PF04703 FaeA: FaeA-like prote 48.4 24 0.00051 28.1 3.4 28 396-423 13-40 (62)
226 PRK10046 dpiA two-component re 47.6 28 0.0006 33.1 4.5 26 398-423 177-202 (225)
227 TIGR03541 reg_near_HchA LuxR f 47.4 19 0.00042 35.0 3.4 28 397-424 185-212 (232)
228 smart00419 HTH_CRP helix_turn_ 47.3 27 0.00059 24.6 3.4 27 398-424 8-34 (48)
229 PF09339 HTH_IclR: IclR helix- 47.0 20 0.00043 26.7 2.7 27 396-422 16-42 (52)
230 PRK13239 alkylmercury lyase; P 46.8 45 0.00097 32.7 5.8 29 395-423 33-61 (206)
231 PRK00423 tfb transcription ini 46.8 1.8E+02 0.0039 29.8 10.5 28 396-423 274-301 (310)
232 PRK10188 DNA-binding transcrip 46.7 24 0.00052 34.7 4.0 29 396-424 192-220 (240)
233 TIGR02531 yecD_yerC TrpR-relat 46.4 50 0.0011 28.0 5.3 26 396-421 48-73 (88)
234 TIGR00498 lexA SOS regulatory 46.4 52 0.0011 31.0 6.1 40 383-422 10-50 (199)
235 PF00392 GntR: Bacterial regul 46.2 23 0.00051 27.3 3.1 27 397-423 23-49 (64)
236 smart00342 HTH_ARAC helix_turn 46.0 87 0.0019 23.9 6.4 36 383-421 38-74 (84)
237 COG1318 Predicted transcriptio 45.8 38 0.00082 32.5 4.9 25 397-421 60-84 (182)
238 PRK11161 fumarate/nitrate redu 44.8 83 0.0018 29.9 7.3 26 398-423 184-209 (235)
239 COG4977 Transcriptional regula 44.7 46 0.00099 34.8 5.8 72 350-421 186-259 (328)
240 PF04760 IF2_N: Translation in 44.6 22 0.00047 26.8 2.6 37 399-435 4-42 (54)
241 COG4566 TtrR Response regulato 44.4 26 0.00056 34.2 3.6 30 390-419 149-178 (202)
242 PF02001 DUF134: Protein of un 44.1 17 0.00037 32.0 2.2 29 397-425 56-84 (106)
243 PRK10219 DNA-binding transcrip 44.1 1E+02 0.0022 25.8 7.0 48 316-363 18-65 (107)
244 PRK10572 DNA-binding transcrip 43.8 2.6E+02 0.0056 27.5 10.9 39 383-421 184-222 (290)
245 PF03444 HrcA_DNA-bdg: Winged 43.7 83 0.0018 26.3 6.1 42 382-423 7-48 (78)
246 PF09012 FeoC: FeoC like trans 43.3 31 0.00068 27.2 3.5 27 396-422 12-38 (69)
247 PF05225 HTH_psq: helix-turn-h 42.8 74 0.0016 23.4 5.1 35 383-420 4-38 (45)
248 PRK09483 response regulator; P 42.7 29 0.00062 31.6 3.7 31 395-425 160-190 (217)
249 cd00569 HTH_Hin_like Helix-tur 42.6 49 0.0011 20.4 3.8 21 398-418 21-41 (42)
250 PRK15369 two component system 42.6 38 0.00081 30.0 4.3 30 396-425 162-191 (211)
251 PF10078 DUF2316: Uncharacteri 42.6 56 0.0012 28.0 5.0 35 388-422 12-47 (89)
252 PRK15418 transcriptional regul 42.2 22 0.00048 36.7 3.0 38 395-432 26-67 (318)
253 PRK09464 pdhR transcriptional 41.6 47 0.001 32.3 5.2 26 398-423 34-59 (254)
254 COG2902 NAD-specific glutamate 41.4 8.4E+02 0.018 30.8 16.3 32 399-430 1467-1498(1592)
255 PRK13918 CRP/FNR family transc 41.2 1.1E+02 0.0023 28.2 7.3 27 398-424 149-175 (202)
256 PRK11179 DNA-binding transcrip 41.1 51 0.0011 30.0 5.0 26 398-423 23-48 (153)
257 PF13545 HTH_Crp_2: Crp-like h 41.1 29 0.00062 27.2 2.9 25 399-423 29-53 (76)
258 TIGR02337 HpaR homoprotocatech 40.9 1.1E+02 0.0023 26.3 6.8 65 349-422 2-66 (118)
259 PF04218 CENP-B_N: CENP-B N-te 40.8 27 0.00058 26.5 2.6 27 395-421 19-45 (53)
260 cd04761 HTH_MerR-SF Helix-Turn 40.7 36 0.00079 24.2 3.2 24 400-423 2-25 (49)
261 PRK11169 leucine-responsive tr 40.7 58 0.0013 30.0 5.3 26 398-423 28-53 (164)
262 PF13551 HTH_29: Winged helix- 40.3 84 0.0018 26.0 5.9 24 398-421 80-110 (112)
263 PRK10403 transcriptional regul 40.2 41 0.00089 30.1 4.2 33 396-428 166-198 (215)
264 TIGR03697 NtcA_cyano global ni 40.1 1.3E+02 0.0029 27.2 7.7 27 398-424 143-169 (193)
265 PF01978 TrmB: Sugar-specific 40.1 29 0.00064 27.0 2.8 26 397-422 21-46 (68)
266 PRK15320 transcriptional activ 40.0 31 0.00067 34.0 3.5 35 389-423 170-204 (251)
267 smart00354 HTH_LACI helix_turn 40.0 30 0.00066 27.4 2.9 23 399-421 1-23 (70)
268 PF00440 TetR_N: Bacterial reg 39.5 89 0.0019 22.6 5.2 33 386-418 4-36 (47)
269 PRK00215 LexA repressor; Valid 39.4 76 0.0017 30.0 6.1 35 388-422 13-48 (205)
270 COG3413 Predicted DNA binding 38.8 34 0.00073 32.9 3.6 28 397-424 177-204 (215)
271 PF01381 HTH_3: Helix-turn-hel 38.2 43 0.00092 24.5 3.3 25 397-421 8-32 (55)
272 COG1476 Predicted transcriptio 37.2 68 0.0015 26.2 4.5 23 397-419 13-35 (68)
273 PRK09935 transcriptional regul 37.2 40 0.00086 30.3 3.6 32 395-426 161-192 (210)
274 smart00346 HTH_ICLR helix_turn 37.2 1.1E+02 0.0023 24.7 5.8 26 397-422 19-44 (91)
275 COG2390 DeoR Transcriptional r 37.2 58 0.0013 33.9 5.2 39 395-433 23-65 (321)
276 TIGR00270 conserved hypothetic 37.1 1.2E+02 0.0026 28.2 6.8 36 383-420 69-104 (154)
277 PF13443 HTH_26: Cro/C1-type H 36.8 31 0.00067 26.1 2.4 34 397-430 9-42 (63)
278 PRK10651 transcriptional regul 36.4 43 0.00094 30.0 3.7 33 394-426 166-198 (216)
279 TIGR02844 spore_III_D sporulat 36.4 88 0.0019 26.1 5.2 25 397-421 18-42 (80)
280 cd07377 WHTH_GntR Winged helix 36.2 73 0.0016 23.7 4.4 25 399-423 26-50 (66)
281 PF08280 HTH_Mga: M protein tr 35.5 41 0.00089 25.9 2.9 29 396-424 17-45 (59)
282 PF00376 MerR: MerR family reg 35.1 41 0.00089 23.9 2.6 23 400-422 1-23 (38)
283 PRK15044 transcriptional regul 35.0 1.3E+02 0.0028 31.1 7.3 70 350-421 162-231 (295)
284 PF13518 HTH_28: Helix-turn-he 35.0 68 0.0015 23.1 3.9 25 399-423 13-37 (52)
285 PF01710 HTH_Tnp_IS630: Transp 34.9 1.2E+02 0.0026 26.6 6.2 30 396-425 69-98 (119)
286 smart00420 HTH_DEOR helix_turn 34.7 1.2E+02 0.0026 21.4 5.2 27 397-423 13-39 (53)
287 PF01371 Trp_repressor: Trp re 34.5 1.1E+02 0.0024 25.9 5.6 29 395-423 46-74 (87)
288 PRK09391 fixK transcriptional 34.1 1.2E+02 0.0026 29.1 6.6 27 398-424 179-205 (230)
289 PRK09390 fixJ response regulat 33.7 88 0.0019 27.4 5.2 27 398-424 156-182 (202)
290 PF08535 KorB: KorB domain; I 33.4 48 0.001 27.7 3.3 28 398-425 3-30 (93)
291 PF08220 HTH_DeoR: DeoR-like h 33.3 90 0.0019 23.8 4.5 26 397-422 13-38 (57)
292 PF02082 Rrf2: Transcriptional 32.9 62 0.0014 26.3 3.8 25 399-423 26-50 (83)
293 PF13411 MerR_1: MerR HTH fami 32.8 46 0.001 25.6 2.9 24 400-423 2-25 (69)
294 COG3769 Predicted hydrolase (H 32.5 90 0.0019 31.4 5.3 41 380-420 102-146 (274)
295 PF00165 HTH_AraC: Bacterial r 31.7 70 0.0015 22.5 3.4 28 395-422 5-32 (42)
296 TIGR02147 Fsuc_second hypothet 31.5 4E+02 0.0087 27.1 10.0 28 396-423 135-164 (271)
297 PRK03837 transcriptional regul 31.4 1E+02 0.0022 29.6 5.6 27 397-423 36-62 (241)
298 TIGR02297 HpaA 4-hydroxyphenyl 31.4 5E+02 0.011 25.3 10.7 38 384-421 188-225 (287)
299 PRK09975 DNA-binding transcrip 31.3 1.1E+02 0.0024 28.4 5.7 42 377-418 9-51 (213)
300 TIGR03070 couple_hipB transcri 30.5 63 0.0014 23.4 3.2 25 397-421 14-38 (58)
301 COG2524 Predicted transcriptio 30.3 95 0.0021 31.8 5.2 43 381-423 8-50 (294)
302 TIGR00180 parB_part ParB-like 29.9 1.5E+02 0.0032 27.9 6.3 36 398-433 120-155 (187)
303 PF13551 HTH_29: Winged helix- 29.7 56 0.0012 27.1 3.1 25 400-424 14-38 (112)
304 PF10975 DUF2802: Protein of u 29.5 2E+02 0.0044 23.3 6.1 25 397-421 43-67 (70)
305 TIGR02944 suf_reg_Xantho FeS a 29.4 89 0.0019 27.4 4.4 28 396-423 23-50 (130)
306 PHA01976 helix-turn-helix prot 29.1 73 0.0016 24.4 3.4 25 397-421 14-38 (67)
307 smart00088 PINT motif in prote 28.5 2E+02 0.0042 23.1 6.0 37 396-432 22-58 (88)
308 smart00753 PAM PCI/PINT associ 28.5 2E+02 0.0042 23.1 6.0 37 396-432 22-58 (88)
309 PRK13413 mpi multiple promoter 28.2 2.2E+02 0.0047 26.9 7.1 26 396-421 170-195 (200)
310 PRK11511 DNA-binding transcrip 28.2 92 0.002 27.4 4.3 39 254-292 10-48 (127)
311 PF12802 MarR_2: MarR family; 28.1 85 0.0018 23.4 3.6 24 399-422 22-45 (62)
312 smart00344 HTH_ASNC helix_turn 28.1 1.5E+02 0.0033 24.7 5.5 25 398-422 17-41 (108)
313 PRK14999 histidine utilization 28.0 1.5E+02 0.0033 28.7 6.2 26 397-422 35-60 (241)
314 smart00418 HTH_ARSR helix_turn 28.0 88 0.0019 22.5 3.6 28 396-423 8-35 (66)
315 PF05138 PaaA_PaaC: Phenylacet 28.0 2.1E+02 0.0045 28.9 7.3 109 237-365 10-119 (263)
316 PRK13503 transcriptional activ 27.7 2.2E+02 0.0047 27.6 7.3 27 383-412 224-250 (278)
317 PRK10402 DNA-binding transcrip 27.7 1.7E+02 0.0037 27.9 6.4 26 399-424 170-195 (226)
318 TIGR00373 conserved hypothetic 27.7 67 0.0015 29.8 3.5 26 398-423 28-53 (158)
319 PRK10371 DNA-binding transcrip 27.4 3.7E+02 0.008 27.1 9.1 57 308-365 197-253 (302)
320 PF13560 HTH_31: Helix-turn-he 27.2 1.2E+02 0.0027 23.1 4.4 25 397-421 13-37 (64)
321 PHA02943 hypothetical protein; 27.1 2E+02 0.0043 27.3 6.3 25 398-422 24-48 (165)
322 smart00351 PAX Paired Box doma 26.8 1.3E+02 0.0027 26.7 4.9 32 398-429 33-64 (125)
323 PRK15121 right oriC-binding tr 26.7 1.4E+02 0.0031 29.7 5.9 40 381-420 4-43 (289)
324 cd01104 HTH_MlrA-CarA Helix-Tu 26.7 78 0.0017 24.2 3.2 23 400-422 2-24 (68)
325 COG1342 Predicted DNA-binding 26.7 64 0.0014 28.1 2.8 28 397-424 48-75 (99)
326 PRK09764 DNA-binding transcrip 26.6 1.7E+02 0.0036 28.4 6.2 26 397-422 28-53 (240)
327 TIGR03826 YvyF flagellar opero 26.5 1.5E+02 0.0034 27.2 5.5 41 255-295 32-72 (137)
328 PRK09480 slmA division inhibit 26.5 1.4E+02 0.003 27.1 5.3 44 372-415 4-47 (194)
329 PRK11753 DNA-binding transcrip 26.3 3.1E+02 0.0067 25.3 7.8 26 398-423 168-193 (211)
330 TIGR01321 TrpR trp operon repr 26.3 1.8E+02 0.004 25.1 5.6 25 397-421 54-78 (94)
331 PRK10079 phosphonate metabolis 26.0 1E+02 0.0022 29.9 4.5 26 396-421 33-58 (241)
332 PRK04841 transcriptional regul 25.9 71 0.0015 36.6 4.0 29 395-423 850-878 (903)
333 PRK09958 DNA-binding transcrip 25.9 94 0.002 27.9 4.1 34 392-425 152-185 (204)
334 TIGR00738 rrf2_super rrf2 fami 25.6 1.3E+02 0.0027 26.2 4.7 26 398-423 25-50 (132)
335 smart00422 HTH_MERR helix_turn 25.5 85 0.0018 24.0 3.2 23 400-422 2-24 (70)
336 PRK09726 antitoxin HipB; Provi 25.2 1.7E+02 0.0038 24.0 5.2 33 397-430 24-56 (88)
337 PF04255 DUF433: Protein of un 25.1 1.1E+02 0.0024 23.3 3.7 26 396-421 29-55 (56)
338 PRK10360 DNA-binding transcrip 25.0 84 0.0018 28.0 3.5 30 395-424 149-178 (196)
339 COG2344 AT-rich DNA-binding pr 25.0 1.6E+02 0.0035 28.9 5.6 52 371-422 5-56 (211)
340 PRK09685 DNA-binding transcrip 24.9 3E+02 0.0064 27.2 7.8 80 303-411 197-277 (302)
341 PRK09393 ftrA transcriptional 24.8 1.4E+02 0.0031 30.1 5.6 41 382-422 218-258 (322)
342 COG1654 BirA Biotin operon rep 24.8 1.6E+02 0.0034 24.6 4.8 29 396-424 17-45 (79)
343 PF12840 HTH_20: Helix-turn-he 24.8 1.4E+02 0.0031 22.7 4.3 28 396-423 22-49 (61)
344 TIGR01610 phage_O_Nterm phage 24.6 2E+02 0.0044 24.1 5.6 27 396-422 45-71 (95)
345 PF08765 Mor: Mor transcriptio 24.6 2E+02 0.0043 24.8 5.6 26 398-423 72-97 (108)
346 cd04764 HTH_MlrA-like_sg1 Heli 24.2 94 0.002 24.0 3.2 24 400-423 2-25 (67)
347 COG4565 CitB Response regulato 24.0 1.3E+02 0.0028 29.9 4.8 30 394-423 169-198 (224)
348 cd00131 PAX Paired Box domain 23.8 1.5E+02 0.0033 26.5 4.9 33 397-429 32-64 (128)
349 smart00530 HTH_XRE Helix-turn- 23.7 1E+02 0.0022 20.7 3.2 24 397-420 9-32 (56)
350 TIGR02607 antidote_HigA addict 23.5 95 0.0021 24.4 3.2 32 397-429 17-48 (78)
351 PF14394 DUF4423: Domain of un 23.5 1.3E+02 0.0029 28.2 4.7 28 396-423 37-66 (171)
352 COG2207 AraC AraC-type DNA-bin 23.4 2.8E+02 0.006 22.8 6.3 51 315-365 32-82 (127)
353 PF11268 DUF3071: Protein of u 23.4 86 0.0019 29.8 3.4 24 395-418 66-89 (170)
354 PF06970 RepA_N: Replication i 23.3 83 0.0018 25.9 2.9 22 399-420 53-74 (76)
355 PRK11014 transcriptional repre 23.2 1.2E+02 0.0025 27.2 4.1 28 396-423 23-50 (141)
356 PF15545 Toxin_67: Putative to 23.0 86 0.0019 25.6 2.8 30 347-376 6-35 (70)
357 smart00342 HTH_ARAC helix_turn 23.0 2.6E+02 0.0056 21.2 5.6 60 269-331 1-62 (84)
358 TIGR02325 C_P_lyase_phnF phosp 22.8 2E+02 0.0044 27.4 5.9 26 397-422 31-56 (238)
359 TIGR00122 birA_repr_reg BirA b 22.5 1.6E+02 0.0034 22.9 4.2 26 398-423 13-38 (69)
360 smart00531 TFIIE Transcription 22.4 87 0.0019 28.6 3.1 27 398-424 15-41 (147)
361 TIGR02297 HpaA 4-hydroxyphenyl 22.3 2.6E+02 0.0056 27.3 6.7 29 383-414 239-267 (287)
362 PRK12702 mannosyl-3-phosphogly 22.3 1.7E+02 0.0037 30.4 5.5 41 382-422 101-147 (302)
363 COG1725 Predicted transcriptio 22.2 1E+02 0.0022 27.9 3.5 26 397-422 34-59 (125)
364 PRK10371 DNA-binding transcrip 22.0 1.9E+02 0.004 29.2 5.7 39 383-421 192-230 (302)
365 PRK09492 treR trehalose repres 22.0 70 0.0015 31.4 2.6 24 398-421 4-27 (315)
366 PRK09978 DNA-binding transcrip 21.8 4.1E+02 0.0088 27.1 8.1 56 308-364 147-202 (274)
367 TIGR02405 trehalos_R_Ecol treh 21.7 77 0.0017 31.3 2.9 23 399-421 2-24 (311)
368 PRK10703 DNA-binding transcrip 21.7 78 0.0017 31.5 2.9 23 399-421 2-24 (341)
369 COG2522 Predicted transcriptio 21.6 2.6E+02 0.0056 25.2 5.8 28 397-424 21-48 (119)
370 PRK10014 DNA-binding transcrip 21.5 78 0.0017 31.5 2.9 24 398-421 6-29 (342)
371 PRK13503 transcriptional activ 21.4 2.1E+02 0.0046 27.7 5.9 38 384-421 173-210 (278)
372 cd01392 HTH_LacI Helix-turn-he 21.3 72 0.0016 23.0 2.0 19 403-421 2-20 (52)
373 PRK15044 transcriptional regul 21.2 6.7E+02 0.015 26.0 9.5 38 255-292 194-231 (295)
374 PRK09940 transcriptional regul 21.2 4.2E+02 0.009 26.7 7.9 56 308-364 139-194 (253)
375 PF05344 DUF746: Domain of Unk 21.1 1.5E+02 0.0033 24.0 3.8 36 389-424 4-39 (65)
376 KOG0917 Uncharacterized conser 21.1 77 0.0017 32.6 2.7 82 45-142 10-92 (338)
377 PRK15008 HTH-type transcriptio 21.1 2.4E+02 0.0051 26.5 5.9 40 379-418 18-58 (212)
378 PRK09526 lacI lac repressor; R 21.0 88 0.0019 31.1 3.1 24 398-421 5-28 (342)
379 PF13022 HTH_Tnp_1_2: Helix-tu 20.9 1.1E+02 0.0024 28.4 3.4 29 391-419 27-55 (142)
380 cd00090 HTH_ARSR Arsenical Res 20.8 1.2E+02 0.0027 22.4 3.3 25 399-423 21-45 (78)
381 TIGR03337 phnR transcriptional 20.8 2.4E+02 0.0052 26.8 6.0 26 397-422 24-49 (231)
382 PF01726 LexA_DNA_bind: LexA D 20.6 3.4E+02 0.0075 21.5 5.8 19 264-282 20-38 (65)
383 PF13413 HTH_25: Helix-turn-he 20.4 1.3E+02 0.0028 23.6 3.3 26 395-420 7-32 (62)
384 PRK11512 DNA-binding transcrip 20.2 5.4E+02 0.012 22.8 7.8 26 397-422 53-78 (144)
385 PRK09392 ftrB transcriptional 20.1 3.1E+02 0.0068 25.9 6.6 26 399-424 174-199 (236)
386 TIGR02404 trehalos_R_Bsub treh 20.0 1E+02 0.0022 29.6 3.2 26 397-422 23-48 (233)
No 1
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=100.00 E-value=6.4e-48 Score=400.98 Aligned_cols=233 Identities=26% Similarity=0.419 Sum_probs=217.9
Q ss_pred CCCChhHHHHHHhccCCCCCCChHHHHHHHHHhHHHHH--------------------HHHHHHHHHHHhCCCCchHHHH
Q 012638 217 LKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVAN--------------------LERIKTTLEKESGKAASLNCWA 276 (459)
Q Consensus 217 ~~~p~~~~~~~~~~~~~~~lLt~~eE~eL~~~i~~~~~--------------------le~~~~~l~~~~gr~pt~~ewa 276 (459)
..||...|+ ...++.||||++||++|+++||.++. |++++..|++++|++||..+||
T Consensus 58 ~~d~v~~yl---~~igr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa 134 (415)
T PRK07598 58 STDLVRLYL---QEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWA 134 (415)
T ss_pred CCChHHHHH---HhcccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHH
Confidence 347777777 56677899999999999999999999 8999999999999999999999
Q ss_pred HH----------------------cCCCHHHHHHHHHhchHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHH
Q 012638 277 QA----------------------AGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVL 334 (459)
Q Consensus 277 ~a----------------------~g~deeeL~~~l~~G~~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLi 334 (459)
.+ +|+++++|+..++.|..||++||.+|+++|+++|++|.++|++++||||||++|||
T Consensus 135 ~~~~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~ 214 (415)
T PRK07598 135 KTADISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLE 214 (415)
T ss_pred HHhCCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHH
Confidence 54 45666777777889988999999999999999999999999999999999999999
Q ss_pred HhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHH
Q 012638 335 QGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAE 414 (459)
Q Consensus 335 rAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~ 414 (459)
+|+++|||.+|++|+||++||||++|.+++++++++|++|.|+.+.+++|+++...|.+.+|+.|+.+|||+.|||++++
T Consensus 215 ravekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~ 294 (415)
T PRK07598 215 RAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQ 294 (415)
T ss_pred HHHHHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhccCCccccccCCCCCCccccCCCCCCCCcc
Q 012638 415 IRSASECLRIVGSIDQKIGDCLNAKYLNIPPFFFPSFA 452 (459)
Q Consensus 415 Vk~~l~~ar~~~SLD~~v~~d~~~~l~e~i~D~~~~~~ 452 (459)
|+.++..++.++|||.+++++++.++.|+++++..+|+
T Consensus 295 vr~~l~~~~~~~SLd~~vg~~~d~~l~d~l~~~~~~pe 332 (415)
T PRK07598 295 VREVLLRVPRSVSLETKVGKDKDTELGDLLETDDISPE 332 (415)
T ss_pred HHHHHHHccCCcccccccCCCccccHHHhccCCCCCHH
Confidence 99999999999999999999999999999988766654
No 2
>PRK05949 RNA polymerase sigma factor; Validated
Probab=100.00 E-value=8.6e-45 Score=368.75 Aligned_cols=232 Identities=32% Similarity=0.471 Sum_probs=219.9
Q ss_pred CCChhHHHHHHhccCCCCCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhchHHH
Q 012638 218 KQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCR 297 (459)
Q Consensus 218 ~~p~~~~~~~~~~~~~~~lLt~~eE~eL~~~i~~~~~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l~~G~~Ar 297 (459)
.++...|+ ......||||++||++|++.|+.++.+++.+..|+..+|+.|+..+||.++++++.+|+..++.|+.|+
T Consensus 17 ~d~~~~yl---~~i~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~ 93 (327)
T PRK05949 17 ADMVRTYL---HEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAK 93 (327)
T ss_pred CCHHHHHH---HHcCCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHH
Confidence 35555555 355678999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccch
Q 012638 298 EELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKL 377 (459)
Q Consensus 298 e~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~v 377 (459)
+.||..|+++|+++|++|.+++.+++||+||||+|||+++++|||.+|++|+|||+||||++|.++|++++++||+|.|+
T Consensus 94 ~~Li~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~~~ 173 (327)
T PRK05949 94 QKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHI 173 (327)
T ss_pred HHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccCCCCCCccccCCCCCCCCcc
Q 012638 378 NREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPPFFFPSFA 452 (459)
Q Consensus 378 ~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~~d~~~~l~e~i~D~~~~~~ 452 (459)
.+.+++++++...+..++|+.||.+|||+.+||++++|..++..++.++|||.|++++++.++.|+++|+.++|+
T Consensus 174 ~~~~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~l~d~~~~pe 248 (327)
T PRK05949 174 TEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEGPSPD 248 (327)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCccHHhhcCCCCCCHH
Confidence 999999999999999999999999999999999999999999999999999999998888899999998766655
No 3
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=100.00 E-value=1.1e-44 Score=362.75 Aligned_cols=229 Identities=31% Similarity=0.505 Sum_probs=216.5
Q ss_pred hhHHHHHHhccCCCCCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhchHHHHHH
Q 012638 221 TIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREEL 300 (459)
Q Consensus 221 ~~~~~~~~~~~~~~~lLt~~eE~eL~~~i~~~~~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l~~G~~Are~L 300 (459)
...|+ ......||||++||++|++.++.++.+++.+.+|+++.|++|+..+||+++|+++.+|+.+++.|..|+++|
T Consensus 3 ~~~yl---~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~L 79 (298)
T TIGR02997 3 VRLYL---QEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKM 79 (298)
T ss_pred HHHHH---HHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHH
Confidence 34455 345678999999999999999999999999999999999999999999999999999999999998899999
Q ss_pred HHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccchHHH
Q 012638 301 IKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNRE 380 (459)
Q Consensus 301 I~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~v~e~ 380 (459)
|.+|+++|+++|++|.++|.+++|||||||+|||+|+++|||.+|++|+||++||||++|.+++.++++++|+|.++...
T Consensus 80 v~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~I~r~i~~~~r~vr~p~~~~~~ 159 (298)
T TIGR02997 80 IKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEK 159 (298)
T ss_pred HHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHHHHHHHHhcCCCeeCcHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccCCCCCCccccCCCCCCCCcc
Q 012638 381 ISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPPFFFPSFA 452 (459)
Q Consensus 381 i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~~d~~~~l~e~i~D~~~~~~ 452 (459)
+++++++...+...+|+.||.+|||+.+|+++++|..++..+..++|||.+++++++.++.++++|+.+.|+
T Consensus 160 ~~~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~~~~~pe 231 (298)
T TIGR02997 160 LNKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDDGESPE 231 (298)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCcchHHHhccCCCCCHH
Confidence 999999999999999999999999999999999999999999999999999987777788898888666554
No 4
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=1.2e-44 Score=373.11 Aligned_cols=231 Identities=27% Similarity=0.502 Sum_probs=218.0
Q ss_pred CChhHHHHHHhccCCCCCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhchHHHH
Q 012638 219 QPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCRE 298 (459)
Q Consensus 219 ~p~~~~~~~~~~~~~~~lLt~~eE~eL~~~i~~~~~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l~~G~~Are 298 (459)
++...|+ ......||||++||++|+++|+.++.+++++.+|+++.|++|+..+||.++|+++.+|.+++..|..|++
T Consensus 63 d~l~~Yl---~~i~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~ 139 (373)
T PRK07406 63 DSIRVYL---QEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKE 139 (373)
T ss_pred CHHHHHH---HHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHH
Confidence 4444455 3445689999999999999999999999999999999999999999999999999999999999988999
Q ss_pred HHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccchH
Q 012638 299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLN 378 (459)
Q Consensus 299 ~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~v~ 378 (459)
+||.+|+++|+++|++|.+++.+++||+|||+||||+|+++|||.+|++|+|||+||||++|.++|++++++||+|.++.
T Consensus 140 ~Li~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~~ 219 (373)
T PRK07406 140 KMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLY 219 (373)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccCCCCCCccccCCCCCCCCcc
Q 012638 379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPPFFFPSFA 452 (459)
Q Consensus 379 e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~~d~~~~l~e~i~D~~~~~~ 452 (459)
+.+++|+++...|.+.+|+.||.+|||+.||+++++|..++..+..++|||.|++++++.++.|+++|+.+.|+
T Consensus 220 ~~~~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~~~l~d~l~d~~~~pe 293 (373)
T PRK07406 220 ETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADGETPE 293 (373)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCcccHHHhcCCCCCCHH
Confidence 99999999999999999999999999999999999999999988899999999988888899999998765554
No 5
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=1.6e-43 Score=357.97 Aligned_cols=231 Identities=28% Similarity=0.423 Sum_probs=218.5
Q ss_pred CChhHHHHHHhccCCCCCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhchHHHH
Q 012638 219 QPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCRE 298 (459)
Q Consensus 219 ~p~~~~~~~~~~~~~~~lLt~~eE~eL~~~i~~~~~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l~~G~~Are 298 (459)
+|...|+ ......||||++||++|+++|+.++.+++++..|++++|+.|+..+||.++++++.+|+..++.|+.|++
T Consensus 8 ~~~~~yl---~~i~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~ 84 (317)
T PRK07405 8 DLVRTYL---REIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKR 84 (317)
T ss_pred cHHHHHH---HHccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHH
Confidence 4555555 3456689999999999999999999999999999999999999999999999999999999999988999
Q ss_pred HHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccchH
Q 012638 299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLN 378 (459)
Q Consensus 299 ~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~v~ 378 (459)
+||..|+++|+++|++|.+++.+++||+||||+|||+++++|||.+|++|+|||+||||++|.++|++++++||+|.++.
T Consensus 85 ~L~~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir~p~~~~ 164 (317)
T PRK07405 85 KMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHIT 164 (317)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCccCChHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccCCCCCCccccCCCCCCCCcc
Q 012638 379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPPFFFPSFA 452 (459)
Q Consensus 379 e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~~d~~~~l~e~i~D~~~~~~ 452 (459)
..+++++++...+...+|+.||.+|||+.+|+++++|..++...+.++|||.|++++++.++.++++|+.+.|+
T Consensus 165 ~~~~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~~~d~~~~pe 238 (317)
T PRK07405 165 EKLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTGASPE 238 (317)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCccHHHhhcCCCCCHH
Confidence 99999999999999999999999999999999999999999988899999999988888899999998765554
No 6
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=100.00 E-value=3e-41 Score=342.15 Aligned_cols=224 Identities=29% Similarity=0.440 Sum_probs=203.6
Q ss_pred ccCCCCCCChHHHHHHHHHhHHHHHHHHHHHHHHH-HhCCCCchH---------------HHHHHcCCCH-HHHHHHHHh
Q 012638 230 NSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEK-ESGKAASLN---------------CWAQAAGVSE-RVLKQHLAF 292 (459)
Q Consensus 230 ~~~~~~lLt~~eE~eL~~~i~~~~~le~~~~~l~~-~~gr~pt~~---------------ewa~a~g~de-eeL~~~l~~ 292 (459)
.....++++.++|.++.+.++....+......+.. .++..|+.. +|+.....++ ..|..++..
T Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Ee~~la~~~~~ 96 (342)
T COG0568 17 EIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEEEKALARRLKR 96 (342)
T ss_pred HhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHHHHHHHHHHHc
Confidence 34456999999999999999988877777777766 667888876 5555555444 678889999
Q ss_pred ch--H-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcc
Q 012638 293 GW--Y-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (459)
Q Consensus 293 G~--~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr 369 (459)
|. . |+.+||.+|+++|++||++|.|+|+++.||||||+||||+|++||||.+|++|||||+||||++|.++|.++.+
T Consensus 97 g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAVekFdp~rG~kFsTYA~wWIrqaI~raI~~q~r 176 (342)
T COG0568 97 GERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQAITRAIADQAR 176 (342)
T ss_pred CCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHHHHhcCcccCCcchhHHHHHHHHHHHHHHHHhcc
Confidence 94 3 99999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccCCCCCCccccCCCCCCC
Q 012638 370 GIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPPFFFP 449 (459)
Q Consensus 370 ~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~~d~~~~l~e~i~D~~~ 449 (459)
+||+|.|+.+.++++.++.+.|.+.+++.|+++|||+.||+++++|..++..++.++|||.|+|++++..++|+++|+.+
T Consensus 177 tIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd~~ig~ded~~l~d~leD~~~ 256 (342)
T COG0568 177 TIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDDEDSELGDFLEDDKS 256 (342)
T ss_pred hhhHhHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccCCcCCCCcccHHHHHhhcCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999865
Q ss_pred -Cccc
Q 012638 450 -SFAI 453 (459)
Q Consensus 450 -~~~~ 453 (459)
.|++
T Consensus 257 ~~p~~ 261 (342)
T COG0568 257 VSPED 261 (342)
T ss_pred CCHHH
Confidence 5543
No 7
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=100.00 E-value=4.8e-40 Score=349.52 Aligned_cols=215 Identities=28% Similarity=0.419 Sum_probs=191.5
Q ss_pred CCChhHHHHHHhccCCCCCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhchHHH
Q 012638 218 KQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCR 297 (459)
Q Consensus 218 ~~p~~~~~~~~~~~~~~~lLt~~eE~eL~~~i~~~~~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l~~G~~Ar 297 (459)
.+|...|+ ......||||++||++|+++|+.+..+++... ....|+.+ ...+|...+..|..|+
T Consensus 210 ~d~l~~YL---~~i~~~~lLt~eEE~~La~~i~~g~~~~~~~~----------~~~~~~~~---~~~~l~~~~~~g~~Ar 273 (509)
T PRK05901 210 ADPVKAYL---KQIGKVKLLNAEEEVELAKRIEAGLYAEELLA----------EGEKLDPE---LRRDLQWIGRDGKRAK 273 (509)
T ss_pred ccHHHHHH---HHhccCCCCCHHHHHHHHHHHHhCCchhhhhh----------hcccchhh---hhhhhhhhccchHHHH
Confidence 35555555 23456799999999999999998866555321 11234422 3567888899999999
Q ss_pred HHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccch
Q 012638 298 EELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKL 377 (459)
Q Consensus 298 e~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~v 377 (459)
++||.+|+|||+++|++|.++|++++||||||+|||++|+++|||++|++|+|||+||||++|.++|+++.+.||+|.++
T Consensus 274 ~~LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP~~~ 353 (509)
T PRK05901 274 NHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHM 353 (509)
T ss_pred HHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecCHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccCCCCCCccccCCCCCC
Q 012638 378 NREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPPFFF 448 (459)
Q Consensus 378 ~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~~d~~~~l~e~i~D~~ 448 (459)
.+.+++|.++.+.|.+.+|+.||.+|||+.|||++++|..++...+.++|||.|++++++.++.|+|+|+.
T Consensus 354 ~e~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~l~d~l~D~~ 424 (509)
T PRK05901 354 VETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSE 424 (509)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCcccHHHhccCCC
Confidence 99999999999999999999999999999999999999999999999999999999888888999999874
No 8
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=100.00 E-value=1.5e-39 Score=330.01 Aligned_cols=215 Identities=27% Similarity=0.411 Sum_probs=191.5
Q ss_pred CCChhHHHHHHhccCCCCCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhchHHH
Q 012638 218 KQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCR 297 (459)
Q Consensus 218 ~~p~~~~~~~~~~~~~~~lLt~~eE~eL~~~i~~~~~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l~~G~~Ar 297 (459)
+++...|+ ......||||++||++|+++|+.+..++.. |+..+|+... ...+|...++.|..|+
T Consensus 25 ~~~~~~Yl---~~i~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~ 88 (324)
T PRK07921 25 ADLVRVYL---NGIGKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAAR 88 (324)
T ss_pred CChHHHHH---HHhcccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHH
Confidence 35555555 345668999999999999999988776654 1122232111 3567889999999999
Q ss_pred HHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccch
Q 012638 298 EELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKL 377 (459)
Q Consensus 298 e~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~v 377 (459)
++||..|+++|+++|++|.+++.+++||+|||+||||+|+++|||++|++|+|||+||||++|.++|+++++.|++|.++
T Consensus 89 ~~Lv~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~~~ 168 (324)
T PRK07921 89 RHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHL 168 (324)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccCCCCCCccccCCCCCC
Q 012638 378 NREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPPFFF 448 (459)
Q Consensus 378 ~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~~d~~~~l~e~i~D~~ 448 (459)
.+.++++.++...|...+|+.||.+|||+.||+++++|..++..+..++|||.|++++++.++.|+++|+.
T Consensus 169 ~~~~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~ 239 (324)
T PRK07921 169 VEQVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSE 239 (324)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCchHHHHhcCCC
Confidence 99999999999999999999999999999999999999999988888999999998877788999999863
No 9
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=3.1e-34 Score=295.50 Aligned_cols=187 Identities=27% Similarity=0.449 Sum_probs=171.1
Q ss_pred CChhHHHHHHhccCCCCCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhchHHHH
Q 012638 219 QPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCRE 298 (459)
Q Consensus 219 ~p~~~~~~~~~~~~~~~lLt~~eE~eL~~~i~~~~~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l~~G~~Are 298 (459)
++...|+ ......|+||++||.+|++.++.+ +..|++
T Consensus 96 d~~~~yl---~~i~~~~~l~~~ee~~L~~~~~~G----------------------------------------d~~A~~ 132 (367)
T PRK09210 96 DPVRMYL---KEIGRVPLLTAEEEIELAKRIEEG----------------------------------------DEEAKQ 132 (367)
T ss_pred cHHHHHH---HHhhccCCCCHHHHHHHHHHHHhh----------------------------------------HHHHHH
Confidence 4444444 344568999999999998866432 123899
Q ss_pred HHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccchH
Q 012638 299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLN 378 (459)
Q Consensus 299 ~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~v~ 378 (459)
+||..|+++|+++|++|.+++.+++||+|||+||||+|+++|||.+|++|+|||+|||+++|.++|+++.+++|+|.|+.
T Consensus 133 ~Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~~~~ 212 (367)
T PRK09210 133 RLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMV 212 (367)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccCCCCCCccccCCCCCC
Q 012638 379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPPFFF 448 (459)
Q Consensus 379 e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~~d~~~~l~e~i~D~~ 448 (459)
+.++++.++.+.|...+|+.||.+|||+.|||++++|..++..++.++|||.|++++++.++.|+++|+.
T Consensus 213 ~~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~i~d~~ 282 (367)
T PRK09210 213 ETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQD 282 (367)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCCCcchhhhhccCCC
Confidence 9999999999999999999999999999999999999999999989999999999888889999998874
No 10
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=8.1e-34 Score=309.76 Aligned_cols=173 Identities=27% Similarity=0.533 Sum_probs=161.0
Q ss_pred HHHcCCCH---HHHHHHHHhch----HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCch
Q 012638 276 AQAAGVSE---RVLKQHLAFGW----YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKF 348 (459)
Q Consensus 276 a~a~g~de---eeL~~~l~~G~----~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rF 348 (459)
....+++. ..+.++++.|+ .|+++||.+|++||++||++|.++|++++||||||+|||++|+++|||.+|++|
T Consensus 354 e~~~~Ls~eElk~l~~~i~~g~~~~~~a~~~Li~~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~F 433 (619)
T PRK05658 354 EEETGLTIEELKEINRQISKGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 433 (619)
T ss_pred HHHhCCCHHHHHHHHHHHhccchhhhHHHHHHHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCch
Confidence 33445554 34567778885 389999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHHHHHHhhccccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCcc
Q 012638 349 STYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSI 428 (459)
Q Consensus 349 STYa~~wIrnaI~d~Lrk~sr~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SL 428 (459)
+|||+||||++|.++|+++.++||+|.|+.+.+++++++...+.+++|+.||.+|||+.||+|+++|..++..+..++||
T Consensus 434 stYA~~wIr~aI~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~Sl 513 (619)
T PRK05658 434 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISL 513 (619)
T ss_pred HHHhHHHHHHHHHHHHHHcCCceecCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCcC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCCCCCCccccCCCCCC
Q 012638 429 DQKIGDCLNAKYLNIPPFFF 448 (459)
Q Consensus 429 D~~v~~d~~~~l~e~i~D~~ 448 (459)
|.|++++++.++.|+++|+.
T Consensus 514 d~~i~~~~~~~l~d~i~d~~ 533 (619)
T PRK05658 514 ETPIGDDEDSHLGDFIEDKN 533 (619)
T ss_pred CCCCCCCCCCchhhhcCCCC
Confidence 99999888889999999863
No 11
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=99.98 E-value=4.4e-32 Score=267.96 Aligned_cols=154 Identities=22% Similarity=0.309 Sum_probs=142.0
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccc
Q 012638 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP 374 (459)
Q Consensus 295 ~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP 374 (459)
.++++||.+|++||+++|++|.++|++++||||||+|||++|+++|||++|++|+|||+|||+++|.++++++.+.|++|
T Consensus 40 ~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~iGLi~AierFDp~~G~~FsTYA~~~Irg~I~~~lr~~~~~ir~P 119 (264)
T PRK07122 40 RQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVP 119 (264)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHcCCccccC
Confidence 38899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHh--hccCCccccccCCCCC--CccccCCCCCC
Q 012638 375 CKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC--LRIVGSIDQKIGDCLN--AKYLNIPPFFF 448 (459)
Q Consensus 375 ~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~--ar~~~SLD~~v~~d~~--~~l~e~i~D~~ 448 (459)
.++.+..++++++...|.+.+|+.||.+|||+.||+++++|..++.. ...++|||.+++++++ ..+.+.++|++
T Consensus 120 r~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~~~d~~~~~~ 197 (264)
T PRK07122 120 RRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSGDDDARAIADTLGDVD 197 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccccccCCCCCcccchhccCCcH
Confidence 99999999999999999999999999999999999999999998764 4568999999875433 35666766654
No 12
>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=99.98 E-value=1.1e-31 Score=260.18 Aligned_cols=153 Identities=33% Similarity=0.592 Sum_probs=146.9
Q ss_pred HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccccccc
Q 012638 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC 375 (459)
Q Consensus 296 Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~ 375 (459)
|+++||..|+++|+++|++|.+++.+++||+|||++||++|+++|||.+|++|+|||+||||++|.++++++.+.+++|.
T Consensus 1 a~~~Li~~~~~lv~~ia~~~~~~~~~~eDLiQeG~igL~~A~~~fd~~~g~~FstYA~~~Ir~~I~~~l~~~~~~vrip~ 80 (238)
T TIGR02393 1 AKKQLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80 (238)
T ss_pred CHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCChHHHhHHHHHHHHHHHHHHcCCcEEeCH
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccCCCCCCccccCCCCCC
Q 012638 376 KLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPPFFF 448 (459)
Q Consensus 376 ~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~~d~~~~l~e~i~D~~ 448 (459)
++.+.++++.++...|...+|+.||.+|||+.||+++++|..++.....++|||.+++++++.++.|+++|+.
T Consensus 81 ~~~~~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~ 153 (238)
T TIGR02393 81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDTS 153 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCCCCCCcccHHHHhcCCC
Confidence 9999999999999999999999999999999999999999999888888999999998777778999998875
No 13
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=99.97 E-value=1.5e-30 Score=255.66 Aligned_cols=160 Identities=24% Similarity=0.339 Sum_probs=145.0
Q ss_pred HhchH-HHHHHHHHhHHHHHHHHHHhhCC-CCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhc
Q 012638 291 AFGWY-CREELIKSTRPLVLFLARNYRGL-GIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA 368 (459)
Q Consensus 291 ~~G~~-Are~LI~~nlrLV~sIAkry~g~-g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~s 368 (459)
..|+. |+++||..|+++|+++|++|.+. +.+++||+|||+||||+|+++|||++|++|+|||+|||+|+|.++++++.
T Consensus 20 ~~gd~~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~ 99 (256)
T PRK07408 20 QNPSIALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKS 99 (256)
T ss_pred HCCCHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHHcC
Confidence 46665 99999999999999999999876 66799999999999999999999999999999999999999999999999
Q ss_pred cccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHH--hhccCCccccccCCCCC--CccccCC
Q 012638 369 RGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASE--CLRIVGSIDQKIGDCLN--AKYLNIP 444 (459)
Q Consensus 369 r~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~--~ar~~~SLD~~v~~d~~--~~l~e~i 444 (459)
+.+|+|.++.+.+++++++...|.+.+|+.||.+|||+.||+++++|..++. ....++|||.+++++++ .++.+.+
T Consensus 100 ~~vr~pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~~ 179 (256)
T PRK07408 100 PTVRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQDEDGSTSLGDLL 179 (256)
T ss_pred CeeeeCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCCCCCCcccccccc
Confidence 9999999999999999999999999999999999999999999999999865 34568999999865433 4678888
Q ss_pred CCCCCC
Q 012638 445 PFFFPS 450 (459)
Q Consensus 445 ~D~~~~ 450 (459)
+|+...
T Consensus 180 ~d~~~~ 185 (256)
T PRK07408 180 PDPRYR 185 (256)
T ss_pred CCcccc
Confidence 887543
No 14
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=99.97 E-value=3.5e-30 Score=257.60 Aligned_cols=183 Identities=22% Similarity=0.292 Sum_probs=154.2
Q ss_pred ccCCCCCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhchH-HHHHHHHHhHHHH
Q 012638 230 NSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWY-CREELIKSTRPLV 308 (459)
Q Consensus 230 ~~~~~~lLt~~eE~eL~~~i~~~~~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l~~G~~-Are~LI~~nlrLV 308 (459)
+..+.|+||+++|.+|+++++ ..|+. |+++||..|+++|
T Consensus 14 ~~~~~~~l~~~~e~~L~~~~~----------------------------------------~~gd~~A~~~Lv~~~~~lV 53 (289)
T PRK07500 14 SAMKAPYLEREEEHALAYRWK----------------------------------------DHRDEDALHRIISAHMRLV 53 (289)
T ss_pred HHhcCCCCCHHHHHHHHHHHH----------------------------------------HCCCHHHHHHHHHHhHHHH
Confidence 345679999999998887542 12444 9999999999999
Q ss_pred HHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccchHH--HHHHHHH
Q 012638 309 LFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNR--EISKIQK 386 (459)
Q Consensus 309 ~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~v~e--~i~kI~k 386 (459)
+++|++|.+++.+++||+||||+|||+|+++|||.+|.+|+|||+|||+++|.++|+++.+.+|+|.+..+ ...++.+
T Consensus 54 ~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I~~~lr~~~~~iR~p~~~~~~~~~~~~~~ 133 (289)
T PRK07500 54 ISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRR 133 (289)
T ss_pred HHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHCCCceecCccHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999998655 3345555
Q ss_pred HHHHHHH---HcCCCCCHHHHHHHhCCCHHHHHHHHH-hhccCCccccccCCCCC--CccccCCCCCCCCcc
Q 012638 387 ARKALTN---SHGKYPEDIEIAKYTGLSLAEIRSASE-CLRIVGSIDQKIGDCLN--AKYLNIPPFFFPSFA 452 (459)
Q Consensus 387 a~~~L~~---~lgr~PT~eEIAe~LGIS~e~Vk~~l~-~ar~~~SLD~~v~~d~~--~~l~e~i~D~~~~~~ 452 (459)
+...+.. .+++.||.+|||+.||+++++|..+.. ....++|||.+++++++ .++.|+++|+.+.|+
T Consensus 134 ~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~i~d~~~~pe 205 (289)
T PRK07500 134 LRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDDSPLPD 205 (289)
T ss_pred HHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCCCCCCcccHHHhccCCCCCch
Confidence 5555544 679999999999999999999987753 34578999999976554 368999998866554
No 15
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=99.97 E-value=3.5e-29 Score=245.10 Aligned_cols=154 Identities=24% Similarity=0.257 Sum_probs=142.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccc
Q 012638 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP 374 (459)
Q Consensus 295 ~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP 374 (459)
.|+++||..|.++|+++|++|.+++.+++||+|||++|||+++++||+.+|.+|+||+++||+|.|.++++++. .+++|
T Consensus 34 ~a~~~L~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~~lr~~~-~ir~p 112 (254)
T TIGR02850 34 TAREKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVS 112 (254)
T ss_pred HHHHHHHHHhHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CccCc
Confidence 39999999999999999999999999999999999999999999999999999999999999999999999874 78999
Q ss_pred cchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccCCCCC--CccccCCCCCCC
Q 012638 375 CKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLN--AKYLNIPPFFFP 449 (459)
Q Consensus 375 ~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~~d~~--~~l~e~i~D~~~ 449 (459)
.++.+...++.++...+..++|+.||.+|||+.||+++++|..++.....++|||.++.++++ .++.+.++|+..
T Consensus 113 ~~~~~~~~~~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~~~d~~~ 189 (254)
T TIGR02850 113 RSLRDIAYKALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDEKN 189 (254)
T ss_pred hHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCCCCCcchhhhhcCCccc
Confidence 999999999999999999999999999999999999999999999988889999999864433 457888887644
No 16
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=99.96 E-value=6.2e-29 Score=247.92 Aligned_cols=159 Identities=27% Similarity=0.380 Sum_probs=133.9
Q ss_pred hchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccc
Q 012638 292 FGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG 370 (459)
Q Consensus 292 ~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~ 370 (459)
.|+. |+++||..|+++|+++|++|.+.+.+++||+|||++||++|+++|||.+|++|+|||+|||+++|.++++++.+.
T Consensus 44 ~Gd~~a~~~Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~~~l~~~~~~ 123 (284)
T PRK06596 44 HGDLEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRI 123 (284)
T ss_pred cCCHHHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHcCCe
Confidence 3554 999999999999999999999999999999999999999999999999999999999999999999999998778
Q ss_pred cccccchHH--HHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhh-ccCCccccccCCCC--CCccccCCC
Q 012638 371 IKIPCKLNR--EISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL-RIVGSIDQKIGDCL--NAKYLNIPP 445 (459)
Q Consensus 371 irlP~~v~e--~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~a-r~~~SLD~~v~~d~--~~~l~e~i~ 445 (459)
+++|.+... ...++.+....+. .++.||.+|||+.||+++++|..++... ..++|||.++++++ +.++.++++
T Consensus 124 vr~p~~~~~~~~~~~~~~~~~~l~--~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~~~l~ 201 (284)
T PRK06596 124 VKVATTKAQRKLFFNLRKAKKRLG--WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLE 201 (284)
T ss_pred eeccchHHHHHHHHHHHHHHHHhc--cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCCCCCcchHHHHcC
Confidence 999987542 3334444444443 3489999999999999999999987543 46899999987553 356889999
Q ss_pred CCCCCcc
Q 012638 446 FFFPSFA 452 (459)
Q Consensus 446 D~~~~~~ 452 (459)
|+.+.|+
T Consensus 202 d~~~~p~ 208 (284)
T PRK06596 202 DKSSDPA 208 (284)
T ss_pred CCCCCch
Confidence 8865554
No 17
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=99.96 E-value=2.6e-28 Score=241.26 Aligned_cols=160 Identities=27% Similarity=0.386 Sum_probs=132.3
Q ss_pred hchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccc
Q 012638 292 FGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG 370 (459)
Q Consensus 292 ~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~ 370 (459)
.|+. |+++||..|+++|+++|++|.+++.+++||+|||++||++|+++|||++|++|+|||+|||+++|.++++++.+.
T Consensus 31 ~gd~~a~~~Lv~~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA~~~Ir~~i~~~l~~~~~~ 110 (270)
T TIGR02392 31 HGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRL 110 (270)
T ss_pred CCCHHHHHHHHHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhhHHHHHHHHHHHHHHcCCc
Confidence 4554 999999999999999999999999999999999999999999999999999999999999999999999988778
Q ss_pred cccccchH--HHHHHHHHHHHHHHHHcCCCC-CHHHHHHHhCCCHHHHHHHHHhhc-cCCccccccCCCCC--CccccCC
Q 012638 371 IKIPCKLN--REISKIQKARKALTNSHGKYP-EDIEIAKYTGLSLAEIRSASECLR-IVGSIDQKIGDCLN--AKYLNIP 444 (459)
Q Consensus 371 irlP~~v~--e~i~kI~ka~~~L~~~lgr~P-T~eEIAe~LGIS~e~Vk~~l~~ar-~~~SLD~~v~~d~~--~~l~e~i 444 (459)
+++|.+.. +...++.++...+. ..+.| +.+|||+.||+++++|..++.... .++|||.+++++++ .++.+++
T Consensus 111 ir~p~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~l 188 (270)
T TIGR02392 111 VKVATTKAQRKLFFNLRKMKKRLQ--GWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDDEDDGGAPIAYL 188 (270)
T ss_pred eecCchHHHHHHHHHHHHHHHHHh--cCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCCCCCccccHHHHh
Confidence 99997643 34445555554442 12455 699999999999999999865443 47999999976544 3678888
Q ss_pred CCCCCCccc
Q 012638 445 PFFFPSFAI 453 (459)
Q Consensus 445 ~D~~~~~~~ 453 (459)
+|+.++|+.
T Consensus 189 ~d~~~~pe~ 197 (270)
T TIGR02392 189 VDKTSDPED 197 (270)
T ss_pred cCCCCChHH
Confidence 887655543
No 18
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=99.96 E-value=8.2e-28 Score=235.78 Aligned_cols=156 Identities=24% Similarity=0.249 Sum_probs=142.8
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccc
Q 012638 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP 374 (459)
Q Consensus 295 ~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP 374 (459)
.|+++||..|.++|+++|++|.+++.+++||+|||++|||+|+++||+.+|.+|+||+++||+|+|.++++++. .+++|
T Consensus 37 ~a~~~l~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~~~lr~~~-~vrip 115 (258)
T PRK08215 37 EAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVS 115 (258)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-ceEec
Confidence 38999999999999999999999999999999999999999999999999999999999999999999999884 88999
Q ss_pred cchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccCCCCC--CccccCCCCCCCCc
Q 012638 375 CKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLN--AKYLNIPPFFFPSF 451 (459)
Q Consensus 375 ~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~~d~~--~~l~e~i~D~~~~~ 451 (459)
.++.....++.++...+..++|+.|+.+|||+.|||++++|..++.....++|||.+++++++ .++.|.++|+...+
T Consensus 116 ~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~~~ 194 (258)
T PRK08215 116 RSLRDIAYKALQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQISDEKNKD 194 (258)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCCCCcchhhhhhccCccccH
Confidence 999999999999999999999999999999999999999999998888888999999865543 34677887765433
No 19
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=99.96 E-value=1.5e-27 Score=242.48 Aligned_cols=185 Identities=25% Similarity=0.439 Sum_probs=164.9
Q ss_pred HHHHHHhc-cCCCCCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhchH-HHHHH
Q 012638 223 FSAERALN-SRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWY-CREEL 300 (459)
Q Consensus 223 ~~~~~~~~-~~~~~lLt~~eE~eL~~~i~~~~~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l~~G~~-Are~L 300 (459)
+.++.|.+ ++..|+||+++|.+|.+. ++.|+. |+++|
T Consensus 53 ~~~~~y~~~~~~~~~l~~~ee~~li~~-----------------------------------------~~~Gd~~A~~~L 91 (325)
T PRK05657 53 DATQLYLNEIGYSPLLTAEEEVYFARR-----------------------------------------ALRGDFAARQRM 91 (325)
T ss_pred cHHHHHHHHHhcCCCCCHHHHHHHHHH-----------------------------------------HHcCCHHHHHHH
Confidence 33444554 345788888888776663 334544 99999
Q ss_pred HHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccchHHH
Q 012638 301 IKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNRE 380 (459)
Q Consensus 301 I~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~v~e~ 380 (459)
|..|.++|+++|++|++++.+++||+||||+|+|+++++||+.+|++|+||++||||++|.++++++.+.+++|.++...
T Consensus 92 i~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~~i~~~~r~ir~p~~~~~~ 171 (325)
T PRK05657 92 IESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVKE 171 (325)
T ss_pred HHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHcCCccccCHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999988
Q ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccCCCCCCccccCCCCCC
Q 012638 381 ISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPPFFF 448 (459)
Q Consensus 381 i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~~d~~~~l~e~i~D~~ 448 (459)
++.+.++...|...+++.|+.+|||+.||+++++|..++.....++|||.+++++...++.|.++|+.
T Consensus 172 l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~~~~~~~~l~d~l~d~~ 239 (325)
T PRK05657 172 LNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQ 239 (325)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCCCCCCCcchhhhccCCC
Confidence 88888999999999999999999999999999999999988778899999998777788999988764
No 20
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=99.95 E-value=3.7e-27 Score=231.86 Aligned_cols=157 Identities=22% Similarity=0.281 Sum_probs=138.5
Q ss_pred HhchH-HHHHHHHHhHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHh
Q 012638 291 AFGWY-CREELIKSTRPLVLFLARNYRG---LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVAR 366 (459)
Q Consensus 291 ~~G~~-Are~LI~~nlrLV~sIAkry~g---~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk 366 (459)
..|+. |+++||..|+|+|+++|++|.+ .+.+.+||+|||+||||+|+++|||++|++|+|||+|||+++|.+++|+
T Consensus 18 ~~~~~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i~~~lr~ 97 (257)
T PRK05911 18 STQEIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRK 97 (257)
T ss_pred hcCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHh
Confidence 34654 9999999999999999999863 3568999999999999999999999999999999999999999999998
Q ss_pred hccccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhc--cCCccccccCC--C--CCCcc
Q 012638 367 HARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR--IVGSIDQKIGD--C--LNAKY 440 (459)
Q Consensus 367 ~sr~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar--~~~SLD~~v~~--d--~~~~l 440 (459)
+. ++|.++.+..+++.++...|.+.+|+.|+.+|||+.|||++++|..++..++ .++|||.++.. + ++.++
T Consensus 98 ~~---~~pr~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~Sld~~~~~~~~~~~~~~l 174 (257)
T PRK05911 98 QD---WVPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPCQSDDEAGLAL 174 (257)
T ss_pred cC---CCCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHHhhccceeeccccCCCCCCCccccch
Confidence 74 4899999999999999999999999999999999999999999999887664 36899998743 2 23568
Q ss_pred ccCCCCCCCC
Q 012638 441 LNIPPFFFPS 450 (459)
Q Consensus 441 ~e~i~D~~~~ 450 (459)
.+.++|+.+.
T Consensus 175 ~~~l~d~~~~ 184 (257)
T PRK05911 175 EERIADERAE 184 (257)
T ss_pred hhhccCCCCC
Confidence 8889887543
No 21
>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=99.95 E-value=5.1e-27 Score=225.84 Aligned_cols=160 Identities=25% Similarity=0.276 Sum_probs=146.8
Q ss_pred HHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHh
Q 012638 288 QHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVAR 366 (459)
Q Consensus 288 ~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk 366 (459)
.+++.|+. |+++||..|.++|+++|++|.+++.+++||+|||++|||+++++||+.+|.+|+||+++||+|.|.+++|+
T Consensus 3 ~~~~~gd~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~lr~ 82 (231)
T TIGR02885 3 KLAQNGDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRD 82 (231)
T ss_pred HHHHcCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHh
Confidence 44566766 99999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred hccccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccCCCCC--CccccCC
Q 012638 367 HARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLN--AKYLNIP 444 (459)
Q Consensus 367 ~sr~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~~d~~--~~l~e~i 444 (459)
+. .+++|.++.+...++.++...|..++|+.||.+|||+.||+++++|..++..+..+.|||.+++++++ .++.|.+
T Consensus 83 ~~-~i~~p~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~ 161 (231)
T TIGR02885 83 DG-IIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPIYLLDQI 161 (231)
T ss_pred CC-CeECCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCCCCCcchhhhhc
Confidence 85 78999999999999999999999999999999999999999999999999888889999999875543 3567778
Q ss_pred CCCC
Q 012638 445 PFFF 448 (459)
Q Consensus 445 ~D~~ 448 (459)
+|+.
T Consensus 162 ~~~~ 165 (231)
T TIGR02885 162 ADKG 165 (231)
T ss_pred CCCC
Confidence 7764
No 22
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=99.95 E-value=4.1e-27 Score=230.74 Aligned_cols=170 Identities=28% Similarity=0.337 Sum_probs=149.8
Q ss_pred HHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCC-CHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHH
Q 012638 284 RVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGI-PFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS 361 (459)
Q Consensus 284 eeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~-d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~ 361 (459)
+.+....+.|+. ++ .||+.|+|||.++|++|.+++. +.+||+|.|+|||++|+++|||++|.+|+|||...|+++|+
T Consensus 12 ~~~~~~~~~g~~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~ 90 (247)
T COG1191 12 EKLLEYYAEGDEEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEIL 90 (247)
T ss_pred HHHHHHHHhcCHHHH-HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHH
Confidence 456667778877 88 9999999999999999998877 99999999999999999999999999999999999999999
Q ss_pred HHHHhhccccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhc--cCCccccccCCCCCCc
Q 012638 362 KMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR--IVGSIDQKIGDCLNAK 439 (459)
Q Consensus 362 d~Lrk~sr~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar--~~~SLD~~v~~d~~~~ 439 (459)
+++|++. .+++|+.+++..+++..+..+|..++|+.||++|||+.|||+.++|...+.... ..+|+|..+..+++..
T Consensus 91 d~LR~~~-~v~vpR~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~d~~ 169 (247)
T COG1191 91 DYLRKND-SVKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDDD 169 (247)
T ss_pred HHHHhCC-CccCcHHHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhccccccc
Confidence 9999998 999999999999999999999999999999999999999999999999988764 6789998776444444
Q ss_pred cccCCCCCCCCccchh
Q 012638 440 YLNIPPFFFPSFAIWE 455 (459)
Q Consensus 440 l~e~i~D~~~~~~~~e 455 (459)
..+.+.++....+.|+
T Consensus 170 ~~~~~~~~~~~~~~~~ 185 (247)
T COG1191 170 VDDQIENPDDGVEKEE 185 (247)
T ss_pred hhhccccchhHHHHHH
Confidence 5555555544444444
No 23
>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=99.94 E-value=1.2e-25 Score=215.49 Aligned_cols=154 Identities=32% Similarity=0.399 Sum_probs=140.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccc
Q 012638 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP 374 (459)
Q Consensus 295 ~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP 374 (459)
.|+++||..|.++|+++|++|.+++.+++||+|||++|||+|+++||+.+|.+|+||+++||+|.|.++++++.+.+++|
T Consensus 3 ~a~~~lv~~y~~~v~~~a~~~~~~~~~~eDl~Qe~~i~l~~a~~~f~~~~~~~F~ty~~~~i~~~~~~~~r~~~~~~ri~ 82 (227)
T TIGR02980 3 EAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTWAVRVP 82 (227)
T ss_pred HHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCcHHHHHHHHHHHHHHHHHHcCCceecC
Confidence 48999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhcc--CCccccccCCCC--CCccccCCCCCC
Q 012638 375 CKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRI--VGSIDQKIGDCL--NAKYLNIPPFFF 448 (459)
Q Consensus 375 ~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~--~~SLD~~v~~d~--~~~l~e~i~D~~ 448 (459)
.++.+...+++++...+...+|+.|+.+|+|+.||+++++|..++..... +.|||.++++++ +.++.+.+++++
T Consensus 83 ~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~d~~~~~~ 160 (227)
T TIGR02980 83 RRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIEDDDGDPIALLDTLGDED 160 (227)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCCCCCCCcccccccCCcc
Confidence 99999999999999999999999999999999999999999998887665 899999986332 334556665543
No 24
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=99.93 E-value=1.2e-24 Score=214.77 Aligned_cols=149 Identities=30% Similarity=0.353 Sum_probs=132.8
Q ss_pred HHHHHHHHhHHHHHHHHHHhh-C--CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccc
Q 012638 296 CREELIKSTRPLVLFLARNYR-G--LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIK 372 (459)
Q Consensus 296 Are~LI~~nlrLV~sIAkry~-g--~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~ir 372 (459)
|++.|+..|.++|+.+|++|. + .+.+++||+|||++|||+|+++||+.+|++|+||++|||+|.|++++|+. ++
T Consensus 32 a~~~l~~~y~~lv~~~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i~d~~R~~---~~ 108 (268)
T PRK06288 32 IREYLILKYSPLVKYVAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSI---DW 108 (268)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhc---Cc
Confidence 899999999999999999986 3 46789999999999999999999999899999999999999999999965 56
Q ss_pred cccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhh--ccCCccccccCC-C--CCCccccCCCCC
Q 012638 373 IPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL--RIVGSIDQKIGD-C--LNAKYLNIPPFF 447 (459)
Q Consensus 373 lP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~a--r~~~SLD~~v~~-d--~~~~l~e~i~D~ 447 (459)
+|.++.....+++++...|...+++.||.+|||+.+|++++.|..++... ..++|||.++.. + +..++.+.++++
T Consensus 109 ~p~~~~~~~~~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~l~~~~~~~ 188 (268)
T PRK06288 109 IPRSVRQKARQIERAIAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGDEVSLMDTLESP 188 (268)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhccCCCcccchhhhhccCC
Confidence 89999999999999999999999999999999999999999999988765 457899998742 2 235677888765
No 25
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=99.93 E-value=1.2e-24 Score=212.63 Aligned_cols=156 Identities=25% Similarity=0.270 Sum_probs=143.1
Q ss_pred HHHHHHHHHh-chH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHH
Q 012638 283 ERVLKQHLAF-GWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (459)
Q Consensus 283 eeeL~~~l~~-G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI 360 (459)
+.+|+.+++. |+. |+++||..|.++|+.+|++|.+++.+++||+|||++|||+++++||+..|.+|.||+++||+|.|
T Consensus 15 ~~~li~~~~~~gd~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~~ 94 (255)
T TIGR02941 15 VIQWIAEFQQNQNGEAQEKLVDHYQNLVYSIAYKYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEI 94 (255)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHHH
Confidence 4557777777 565 99999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhccccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhh--ccCCccccccCCCCCC
Q 012638 361 SKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL--RIVGSIDQKIGDCLNA 438 (459)
Q Consensus 361 ~d~Lrk~sr~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~a--r~~~SLD~~v~~d~~~ 438 (459)
.++++++...+++|.++.+..++++.+...+...+|+.|+.+|||+.+||+.+.+..++... ..+.|||.+++.+++.
T Consensus 95 ~~~lr~~~~~iri~~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~ 174 (255)
T TIGR02941 95 KRYLRDKTWSVHVPRRIKELGPKIKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSDG 174 (255)
T ss_pred HHHHHHcCCCcCCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCCCCC
Confidence 99999998899999999999999999999999999999999999999999999999887654 3578999998755443
No 26
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=99.92 E-value=3.4e-24 Score=209.41 Aligned_cols=162 Identities=22% Similarity=0.265 Sum_probs=140.6
Q ss_pred CHHHHHHHHH-hchH-HHHHHHHHhHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHH
Q 012638 282 SERVLKQHLA-FGWY-CREELIKSTRPLVLFLARNYRG---LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI 356 (459)
Q Consensus 282 deeeL~~~l~-~G~~-Are~LI~~nlrLV~sIAkry~g---~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wI 356 (459)
++..|+++++ .|+. |+++||..|.++|+++|++|.+ ++.+++||+|||++|||+++++||+.+|.+|+||+++||
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 3566777744 4566 9999999999999999999976 688999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhccccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHH--hhccCCccccccCC
Q 012638 357 RKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASE--CLRIVGSIDQKIGD 434 (459)
Q Consensus 357 rnaI~d~Lrk~sr~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~--~ar~~~SLD~~v~~ 434 (459)
+|.|++++|++. ++|.++.+.+++++++...+.+.+|+.|+.+|||+.||+++++|..++. ....++|||.++.+
T Consensus 87 rn~~~d~lR~~~---~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~ 163 (251)
T PRK07670 87 RGAIIDGLRKED---WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHD 163 (251)
T ss_pred HHHHHHHHHhcC---CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCccccC
Confidence 999999999864 6899999999999999999999999999999999999999999999876 34578999999865
Q ss_pred CCC-CccccCCCC
Q 012638 435 CLN-AKYLNIPPF 446 (459)
Q Consensus 435 d~~-~~l~e~i~D 446 (459)
+++ .++.+.++|
T Consensus 164 ~~~~~~~~~~~~~ 176 (251)
T PRK07670 164 QDDGENVSVTIRD 176 (251)
T ss_pred CCCcchhhhhhcC
Confidence 443 334444444
No 27
>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=99.92 E-value=9.2e-24 Score=210.29 Aligned_cols=166 Identities=27% Similarity=0.498 Sum_probs=153.3
Q ss_pred HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHH
Q 012638 283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS 361 (459)
Q Consensus 283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~ 361 (459)
+.+|+..++.|+. |++.||..|.++|+++|++|.+++.+++||+|||+||||+|+++||+.+|++|+||+.|||+.++.
T Consensus 33 ~~~li~~~~~gd~~a~~~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ain 112 (285)
T TIGR02394 33 EIAYARRALAGDFEARKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIE 112 (285)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHHH
Confidence 4678888999977 999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhccccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccCCCCCCccc
Q 012638 362 KMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYL 441 (459)
Q Consensus 362 d~Lrk~sr~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~~d~~~~l~ 441 (459)
++++++.+.+++|.++....+.+.+....+...+|+.|+.+++|+.+|+++..|..++..+...+|||.++.+++..++.
T Consensus 113 ~~i~~~~~~~~~p~~~~~~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~ 192 (285)
T TIGR02394 113 RAIMNQARTIRLPVHVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLL 192 (285)
T ss_pred HHHHHcCCceeCcHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCCCCCCCcchh
Confidence 99999999999999999999988888888888889999999999999999999999999888899999988766666777
Q ss_pred cCCCCCC
Q 012638 442 NIPPFFF 448 (459)
Q Consensus 442 e~i~D~~ 448 (459)
+.++++.
T Consensus 193 ~~~~~~~ 199 (285)
T TIGR02394 193 DTIADEQ 199 (285)
T ss_pred hhhcCCC
Confidence 7776553
No 28
>PRK05572 sporulation sigma factor SigF; Validated
Probab=99.91 E-value=1.3e-23 Score=205.44 Aligned_cols=164 Identities=25% Similarity=0.340 Sum_probs=146.8
Q ss_pred HHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHH
Q 012638 284 RVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISK 362 (459)
Q Consensus 284 eeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d 362 (459)
..|+..+..|+. |+++||..|.++|+++|++|.+++.+++||+|||++++|+++++||+.+|.+|.||+++||++.|.+
T Consensus 20 ~~li~~~~~gd~~a~~~L~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~ 99 (252)
T PRK05572 20 KELIKKSQDGDQEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQR 99 (252)
T ss_pred HHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHH
Confidence 445666777876 9999999999999999999999999999999999999999999999988889999999999999999
Q ss_pred HHHhhccccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccCCCCC--Ccc
Q 012638 363 MVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLN--AKY 440 (459)
Q Consensus 363 ~Lrk~sr~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~~d~~--~~l 440 (459)
++++. ..+++|..+.+...+++++...+..++|+.|+.+|||+.+|++++.|..++.....+.||+.++.+++. .++
T Consensus 100 ~lr~~-~~~r~~~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~ 178 (252)
T PRK05572 100 FLRDD-GTVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGDPITL 178 (252)
T ss_pred HHHhC-CCCCCCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCcccCCCCcchh
Confidence 99987 478999999999999999999999999999999999999999999999998888889999998865443 245
Q ss_pred ccCCCCCC
Q 012638 441 LNIPPFFF 448 (459)
Q Consensus 441 ~e~i~D~~ 448 (459)
.|.++++.
T Consensus 179 ~d~~~~~~ 186 (252)
T PRK05572 179 LDQIADQS 186 (252)
T ss_pred hhhcCCCc
Confidence 56665543
No 29
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=99.90 E-value=3.7e-23 Score=200.68 Aligned_cols=138 Identities=20% Similarity=0.223 Sum_probs=123.6
Q ss_pred HHHHHHHHhHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccc
Q 012638 296 CREELIKSTRPLVLFLARNYRG---LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIK 372 (459)
Q Consensus 296 Are~LI~~nlrLV~sIAkry~g---~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~ir 372 (459)
....|+..|+|+|+++|++|.. .+.+.+||+|||++|||+|+++||+.+| +|+||++|||+|+|.+++++.. +
T Consensus 16 ~~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~il~~lr~~~---~ 91 (231)
T PRK12427 16 EEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELRELD---W 91 (231)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHHHHhcC---C
Confidence 3557899999999999999875 4679999999999999999999998666 8999999999999999999753 5
Q ss_pred cccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHh--hccCCccccccCCCCC
Q 012638 373 IPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC--LRIVGSIDQKIGDCLN 437 (459)
Q Consensus 373 lP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~--ar~~~SLD~~v~~d~~ 437 (459)
.|+.+....++++++...+.+++|+.||.+|||+.||+++++|..++.. +..++|||.+++++++
T Consensus 92 ~~r~vr~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~ 158 (231)
T PRK12427 92 RPRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALEAH 158 (231)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccCCCc
Confidence 7888999999999999999999999999999999999999999998764 4568999999876544
No 30
>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=99.90 E-value=3.7e-23 Score=198.36 Aligned_cols=145 Identities=29% Similarity=0.393 Sum_probs=129.8
Q ss_pred HHHHhHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccc
Q 012638 300 LIKSTRPLVLFLARNYRG---LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCK 376 (459)
Q Consensus 300 LI~~nlrLV~sIAkry~g---~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~ 376 (459)
|+..|.++|+.+|++|.+ ++.+++||+|||++|||+|+++|||.+|++|+||+++||+|.+++++|+.. ++|.+
T Consensus 1 L~~~~~~lv~~~a~~~~~~~~~~~~~eDl~Qe~~~~l~~a~~~fd~~~~~~f~t~~~~~i~~~~~~~lr~~~---~~p~~ 77 (224)
T TIGR02479 1 LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLD---WVPRS 77 (224)
T ss_pred CHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHHcC---ccCHH
Confidence 688999999999999986 789999999999999999999999999999999999999999999999763 68999
Q ss_pred hHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhh--ccCCccccccCCC-CCCccccCCCCC
Q 012638 377 LNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL--RIVGSIDQKIGDC-LNAKYLNIPPFF 447 (459)
Q Consensus 377 v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~a--r~~~SLD~~v~~d-~~~~l~e~i~D~ 447 (459)
+...++++.++...|...+|+.|+.+|||+.||++++.|..++..+ ..++|+|.++.++ +..++.+.++++
T Consensus 78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~ 151 (224)
T TIGR02479 78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLIDRIEDD 151 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcccCCCccchhhhhcccc
Confidence 9999999999999999999999999999999999999999998654 3568999877643 445677777643
No 31
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=99.90 E-value=9.1e-23 Score=199.67 Aligned_cols=167 Identities=25% Similarity=0.238 Sum_probs=146.8
Q ss_pred HHHHHHHHHh-chH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHH
Q 012638 283 ERVLKQHLAF-GWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (459)
Q Consensus 283 eeeL~~~l~~-G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI 360 (459)
+..|+..++. |+. |+++||..|.++|+++|++|.+++.+++||+||||+|||+++++||+.+|.+|+||+++||+|.|
T Consensus 15 ~~~li~~~~~~gd~~a~~~l~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~tyl~~~i~n~~ 94 (257)
T PRK08583 15 VNKWIAEYQENQDEEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEI 94 (257)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHH
Confidence 4557777764 665 99999999999999999999999999999999999999999999999988899999999999999
Q ss_pred HHHHHhhccccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhh--ccCCccccccCCCCC-
Q 012638 361 SKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL--RIVGSIDQKIGDCLN- 437 (459)
Q Consensus 361 ~d~Lrk~sr~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~a--r~~~SLD~~v~~d~~- 437 (459)
.++++++...+++|.++.+..+++..+...+...+++.|+.+|+|+.+|++.+.|..++... ..++|||.+++.+++
T Consensus 95 ~~~lr~~~~~~~i~r~~~~~~~~~~~~~~~~~~~~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~~~~ 174 (257)
T PRK08583 95 KRYLRDKTWSVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSDG 174 (257)
T ss_pred HHHHHhcCCCcCCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCCCCC
Confidence 99999999999999999999999999999999999999999999999999999998877654 357899999865433
Q ss_pred --CccccCCCCCCC
Q 012638 438 --AKYLNIPPFFFP 449 (459)
Q Consensus 438 --~~l~e~i~D~~~ 449 (459)
..+.+.++++..
T Consensus 175 ~~~~~~~~~~~~e~ 188 (257)
T PRK08583 175 STVTLLDIVGQQED 188 (257)
T ss_pred ccchHhhhcCCcch
Confidence 334555555543
No 32
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=99.88 E-value=6.1e-22 Score=191.57 Aligned_cols=143 Identities=29% Similarity=0.422 Sum_probs=128.6
Q ss_pred hchHHHHHHHHHhHHHHHHHHHHhh---CCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhc
Q 012638 292 FGWYCREELIKSTRPLVLFLARNYR---GLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA 368 (459)
Q Consensus 292 ~G~~Are~LI~~nlrLV~sIAkry~---g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~s 368 (459)
.|.-++++|+..|.++|+++|++|+ +++.+++||+||||+|||+++++||+.+|.+|+||+++||+|.|.+++|++.
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 4666999999999999999999997 6789999999999999999999999998999999999999999999999875
Q ss_pred cccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhh--ccCCccccccCCCCC
Q 012638 369 RGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL--RIVGSIDQKIGDCLN 437 (459)
Q Consensus 369 r~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~a--r~~~SLD~~v~~d~~ 437 (459)
+ +|..+......+.++...+.+.+++.|+.+|||+.||+++++|..++... ..++|+|.+++++++
T Consensus 85 ~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~~ 152 (236)
T PRK06986 85 W---VPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGD 152 (236)
T ss_pred C---CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccccCCCc
Confidence 3 68888888888899999999999999999999999999999999888753 356799998876554
No 33
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=99.79 E-value=8.1e-18 Score=162.71 Aligned_cols=170 Identities=22% Similarity=0.252 Sum_probs=127.6
Q ss_pred HHHHhHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHH
Q 012638 245 MSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFS 323 (459)
Q Consensus 245 L~~~i~~~~~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~E 323 (459)
|.--++..+.|.+....+ ++.|.+.. .++..|+..+..|+. |++.|+..|.++|+++|.+|.+++.+++
T Consensus 8 ~~~~~~~~~~~~~~~~~~----~~~~~~~~------~~e~~l~~~~~~gd~~a~~~l~~~y~~~l~~~a~~~~~~~~dae 77 (233)
T PRK05803 8 LLYIVKEILFLVSYVKNN----SFPQPLSE------EEERKYLELMKEGDEEARNILIERNLRLVAHIVKKFENTGEDVD 77 (233)
T ss_pred HHHHHHHHHHHHHHHHHh----cccCCCCH------HHHHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHH
Confidence 334456666766666554 44444332 124567888888877 9999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccc---cc-------------------cc---chH
Q 012638 324 DLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGI---KI-------------------PC---KLN 378 (459)
Q Consensus 324 DLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~i---rl-------------------P~---~v~ 378 (459)
|++|||++++|+++++||+.+|.+|.||+++|++|.+++++|+..+.. .+ +. ...
T Consensus 78 DlvQE~fi~l~~~~~~f~~~~~~~f~~wl~~i~rn~~id~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (233)
T PRK05803 78 DLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRNLKKTKKEVSLQDPIGVDKEGNEISLIDILGSEEDDVI 157 (233)
T ss_pred HHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHHhccccCCCccccccCCCCcCcccHHHHccCCCCCHH
Confidence 999999999999999999988889999999999999999999764321 00 00 000
Q ss_pred ------HHHHHHHHHHHHHHHHc------------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 379 ------REISKIQKARKALTNSH------------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 379 ------e~i~kI~ka~~~L~~~l------------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
+....+.++...|+... ..+.|++|||+.||||.++|+..+++++.
T Consensus 158 ~~~~~~~~~~~l~~~l~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~ 221 (233)
T PRK05803 158 EQVELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALK 221 (233)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 11223555555444332 25679999999999999999999877764
No 34
>TIGR02895 spore_sigI RNA polymerase sigma-I factor. Members of this sigma factor protein family are strictly limited to endospore-forming species in the Firmicutes lineage of bacteria, but are not universally present among such species. Sigma-I was shown to be induced by heat shock (PubMed:11157964) in Bacillus subtilis and is suggested by its phylogenetic profile to be connected to the program of sporulation (PubMed:16311624).
Probab=99.78 E-value=3.1e-18 Score=165.70 Aligned_cols=129 Identities=17% Similarity=0.276 Sum_probs=114.5
Q ss_pred HHHhchHHHHHHHHHhHHHHHHHHHHhhCCC--CCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHh
Q 012638 289 HLAFGWYCREELIKSTRPLVLFLARNYRGLG--IPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVAR 366 (459)
Q Consensus 289 ~l~~G~~Are~LI~~nlrLV~sIAkry~g~g--~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk 366 (459)
.++.|+..+++||..|.|+|.++|.+|.++. .+.+|++|+|++|||+|+++||+++|.+|.|||.++|++.|++++|+
T Consensus 3 ~~~~gd~~~e~LI~~Y~plI~~~a~~~~~~~~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~sya~~~Ir~~i~dylRk 82 (218)
T TIGR02895 3 PIQPGNEEREELIRQYKPFIAKIVSSVCGRYIDTKSDDELSIGLIAFNEAIESYDSNKGKSFLSFAKLIIKRRLIDYIRK 82 (218)
T ss_pred hhhcCChHHHHHHHHhHHHHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence 5678888899999999999999999998775 58999999999999999999999999999999999999999999998
Q ss_pred hc---cccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHH------HhCCCHHHHHH
Q 012638 367 HA---RGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAK------YTGLSLAEIRS 417 (459)
Q Consensus 367 ~s---r~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe------~LGIS~e~Vk~ 417 (459)
.. ..+++|....+....+..+..++..++++.|+.+||+. ..||+.+.+.+
T Consensus 83 ~~k~~~~v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~~~~~L~~~gi~~~dLv~ 142 (218)
T TIGR02895 83 NQKYQNLLYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILEYKKLLKQFGIEFVELVK 142 (218)
T ss_pred cccccCeeeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcCCcHHHHhh
Confidence 87 45688876666677888888899999999999999997 45888877653
No 35
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=99.76 E-value=3.7e-17 Score=157.66 Aligned_cols=142 Identities=24% Similarity=0.356 Sum_probs=115.0
Q ss_pred HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHH
Q 012638 283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS 361 (459)
Q Consensus 283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~ 361 (459)
+..|+..++.|+. |++.|+..|.++|+++|.+|.++..+++|++||+|+++|+++++|++.++.+|.||+++|++|.|+
T Consensus 35 ~~~li~~~~~gd~~af~~l~~~y~~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~~ 114 (227)
T TIGR02846 35 EKKYLDRLKEGDEEARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEIL 114 (227)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHHH
Confidence 5678888999987 999999999999999999999999999999999999999999999998888899999999999999
Q ss_pred HHHHhhccccc-c---------------------cc---c------hHHHHHHHHHHHHHHHHHc------------CCC
Q 012638 362 KMVARHARGIK-I---------------------PC---K------LNREISKIQKARKALTNSH------------GKY 398 (459)
Q Consensus 362 d~Lrk~sr~ir-l---------------------P~---~------v~e~i~kI~ka~~~L~~~l------------gr~ 398 (459)
+++|+..+..+ . +. . ..+....|.+++..|+... ..+
T Consensus 115 d~~Rk~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~il~l~y~~~~~e~ 194 (227)
T TIGR02846 115 MHLRALKKTKGEVSLQDPIGVDKEGNEISLIDILGSDGDSVIEQVELNLEIKKLYKKLSVLDGREREVIEMRYGLGDGRR 194 (227)
T ss_pred HHHHHHhccccceeccccccCCcccCcccHHHHhcCCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHcCCCCCC
Confidence 99997654211 0 00 0 0012233555555554432 156
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 399 PEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 399 PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
.|++|||+.||+|+++|+..+++++.
T Consensus 195 ~S~~EIAe~lgis~~tV~~~~~rAl~ 220 (227)
T TIGR02846 195 KTQREIAKILGISRSYVSRIEKRALM 220 (227)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 79999999999999999999887764
No 36
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=99.75 E-value=1.5e-17 Score=160.35 Aligned_cols=143 Identities=24% Similarity=0.392 Sum_probs=116.3
Q ss_pred CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHH
Q 012638 282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (459)
Q Consensus 282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI 360 (459)
.+..|+..++.|+. |++.|+..|.++|+.+|++|.+++.+++|++||+|+++|+++++|++..+++|.||++++++|.+
T Consensus 38 ~~~~L~~~~~~gd~~af~~l~~~y~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~ 117 (234)
T PRK08301 38 EEEYLLNKLPKGDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEI 117 (234)
T ss_pred HHHHHHHHHHccCHHHHHHHHHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHH
Confidence 36778888999987 99999999999999999999999999999999999999999999999877889999999999999
Q ss_pred HHHHHhhccccc-c----c-----------------c--ch----H---HHHHHHHHHHHHHHHHc------------CC
Q 012638 361 SKMVARHARGIK-I----P-----------------C--KL----N---REISKIQKARKALTNSH------------GK 397 (459)
Q Consensus 361 ~d~Lrk~sr~ir-l----P-----------------~--~v----~---e~i~kI~ka~~~L~~~l------------gr 397 (459)
++++|++.+... . + . .. . .....+.++...|+... ..
T Consensus 118 ~d~lRk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~v~~L~y~l~~~e 197 (234)
T PRK08301 118 LMYLRRNNKVKAEVSFDEPLNIDWDGNELLLSDVLGTDNDIIYKDIEDEVDRKLLKKALKKLSDREKQIMELRFGLNGGE 197 (234)
T ss_pred HHHHHHHhccccccccccccccccCCCcccHHHhccCcccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCC
Confidence 999997654211 0 0 0 00 0 11223566666665442 25
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 398 YPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 398 ~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
+.|++|||+.||||+++|+..+++++.
T Consensus 198 g~s~~EIA~~lgis~~tVk~~~~rA~~ 224 (234)
T PRK08301 198 EKTQKEVADMLGISQSYISRLEKRIIK 224 (234)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 789999999999999999999888764
No 37
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=99.74 E-value=4.6e-17 Score=151.65 Aligned_cols=144 Identities=18% Similarity=0.200 Sum_probs=114.0
Q ss_pred CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 012638 281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (459)
Q Consensus 281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrna 359 (459)
|++..|+..++.|+. |++.|+..|.+.|+++|++++++..+++|++||+++++|+++.+|++..+..|.||++.+|++.
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 567888999999987 9999999999999999999999999999999999999999999999987779999999999999
Q ss_pred HHHHHHhhcccccc----------------------------ccch-------HHHHHHHHHHHHHHHHH--------cC
Q 012638 360 ISKMVARHARGIKI----------------------------PCKL-------NREISKIQKARKALTNS--------HG 396 (459)
Q Consensus 360 I~d~Lrk~sr~irl----------------------------P~~v-------~e~i~kI~ka~~~L~~~--------lg 396 (459)
+.+++++..+..+. +... .+....+.++...|... .-
T Consensus 84 ~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~~~~~ 163 (198)
T TIGR02859 84 IITAIKTATRQKHIPLNSYVSLNKPIYDEESDRTLLDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVLQSYL 163 (198)
T ss_pred HHHHHHHHHHhcccchhhhcCcccccccccccchHHHHhhccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence 98888743111100 0000 11122344555553222 23
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
.+.|++|||+.||+|+++|+.++++++.
T Consensus 164 ~~~s~~eIA~~l~~s~~tV~~~l~r~r~ 191 (198)
T TIGR02859 164 DGKSYQEIACDLNRHVKSIDNALQRVKR 191 (198)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6789999999999999999999998875
No 38
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=99.74 E-value=6.4e-17 Score=152.04 Aligned_cols=145 Identities=21% Similarity=0.254 Sum_probs=113.0
Q ss_pred CCCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHH
Q 012638 280 GVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK 358 (459)
Q Consensus 280 g~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrn 358 (459)
.++...|+..++.|+. |++.|+..|.++|+.+|++|.++..+++|++||+++++|+++.+||+.++.+|.||++.+++|
T Consensus 8 ~~~~~~l~~~~~~~d~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~~n 87 (208)
T PRK08295 8 ELEDEELVELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITR 87 (208)
T ss_pred CCChHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHH
Confidence 4567788888889987 999999999999999999999999999999999999999999999998777999999999999
Q ss_pred HHHHHHHhhcccccccc-----------------------------chH------HHHHHH-HHHHHHHHHH-------c
Q 012638 359 SISKMVARHARGIKIPC-----------------------------KLN------REISKI-QKARKALTNS-------H 395 (459)
Q Consensus 359 aI~d~Lrk~sr~irlP~-----------------------------~v~------e~i~kI-~ka~~~L~~~-------l 395 (459)
.+.+++++..+..+.+. ... +....+ ..+...|+.. .
T Consensus 88 ~~~d~~r~~~r~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~~r~vl~l~ 167 (208)
T PRK08295 88 QIITAIKTANRQKHIPLNSYVSLDKPIYDEESDRTLLDVISEAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLELY 167 (208)
T ss_pred HHHHHHHHhhhhccccccceeecCCcccCCccchhHHHHhcCcccCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence 99999985433211110 000 011111 1122222211 3
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
-.+.+++|||+.||+|+++|+.++.+++.
T Consensus 168 ~e~~s~~EIA~~lgis~~tV~~~l~rar~ 196 (208)
T PRK08295 168 LDGKSYQEIAEELNRHVKSIDNALQRVKR 196 (208)
T ss_pred HccCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 46789999999999999999999998875
No 39
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=99.73 E-value=5.7e-17 Score=150.48 Aligned_cols=143 Identities=17% Similarity=0.129 Sum_probs=117.1
Q ss_pred CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 012638 281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (459)
Q Consensus 281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrna 359 (459)
++++.|+..+..|+. |++.|+..|.++|+.+|++|.+++.+++|++||+|+++|+++.+|++. +.+|.||++.+++|.
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 567789999999987 999999999999999999999999999999999999999999999975 358999999999999
Q ss_pred HHHHHHhhccccc--ccc---------c---hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHH
Q 012638 360 ISKMVARHARGIK--IPC---------K---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRS 417 (459)
Q Consensus 360 I~d~Lrk~sr~ir--lP~---------~---v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~ 417 (459)
+.+++|++..... ++. . ..+....+.++...|+.+. -.+.+++|||+.||+|..+|+.
T Consensus 84 ~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~ 163 (186)
T PRK05602 84 CYDRLRRRREVPVEDAPDVPDPAPGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALES 163 (186)
T ss_pred HHHHHHhcCCCCcccccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHhcCCCHHHHHHHhCcCHHHHHH
Confidence 9999997754211 110 0 0122334556666555432 3578999999999999999999
Q ss_pred HHHhhcc
Q 012638 418 ASECLRI 424 (459)
Q Consensus 418 ~l~~ar~ 424 (459)
.+++++.
T Consensus 164 ~l~Rar~ 170 (186)
T PRK05602 164 LLARGRR 170 (186)
T ss_pred HHHHHHH
Confidence 9998875
No 40
>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=99.73 E-value=6.7e-17 Score=156.58 Aligned_cols=142 Identities=24% Similarity=0.385 Sum_probs=115.6
Q ss_pred HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHH
Q 012638 283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS 361 (459)
Q Consensus 283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~ 361 (459)
+..|+..+..|+. |++.|+..|.+.|+++|++|.+++.+++|++||+++++|+++++|++..+++|.||++++++|.++
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 5678888888877 999999999999999999999999999999999999999999999988777899999999999999
Q ss_pred HHHHhhccccc-cc----------------------c-----ch---HHHHHHHHHHHHHHHHHc------------CCC
Q 012638 362 KMVARHARGIK-IP----------------------C-----KL---NREISKIQKARKALTNSH------------GKY 398 (459)
Q Consensus 362 d~Lrk~sr~ir-lP----------------------~-----~v---~e~i~kI~ka~~~L~~~l------------gr~ 398 (459)
+++|++.+... .+ . .. ......+..++..|+... ..+
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 99998654211 00 0 00 011233666666665442 156
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 399 PEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 399 PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
.|++|||+.||+|+++|+..+++++.
T Consensus 199 ~s~~EIA~~Lgis~~tV~~~l~ra~~ 224 (234)
T TIGR02835 199 KTQKEVADMLGISQSYISRLEKRILK 224 (234)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 89999999999999999999887764
No 41
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=99.72 E-value=1.3e-16 Score=149.13 Aligned_cols=142 Identities=18% Similarity=0.143 Sum_probs=116.1
Q ss_pred CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 012638 281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (459)
Q Consensus 281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrna 359 (459)
++++.|+..++.|+. |++.|+..|.+.|+++|+++.++..+++|++||+|+++|+++++|++. ..|.+|++++++|.
T Consensus 11 ~~~~~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~~~~~~~~--~~f~~wl~~i~~n~ 88 (194)
T PRK12513 11 ASDEALMLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPR--ARFRTWLYQIARNL 88 (194)
T ss_pred CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CchHHHHHHHHHHH
Confidence 457788999999977 999999999999999999999999999999999999999999999974 36999999999999
Q ss_pred HHHHHHhhcccccccc------------c--------hHHHHHHHHHHHHHHHHHcC--------CCCCHHHHHHHhCCC
Q 012638 360 ISKMVARHARGIKIPC------------K--------LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLS 411 (459)
Q Consensus 360 I~d~Lrk~sr~irlP~------------~--------v~e~i~kI~ka~~~L~~~lg--------r~PT~eEIAe~LGIS 411 (459)
+++++|++.+....+. . ..+....+..+...|+.... .+.|++|||+.||||
T Consensus 89 ~~~~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis 168 (194)
T PRK12513 89 LIDHWRRHGARQAPSLDADEQLHALADDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVP 168 (194)
T ss_pred HHHHHHHhccccccccccchhhhhcCCCCCCHHHHHHHHHHHHHHHHHHHhCCHhHhhheeeehccCCCHHHHHHHHCCC
Confidence 9999998765332210 0 01122345566666655432 568999999999999
Q ss_pred HHHHHHHHHhhcc
Q 012638 412 LAEIRSASECLRI 424 (459)
Q Consensus 412 ~e~Vk~~l~~ar~ 424 (459)
+++|+..+.+++.
T Consensus 169 ~~tV~~~l~ra~~ 181 (194)
T PRK12513 169 EETVKSRLRYALQ 181 (194)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999888875
No 42
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=99.71 E-value=1.4e-16 Score=148.74 Aligned_cols=144 Identities=16% Similarity=0.122 Sum_probs=115.1
Q ss_pred CCCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCC---CCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHH
Q 012638 280 GVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLG---IPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYW 355 (459)
Q Consensus 280 g~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g---~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~w 355 (459)
.++++.|+..+..|+. |+++|+..|.++|+.+|.++.+++ .+++|++||+++++|+++++|++..+ +|.||++.+
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 4678889999999987 999999999999999999998853 57999999999999999999997544 799999999
Q ss_pred HHHHHHHHHHhhccccccc---c-------c------hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCC
Q 012638 356 IRKSISKMVARHARGIKIP---C-------K------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLS 411 (459)
Q Consensus 356 IrnaI~d~Lrk~sr~irlP---~-------~------v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS 411 (459)
++|.+++++|++.+..... . . ..+....+.++...|+... -.+.+++|||+.||+|
T Consensus 81 arn~~~d~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIAe~lgis 160 (189)
T PRK06811 81 SKYKAIDYKRKLTKNNEIDSIDEFILISEESIENEIILKENKEEILKLINDLEKLDREIFIRRYLLGEKIEEIAKKLGLT 160 (189)
T ss_pred HHHHHHHHHHHhccccccccchhhhhcccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHccCCHHHHHHHHCCC
Confidence 9999999999866432211 0 0 0112233555555554432 2678999999999999
Q ss_pred HHHHHHHHHhhcc
Q 012638 412 LAEIRSASECLRI 424 (459)
Q Consensus 412 ~e~Vk~~l~~ar~ 424 (459)
..+|+..+.+++.
T Consensus 161 ~~~V~~~l~Ra~~ 173 (189)
T PRK06811 161 RSAIDNRLSRGRK 173 (189)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999998864
No 43
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=99.71 E-value=1.4e-16 Score=149.41 Aligned_cols=142 Identities=18% Similarity=0.098 Sum_probs=114.8
Q ss_pred CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHH
Q 012638 282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (459)
Q Consensus 282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI 360 (459)
+...|+..+..|+. |+++|+..|.++|+++|.+|.++..+++|++||+++++|+++++||+.+| .|.+|++.+++|.+
T Consensus 16 ~~~~li~~~~~g~~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi~l~~~~~~~~~~~~-~~~~wl~~ia~n~~ 94 (194)
T PRK09646 16 DLDALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SALAWLLTLAHRRA 94 (194)
T ss_pred cHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCcccc-cHHHHHHHHHHHHH
Confidence 45678888899977 99999999999999999999999999999999999999999999998665 79999999999999
Q ss_pred HHHHHhhcccccc---------cc---ch------HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHH
Q 012638 361 SKMVARHARGIKI---------PC---KL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAE 414 (459)
Q Consensus 361 ~d~Lrk~sr~irl---------P~---~v------~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~ 414 (459)
++++|++.+..+. +. .. .+....+..++..|+... ..+.+++|||+.||+|+++
T Consensus 95 ~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~EIA~~Lgis~~t 174 (194)
T PRK09646 95 VDRVRSEQAASQREVRYGARNVDPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAYYGGLTYREVAERLAVPLGT 174 (194)
T ss_pred HHHHHhhccccccccccccccccccccchHHHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCChHh
Confidence 9999986532111 00 00 112233555555554432 3678999999999999999
Q ss_pred HHHHHHhhcc
Q 012638 415 IRSASECLRI 424 (459)
Q Consensus 415 Vk~~l~~ar~ 424 (459)
|+..+.+++.
T Consensus 175 Vk~~l~ra~~ 184 (194)
T PRK09646 175 VKTRMRDGLI 184 (194)
T ss_pred HHHHHHHHHH
Confidence 9999998875
No 44
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=99.69 E-value=4.6e-16 Score=144.80 Aligned_cols=141 Identities=18% Similarity=0.193 Sum_probs=112.1
Q ss_pred HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCC----CCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHH
Q 012638 283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGL----GIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIR 357 (459)
Q Consensus 283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~----g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIr 357 (459)
...|+..+..|+. |+++|+..|.+.|+.+|.++.++ ..+++|++||+++++|+++.+|+.. +..|.||++.+++
T Consensus 11 ~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~~~~wl~~i~~ 89 (189)
T PRK09648 11 LDALVAEAVAGDRRALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITALPRYRDQ-GRPFLAFVYGIAA 89 (189)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHHHHHHhcc-CCcHHHHHHHHHH
Confidence 3567888899977 99999999999999999998765 4689999999999999999999864 4589999999999
Q ss_pred HHHHHHHHhhcccccccc-----------ch------HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCH
Q 012638 358 KSISKMVARHARGIKIPC-----------KL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSL 412 (459)
Q Consensus 358 naI~d~Lrk~sr~irlP~-----------~v------~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~ 412 (459)
|.+++++|++.+....+. .. .+....+.+++..|+... ..+.+++|||+.||+|+
T Consensus 90 n~~~d~~r~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~ 169 (189)
T PRK09648 90 HKVADAHRAAGRDKAVPTEEVPERPSDDAGPEERALRSESSNRMRELLDTLPEKQREILILRVVVGLSAEETAEAVGSTP 169 (189)
T ss_pred HHHHHHHHHhCCCccccccccccccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCH
Confidence 999999998765322110 00 112233555555555432 35789999999999999
Q ss_pred HHHHHHHHhhcc
Q 012638 413 AEIRSASECLRI 424 (459)
Q Consensus 413 e~Vk~~l~~ar~ 424 (459)
++|+..+.+++.
T Consensus 170 ~tV~~~l~Ra~~ 181 (189)
T PRK09648 170 GAVRVAQHRALA 181 (189)
T ss_pred HHHHHHHHHHHH
Confidence 999999988764
No 45
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=99.69 E-value=3.6e-16 Score=144.72 Aligned_cols=143 Identities=21% Similarity=0.188 Sum_probs=114.8
Q ss_pred CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 012638 281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (459)
Q Consensus 281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrna 359 (459)
+++.+|+..++.|+. |++.|+..|.+.|+.+|++|.+++.+++|++||+++++|+++++|++.. ..|.+|++++++|.
T Consensus 8 ~~~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~-~~~~~wl~~ia~n~ 86 (186)
T PRK13919 8 LSDEALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRR-GSARAWLLALAHHA 86 (186)
T ss_pred cCHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCccc-cchHHHHHHHHHHH
Confidence 457788888889987 9999999999999999999999999999999999999999999998754 36999999999999
Q ss_pred HHHHHHhhccccc-c------c------cc--h---HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHH
Q 012638 360 ISKMVARHARGIK-I------P------CK--L---NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLA 413 (459)
Q Consensus 360 I~d~Lrk~sr~ir-l------P------~~--v---~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e 413 (459)
+++++|++.+... + + .. . ......+.++...|+... -.+.+++|||+.||||++
T Consensus 87 ~~d~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~ 166 (186)
T PRK13919 87 AVDHVRRRAARPQPLEPDEREPEAFDLPGPGLDEEGHLDRTRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLG 166 (186)
T ss_pred HHHHHHhhhcccccccccccccccccCCCccccHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHH
Confidence 9999997653211 1 0 00 0 011223556666554443 367899999999999999
Q ss_pred HHHHHHHhhcc
Q 012638 414 EIRSASECLRI 424 (459)
Q Consensus 414 ~Vk~~l~~ar~ 424 (459)
+|+..+++++.
T Consensus 167 ~V~~~l~ra~~ 177 (186)
T PRK13919 167 TLKTRARRALS 177 (186)
T ss_pred HHHHHHHHHHH
Confidence 99999998875
No 46
>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=99.69 E-value=4.2e-16 Score=142.38 Aligned_cols=142 Identities=14% Similarity=0.069 Sum_probs=115.3
Q ss_pred CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 012638 281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (459)
Q Consensus 281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrna 359 (459)
|+++.|+..+..|+. |++.++..|.+.|+++|.++.++..+++|++||+++.+|+..++|++. .+|.||++.+++|.
T Consensus 1 ~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~--~~~~~wl~~i~~n~ 78 (169)
T TIGR02954 1 MNDEELVKKAKRGNKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHP--KYFNTWLTRILINE 78 (169)
T ss_pred CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCc--cccHHHHHHHHHHH
Confidence 457788888999977 999999999999999999999999999999999999999999999974 36999999999999
Q ss_pred HHHHHHhhccccccccc----------hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHh
Q 012638 360 ISKMVARHARGIKIPCK----------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASEC 421 (459)
Q Consensus 360 I~d~Lrk~sr~irlP~~----------v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ 421 (459)
+++++|+..+...++.. ..+....+..+...|+... -.+.+++|||+.||||+++|+..+.+
T Consensus 79 ~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eiA~~lgis~~tv~~~l~R 158 (169)
T TIGR02954 79 CIDLLKKKKKVIPFDPNTSIEKGECETHADSRLDLYKAIDTLNDKYQTAIILRYYHDLTIKEIAEVMNKPEGTVKTYLHR 158 (169)
T ss_pred HHHHHHhcCCcCccccccccccchhhhchHHHHHHHHHHHhCCHHHhHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 99999987654322111 0111123555555554433 36789999999999999999999998
Q ss_pred hcc
Q 012638 422 LRI 424 (459)
Q Consensus 422 ar~ 424 (459)
++.
T Consensus 159 a~~ 161 (169)
T TIGR02954 159 ALK 161 (169)
T ss_pred HHH
Confidence 875
No 47
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=99.69 E-value=3.7e-16 Score=144.01 Aligned_cols=142 Identities=15% Similarity=0.060 Sum_probs=113.7
Q ss_pred CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHH
Q 012638 282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (459)
Q Consensus 282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI 360 (459)
+...|+..+..|+. |+++|+..|.+.|+.+|.++.++..+++|++||+|+++|+++++|++.. ..|.||++.+++|.+
T Consensus 5 ~~~~li~~~~~g~~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~~-~~~~~wl~~ia~n~~ 83 (179)
T PRK12514 5 DIEKLIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSG-LSPMTWLITIARNHA 83 (179)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHH
Confidence 45677888888977 9999999999999999999999999999999999999999999998654 369999999999999
Q ss_pred HHHHHhhcccc-cc------------ccch---HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHH
Q 012638 361 SKMVARHARGI-KI------------PCKL---NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIR 416 (459)
Q Consensus 361 ~d~Lrk~sr~i-rl------------P~~v---~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk 416 (459)
++++|++.+.. .+ |... .+....+..+...|+... -.+.|++|||+.||||+++|+
T Consensus 84 ~d~~R~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tV~ 163 (179)
T PRK12514 84 IDRLRARKAVAVDIDEAHDLADPSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMR 163 (179)
T ss_pred HHHHHhcCCcccccccchhccccCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCChHHHH
Confidence 99999765421 00 0000 111233555555555433 257899999999999999999
Q ss_pred HHHHhhcc
Q 012638 417 SASECLRI 424 (459)
Q Consensus 417 ~~l~~ar~ 424 (459)
..+.+++.
T Consensus 164 ~~l~Rar~ 171 (179)
T PRK12514 164 TWLRRSLL 171 (179)
T ss_pred HHHHHHHH
Confidence 99998875
No 48
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=99.69 E-value=6.7e-16 Score=143.97 Aligned_cols=143 Identities=15% Similarity=0.111 Sum_probs=116.1
Q ss_pred CCCHHHHHHHHHh---chH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHH
Q 012638 280 GVSERVLKQHLAF---GWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYW 355 (459)
Q Consensus 280 g~deeeL~~~l~~---G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~w 355 (459)
.++++.|+..++. |+. |++.|+..|.+.|+.+|.+|.++..+++|++||+|+++|+++++|++. .+|.||++++
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 4677888888885 466 999999999999999999999999999999999999999999999963 4799999999
Q ss_pred HHHHHHHHHHhhccccccc---------c---c---hHHHHHHHHHHHHHHHHHcC--------CCCCHHHHHHHhCCCH
Q 012638 356 IRKSISKMVARHARGIKIP---------C---K---LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSL 412 (459)
Q Consensus 356 IrnaI~d~Lrk~sr~irlP---------~---~---v~e~i~kI~ka~~~L~~~lg--------r~PT~eEIAe~LGIS~ 412 (459)
++|.+++++|+..+..... . . ..+....+.++...|+.... .+.+++|||+.||||.
T Consensus 85 a~n~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~lgis~ 164 (188)
T PRK09640 85 TYNECITQYRKERRKRRLMDALSLDPLEEASEEKAPKPEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMGL 164 (188)
T ss_pred HHHHHHHHHHHhcccccCcchhhhcccccccccccccHHHHHHHHHHHHhcChhheeeeeeHHhcCCCHHHHHHHHCCCH
Confidence 9999999999754322111 0 0 11233456677777765532 4579999999999999
Q ss_pred HHHHHHHHhhcc
Q 012638 413 AEIRSASECLRI 424 (459)
Q Consensus 413 e~Vk~~l~~ar~ 424 (459)
++|+..+.+++.
T Consensus 165 ~tV~~~l~Ra~~ 176 (188)
T PRK09640 165 SATKMRYKRALD 176 (188)
T ss_pred HHHHHHHHHHHH
Confidence 999999998875
No 49
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=99.69 E-value=3.9e-16 Score=144.84 Aligned_cols=143 Identities=16% Similarity=0.095 Sum_probs=115.7
Q ss_pred CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 012638 281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (459)
Q Consensus 281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrna 359 (459)
++..+|+..+..|+. |++.|+..|.+.|+.+|.++.++..+++|++||+|+.+|+.+++|++.. ..|.||++.+++|.
T Consensus 8 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~-~~~~~wL~~iarn~ 86 (182)
T PRK12537 8 FDYEACLLACARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPAR-GSARGWIYSVTRHL 86 (182)
T ss_pred hhHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCccc-ccHHHHHHHHHHHH
Confidence 345678889999977 9999999999999999999999999999999999999999999998644 37999999999999
Q ss_pred HHHHHHhhcccccccc-----------c-----hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHH
Q 012638 360 ISKMVARHARGIKIPC-----------K-----LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEI 415 (459)
Q Consensus 360 I~d~Lrk~sr~irlP~-----------~-----v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~V 415 (459)
++++++++.+...... . ..+....+.++...|+... -.+.+++|||+.||||+++|
T Consensus 87 ~~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~~~s~~eIA~~lgis~~tV 166 (182)
T PRK12537 87 ALNVLRDTRREVVLDDDAEETAQTLHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTV 166 (182)
T ss_pred HHHHHHhccccCccccchhhhcccccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCChhhH
Confidence 9999998864322110 0 0112234555555554433 36789999999999999999
Q ss_pred HHHHHhhcc
Q 012638 416 RSASECLRI 424 (459)
Q Consensus 416 k~~l~~ar~ 424 (459)
+..+.+++.
T Consensus 167 ~~~l~ra~~ 175 (182)
T PRK12537 167 KAWIKRSLK 175 (182)
T ss_pred HHHHHHHHH
Confidence 999998875
No 50
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=99.68 E-value=3.8e-16 Score=146.72 Aligned_cols=145 Identities=17% Similarity=0.148 Sum_probs=116.9
Q ss_pred CCCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHH
Q 012638 280 GVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK 358 (459)
Q Consensus 280 g~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrn 358 (459)
.+++..|+.++..|+. |++.|+..|.+.|+.+|.++.++..+++|++||+++++|+.+.+|++.. ..|.||++.+++|
T Consensus 10 ~~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~-~~~~~wl~~ia~n 88 (196)
T PRK12524 10 DVSDEALLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGE-ARVSTWLYRVVCN 88 (196)
T ss_pred CcCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhcccccc-chHHHHHHHHHHH
Confidence 4567889999999977 9999999999999999999999999999999999999999999998533 4799999999999
Q ss_pred HHHHHHHhhccc-ccc---c------c---c---hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHH
Q 012638 359 SISKMVARHARG-IKI---P------C---K---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAE 414 (459)
Q Consensus 359 aI~d~Lrk~sr~-irl---P------~---~---v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~ 414 (459)
.+++++|++.+. ..+ + . . ..+....+.++...|+... -.+.+++|||+.||||+.+
T Consensus 89 ~~~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~L~~~~g~s~~eIA~~lgis~~t 168 (196)
T PRK12524 89 LCTDRLRRRRRASVDLDDAPEPADAAPGAEEALIEGDRMRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEA 168 (196)
T ss_pred HHHHHHHhhcCCCCCccccccccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHH
Confidence 999999975432 111 0 0 0 0112234555666555432 3678999999999999999
Q ss_pred HHHHHHhhccC
Q 012638 415 IRSASECLRIV 425 (459)
Q Consensus 415 Vk~~l~~ar~~ 425 (459)
|+..+++++..
T Consensus 169 V~~~l~Ra~~~ 179 (196)
T PRK12524 169 VESLTARGKRA 179 (196)
T ss_pred HHHHHHHHHHH
Confidence 99999998753
No 51
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=99.68 E-value=4.9e-16 Score=139.26 Aligned_cols=128 Identities=16% Similarity=0.144 Sum_probs=102.9
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccc----
Q 012638 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG---- 370 (459)
Q Consensus 295 ~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~---- 370 (459)
.|+++|+..|.++|+.+++++ +...+++|++|||++++|+++++|++..| .|.||++.+++|.+++++|++.+.
T Consensus 4 ~af~~l~~~y~~~l~~~~~~~-~~~~~aeDi~Qe~~l~l~~~~~~~~~~~~-~f~~wl~~i~~n~~ld~~rk~~~~~~~~ 81 (154)
T PRK06759 4 ATFTEAVVLYEGLIVNQIKKL-GIYQDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYILERLKKEFAVQEKC 81 (154)
T ss_pred ccHHHHHHHHHHHHHHHHHHh-CCcccHHHHHHHHHHHHHHHHHHhCccCC-chHHHHHHHHHHHHHHHHHHHHhhcccc
Confidence 489999999999999999986 56789999999999999999999998666 799999999999999999987421
Q ss_pred --cccccc---hHHHHHHHHHHHHHHHHH--------cCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 371 --IKIPCK---LNREISKIQKARKALTNS--------HGKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 371 --irlP~~---v~e~i~kI~ka~~~L~~~--------lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
...|.. ..+....+..+...|+.. +..+.|++|||+.||+|+++|+..+.+++.
T Consensus 82 ~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~ii~l~~~~~~s~~EIA~~l~is~~tV~~~~~ra~~ 148 (154)
T PRK06759 82 VCVGEYEDHFHFEDVEMKVKDFMSVLDEKEKYIIFERFFVGKTMGEIALETEMTYYQVRWIYRQALE 148 (154)
T ss_pred cccCCCcccccHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 111222 122334456666555443 246789999999999999999999988764
No 52
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=99.68 E-value=6.6e-16 Score=142.45 Aligned_cols=140 Identities=14% Similarity=0.069 Sum_probs=111.8
Q ss_pred HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHH
Q 012638 283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS 361 (459)
Q Consensus 283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~ 361 (459)
++.|+..+..|+. |+++|+..|.+.|+.+|.+|.++..+++|++||+++++|+++.+|++.. .|.||++.+++|.+.
T Consensus 5 ~~~li~~~~~gd~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~ 82 (187)
T TIGR02948 5 IKKRIKEVRKGDENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQR--KFSTWLYRIATNLTI 82 (187)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHHH
Confidence 4567888899977 9999999999999999999999999999999999999999999999865 699999999999999
Q ss_pred HHHHhhcccccccc-------------------ch------HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHh
Q 012638 362 KMVARHARGIKIPC-------------------KL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYT 408 (459)
Q Consensus 362 d~Lrk~sr~irlP~-------------------~v------~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~L 408 (459)
+++|+..+...... .. .+....+.++...|+... ..+.+++|||+.|
T Consensus 83 ~~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l 162 (187)
T TIGR02948 83 DRLRKRKPDFYLDDEVQGTDGLTMESQLAADEAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKYMEDLSLKEISEIL 162 (187)
T ss_pred HHHHhhcccccccccccCccccccccccccCcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhHHhcCCCHHHHHHHH
Confidence 99997654211000 00 011223445555544332 3568999999999
Q ss_pred CCCHHHHHHHHHhhcc
Q 012638 409 GLSLAEIRSASECLRI 424 (459)
Q Consensus 409 GIS~e~Vk~~l~~ar~ 424 (459)
|+|+++|+..+++++.
T Consensus 163 gis~~~v~~~l~Rar~ 178 (187)
T TIGR02948 163 DLPVGTVKTRIHRGRE 178 (187)
T ss_pred CCCHHHHHHHHHHHHH
Confidence 9999999999998875
No 53
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=99.68 E-value=8.3e-16 Score=140.90 Aligned_cols=143 Identities=16% Similarity=0.048 Sum_probs=116.0
Q ss_pred CCCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHH
Q 012638 280 GVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK 358 (459)
Q Consensus 280 g~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrn 358 (459)
.|++..++..+..|+. |++.|+..|.+.|+.+|+++.++..+++|++||+++++|+++++|++. .+|.+|++.+++|
T Consensus 2 ~~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~--~~~~~wl~~i~~n 79 (176)
T PRK09638 2 QMDEKELIQKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGR--SKFSTWLISIASR 79 (176)
T ss_pred CccHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHH
Confidence 4567888888999987 999999999999999999999999999999999999999999999874 4799999999999
Q ss_pred HHHHHHHhhcccccccc-------c-h-------HHHHHHHHHHHHHHHHHcC--------CCCCHHHHHHHhCCCHHHH
Q 012638 359 SISKMVARHARGIKIPC-------K-L-------NREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEI 415 (459)
Q Consensus 359 aI~d~Lrk~sr~irlP~-------~-v-------~e~i~kI~ka~~~L~~~lg--------r~PT~eEIAe~LGIS~e~V 415 (459)
.+++++|+..+...... . . ......+.++...|+.... .+.+++|||+.||+|+.+|
T Consensus 80 ~~~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l~is~~~V 159 (176)
T PRK09638 80 LYKDHLRKQKREKLRLQRAKEETLRKEKWEAAIKGAEWSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTV 159 (176)
T ss_pred HHHHHHHHhccccchhhhcccccCCccchHHHHHhhhHHHHHHHHHcCCHHHhheeeehhhcCCCHHHHHHHHCCChhHH
Confidence 99999998754322110 0 0 1122345555555555432 5679999999999999999
Q ss_pred HHHHHhhcc
Q 012638 416 RSASECLRI 424 (459)
Q Consensus 416 k~~l~~ar~ 424 (459)
+..+.+++.
T Consensus 160 ~~~l~ra~~ 168 (176)
T PRK09638 160 KSRVHHGIK 168 (176)
T ss_pred HHHHHHHHH
Confidence 999988875
No 54
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=99.67 E-value=1e-15 Score=143.60 Aligned_cols=142 Identities=16% Similarity=0.107 Sum_probs=116.9
Q ss_pred CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 012638 281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (459)
Q Consensus 281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrna 359 (459)
+++..++..+..|+. +++.|+..|.+.|+++|.++.++..+++|++||+|+.+|+++++|++. ..|.+|++.+++|.
T Consensus 12 ~~~~~l~~~~~~gd~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~--~~f~~wL~~i~rn~ 89 (192)
T PRK09643 12 RSDAELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGD--AAVSSWLHRIVVNA 89 (192)
T ss_pred cCHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCC--CccHHHHHHHHHHH
Confidence 457888899999987 999999999999999999999999999999999999999999999975 36999999999999
Q ss_pred HHHHHHhhccccccc-----------cc---hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHH
Q 012638 360 ISKMVARHARGIKIP-----------CK---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRS 417 (459)
Q Consensus 360 I~d~Lrk~sr~irlP-----------~~---v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~ 417 (459)
+++++|+..+....+ .. ..+....+..+...|+... -.+.+++|||+.||+|.++|+.
T Consensus 90 ~~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~i~~l~~~~g~s~~EIA~~lg~s~~tV~~ 169 (192)
T PRK09643 90 CLDRLRRAKARPTVPLDDVYPVAQLERDPTARVETALAVQRALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKS 169 (192)
T ss_pred HHHHHHccccCCCCCccccccccCCcccHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHH
Confidence 999999765432211 01 1122345666666665543 2668999999999999999999
Q ss_pred HHHhhcc
Q 012638 418 ASECLRI 424 (459)
Q Consensus 418 ~l~~ar~ 424 (459)
.+.+++.
T Consensus 170 rl~rar~ 176 (192)
T PRK09643 170 RCARGRA 176 (192)
T ss_pred HHHHHHH
Confidence 9998875
No 55
>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=99.67 E-value=9.3e-16 Score=139.14 Aligned_cols=137 Identities=15% Similarity=0.067 Sum_probs=109.2
Q ss_pred HHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHH
Q 012638 287 KQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVA 365 (459)
Q Consensus 287 ~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lr 365 (459)
+..+.+|+. |++.|+..|.+.|++++.++.++..+++|++||+++++|+++++|+...+ .|.+|++.+++|.+++++|
T Consensus 2 i~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~~R 80 (170)
T TIGR02952 2 LERAQDREEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVNDYFR 80 (170)
T ss_pred hHHHHccCHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHHHHH
Confidence 456777876 99999999999999999999998899999999999999999999997544 8999999999999999999
Q ss_pred hhcccccccc-----------ch------HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHH
Q 012638 366 RHARGIKIPC-----------KL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASE 420 (459)
Q Consensus 366 k~sr~irlP~-----------~v------~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~ 420 (459)
++.+....+. .. .+....+.++...|+... -.+.+++|||+.||||+++|+..+.
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~eIA~~l~is~~tv~~~l~ 160 (170)
T TIGR02952 81 GSKRHPLFSLDVFKELLSNEPNPEEAILKEEANEKLLKALKILTPKQQHVIALRFGQNLPIAEVARILGKTEGAVKILQF 160 (170)
T ss_pred hcCCCCCCcHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 7654322110 00 112233455555554432 3678999999999999999999999
Q ss_pred hhcc
Q 012638 421 CLRI 424 (459)
Q Consensus 421 ~ar~ 424 (459)
+++.
T Consensus 161 ra~~ 164 (170)
T TIGR02952 161 RAIK 164 (170)
T ss_pred HHHH
Confidence 8864
No 56
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=99.67 E-value=9.3e-16 Score=141.44 Aligned_cols=142 Identities=15% Similarity=0.086 Sum_probs=113.6
Q ss_pred CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 012638 281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (459)
Q Consensus 281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrna 359 (459)
...+.|+..++.|+. |++.++..|.++|+++|+++.++..+++|++||++++||+++.+|++.. +|.||++.+++|.
T Consensus 3 ~~~~~li~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn~ 80 (187)
T PRK09641 3 LLIKRLIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATNL 80 (187)
T ss_pred hHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHHH
Confidence 345678888999987 9999999999999999999999999999999999999999999999853 7999999999999
Q ss_pred HHHHHHhhcccccc----------------ccc---h------HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHH
Q 012638 360 ISKMVARHARGIKI----------------PCK---L------NREISKIQKARKALTNSH--------GKYPEDIEIAK 406 (459)
Q Consensus 360 I~d~Lrk~sr~irl----------------P~~---v------~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe 406 (459)
+++++|++.+.... +.. . .+....+.++...|+... -.+.+++|||+
T Consensus 81 ~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~~~~~s~~eIA~ 160 (187)
T PRK09641 81 TIDRLRKRKPDYYLDAEVAGTEGLTMYSQLAADDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISE 160 (187)
T ss_pred HHHHHHhcCccccccccccCCcchhhhcccccCcCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHhhCCCHHHHHH
Confidence 99999987542211 000 0 111123555555554432 25689999999
Q ss_pred HhCCCHHHHHHHHHhhcc
Q 012638 407 YTGLSLAEIRSASECLRI 424 (459)
Q Consensus 407 ~LGIS~e~Vk~~l~~ar~ 424 (459)
.||||+++|+..+++++.
T Consensus 161 ~lgis~~~v~~~l~Rar~ 178 (187)
T PRK09641 161 ILDLPVGTVKTRIHRGRE 178 (187)
T ss_pred HHCCCHHHHHHHHHHHHH
Confidence 999999999999998875
No 57
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=99.67 E-value=7.9e-16 Score=144.32 Aligned_cols=141 Identities=14% Similarity=0.050 Sum_probs=112.3
Q ss_pred HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHH
Q 012638 283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS 361 (459)
Q Consensus 283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~ 361 (459)
...|+..+..|+. |++.|+..|.+.|+.+|.++.++..+++|++||+++.+|+...+|++.++ .|.||++.+++|.++
T Consensus 14 ~~~li~~~~~~d~~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l~l~~~~~~~~~~~~-~~~~wL~~iarn~~l 92 (194)
T PRK12531 14 WLECMEKVKSRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYTIIRNLCF 92 (194)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-hHHHHHHHHHHHHHH
Confidence 3467888899987 99999999999999999999999999999999999999999999997544 799999999999999
Q ss_pred HHHHhhccccc-c------cc---------c-hH---HHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHH
Q 012638 362 KMVARHARGIK-I------PC---------K-LN---REISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLA 413 (459)
Q Consensus 362 d~Lrk~sr~ir-l------P~---------~-v~---e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e 413 (459)
+++|+..+... . +. . .. .....+.++...|+... -.+.+++|||+.||||++
T Consensus 93 d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~l~~~l~~Lp~~~r~v~~l~~~eg~s~~EIA~~lgis~~ 172 (194)
T PRK12531 93 DLLRKQKGKDLHIHADDIWPSDYYPPDLVDHYSPEQDMLKEQVMKFLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLG 172 (194)
T ss_pred HHHHHhcccccccchhhcccccccccccccccCHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCcCHH
Confidence 99998653211 0 00 0 00 11133455555554432 257899999999999999
Q ss_pred HHHHHHHhhcc
Q 012638 414 EIRSASECLRI 424 (459)
Q Consensus 414 ~Vk~~l~~ar~ 424 (459)
+|+..+++++.
T Consensus 173 tVk~rl~ra~~ 183 (194)
T PRK12531 173 TVKSRLRLAVE 183 (194)
T ss_pred HHHHHHHHHHH
Confidence 99999998875
No 58
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=99.66 E-value=9.7e-16 Score=142.17 Aligned_cols=141 Identities=16% Similarity=0.041 Sum_probs=113.7
Q ss_pred HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHH
Q 012638 283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS 361 (459)
Q Consensus 283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~ 361 (459)
...+...+..|+. +++.|+..|.++|+.+|+++.++..+++|++||+|+++|+++++|++.++ .|.||++.+++|.++
T Consensus 12 ~~~l~~~~~~~~~~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~~n~~~ 90 (187)
T PRK12534 12 TGRLLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIARNKAI 90 (187)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHH
Confidence 4567777778876 99999999999999999999999999999999999999999999998654 689999999999999
Q ss_pred HHHHhhccccc------cc---------cc---hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHH
Q 012638 362 KMVARHARGIK------IP---------CK---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEI 415 (459)
Q Consensus 362 d~Lrk~sr~ir------lP---------~~---v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~V 415 (459)
+++|++.+... .+ .. ..+....+..+...|+... -.+.+++|||+.||||+++|
T Consensus 91 d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~~v 170 (187)
T PRK12534 91 DHLRANAPQRRNVALDDAGELRAADASPLERTERASTRRRIDHCLAELEPPRSELIRTAFFEGITYEELAARTDTPIGTV 170 (187)
T ss_pred HHHHhcccccccccccchhhhccccCChhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCChhHH
Confidence 99997643210 11 00 1122345666666664432 36789999999999999999
Q ss_pred HHHHHhhcc
Q 012638 416 RSASECLRI 424 (459)
Q Consensus 416 k~~l~~ar~ 424 (459)
+..+++++.
T Consensus 171 ~~~l~Rar~ 179 (187)
T PRK12534 171 KSWIRRGLA 179 (187)
T ss_pred HHHHHHHHH
Confidence 999998875
No 59
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=99.66 E-value=1.5e-15 Score=147.87 Aligned_cols=143 Identities=18% Similarity=0.129 Sum_probs=115.2
Q ss_pred CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 012638 281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (459)
Q Consensus 281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrna 359 (459)
.++..|+..++.|+. |++.|+..|.+.|+.+++++.++..+++|++||+|+++|+++++|++..+ .|.+|++.+++|.
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 356778888899987 99999999999999999999999999999999999999999999986544 7999999999999
Q ss_pred HHHHHHhhccccc--c-------ccc-----hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHH
Q 012638 360 ISKMVARHARGIK--I-------PCK-----LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRS 417 (459)
Q Consensus 360 I~d~Lrk~sr~ir--l-------P~~-----v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~ 417 (459)
+++++|++.+... . |.. ..+....+..+...|+... -.+.+++|||+.||+|+++|+.
T Consensus 127 ~id~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~L~~Lp~~~R~v~~L~~~eg~s~~EIA~~Lgis~~tVk~ 206 (233)
T PRK12538 127 CIDLRRKPRTENVDAVPEVADGKPDAVSVIERNELSDLLEAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVES 206 (233)
T ss_pred HHHHHHhhcccccccccccccCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHhcCCCHHHHHHHHCcCHHHHHH
Confidence 9999997642211 1 110 0112234566666665543 2668999999999999999999
Q ss_pred HHHhhcc
Q 012638 418 ASECLRI 424 (459)
Q Consensus 418 ~l~~ar~ 424 (459)
.+++++.
T Consensus 207 ~l~RAr~ 213 (233)
T PRK12538 207 LLKRGRQ 213 (233)
T ss_pred HHHHHHH
Confidence 9998875
No 60
>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=99.65 E-value=2.7e-15 Score=138.66 Aligned_cols=142 Identities=15% Similarity=0.080 Sum_probs=113.4
Q ss_pred CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 012638 281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (459)
Q Consensus 281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrna 359 (459)
.++..|+..+..|+. |++.|+..|.+.|+.+|+++.++..+++|++||+++++|+++.+|++. .+|.+|++.+++|.
T Consensus 5 ~~d~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~--~~~~~wl~~iarn~ 82 (190)
T TIGR02939 5 ELDLELVERVQRGEKQAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGD--SAFYTWLYRIAVNT 82 (190)
T ss_pred ccHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCC--CccHhHHHHHHHHH
Confidence 346678888999987 999999999999999999999999999999999999999999999975 36999999999999
Q ss_pred HHHHHHhhccccccc----------------------cc---hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHH
Q 012638 360 ISKMVARHARGIKIP----------------------CK---LNREISKIQKARKALTNSH--------GKYPEDIEIAK 406 (459)
Q Consensus 360 I~d~Lrk~sr~irlP----------------------~~---v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe 406 (459)
++++++++.+..... .. ..+....+..+...|+... -.+.+++|||+
T Consensus 83 ~~~~~r~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~EIA~ 162 (190)
T TIGR02939 83 AKNHLVAQGRRPPTSDVEIEDAEHFEGADRLREIDTPERLLLSRELEQTVMRAVEALPEDLRTAITLRELEGLSYEDIAR 162 (190)
T ss_pred HHHHHHHhccCCCcccccccchhhhcccccccccCChHHHHHHHHHHHHHHHHHHcCCHHHhhhhhhhhhcCCCHHHHHH
Confidence 999998655422110 00 0011123555555554433 25679999999
Q ss_pred HhCCCHHHHHHHHHhhcc
Q 012638 407 YTGLSLAEIRSASECLRI 424 (459)
Q Consensus 407 ~LGIS~e~Vk~~l~~ar~ 424 (459)
.|||++.+|+..+++++.
T Consensus 163 ~lgis~~tv~~~l~rar~ 180 (190)
T TIGR02939 163 IMDCPVGTVRSRIFRARE 180 (190)
T ss_pred HHCcCHHHHHHHHHHHHH
Confidence 999999999999998875
No 61
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=99.65 E-value=1.9e-15 Score=140.98 Aligned_cols=141 Identities=21% Similarity=0.192 Sum_probs=112.3
Q ss_pred CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHH
Q 012638 282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (459)
Q Consensus 282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI 360 (459)
+..+|+..+..|+. |++.|+..|.+.|+.+|+++.++..+++|++||+++++|+. ..|++..+ .|.||++++++|.+
T Consensus 15 ~~~~l~~~~~~gd~~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn~~ 92 (194)
T PRK12519 15 SDAELFSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRSRA 92 (194)
T ss_pred cHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHHHH
Confidence 46778888899987 99999999999999999999999999999999999999976 67887554 79999999999999
Q ss_pred HHHHHhhcccccc------------cc-c------hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHH
Q 012638 361 SKMVARHARGIKI------------PC-K------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLA 413 (459)
Q Consensus 361 ~d~Lrk~sr~irl------------P~-~------v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e 413 (459)
++++|++.+.... +. . ..+....+..+...|+... -.+.+++|||+.||+|+.
T Consensus 93 ~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~~~g~s~~EIA~~lgis~~ 172 (194)
T PRK12519 93 IDRLRSRRSRQRLLERWQQELLGEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLG 172 (194)
T ss_pred HHHHHhcccccchhhhhhhhhcccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhhhcCCCHHHHHHHhCCCHH
Confidence 9999976542111 00 0 0111234555555555443 256899999999999999
Q ss_pred HHHHHHHhhcc
Q 012638 414 EIRSASECLRI 424 (459)
Q Consensus 414 ~Vk~~l~~ar~ 424 (459)
+|+..+.+++.
T Consensus 173 tV~~~l~Ra~~ 183 (194)
T PRK12519 173 TVKARARQGLL 183 (194)
T ss_pred HHHHHHHHHHH
Confidence 99999888764
No 62
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=99.64 E-value=3.4e-15 Score=138.39 Aligned_cols=140 Identities=15% Similarity=0.067 Sum_probs=111.5
Q ss_pred HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhC-CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHH
Q 012638 283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRG-LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (459)
Q Consensus 283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g-~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI 360 (459)
...++..+..|+. |+++|+..|.+.|+.+|.++.+ ...+++|++||+++++|+.++.|++. ..|.+|++.+++|.+
T Consensus 8 ~~~~~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~--~~~~~wl~~iarN~~ 85 (181)
T PRK12536 8 LRALLLRGLAGDAAAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRAD--QPLTAWVHAIARYKL 85 (181)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCC--CchHHHHHHHHHHHH
Confidence 4567788888877 9999999999999999988764 57899999999999999999999974 469999999999999
Q ss_pred HHHHHhhccccccc--------------cchHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHH
Q 012638 361 SKMVARHARGIKIP--------------CKLNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSA 418 (459)
Q Consensus 361 ~d~Lrk~sr~irlP--------------~~v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~ 418 (459)
++++|++.+..... ....+....+.++...|+... -.+.+++|||+.||||+++|+..
T Consensus 86 ~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tV~~~ 165 (181)
T PRK12536 86 MDFLRSRARREALHDPLDDESELFATSDDEAAEARRDLGKLLEQLPDRQRLPIVHVKLEGLSVAETAQLTGLSESAVKVG 165 (181)
T ss_pred HHHHHHHhccccccCCccchhhhcCCCCcchHHHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHH
Confidence 99999864422110 011223334566666554432 25689999999999999999999
Q ss_pred HHhhcc
Q 012638 419 SECLRI 424 (459)
Q Consensus 419 l~~ar~ 424 (459)
+++++.
T Consensus 166 l~rar~ 171 (181)
T PRK12536 166 IHRGLK 171 (181)
T ss_pred HHHHHH
Confidence 998875
No 63
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=99.64 E-value=2.7e-15 Score=142.41 Aligned_cols=140 Identities=14% Similarity=0.073 Sum_probs=110.7
Q ss_pred HHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHH
Q 012638 284 RVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISK 362 (459)
Q Consensus 284 eeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d 362 (459)
..|...+..|+. |+++|+..|.+.|+.++.++.++..+++|++||+|+++|+++.+|++.++ .|.||++++++|.+++
T Consensus 26 ~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wl~~I~rn~~~d 104 (206)
T PRK12526 26 QWLILVAISRDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYTVMRNAAFD 104 (206)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCccc-chhHHHHHHHHHHHHH
Confidence 345666787877 99999999999999999999999999999999999999999999997665 6999999999999999
Q ss_pred HHHhhcccccc-------cc-------c-h-HH-----HHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHH
Q 012638 363 MVARHARGIKI-------PC-------K-L-NR-----EISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLA 413 (459)
Q Consensus 363 ~Lrk~sr~irl-------P~-------~-v-~e-----~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e 413 (459)
++|++.+.... |. . . .+ ....+.++...|+.+. ..+.|++|||+.||+|++
T Consensus 105 ~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~EIA~~lgis~~ 184 (206)
T PRK12526 105 MLRKIKAKKEQNLGDDIWPIEQALAESQSESEEFSDHLMDKQILSYIEKLPEAQQTVVKGVYFQELSQEQLAQQLNVPLG 184 (206)
T ss_pred HHHHhccccccccccccchhhhhcccccCchHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHH
Confidence 99976532110 10 0 0 00 1123455555554432 367899999999999999
Q ss_pred HHHHHHHhhcc
Q 012638 414 EIRSASECLRI 424 (459)
Q Consensus 414 ~Vk~~l~~ar~ 424 (459)
+|+..+++++.
T Consensus 185 tV~~~l~Ra~~ 195 (206)
T PRK12526 185 TVKSRLRLALA 195 (206)
T ss_pred HHHHHHHHHHH
Confidence 99999998875
No 64
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=99.64 E-value=4.1e-15 Score=143.69 Aligned_cols=142 Identities=16% Similarity=0.130 Sum_probs=115.8
Q ss_pred CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 012638 281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (459)
Q Consensus 281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrna 359 (459)
+++..|+..+..|+. |++.|+..|.+.|+.+|+++.+...+++|++||+|+++|+++++|++. ..|.||++++++|.
T Consensus 15 ~~~~~l~~~~~~gd~~a~~~l~~~y~~~l~~~a~~~~~~~~~AEDlvQE~fi~l~~~~~~~~~~--~~~~~wL~~iarn~ 92 (231)
T PRK11922 15 ASDRELVARVLAGDEAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGD--ASLSTWLSRIVLNE 92 (231)
T ss_pred ccHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHhcCCC--chhHHHHHHHHHHH
Confidence 456778888888977 999999999999999999999999999999999999999999999985 47999999999999
Q ss_pred HHHHHHhhcccccccc------------------c--------hHHHHHHHHHHHHHHHHHcC--------CCCCHHHHH
Q 012638 360 ISKMVARHARGIKIPC------------------K--------LNREISKIQKARKALTNSHG--------KYPEDIEIA 405 (459)
Q Consensus 360 I~d~Lrk~sr~irlP~------------------~--------v~e~i~kI~ka~~~L~~~lg--------r~PT~eEIA 405 (459)
+++++|+..+...++. + ..+....+.+++..|+.... .+.+++|||
T Consensus 93 ~~d~~Rk~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA 172 (231)
T PRK11922 93 ALGRLRRRRRLVNLAEMVMASTIAGGERTPLADPAEDPERAAARREIRALLERAIDALPDAFRAVFVLRVVEELSVEETA 172 (231)
T ss_pred HHHHHHhhcccccchhcccccccccccccccCcccCChHHHHHHHHHHHHHHHHHHhCCHHHhhhheeehhcCCCHHHHH
Confidence 9999997654322210 0 01122345666666655432 568999999
Q ss_pred HHhCCCHHHHHHHHHhhcc
Q 012638 406 KYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 406 e~LGIS~e~Vk~~l~~ar~ 424 (459)
+.||+|.++|+..+++++.
T Consensus 173 e~lgis~~tVk~~l~Rar~ 191 (231)
T PRK11922 173 QALGLPEETVKTRLHRARR 191 (231)
T ss_pred HHHCcCHHHHHHHHHHHHH
Confidence 9999999999999988864
No 65
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=99.64 E-value=4.3e-15 Score=138.52 Aligned_cols=141 Identities=12% Similarity=0.063 Sum_probs=111.8
Q ss_pred CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHH
Q 012638 282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (459)
Q Consensus 282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI 360 (459)
+++.|+..++.|+. |++.|+..|.+.|+.+++++.++..+++|++||+++++|+++.+|++.. .|.+|++.+++|.+
T Consensus 6 ~~~~ll~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~l~~~~~~~~~~~--~~~~wl~~ia~n~~ 83 (193)
T PRK11923 6 EDQQLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDS--AFYTWLYRIAINTA 83 (193)
T ss_pred cHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHhCcCCCC--ccHhHHHHHHHHHH
Confidence 35677888899977 9999999999999999999999999999999999999999999999864 59999999999999
Q ss_pred HHHHHhhccccc---ccc-------------c---------hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHH
Q 012638 361 SKMVARHARGIK---IPC-------------K---------LNREISKIQKARKALTNSH--------GKYPEDIEIAKY 407 (459)
Q Consensus 361 ~d~Lrk~sr~ir---lP~-------------~---------v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~ 407 (459)
+++++++.+... .+. . ..+....+.++...|+... -.+.+++|||+.
T Consensus 84 ~d~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~ 163 (193)
T PRK11923 84 KNHLVSRGRRPPDSDVSSEDAEFYDGDHALKDIESPERALLRDEIEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASV 163 (193)
T ss_pred HHHHHHhcCCCccccccccchhhhcccccccCcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHHhhHHhcCCCHHHHHHH
Confidence 999987544321 000 0 0011123444555444432 256799999999
Q ss_pred hCCCHHHHHHHHHhhcc
Q 012638 408 TGLSLAEIRSASECLRI 424 (459)
Q Consensus 408 LGIS~e~Vk~~l~~ar~ 424 (459)
||+|+.+|+..+.+++.
T Consensus 164 lgis~~tv~~~l~Rar~ 180 (193)
T PRK11923 164 MQCPVGTVRSRIFRARE 180 (193)
T ss_pred HCCCHHHHHHHHHHHHH
Confidence 99999999999988875
No 66
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=99.64 E-value=2e-15 Score=137.43 Aligned_cols=134 Identities=17% Similarity=0.118 Sum_probs=106.1
Q ss_pred HHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhh
Q 012638 289 HLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARH 367 (459)
Q Consensus 289 ~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~ 367 (459)
+++.|+. |+++|+..|.++|+.++++|.+++.+.+|++||++++||+++++|+ .+.+|.||++.++++.+.+++++.
T Consensus 3 ~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~r~~ 80 (182)
T PRK09652 3 RVQRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR--GGAAFYTWLYRIARNTAINYLRKQ 80 (182)
T ss_pred hhhcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHHHHHHHHcc
Confidence 4677876 9999999999999999999999999999999999999999999999 345899999999999999999976
Q ss_pred ccccccc-------c---------c---h------HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHH
Q 012638 368 ARGIKIP-------C---------K---L------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAE 414 (459)
Q Consensus 368 sr~irlP-------~---------~---v------~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~ 414 (459)
.+....+ . . . .+....+..+...|+... ..+.+++|||+.||||+.+
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~t 160 (182)
T PRK09652 81 GRRPPASDVDAEEAEDFDLADALRDISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGT 160 (182)
T ss_pred cCCCCccccccccccccccccccccccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHH
Confidence 5433211 0 0 0 012233444444443332 3678999999999999999
Q ss_pred HHHHHHhhcc
Q 012638 415 IRSASECLRI 424 (459)
Q Consensus 415 Vk~~l~~ar~ 424 (459)
|+..+.+++.
T Consensus 161 V~~~l~ra~~ 170 (182)
T PRK09652 161 VRSRIFRARE 170 (182)
T ss_pred HHHHHHHHHH
Confidence 9999887764
No 67
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=99.64 E-value=4.3e-15 Score=138.08 Aligned_cols=140 Identities=11% Similarity=0.051 Sum_probs=112.3
Q ss_pred HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHH----HhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHH
Q 012638 283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLAR----NYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIR 357 (459)
Q Consensus 283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAk----ry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIr 357 (459)
...|+..+..|+. |+++|+..|.+.|+.+|+ ++.++..+++|++||+++.+|++++.|++.. .|.+|++.+++
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 5677888889976 999999999999999987 4557889999999999999999999999753 69999999999
Q ss_pred HHHHHHHHhhccc-cccc---------c---chHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHH
Q 012638 358 KSISKMVARHARG-IKIP---------C---KLNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIR 416 (459)
Q Consensus 358 naI~d~Lrk~sr~-irlP---------~---~v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk 416 (459)
|.+++++|+..+. ...+ . ...+....+..+...|+... -.+.+++|||+.||||+++|+
T Consensus 86 n~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~ 165 (184)
T PRK12539 86 YKLIDHLRRTRASLADVPIDDADELVAHDDHAAVESTLDLGRLLARLPEKMRLAIQAVKLEGLSVAEAATRSGMSESAVK 165 (184)
T ss_pred HHHHHHHHHHhccccccChhhhccccCCcHHhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCcHHHHHHHHCcCHHHHH
Confidence 9999999986542 1111 0 01223345666666665543 257899999999999999999
Q ss_pred HHHHhhcc
Q 012638 417 SASECLRI 424 (459)
Q Consensus 417 ~~l~~ar~ 424 (459)
..+.+++.
T Consensus 166 ~~l~ra~~ 173 (184)
T PRK12539 166 VSVHRGLK 173 (184)
T ss_pred HHHHHHHH
Confidence 99998875
No 68
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=99.63 E-value=1.7e-15 Score=140.74 Aligned_cols=134 Identities=16% Similarity=0.108 Sum_probs=107.2
Q ss_pred HhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcc
Q 012638 291 AFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (459)
Q Consensus 291 ~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr 369 (459)
..|+. |+++|+..|.+.|+.+|.+++++..+++|++||+|+.+|+++++|+...+..|.||++.+++|.+++++|++.+
T Consensus 4 ~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn~~~d~~Rk~~~ 83 (185)
T PRK12542 4 TNNDYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRKNKR 83 (185)
T ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 45665 99999999999999999999999999999999999999999999986544579999999999999999998754
Q ss_pred ccccc------------cch------HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 370 GIKIP------------CKL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 370 ~irlP------------~~v------~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
..... ... .+....|.++...|+... -.+.+++|||+.||+|+++|+..+.+++
T Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tVk~~l~Rar 163 (185)
T PRK12542 84 HETFLEEYERESIEAVDENIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERAR 163 (185)
T ss_pred hhhhhhhccccchhhhhccHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 32210 000 011233555555555443 3568999999999999999999999887
Q ss_pred c
Q 012638 424 I 424 (459)
Q Consensus 424 ~ 424 (459)
.
T Consensus 164 ~ 164 (185)
T PRK12542 164 K 164 (185)
T ss_pred H
Confidence 6
No 69
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=99.63 E-value=5.1e-15 Score=137.93 Aligned_cols=143 Identities=13% Similarity=0.076 Sum_probs=115.0
Q ss_pred CCCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHH
Q 012638 280 GVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK 358 (459)
Q Consensus 280 g~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrn 358 (459)
.+++..|+..+..|+. |++.|+..|.+.|+.++.++.++..+++|++||+|+.+|++.++|++. ..|.||++.+++|
T Consensus 6 ~~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~~~~~~~--~~~~~wl~~i~~n 83 (189)
T PRK12515 6 ATTDEMLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIARF 83 (189)
T ss_pred ccCHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CChHHHHHHHHHH
Confidence 4577889999999987 999999999999999999999999999999999999999999999974 4799999999999
Q ss_pred HHHHHHHhhcccccc-------cc---ch------HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHH
Q 012638 359 SISKMVARHARGIKI-------PC---KL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAE 414 (459)
Q Consensus 359 aI~d~Lrk~sr~irl-------P~---~v------~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~ 414 (459)
.+++++++..+.... +. .. .+....+.++...|+... -.+.+++|||+.||+|+++
T Consensus 84 ~~~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~t 163 (189)
T PRK12515 84 KALSALRRRKHEEIDDEAAAAIEDGADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPEST 163 (189)
T ss_pred HHHHHHHccCCCCCccccccccCCCCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHH
Confidence 999999976432111 00 00 011223445555444432 3678999999999999999
Q ss_pred HHHHHHhhcc
Q 012638 415 IRSASECLRI 424 (459)
Q Consensus 415 Vk~~l~~ar~ 424 (459)
|+..+.+++.
T Consensus 164 V~~~l~Rar~ 173 (189)
T PRK12515 164 VKTRMFYARK 173 (189)
T ss_pred HHHHHHHHHH
Confidence 9999998875
No 70
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=99.62 E-value=5.8e-15 Score=136.14 Aligned_cols=140 Identities=16% Similarity=0.145 Sum_probs=108.9
Q ss_pred HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCC-----CHHHHHHHHHHHHHH-hhhhcCCCCCCchhhHHHHH
Q 012638 283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGI-----PFSDLLQAGNVGVLQ-GAERFDHTRGYKFSTYVQYW 355 (459)
Q Consensus 283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~-----d~EDLIQEG~IGLir-AieKFDp~kG~rFSTYa~~w 355 (459)
...|+..+..|+. |+++|+..|.+.|+.+|++|.++.. +++|++||+|+.+|+ ...+|++. ..|.||++.+
T Consensus 4 ~~~li~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~--~~~~~wl~~i 81 (183)
T TIGR02999 4 VTELLQQWQNGDAAARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR--AHFFAAAAKA 81 (183)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCCch--HHHHHHHHHH
Confidence 4567888899987 9999999999999999999999877 899999999999998 78889764 3699999999
Q ss_pred HHHHHHHHHHhhccccc------c------cc---chHHHHHHHHHHHHH---HHHHc--------CCCCCHHHHHHHhC
Q 012638 356 IRKSISKMVARHARGIK------I------PC---KLNREISKIQKARKA---LTNSH--------GKYPEDIEIAKYTG 409 (459)
Q Consensus 356 IrnaI~d~Lrk~sr~ir------l------P~---~v~e~i~kI~ka~~~---L~~~l--------gr~PT~eEIAe~LG 409 (459)
++|.+++++|++.+..+ . |. ...+....+..+... |+... ..+.|++|||+.||
T Consensus 82 ~~n~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lg 161 (183)
T TIGR02999 82 MRRILVDHARRRRAQKRGGGAVRVPLDEVLPDAEADLDEELLDLDDALDKLAQVDPRQAEVVELRFFAGLTVEEIAELLG 161 (183)
T ss_pred HHHHHHHHHHHHHHHhccCCccccccccccCCCCccHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHcCCCHHHHHHHhC
Confidence 99999999987543211 0 11 111222223333333 44332 36789999999999
Q ss_pred CCHHHHHHHHHhhcc
Q 012638 410 LSLAEIRSASECLRI 424 (459)
Q Consensus 410 IS~e~Vk~~l~~ar~ 424 (459)
||+++|+..+++++.
T Consensus 162 is~~tVk~~l~Rar~ 176 (183)
T TIGR02999 162 VSVRTVERDWRFARA 176 (183)
T ss_pred CCHHHHHHHHHHHHH
Confidence 999999999998875
No 71
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=99.62 E-value=9.8e-15 Score=135.62 Aligned_cols=135 Identities=20% Similarity=0.188 Sum_probs=110.9
Q ss_pred HHHHhch-HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHh
Q 012638 288 QHLAFGW-YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVAR 366 (459)
Q Consensus 288 ~~l~~G~-~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk 366 (459)
.....|+ .+++.++..|.+.++.+|++++++..+++||+||+|+.+|+++..| .. +..|.||++.+++|.++|++|+
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~-~~~~~~wl~~Ia~n~~iD~~R~ 84 (182)
T COG1595 7 AEALRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RG-RSSFKAWLYRIARNLAIDRLRK 84 (182)
T ss_pred HHHHhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CC-CCchHHHHHHHHHHHHHHHHHH
Confidence 3344454 4999999999999999999999998899999999999999999999 33 3479999999999999999997
Q ss_pred hcccccc-c-------------cch-----HHHHHHHHHHHHHHHHHcC--------CCCCHHHHHHHhCCCHHHHHHHH
Q 012638 367 HARGIKI-P-------------CKL-----NREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSAS 419 (459)
Q Consensus 367 ~sr~irl-P-------------~~v-----~e~i~kI~ka~~~L~~~lg--------r~PT~eEIAe~LGIS~e~Vk~~l 419 (459)
..+.... + ... .+....+.++...|+.... .+.|++|||+.||||+++|+..+
T Consensus 85 ~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~~~gls~~EIA~~l~i~~~tVks~l 164 (182)
T COG1595 85 RKRRRARVEEADLLPEEADPAPDLAELLLAEEELERLRRALARLPPRQREAFLLRYLEGLSYEEIAEILGISVGTVKSRL 164 (182)
T ss_pred hcccccccccccccccccCcccccchHHHHHHHHHHHHHHHHhCCHHHhHHhhhHhhcCCCHHHHHHHHCCCHHHHHHHH
Confidence 7654321 0 111 2444567788887777653 67899999999999999999999
Q ss_pred Hhhcc
Q 012638 420 ECLRI 424 (459)
Q Consensus 420 ~~ar~ 424 (459)
++++.
T Consensus 165 ~ra~~ 169 (182)
T COG1595 165 HRARK 169 (182)
T ss_pred HHHHH
Confidence 98875
No 72
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=99.61 E-value=7.4e-15 Score=137.11 Aligned_cols=141 Identities=18% Similarity=0.090 Sum_probs=113.1
Q ss_pred HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHH
Q 012638 283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS 361 (459)
Q Consensus 283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~ 361 (459)
...|+.++..|+. |+++|+..|.+.|+.++. +.++..+++|++||+|+.+|+..++|++. ..|.+|++.+++|.++
T Consensus 11 ~~~l~~~~~~gd~~af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~flkl~~~~~~~~~~--~~~~~Wl~~Iarn~~~ 87 (185)
T PRK09649 11 VTALALSAAKGNGRALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVA 87 (185)
T ss_pred HHHHHHHHHccCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHhccccCcc--chHHHHHHHHHHHHHH
Confidence 3567888889987 999999999999999995 67888999999999999999999999964 3799999999999999
Q ss_pred HHHHhhcccccc-----ccc---------hHHHHHHHHHHHHHHHHHcC--------CCCCHHHHHHHhCCCHHHHHHHH
Q 012638 362 KMVARHARGIKI-----PCK---------LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSAS 419 (459)
Q Consensus 362 d~Lrk~sr~irl-----P~~---------v~e~i~kI~ka~~~L~~~lg--------r~PT~eEIAe~LGIS~e~Vk~~l 419 (459)
+++|++.+.... +.. ..+....+.++...|+.... .+.|++|||+.||+|+++|+..+
T Consensus 88 d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l 167 (185)
T PRK09649 88 DHIRHVRSRPRTTRGARPEHLIDGDRHARGFEDLVEVTTMIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRV 167 (185)
T ss_pred HHHHHhccccccccccchhhccChhhhhhhHHHHHHHHHHHHhCCHHHhHHhhhHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 999975432211 110 01223446666666655542 66899999999999999999999
Q ss_pred HhhccCC
Q 012638 420 ECLRIVG 426 (459)
Q Consensus 420 ~~ar~~~ 426 (459)
.+++..+
T Consensus 168 ~Rar~~L 174 (185)
T PRK09649 168 ARARDAL 174 (185)
T ss_pred HHHHHHH
Confidence 9988643
No 73
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=99.61 E-value=9.1e-15 Score=143.46 Aligned_cols=144 Identities=12% Similarity=-0.020 Sum_probs=115.9
Q ss_pred cCCCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHH-------hhhhcCCCCCCchhh
Q 012638 279 AGVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQ-------GAERFDHTRGYKFST 350 (459)
Q Consensus 279 ~g~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLir-------AieKFDp~kG~rFST 350 (459)
++.++..|+..++.|+. |++.|+..|.+.|+.++.++.++..+++|++||+|+.+|. .+.+|++. ..|.|
T Consensus 22 ~~~~d~~Li~~~~~gd~~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~--~~~~t 99 (244)
T TIGR03001 22 LHAADLYLACACAQGEPAALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGR--GPLLS 99 (244)
T ss_pred ccccHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccchhhhhhccCCC--CchHh
Confidence 45567889999999987 9999999999999999999999999999999999999994 78889864 37999
Q ss_pred HHHHHHHHHHHHHHHhhcccccccc---------c---hH----------HHHHHHHHHHHHHHHHc--------CCCCC
Q 012638 351 YVQYWIRKSISKMVARHARGIKIPC---------K---LN----------REISKIQKARKALTNSH--------GKYPE 400 (459)
Q Consensus 351 Ya~~wIrnaI~d~Lrk~sr~irlP~---------~---v~----------e~i~kI~ka~~~L~~~l--------gr~PT 400 (459)
|++.+++|.+++++|++.+...+.. . .. +....|.+++.+|+... -.+.|
T Consensus 100 WL~~Ia~N~~id~lRk~~r~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~e~~~~l~~aL~~Lp~~~R~v~~L~~~eg~S 179 (244)
T TIGR03001 100 WVRIVATRIALELQAQERRHSPVEEPTELAALPAPGSDPELDLLRERYRQDFRQALREALAALSERERHLLRLHFVDGLS 179 (244)
T ss_pred HHHHHHHHHHHHHHHHhcccCccccccccccccCCCCCHHHHHHHHhhHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCC
Confidence 9999999999999997654222110 0 00 12234666666666543 26789
Q ss_pred HHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 401 DIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 401 ~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
++|||+.||||+++|+..+.+++.
T Consensus 180 ~~EIA~~Lgis~~TVk~rl~RAr~ 203 (244)
T TIGR03001 180 MDRIGAMYQVHRSTVSRWVAQARE 203 (244)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHH
Confidence 999999999999999999888764
No 74
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=99.60 E-value=8.9e-15 Score=131.55 Aligned_cols=128 Identities=14% Similarity=0.130 Sum_probs=103.1
Q ss_pred HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccccccc
Q 012638 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC 375 (459)
Q Consensus 296 Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~ 375 (459)
|++.++..|.+.|+.+|+++.++..++||++||+++.+|+++++|++.. .|.||++.+++|.++++++++.+......
T Consensus 2 ~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~~~~ 79 (159)
T TIGR02989 2 AFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRDRLVFD 79 (159)
T ss_pred HHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhcccccccC
Confidence 7899999999999999999999999999999999999999999999753 69999999999999999998755322100
Q ss_pred c-----------------hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhccC
Q 012638 376 K-----------------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRIV 425 (459)
Q Consensus 376 ~-----------------v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~ 425 (459)
. ..+....+.+++..|+... -.+.+++|||+.||||+++|+..+++++..
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~v~~l~~~~g~~~~eIA~~l~is~~tv~~~l~Rar~~ 154 (159)
T TIGR02989 80 DELLEALAAEAEATEADRSEDELQALEGCLEKLPERQRELLQLRYQRGVSLTALAEQLGRTVNAVYKALSRLRVR 154 (159)
T ss_pred HHHHHHHHhhcccchHhhHHHHHHHHHHHHHHCCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 0 0111223455555554432 367899999999999999999999988753
No 75
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=99.60 E-value=2.4e-14 Score=132.52 Aligned_cols=138 Identities=15% Similarity=0.090 Sum_probs=109.7
Q ss_pred HHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCC----CCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 012638 285 VLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGL----GIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (459)
Q Consensus 285 eL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~----g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrna 359 (459)
.|+..+..|+. |+++|+..|.+.|+.+|.+++++ ..+++|++||+++.+|...++|+.. ..|.+|++.+++|.
T Consensus 11 ~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~--~~~~~wl~~i~rn~ 88 (184)
T PRK12512 11 DLMRSANAGDAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWLFAIARNK 88 (184)
T ss_pred HHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCcc--ccHHHHHHHHHHHH
Confidence 46677788876 99999999999999999998762 4689999999999999999999873 47999999999999
Q ss_pred HHHHHHhhccccccc---------cc---hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHH
Q 012638 360 ISKMVARHARGIKIP---------CK---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSAS 419 (459)
Q Consensus 360 I~d~Lrk~sr~irlP---------~~---v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l 419 (459)
+.+++|++.+....+ .. .......+.++...|+... -.+.+++|||+.||+|+.+|+..+
T Consensus 89 ~~d~~Rr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l~is~~tV~~~l 168 (184)
T PRK12512 89 LIDALRRRGRRVFVDIDDFAETLPAEPATETLPAGDVGRHLETLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVRVAL 168 (184)
T ss_pred HHHHHHhhcccccCCchhccccccccchhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 999999876532221 10 1122344555666555543 257899999999999999999999
Q ss_pred Hhhcc
Q 012638 420 ECLRI 424 (459)
Q Consensus 420 ~~ar~ 424 (459)
.+++.
T Consensus 169 ~ra~~ 173 (184)
T PRK12512 169 HRGLA 173 (184)
T ss_pred HHHHH
Confidence 98875
No 76
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=99.58 E-value=3.8e-14 Score=128.70 Aligned_cols=137 Identities=20% Similarity=0.167 Sum_probs=108.6
Q ss_pred HHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHH
Q 012638 286 LKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMV 364 (459)
Q Consensus 286 L~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~L 364 (459)
|...+..|+. |++.++..|.+.|+++|+++.++..+++|++||++++||.++++|+ .+.+|.+|++.++++.+++++
T Consensus 3 ~~~~~~~~~~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~~~d~~ 80 (179)
T PRK11924 3 LMPVDATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNVCYDLL 80 (179)
T ss_pred HHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHHHHHHH
Confidence 5667788876 9999999999999999999999999999999999999999999998 345899999999999999999
Q ss_pred Hhhcccccccc-------------c------hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHH
Q 012638 365 ARHARGIKIPC-------------K------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRS 417 (459)
Q Consensus 365 rk~sr~irlP~-------------~------v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~ 417 (459)
++..+...... . ..+....+.++...|+... ..+.+++|||+.||||..+|+.
T Consensus 81 r~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~~~~~~eIA~~lgis~~tv~~ 160 (179)
T PRK11924 81 RRRRREKAVLSDDALEPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKS 160 (179)
T ss_pred HhcccccccCcccccccccCCccCCHHHHHhhHHHHHHHHHHHHhCCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHH
Confidence 97654332110 0 0112233444444443332 3578999999999999999999
Q ss_pred HHHhhcc
Q 012638 418 ASECLRI 424 (459)
Q Consensus 418 ~l~~ar~ 424 (459)
.+.+++.
T Consensus 161 ~~~ra~~ 167 (179)
T PRK11924 161 RLRRARQ 167 (179)
T ss_pred HHHHHHH
Confidence 9888764
No 77
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=99.58 E-value=2.6e-14 Score=131.22 Aligned_cols=127 Identities=10% Similarity=0.101 Sum_probs=102.9
Q ss_pred HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccc-
Q 012638 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP- 374 (459)
Q Consensus 296 Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP- 374 (459)
.+++|+..|.++|+.+|++|.++..+++|++||+++.+|+++++|++.. +|.+|++.+++|.+++++|++.+....+
T Consensus 4 ~~~~l~~~y~~~i~~~~~~~~~~~~daeDvvQe~~i~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~Rk~~~~~~~~~ 81 (173)
T PRK12522 4 KVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVE--NYKKWITTICVRTFYDFYRKKKRWKDRIL 81 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcCCcc--chHHHHHHHHHHHHHHHHHHhcccccccc
Confidence 6899999999999999999999999999999999999999999999753 7999999999999999999765432110
Q ss_pred --------------c--ch------HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 375 --------------C--KL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 375 --------------~--~v------~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
. .. .+....+.++...|+... -.+.+++|||+.||||+++|+..+.+++.
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~~~s~~EIA~~lgis~~tV~~~l~Ra~~ 161 (173)
T PRK12522 82 DLFHKEDGGEIEFADDVNISEEFIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKK 161 (173)
T ss_pred cccchhhhhhhccccCCCChHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 0 00 112234555555555533 36789999999999999999999998875
No 78
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=99.57 E-value=1.8e-14 Score=134.41 Aligned_cols=127 Identities=17% Similarity=0.128 Sum_probs=103.2
Q ss_pred HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccccccc
Q 012638 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC 375 (459)
Q Consensus 296 Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~ 375 (459)
+|+.|+..|.+.|+.+|.+++++..+++|++||.|+.+|+.+++|++. .+|.||++.+++|.+++++|++.+....+.
T Consensus 3 ~~~~l~~~~~~~l~~~a~~~~~~~~~AeDivQevfl~~~~~~~~~~~~--~~~~~WL~~ia~n~~~d~~Rk~~r~~~~~~ 80 (191)
T PRK12520 3 IAPAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQ--SSLKTYLVGILKHKIIDAIRSGRREVRLSL 80 (191)
T ss_pred chHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--ccHHHHHHHHHHHHHHHHHHhhcCcCcccc
Confidence 689999999999999999999999999999999999999999999864 369999999999999999998754322111
Q ss_pred ------------------------------ch------HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCC
Q 012638 376 ------------------------------KL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLS 411 (459)
Q Consensus 376 ------------------------------~v------~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS 411 (459)
.. .+....|..++..|+... -.+.|++|||+.||||
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis 160 (191)
T PRK12520 81 DDADEQSDDDLFDALFAADGHYREPPSDWGDPDAALSRREFFEVLQACVDRLPPRTGRVFMMREWLELETEEICQELQIT 160 (191)
T ss_pred cccccchhhhhhhhhcccccccccCccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCC
Confidence 00 011233556666665543 2568999999999999
Q ss_pred HHHHHHHHHhhcc
Q 012638 412 LAEIRSASECLRI 424 (459)
Q Consensus 412 ~e~Vk~~l~~ar~ 424 (459)
+++|+..+.+++.
T Consensus 161 ~~tV~~~l~Rar~ 173 (191)
T PRK12520 161 ATNAWVLLYRARM 173 (191)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999998875
No 79
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=99.57 E-value=2.4e-14 Score=132.51 Aligned_cols=131 Identities=12% Similarity=0.075 Sum_probs=104.4
Q ss_pred hchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccc
Q 012638 292 FGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG 370 (459)
Q Consensus 292 ~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~ 370 (459)
.|+. |++.|+..|.+.|+.++++|.++..+++|++||+++.+|+++.+|++.. .|.+|++.+++|.+.+++++..+.
T Consensus 3 ~~d~~af~~l~~~~~~~l~~~~~~~~~~~~daeDl~Qevfl~l~~~~~~~~~~~--~f~~wl~~iarn~~~~~~r~~~~~ 80 (179)
T PRK12543 3 SGDQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNR--PFRFWLIGLVIKQIHSWRRKRWRR 80 (179)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--ChHHHHHHHHHHHHHHHHHhhccc
Confidence 4555 9999999999999999999999999999999999999999999999864 699999999999999999865421
Q ss_pred cc---------------cccch--HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 371 IK---------------IPCKL--NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 371 ir---------------lP~~v--~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
.+ .|.++ .+....+.++...|+... -.+.+++|||+.||||+++|+..+.+++.
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~i~~l~~~e~~s~~EIA~~lgis~~tV~~~l~ra~~ 159 (179)
T PRK12543 81 FRIFEKAEEQRKPVSIDFSEDVLSKESNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALK 159 (179)
T ss_pred cccccccccccccccccChHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHccCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 11 11110 122344555555555443 26689999999999999999999888765
No 80
>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=99.56 E-value=3.4e-14 Score=132.84 Aligned_cols=131 Identities=12% Similarity=-0.002 Sum_probs=105.7
Q ss_pred hchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccc
Q 012638 292 FGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG 370 (459)
Q Consensus 292 ~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~ 370 (459)
.|+. +|++|+..|.+.|+.+|.+++++..+++|++||+|+.+|+++.+|++. .+|.||++.+++|.+++++|++.+.
T Consensus 7 ~~~~~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~~~~~~~~~--~~~~~wL~~iarN~~~d~~Rk~~~~ 84 (193)
T TIGR02947 7 TQRAQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPG--TNLKAWLYRILTNTYINSYRKAQRR 84 (193)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcccCCC--CcchHHHHHHHHHHHHHHHHHhcCC
Confidence 3444 999999999999999999999999999999999999999999999864 4699999999999999999976543
Q ss_pred cccc--------------cc------hH-------HHHHHHHHHHHHHHHHcC--------CCCCHHHHHHHhCCCHHHH
Q 012638 371 IKIP--------------CK------LN-------REISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEI 415 (459)
Q Consensus 371 irlP--------------~~------v~-------e~i~kI~ka~~~L~~~lg--------r~PT~eEIAe~LGIS~e~V 415 (459)
.... .+ .. +....+..+...|+.... .+.+++|||+.||||+++|
T Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~r~i~~L~~~~g~s~~EIA~~lgis~~tV 164 (193)
T TIGR02947 85 PQQSDDDDIEDWQLAKAASHTSNGLRSAELEALDGLPDQDIKDALQGLPEEFRQAVYLADVEGFAYKEIAEIMGTPIGTV 164 (193)
T ss_pred cccccchhhhhhhhccccccccccccchhHHHHhhhhHHHHHHHHHhCCHHHhhheeehhhcCCCHHHHHHHHCCCHHHH
Confidence 2110 00 00 112446666766666543 5689999999999999999
Q ss_pred HHHHHhhcc
Q 012638 416 RSASECLRI 424 (459)
Q Consensus 416 k~~l~~ar~ 424 (459)
+..+.+++.
T Consensus 165 k~~l~Rar~ 173 (193)
T TIGR02947 165 MSRLHRGRK 173 (193)
T ss_pred HHHHHHHHH
Confidence 999998875
No 81
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=99.56 E-value=5.6e-14 Score=128.66 Aligned_cols=135 Identities=16% Similarity=0.093 Sum_probs=104.6
Q ss_pred HHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHH
Q 012638 287 KQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVA 365 (459)
Q Consensus 287 ~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lr 365 (459)
+..++.|+. |++.|+..|.+.|+.+|+++.+ ..+++|++||+|+.+|+.+++|++. ..|.+|++.+++|.+++++|
T Consensus 2 ~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R 78 (175)
T PRK12518 2 ILRCQRGDRQSFRQLYRRYQQKVRSTLYQLCG-RELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATDARR 78 (175)
T ss_pred hhHHHcCCHHHHHHHHHHHHHHHHHHHHHHcC-HhHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHHHHH
Confidence 456678876 9999999999999999999875 4789999999999999999999974 47999999999999999999
Q ss_pred hhcccc----ccc--------cc---h--HHHHHHHHHHHHHHHHHcC--------CCCCHHHHHHHhCCCHHHHHHHHH
Q 012638 366 RHARGI----KIP--------CK---L--NREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASE 420 (459)
Q Consensus 366 k~sr~i----rlP--------~~---v--~e~i~kI~ka~~~L~~~lg--------r~PT~eEIAe~LGIS~e~Vk~~l~ 420 (459)
+..+.. ..+ .. . .+....+.++...|+.... .+.+++|||+.||+|+++|+..+.
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~eIA~~lg~s~~tv~~~l~ 158 (175)
T PRK12518 79 QFAQRPSRIQDDSLNDQPSRPSDTPDLMQLHYQDLVQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLF 158 (175)
T ss_pred HhhccccchhcccccccccCCCCcHHHHHHHHHHHHHHHHHhCCHHHeeeeeehHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 764311 110 00 0 0111224455555554432 567999999999999999999999
Q ss_pred hhcc
Q 012638 421 CLRI 424 (459)
Q Consensus 421 ~ar~ 424 (459)
+++.
T Consensus 159 Rar~ 162 (175)
T PRK12518 159 YARR 162 (175)
T ss_pred HHHH
Confidence 8875
No 82
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=99.56 E-value=5.6e-14 Score=130.24 Aligned_cols=128 Identities=16% Similarity=0.057 Sum_probs=103.0
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccc
Q 012638 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP 374 (459)
Q Consensus 295 ~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP 374 (459)
.|+++|+..|.+.|+++|.+++++..+++|++||+++.+|+++.+|++. ..|.||++.+++|.+++++|+..+....+
T Consensus 16 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~--~~~~awl~~ia~n~~~d~~Rk~~~~~~~~ 93 (179)
T PRK09415 16 DLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGK--SSLKTWLYRIAINHCKDYLKSWHNKKVIV 93 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--cccHHHHHHHHHHHHHHHHHhhccccccc
Confidence 4999999999999999999999999999999999999999999999874 36999999999999999999753221110
Q ss_pred ---------------cc---hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 375 ---------------CK---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 375 ---------------~~---v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
.. ..+....+.++...|+... -.+.|++|||+.||||+++|+..+.+++.
T Consensus 94 ~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tv~~~l~Ra~~ 169 (179)
T PRK09415 94 TEDIFTYMESQKESVEEEVIQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKE 169 (179)
T ss_pred cccccccccccccCcHHHHHHHHHHHHHHHHHHhCCHHHhhHhHhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 00 1122334555555555543 25679999999999999999999998875
No 83
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=99.55 E-value=5.4e-14 Score=131.92 Aligned_cols=128 Identities=13% Similarity=0.108 Sum_probs=104.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccc
Q 012638 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP 374 (459)
Q Consensus 295 ~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP 374 (459)
.++++|+..|.+.|+.+|.+++++..+++|++||.|+.+|+..++|+.. ..|.+|++++++|.+++++|++.+.....
T Consensus 10 ~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~awL~~Ia~n~~~d~~R~~~~~~~~~ 87 (187)
T PRK12516 10 PPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVG--TNMKAWLFTILRNEFYSQMRKRGREVQDT 87 (187)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCc--ccHHHHHHHHHHHHHHHHHHhhcCCcccc
Confidence 4999999999999999999999999999999999999999999999864 36999999999999999999876432111
Q ss_pred c---------c----hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 375 C---------K----LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 375 ~---------~----v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
. . .......+..++..|+... ..+.+++|||+.||||+++|+..+.+++.
T Consensus 88 ~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~i~~L~~~~g~s~~EIA~~Lgis~~tVk~~l~Rar~ 158 (187)
T PRK12516 88 DGMFTEQLAVHPSQYGTLDLQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQ 158 (187)
T ss_pred ccccccccCCCcchhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 0 0 1112344666666665543 36789999999999999999999998875
No 84
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=99.55 E-value=5.3e-14 Score=128.82 Aligned_cols=130 Identities=13% Similarity=0.007 Sum_probs=103.2
Q ss_pred hHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccccc
Q 012638 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI 373 (459)
Q Consensus 294 ~~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irl 373 (459)
..+++.|+..|.+.|+++|.++.++..+++|++||.|+.+|+..++|++.. ..|.+|++.+++|.+++++|++.+....
T Consensus 8 ~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~~~~~~~~~~-~~~~~wL~~iarn~~~d~~Rk~~~~~~~ 86 (173)
T PRK09645 8 AALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTG-RSARAWLFTVARNLVIDERRSARARPVE 86 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHHHHHHHhhcccccc
Confidence 349999999999999999999999999999999999999999999997532 4799999999999999999976432111
Q ss_pred --------cc-----ch--HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 374 --------PC-----KL--NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 374 --------P~-----~v--~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
|. .+ ......+..+...|+... -.+.+++|||+.||||+++|+..+++++.
T Consensus 87 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~ 160 (173)
T PRK09645 87 GGDDVLGVPEQSAPDEVDRALDRLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALR 160 (173)
T ss_pred cccccccCCCCCCchHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 10 01 011123556666555543 36789999999999999999999998875
No 85
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=99.55 E-value=5.5e-14 Score=122.22 Aligned_cols=126 Identities=25% Similarity=0.300 Sum_probs=101.0
Q ss_pred HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccccc--
Q 012638 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI-- 373 (459)
Q Consensus 296 Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irl-- 373 (459)
|++.++..|.++|+++++++.+++.+.+|++|||+++++++++.|++. .+|.||+++++++.+.++++++.+ .+.
T Consensus 2 a~~~l~~~~~~~v~~~~~~~~~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~rk~~~-~~~~~ 78 (158)
T TIGR02937 2 AFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRR-LRREL 78 (158)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHHHHHHHHhcc-CCcch
Confidence 789999999999999999999999999999999999999999999997 689999999999999999998764 110
Q ss_pred ------------ccc---hHHHHHHHHHHHHHHHHH--------cCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 374 ------------PCK---LNREISKIQKARKALTNS--------HGKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 374 ------------P~~---v~e~i~kI~ka~~~L~~~--------lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
|.. .......+.++...|+.. +..+.+.+|||+.+|+|+.+|...+..++.
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~ii~~~~~~g~s~~eIA~~l~~s~~~v~~~~~~~~~ 152 (158)
T TIGR02937 79 DLLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARK 152 (158)
T ss_pred hhhhhcccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 000 112223344444444322 246789999999999999999999887754
No 86
>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=99.55 E-value=5.6e-14 Score=127.16 Aligned_cols=131 Identities=15% Similarity=0.023 Sum_probs=104.1
Q ss_pred hchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccc
Q 012638 292 FGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG 370 (459)
Q Consensus 292 ~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~ 370 (459)
.|+. +++.|+..|.+.|+.+|.++.++..+++|++||+|+.+|++.++|+. ...|.+|++.+++|.+++++|++.+.
T Consensus 2 ~~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~--~~~~~~wl~~i~~n~~~d~~rk~~~~ 79 (162)
T TIGR02983 2 SATEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRD--PDAPDAYVRRVLVNLARSRWRRRRLL 79 (162)
T ss_pred CCcHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCC--cccHHHHHHHHHHHHHHHHHHhhccc
Confidence 3554 99999999999999999999999999999999999999999999964 34799999999999999999976541
Q ss_pred ccc----cc----c---hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 371 IKI----PC----K---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 371 irl----P~----~---v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
... |. . .......|..+...|+... -.+.+++|||+.||+|+++|+..+.+++.
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ra~~ 152 (162)
T TIGR02983 80 ELPTRELPDAAAPDPAPDVALRAALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALA 152 (162)
T ss_pred cccccccCcccCCccchhHHHHHHHHHHHHhCCHHHHHHhhhHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 100 10 0 1123334555555554433 25689999999999999999999998875
No 87
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=99.54 E-value=7.6e-14 Score=141.56 Aligned_cols=139 Identities=18% Similarity=0.104 Sum_probs=111.6
Q ss_pred HHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHH
Q 012638 284 RVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISK 362 (459)
Q Consensus 284 eeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d 362 (459)
.+|+..++.|+. |+++|+..|.+.|+.+|++++++..+++|++||.|+.+|+.+++|++. ..|.+|++.+++|.+++
T Consensus 7 ~~l~~~~~~gd~~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d 84 (339)
T PRK08241 7 AALLARAAAGDRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGR--SSLRTWLYRIATNVCLD 84 (339)
T ss_pred HHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhhhccccc--cchHHHHHHHHHHHHHH
Confidence 478889999987 999999999999999999999999999999999999999999999853 47999999999999999
Q ss_pred HHHhhccccc---c-----------------------cc-----------ch---HHH-HHHHHHHHHHHHHHcC-----
Q 012638 363 MVARHARGIK---I-----------------------PC-----------KL---NRE-ISKIQKARKALTNSHG----- 396 (459)
Q Consensus 363 ~Lrk~sr~ir---l-----------------------P~-----------~v---~e~-i~kI~ka~~~L~~~lg----- 396 (459)
++|++.+... . +. .. .+. ...+..++..|+....
T Consensus 85 ~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L 164 (339)
T PRK08241 85 ALEGRARRPLPTDLGAPAADPVDELVERPEVPWLEPYPDALLDPAAADPAARVVARESVRLAFVAALQHLPPRQRAVLIL 164 (339)
T ss_pred HHHhhccccCccccCCCcCcccccccccccccccCCCCcccccccCCChHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhh
Confidence 9997643210 0 00 00 011 1235556666655432
Q ss_pred ---CCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 397 ---KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 397 ---r~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
.+.+++|||+.||+|+++|+..+.+++.
T Consensus 165 ~~~~g~s~~EIA~~lgis~~tVk~~l~RAr~ 195 (339)
T PRK08241 165 RDVLGWSAAEVAELLDTSVAAVNSALQRARA 195 (339)
T ss_pred HHhhCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 5679999999999999999999888764
No 88
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=99.54 E-value=6e-14 Score=130.07 Aligned_cols=135 Identities=9% Similarity=-0.018 Sum_probs=104.8
Q ss_pred HHhchH-HHHHHHHHhHHHHHHHHHHhhC--CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHh
Q 012638 290 LAFGWY-CREELIKSTRPLVLFLARNYRG--LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVAR 366 (459)
Q Consensus 290 l~~G~~-Are~LI~~nlrLV~sIAkry~g--~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk 366 (459)
+..|+. ||+.|+..|.+.|+.++.++++ +..+++|++||.|+.+|+..++|+......|.||++.+++|.+++++|+
T Consensus 7 ~~~~d~~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~~Rk 86 (178)
T PRK12529 7 CLSADRDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSWRRR 86 (178)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHHHHH
Confidence 345655 9999999999999998766665 4678999999999999999999975434579999999999999999997
Q ss_pred hccccc-------c-------ccc---hHHHHHHHHHHHHHHHHHcC--------CCCCHHHHHHHhCCCHHHHHHHHHh
Q 012638 367 HARGIK-------I-------PCK---LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASEC 421 (459)
Q Consensus 367 ~sr~ir-------l-------P~~---v~e~i~kI~ka~~~L~~~lg--------r~PT~eEIAe~LGIS~e~Vk~~l~~ 421 (459)
+.+... . |.. ..+....|.+++.+|+.+.. .+.|++|||+.||||+++|+..+++
T Consensus 87 ~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~r 166 (178)
T PRK12529 87 QSLELAWLEALATLPEPLHPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQ 166 (178)
T ss_pred HHHHhhhhhHhhhccCcCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 643110 1 111 11233456677777766543 5689999999999999999999888
Q ss_pred hcc
Q 012638 422 LRI 424 (459)
Q Consensus 422 ar~ 424 (459)
+..
T Consensus 167 Al~ 169 (178)
T PRK12529 167 AYV 169 (178)
T ss_pred HHH
Confidence 764
No 89
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=99.53 E-value=1.1e-13 Score=126.32 Aligned_cols=128 Identities=13% Similarity=0.107 Sum_probs=103.4
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccc
Q 012638 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP 374 (459)
Q Consensus 295 ~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP 374 (459)
..|.+++..|.+.|+.+|+++.++..+++|++||+++.+|+..++|+.. ..|.+|++.+++|.+++++|++++.....
T Consensus 6 ~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R~~~~~~~~~ 83 (164)
T PRK12547 6 KNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMG--TNLKAWLFTILRNEFYSQMRKRGREVQDS 83 (164)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCc--ccHHHHHHHHHHHHHHHHHHhhccccccc
Confidence 4789999999999999999999999999999999999999999999864 36999999999999999999765432110
Q ss_pred ---------cc----hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 375 ---------CK----LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 375 ---------~~----v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
.+ .......+..+...|+... -.+.+++|||+.||||+++|+..+.+++.
T Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~ 154 (164)
T PRK12547 84 DGVFTARVAVHPAQYGSLDLQDFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARN 154 (164)
T ss_pred cccccccCCCCchhhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 00 0112234556666655543 26789999999999999999999998875
No 90
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=99.53 E-value=1.1e-13 Score=127.53 Aligned_cols=133 Identities=17% Similarity=0.098 Sum_probs=102.0
Q ss_pred hchH-HHHHHHHHhHHHHHHHHHHhh----CCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHh
Q 012638 292 FGWY-CREELIKSTRPLVLFLARNYR----GLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVAR 366 (459)
Q Consensus 292 ~G~~-Are~LI~~nlrLV~sIAkry~----g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk 366 (459)
.|+. |++.|+..|.+.|+.+|++|. ++..+++|++||+++.+|+++.+|+...+.+|.+|++.+++|.+++++++
T Consensus 3 ~~~~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r~ 82 (189)
T TIGR02984 3 GGDQEALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNVLADALRR 82 (189)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHHHHHHH
Confidence 4665 999999999999999999875 35679999999999999999999987655689999999999999999986
Q ss_pred hc----ccc--ccc-------------------------cc---hHHHHHHHHHHHHHHHHHc--------CCCCCHHHH
Q 012638 367 HA----RGI--KIP-------------------------CK---LNREISKIQKARKALTNSH--------GKYPEDIEI 404 (459)
Q Consensus 367 ~s----r~i--rlP-------------------------~~---v~e~i~kI~ka~~~L~~~l--------gr~PT~eEI 404 (459)
+. +.. ..+ .. ..+....+.++...|+... ..+.+++||
T Consensus 83 ~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vi~l~~~~g~s~~eI 162 (189)
T TIGR02984 83 HLGAQKRDIRREQSLDAGGRLDESSVRLAAQLAADGPSPSQVAARREAAVRLAQALAKLPEDYREVILLRHLEGLSFAEV 162 (189)
T ss_pred HHHHHhhhcccccCCCcccccCCcchhHHHHccCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCHHHH
Confidence 51 110 000 00 0112233444555444332 367899999
Q ss_pred HHHhCCCHHHHHHHHHhhcc
Q 012638 405 AKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 405 Ae~LGIS~e~Vk~~l~~ar~ 424 (459)
|+.||||+++|+..+++++.
T Consensus 163 A~~lgis~~~v~~~l~Ra~~ 182 (189)
T TIGR02984 163 AERMDRSEGAVSMLWVRGLA 182 (189)
T ss_pred HHHHCcCHHHHHHHHHHHHH
Confidence 99999999999999988764
No 91
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=99.53 E-value=1.3e-13 Score=125.06 Aligned_cols=127 Identities=17% Similarity=0.101 Sum_probs=100.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccccc-
Q 012638 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI- 373 (459)
Q Consensus 295 ~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irl- 373 (459)
.|+++++..|.+.|+.+|.+++++..+++|++||+++.+|+..++|++. .|.||++.+++|.+++++|++.+....
T Consensus 5 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDv~Qe~f~~~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~~~~~ 81 (161)
T PRK12541 5 QSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE---EIRPWLFTIAYNAFIDWYRKEKKYKTTT 81 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhHHHccCC---ChHHHHHHHHHHHHHHHHHhcccccccc
Confidence 3899999999999999999999999999999999999999999999863 599999999999999999976532211
Q ss_pred ---------ccc-----hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 374 ---------PCK-----LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 374 ---------P~~-----v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
|.. ..+....+..+...|+... -.+.+++|||+.||+|+++|+..+.+++.
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~Rar~ 154 (161)
T PRK12541 82 IEEFHLPNVPSTEHEYFIKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRK 154 (161)
T ss_pred hhhhhccCCCCcHHHHHHHhHHHHHHHHHHHCCHHHHHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 000 0111222334444444432 36789999999999999999999998875
No 92
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=99.52 E-value=1.7e-13 Score=129.67 Aligned_cols=138 Identities=19% Similarity=0.049 Sum_probs=109.4
Q ss_pred HHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHH
Q 012638 284 RVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISK 362 (459)
Q Consensus 284 eeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d 362 (459)
.+|+..+..|+. |++.|+..|.+.++.+++ +.++..+++|++||.|+.+|+..++|++. ..|.+|++.+++|.+++
T Consensus 13 ~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~-~~~~~~~AEDivQevflkl~~~~~~~~~~--~~~~~WL~~Iarn~~id 89 (196)
T PRK12535 13 TDLALAAGRGDRAALTEFIRETQDDVWRLLA-HLGGHDIADDLTQETYLRVMSALPRFAAR--SSARTWLLSLARRVWVD 89 (196)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHHhhhcCCc--ccHHHHHHHHHHHHHHH
Confidence 567778888877 999999999999999975 57888899999999999999999999863 37999999999999999
Q ss_pred HHHhhcccccc--------------cc--chHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHH
Q 012638 363 MVARHARGIKI--------------PC--KLNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSA 418 (459)
Q Consensus 363 ~Lrk~sr~irl--------------P~--~v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~ 418 (459)
++|++.+..+. |. ...+....+.+++..|+... -.+.+++|||+.||+|+++|+..
T Consensus 90 ~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIAe~lgis~~tV~~~ 169 (196)
T PRK12535 90 NIRHDMARPRKSATEYEDAAATTASNETTGSWSEWIDVRTLIDALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSR 169 (196)
T ss_pred HHHhhccCCCcccccccccccccCCcchhHHHHHHHHHHHHHHcCCHHHHHHhhhHHHhCCCHHHHHHHhCCCHHHHHHH
Confidence 99976432211 00 01122234566666665543 25679999999999999999999
Q ss_pred HHhhcc
Q 012638 419 SECLRI 424 (459)
Q Consensus 419 l~~ar~ 424 (459)
+.+++.
T Consensus 170 l~Rar~ 175 (196)
T PRK12535 170 VARARA 175 (196)
T ss_pred HHHHHH
Confidence 998875
No 93
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=99.51 E-value=6.7e-14 Score=128.56 Aligned_cols=132 Identities=15% Similarity=0.066 Sum_probs=102.5
Q ss_pred HhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcc
Q 012638 291 AFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (459)
Q Consensus 291 ~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr 369 (459)
+.|+. |+.+|+..|.+.|+.+|.+++++..+++|++||+|+.+|+. ..|+.. ..|.||++.+++|.+++++|++.+
T Consensus 5 ~~~~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~~~d~~Rk~~~ 81 (172)
T PRK12523 5 QSPHSELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRRAAL 81 (172)
T ss_pred CCCCcHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHHHHHHHHHHHH
Confidence 56765 99999999999999999999999999999999999999986 446543 369999999999999999997643
Q ss_pred ccc-------cc-------cc---hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 370 GIK-------IP-------CK---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 370 ~ir-------lP-------~~---v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
... .+ .. ..+....+..++..|+... -.+.+++|||+.||||+++|+..+.+++.
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~ 161 (172)
T PRK12523 82 EQAYLAELALVPEAEQPSPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGLR 161 (172)
T ss_pred HHHHHHHHhhcccccCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 210 00 00 0122234556666555443 36789999999999999999999988765
Q ss_pred C
Q 012638 425 V 425 (459)
Q Consensus 425 ~ 425 (459)
.
T Consensus 162 ~ 162 (172)
T PRK12523 162 Q 162 (172)
T ss_pred H
Confidence 3
No 94
>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=99.51 E-value=1.2e-13 Score=123.13 Aligned_cols=127 Identities=17% Similarity=0.087 Sum_probs=99.7
Q ss_pred HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccccc--
Q 012638 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI-- 373 (459)
Q Consensus 296 Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irl-- 373 (459)
|+++|+..|.+.|+.+++++.++..+.+|++||+++++|+++.+|++. .+|.+|++.++++.+.+++++..+....
T Consensus 2 a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~--~~~~~wl~~i~r~~~~d~~r~~~~~~~~~~ 79 (161)
T TIGR02985 2 AFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEV--ESFKAYLFTIVKNRSLNYLRHKQVEEKYQE 79 (161)
T ss_pred hHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc--ccHHHHHHHHHHHHHHHHHHHHHhHhHHHH
Confidence 789999999999999999999999999999999999999999999874 4799999999999999999876532111
Q ss_pred ------c--------cc---hHHHHHHHHHHHHHHHHH--------cCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 374 ------P--------CK---LNREISKIQKARKALTNS--------HGKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 374 ------P--------~~---v~e~i~kI~ka~~~L~~~--------lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
+ .. ..+....+..+...|+.. ...+.+.+|||+.||+|..+|+..+++++.
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~il~l~~~~~~~~~eIA~~lgis~~tv~~~~~ra~~ 155 (161)
T TIGR02985 80 EILEIEVDELSENDPEEELEAKELQLIIYKAIEKLPEQCRKIFILSRFEGKSYKEIAEELGISVKTVEYHISKALK 155 (161)
T ss_pred HHHhhcccccCCCCcHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 0 00 011222344444433222 235789999999999999999999988764
No 95
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=99.50 E-value=1.5e-13 Score=125.20 Aligned_cols=125 Identities=16% Similarity=0.004 Sum_probs=100.1
Q ss_pred HHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccc--
Q 012638 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP-- 374 (459)
Q Consensus 297 re~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP-- 374 (459)
++.|+..|.+.|+.+|+++.++..+++|++||+++.+|+++++|++. +|.+|++.+++|.+++++|+.++.....
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wL~~i~~n~~~d~~R~~~~~~~~~~~ 79 (165)
T PRK09644 3 IEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYHTFIDFVRKEKKVSFVGTD 79 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc---chHHHHHHHHHHHHHHHHHhhhhccccchh
Confidence 67899999999999999999999999999999999999999999863 5999999999999999999876432211
Q ss_pred ----------cc---hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 375 ----------CK---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 375 ----------~~---v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
.. ..+....+.++...|+... -.+.+++|||+.||+|+++|+..+++++.
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Rar~ 150 (165)
T PRK09644 80 EIEAIQAESTEEYVVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRK 150 (165)
T ss_pred HHhhhcccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 01 0112234445555444432 25679999999999999999999998875
No 96
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=99.50 E-value=2e-13 Score=131.62 Aligned_cols=131 Identities=15% Similarity=0.053 Sum_probs=104.9
Q ss_pred HhchHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccc
Q 012638 291 AFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG 370 (459)
Q Consensus 291 ~~G~~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~ 370 (459)
.....+++.|+..|.+.|+.+++++.++..+++|++||+|+.+|+.+++|++ + .|.+|++++++|.++++++++++.
T Consensus 14 ~~~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~--~-~~~aWL~~IarN~~~d~~Rk~~~~ 90 (216)
T PRK12533 14 AARGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRG--D-NARPWLLAIVRHTWYSEWRRRANA 90 (216)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCc--c-chHhHHHHHHHHHHHHHHHhhccc
Confidence 3345599999999999999999999999999999999999999999999985 2 599999999999999999976532
Q ss_pred ccc------cc------------c------hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHH
Q 012638 371 IKI------PC------------K------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSA 418 (459)
Q Consensus 371 irl------P~------------~------v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~ 418 (459)
... +. . ..+....+.+++..|+... -.+.+++|||+.||||+++|+..
T Consensus 91 ~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y~eg~s~~EIAe~LgiS~~tVk~~ 170 (216)
T PRK12533 91 HEVAAPDTLDDADSLDDWQPAGEDPLALLLRAEDVRLVNAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSR 170 (216)
T ss_pred ccccccccccccccccccccCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHhHhhhHHhcCCCHHHHHHHHCCCHHHHHHH
Confidence 110 00 0 0123344666666665543 25689999999999999999999
Q ss_pred HHhhcc
Q 012638 419 SECLRI 424 (459)
Q Consensus 419 l~~ar~ 424 (459)
+++++.
T Consensus 171 L~RAr~ 176 (216)
T PRK12533 171 LARARR 176 (216)
T ss_pred HHHHHH
Confidence 998875
No 97
>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=99.49 E-value=2.1e-13 Score=137.04 Aligned_cols=130 Identities=17% Similarity=0.070 Sum_probs=103.1
Q ss_pred chH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccc
Q 012638 293 GWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGI 371 (459)
Q Consensus 293 G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~i 371 (459)
|+. |+++|+..|.+.|+++|++++++..+++|++||.|+.+|+.+++|+.. ..|.||++++++|.+++++|++.+..
T Consensus 2 gd~~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~~~~ 79 (324)
T TIGR02960 2 VDGAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGR--SSVRTWLYRIATNACLDALEARQRRP 79 (324)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCcc--cchHHHHHHHHHHHHHHHHHhccCCc
Confidence 554 999999999999999999999999999999999999999999999864 36999999999999999999764321
Q ss_pred c--------------------------ccc-----------c---h---HHH-HHHHHHHHHHHHHHc--------CCCC
Q 012638 372 K--------------------------IPC-----------K---L---NRE-ISKIQKARKALTNSH--------GKYP 399 (459)
Q Consensus 372 r--------------------------lP~-----------~---v---~e~-i~kI~ka~~~L~~~l--------gr~P 399 (459)
. ++. . . .+. ...+..++..|+... -.+.
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~ 159 (324)
T TIGR02960 80 RPVGLGAPSADGTAAASEAAEVTWLEPLPDLTLDLDDPAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRDVLGW 159 (324)
T ss_pred CccccCCCCCcccccccccccccccCCCCccccccccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHHhCC
Confidence 1 000 0 0 011 123455555555543 2568
Q ss_pred CHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 400 EDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 400 T~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
+++|||+.||||+++|+..+.+++.
T Consensus 160 s~~EIA~~lgis~~tV~~~l~Rar~ 184 (324)
T TIGR02960 160 RAAETAELLGTSTASVNSALQRARA 184 (324)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 9999999999999999999998875
No 98
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=99.49 E-value=4.8e-13 Score=131.14 Aligned_cols=91 Identities=19% Similarity=0.293 Sum_probs=82.1
Q ss_pred CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCC--CHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHH
Q 012638 282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGI--PFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK 358 (459)
Q Consensus 282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~--d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrn 358 (459)
+.+.|+..++.|+. |++.|+..|.++|+++|.+++++.. +.+|++|||++++|+++++||+.+|.+|.||++++|+|
T Consensus 4 ~~~~Li~~~~~gD~~AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~awl~~Iirn 83 (237)
T PRK08311 4 SLEDILEKIKNGDEELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELVIKR 83 (237)
T ss_pred cHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHH
Confidence 45677888899977 9999999999999999999998875 59999999999999999999999888899999999999
Q ss_pred HHHHHHHhhccccc
Q 012638 359 SISKMVARHARGIK 372 (459)
Q Consensus 359 aI~d~Lrk~sr~ir 372 (459)
.+++++|++.+...
T Consensus 84 ~~iDylRk~~~~~~ 97 (237)
T PRK08311 84 RLIDYFRKESKHNL 97 (237)
T ss_pred HHHHHHHHhhcccc
Confidence 99999998766433
No 99
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=99.48 E-value=3e-13 Score=122.63 Aligned_cols=127 Identities=17% Similarity=0.096 Sum_probs=100.5
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccc---
Q 012638 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGI--- 371 (459)
Q Consensus 295 ~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~i--- 371 (459)
.|+++|+..|.+.|+.+|.+++++..+++|++||+|+.+|+..+.|++ ..|.+|++++++|.+++++|++.+..
T Consensus 4 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~---~~~~~wl~~i~~n~~~d~~R~~~~~~~~~ 80 (161)
T PRK12528 4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQI---IEPRAFLTTIAKRVLCNHYRRQDLERAYL 80 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhccccccc---cCHHHHHHHHHHHHHHHHHHHHHHHHhhH
Confidence 489999999999999999999999999999999999999999988864 26999999999999999999754211
Q ss_pred ----cccc----c------hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 372 ----KIPC----K------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 372 ----rlP~----~------v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
..|. . ..+....+.++...|+... -.+.+++|||+.||+|+++|+..+.+++.
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~~g~s~~EIA~~l~is~~tV~~~l~ra~~ 155 (161)
T PRK12528 81 EALAQLPERVAPSEEERAIILETLVELDQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAM 155 (161)
T ss_pred HHhhccccccCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 0110 0 0122234555555555433 36789999999999999999999888754
No 100
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=99.48 E-value=2e-13 Score=123.43 Aligned_cols=121 Identities=11% Similarity=0.060 Sum_probs=95.7
Q ss_pred HHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccc-cc-----
Q 012638 301 IKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIK-IP----- 374 (459)
Q Consensus 301 I~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~ir-lP----- 374 (459)
+..|.+.|+.+|.+++++..+++|++||+|+.+|+++++|++. .|.||++.+++|.+++++|++.+... ..
T Consensus 1 ~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~~~~~~ 77 (160)
T PRK09642 1 MQTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFR---GLKTWMARIATNHAIDYKRKKARENEELSLCKET 77 (160)
T ss_pred CchHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcccccccc---hhHHHHHHHHHHHHHHHHHHhcccccccccchhh
Confidence 3578999999999999999999999999999999999999863 49999999999999999997654211 00
Q ss_pred -----c--ch------HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 375 -----C--KL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 375 -----~--~v------~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
. .. .+....+.++...|+... -.+.|++|||+.||+|+++|+..+.+++.
T Consensus 78 ~~~~~~~~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~ 148 (160)
T PRK09642 78 EENIKSSHNIEDLLLTKEQKLLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARK 148 (160)
T ss_pred hhhccCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 0 00 011233555566555543 36789999999999999999999998875
No 101
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=99.47 E-value=6.5e-13 Score=124.14 Aligned_cols=127 Identities=16% Similarity=0.156 Sum_probs=103.1
Q ss_pred HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccccc--
Q 012638 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI-- 373 (459)
Q Consensus 296 Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irl-- 373 (459)
++..++..|.+.|+.+|.+++++..+++|++||+|+.+|+..++|++.. .|.+|++.+++|.++++++++.+....
T Consensus 6 ~~~~~~~~~~~~l~~~~~~~~~~~~~AEDivQevflkl~~~~~~~~~~~--~~~~WL~~Ia~n~~~d~~Rk~~~~~~~~~ 83 (182)
T PRK12540 6 SLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGS--NLPAWLFTILRNLFRSDYRKRRREVEDAD 83 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCc--hHHHHHHHHHHHHHHHHHHhccccccccc
Confidence 6789999999999999999999999999999999999999999998753 699999999999999999986543211
Q ss_pred --------ccc---hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 374 --------PCK---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 374 --------P~~---v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
+.. .......+..++..|+... -.+.+++|||+.||||+++|+..+.+++.
T Consensus 84 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RAr~ 153 (182)
T PRK12540 84 GSYAKTLKSQPGQNAHLEFEEFRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARS 153 (182)
T ss_pred ccccccccCCCchHHHHHHHHHHHHHHhCCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 000 1112234566666665543 36789999999999999999999998875
No 102
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=99.46 E-value=6.4e-13 Score=120.51 Aligned_cols=125 Identities=15% Similarity=0.050 Sum_probs=99.2
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccc
Q 012638 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP 374 (459)
Q Consensus 295 ~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP 374 (459)
.++++|+..|.+.|+.+|.++.++..+++|++||+|+.+|++ .|+. +..|.||++.+++|.+++++|+..+.....
T Consensus 3 ~~f~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fi~~~~~--~~~~--~~~~~~wl~~i~rn~~~d~~rk~~~~~~~~ 78 (166)
T PRK09639 3 ETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKG--IENEKGWLIKSARNVAYNYLRSEKRRRARI 78 (166)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH--hccc--ccchHHHHHHHHHHHHHHHHHHhccccccc
Confidence 489999999999999999999999999999999999999999 6764 347999999999999999999865432111
Q ss_pred ---------------cch---HHHHHHHHHHHHHHHH--------HcCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 375 ---------------CKL---NREISKIQKARKALTN--------SHGKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 375 ---------------~~v---~e~i~kI~ka~~~L~~--------~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
... .+....+.++...|+. .+ .+.+++|||+.||+|+.+|+..+.+++.
T Consensus 79 ~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~-~g~s~~eIA~~lgis~~tV~~~i~ra~~ 153 (166)
T PRK09639 79 LGEFQWQEVDNEPSPEEIWIRKEEITKVQEVLAKMTERDRTVLLLRF-SGYSYKEIAEALGIKESSVGTTLARAKK 153 (166)
T ss_pred cchhhhhhccCCCChHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 000 1222334455544433 24 7789999999999999999999988875
No 103
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=99.45 E-value=9.2e-13 Score=125.49 Aligned_cols=130 Identities=24% Similarity=0.201 Sum_probs=103.3
Q ss_pred hchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccc
Q 012638 292 FGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG 370 (459)
Q Consensus 292 ~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~ 370 (459)
.|+. ++++|+..|.+.|+.++.++.++..+++|++||+++.+|+...+|++ + +|.+|++.+++|.+++++|+..+.
T Consensus 24 ~~d~~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~~~d~~Rk~~~~ 100 (203)
T PRK09647 24 KATMPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNLFLDMVRRRARI 100 (203)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHHHHHHHHhcccC
Confidence 3454 99999999999999999999999999999999999999999999985 3 699999999999999999987431
Q ss_pred --cccc-------c------c---hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 371 --IKIP-------C------K---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 371 --irlP-------~------~---v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
..++ . . ..+....+..++..|+... ..+.+++|||+.||||+++|+..+.+++.
T Consensus 101 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~L~~~~r~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RArk 180 (203)
T PRK09647 101 RMEALPEDYDRVPGDEPNPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQ 180 (203)
T ss_pred ccccccccccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 1010 0 0 0112233455555554432 36789999999999999999999998875
No 104
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=99.45 E-value=7.3e-13 Score=124.06 Aligned_cols=125 Identities=16% Similarity=0.102 Sum_probs=98.4
Q ss_pred HHHHHHhHHHHHHHHHHhhCCCCC-HHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccc--
Q 012638 298 EELIKSTRPLVLFLARNYRGLGIP-FSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP-- 374 (459)
Q Consensus 298 e~LI~~nlrLV~sIAkry~g~g~d-~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP-- 374 (459)
+..+..|.+.|+.+|++++++..+ ++|++||+|+.+|+++++|++. .+|.||++.+++|.+++++|++++.....
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 466788999999999999999888 9999999999999999999864 37999999999999999999875432110
Q ss_pred ----------------------c----c---------hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCC
Q 012638 375 ----------------------C----K---------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLS 411 (459)
Q Consensus 375 ----------------------~----~---------v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS 411 (459)
. . ..+....+.++...|+... -.+.+++|||+.||||
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~L~~~~g~s~~EIA~~lgis 165 (195)
T PRK12532 86 LDDELLDEAFESHFSQNGHWTPEGQPQHWNTPEKSLNNNEFQKILQSCLYNLPENTARVFTLKEILGFSSDEIQQMCGIS 165 (195)
T ss_pred ccccccchhhhhhhccccccccccCccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHHhCCCHHHHHHHHCCC
Confidence 0 0 0112233555555555432 2568999999999999
Q ss_pred HHHHHHHHHhhcc
Q 012638 412 LAEIRSASECLRI 424 (459)
Q Consensus 412 ~e~Vk~~l~~ar~ 424 (459)
+++|+..+.+++.
T Consensus 166 ~~tVk~~l~Rar~ 178 (195)
T PRK12532 166 TSNYHTIMHRARE 178 (195)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999998875
No 105
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=99.45 E-value=5.5e-13 Score=126.23 Aligned_cols=124 Identities=15% Similarity=0.042 Sum_probs=98.1
Q ss_pred HHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccc---c
Q 012638 299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP---C 375 (459)
Q Consensus 299 ~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP---~ 375 (459)
.++..|.+.|+.+|++++++..+++|++||+|+.+|+.+++|++. ..|.||++.+++|.+++++|++.+...++ .
T Consensus 12 ~~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~~~ 89 (201)
T PRK12545 12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQ--SAHKTWVFGILRNKLIDTLRARQRTVNLSALDA 89 (201)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhcccc--chHHHHHHHHHHHHHHHHHHhhccccccccccc
Confidence 458899999999999999999999999999999999999999975 36999999999999999999876432211 0
Q ss_pred -----------------------------chH------HHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCH
Q 012638 376 -----------------------------KLN------REISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSL 412 (459)
Q Consensus 376 -----------------------------~v~------e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~ 412 (459)
... +....+.++...|+... ..+.+++|||+.||+|+
T Consensus 90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~v~~L~~~eg~s~~EIA~~lgis~ 169 (201)
T PRK12545 90 ELDGEALLDRELFKDNGHWAAHAKPRPWPKPETILQQQQFWTLFETCLDHLPEQIGRVFMMREFLDFEIDDICTELTLTA 169 (201)
T ss_pred ccchhhhhhhhhhcccccccccccCcCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCH
Confidence 000 11123455555554432 36789999999999999
Q ss_pred HHHHHHHHhhcc
Q 012638 413 AEIRSASECLRI 424 (459)
Q Consensus 413 e~Vk~~l~~ar~ 424 (459)
++|+..+.+++.
T Consensus 170 ~tVk~~l~RAr~ 181 (201)
T PRK12545 170 NHCSVLLYRART 181 (201)
T ss_pred HHHHHHHHHHHH
Confidence 999999998875
No 106
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=99.44 E-value=1.4e-12 Score=121.71 Aligned_cols=126 Identities=15% Similarity=0.115 Sum_probs=99.8
Q ss_pred HHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccc
Q 012638 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCK 376 (459)
Q Consensus 297 re~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~ 376 (459)
++.|+..|.+.|+.+|.++.++..+++|++||.++.+|+.+..|++. .+|.||++.+++|.+++++|++.+...++..
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~aeDi~QEvflkl~~~~~~~~~~--~~~~~wL~~i~~n~~~d~~Rk~~~~~~~~~~ 80 (181)
T PRK09637 3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDG--SSIKSWLYQIANNTIIDFYRKKNRSEELPDD 80 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHhHHHhccc--cchHHHHHHHHHHHHHHHHHhccccCCcchh
Confidence 67899999999999999999999999999999999999999999853 4799999999999999999977544332210
Q ss_pred ------------hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 377 ------------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 377 ------------v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
..+....+..+...|+... -.+.+.+|||+.||+|+++|+..+.+++.
T Consensus 81 ~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~~~~EIA~~lgis~~tV~~~l~Rar~ 148 (181)
T PRK09637 81 LLFEDEEREENAKKELAPCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRV 148 (181)
T ss_pred hhccCCChhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 0111223334444443322 36789999999999999999999888864
No 107
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=99.44 E-value=9.2e-13 Score=123.42 Aligned_cols=125 Identities=13% Similarity=0.062 Sum_probs=98.8
Q ss_pred HHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccc---
Q 012638 298 EELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP--- 374 (459)
Q Consensus 298 e~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP--- 374 (459)
+..|..|.+.|+.+|.+++++..+++|++||+|+.+|+..++|++. .+|.||++++++|.+++++|++.+.....
T Consensus 10 ~~~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~~~~ 87 (189)
T PRK12530 10 SLEIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQ--SALKTWIFAILKNKIIDLIRYRKRFVNESELI 87 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCC--ccHHHHHHHHHHHHHHHHHHhhccCCCccccc
Confidence 4567888999999999999999999999999999999999999875 36999999999999999999775432110
Q ss_pred ----------------------cc--h-------HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHH
Q 012638 375 ----------------------CK--L-------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEI 415 (459)
Q Consensus 375 ----------------------~~--v-------~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~V 415 (459)
.. . .+....+..++.+|+... -.+.|++|||+.||+|+++|
T Consensus 88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tV 167 (189)
T PRK12530 88 EEDSPNSFFDEKGHWKPEYYEPSEWQEVENTVYKEEFWLIFEACLNHLPAQQARVFMMREYLELSSEQICQECDISTSNL 167 (189)
T ss_pred ccccchhhhcccccccccccCCccccCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHhHHHHcCCCHHHHHHHHCCCHHHH
Confidence 00 0 011123555666665543 25789999999999999999
Q ss_pred HHHHHhhcc
Q 012638 416 RSASECLRI 424 (459)
Q Consensus 416 k~~l~~ar~ 424 (459)
+..+.+++.
T Consensus 168 k~~l~RAr~ 176 (189)
T PRK12530 168 HVLLYRARL 176 (189)
T ss_pred HHHHHHHHH
Confidence 999998875
No 108
>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=99.44 E-value=7.7e-13 Score=118.36 Aligned_cols=121 Identities=17% Similarity=0.038 Sum_probs=96.5
Q ss_pred HHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccccc-----c-
Q 012638 301 IKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI-----P- 374 (459)
Q Consensus 301 I~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irl-----P- 374 (459)
+..|.+.|+.+|.++.++..+++|++||+++.+|+.+++|++ .+|.||++.++++.++++++++.+.... +
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 357899999999999999999999999999999999999997 3799999999999999999976432211 0
Q ss_pred ---------cch---HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 375 ---------CKL---NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 375 ---------~~v---~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
... .+....+.++...|+... ..+.+++|||+.||+|+++|+..+.+++.
T Consensus 78 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~ 147 (154)
T TIGR02950 78 LEQHPVESPEHHLLIKIEQEEITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARK 147 (154)
T ss_pred ccccccCChhHHHHHHHHHHHHHHHHHhCCHhheeeeeehhhccCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 000 112234666666665543 25679999999999999999999998875
No 109
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=99.43 E-value=1.2e-12 Score=125.01 Aligned_cols=126 Identities=16% Similarity=0.137 Sum_probs=99.6
Q ss_pred HHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccccccc-
Q 012638 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC- 375 (459)
Q Consensus 297 re~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~- 375 (459)
-..++..|.+.|+.+|++++++..+++|++||+|+.+|+.+.+|+.. .+|.+|++++++|.+++++|++.+....+.
T Consensus 20 ~~~~~~~~~~~l~~~~~~~~~d~~~AEDivQEvfikl~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~~~~~~~~~ 97 (206)
T PRK12544 20 DPVFLEDLRKQMIKFATLQLSDLHLAEDAVQEALIGALKNADSFAGR--AAFKTWVFAILKNKIIDLLRQKKRHVSASSL 97 (206)
T ss_pred hHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhhccccccccc
Confidence 46889999999999999999999999999999999999999999864 369999999999999999997654322110
Q ss_pred ---------------------------------ch---HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCC
Q 012638 376 ---------------------------------KL---NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLS 411 (459)
Q Consensus 376 ---------------------------------~v---~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS 411 (459)
.. .+....+..++..|+... -.+.+++|||+.||+|
T Consensus 98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~L~~L~~~~r~v~~L~~~~g~s~~EIAe~lgis 177 (206)
T PRK12544 98 LRDEEEEEDFEELFDESGHWQKDERPQAWGNPEESLEQEQFWRIFEACLDGLPAKYARVFMMREFIELETNEICHAVDLS 177 (206)
T ss_pred ccccchhhHHHHhhcccccccccccccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcC
Confidence 00 011123444555554432 2578999999999999
Q ss_pred HHHHHHHHHhhcc
Q 012638 412 LAEIRSASECLRI 424 (459)
Q Consensus 412 ~e~Vk~~l~~ar~ 424 (459)
+++|+..+++++.
T Consensus 178 ~~tV~~~l~RAr~ 190 (206)
T PRK12544 178 VSNLNVLLYRARL 190 (206)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999998875
No 110
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=99.43 E-value=2e-12 Score=121.29 Aligned_cols=130 Identities=13% Similarity=-0.003 Sum_probs=103.3
Q ss_pred chHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccc
Q 012638 293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIK 372 (459)
Q Consensus 293 G~~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~ir 372 (459)
...+++.++..|.+.|+.+|.++.++..+++|++||+|+.+|+.+..|++. ..|.+|++.+++|.+++..+++.+...
T Consensus 21 ~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~--~~~~~wL~~Iarn~~~~~~r~~~~~~~ 98 (188)
T PRK12517 21 KQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDE--KAAKAWLITILRRENARRFERKQFDLV 98 (188)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCc--cchHHHHHHHHHHHHHHHHHHhccCcc
Confidence 345999999999999999999999999999999999999999999999864 369999999999999888776432211
Q ss_pred ------ccc---c---hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 373 ------IPC---K---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 373 ------lP~---~---v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
.+. . .......+..++..|+... ..+.+++|||+.||||+++|+..+.+++.
T Consensus 99 ~~~~~~~~~~~~~~~e~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~ 170 (188)
T PRK12517 99 DIEDDSIEDDASHSSEEEMEQEWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARN 170 (188)
T ss_pred CcccccccCccccChhHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 010 0 0111234666666665543 25689999999999999999999998875
No 111
>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=99.42 E-value=1.3e-12 Score=120.20 Aligned_cols=121 Identities=19% Similarity=0.168 Sum_probs=96.0
Q ss_pred HHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccch----
Q 012638 302 KSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKL---- 377 (459)
Q Consensus 302 ~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~v---- 377 (459)
..|.+.|+.+++++.++..+++|++||+++.+|+++++|+.. .+|.+|++.+++|.+++++|+..+...++...
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 468899999999999999999999999999999999999963 48999999999999999999876544332111
Q ss_pred --------HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 378 --------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 378 --------~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
.+....+.++...|+... -.+.+++|||+.||||+.+|+..+.+++.
T Consensus 80 ~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~ 142 (170)
T TIGR02959 80 SAREETFVKELSQCIPPMIKELPDEYREAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQRGRK 142 (170)
T ss_pred CccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 111223444444443332 36789999999999999999999998875
No 112
>PF04542 Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR007627 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [, ]. The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation [, ].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1OR7_B 1H3L_B 2Z2S_C 2Q1Z_C 2O7G_B 1SMY_F 1IW7_P 2BE5_F 2A6E_F 2CW0_F ....
Probab=99.42 E-value=6.4e-13 Score=103.84 Aligned_cols=70 Identities=24% Similarity=0.375 Sum_probs=67.1
Q ss_pred HHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcc
Q 012638 300 LIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (459)
Q Consensus 300 LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr 369 (459)
|++.|.++|+++|.+|.+++.+.+|++||++++||+++++||+.++..|.+|++.+++|.++++++++.+
T Consensus 1 L~~~~~~~l~~~~~~~~~~~~~~eD~~qe~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~r~~~r 70 (71)
T PF04542_consen 1 LYERYYPLLYRYARRYTGDPEDAEDLVQEAFIKLWRAIDSYDPDRGDSFRAWLFRIARNRILDYLRKRRR 70 (71)
T ss_dssp HHHHTHHHHHHHHHTCTTCSSHHHHHHHHHHHHHHHHHHHTSTTSSSHHHHHHHHHHHHHHHHHHHCSSS
T ss_pred CHHHHHHHHHHHHHHHhCCHhhHHHHhhHHHHHHHhhhhcccccccCCHHHHHHHHHHHHHHHHHHHhcC
Confidence 7899999999999999999999999999999999999999999999899999999999999999998764
No 113
>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=99.41 E-value=1.5e-12 Score=122.04 Aligned_cols=125 Identities=14% Similarity=0.051 Sum_probs=98.8
Q ss_pred HHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccccccc--
Q 012638 298 EELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC-- 375 (459)
Q Consensus 298 e~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~-- 375 (459)
.+.+..|.+.|+.+|++++++..+++|++||+|+++|+..++|++. .+|.||++.+++|.+++++|++.+....+.
T Consensus 5 ~~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R~~~r~~~~~~~~ 82 (188)
T TIGR02943 5 PQELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKNKIIDALRAKGREVKVSDLD 82 (188)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHHHHHHHHHhhcccCCccccc
Confidence 3678899999999999999999999999999999999999999964 479999999999999999997654322110
Q ss_pred -------------------------c---------hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHH
Q 012638 376 -------------------------K---------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLA 413 (459)
Q Consensus 376 -------------------------~---------v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e 413 (459)
. ..+....+.+++..|+... -.+.+++|||+.||+|++
T Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~lgis~~ 162 (188)
T TIGR02943 83 DELDDEAFNALFTQNGHWAQHGQPQHWNTPEKQLENKEFWEVFEACLYHLPEQTARVFMMREVLGFESDEICQELEISTS 162 (188)
T ss_pred cccccchhhhhhccccchhccccccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHhCCCHH
Confidence 0 0011133455555554432 367899999999999999
Q ss_pred HHHHHHHhhcc
Q 012638 414 EIRSASECLRI 424 (459)
Q Consensus 414 ~Vk~~l~~ar~ 424 (459)
+|+..+.+++.
T Consensus 163 tvk~rl~Rar~ 173 (188)
T TIGR02943 163 NCHVLLYRARL 173 (188)
T ss_pred HHHHHHHHHHH
Confidence 99999998875
No 114
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=99.41 E-value=2.9e-12 Score=120.62 Aligned_cols=126 Identities=17% Similarity=0.202 Sum_probs=99.7
Q ss_pred HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccc-
Q 012638 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP- 374 (459)
Q Consensus 296 Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP- 374 (459)
+++.|+. |.+.|+++|++++++..+++|++||.|+.+|+.+..|+.. ..|.+|++.+++|.+++++|++.+.....
T Consensus 9 ~~~~l~~-~~~~l~~~a~~~l~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n~~~d~~Rk~~r~~~~~~ 85 (188)
T PRK12546 9 PRDELVE-HLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSDRRKHKREVPDPE 85 (188)
T ss_pred HHHHHHH-HHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHHHHHHHHHHhcccccCcc
Confidence 5666655 7799999999999999999999999999999999999863 36999999999999999999876432110
Q ss_pred -----------cc-hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 375 -----------CK-LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 375 -----------~~-v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
.. .......+..+...|+... -.+.+++|||+.||||+.+|+..+.+++.
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~v~~L~~~~g~s~~EIA~~LgiS~~tVk~~l~Rar~ 155 (188)
T PRK12546 86 GVHAASLAVKPAHDGRLAMSDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARA 155 (188)
T ss_pred cccccccccCCcchhHHHHHHHHHHHHhCCHHHhHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 00 0111234566666665543 25689999999999999999999998875
No 115
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=99.38 E-value=4.5e-12 Score=116.75 Aligned_cols=127 Identities=13% Similarity=0.082 Sum_probs=99.2
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccc---
Q 012638 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGI--- 371 (459)
Q Consensus 295 ~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~i--- 371 (459)
.|++.++..|.+.|+.++.++.++..+++|++||.|+.+|+. ..|++.. +|.+|++.+++|.+++++|++.+..
T Consensus 10 ~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~-~~~~~~~--~~~~wL~~iarn~~~d~~R~~~~~~~~~ 86 (172)
T PRK09651 10 LTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRNALEKAYL 86 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhh-ccccccc--CHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 489999999999999999999999999999999999999998 3565432 5999999999999999999754211
Q ss_pred ----cc-----ccc--h---HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 372 ----KI-----PCK--L---NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 372 ----rl-----P~~--v---~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
.+ |.. . .+....+..+...|+.+. ..+.+++|||+.||+|+++|+..+.+++.
T Consensus 87 ~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~ 161 (172)
T PRK09651 87 EMLALMPEGGAPSPEERESQLETLQLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKATE 161 (172)
T ss_pred hHHhhccccCCCChHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhhhccCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 01 110 0 122334566666665543 36689999999999999999999988764
No 116
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=99.38 E-value=4.5e-12 Score=118.60 Aligned_cols=127 Identities=13% Similarity=0.074 Sum_probs=100.1
Q ss_pred HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccc-
Q 012638 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP- 374 (459)
Q Consensus 296 Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP- 374 (459)
..+..+..+++.|+.+|.++.++..+++|++||.|+.+|+....|+.. .+|.||++.+++|.+++++|++.+.....
T Consensus 5 ~~~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~Rk~~~~~~~~~ 82 (182)
T PRK12511 5 SKRFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSG--GNLRTWLMSILHNAFIDELRRRRVEARRAD 82 (182)
T ss_pred chhhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCc--cchHHHHHHHHHHHHHHHHHhhcccccccc
Confidence 345568899999999999999999999999999999999999999864 37999999999999999999865421110
Q ss_pred -----------cc--hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 375 -----------CK--LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 375 -----------~~--v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
.. .......+.++...|+... -.+.+++|||+.||||+++|+..+.+++.
T Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~eg~s~~EIA~~lgis~~tV~~~l~Rar~ 153 (182)
T PRK12511 83 ELAVLADASLPAAQEHAVRLAQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARA 153 (182)
T ss_pred chhhccccCCCcchHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 00 1112234555666555543 26789999999999999999999988875
No 117
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=99.33 E-value=1.1e-11 Score=120.96 Aligned_cols=133 Identities=15% Similarity=-0.055 Sum_probs=100.4
Q ss_pred HHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHH
Q 012638 287 KQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVA 365 (459)
Q Consensus 287 ~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lr 365 (459)
.+....|+. +++.+++.| +.|+.+|.++.++..+++||+||.|+.+|+. |+.. ..|.||++.+++|.+++++|
T Consensus 9 ~~~~~~~~~~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~~---~~~~--~~~~~WL~~IarN~~id~~R 82 (228)
T PRK06704 9 LKNHIDMNHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQK---YSNK--DICMTLVYKIARNRWLDQIK 82 (228)
T ss_pred HhcccCCCHHHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH---cCcc--ccHHHHHHHHHHHHHHHHHh
Confidence 444555655 888877777 7899999999999999999999999999986 5543 25999999999999999999
Q ss_pred hhcccccccc--------c-hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhccC
Q 012638 366 RHARGIKIPC--------K-LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRIV 425 (459)
Q Consensus 366 k~sr~irlP~--------~-v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~ 425 (459)
++.+...+.. . ..+....+..+...|+... ..+.|++|||+.||||+++|+..+.+++..
T Consensus 83 k~k~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~R~v~lL~~~eg~S~~EIAe~LgiS~~tVksrL~Rark~ 159 (228)
T PRK06704 83 SKSVHEKIRDQITFEEPHEKIADLHEMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNR 159 (228)
T ss_pred ccccccccccccccCChHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHhhCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 7654322111 0 1122233455555555543 256799999999999999999999998864
No 118
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=99.33 E-value=1.2e-11 Score=111.91 Aligned_cols=123 Identities=15% Similarity=0.142 Sum_probs=94.5
Q ss_pred HHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccc------
Q 012638 299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIK------ 372 (459)
Q Consensus 299 ~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~ir------ 372 (459)
+++..|.+.|+.+|.++.++..+++|++||+++++|+....|++. .|.+|++.+++|.+++++|++++...
T Consensus 2 ~~~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~---~~~~wl~~iarn~~~d~~R~~~~~~~~~~~~~ 78 (163)
T PRK07037 2 DVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVK---QPVAYLFRIVRNLAIDHYRRQALENKYHGDEE 78 (163)
T ss_pred hHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhccccCCcc---cHHHHHHHHHHHHHHHHHHhhccccccccccc
Confidence 467889999999999999999999999999999999998888753 48899999999999999997653211
Q ss_pred ----ccc---c------hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 373 ----IPC---K------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 373 ----lP~---~------v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
.+. . ..+....+.++...|+... -.+.+++|||+.||+|+++|+..+.+++.
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~EIA~~lgis~~tV~~~l~ra~~ 151 (163)
T PRK07037 79 DGLDVPSPEASPEAALINRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALV 151 (163)
T ss_pred cccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 110 0 0112233444555444332 36789999999999999999999887764
No 119
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=99.32 E-value=1.2e-11 Score=112.03 Aligned_cols=121 Identities=12% Similarity=0.030 Sum_probs=94.2
Q ss_pred HHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccccc-------
Q 012638 301 IKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI------- 373 (459)
Q Consensus 301 I~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irl------- 373 (459)
+..|.+.++.++.+++++..+++|++||+++.+|+..+.|++ + +|.||++.+++|.+++++|++.+....
T Consensus 1 ~~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~--~-~~~~wL~~ia~n~~~d~~R~~~~~~~~~~~~~~~ 77 (159)
T PRK12527 1 MENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQI--E-HPRAFLYRTALNLVVDRHRRHRVRQAEPLEVLDE 77 (159)
T ss_pred ChhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhccccccc--c-chHHHHHHHHHHHHHHHHHHHhcccccchhhhhc
Confidence 357889999999999999999999999999999999999875 2 799999999999999999975321110
Q ss_pred ------c--cch---HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 374 ------P--CKL---NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 374 ------P--~~v---~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
| ... .+....+..+...|+... ..+.+++|||+.||+|+++|+..+.+++.
T Consensus 78 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~ra~~ 147 (159)
T PRK12527 78 EERLHSPSPQTRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMK 147 (159)
T ss_pred cccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 0 000 112234556666555543 36789999999999999999999988865
No 120
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=99.31 E-value=2.3e-11 Score=111.51 Aligned_cols=127 Identities=12% Similarity=0.010 Sum_probs=97.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccc---
Q 012638 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGI--- 371 (459)
Q Consensus 295 ~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~i--- 371 (459)
.++.+++..|.+.++.+|.+++++..+++|++||.|+.+|+..+.++. ..|.+|++++++|.+++++|+.....
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 489999999999999999999999999999999999999986665542 36999999999999999998653210
Q ss_pred ----cccc----c------hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 372 ----KIPC----K------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 372 ----rlP~----~------v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
..|. . ..+....+.+++..|+... -.+.+++|||+.||+|+++|+..+.++..
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~eg~s~~EIA~~l~is~~tV~~~l~ra~~ 160 (168)
T PRK12525 86 QSLAEAPEAVQPSPEEQWMVIETLLAIDRLLDGLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAFK 160 (168)
T ss_pred HHHhcccccccCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 0110 0 1112233455555554443 36789999999999999999999887754
No 121
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=99.25 E-value=5.1e-11 Score=119.11 Aligned_cols=125 Identities=16% Similarity=0.054 Sum_probs=95.6
Q ss_pred HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccc--c--
Q 012638 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG--I-- 371 (459)
Q Consensus 296 Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~--i-- 371 (459)
...+++..|.+.++.+|++++++..++||++||.++. |.....|+. ..|.||++++++|.+++++|++.+. .
T Consensus 5 ~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~-~~~~~~~~~---~~~~~WL~~Ia~n~~~d~lR~~~~~~~~~~ 80 (293)
T PRK09636 5 DAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQI---RDPRAWLTRVVTRLCLDRLRSARHRRETYV 80 (293)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHhcccccc---cCHHHHHHHHHHHHHHHHHHhhhccccccc
Confidence 4678999999999999999999999999999999999 556677762 4799999999999999999975421 1
Q ss_pred --ccccch-------------HHH-HHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 372 --KIPCKL-------------NRE-ISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 372 --rlP~~v-------------~e~-i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
.+|... .+. ...+..+...|+... -.+.+++|||+.||+|+++|+..+++++.
T Consensus 81 ~~~~~e~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~R~v~~L~~~~g~s~~EIA~~lg~s~~tVk~~l~RAr~ 157 (293)
T PRK09636 81 GPWLPEPVVEELDDPLEAVVAAEDLSLALMLALERLSPLERAAFLLHDVFGVPFDEIASTLGRSPAACRQLASRARK 157 (293)
T ss_pred CCcCCcCCCCCCCChHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 111110 111 122445555554443 25689999999999999999999998865
No 122
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=99.20 E-value=3.5e-11 Score=97.47 Aligned_cols=74 Identities=30% Similarity=0.359 Sum_probs=64.0
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccCCCCCCccccCCCCC-CCCcc
Q 012638 379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPPFF-FPSFA 452 (459)
Q Consensus 379 e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~~d~~~~l~e~i~D~-~~~~~ 452 (459)
+.+++|.++..+|.+++||.||.+|||+.|||++++|..++.+++.++|||.+++.+++.++.++|+|+ .++|+
T Consensus 1 E~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~~~~l~~~i~d~~~~~P~ 75 (78)
T PF04539_consen 1 EKLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDEDDSTLGDFIEDDDAPSPE 75 (78)
T ss_dssp HHHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSSSEEGGGSSB-SSS--HH
T ss_pred ChHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCCCCchhheecCCCCCChh
Confidence 467899999999999999999999999999999999999999999999999999999899999999998 56654
No 123
>PRK09191 two-component response regulator; Provisional
Probab=99.18 E-value=9.7e-11 Score=112.58 Aligned_cols=121 Identities=16% Similarity=0.034 Sum_probs=94.7
Q ss_pred HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccccccc
Q 012638 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC 375 (459)
Q Consensus 296 Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~ 375 (459)
|+.+|+..|.+.|+++|.++.++..+++|++||+|+.+|+...+|++. ..|.||+++++++...+...... ....|.
T Consensus 2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~--~~~~~wl~~~~~~~~~~~~~~~~-~~~~~~ 78 (261)
T PRK09191 2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEA--SSPRVGLYRLFHRLWSSAGANDP-EPGSPF 78 (261)
T ss_pred chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCC--cchhhHHHHHHHHHhccccccCC-CCCCCc
Confidence 578999999999999999999999999999999999999999999874 46999999999887644322110 001111
Q ss_pred chHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 376 KLNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 376 ~v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
...+.+++..|+... -.+.|++|||+.||+|+++|+..+.+++.
T Consensus 79 -----~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~l~~s~~tV~~~l~ra~~ 130 (261)
T PRK09191 79 -----EARAERRLAGLTPLPRQAFLLTALEGFSVEEAAEILGVDPAEAEALLDDARA 130 (261)
T ss_pred -----hHHHHHHHHhCCHHHhHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 115666666665543 25689999999999999999999887764
No 124
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=99.18 E-value=1.7e-10 Score=115.00 Aligned_cols=122 Identities=17% Similarity=0.046 Sum_probs=90.6
Q ss_pred HHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccc------c
Q 012638 299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGI------K 372 (459)
Q Consensus 299 ~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~i------r 372 (459)
+++..|.+.++.+|++++++..++||++||+++.+++. .|+. ...|.+|++++++|.++|++|++.+.. .
T Consensus 1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~--~~~~~awL~~Ia~n~~ld~lR~~~~~~~~~~~~~ 76 (281)
T TIGR02957 1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQ--IENPKAYLTKVVTRRCIDVLRSARARREVYVGPW 76 (281)
T ss_pred ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Cccc--ccCHHHHHHHHHHHHHHHHHHHhhhcccccCCCC
Confidence 47899999999999999999999999999999998775 5543 236999999999999999999764211 1
Q ss_pred cccch----------HHHHH----HHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 373 IPCKL----------NREIS----KIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 373 lP~~v----------~e~i~----kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
+|... ..... .+..+...|+... -.+.+++|||+.||+|+.+|+..+++++.
T Consensus 77 ~~e~~~~~~~~~~~~~~~~e~~~~~l~~~l~~L~~~~R~v~~L~~~~g~s~~EIA~~lg~s~~tVr~~l~RAr~ 150 (281)
T TIGR02957 77 LPEPLLTTSADPAESVELAESLSMAYLLLLERLSPLERAVFVLREVFDYPYEEIASIVGKSEANCRQLVSRARR 150 (281)
T ss_pred CCcccCCCCCChHHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 22110 01111 1233333333322 25689999999999999999999998875
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=99.17 E-value=1.3e-10 Score=103.34 Aligned_cols=113 Identities=16% Similarity=0.140 Sum_probs=83.8
Q ss_pred HHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhh-----cCCCCCCchhhHHHHHHHHHHHHHHHhhcccc
Q 012638 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAER-----FDHTRGYKFSTYVQYWIRKSISKMVARHARGI 371 (459)
Q Consensus 297 re~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieK-----FDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~i 371 (459)
++.++..|.++|+.+|++|... +| +||.++.+|....+ |++. ..|.||++.+++|.+++++|++.+..
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 4689999999999999999652 34 49999999999865 5542 47999999999999999999765421
Q ss_pred ccc-------------cc--hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHH
Q 012638 372 KIP-------------CK--LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIR 416 (459)
Q Consensus 372 rlP-------------~~--v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk 416 (459)
... .. ..+....+.++...|+... -.+.|++|||+.||||+++|+
T Consensus 74 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~~~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 74 KIIYNSEITDIKLSLINVYSSNDLEFEFNDLISILPNKQKKIIYMKFFEDMKEIDIAKKLHISRQSVY 141 (142)
T ss_pred hhhhhhhhhccccchhHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHhhc
Confidence 110 00 0112234566666666543 266899999999999999986
No 126
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=99.17 E-value=2.6e-10 Score=114.72 Aligned_cols=127 Identities=10% Similarity=-0.110 Sum_probs=96.1
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccc-c--
Q 012638 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG-I-- 371 (459)
Q Consensus 295 ~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~-i-- 371 (459)
..+..++..|.+.++.+|+++.++..++||++||.|+.+|++...+ ...|.+|++.+++|.|+|++|+..+. .
T Consensus 5 ~~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~----~~~~~aWL~~Ia~n~~id~lRk~~~rr~~~ 80 (290)
T PRK09635 5 DPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGD----IDDERGWLIVVTSRLCLDHIKSASTRRERP 80 (290)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCccc----cccHHHHHHHHHHHHHHHHHhhhhccCcCc
Confidence 3688999999999999999999999999999999999999987543 13699999999999999999974321 1
Q ss_pred -----ccccc-------h------H-HHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 372 -----KIPCK-------L------N-REISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 372 -----rlP~~-------v------~-e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
..|.. - . +....+..+...|+... ..+.+++|||+.||+|+.+|+..+++++.
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~al~~~L~~L~p~~R~vf~L~~~~g~s~~EIA~~Lgis~~tVr~~l~RAr~ 160 (290)
T PRK09635 81 QDIAAWHDGDASVSSVDPADRVTLDDEVRLALLIMLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARR 160 (290)
T ss_pred ccccccCccccCCCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHHhCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 11100 0 0 01123444444444332 25689999999999999999999998875
Q ss_pred C
Q 012638 425 V 425 (459)
Q Consensus 425 ~ 425 (459)
.
T Consensus 161 ~ 161 (290)
T PRK09635 161 K 161 (290)
T ss_pred H
Confidence 3
No 127
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=99.07 E-value=6.8e-10 Score=100.00 Aligned_cols=105 Identities=11% Similarity=0.024 Sum_probs=77.6
Q ss_pred CCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccc----------------------
Q 012638 317 GLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP---------------------- 374 (459)
Q Consensus 317 g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP---------------------- 374 (459)
++..+++|++||+|+.+|+....+ + +..|.+|++.+++|.+++++|++.+.....
T Consensus 2 ~~~~~AeDivQe~fl~~~~~~~~~-~--~~~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 78 (161)
T PRK09047 2 RDDDAALDIVQDAMIKLAEKYGDR-P--AAEWPPLFQRILQNRIHDWFRRQKVRNTWVSLFSSFSDDDDDDDFDPLETLD 78 (161)
T ss_pred CCHHHHHHHHHHHHHHHHHHHhhc-c--cCchHHHHHHHHHHHHHHHHHhhcccccccccccccccccccccccHHHHhc
Confidence 445679999999999999998863 3 357999999999999999999765321110
Q ss_pred ------cch------HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 375 ------CKL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 375 ------~~v------~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
... .+....+.++...|+... ..+.+++|||+.||||+++|+..+.+++.
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~ 148 (161)
T PRK09047 79 SADEGAESPADKLERAQVLQLIEEAIQKLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATH 148 (161)
T ss_pred cccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 000 112234555666555543 36789999999999999999999998875
No 128
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=98.85 E-value=7.3e-08 Score=90.55 Aligned_cols=141 Identities=16% Similarity=0.112 Sum_probs=100.8
Q ss_pred HHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCC---CCCHHH--HHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHH
Q 012638 284 RVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGL---GIPFSD--LLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIR 357 (459)
Q Consensus 284 eeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~---g~d~ED--LIQEG~IGLirAieKFDp~kG~rFSTYa~~wIr 357 (459)
.+|+.+++.|+. |.++|+..|.+.++.+|+++... +.+.+| |++|.|+.+++.-...+...-..|..|+...++
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 578899999988 99999999999999999987633 345555 577888877773333233323469999999999
Q ss_pred HHHHHHHHhhcccccc------c---------cchHHHHHHHHHHHHHHHH-----------HcCCCCCHHHHHHHhCCC
Q 012638 358 KSISKMVARHARGIKI------P---------CKLNREISKIQKARKALTN-----------SHGKYPEDIEIAKYTGLS 411 (459)
Q Consensus 358 naI~d~Lrk~sr~irl------P---------~~v~e~i~kI~ka~~~L~~-----------~lgr~PT~eEIAe~LGIS 411 (459)
+.++|++|++....|- + ....+..-.+.++...|.. ..-.+.|.+|||+.||||
T Consensus 85 r~lid~~R~~~a~KRg~~~~~~~l~~~~~~~~~~~~~~~~~l~e~l~~L~~l~~~~~~~v~l~~~~Gls~~EIA~~lgiS 164 (185)
T PF07638_consen 85 RKLIDHARRRQAQKRGGDQVRVELDERADSGDEPSPEELLELEEALERLLALDPRQRRVVELRFFEGLSVEEIAERLGIS 164 (185)
T ss_pred HHHHHHHHHHHHHhcCCCCcccchhhhhccccCCCHHHHHHHHHHHHHHHccCHHHHHHHHHHHHCCCCHHHHHHHHCcC
Confidence 9999999976554331 1 1122233334444443322 123568999999999999
Q ss_pred HHHHHHHHHhhcc
Q 012638 412 LAEIRSASECLRI 424 (459)
Q Consensus 412 ~e~Vk~~l~~ar~ 424 (459)
+.+|+..++.++.
T Consensus 165 ~~tV~r~l~~aR~ 177 (185)
T PF07638_consen 165 ERTVRRRLRRARA 177 (185)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999988763
No 129
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=96.46 E-value=0.062 Score=52.37 Aligned_cols=35 Identities=17% Similarity=0.311 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 012638 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (459)
Q Consensus 254 ~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~ 288 (459)
++.+....+...+|++||.++.|+.+|++.+.+..
T Consensus 88 ~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~ 122 (238)
T TIGR02393 88 KLIKAERQLTQELGREPTDEELAERMGMPAEKVRE 122 (238)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 44556677888899999999999999999887654
No 130
>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=96.29 E-value=0.0011 Score=47.14 Aligned_cols=34 Identities=12% Similarity=0.049 Sum_probs=24.9
Q ss_pred ChhHHHHHHhccCCCCCCChHHHHHHHHHhHHHHHHH
Q 012638 220 PTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLE 256 (459)
Q Consensus 220 p~~~~~~~~~~~~~~~lLt~~eE~eL~~~i~~~~~le 256 (459)
|...|+ ....+.||||++||++|+++|+.+...+
T Consensus 3 ~l~~Yl---~ei~~~~LLt~eeE~~LA~~i~~g~~~a 36 (37)
T PF00140_consen 3 SLRLYL---KEIGRYPLLTAEEEIELARRIRKGDEAA 36 (37)
T ss_dssp HHHHHH---HHHHHS-EETTHHHHHHHHHHHHHHHHH
T ss_pred HHHHHH---HHHcCCCCCCHHHHHHHHHHHHHhHHhc
Confidence 444555 3345679999999999999999987653
No 131
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=96.08 E-value=0.088 Score=51.73 Aligned_cols=36 Identities=17% Similarity=0.178 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHH
Q 012638 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQH 289 (459)
Q Consensus 254 ~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~ 289 (459)
.+.+....+...+|+.|+..++|+..|++.+++...
T Consensus 110 ~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~ 145 (251)
T PRK07670 110 KVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEAT 145 (251)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHH
Confidence 345556667778899999999999999998886653
No 132
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=95.95 E-value=0.12 Score=54.20 Aligned_cols=128 Identities=13% Similarity=0.166 Sum_probs=72.3
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhchHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHH-HHH
Q 012638 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAG-NVG 332 (459)
Q Consensus 254 ~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l~~G~~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG-~IG 332 (459)
++.+....|...+|+.||.++.|..+|++.+.+...+.. +.. ...+++.+.++ -..
T Consensus 217 ~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~-------------------~~~----~~SLd~~~~~~~~~~ 273 (367)
T PRK09210 217 KLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKI-------------------AQE----PVSLETPIGEEDDSH 273 (367)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHH-------------------hcC----CCCcCCCCCCCCcch
Confidence 455667788888999999999999999999886543221 111 11111111110 011
Q ss_pred HHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccchHHHHHHHHHHHHHHHHHcC----CCCCHHHHHHHh
Q 012638 333 VLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHG----KYPEDIEIAKYT 408 (459)
Q Consensus 333 LirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~v~e~i~kI~ka~~~L~~~lg----r~PT~eEIAe~L 408 (459)
+...+. |..............++..+.++|. .+|..-. .-|...+| ...|.+|||+.|
T Consensus 274 l~d~i~--d~~~~~p~~~~~~~~~~~~l~~~l~------~L~~rEr----------~Vl~lrygl~~~~~~tl~EIa~~l 335 (367)
T PRK09210 274 LGDFIE--DQDATSPADHAAYELLKEQLEDVLD------TLTDREE----------NVLRLRFGLDDGRTRTLEEVGKVF 335 (367)
T ss_pred hhhhcc--CCCCCCHHHHHHHHHHHHHHHHHHH------hCCHHHH----------HHHHHHhccCCCCCccHHHHHHHH
Confidence 111111 1111223444455556666666664 2332211 11222233 678999999999
Q ss_pred CCCHHHHHHHHHhh
Q 012638 409 GLSLAEIRSASECL 422 (459)
Q Consensus 409 GIS~e~Vk~~l~~a 422 (459)
|||.++|+.+...+
T Consensus 336 gvs~erVrQi~~~A 349 (367)
T PRK09210 336 GVTRERIRQIEAKA 349 (367)
T ss_pred CCCHHHHHHHHHHH
Confidence 99999999886654
No 133
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=95.82 E-value=0.047 Score=54.06 Aligned_cols=35 Identities=20% Similarity=0.280 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 012638 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (459)
Q Consensus 254 ~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~ 288 (459)
++.+.+..|...+|++|+.++.|+.+|++.+++..
T Consensus 114 ~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~ 148 (256)
T PRK07408 114 QAKKVRQELRQELGRQPTDQEIAQALDISLEEWQE 148 (256)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHH
Confidence 45567778888999999999999999999887654
No 134
>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=95.82 E-value=0.035 Score=44.37 Aligned_cols=57 Identities=21% Similarity=0.243 Sum_probs=47.8
Q ss_pred HHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhh----C--CCCCHHHHHHHHHHHHHHhhhhcC
Q 012638 285 VLKQHLAFGWY-CREELIKSTRPLVLFLARNYR----G--LGIPFSDLLQAGNVGVLQGAERFD 341 (459)
Q Consensus 285 eL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~----g--~g~d~EDLIQEG~IGLirAieKFD 341 (459)
+++.++.+|+. |.+++++.|.|++.+.+.|-. | .+.--+|+-|+--..|+.++-+|+
T Consensus 2 ~vI~~A~~GD~~A~~~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kLi~~I~~F~ 65 (65)
T PF12645_consen 2 EVIKAAKQGDPEAMEEILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKLIEAILKFE 65 (65)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHHHHHHHccC
Confidence 35677889987 999999999999999997722 2 244559999999999999999996
No 135
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=95.76 E-value=0.26 Score=48.95 Aligned_cols=35 Identities=26% Similarity=0.284 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 012638 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (459)
Q Consensus 254 ~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~ 288 (459)
.+.+.+..|+..+|++||.++.|...|++.+.+..
T Consensus 119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~ 153 (268)
T PRK06288 119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYNS 153 (268)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHH
Confidence 45566778888899999999999999999877654
No 136
>PRK05949 RNA polymerase sigma factor; Validated
Probab=95.70 E-value=0.14 Score=52.86 Aligned_cols=35 Identities=11% Similarity=0.275 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 012638 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (459)
Q Consensus 254 ~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~ 288 (459)
++.+.+..+...+|++|+.++.|+.+|++.+.+..
T Consensus 179 ~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~ 213 (327)
T PRK05949 179 KIKKTQRELSQKLGRSATPAEIAKELELEPSQIRE 213 (327)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHH
Confidence 45556667778889999999999999999877654
No 137
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=95.38 E-value=0.27 Score=49.05 Aligned_cols=35 Identities=20% Similarity=0.305 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 012638 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (459)
Q Consensus 254 ~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~ 288 (459)
++.+....|...+|+.||.++.|+..|++.+++..
T Consensus 128 ~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~ 162 (264)
T PRK07122 128 RLGRATAELSQRLGRAPTASELAAELGMDREEVVE 162 (264)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 34456667777889999999999999999988754
No 138
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=95.37 E-value=0.23 Score=49.31 Aligned_cols=29 Identities=17% Similarity=0.022 Sum_probs=25.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
..+.|.+|||+.||+|.++|+.+..++..
T Consensus 219 ~e~~t~~EIA~~lgis~~~V~~~~~ral~ 247 (257)
T PRK05911 219 YEELVLKEIGKILGVSESRVSQIHSKALL 247 (257)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 46789999999999999999999887653
No 139
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=95.30 E-value=0.36 Score=48.25 Aligned_cols=126 Identities=14% Similarity=0.073 Sum_probs=73.7
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhchHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHH
Q 012638 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGV 333 (459)
Q Consensus 254 ~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l~~G~~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGL 333 (459)
+++.+..+|+.++||+||.++.|+..|++.++....+..+. -..+.++--.....+.. +
T Consensus 111 ~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~----------~~~~~sld~~~~~~~d~--~--------- 169 (247)
T COG1191 111 RIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAIN----------GSQLLSLDEDVLKDDDD--D--------- 169 (247)
T ss_pred HHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhc----------cccccchhhhhcccccc--c---------
Confidence 45667888999999999999999999999988765433322 11111111111111110 0
Q ss_pred HHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHH
Q 012638 334 LQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLA 413 (459)
Q Consensus 334 irAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e 413 (459)
+. ..-+..+..+-.+...+.+..++. .+|.. -. .-+.-.+..+.|..|||+.||||+.
T Consensus 170 ---~~---~~~~~~~~~~~~~~~~~~l~~ai~------~L~ER----Ek------~Vl~l~y~eelt~kEI~~~LgISes 227 (247)
T COG1191 170 ---VD---DQIENPDDGVEKEELLEILKEAIE------PLPER----EK------LVLVLRYKEELTQKEIAEVLGISES 227 (247)
T ss_pred ---hh---hccccchhHHHHHHHHHHHHHHHH------ccCHH----HH------HHHHHHHHhccCHHHHHHHhCccHH
Confidence 11 112234555556666666666664 12211 11 1111223457899999999999999
Q ss_pred HHHHHHHhh
Q 012638 414 EIRSASECL 422 (459)
Q Consensus 414 ~Vk~~l~~a 422 (459)
.|-.+...+
T Consensus 228 ~VSql~kka 236 (247)
T COG1191 228 RVSRLHKKA 236 (247)
T ss_pred HHHHHHHHH
Confidence 998776544
No 140
>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=95.16 E-value=0.41 Score=46.05 Aligned_cols=35 Identities=26% Similarity=0.333 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 012638 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (459)
Q Consensus 254 ~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~ 288 (459)
++.+...+|...+|+.|+.++.|+.+|++.+.+..
T Consensus 84 ~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~ 118 (224)
T TIGR02479 84 KLERAIRELEARLGREPTEEEIAEELGMDLKEYRQ 118 (224)
T ss_pred HHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHH
Confidence 45566777888899999999999999999877654
No 141
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=95.11 E-value=0.32 Score=48.84 Aligned_cols=28 Identities=18% Similarity=0.061 Sum_probs=25.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
.+.|++|||+.||||+++|+.++++++.
T Consensus 241 e~~s~~EIA~~Lgis~~tVk~~l~rAlk 268 (285)
T TIGR02394 241 EPATLEEVAAEVGLTRERVRQIQVEALK 268 (285)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5679999999999999999999988864
No 142
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=95.04 E-value=0.43 Score=52.30 Aligned_cols=128 Identities=15% Similarity=0.177 Sum_probs=70.4
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhchHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHH-HHHH
Q 012638 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQA-GNVG 332 (459)
Q Consensus 254 ~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l~~G~~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQE-G~IG 332 (459)
++.++...|...+|+.||.++.|+.+|++.+.+....+ +....+.+++.+.+ +-..
T Consensus 359 kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~-----------------------~~~~~~SLD~~i~~d~~~~ 415 (509)
T PRK05901 359 KLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQK-----------------------YNREPISLDKTIGKEGDSQ 415 (509)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH-----------------------hcCCCcccccccccCCccc
Confidence 45567778888899999999999999999887654221 11122223332211 1111
Q ss_pred HHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccchHHHHHHHHHHHHHHHHHc----CCCCCHHHHHHHh
Q 012638 333 VLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSH----GKYPEDIEIAKYT 408 (459)
Q Consensus 333 LirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~v~e~i~kI~ka~~~L~~~l----gr~PT~eEIAe~L 408 (459)
+...+. |...............+..+..+|. .+|.. -.. -|...+ +...|.+|||+.|
T Consensus 416 l~d~l~--D~~~~~p~~~~~~~~l~~~L~~aL~------~L~eR----Er~------VI~lRyGL~~~e~~TL~EIa~~l 477 (509)
T PRK05901 416 FGDFIE--DSEAVSPVDAVSFTLLQDQLQEVLE------TLSER----EAG------VIRMRFGLTDGQPKTLDEIGQVY 477 (509)
T ss_pred HHHhcc--CCCCCCHHHHHHHHHHHHHHHHHHh------hCCHH----HHH------HHHHHhhccCCCCCCHHHHHHHH
Confidence 222111 1111112333334444444444443 12211 111 122223 4678999999999
Q ss_pred CCCHHHHHHHHHhh
Q 012638 409 GLSLAEIRSASECL 422 (459)
Q Consensus 409 GIS~e~Vk~~l~~a 422 (459)
|||.++|+.+...+
T Consensus 478 GVSrERVRQIe~kA 491 (509)
T PRK05901 478 GVTRERIRQIESKT 491 (509)
T ss_pred CCCHHHHHHHHHHH
Confidence 99999999876554
No 143
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=95.02 E-value=0.41 Score=51.24 Aligned_cols=37 Identities=11% Similarity=0.313 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHH
Q 012638 253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQH 289 (459)
Q Consensus 253 ~~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~ 289 (459)
-++.+.+..|...+|+.|+.++.|+++|++.+.+...
T Consensus 262 ~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~ 298 (415)
T PRK07598 262 NKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREV 298 (415)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 3566777788888999999999999999999887653
No 144
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=94.88 E-value=0.49 Score=48.88 Aligned_cols=35 Identities=29% Similarity=0.470 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 012638 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (459)
Q Consensus 254 ~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~ 288 (459)
++.+++..|...+|+.||.++.|..+|++.+.+..
T Consensus 174 ~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~ 208 (324)
T PRK07921 174 KLARIKRELHQQLGREATDEELAEESGIPEEKIAD 208 (324)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHH
Confidence 45667778888899999999999999999887654
No 145
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=94.67 E-value=0.23 Score=47.94 Aligned_cols=34 Identities=32% Similarity=0.446 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 012638 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (459)
Q Consensus 255 le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~ 288 (459)
+.+....+...+|+.||.++.|+..|++.+++..
T Consensus 99 ~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~ 132 (231)
T TIGR02885 99 IRYMKEELSKELGREPTINELAEALGVSPEEIVM 132 (231)
T ss_pred HHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHH
Confidence 3445567777889999999999999999877654
No 146
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=94.65 E-value=0.54 Score=47.61 Aligned_cols=35 Identities=14% Similarity=0.308 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 012638 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (459)
Q Consensus 254 ~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~ 288 (459)
++.+.+..+...+|+.|+.++.|..+|++.+.+..
T Consensus 162 ~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~ 196 (298)
T TIGR02997 162 KIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRE 196 (298)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 44555667777889999999999999999887654
No 147
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=94.25 E-value=0.43 Score=47.06 Aligned_cols=36 Identities=14% Similarity=0.147 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHH
Q 012638 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQH 289 (459)
Q Consensus 254 ~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~ 289 (459)
++.+....+..++|++||.++.|+..|++.+.+...
T Consensus 121 ~~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~ 156 (254)
T TIGR02850 121 KALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFA 156 (254)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHH
Confidence 344556677788899999999999999998887653
No 148
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=94.05 E-value=0.14 Score=41.06 Aligned_cols=38 Identities=26% Similarity=0.408 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHH
Q 012638 253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL 290 (459)
Q Consensus 253 ~~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l 290 (459)
.++.+++.+|+.++||.||.++.|+.+|++.+++...+
T Consensus 4 ~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l 41 (78)
T PF04539_consen 4 RKIERARRELEQELGREPTDEEIAEELGISVEEVRELL 41 (78)
T ss_dssp HHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHH
Confidence 46778889999999999999999999999998876543
No 149
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=93.89 E-value=0.62 Score=47.11 Aligned_cols=28 Identities=11% Similarity=-0.003 Sum_probs=25.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
.+.|.+|||+.||||.++|+.+.+.+..
T Consensus 244 ~~~t~~EIa~~lgvs~~~V~q~~~~Al~ 271 (289)
T PRK07500 244 DGATLEALGEELGISKERVRQIEARALE 271 (289)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6789999999999999999999887754
No 150
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=93.88 E-value=0.74 Score=47.29 Aligned_cols=36 Identities=14% Similarity=0.375 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 012638 253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (459)
Q Consensus 253 ~~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~ 288 (459)
.++.+.+..+...+|+.||.++.|.++|++.+.+..
T Consensus 168 ~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~ 203 (317)
T PRK07405 168 NKIKKAQRQLSQQLGRAATIGELAEELELTPKQVRE 203 (317)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHH
Confidence 345666777788889999999999999998877654
No 151
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=93.87 E-value=1.1 Score=43.36 Aligned_cols=29 Identities=14% Similarity=-0.011 Sum_probs=25.7
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
..+.|++|||+.||||+++|+..+.+++.
T Consensus 198 ~~g~s~~EIA~~lgis~~tV~~~~~ra~~ 226 (236)
T PRK06986 198 QEELNLKEIGAVLGVSESRVSQIHSQAIK 226 (236)
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 46789999999999999999999887764
No 152
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=93.60 E-value=1.1 Score=47.17 Aligned_cols=35 Identities=14% Similarity=0.230 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 012638 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (459)
Q Consensus 254 ~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~ 288 (459)
++.+....|...+|+.||.++.|+.+|++.+.+..
T Consensus 224 ~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~ 258 (373)
T PRK07406 224 RIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRF 258 (373)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 45566777888889999999999999999887643
No 153
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=93.37 E-value=0.51 Score=46.37 Aligned_cols=30 Identities=10% Similarity=0.016 Sum_probs=25.7
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 395 HGKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 395 lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
+..+.|++|||+.||+|+++|+..++.+..
T Consensus 218 ~~~g~s~~eIA~~lgis~~~V~~~~~ra~~ 247 (255)
T TIGR02941 218 FEENLSQKETGERLGISQMHVSRLQRQAIS 247 (255)
T ss_pred HcCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 356789999999999999999998877653
No 154
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=92.80 E-value=0.11 Score=38.95 Aligned_cols=31 Identities=19% Similarity=0.062 Sum_probs=23.4
Q ss_pred HcCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 394 SHGKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 394 ~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
.+..+.|++|||+.+|+|+.+|+..+.+++.
T Consensus 22 ~~~~g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 22 RYFQGMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp HHTS---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred HHHHCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 3467889999999999999999999988763
No 155
>PRK05572 sporulation sigma factor SigF; Validated
Probab=92.79 E-value=1.7 Score=42.71 Aligned_cols=34 Identities=24% Similarity=0.357 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHH
Q 012638 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLK 287 (459)
Q Consensus 254 ~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~ 287 (459)
++.+....+..+.|+.|+..+.|++.|++.+.+.
T Consensus 119 ~~~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v~ 152 (252)
T PRK05572 119 KIRKDKDELSKELGREPTIEELAEYLGVTPEEVV 152 (252)
T ss_pred HHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHH
Confidence 3455566777778999999999999999887653
No 156
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=92.69 E-value=1.8 Score=42.72 Aligned_cols=34 Identities=15% Similarity=0.152 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 012638 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (459)
Q Consensus 255 le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~ 288 (459)
+.+....+...+|+.|+..+.|..+|++.+.+..
T Consensus 125 ~~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~ 158 (258)
T PRK08215 125 ALQVREKLINENSKEPTVEEIAKELEVPREEVVF 158 (258)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHH
Confidence 3445667777889999999999999999888654
No 157
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=91.90 E-value=2.7 Score=41.02 Aligned_cols=34 Identities=6% Similarity=0.120 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 012638 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (459)
Q Consensus 255 le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~ 288 (459)
+.+....+...+|+.|+.++.|+.+|++.+++..
T Consensus 103 i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~ 136 (231)
T PRK12427 103 TNDAIREIAKRLGHEPNFEEISAELNLTAEEYQE 136 (231)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHH
Confidence 4455677778889999999999999999887654
No 158
>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=91.64 E-value=0.79 Score=44.02 Aligned_cols=29 Identities=17% Similarity=0.020 Sum_probs=25.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
..+.|++|||+.||+|..+|...+.++..
T Consensus 192 ~~~~s~~eIA~~lgis~~~v~~~~~ra~~ 220 (227)
T TIGR02980 192 FEDKTQSEIAERLGISQMHVSRLLRRALK 220 (227)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 45789999999999999999999887754
No 159
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=91.62 E-value=0.59 Score=37.30 Aligned_cols=44 Identities=18% Similarity=0.240 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCC-HHHHHHHHHhh
Q 012638 379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLS-LAEIRSASECL 422 (459)
Q Consensus 379 e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS-~e~Vk~~l~~a 422 (459)
+...+|-.++.+...+.|..||..|||+.+|++ ..+|...+...
T Consensus 6 ~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~L 50 (65)
T PF01726_consen 6 ERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKAL 50 (65)
T ss_dssp HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHH
Confidence 344566677777788889999999999999997 99999887754
No 160
>PHA02547 55 RNA polymerase sigma factor; Provisional
Probab=91.06 E-value=0.66 Score=43.91 Aligned_cols=64 Identities=16% Similarity=0.185 Sum_probs=51.2
Q ss_pred HHHHHHHHHHhhCCCCC---HHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhc
Q 012638 305 RPLVLFLARNYRGLGIP---FSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA 368 (459)
Q Consensus 305 lrLV~sIAkry~g~g~d---~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~s 368 (459)
+..+-.+.++|--++-. -+|.|.+|.-.+++.+..||+.+...+.+|++.++-++..+.|.+..
T Consensus 47 mkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~kEk 113 (179)
T PHA02547 47 MKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIKKEK 113 (179)
T ss_pred HHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHHHHH
Confidence 44445555555333433 59999999999999999999999999999999999999999887653
No 161
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=90.83 E-value=2.1 Score=47.90 Aligned_cols=35 Identities=23% Similarity=0.402 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 012638 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (459)
Q Consensus 254 ~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~ 288 (459)
++.++...+...+|++||.++.|..+|++.+.+..
T Consensus 468 k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~ 502 (619)
T PRK05658 468 KLNRISRQMLQEIGREPTPEELAERLGMPEDKVRK 502 (619)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 45566777888899999999999999999887654
No 162
>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=90.75 E-value=0.68 Score=34.22 Aligned_cols=31 Identities=19% Similarity=-0.037 Sum_probs=25.7
Q ss_pred HHcCCCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 393 NSHGKYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 393 ~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
..+..+.|.+|||+.||+|.++|+.+...+.
T Consensus 15 ~~y~~~~t~~eIa~~lg~s~~~V~~~~~~al 45 (50)
T PF04545_consen 15 LRYFEGLTLEEIAERLGISRSTVRRILKRAL 45 (50)
T ss_dssp HHHTST-SHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred HHhcCCCCHHHHHHHHCCcHHHHHHHHHHHH
Confidence 3457788999999999999999999887664
No 163
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=89.22 E-value=4.5 Score=41.73 Aligned_cols=29 Identities=14% Similarity=0.038 Sum_probs=26.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
..+.|++|||+.||||+++|+.++++++.
T Consensus 280 ~e~~s~~EIA~~Lgis~~tV~~~~~rAl~ 308 (325)
T PRK05657 280 YEAATLEDVAREIGLTRERVRQIQVEALR 308 (325)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 45789999999999999999999888865
No 164
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=88.54 E-value=2.9 Score=41.10 Aligned_cols=30 Identities=10% Similarity=-0.028 Sum_probs=26.0
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 395 HGKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 395 lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
+..+.|++|||+.||||+++|+..+++++.
T Consensus 218 ~~~g~s~~eIA~~l~is~~tV~~~~~ra~~ 247 (257)
T PRK08583 218 FIENLSQKETGERLGISQMHVSRLQRQAIK 247 (257)
T ss_pred HhCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 356889999999999999999999887654
No 165
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=86.30 E-value=10 Score=38.18 Aligned_cols=27 Identities=19% Similarity=0.129 Sum_probs=23.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
.+.|.+|||+.||||.++|+.+.+.+.
T Consensus 247 ~~~Tl~EIA~~lgvS~~rVrqi~~~Al 273 (284)
T PRK06596 247 DKSTLQELAAEYGVSAERVRQIEKNAM 273 (284)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 578999999999999999999877653
No 166
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=83.02 E-value=6.1 Score=41.54 Aligned_cols=125 Identities=20% Similarity=0.062 Sum_probs=81.2
Q ss_pred HHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccch
Q 012638 298 EELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKL 377 (459)
Q Consensus 298 e~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~v 377 (459)
+..+..-.+.++.---+|.++-.-.|+.+||+|+...+..-+=-+-+ .-..|++-..||.-+|.+|++.+....|.+.
T Consensus 8 e~~~r~~~~r~~a~L~r~~rd~dlAEEa~~dA~~~Ale~WPr~G~P~--~PaAWL~~v~R~~aiD~~Rr~~~~~~~~~el 85 (415)
T COG4941 8 EAAARIERPRAMAALARYLRDLDLAEEALQDAFAAALERWPRAGPPR--NPAAWLIAVGRNRAIDRVRRRARRDAAPPEL 85 (415)
T ss_pred HHHHHHhhhHHHHHHHHHhcccchHHHHHHHHHHHHHHhCcccCCCC--ChHHHHHHHHhhhHHHHHHHHHHhccCChhh
Confidence 34445555666666666777767789999999876554443333322 4689999999999999999987766555443
Q ss_pred HHHH--HHHHHH----------------------------HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 378 NREI--SKIQKA----------------------------RKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 378 ~e~i--~kI~ka----------------------------~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
.... ..+..+ .-.|.-.+--+.|.+|||...=+++.++...+.+++.
T Consensus 86 ~~~~e~~e~~~a~~~~d~~i~Dd~LRLiFvccHPal~~~~riALtLR~v~GLs~~eIArAFLv~e~am~QRivRAK~ 162 (415)
T COG4941 86 LLSDEDEEMEEAEALDDEHIRDDRLRLIFVCCHPALPPEQRIALTLRLVGGLSTAEIARAFLVPEAAMAQRIVRAKA 162 (415)
T ss_pred cccccchhhhccccccccccchhhHHhhhhhcCCCCChhhHHHHHHHHHcCCcHHHHHHHHcCCcHHHHHHHHHHHH
Confidence 2221 111111 0011111123569999999999999999888877764
No 167
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=80.79 E-value=2 Score=35.38 Aligned_cols=25 Identities=20% Similarity=0.106 Sum_probs=22.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHh
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASEC 421 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~ 421 (459)
.+.|+.|||+.||+|+.+|+..+..
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 5789999999999999999998774
No 168
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=79.44 E-value=4.4 Score=28.56 Aligned_cols=29 Identities=24% Similarity=0.161 Sum_probs=25.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
..+.+..+||+.+|++..+|...++.++.
T Consensus 24 ~~~~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 24 GEGLSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 36789999999999999999998877653
No 169
>PHA02591 hypothetical protein; Provisional
Probab=78.57 E-value=4.5 Score=33.81 Aligned_cols=25 Identities=28% Similarity=0.216 Sum_probs=22.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHh
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASEC 421 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~ 421 (459)
++.|.++||+.||++..+|+.+++.
T Consensus 58 qGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 58 KGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 5889999999999999999998763
No 170
>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=78.46 E-value=6.5 Score=28.66 Aligned_cols=24 Identities=25% Similarity=0.201 Sum_probs=19.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHh
Q 012638 398 YPEDIEIAKYTGLSLAEIRSASEC 421 (459)
Q Consensus 398 ~PT~eEIAe~LGIS~e~Vk~~l~~ 421 (459)
..++.+||+.+|+|..+|...++.
T Consensus 17 r~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 17 RRSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp TS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CccHHHHHHHHCcCHHHHHHHHHH
Confidence 468999999999999999988765
No 171
>PRK00118 putative DNA-binding protein; Validated
Probab=77.94 E-value=4 Score=35.73 Aligned_cols=30 Identities=13% Similarity=-0.178 Sum_probs=26.3
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 395 HGKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 395 lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
...+.|+.|||+.+|+|..+|...+.+++.
T Consensus 30 y~eg~S~~EIAe~lGIS~~TV~r~L~RArk 59 (104)
T PRK00118 30 YLDDYSLGEIAEEFNVSRQAVYDNIKRTEK 59 (104)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 345789999999999999999999887764
No 172
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=77.38 E-value=44 Score=35.19 Aligned_cols=36 Identities=28% Similarity=0.417 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHH
Q 012638 252 VANLERIKTTLEKESGKAASLNCWAQAAGVSERVLK 287 (459)
Q Consensus 252 ~~~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~ 287 (459)
.-++-+++.+|...+|++|+.++.|+..|++..+..
T Consensus 188 ~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~ 223 (342)
T COG0568 188 INKLRRVKRELLQELGREPTPEEIAEELGVSPDKVR 223 (342)
T ss_pred HHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHH
Confidence 345666778888889999999999999999887543
No 173
>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=75.67 E-value=3.6 Score=30.07 Aligned_cols=23 Identities=26% Similarity=0.083 Sum_probs=17.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Q 012638 398 YPEDIEIAKYTGLSLAEIRSASE 420 (459)
Q Consensus 398 ~PT~eEIAe~LGIS~e~Vk~~l~ 420 (459)
+.++.+||+.+||+..+|..++.
T Consensus 21 G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 21 GMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp T--HHHHHHHTTS-HHHHHHHHC
T ss_pred CCCHHHHHHHHCcCHHHHHHHHh
Confidence 58999999999999999988763
No 174
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=75.55 E-value=4 Score=29.47 Aligned_cols=28 Identities=18% Similarity=0.154 Sum_probs=24.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
.+.+..|||+.+|+|..+|...+..+..
T Consensus 17 ~g~s~~eia~~l~is~~tv~~~~~~~~~ 44 (58)
T smart00421 17 EGLTNKEIAERLGISEKTVKTHLSNIMR 44 (58)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4579999999999999999999887653
No 175
>PRK04217 hypothetical protein; Provisional
Probab=74.74 E-value=4 Score=36.06 Aligned_cols=28 Identities=21% Similarity=0.108 Sum_probs=25.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
.+.|++|||+.+|||..+|...+..++.
T Consensus 57 eGlS~~EIAk~LGIS~sTV~r~L~RArk 84 (110)
T PRK04217 57 EGLTQEEAGKRMGVSRGTVWRALTSARK 84 (110)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 5679999999999999999999888765
No 176
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=74.68 E-value=5.6 Score=29.06 Aligned_cols=27 Identities=22% Similarity=0.021 Sum_probs=18.6
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHh
Q 012638 395 HGKYPEDIEIAKYTGLSLAEIRSASEC 421 (459)
Q Consensus 395 lgr~PT~eEIAe~LGIS~e~Vk~~l~~ 421 (459)
+..+.|..|||+.||.+..+|...+++
T Consensus 17 ~~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 17 LEQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp HCS---HHHHHHHTT--HHHHHHHHHH
T ss_pred HHcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 456799999999999999999887654
No 177
>PRK06930 positive control sigma-like factor; Validated
Probab=74.52 E-value=4.7 Score=37.95 Aligned_cols=30 Identities=23% Similarity=0.184 Sum_probs=26.7
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 395 HGKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 395 lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
+..+.|+.|||+.||+|+++|+..+.+++.
T Consensus 127 ~~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~ 156 (170)
T PRK06930 127 RGYGLSYSEIADYLNIKKSTVQSMIERAEK 156 (170)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 456889999999999999999999888764
No 178
>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=74.25 E-value=3.4 Score=28.75 Aligned_cols=25 Identities=24% Similarity=0.319 Sum_probs=19.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 399 PEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 399 PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
.|.+|||+.+|++.++|-.++...+
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l~ 27 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKLE 27 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHHH
Confidence 4789999999999999998877554
No 179
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=73.77 E-value=8.5 Score=28.28 Aligned_cols=26 Identities=15% Similarity=0.173 Sum_probs=22.4
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHh
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASEC 421 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ 421 (459)
....|..+||+.+|++..+|..++..
T Consensus 25 ~~~~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 25 RESRSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred hhcCCHHHHHHHHCCCHHHHHHHHHh
Confidence 33479999999999999999998764
No 180
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=72.25 E-value=8 Score=28.79 Aligned_cols=27 Identities=30% Similarity=0.201 Sum_probs=22.5
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 398 YPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 398 ~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
..|.+|||+.||+|..+|...+...+.
T Consensus 15 ~it~~eLa~~l~vS~rTi~~~i~~L~~ 41 (55)
T PF08279_consen 15 PITAKELAEELGVSRRTIRRDIKELRE 41 (55)
T ss_dssp SBEHHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 389999999999999999998876553
No 181
>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=71.78 E-value=5.7 Score=28.83 Aligned_cols=28 Identities=18% Similarity=0.182 Sum_probs=24.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
.+.+..|||+.+|++..+|+..++.++.
T Consensus 14 ~~~s~~eia~~l~~s~~tv~~~~~~~~~ 41 (57)
T cd06170 14 EGKTNKEIADILGISEKTVKTHLRNIMR 41 (57)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4579999999999999999999887654
No 182
>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=71.75 E-value=5.8 Score=30.61 Aligned_cols=27 Identities=15% Similarity=0.071 Sum_probs=24.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
|..+..|||+.|||+..++...++.+-
T Consensus 22 R~~tl~elA~~lgis~st~~~~LRrae 48 (53)
T PF04967_consen 22 RRITLEELAEELGISKSTVSEHLRRAE 48 (53)
T ss_pred CcCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 667999999999999999999988764
No 183
>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=71.03 E-value=4.5 Score=30.76 Aligned_cols=32 Identities=19% Similarity=0.126 Sum_probs=25.2
Q ss_pred HHcCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 393 NSHGKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 393 ~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
..+..+.+..|||+.+|+++.+|+..+.....
T Consensus 13 ~~l~~G~~~~eIA~~l~is~~tV~~~~~~i~~ 44 (58)
T PF00196_consen 13 RLLAQGMSNKEIAEELGISEKTVKSHRRRIMK 44 (58)
T ss_dssp HHHHTTS-HHHHHHHHTSHHHHHHHHHHHHHH
T ss_pred HHHHhcCCcchhHHhcCcchhhHHHHHHHHHH
Confidence 33456889999999999999999988776543
No 184
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=70.75 E-value=11 Score=32.32 Aligned_cols=40 Identities=15% Similarity=0.120 Sum_probs=29.4
Q ss_pred HHHHHHHHHHcC-CCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 385 QKARKALTNSHG-KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 385 ~ka~~~L~~~lg-r~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
+....+|...+. ...|++|||..||+++.+|+.+++..+.
T Consensus 9 ~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~lekil~~tqr 49 (97)
T COG4367 9 QRTKQELQANFELCPLSDEEIATALNWTEVKLEKILQVTQR 49 (97)
T ss_pred HHHHHHHHHhhhhccccHHHHHHHhCCCHHHHHHHHHHhhc
Confidence 334445544433 4579999999999999999999876544
No 185
>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=70.52 E-value=9.6 Score=30.25 Aligned_cols=29 Identities=21% Similarity=0.144 Sum_probs=23.9
Q ss_pred HHHHHcCCCCCHHHHHHHhCCCHHHHHHH
Q 012638 390 ALTNSHGKYPEDIEIAKYTGLSLAEIRSA 418 (459)
Q Consensus 390 ~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~ 418 (459)
++..+.+-..+..+||+.||++..+|+.-
T Consensus 14 e~y~~~~g~i~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 14 EIYKESNGKIKLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred HHHHHhCCCccHHHHHHHHCCCHHHHHHH
Confidence 34455677899999999999999999864
No 186
>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=70.20 E-value=14 Score=26.76 Aligned_cols=26 Identities=19% Similarity=0.156 Sum_probs=20.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhh
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECL 422 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~a 422 (459)
...|..|||+.+|+|..+|...++..
T Consensus 16 ~~~t~~ela~~~~is~~tv~~~l~~L 41 (48)
T PF13412_consen 16 PRITQKELAEKLGISRSTVNRYLKKL 41 (48)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 34899999999999999999987754
No 187
>PF14502 HTH_41: Helix-turn-helix domain
Probab=69.17 E-value=6.5 Score=29.91 Aligned_cols=35 Identities=20% Similarity=0.212 Sum_probs=28.2
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhhc--cCCcccc
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASECLR--IVGSIDQ 430 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar--~~~SLD~ 430 (459)
.|-||+.|.++.++++.++|+.++.... ..++|..
T Consensus 4 dRi~tI~e~~~~~~vs~GtiQ~Alk~Le~~gaI~Le~ 40 (48)
T PF14502_consen 4 DRIPTISEYSEKFGVSRGTIQNALKFLEENGAIKLES 40 (48)
T ss_pred cccCCHHHHHHHhCcchhHHHHHHHHHHHCCcEEeee
Confidence 4779999999999999999999988764 3445543
No 188
>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=66.98 E-value=6.8 Score=35.92 Aligned_cols=28 Identities=21% Similarity=0.050 Sum_probs=24.4
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
..+.|++|||+.||+|..+|+.+.+.++
T Consensus 19 ~~GlTq~EIAe~LgiS~stV~~~e~ra~ 46 (137)
T TIGR00721 19 EKGLSQKEIAKELKTTRANVSAIEKRAM 46 (137)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHhHH
Confidence 4688999999999999999998877654
No 189
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=66.85 E-value=11 Score=28.73 Aligned_cols=46 Identities=20% Similarity=0.228 Sum_probs=29.8
Q ss_pred cccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHH
Q 012638 373 IPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSA 418 (459)
Q Consensus 373 lP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~ 418 (459)
+|....+.+...-++...|..+--...+-.|||+.+|++..+|+.=
T Consensus 3 Ip~~ti~RL~~Y~r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRKD 48 (50)
T PF06971_consen 3 IPKATIRRLPLYLRYLEQLKEEGVERVSSQELAEALGITPAQVRKD 48 (50)
T ss_dssp -SHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHcCCeeECHHHHHHHHCCCHHHhccc
Confidence 4544455555555666666655445679999999999999999763
No 190
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=66.67 E-value=19 Score=27.23 Aligned_cols=27 Identities=26% Similarity=0.258 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
...+..|||+.+|++..+|..++....
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~ 50 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELE 50 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 347999999999999999999887654
No 191
>PF13730 HTH_36: Helix-turn-helix domain
Probab=65.24 E-value=7.8 Score=28.83 Aligned_cols=27 Identities=30% Similarity=0.421 Sum_probs=23.3
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhh
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASECL 422 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~a 422 (459)
+--||.+.||+.+|++..+|..++...
T Consensus 23 ~~~pS~~~la~~~g~s~~Tv~~~i~~L 49 (55)
T PF13730_consen 23 GCFPSQETLAKDLGVSRRTVQRAIKEL 49 (55)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 345899999999999999999987754
No 192
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=64.95 E-value=6.9 Score=28.53 Aligned_cols=26 Identities=27% Similarity=0.052 Sum_probs=18.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 398 YPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 398 ~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
+.|..+||+.+|+|..+|...++..+
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT---
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHcc
Confidence 67999999999999999999887654
No 193
>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=62.98 E-value=8.5 Score=28.70 Aligned_cols=23 Identities=17% Similarity=0.154 Sum_probs=20.6
Q ss_pred CHHHHHHHhCCCHHHHHHHHHhh
Q 012638 400 EDIEIAKYTGLSLAEIRSASECL 422 (459)
Q Consensus 400 T~eEIAe~LGIS~e~Vk~~l~~a 422 (459)
|..+||+.+|+|..+|..+++-.
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~~ 23 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNGP 23 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTTC
T ss_pred CHHHHHHHHCcCHHHHHHHHhCC
Confidence 67899999999999999998754
No 194
>PF12728 HTH_17: Helix-turn-helix domain
Probab=62.33 E-value=11 Score=27.71 Aligned_cols=25 Identities=16% Similarity=0.004 Sum_probs=21.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 399 PEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 399 PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
.|.+|+|+.|||+..+|....+...
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g~ 26 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQGK 26 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 4789999999999999999887554
No 195
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=62.04 E-value=9.7 Score=35.08 Aligned_cols=28 Identities=29% Similarity=0.223 Sum_probs=23.8
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
..+.|++|||+.||+|..+|+.+.+.++
T Consensus 19 ~~GlTq~EIAe~LGiS~~tVs~ie~ra~ 46 (141)
T PRK03975 19 ERGLTQQEIADILGTSRANVSSIEKRAR 46 (141)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4678999999999999999998766543
No 196
>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=61.62 E-value=13 Score=37.13 Aligned_cols=26 Identities=23% Similarity=0.133 Sum_probs=22.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhh
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECL 422 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~a 422 (459)
.+.|..|||+.||||.++|+.+...+
T Consensus 235 ~~~t~~eIA~~lgvS~~~V~q~~~~A 260 (270)
T TIGR02392 235 DKLTLQELAAEYGVSAERIRQIEKNA 260 (270)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 46899999999999999999876655
No 197
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=61.48 E-value=12 Score=26.36 Aligned_cols=25 Identities=20% Similarity=0.062 Sum_probs=21.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 399 PEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 399 PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
.|.+|+|+.|||+..+|....+...
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g~ 26 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEGE 26 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcCC
Confidence 4789999999999999999887654
No 198
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=60.93 E-value=22 Score=27.75 Aligned_cols=27 Identities=19% Similarity=0.062 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
.+.++.|||+.||++..+|..-..+..
T Consensus 12 ~G~~~~eIA~~Lg~~~~TV~~W~~r~~ 38 (58)
T PF06056_consen 12 QGWSIKEIAEELGVPRSTVYSWKDRYK 38 (58)
T ss_pred cCCCHHHHHHHHCCChHHHHHHHHhhC
Confidence 588999999999999999998766544
No 199
>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=60.40 E-value=18 Score=31.51 Aligned_cols=33 Identities=15% Similarity=-0.037 Sum_probs=24.4
Q ss_pred HHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 392 TNSHGKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 392 ~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
..-+..+.|..|||+.+|||...|.+.++++..
T Consensus 27 ~lyy~eDlSlsEIAe~~~iSRqaV~d~ikr~~~ 59 (101)
T PF04297_consen 27 ELYYEEDLSLSEIAEELGISRQAVYDSIKRAEK 59 (101)
T ss_dssp HHHCTS---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred HHHHccCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 334567899999999999999999999888764
No 200
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=60.20 E-value=12 Score=35.93 Aligned_cols=33 Identities=15% Similarity=0.078 Sum_probs=26.7
Q ss_pred HHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 391 LTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 391 L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
+...+.++.+.+|||+.|++|+.||+.......
T Consensus 156 VL~lla~G~snkeIA~~L~iS~~TVk~h~~~i~ 188 (211)
T COG2197 156 VLRLLAEGLSNKEIAEELNLSEKTVKTHVSNIL 188 (211)
T ss_pred HHHHHHCCCCHHHHHHHHCCCHhHHHHHHHHHH
Confidence 334456799999999999999999998766543
No 201
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=60.15 E-value=13 Score=35.63 Aligned_cols=38 Identities=8% Similarity=0.121 Sum_probs=29.3
Q ss_pred HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 386 KARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 386 ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
.-..+.......+.|.+|||+.||||+.+|+.......
T Consensus 140 ~RE~eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~I~ 177 (207)
T PRK15411 140 RTESSMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIK 177 (207)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHH
Confidence 33344444556789999999999999999999876543
No 202
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=59.43 E-value=24 Score=28.78 Aligned_cols=36 Identities=17% Similarity=0.049 Sum_probs=24.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccc
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQK 431 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~ 431 (459)
.++.|..|+|+.||++..+|..+++--...+|+|.-
T Consensus 29 ~~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L 64 (80)
T PF13744_consen 29 ERGLTQAELAERLGISQPRVSRLENGKIDDFSLDTL 64 (80)
T ss_dssp CCT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHHH
T ss_pred HcCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHHH
Confidence 467899999999999999999888643444677654
No 203
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=59.09 E-value=13 Score=27.33 Aligned_cols=26 Identities=31% Similarity=0.425 Sum_probs=23.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 398 YPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 398 ~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
-||..|||+.+|+|..+|..++....
T Consensus 20 l~s~~~la~~~~vs~~tv~~~l~~L~ 45 (60)
T smart00345 20 LPSERELAAQLGVSRTTVREALSRLE 45 (60)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45999999999999999999887654
No 204
>PRK14082 hypothetical protein; Provisional
Probab=59.03 E-value=29 Score=28.03 Aligned_cols=54 Identities=19% Similarity=0.109 Sum_probs=41.7
Q ss_pred HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhH
Q 012638 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTY 351 (459)
Q Consensus 296 Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTY 351 (459)
..+.+|..+.|.+.+-... ....+.+||.||--|.+++-+..++-..+.-|--|
T Consensus 10 e~e~ii~~FepkIkKsL~~--T~yqeREDLeQElk~Ki~eK~~~~~~~e~PGF~ef 63 (65)
T PRK14082 10 EIEHLIENFSPMIKKKLSN--TSYQEREDLEQELKIKIIEKADMLLCQEVPGFWEF 63 (65)
T ss_pred HHHHHHHHccHHHHHHHhc--CChhhHHHHHHHHHHHHHHHHHHhhcccCCcHHHh
Confidence 5678888888888765542 23467899999999999999999987666556544
No 205
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=58.18 E-value=29 Score=30.63 Aligned_cols=41 Identities=7% Similarity=-0.040 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhh
Q 012638 382 SKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL 422 (459)
Q Consensus 382 ~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~a 422 (459)
..+.++...+...+...++.++||+.+|+++..+....+..
T Consensus 9 ~~i~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 9 ITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 44566677777777788999999999999999998776543
No 206
>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=57.11 E-value=22 Score=35.48 Aligned_cols=29 Identities=17% Similarity=0.138 Sum_probs=25.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
..+.|..|||+.||||+.+|+..++.+..
T Consensus 203 a~G~s~~eIA~~L~IS~~TVk~hl~~i~~ 231 (247)
T TIGR03020 203 RDGKTNEEIAAILGISSLTVKNHLQHIFK 231 (247)
T ss_pred HCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 46789999999999999999998887653
No 207
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=56.94 E-value=16 Score=34.10 Aligned_cols=34 Identities=21% Similarity=0.032 Sum_probs=27.1
Q ss_pred HHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 390 ALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 390 ~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
+....+..+.|..|||+.|+||..||+..+....
T Consensus 157 evl~~~~~G~s~~eIA~~l~iS~~TV~~h~~~i~ 190 (216)
T PRK10840 157 EVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAM 190 (216)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3334446789999999999999999999876543
No 208
>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]
Probab=56.46 E-value=19 Score=34.70 Aligned_cols=35 Identities=17% Similarity=-0.123 Sum_probs=28.2
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhhccCCcccc
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQ 430 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~ 430 (459)
.++.+..|||++|++|.+++..++.++..-.+--+
T Consensus 16 ~~Glt~gEIAdELNvSreTa~WL~~r~~~~~~~~~ 50 (203)
T COG0856 16 SKGLTTGEIADELNVSRETATWLLTRAFKKESVPA 50 (203)
T ss_pred HCCCcHHHhhhhhhhhHHHHHHHHhhhhhccCCCC
Confidence 46899999999999999999999887654333333
No 209
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=56.05 E-value=17 Score=35.81 Aligned_cols=38 Identities=8% Similarity=-0.074 Sum_probs=29.5
Q ss_pred HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 386 KARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 386 ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
.-..++...+.++.|.+|||+.|+|++.+|+.......
T Consensus 146 ~RE~eVL~Lia~G~SnkEIA~~L~IS~~TVk~hvs~I~ 183 (217)
T PRK13719 146 KYQNDVFILYSFGFSHEYIAQLLNITVGSSKNKISEIL 183 (217)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 33344445557799999999999999999999876554
No 210
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=55.76 E-value=21 Score=34.07 Aligned_cols=31 Identities=16% Similarity=-0.054 Sum_probs=26.8
Q ss_pred HcCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 394 SHGKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 394 ~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
....+.|.+|||+.||||..+|+..+....+
T Consensus 174 ~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~ 204 (239)
T PRK10430 174 HQDYEFSTDELANAVNISRVSCRKYLIWLVN 204 (239)
T ss_pred CCCCCcCHHHHHHHhCchHHHHHHHHHHHHh
Confidence 3467889999999999999999999887644
No 211
>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=55.73 E-value=25 Score=27.45 Aligned_cols=38 Identities=24% Similarity=0.209 Sum_probs=29.1
Q ss_pred HHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 385 QKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 385 ~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
-+++..|.. -+..++..+||+.||++..+|-..++...
T Consensus 10 L~~Iy~l~~-~~~~v~~~~iA~~L~vs~~tvt~ml~~L~ 47 (60)
T PF01325_consen 10 LKAIYELSE-EGGPVRTKDIAERLGVSPPTVTEMLKRLA 47 (60)
T ss_dssp HHHHHHHHH-CTSSBBHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHc-CCCCccHHHHHHHHCCChHHHHHHHHHHH
Confidence 345555655 56788999999999999999998887653
No 212
>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=54.98 E-value=18 Score=25.18 Aligned_cols=24 Identities=21% Similarity=0.160 Sum_probs=21.0
Q ss_pred CHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 400 EDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 400 T~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
+..|+|+.+||+..+|........
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcCC
Confidence 678999999999999998877654
No 213
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=54.01 E-value=20 Score=34.64 Aligned_cols=35 Identities=17% Similarity=0.030 Sum_probs=27.7
Q ss_pred HHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 389 KALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 389 ~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
.++......+.|..|||+.|++|..+|+..+....
T Consensus 139 rEVLrLLAqGkTnKEIAe~L~IS~rTVkth~srIm 173 (198)
T PRK15201 139 RHLLKLIASGYHLSETAALLSLSEEQTKSLRRSIM 173 (198)
T ss_pred HHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 33444456789999999999999999998877554
No 214
>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=53.49 E-value=28 Score=29.02 Aligned_cols=28 Identities=21% Similarity=0.285 Sum_probs=21.4
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
|+..|..++|..+|+++++|..++....
T Consensus 36 G~PVt~~~LA~a~g~~~e~v~~~L~~~p 63 (77)
T PF12324_consen 36 GQPVTVEQLAAALGWPVEEVRAALAAMP 63 (77)
T ss_dssp TS-B-HHHHHHHHT--HHHHHHHHHH-T
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHhCC
Confidence 8889999999999999999999998664
No 215
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=53.46 E-value=20 Score=34.59 Aligned_cols=34 Identities=12% Similarity=-0.014 Sum_probs=27.0
Q ss_pred HHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 390 ALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 390 ~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
+....+.++.|.+|||+.|+||+.||+.......
T Consensus 141 eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~I~ 174 (207)
T PRK11475 141 EILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVM 174 (207)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3344456789999999999999999998876543
No 216
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=53.10 E-value=32 Score=25.69 Aligned_cols=29 Identities=17% Similarity=0.221 Sum_probs=24.2
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 395 HGKYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 395 lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
...+.+..|||..+|++..+|...+....
T Consensus 16 ~~~G~s~~eia~~l~is~~tV~~h~~~i~ 44 (65)
T COG2771 16 VAQGKSNKEIARILGISEETVKTHLRNIY 44 (65)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 34568999999999999999998877553
No 217
>PRK13870 transcriptional regulator TraR; Provisional
Probab=52.06 E-value=13 Score=36.60 Aligned_cols=29 Identities=17% Similarity=0.035 Sum_probs=25.6
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
..+.|..|||.+||||+.+|+..++.++.
T Consensus 186 A~GKT~~EIa~ILgISe~TV~~Hl~na~~ 214 (234)
T PRK13870 186 AVGKTMEEIADVEGVKYNSVRVKLREAMK 214 (234)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 35789999999999999999999887764
No 218
>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=51.99 E-value=50 Score=30.34 Aligned_cols=44 Identities=23% Similarity=0.106 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCC
Q 012638 383 KIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVG 426 (459)
Q Consensus 383 kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~ 426 (459)
...++..-|...-++..|..|||+.+|+++..|...++-.|-.+
T Consensus 31 ~f~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~IreGRL~~ 74 (137)
T TIGR03826 31 EFEKVYKFLRKHENRQATVSEIVEETGVSEKLILKFIREGRLQL 74 (137)
T ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCCeec
Confidence 33444444444445668999999999999999999998877543
No 219
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=51.48 E-value=44 Score=28.12 Aligned_cols=38 Identities=16% Similarity=-0.023 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHh
Q 012638 384 IQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC 421 (459)
Q Consensus 384 I~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ 421 (459)
+.++...+...+...++.++||+.+|+|...+..+.+.
T Consensus 7 ~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~ 44 (107)
T PRK10219 7 IQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRT 44 (107)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 55566666667778899999999999999999876554
No 220
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=50.25 E-value=25 Score=29.69 Aligned_cols=28 Identities=32% Similarity=0.273 Sum_probs=23.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
..+..+.+||+.|++++.+|+.++...-
T Consensus 63 ~~Gv~v~~I~~~l~~~~~~v~~al~~L~ 90 (102)
T PF08784_consen 63 EEGVHVDEIAQQLGMSENEVRKALDFLS 90 (102)
T ss_dssp TTTEEHHHHHHHSTS-HHHHHHHHHHHH
T ss_pred CCcccHHHHHHHhCcCHHHHHHHHHHHH
Confidence 4578999999999999999999887543
No 221
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=50.05 E-value=33 Score=30.50 Aligned_cols=32 Identities=22% Similarity=0.279 Sum_probs=25.3
Q ss_pred HHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhh
Q 012638 390 ALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL 422 (459)
Q Consensus 390 ~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~a 422 (459)
.+-+..++ .++.|||+.+|+|..+|..+++..
T Consensus 15 ~~L~~d~r-~~~~eia~~lglS~~~v~~Ri~~L 46 (154)
T COG1522 15 RLLQEDAR-ISNAELAERVGLSPSTVLRRIKRL 46 (154)
T ss_pred HHHHHhCC-CCHHHHHHHHCCCHHHHHHHHHHH
Confidence 33344454 899999999999999999987765
No 222
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=49.74 E-value=52 Score=26.09 Aligned_cols=30 Identities=23% Similarity=0.348 Sum_probs=24.5
Q ss_pred HcCC-CCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 394 SHGK-YPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 394 ~lgr-~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
..|. ..+..|||+.|||+..+|...+....
T Consensus 17 ~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~ 47 (68)
T smart00550 17 NSGDETSTALQLAKNLGLPKKEVNRVLYSLE 47 (68)
T ss_pred HCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3344 48999999999999999999887544
No 223
>PRK12423 LexA repressor; Provisional
Probab=49.05 E-value=44 Score=31.93 Aligned_cols=41 Identities=24% Similarity=0.232 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHhCC-CHHHHHHHHHhh
Q 012638 382 SKIQKARKALTNSHGKYPEDIEIAKYTGL-SLAEIRSASECL 422 (459)
Q Consensus 382 ~kI~ka~~~L~~~lgr~PT~eEIAe~LGI-S~e~Vk~~l~~a 422 (459)
..|-........+.|..||..|||+.+|+ +...|+..+...
T Consensus 9 ~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L 50 (202)
T PRK12423 9 AAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQAL 50 (202)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHH
Confidence 33444444444556778999999999994 899998776654
No 224
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=48.83 E-value=28 Score=33.66 Aligned_cols=30 Identities=17% Similarity=-0.022 Sum_probs=25.3
Q ss_pred HcCCCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 394 SHGKYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 394 ~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
....+.|++|||+.|++|+.+|+..+....
T Consensus 166 l~~~G~s~~eIA~~L~iS~~TVk~~~~~i~ 195 (216)
T PRK10100 166 KLRIGASNNEIARSLFISENTVKTHLYNLF 195 (216)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 334578999999999999999999877654
No 225
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=48.41 E-value=24 Score=28.09 Aligned_cols=28 Identities=32% Similarity=0.213 Sum_probs=22.6
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
...++..|||+.+||+.-+++.++....
T Consensus 13 ~~p~~T~eiA~~~gls~~~aR~yL~~Le 40 (62)
T PF04703_consen 13 NGPLKTREIADALGLSIYQARYYLEKLE 40 (62)
T ss_dssp TS-EEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 5568999999999999999999987653
No 226
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=47.57 E-value=28 Score=33.06 Aligned_cols=26 Identities=15% Similarity=0.004 Sum_probs=23.3
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 398 YPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 398 ~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
+.|.+|||+.||||+.||+..+....
T Consensus 177 g~s~~eIa~~l~iS~~Tv~~~~~~~~ 202 (225)
T PRK10046 177 QHTAETVAQALTISRTTARRYLEYCA 202 (225)
T ss_pred CcCHHHHHHHhCccHHHHHHHHHHHH
Confidence 57999999999999999999887654
No 227
>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=47.41 E-value=19 Score=35.03 Aligned_cols=28 Identities=18% Similarity=0.138 Sum_probs=25.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
.+.|..|||++||||+.+|+..+..++.
T Consensus 185 ~G~t~~eIa~~l~is~~Tv~~~l~~~~~ 212 (232)
T TIGR03541 185 LGRRQADIAAILGISERTVENHLRSARR 212 (232)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 5789999999999999999999887754
No 228
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=47.32 E-value=27 Score=24.58 Aligned_cols=27 Identities=22% Similarity=0.181 Sum_probs=23.1
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 398 YPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 398 ~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
.++..+||+.+|++..+|..++.....
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~ 34 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEK 34 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 468899999999999999998876543
No 229
>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=47.04 E-value=20 Score=26.68 Aligned_cols=27 Identities=26% Similarity=0.233 Sum_probs=22.2
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhh
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASECL 422 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~a 422 (459)
+...+..|||+.+|++..++..++...
T Consensus 16 ~~~~t~~eia~~~gl~~stv~r~L~tL 42 (52)
T PF09339_consen 16 GGPLTLSEIARALGLPKSTVHRLLQTL 42 (52)
T ss_dssp BSCEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 445699999999999999999988754
No 230
>PRK13239 alkylmercury lyase; Provisional
Probab=46.84 E-value=45 Score=32.71 Aligned_cols=29 Identities=17% Similarity=0.268 Sum_probs=26.8
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 395 HGKYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 395 lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
.|+.||..+||+.+|+++++|+.+|+...
T Consensus 33 ~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 33 KGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 58999999999999999999999998765
No 231
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=46.75 E-value=1.8e+02 Score=29.80 Aligned_cols=28 Identities=21% Similarity=0.337 Sum_probs=22.6
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
|...|.+|||...|++..+|+...+...
T Consensus 274 g~~~t~keIa~v~~Vs~~tI~~~ykel~ 301 (310)
T PRK00423 274 GERRTQREVAEVAGVTEVTVRNRYKELA 301 (310)
T ss_pred CCCCCHHHHHHHcCCCHHHHHHHHHHHH
Confidence 4445999999999999999988766443
No 232
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=46.72 E-value=24 Score=34.70 Aligned_cols=29 Identities=14% Similarity=0.084 Sum_probs=25.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
..+.|..|||++||||+.+|+..+..++.
T Consensus 192 a~G~t~~eIa~~l~is~~TV~~h~~~~~~ 220 (240)
T PRK10188 192 AEGKTSAEIAMILSISENTVNFHQKNMQK 220 (240)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 35789999999999999999998887764
No 233
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=46.39 E-value=50 Score=27.98 Aligned_cols=26 Identities=27% Similarity=0.277 Sum_probs=22.2
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHh
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASEC 421 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ 421 (459)
..+.|..|||+.+|+|..+|..+.++
T Consensus 48 ~~G~S~~eIA~~LgISrsTIyRi~R~ 73 (88)
T TIGR02531 48 KQGKTYSDIEAETGASTATISRVKRC 73 (88)
T ss_pred HCCCCHHHHHHHHCcCHHHHHHHHHh
Confidence 45679999999999999999986653
No 234
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=46.36 E-value=52 Score=30.99 Aligned_cols=40 Identities=25% Similarity=0.254 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHhCCC-HHHHHHHHHhh
Q 012638 383 KIQKARKALTNSHGKYPEDIEIAKYTGLS-LAEIRSASECL 422 (459)
Q Consensus 383 kI~ka~~~L~~~lgr~PT~eEIAe~LGIS-~e~Vk~~l~~a 422 (459)
+|-..+.+...+.+..||..|||+.+|++ ..+|...+...
T Consensus 10 ~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L 50 (199)
T TIGR00498 10 EVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKAL 50 (199)
T ss_pred HHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHH
Confidence 34444444445567789999999999998 99999887754
No 235
>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=46.25 E-value=23 Score=27.29 Aligned_cols=27 Identities=30% Similarity=0.457 Sum_probs=20.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
+-|+..+||+.+|+|..+|+.++....
T Consensus 23 ~lps~~~la~~~~vsr~tvr~al~~L~ 49 (64)
T PF00392_consen 23 RLPSERELAERYGVSRTTVREALRRLE 49 (64)
T ss_dssp BE--HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred EeCCHHHHHHHhccCCcHHHHHHHHHH
Confidence 346999999999999999999987653
No 236
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=45.96 E-value=87 Score=23.90 Aligned_cols=36 Identities=25% Similarity=0.278 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHhCC-CHHHHHHHHHh
Q 012638 383 KIQKARKALTNSHGKYPEDIEIAKYTGL-SLAEIRSASEC 421 (459)
Q Consensus 383 kI~ka~~~L~~~lgr~PT~eEIAe~LGI-S~e~Vk~~l~~ 421 (459)
++..+...+... ..+.++||..+|+ +...+....+.
T Consensus 38 r~~~a~~~l~~~---~~~~~~ia~~~g~~s~~~f~r~Fk~ 74 (84)
T smart00342 38 RLERARRLLRDT---DLSVTEIALRVGFSSQSYFSRAFKK 74 (84)
T ss_pred HHHHHHHHHHcC---CCCHHHHHHHhCCCChHHHHHHHHH
Confidence 455555555432 6899999999999 99888776654
No 237
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=45.83 E-value=38 Score=32.46 Aligned_cols=25 Identities=20% Similarity=0.036 Sum_probs=22.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHh
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASEC 421 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~ 421 (459)
-+.|+.|||+.+|.++.+|++.+.-
T Consensus 60 ag~Ti~EIAeelG~TeqTir~hlkg 84 (182)
T COG1318 60 AGMTISEIAEELGRTEQTVRNHLKG 84 (182)
T ss_pred ccCcHHHHHHHhCCCHHHHHHHHhc
Confidence 3679999999999999999998763
No 238
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=44.78 E-value=83 Score=29.86 Aligned_cols=26 Identities=19% Similarity=0.257 Sum_probs=22.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 398 YPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 398 ~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
..|.++||+.+|++.++|-.+++..+
T Consensus 184 ~lt~~~iA~~lG~sr~tvsR~l~~l~ 209 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETISRLLGRFQ 209 (235)
T ss_pred cccHHHHHHHhCCcHHHHHHHHHHHH
Confidence 36899999999999999999887654
No 239
>COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]
Probab=44.72 E-value=46 Score=34.84 Aligned_cols=72 Identities=13% Similarity=0.146 Sum_probs=51.4
Q ss_pred hHHHHHHHHHHHHHHHhhcccccccc--chHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHh
Q 012638 350 TYVQYWIRKSISKMVARHARGIKIPC--KLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC 421 (459)
Q Consensus 350 TYa~~wIrnaI~d~Lrk~sr~irlP~--~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ 421 (459)
+.+....++.+.+.+|.-...-++|. ...-.-.+|.+++..+.+.+.+..+.+|||+.+|+|..++..+.+.
T Consensus 186 ~~a~~va~~lv~~~~R~~~~~Q~~~~~~~~~~~~~~l~~~i~~me~nle~plsl~~LA~~~~~S~R~leRlF~~ 259 (328)
T COG4977 186 ALANRVARQLVVDPIRSGGDRQRLPLLGRLGHRDPRLLRAIELMEANLEEPLSLEELADRAGLSRRQLERLFRA 259 (328)
T ss_pred HHHHHHHHHhhhccccCCCccccccccccCCCCCHHHHHHHHHHHHhhcCCcCHHHHHHHhCCCHHHHHHHHHH
Confidence 45566777777777775332222332 2233446788888888888999999999999999999999876554
No 240
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=44.64 E-value=22 Score=26.78 Aligned_cols=37 Identities=30% Similarity=0.263 Sum_probs=24.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHH-Hhhcc-CCccccccCCC
Q 012638 399 PEDIEIAKYTGLSLAEIRSAS-ECLRI-VGSIDQKIGDC 435 (459)
Q Consensus 399 PT~eEIAe~LGIS~e~Vk~~l-~~ar~-~~SLD~~v~~d 435 (459)
.++.|+|+.+|++...|-..+ ..... ..+.++.++++
T Consensus 4 i~V~elAk~l~v~~~~ii~~l~~~~Gi~~~~~~~~ld~e 42 (54)
T PF04760_consen 4 IRVSELAKELGVPSKEIIKKLFKELGIMVKSINSSLDEE 42 (54)
T ss_dssp E-TTHHHHHHSSSHHHHHHHH-HHHTS---SSSS-EETT
T ss_pred eEHHHHHHHHCcCHHHHHHHHHHhCCcCcCCCCCcCCHH
Confidence 367899999999999998888 42333 36666666544
No 241
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=44.36 E-value=26 Score=34.17 Aligned_cols=30 Identities=13% Similarity=-0.011 Sum_probs=23.2
Q ss_pred HHHHHcCCCCCHHHHHHHhCCCHHHHHHHH
Q 012638 390 ALTNSHGKYPEDIEIAKYTGLSLAEIRSAS 419 (459)
Q Consensus 390 ~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l 419 (459)
+.....-++...++||..||||+.||+...
T Consensus 149 qVl~~vV~G~~NKqIA~dLgiS~rTVe~HR 178 (202)
T COG4566 149 QVLDLVVRGLMNKQIAFDLGISERTVELHR 178 (202)
T ss_pred HHHHHHHcCcccHHHHHHcCCchhhHHHHH
Confidence 333333477899999999999999998653
No 242
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=44.10 E-value=17 Score=32.00 Aligned_cols=29 Identities=21% Similarity=0.102 Sum_probs=26.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhhccC
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECLRIV 425 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~ar~~ 425 (459)
.+.+++|-|+.||||..|+..++..||..
T Consensus 56 egl~QeeaA~~MgVSR~T~~ril~~ARkK 84 (106)
T PF02001_consen 56 EGLSQEEAAERMGVSRPTFQRILESARKK 84 (106)
T ss_pred cCCCHHHHHHHcCCcHHHHHHHHHHHHHH
Confidence 46899999999999999999999998863
No 243
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=44.07 E-value=1e+02 Score=25.84 Aligned_cols=48 Identities=4% Similarity=-0.072 Sum_probs=31.4
Q ss_pred hCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHH
Q 012638 316 RGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKM 363 (459)
Q Consensus 316 ~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~ 363 (459)
.....+++||.+...+..-.--..|...-|..|..|+...--......
T Consensus 18 ~~~~~~~~~lA~~~~~S~~~l~r~f~~~~g~s~~~~i~~~Rl~~a~~~ 65 (107)
T PRK10219 18 IDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVE 65 (107)
T ss_pred cCCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 345688999998888777666666765567777777655433333333
No 244
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=43.82 E-value=2.6e+02 Score=27.50 Aligned_cols=39 Identities=10% Similarity=0.063 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHh
Q 012638 383 KIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC 421 (459)
Q Consensus 383 kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ 421 (459)
.+.++...+........+.+++|+.+|+|...+..+.+.
T Consensus 184 ~i~~~~~~i~~~~~~~isl~~lA~~~~lS~~~l~r~Fk~ 222 (290)
T PRK10572 184 RVREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQ 222 (290)
T ss_pred HHHHHHHHHHhcccCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 455666666667778899999999999999988876554
No 245
>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=43.72 E-value=83 Score=26.33 Aligned_cols=42 Identities=31% Similarity=0.195 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 382 SKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 382 ~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
..|-+++-++..+.++...-++||+.+|++..+|++.+....
T Consensus 7 ~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le 48 (78)
T PF03444_consen 7 REILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADLE 48 (78)
T ss_pred HHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHH
Confidence 344455555556668888999999999999999999887554
No 246
>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=43.34 E-value=31 Score=27.21 Aligned_cols=27 Identities=22% Similarity=0.158 Sum_probs=21.3
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhh
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASECL 422 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~a 422 (459)
+...|..|||..+|++++.|+.++...
T Consensus 12 ~~~~S~~eLa~~~~~s~~~ve~mL~~l 38 (69)
T PF09012_consen 12 RGRVSLAELAREFGISPEAVEAMLEQL 38 (69)
T ss_dssp S-SEEHHHHHHHTT--HHHHHHHHHHH
T ss_pred cCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 456799999999999999999998764
No 247
>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=42.82 E-value=74 Score=23.39 Aligned_cols=35 Identities=29% Similarity=0.305 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHH
Q 012638 383 KIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASE 420 (459)
Q Consensus 383 kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~ 420 (459)
.|..|+..+. .|. .++.+.|+..|||..++...++
T Consensus 4 ~l~~Ai~~v~--~g~-~S~r~AA~~ygVp~sTL~~r~~ 38 (45)
T PF05225_consen 4 DLQKAIEAVK--NGK-MSIRKAAKKYGVPRSTLRRRLR 38 (45)
T ss_dssp HHHHHHHHHH--TTS-S-HHHHHHHHT--HHHHHHHHH
T ss_pred HHHHHHHHHH--hCC-CCHHHHHHHHCcCHHHHHHHHc
Confidence 4566666655 344 9999999999999999997655
No 248
>PRK09483 response regulator; Provisional
Probab=42.65 E-value=29 Score=31.64 Aligned_cols=31 Identities=19% Similarity=-0.037 Sum_probs=26.0
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhhccC
Q 012638 395 HGKYPEDIEIAKYTGLSLAEIRSASECLRIV 425 (459)
Q Consensus 395 lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~ 425 (459)
+..+.+..|||+.|+++..+|+...+.....
T Consensus 160 ~~~G~~~~~Ia~~l~is~~TV~~~~~~i~~K 190 (217)
T PRK09483 160 ITKGQKVNEISEQLNLSPKTVNSYRYRMFSK 190 (217)
T ss_pred HHCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 3567899999999999999999988766543
No 249
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=42.64 E-value=49 Score=20.44 Aligned_cols=21 Identities=24% Similarity=0.154 Sum_probs=18.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHH
Q 012638 398 YPEDIEIAKYTGLSLAEIRSA 418 (459)
Q Consensus 398 ~PT~eEIAe~LGIS~e~Vk~~ 418 (459)
..+..+||+.+|++..+|...
T Consensus 21 ~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 21 GESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCCHHHHHHHHCCCHHHHHHh
Confidence 459999999999999998754
No 250
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=42.64 E-value=38 Score=29.97 Aligned_cols=30 Identities=10% Similarity=0.048 Sum_probs=25.4
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhhccC
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASECLRIV 425 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~ 425 (459)
..+.+.+|||+.|+++..+|+..+...+..
T Consensus 162 ~~g~~~~~Ia~~l~~s~~tv~~~~~~~~~k 191 (211)
T PRK15369 162 TEGYTNRDIAEQLSISIKTVETHRLNMMRK 191 (211)
T ss_pred HCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 456799999999999999999988876543
No 251
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=42.56 E-value=56 Score=27.97 Aligned_cols=35 Identities=17% Similarity=0.017 Sum_probs=26.6
Q ss_pred HHHHHHHc-CCCCCHHHHHHHhCCCHHHHHHHHHhh
Q 012638 388 RKALTNSH-GKYPEDIEIAKYTGLSLAEIRSASECL 422 (459)
Q Consensus 388 ~~~L~~~l-gr~PT~eEIAe~LGIS~e~Vk~~l~~a 422 (459)
..+|.+.+ .-+.|.++||..||++.+.|..++..-
T Consensus 12 ~~ELq~nf~~~~ls~~~ia~dL~~s~~~le~vL~l~ 47 (89)
T PF10078_consen 12 RQELQANFELSGLSLEQIAADLGTSPEHLEQVLNLK 47 (89)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC
Confidence 33444433 247899999999999999999988643
No 252
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=42.16 E-value=22 Score=36.67 Aligned_cols=38 Identities=18% Similarity=0.084 Sum_probs=31.3
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhhcc----CCcccccc
Q 012638 395 HGKYPEDIEIAKYTGLSLAEIRSASECLRI----VGSIDQKI 432 (459)
Q Consensus 395 lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~----~~SLD~~v 432 (459)
+..+.|..|||+.||||.-+|..++..||. .+.++.|.
T Consensus 26 Y~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~I~I~~~~ 67 (318)
T PRK15418 26 YHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQINSRF 67 (318)
T ss_pred HhcCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEEEEEeCCC
Confidence 346889999999999999999999999985 24565554
No 253
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=41.64 E-value=47 Score=32.32 Aligned_cols=26 Identities=31% Similarity=0.387 Sum_probs=23.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 398 YPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 398 ~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
-|+..|||+.+|+|...|+.++....
T Consensus 34 LpsE~eLa~~lgVSRtpVREAL~~L~ 59 (254)
T PRK09464 34 LPPERELAKQFDVSRPSLREAIQRLE 59 (254)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 46999999999999999999988653
No 254
>COG2902 NAD-specific glutamate dehydrogenase [Amino acid transport and metabolism]
Probab=41.38 E-value=8.4e+02 Score=30.83 Aligned_cols=32 Identities=28% Similarity=0.294 Sum_probs=25.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHhhccCCcccc
Q 012638 399 PEDIEIAKYTGLSLAEIRSASECLRIVGSIDQ 430 (459)
Q Consensus 399 PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~ 430 (459)
|.+-+||+..|+++.+|..+..+....++||-
T Consensus 1467 ~dii~ia~~~~~~~~~~Ak~yf~v~~~~~~~~ 1498 (1592)
T COG2902 1467 LDIIDIADITGIDVAEVAKAYFAVSDALGLDW 1498 (1592)
T ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHHHhCchH
Confidence 57789999999999999988776666666654
No 255
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=41.23 E-value=1.1e+02 Score=28.25 Aligned_cols=27 Identities=19% Similarity=0.137 Sum_probs=23.3
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 398 YPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 398 ~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
..|.++||..+|++.++|-..+...+.
T Consensus 149 ~~t~~~iA~~lG~tretvsR~l~~l~~ 175 (202)
T PRK13918 149 YATHDELAAAVGSVRETVTKVIGELSR 175 (202)
T ss_pred cCCHHHHHHHhCccHHHHHHHHHHHHH
Confidence 358999999999999999998887653
No 256
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=41.10 E-value=51 Score=29.96 Aligned_cols=26 Identities=27% Similarity=0.249 Sum_probs=23.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 398 YPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 398 ~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
..++.|||+.+|+|..+|..+++...
T Consensus 23 R~s~~eiA~~lglS~~tV~~Ri~rL~ 48 (153)
T PRK11179 23 RTPYAELAKQFGVSPGTIHVRVEKMK 48 (153)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 46899999999999999999988764
No 257
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=41.06 E-value=29 Score=27.18 Aligned_cols=25 Identities=24% Similarity=0.250 Sum_probs=22.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 399 PEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 399 PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
.|.++||..+|++..+|...++..+
T Consensus 29 lt~~~iA~~~g~sr~tv~r~l~~l~ 53 (76)
T PF13545_consen 29 LTQEEIADMLGVSRETVSRILKRLK 53 (76)
T ss_dssp SSHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 5999999999999999999988765
No 258
>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=40.95 E-value=1.1e+02 Score=26.25 Aligned_cols=65 Identities=9% Similarity=-0.035 Sum_probs=38.5
Q ss_pred hhHHHHHHHHHHHHHHHhhccccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhh
Q 012638 349 STYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL 422 (459)
Q Consensus 349 STYa~~wIrnaI~d~Lrk~sr~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~a 422 (459)
.+|...++.+.+.+.+...-....+...... ....|.. ....+..|||+.+|++..+|...+...
T Consensus 2 ~~~~l~~~~~~~~~~~~~~l~~~~lt~~q~~-------iL~~l~~--~~~~t~~ela~~~~~~~~tvs~~l~~L 66 (118)
T TIGR02337 2 LPLALLQAREAAMSFFRPILAQHGLTEQQWR-------ILRILAE--QGSMEFTQLANQACILRPSLTGILARL 66 (118)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHcCCCHHHHH-------HHHHHHH--cCCcCHHHHHHHhCCCchhHHHHHHHH
Confidence 4566677777777666544222222111111 1122221 345789999999999999998877654
No 259
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=40.76 E-value=27 Score=26.54 Aligned_cols=27 Identities=15% Similarity=0.119 Sum_probs=20.3
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHh
Q 012638 395 HGKYPEDIEIAKYTGLSLAEIRSASEC 421 (459)
Q Consensus 395 lgr~PT~eEIAe~LGIS~e~Vk~~l~~ 421 (459)
+..+++..+||..+||+..+|..++..
T Consensus 19 ~e~g~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 19 LEEGESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp HHCTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 345779999999999999999988764
No 260
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=40.71 E-value=36 Score=24.22 Aligned_cols=24 Identities=29% Similarity=0.165 Sum_probs=20.6
Q ss_pred CHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 400 EDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 400 T~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
+..|+|+.+|++..+|+.......
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHHCCC
Confidence 678999999999999998866554
No 261
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=40.67 E-value=58 Score=30.03 Aligned_cols=26 Identities=23% Similarity=0.239 Sum_probs=22.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 398 YPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 398 ~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
..++.|||+.+|+|..+|..++++..
T Consensus 28 R~s~~eiA~~lglS~~tv~~Ri~rL~ 53 (164)
T PRK11169 28 RISNVELSKRVGLSPTPCLERVRRLE 53 (164)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 36889999999999999999887653
No 262
>PF13551 HTH_29: Winged helix-turn helix
Probab=40.35 E-value=84 Score=26.02 Aligned_cols=24 Identities=21% Similarity=0.094 Sum_probs=18.9
Q ss_pred CCCHHHHHHHh-------CCCHHHHHHHHHh
Q 012638 398 YPEDIEIAKYT-------GLSLAEIRSASEC 421 (459)
Q Consensus 398 ~PT~eEIAe~L-------GIS~e~Vk~~l~~ 421 (459)
..+..+|++.| .++..+|..+++.
T Consensus 80 ~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~~ 110 (112)
T PF13551_consen 80 RWTLEELAEWLIEEEFGIDVSPSTIRRILKR 110 (112)
T ss_pred cccHHHHHHHHHHhccCccCCHHHHHHHHHH
Confidence 46788888865 7888999988875
No 263
>PRK10403 transcriptional regulator NarP; Provisional
Probab=40.23 E-value=41 Score=30.09 Aligned_cols=33 Identities=12% Similarity=0.025 Sum_probs=27.2
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhhccCCcc
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASECLRIVGSI 428 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SL 428 (459)
..+.+.+|||+.+|++..+|+..+...+..+.+
T Consensus 166 ~~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~ 198 (215)
T PRK10403 166 AQGLSNKQIASVLNISEQTVKVHIRNLLRKLNV 198 (215)
T ss_pred HCCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 456899999999999999999998877654433
No 264
>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=40.14 E-value=1.3e+02 Score=27.23 Aligned_cols=27 Identities=22% Similarity=0.078 Sum_probs=23.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 398 YPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 398 ~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
..|.+|||..+|++.++|-.+++..+.
T Consensus 143 ~~t~~~iA~~lG~tretvsR~l~~l~~ 169 (193)
T TIGR03697 143 RLSHQAIAEAIGSTRVTITRLLGDLRK 169 (193)
T ss_pred CCCHHHHHHHhCCcHHHHHHHHHHHHH
Confidence 469999999999999999998887653
No 265
>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=40.10 E-value=29 Score=26.97 Aligned_cols=26 Identities=27% Similarity=0.224 Sum_probs=22.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhh
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECL 422 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~a 422 (459)
...|..|||+.+|+|..+|..+++..
T Consensus 21 ~~~t~~eIa~~l~i~~~~v~~~L~~L 46 (68)
T PF01978_consen 21 GPATAEEIAEELGISRSTVYRALKSL 46 (68)
T ss_dssp CHEEHHHHHHHHTSSHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 35799999999999999999988754
No 266
>PRK15320 transcriptional activator SprB; Provisional
Probab=40.02 E-value=31 Score=34.05 Aligned_cols=35 Identities=23% Similarity=0.087 Sum_probs=28.1
Q ss_pred HHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 389 KALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 389 ~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
.++...+..+.|..|||+.|++|..+|+....+..
T Consensus 170 IEVL~LLAkG~SNKEIAekL~LS~KTVSTYKnRLL 204 (251)
T PRK15320 170 YALLILLSSGHPAIELAKKFGLGTKTVSIYRKKVM 204 (251)
T ss_pred HHHHHHHHcCCCHHHHHHHhccchhhHHHHHHHHH
Confidence 34444556789999999999999999998877654
No 267
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=40.01 E-value=30 Score=27.37 Aligned_cols=23 Identities=17% Similarity=0.237 Sum_probs=19.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHh
Q 012638 399 PEDIEIAKYTGLSLAEIRSASEC 421 (459)
Q Consensus 399 PT~eEIAe~LGIS~e~Vk~~l~~ 421 (459)
++..|||+.+|++..+|..+++-
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln~ 23 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLNG 23 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCC
Confidence 46789999999999999887763
No 268
>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=39.52 E-value=89 Score=22.57 Aligned_cols=33 Identities=15% Similarity=0.061 Sum_probs=24.8
Q ss_pred HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHH
Q 012638 386 KARKALTNSHGKYPEDIEIAKYTGLSLAEIRSA 418 (459)
Q Consensus 386 ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~ 418 (459)
.+...+.+.--...|..+||+.+|++...+...
T Consensus 4 aa~~l~~~~G~~~~s~~~Ia~~~gvs~~~~y~~ 36 (47)
T PF00440_consen 4 AALELFAEKGYEAVSIRDIARRAGVSKGSFYRY 36 (47)
T ss_dssp HHHHHHHHHHTTTSSHHHHHHHHTSCHHHHHHH
T ss_pred HHHHHHHHhCHHhCCHHHHHHHHccchhhHHHH
Confidence 344444445457899999999999999998653
No 269
>PRK00215 LexA repressor; Validated
Probab=39.42 E-value=76 Score=30.01 Aligned_cols=35 Identities=26% Similarity=0.288 Sum_probs=28.1
Q ss_pred HHHHHHHcCCCCCHHHHHHHhCC-CHHHHHHHHHhh
Q 012638 388 RKALTNSHGKYPEDIEIAKYTGL-SLAEIRSASECL 422 (459)
Q Consensus 388 ~~~L~~~lgr~PT~eEIAe~LGI-S~e~Vk~~l~~a 422 (459)
+.+.....+..|+..|||+.+|+ +..+|..++...
T Consensus 13 i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L 48 (205)
T PRK00215 13 IRDHIEETGYPPSRREIADALGLRSPSAVHEHLKAL 48 (205)
T ss_pred HHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHH
Confidence 33344556788999999999999 999999887754
No 270
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=38.79 E-value=34 Score=32.93 Aligned_cols=28 Identities=14% Similarity=0.070 Sum_probs=25.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
|..+..|||+.|||+..++...|+++.+
T Consensus 177 R~~~l~dLA~~lGISkst~~ehLRrAe~ 204 (215)
T COG3413 177 RRVSLKDLAKELGISKSTLSEHLRRAER 204 (215)
T ss_pred ccCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 6679999999999999999999998754
No 271
>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=38.24 E-value=43 Score=24.54 Aligned_cols=25 Identities=24% Similarity=0.199 Sum_probs=20.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHh
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASEC 421 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~ 421 (459)
.+.|..|+|+.+|++..+|..+..-
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 4679999999999999999988764
No 272
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=37.23 E-value=68 Score=26.16 Aligned_cols=23 Identities=26% Similarity=0.174 Sum_probs=20.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHH
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSAS 419 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l 419 (459)
.+.|.+|+|+.+|++.+++-.+-
T Consensus 13 ~~ltQ~elA~~vgVsRQTi~~iE 35 (68)
T COG1476 13 LGLTQEELAKLVGVSRQTIIAIE 35 (68)
T ss_pred hCcCHHHHHHHcCcCHHHHHHHH
Confidence 36799999999999999998753
No 273
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=37.21 E-value=40 Score=30.31 Aligned_cols=32 Identities=16% Similarity=-0.135 Sum_probs=27.1
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhhccCC
Q 012638 395 HGKYPEDIEIAKYTGLSLAEIRSASECLRIVG 426 (459)
Q Consensus 395 lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~ 426 (459)
+..+.+.+|||+.|+++..+|+..+...+..+
T Consensus 161 l~~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl 192 (210)
T PRK09935 161 LVSGLSNKEIADQLLLSNKTVSAHKSNIYGKL 192 (210)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 34569999999999999999999988877543
No 274
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=37.19 E-value=1.1e+02 Score=24.67 Aligned_cols=26 Identities=23% Similarity=0.092 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhh
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECL 422 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~a 422 (459)
...+..|||+.+|++..+|...+...
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l~~L 44 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLNTL 44 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 46899999999999999999988765
No 275
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=37.18 E-value=58 Score=33.89 Aligned_cols=39 Identities=23% Similarity=0.085 Sum_probs=31.9
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhhcc----CCccccccC
Q 012638 395 HGKYPEDIEIAKYTGLSLAEIRSASECLRI----VGSIDQKIG 433 (459)
Q Consensus 395 lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~----~~SLD~~v~ 433 (459)
+..+.|..|||+.||||.-+|..++..++. .++++.++-
T Consensus 23 Y~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I~i~~~~~ 65 (321)
T COG2390 23 YVEGLTQSEIAERLGISRATVSRLLAKAREEGIVKISINSPVE 65 (321)
T ss_pred HhcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEEEeCCCCc
Confidence 456889999999999999999999999874 356665553
No 276
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=37.10 E-value=1.2e+02 Score=28.21 Aligned_cols=36 Identities=8% Similarity=-0.082 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHH
Q 012638 383 KIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASE 420 (459)
Q Consensus 383 kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~ 420 (459)
.+...++.+.. .++.|.+++|+.+|++...|..+-+
T Consensus 69 ~~g~~Ir~~Re--~~glSqeeLA~~lgvs~s~IsriE~ 104 (154)
T TIGR00270 69 DYGIIIRRERE--KRGWSQEQLAKKIQEKESLIKKIEN 104 (154)
T ss_pred HHHHHHHHHHH--HcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 33344444333 3578999999999999999988754
No 277
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=36.78 E-value=31 Score=26.11 Aligned_cols=34 Identities=18% Similarity=0.156 Sum_probs=20.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhhccCCcccc
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQ 430 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~ 430 (459)
++.|..++|+.+||+..+|..+++.-....+++.
T Consensus 9 ~~it~~~La~~~gis~~tl~~~~~~~~~~~~~~~ 42 (63)
T PF13443_consen 9 RGITQKDLARKTGISRSTLSRILNGKPSNPSLDT 42 (63)
T ss_dssp TT--HHHHHHHHT--HHHHHHHHTTT-----HHH
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcccccccHHH
Confidence 4569999999999999999998874433455543
No 278
>PRK10651 transcriptional regulator NarL; Provisional
Probab=36.42 E-value=43 Score=30.04 Aligned_cols=33 Identities=6% Similarity=-0.060 Sum_probs=27.0
Q ss_pred HcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCC
Q 012638 394 SHGKYPEDIEIAKYTGLSLAEIRSASECLRIVG 426 (459)
Q Consensus 394 ~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~ 426 (459)
.+..+.+.++||..++++..+|+..+...+..+
T Consensus 166 ~l~~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl 198 (216)
T PRK10651 166 LIAQGLPNKMIARRLDITESTVKVHVKHMLKKM 198 (216)
T ss_pred HHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHc
Confidence 344678999999999999999999888766543
No 279
>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=36.38 E-value=88 Score=26.11 Aligned_cols=25 Identities=20% Similarity=0.097 Sum_probs=22.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHh
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASEC 421 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~ 421 (459)
..++..+||+.+|+|..+|...+..
T Consensus 18 ~~~ti~dvA~~~gvS~~TVsr~L~~ 42 (80)
T TIGR02844 18 TKATVRETAKVFGVSKSTVHKDVTE 42 (80)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHhcC
Confidence 4679999999999999999987754
No 280
>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=36.25 E-value=73 Score=23.65 Aligned_cols=25 Identities=32% Similarity=0.442 Sum_probs=22.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 399 PEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 399 PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
++..+||+.+|++..+|..++....
T Consensus 26 ~~~~~la~~~~is~~~v~~~l~~L~ 50 (66)
T cd07377 26 PSERELAEELGVSRTTVREALRELE 50 (66)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 6799999999999999999887654
No 281
>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=35.54 E-value=41 Score=25.86 Aligned_cols=29 Identities=24% Similarity=0.168 Sum_probs=24.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
....+..|||+.+|+|..+++..+...+.
T Consensus 17 ~~~~~~~ela~~l~~S~rti~~~i~~L~~ 45 (59)
T PF08280_consen 17 NKWITLKELAKKLNISERTIKNDINELNE 45 (59)
T ss_dssp HTSBBHHHHHHHCTS-HHHHHHHHHHHHT
T ss_pred CCCCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45789999999999999999998876653
No 282
>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=35.06 E-value=41 Score=23.94 Aligned_cols=23 Identities=26% Similarity=0.101 Sum_probs=18.6
Q ss_pred CHHHHHHHhCCCHHHHHHHHHhh
Q 012638 400 EDIEIAKYTGLSLAEIRSASECL 422 (459)
Q Consensus 400 T~eEIAe~LGIS~e~Vk~~l~~a 422 (459)
|+.|+|+.+||++.+|+..-+..
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~G 23 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYEREG 23 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHTT
T ss_pred CHHHHHHHHCCCHHHHHHHHHCC
Confidence 46799999999999999877654
No 283
>PRK15044 transcriptional regulator SirC; Provisional
Probab=35.02 E-value=1.3e+02 Score=31.08 Aligned_cols=70 Identities=13% Similarity=0.076 Sum_probs=44.2
Q ss_pred hHHHHHHHHHHHHHHHhhccccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHh
Q 012638 350 TYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC 421 (459)
Q Consensus 350 TYa~~wIrnaI~d~Lrk~sr~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ 421 (459)
.|....+.-.+..+++++....-+.. ...+....++...+...+.+.++.++||+.+|+|..+++...+.
T Consensus 162 ~~~~~~l~~LLs~~l~~~~~~~~L~~--~~~is~~~kV~~~I~~nl~~~~SLeeLA~~lgmS~~tL~R~Fk~ 231 (295)
T PRK15044 162 DYSYFSLMYLISAFVRKPGGFDFLER--AIKITTKEKVYNIIISDLTRKWSQAEVAGKLFMSVSSLKRKLAA 231 (295)
T ss_pred HHHHHHHHHHHHHHHhcccchhhHHH--HhhhhHHHHHHHHHHhCcccCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 34444444555555554432221111 11233455666677777888999999999999999999987664
No 284
>PF13518 HTH_28: Helix-turn-helix domain
Probab=34.98 E-value=68 Score=23.07 Aligned_cols=25 Identities=24% Similarity=0.162 Sum_probs=22.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 399 PEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 399 PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
.|..+||..+||+..+|...+....
T Consensus 13 ~s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 13 ESVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred CCHHHHHHHHCCCHhHHHHHHHHHH
Confidence 3999999999999999998877654
No 285
>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=34.94 E-value=1.2e+02 Score=26.55 Aligned_cols=30 Identities=27% Similarity=0.174 Sum_probs=25.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhhccC
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASECLRIV 425 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~ 425 (459)
..+.|..|||+.+||+..+|..++....-+
T Consensus 69 ~pd~tl~Ela~~l~Vs~~ti~~~Lkrlg~t 98 (119)
T PF01710_consen 69 NPDATLRELAERLGVSPSTIWRALKRLGIT 98 (119)
T ss_pred CCCcCHHHHHHHcCCCHHHHHHHHHHcCch
Confidence 456788999999999999999999876543
No 286
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=34.71 E-value=1.2e+02 Score=21.35 Aligned_cols=27 Identities=26% Similarity=0.174 Sum_probs=23.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
..++..+||+.+|++..+|...+....
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~L~ 39 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNKLE 39 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 358999999999999999998887654
No 287
>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=34.51 E-value=1.1e+02 Score=25.91 Aligned_cols=29 Identities=38% Similarity=0.472 Sum_probs=23.5
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 395 HGKYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 395 lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
+..+.|+.|||+.+|+|..+|-..-++.+
T Consensus 46 L~~g~syreIa~~tgvS~aTItRvsr~Lk 74 (87)
T PF01371_consen 46 LDEGKSYREIAEETGVSIATITRVSRCLK 74 (87)
T ss_dssp HHTTSSHHHHHHHHTSTHHHHHHHHHHHH
T ss_pred HHCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 34678999999999999999977655443
No 288
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=34.08 E-value=1.2e+02 Score=29.08 Aligned_cols=27 Identities=26% Similarity=0.315 Sum_probs=23.3
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 398 YPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 398 ~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
..|.++||..+|++.++|-.+++..+.
T Consensus 179 ~lt~~~IA~~lGisretlsR~L~~L~~ 205 (230)
T PRK09391 179 PMSRRDIADYLGLTIETVSRALSQLQD 205 (230)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 368999999999999999998876653
No 289
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=33.71 E-value=88 Score=27.42 Aligned_cols=27 Identities=11% Similarity=-0.034 Sum_probs=23.4
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 398 YPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 398 ~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
+.+.++||+.+|++..+|+..+...+.
T Consensus 156 ~~~~~~ia~~l~~s~~tv~~~~~~~~~ 182 (202)
T PRK09390 156 GLSNKVIARDLDISPRTVEVYRANVMT 182 (202)
T ss_pred cCchHHHHHHcCCCHHHHHHHHHHHHH
Confidence 568999999999999999988877654
No 290
>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=33.40 E-value=48 Score=27.68 Aligned_cols=28 Identities=25% Similarity=0.057 Sum_probs=19.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhhccC
Q 012638 398 YPEDIEIAKYTGLSLAEIRSASECLRIV 425 (459)
Q Consensus 398 ~PT~eEIAe~LGIS~e~Vk~~l~~ar~~ 425 (459)
+.|.+|||+.+|.|...|..++....-|
T Consensus 3 G~tq~eIA~~lGks~s~Vs~~l~Ll~lP 30 (93)
T PF08535_consen 3 GWTQEEIAKRLGKSRSWVSNHLALLDLP 30 (93)
T ss_dssp T--HHHHHHHTT--HHHHHHHHGGGS--
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHcCC
Confidence 5689999999999999999998876543
No 291
>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=33.33 E-value=90 Score=23.83 Aligned_cols=26 Identities=27% Similarity=0.137 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhh
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECL 422 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~a 422 (459)
...+.+|||+.+|+|..+|+.-+...
T Consensus 13 ~~~s~~ela~~~~VS~~TiRRDl~~L 38 (57)
T PF08220_consen 13 GKVSVKELAEEFGVSEMTIRRDLNKL 38 (57)
T ss_pred CCEEHHHHHHHHCcCHHHHHHHHHHH
Confidence 46799999999999999999776643
No 292
>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=32.92 E-value=62 Score=26.30 Aligned_cols=25 Identities=28% Similarity=0.307 Sum_probs=21.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 399 PEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 399 PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
.+.+|||+.+|+|...|..+++...
T Consensus 26 ~s~~eiA~~~~i~~~~l~kil~~L~ 50 (83)
T PF02082_consen 26 VSSKEIAERLGISPSYLRKILQKLK 50 (83)
T ss_dssp BEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHh
Confidence 7999999999999999999987654
No 293
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=32.78 E-value=46 Score=25.57 Aligned_cols=24 Identities=25% Similarity=0.123 Sum_probs=21.0
Q ss_pred CHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 400 EDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 400 T~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
|..|+|+.+|||..+|+...+...
T Consensus 2 ti~eva~~~gvs~~tlr~y~~~gl 25 (69)
T PF13411_consen 2 TIKEVAKLLGVSPSTLRYYEREGL 25 (69)
T ss_dssp EHHHHHHHTTTTHHHHHHHHHTTS
T ss_pred cHHHHHHHHCcCHHHHHHHHHhcC
Confidence 578999999999999999877654
No 294
>COG3769 Predicted hydrolase (HAD superfamily) [General function prediction only]
Probab=32.49 E-value=90 Score=31.42 Aligned_cols=41 Identities=29% Similarity=0.353 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHHHHcC----CCCCHHHHHHHhCCCHHHHHHHHH
Q 012638 380 EISKIQKARKALTNSHG----KYPEDIEIAKYTGLSLAEIRSASE 420 (459)
Q Consensus 380 ~i~kI~ka~~~L~~~lg----r~PT~eEIAe~LGIS~e~Vk~~l~ 420 (459)
.+.+|++..+.|....| ...+.+||++.+|+|.+.+.-++.
T Consensus 102 ~l~~ire~l~kLee~~g~~~~~~~d~~ei~e~TGlpre~aaLa~~ 146 (274)
T COG3769 102 VLEKIREKLDKLEEHFGFTTFDDVDDEEIAEWTGLPREQAALAML 146 (274)
T ss_pred hHHHHHHHHHHHHHHhCeeEeccCCHHHHHHHhCCChHHhHHHHH
Confidence 45566666667776665 568999999999999999876654
No 295
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=31.69 E-value=70 Score=22.50 Aligned_cols=28 Identities=14% Similarity=-0.048 Sum_probs=19.9
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhh
Q 012638 395 HGKYPEDIEIAKYTGLSLAEIRSASECL 422 (459)
Q Consensus 395 lgr~PT~eEIAe~LGIS~e~Vk~~l~~a 422 (459)
+....+.++||+.+|++...+..+.+..
T Consensus 5 ~~~~~~l~~iA~~~g~S~~~f~r~Fk~~ 32 (42)
T PF00165_consen 5 LQQKLTLEDIAEQAGFSPSYFSRLFKKE 32 (42)
T ss_dssp T-SS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred ccCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 4556899999999999999988876643
No 296
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=31.49 E-value=4e+02 Score=27.07 Aligned_cols=28 Identities=18% Similarity=0.146 Sum_probs=23.2
Q ss_pred CCCCCHHHHHHHhC--CCHHHHHHHHHhhc
Q 012638 396 GKYPEDIEIAKYTG--LSLAEIRSASECLR 423 (459)
Q Consensus 396 gr~PT~eEIAe~LG--IS~e~Vk~~l~~ar 423 (459)
+-.+++++||+.++ ||.++|+..+....
T Consensus 135 ~~~~~~~~ia~~l~p~is~~ev~~sL~~L~ 164 (271)
T TIGR02147 135 PFADDPEELAKRCFPKISAEQVKESLDLLE 164 (271)
T ss_pred CCCCCHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence 34567889999999 99999999887654
No 297
>PRK03837 transcriptional regulator NanR; Provisional
Probab=31.36 E-value=1e+02 Score=29.59 Aligned_cols=27 Identities=22% Similarity=0.518 Sum_probs=23.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
+-|+..+||+.+|+|...|+.++....
T Consensus 36 ~Lp~E~~Lae~~gVSRt~VREAL~~L~ 62 (241)
T PRK03837 36 QLPSERELMAFFGVGRPAVREALQALK 62 (241)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 346999999999999999999988653
No 298
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=31.35 E-value=5e+02 Score=25.26 Aligned_cols=38 Identities=11% Similarity=0.037 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHh
Q 012638 384 IQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC 421 (459)
Q Consensus 384 I~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ 421 (459)
+.++...+.+......|.++||+.+|+|...+..+.+.
T Consensus 188 ~~~~~~~I~~~~~~~~sl~~lA~~~~~S~~~l~r~Fk~ 225 (287)
T TIGR02297 188 FNRFNFLIEENYKQHLRLPEYADRLGISESRLNDICRR 225 (287)
T ss_pred HHHHHHHHHHhhccCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 34444455556667889999999999999999776554
No 299
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=31.29 E-value=1.1e+02 Score=28.45 Aligned_cols=42 Identities=12% Similarity=0.009 Sum_probs=33.7
Q ss_pred hHHHHHHHHHHHHHHHHHcC-CCCCHHHHHHHhCCCHHHHHHH
Q 012638 377 LNREISKIQKARKALTNSHG-KYPEDIEIAKYTGLSLAEIRSA 418 (459)
Q Consensus 377 v~e~i~kI~ka~~~L~~~lg-r~PT~eEIAe~LGIS~e~Vk~~ 418 (459)
..+...+|-++..++..+.| ...|.++||+..|++.+++...
T Consensus 9 ~~~~r~~Il~aa~~lf~~~G~~~~ti~~Ia~~agvsk~t~Y~~ 51 (213)
T PRK09975 9 ALKTRQELIETAIAQFALRGVSNTTLNDIADAANVTRGAIYWH 51 (213)
T ss_pred HHHHHHHHHHHHHHHHHHcCcccCCHHHHHHHcCCCHHHHHHH
Confidence 44556677777777777777 5799999999999999998753
No 300
>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=30.51 E-value=63 Score=23.37 Aligned_cols=25 Identities=20% Similarity=0.232 Sum_probs=22.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHh
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASEC 421 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~ 421 (459)
...|.+++|+.+|++..+|..+.+-
T Consensus 14 ~gltq~~lA~~~gvs~~~vs~~e~g 38 (58)
T TIGR03070 14 LGLTQADLADLAGVGLRFIRDVENG 38 (58)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 4779999999999999999988753
No 301
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=30.27 E-value=95 Score=31.81 Aligned_cols=43 Identities=19% Similarity=0.157 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 381 ISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 381 i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
...|-++.-.|..+.++...-+|||+.+|..+++|++.++..+
T Consensus 8 QkeIL~aLi~LY~~~~r~IKgeeIA~~l~rnpGTVRNqmq~Lk 50 (294)
T COG2524 8 QKEILQALINLYRRKKRPIKGEEIAEVLNRNPGTVRNQMQSLK 50 (294)
T ss_pred HHHHHHHHHHHHHhcCCCcchHHHHHHHccCcchHHHHHHHHH
Confidence 3445556666666777888899999999999999999887655
No 302
>TIGR00180 parB_part ParB-like partition proteins. This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.
Probab=29.88 E-value=1.5e+02 Score=27.93 Aligned_cols=36 Identities=25% Similarity=0.235 Sum_probs=28.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccC
Q 012638 398 YPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIG 433 (459)
Q Consensus 398 ~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~ 433 (459)
+.+.++||+.+|++...|..++..+.-+-.+...+.
T Consensus 120 g~s~~~iA~~lg~s~~~V~r~l~l~~lp~~v~~~~~ 155 (187)
T TIGR00180 120 SMTQEDLAKKIGKSRAHITNLLRLLKLPSEIQSAIP 155 (187)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHcCCHHHHHHHH
Confidence 468999999999999999999998875545544443
No 303
>PF13551 HTH_29: Winged helix-turn helix
Probab=29.69 E-value=56 Score=27.13 Aligned_cols=25 Identities=24% Similarity=0.135 Sum_probs=22.3
Q ss_pred CHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 400 EDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 400 T~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
+..+||+.+|++..+|...++....
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~ 38 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYRE 38 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHc
Confidence 6999999999999999998887553
No 304
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=29.53 E-value=2e+02 Score=23.29 Aligned_cols=25 Identities=24% Similarity=0.077 Sum_probs=21.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHh
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASEC 421 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~ 421 (459)
.+.+.+||++.+|+|..++.-++..
T Consensus 43 ~Ga~~~el~~~CgL~~aEAeLl~~L 67 (70)
T PF10975_consen 43 QGASVEELMEECGLSRAEAELLLSL 67 (70)
T ss_pred cCCCHHHHHHHcCCCHHHHHHHHHH
Confidence 4579999999999999999877654
No 305
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=29.39 E-value=89 Score=27.39 Aligned_cols=28 Identities=25% Similarity=0.240 Sum_probs=23.8
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
+...+..|||+.+|+|...|..+++...
T Consensus 23 ~~~~s~~eia~~l~is~~~v~~~l~~L~ 50 (130)
T TIGR02944 23 SQPYSAAEIAEQTGLNAPTVSKILKQLS 50 (130)
T ss_pred CCCccHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4457999999999999999999877653
No 306
>PHA01976 helix-turn-helix protein
Probab=29.14 E-value=73 Score=24.35 Aligned_cols=25 Identities=12% Similarity=0.053 Sum_probs=21.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHh
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASEC 421 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~ 421 (459)
+..|.+|+|+.+|++..+|....+-
T Consensus 14 ~glt~~~lA~~~gvs~~~v~~~e~g 38 (67)
T PHA01976 14 RAWSAPELSRRAGVRHSLIYDFEAD 38 (67)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 5689999999999999999887653
No 307
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=28.50 E-value=2e+02 Score=23.15 Aligned_cols=37 Identities=27% Similarity=0.205 Sum_probs=27.2
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhhccCCcccccc
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKI 432 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v 432 (459)
....+.++||+.++++.+.|...+..+-..-.|+..+
T Consensus 22 y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~I 58 (88)
T smart00088 22 YSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKI 58 (88)
T ss_pred hceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEE
Confidence 3467999999999999999988766554333455544
No 308
>smart00753 PAM PCI/PINT associated module.
Probab=28.50 E-value=2e+02 Score=23.15 Aligned_cols=37 Identities=27% Similarity=0.205 Sum_probs=27.2
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhhccCCcccccc
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKI 432 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v 432 (459)
....+.++||+.++++.+.|...+..+-..-.|+..+
T Consensus 22 y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~I 58 (88)
T smart00753 22 YSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKI 58 (88)
T ss_pred hceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEE
Confidence 3467999999999999999988766554333455544
No 309
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=28.21 E-value=2.2e+02 Score=26.90 Aligned_cols=26 Identities=23% Similarity=0.192 Sum_probs=22.7
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHh
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASEC 421 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ 421 (459)
..+.|..+||+.||||..+|..++..
T Consensus 170 ~~g~s~~~iak~lgis~~Tv~r~~k~ 195 (200)
T PRK13413 170 DKGTSKSEIARKLGVSRTTLARFLKT 195 (200)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 44679999999999999999988764
No 310
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=28.17 E-value=92 Score=27.43 Aligned_cols=39 Identities=18% Similarity=0.176 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHh
Q 012638 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAF 292 (459)
Q Consensus 254 ~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l~~ 292 (459)
.++++..-+.......++.+++|+.+|++...|.+.++.
T Consensus 10 ~i~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 10 TIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 445566667777788899999999999999888765553
No 311
>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=28.06 E-value=85 Score=23.38 Aligned_cols=24 Identities=21% Similarity=0.252 Sum_probs=20.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHhh
Q 012638 399 PEDIEIAKYTGLSLAEIRSASECL 422 (459)
Q Consensus 399 PT~eEIAe~LGIS~e~Vk~~l~~a 422 (459)
.+..|||+.+|++..+|..++...
T Consensus 22 ~t~~~la~~l~~~~~~vs~~v~~L 45 (62)
T PF12802_consen 22 LTQSELAERLGISKSTVSRIVKRL 45 (62)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHH
Confidence 699999999999999999887754
No 312
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=28.06 E-value=1.5e+02 Score=24.75 Aligned_cols=25 Identities=28% Similarity=0.247 Sum_probs=22.1
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhh
Q 012638 398 YPEDIEIAKYTGLSLAEIRSASECL 422 (459)
Q Consensus 398 ~PT~eEIAe~LGIS~e~Vk~~l~~a 422 (459)
..+..|||+.+|++..+|...+...
T Consensus 17 ~~~~~~la~~l~~s~~tv~~~l~~L 41 (108)
T smart00344 17 RISLAELAKKVGLSPSTVHNRVKRL 41 (108)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4689999999999999999887765
No 313
>PRK14999 histidine utilization repressor; Provisional
Probab=28.02 E-value=1.5e+02 Score=28.66 Aligned_cols=26 Identities=27% Similarity=0.358 Sum_probs=23.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhh
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECL 422 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~a 422 (459)
+-|+..|||+.+|+|..+|+.++...
T Consensus 35 ~LPsE~eLa~~~gVSR~TVR~Al~~L 60 (241)
T PRK14999 35 RIPSEAELVAQYGFSRMTINRALREL 60 (241)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 56899999999999999999998753
No 314
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=27.97 E-value=88 Score=22.55 Aligned_cols=28 Identities=25% Similarity=0.159 Sum_probs=23.6
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
....+..+|++.+|++..+|..+++...
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~ 35 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLR 35 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3456899999999999999999887653
No 315
>PF05138 PaaA_PaaC: Phenylacetic acid catabolic protein; InterPro: IPR007814 This family includes proteins such as PaaA and PaaC that are part of a catabolic pathway of phenylacetic acid []. These proteins may form part of a dioxygenase complex.; PDB: 3PWQ_K 3PVT_B 1OTK_B 3PW1_B 3PW8_B 3PVR_B 3PVY_B 3Q1G_A 3PF7_B 3PM5_C ....
Probab=27.96 E-value=2.1e+02 Score=28.91 Aligned_cols=109 Identities=17% Similarity=0.135 Sum_probs=63.9
Q ss_pred CChHHHHHHHHHhHHHHHHHHH-HHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhchHHHHHHHHHhHHHHHHHHHHh
Q 012638 237 TIARNEAEMSKGVQVVANLERI-KTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNY 315 (459)
Q Consensus 237 Lt~~eE~eL~~~i~~~~~le~~-~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l~~G~~Are~LI~~nlrLV~sIAkry 315 (459)
++.+--..|.+.|-.+..=+=+ -..+-+-+|+.|++++....+++ |.+.| .|-++.+.++..+
T Consensus 10 ~~~~~~~~L~~~l~~laD~elil~~r~~ew~~~AP~LeediAl~~i--------------a~Del--GHAr~ly~ll~el 73 (263)
T PF05138_consen 10 MPEEYREALIRYLLRLADDELILGQRLSEWCGHAPSLEEDIALANI--------------AQDEL--GHARLLYRLLEEL 73 (263)
T ss_dssp --HHHHHHHHHHHHHHHHHHHHHHHHHHTGGGGSSSHHHHHHHHHH--------------HHHHH--HHHHHHHHHHHHC
T ss_pred hhhhhHHHHHHHHHHHhChHHHhhhHHhHHHhhCCCHHHHHHHHHH--------------HHHHH--HHHHHHHHHHHHH
Confidence 3444445555555544332222 22344567999999876544322 22222 4577888999888
Q ss_pred hCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHH
Q 012638 316 RGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVA 365 (459)
Q Consensus 316 ~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lr 365 (459)
-|.|.+.+||...=.-+=++.+.-|+ ..+..|+..++++.+.+...
T Consensus 74 ~g~G~~~d~la~~R~~~~~rn~~l~e----~p~~dwa~~v~r~~l~d~~~ 119 (263)
T PF05138_consen 74 EGEGRDEDDLAFLRDAREFRNLLLFE----QPNGDWADTVARQFLFDRAG 119 (263)
T ss_dssp HCCCHHHHHHHHHHHTTCS-SSGGGG----S---SHHHHHHHHHHHHHHH
T ss_pred hccCCChhHHHhhcccchhhhhhhhc----cCCCCHHHHHHHHHHHHHHH
Confidence 88887777776554444444444443 35779999999999988664
No 316
>PRK13503 transcriptional activator RhaS; Provisional
Probab=27.74 E-value=2.2e+02 Score=27.62 Aligned_cols=27 Identities=26% Similarity=0.249 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHhCCCH
Q 012638 383 KIQKARKALTNSHGKYPEDIEIAKYTGLSL 412 (459)
Q Consensus 383 kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~ 412 (459)
+|.+|.+.|. ....++.|||..+|.+-
T Consensus 224 Rl~~A~~LL~---~~~~sI~eIA~~~GF~~ 250 (278)
T PRK13503 224 RLLKARHLLR---HSDASVTDIAYRCGFGD 250 (278)
T ss_pred HHHHHHHHHH---cCCCCHHHHHHHhCCCC
Confidence 3444444443 23467888888887654
No 317
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=27.74 E-value=1.7e+02 Score=27.86 Aligned_cols=26 Identities=15% Similarity=0.180 Sum_probs=22.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 399 PEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 399 PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
.+.++||+.+|++.++|-..+...+.
T Consensus 170 ~t~~~lA~~lG~sretvsR~L~~L~~ 195 (226)
T PRK10402 170 EKHTQAAEYLGVSYRHLLYVLAQFIQ 195 (226)
T ss_pred chHHHHHHHHCCcHHHHHHHHHHHHH
Confidence 47899999999999999998886653
No 318
>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=27.70 E-value=67 Score=29.85 Aligned_cols=26 Identities=35% Similarity=0.296 Sum_probs=23.5
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 398 YPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 398 ~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
..|.+|||+.|||+...|+.++....
T Consensus 28 ~~tdEeLa~~Lgi~~~~VRk~L~~L~ 53 (158)
T TIGR00373 28 EFTDEEISLELGIKLNEVRKALYALY 53 (158)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 68999999999999999999987654
No 319
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=27.41 E-value=3.7e+02 Score=27.10 Aligned_cols=57 Identities=12% Similarity=0.248 Sum_probs=36.6
Q ss_pred HHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHH
Q 012638 308 VLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVA 365 (459)
Q Consensus 308 V~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lr 365 (459)
+..|..+|. .....+||.....+..-.-...|...-|..|..|+...-.+...+.|.
T Consensus 197 ~~~i~~~~~-~~~tl~~lA~~~~~S~~~l~r~Fk~~~G~t~~~~l~~~Rl~~A~~lL~ 253 (302)
T PRK10371 197 LGFIAENYD-QALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRALLS 253 (302)
T ss_pred HHHHHHhhc-CCCCHHHHHHHHCcCHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHh
Confidence 334444554 568899998887777666666666555777887776655555555444
No 320
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=27.24 E-value=1.2e+02 Score=23.06 Aligned_cols=25 Identities=12% Similarity=0.114 Sum_probs=19.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHh
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASEC 421 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~ 421 (459)
.+.|.+++|+.+|++..+|..+.+-
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 3679999999999999999987663
No 321
>PHA02943 hypothetical protein; Provisional
Probab=27.06 E-value=2e+02 Score=27.29 Aligned_cols=25 Identities=28% Similarity=0.175 Sum_probs=21.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhh
Q 012638 398 YPEDIEIAKYTGLSLAEIRSASECL 422 (459)
Q Consensus 398 ~PT~eEIAe~LGIS~e~Vk~~l~~a 422 (459)
..|..|||+.||+|-+.|+.++...
T Consensus 24 ~~TtseIAkaLGlS~~qa~~~LyvL 48 (165)
T PHA02943 24 CKTTSRIANKLGVSHSMARNALYQL 48 (165)
T ss_pred CccHHHHHHHHCCCHHHHHHHHHHH
Confidence 4578999999999999999987754
No 322
>smart00351 PAX Paired Box domain.
Probab=26.83 E-value=1.3e+02 Score=26.75 Aligned_cols=32 Identities=16% Similarity=0.034 Sum_probs=26.3
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhhccCCccc
Q 012638 398 YPEDIEIAKYTGLSLAEIRSASECLRIVGSID 429 (459)
Q Consensus 398 ~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD 429 (459)
+.+..+||+.+||+..+|...+++.+..-++.
T Consensus 33 G~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~ 64 (125)
T smart00351 33 GVRPCDISRQLCVSHGCVSKILGRYYETGSIR 64 (125)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcC
Confidence 56899999999999999999988876543433
No 323
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=26.72 E-value=1.4e+02 Score=29.72 Aligned_cols=40 Identities=13% Similarity=-0.039 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHH
Q 012638 381 ISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASE 420 (459)
Q Consensus 381 i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~ 420 (459)
...|.++..-+...+...++.++||+.+|+|...+..+.+
T Consensus 4 ~~~i~~~~~~i~~~~~~~~~l~~lA~~~~~S~~~l~r~F~ 43 (289)
T PRK15121 4 AGIIRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFK 43 (289)
T ss_pred HHHHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3456777777777788889999999999999998887654
No 324
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=26.69 E-value=78 Score=24.19 Aligned_cols=23 Identities=22% Similarity=0.199 Sum_probs=19.9
Q ss_pred CHHHHHHHhCCCHHHHHHHHHhh
Q 012638 400 EDIEIAKYTGLSLAEIRSASECL 422 (459)
Q Consensus 400 T~eEIAe~LGIS~e~Vk~~l~~a 422 (459)
+..|+|+.+||+..+++...+..
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~~ 24 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERRY 24 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHhC
Confidence 67899999999999999876643
No 325
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=26.68 E-value=64 Score=28.13 Aligned_cols=28 Identities=18% Similarity=0.004 Sum_probs=25.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
.+.+.+|-|..||||..++..++..+|.
T Consensus 48 ~~l~QeeAA~rMgISr~Tfwr~l~sAR~ 75 (99)
T COG1342 48 EGLTQEEAALRMGISRQTFWRLLTSARK 75 (99)
T ss_pred hhccHHHHHHHhcccHHHHHHHHHHHHH
Confidence 4679999999999999999999998875
No 326
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=26.63 E-value=1.7e+02 Score=28.43 Aligned_cols=26 Identities=23% Similarity=0.316 Sum_probs=23.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhh
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECL 422 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~a 422 (459)
+-||..|||+.+|++..+|+.++...
T Consensus 28 ~LPsE~eL~~~~~VSR~TvR~Al~~L 53 (240)
T PRK09764 28 ALPTESALQTEFGVSRVTVRQALRQL 53 (240)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 56899999999999999999997753
No 327
>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=26.53 E-value=1.5e+02 Score=27.17 Aligned_cols=41 Identities=22% Similarity=0.393 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhchH
Q 012638 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWY 295 (459)
Q Consensus 255 le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l~~G~~ 295 (459)
.++++.-|.+..++..|..+.+++.|++.+.+.+-++.|+-
T Consensus 32 f~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~IreGRL 72 (137)
T TIGR03826 32 FEKVYKFLRKHENRQATVSEIVEETGVSEKLILKFIREGRL 72 (137)
T ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCCe
Confidence 34455566666678889999999999999999998888853
No 328
>PRK09480 slmA division inhibitor protein; Provisional
Probab=26.51 E-value=1.4e+02 Score=27.13 Aligned_cols=44 Identities=25% Similarity=0.257 Sum_probs=0.0
Q ss_pred ccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHH
Q 012638 372 KIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEI 415 (459)
Q Consensus 372 rlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~V 415 (459)
+.|..-.....-+..+...+..+.|...|.++||+..||+.+++
T Consensus 4 ~~~~~~~~r~~Il~aa~~l~~~~~G~~~ti~~Ia~~agvs~gt~ 47 (194)
T PRK09480 4 KRPKKGERREQILQALAQMLESPPGERITTAKLAARVGVSEAAL 47 (194)
T ss_pred cCCCchhHHHHHHHHHHHHHHhcCCCccCHHHHHHHhCCCHhHH
No 329
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=26.34 E-value=3.1e+02 Score=25.27 Aligned_cols=26 Identities=19% Similarity=0.141 Sum_probs=22.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 398 YPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 398 ~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
..|.++||..+|++.++|-.+++..+
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR~l~~l~ 193 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRVLKMLE 193 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 46889999999999999999887654
No 330
>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=26.30 E-value=1.8e+02 Score=25.09 Aligned_cols=25 Identities=32% Similarity=0.290 Sum_probs=21.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHh
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASEC 421 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~ 421 (459)
.+.|+.|||+.+|||..+|-..-+.
T Consensus 54 ~~~tQrEIa~~lGiS~atIsR~sn~ 78 (94)
T TIGR01321 54 GNMSQREIASKLGVSIATITRGSNN 78 (94)
T ss_pred CCCCHHHHHHHhCCChhhhhHHHhh
Confidence 5789999999999999999765543
No 331
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=26.01 E-value=1e+02 Score=29.93 Aligned_cols=26 Identities=15% Similarity=0.210 Sum_probs=23.3
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHh
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASEC 421 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ 421 (459)
.+-||..|||+.+|+|..||+.++..
T Consensus 33 ~~LPsE~eLa~~~~VSR~TVR~Al~~ 58 (241)
T PRK10079 33 DYLPAEQQLAARYEVNRHTLRRAIDQ 58 (241)
T ss_pred CcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 36799999999999999999999774
No 332
>PRK04841 transcriptional regulator MalT; Provisional
Probab=25.93 E-value=71 Score=36.62 Aligned_cols=29 Identities=14% Similarity=-0.018 Sum_probs=25.1
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 395 HGKYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 395 lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
..++.|++|||+.|+||+.||+..++...
T Consensus 850 ~~~g~~~~~ia~~l~~s~~tv~~h~~~~~ 878 (903)
T PRK04841 850 IYSGYSNEQIAGELDVAATTIKTHIRNLY 878 (903)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 45688999999999999999999877643
No 333
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=25.89 E-value=94 Score=27.90 Aligned_cols=34 Identities=12% Similarity=-0.082 Sum_probs=27.1
Q ss_pred HHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccC
Q 012638 392 TNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIV 425 (459)
Q Consensus 392 ~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~ 425 (459)
...+..+.+.+|||+.++++..+|+......+..
T Consensus 152 l~~l~~g~~~~~I~~~l~~s~~tv~~~~~~l~~K 185 (204)
T PRK09958 152 MRYILDGKDNNDIAEKMFISNKTVSTYKSRLMEK 185 (204)
T ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 3334456799999999999999999988876653
No 334
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=25.57 E-value=1.3e+02 Score=26.23 Aligned_cols=26 Identities=27% Similarity=0.213 Sum_probs=22.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 398 YPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 398 ~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
.++.+|||+.+|+|...|..++....
T Consensus 25 ~~s~~eia~~~~i~~~~v~~il~~L~ 50 (132)
T TIGR00738 25 PVSVKEIAERQGISRSYLEKILRTLR 50 (132)
T ss_pred cCcHHHHHHHHCcCHHHHHHHHHHHH
Confidence 67999999999999999999877543
No 335
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=25.47 E-value=85 Score=24.02 Aligned_cols=23 Identities=26% Similarity=0.215 Sum_probs=19.8
Q ss_pred CHHHHHHHhCCCHHHHHHHHHhh
Q 012638 400 EDIEIAKYTGLSLAEIRSASECL 422 (459)
Q Consensus 400 T~eEIAe~LGIS~e~Vk~~l~~a 422 (459)
+..|+|+.+||+..+++......
T Consensus 2 s~~eva~~~gvs~~tlr~~~~~g 24 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYERIG 24 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCC
Confidence 67899999999999999886643
No 336
>PRK09726 antitoxin HipB; Provisional
Probab=25.20 E-value=1.7e+02 Score=24.01 Aligned_cols=33 Identities=18% Similarity=0.072 Sum_probs=25.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhhccCCcccc
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQ 430 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~ 430 (459)
++.|.+|+|+.+|++..+|..+.+-. ...+++.
T Consensus 24 ~gltq~elA~~~gvs~~tis~~e~g~-~~ps~~~ 56 (88)
T PRK09726 24 NGWTQSELAKKIGIKQATISNFENNP-DNTTLTT 56 (88)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHCCC-CCCCHHH
Confidence 47899999999999999999887633 2335543
No 337
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=25.10 E-value=1.1e+02 Score=23.32 Aligned_cols=26 Identities=31% Similarity=0.247 Sum_probs=19.1
Q ss_pred CCCCCHHHHHHHhC-CCHHHHHHHHHh
Q 012638 396 GKYPEDIEIAKYTG-LSLAEIRSASEC 421 (459)
Q Consensus 396 gr~PT~eEIAe~LG-IS~e~Vk~~l~~ 421 (459)
..+.|.+||++... ++.+.|+.++..
T Consensus 29 ~~G~s~eeI~~~yp~Lt~~~i~aAl~y 55 (56)
T PF04255_consen 29 AAGESPEEIAEDYPSLTLEDIRAALAY 55 (56)
T ss_dssp HTT--HHHHHHHSTT--HHHHHHHHHH
T ss_pred HcCCCHHHHHHHCCCCCHHHHHHHHHh
Confidence 45789999999998 999999998865
No 338
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=24.96 E-value=84 Score=28.04 Aligned_cols=30 Identities=23% Similarity=0.045 Sum_probs=24.8
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 395 HGKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 395 lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
+..+.+.++||+.++++..+|+......+.
T Consensus 149 l~~g~~~~~Ia~~l~~s~~tv~~~~~~l~~ 178 (196)
T PRK10360 149 LAQGMAVKEIAAELGLSPKTVHVHRANLME 178 (196)
T ss_pred HHCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 334679999999999999999988776554
No 339
>COG2344 AT-rich DNA-binding protein [General function prediction only]
Probab=24.96 E-value=1.6e+02 Score=28.87 Aligned_cols=52 Identities=19% Similarity=0.190 Sum_probs=40.4
Q ss_pred cccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhh
Q 012638 371 IKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL 422 (459)
Q Consensus 371 irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~a 422 (459)
..+|......+....+....|..+.-...+-+|||+.+|++..+|+.-+.+.
T Consensus 5 ~~IP~AT~kRL~~YyR~le~l~a~~v~rvsS~els~~~~vdsatIRrDfSYF 56 (211)
T COG2344 5 KKIPKATAKRLPLYYRVLERLHASGVERVSSKELSEALGVDSATIRRDFSYF 56 (211)
T ss_pred ccCCHHHHHHhHHHHHHHHHHHHcCCceecHHHHHHHhCCCHHHHhhhhHHH
Confidence 4577777777777777777777665566899999999999999999765543
No 340
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=24.91 E-value=3e+02 Score=27.16 Aligned_cols=80 Identities=14% Similarity=0.083 Sum_probs=0.0
Q ss_pred HhHHHHHHHHHHhhCCC-CCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccchHHHH
Q 012638 303 STRPLVLFLARNYRGLG-IPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREI 381 (459)
Q Consensus 303 ~nlrLV~sIAkry~g~g-~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~v~e~i 381 (459)
..+..|..++....... +..+++-+...|..-.-...|... |..|..|+..
T Consensus 197 ~~l~~~~~~I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk~~-G~T~~~yi~~--------------------------- 248 (302)
T PRK09685 197 RQFQKVVALIDQSIQEEILRPEWIAGELGISVRSLYRLFAEQ-GLVVAQYIRN--------------------------- 248 (302)
T ss_pred HHHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHc-CCCHHHHHHH---------------------------
Q ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHhCCC
Q 012638 382 SKIQKARKALTNSHGKYPEDIEIAKYTGLS 411 (459)
Q Consensus 382 ~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS 411 (459)
.+|.++...| .......++.|||..+|.+
T Consensus 249 ~RL~~A~~lL-~~~~~~~sI~eIA~~~GF~ 277 (302)
T PRK09685 249 RRLDRCADDL-RPAADDEKITSIAYKWGFS 277 (302)
T ss_pred HHHHHHHHHh-hhhccCCCHHHHHHHhCCC
No 341
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=24.83 E-value=1.4e+02 Score=30.11 Aligned_cols=41 Identities=7% Similarity=-0.030 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhh
Q 012638 382 SKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL 422 (459)
Q Consensus 382 ~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~a 422 (459)
..+.++...+...+...++.++||+.+|+|..++....+..
T Consensus 218 ~~~~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~ 258 (322)
T PRK09393 218 DRLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAA 258 (322)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 45666777777777788999999999999999998876643
No 342
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=24.82 E-value=1.6e+02 Score=24.57 Aligned_cols=29 Identities=21% Similarity=0.303 Sum_probs=24.9
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
+...|-++||+.||||...|...++..+.
T Consensus 17 ~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~ 45 (79)
T COG1654 17 GNFVSGEKLAEELGISRTAVWKHIQQLRE 45 (79)
T ss_pred CCcccHHHHHHHHCccHHHHHHHHHHHHH
Confidence 45679999999999999999988877663
No 343
>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=24.80 E-value=1.4e+02 Score=22.66 Aligned_cols=28 Identities=18% Similarity=0.084 Sum_probs=22.7
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
+...|..|||+.+|++..++..-++...
T Consensus 22 ~~~~t~~ela~~l~~~~~t~s~hL~~L~ 49 (61)
T PF12840_consen 22 NGPMTVSELAEELGISQSTVSYHLKKLE 49 (61)
T ss_dssp CSTBEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 5678999999999999999987766543
No 344
>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=24.65 E-value=2e+02 Score=24.15 Aligned_cols=27 Identities=30% Similarity=0.298 Sum_probs=23.3
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhh
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASECL 422 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~a 422 (459)
...+|..|||+.+|++..+|..++...
T Consensus 45 ~~~is~~eLa~~~g~sr~tVsr~L~~L 71 (95)
T TIGR01610 45 QDRVTATVIAELTGLSRTHVSDAIKSL 71 (95)
T ss_pred CCccCHHHHHHHHCcCHHHHHHHHHHH
Confidence 456899999999999999999887654
No 345
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=24.60 E-value=2e+02 Score=24.82 Aligned_cols=26 Identities=27% Similarity=0.165 Sum_probs=20.4
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 398 YPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 398 ~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
+.+..|||...|+|...|..++...+
T Consensus 72 G~n~~eLA~kyglS~r~I~~Ii~~~~ 97 (108)
T PF08765_consen 72 GMNVRELARKYGLSERQIYRIIKRVR 97 (108)
T ss_dssp SS-HHHHHHHHT--HHHHHHHHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 66899999999999999999988765
No 346
>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=24.23 E-value=94 Score=23.95 Aligned_cols=24 Identities=13% Similarity=0.156 Sum_probs=20.0
Q ss_pred CHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 400 EDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 400 T~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
+..|+|+.+||+..+++.......
T Consensus 2 ~i~evA~~~gvs~~tlR~~~~~g~ 25 (67)
T cd04764 2 TIKEVSEIIGVKPHTLRYYEKEFN 25 (67)
T ss_pred CHHHHHHHHCcCHHHHHHHHHhcC
Confidence 678999999999999998765433
No 347
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=23.96 E-value=1.3e+02 Score=29.90 Aligned_cols=30 Identities=23% Similarity=0.150 Sum_probs=25.9
Q ss_pred HcCCCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 394 SHGKYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 394 ~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
..+...|.+|+|+.+|+|.-+++.++...-
T Consensus 169 ~~~~~~Taeela~~~giSRvTaRRYLeyl~ 198 (224)
T COG4565 169 EPDQELTAEELAQALGISRVTARRYLEYLV 198 (224)
T ss_pred CcCCccCHHHHHHHhCccHHHHHHHHHHHH
Confidence 345678999999999999999999988754
No 348
>cd00131 PAX Paired Box domain
Probab=23.80 E-value=1.5e+02 Score=26.46 Aligned_cols=33 Identities=15% Similarity=0.053 Sum_probs=28.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhhccCCccc
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECLRIVGSID 429 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD 429 (459)
.+.+..+||+.+|++..+|...+++.+..-++.
T Consensus 32 ~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~ 64 (128)
T cd00131 32 SGIRPCDISRQLRVSHGCVSKILNRYYETGSIR 64 (128)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcC
Confidence 367999999999999999999999877655554
No 349
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=23.74 E-value=1e+02 Score=20.69 Aligned_cols=24 Identities=21% Similarity=0.192 Sum_probs=20.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASE 420 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~ 420 (459)
...+..++|+.+|++..+|.....
T Consensus 9 ~~~s~~~la~~~~i~~~~i~~~~~ 32 (56)
T smart00530 9 KGLTQEELAEKLGVSRSTLSRIEN 32 (56)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHC
Confidence 467999999999999999987655
No 350
>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=23.52 E-value=95 Score=24.35 Aligned_cols=32 Identities=19% Similarity=-0.005 Sum_probs=24.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhhccCCccc
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECLRIVGSID 429 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD 429 (459)
.+.|.+++|+.+|++..+|..++.- +..++.+
T Consensus 17 ~~~t~~~lA~~~gis~~tis~~~~g-~~~~~~~ 48 (78)
T TIGR02607 17 LGLSIRALAKALGVSRSTLSRIVNG-RRGITAD 48 (78)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcC-CCCCCHH
Confidence 4679999999999999999998763 3333444
No 351
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=23.50 E-value=1.3e+02 Score=28.22 Aligned_cols=28 Identities=32% Similarity=0.273 Sum_probs=23.9
Q ss_pred CCCCCHHHHHHHh--CCCHHHHHHHHHhhc
Q 012638 396 GKYPEDIEIAKYT--GLSLAEIRSASECLR 423 (459)
Q Consensus 396 gr~PT~eEIAe~L--GIS~e~Vk~~l~~ar 423 (459)
+-.+++.+||+.+ +||.++|+..+....
T Consensus 37 ~~~~d~~~iak~l~p~is~~ev~~sL~~L~ 66 (171)
T PF14394_consen 37 PFAPDPEWIAKRLRPKISAEEVRDSLEFLE 66 (171)
T ss_pred CCCCCHHHHHHHhcCCCCHHHHHHHHHHHH
Confidence 4456999999999 999999999887654
No 352
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=23.43 E-value=2.8e+02 Score=22.82 Aligned_cols=51 Identities=12% Similarity=0.113 Sum_probs=33.9
Q ss_pred hhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHH
Q 012638 315 YRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVA 365 (459)
Q Consensus 315 y~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lr 365 (459)
....+...+++.++.-+.-..-...|....|..|..|+..+-.+.....+.
T Consensus 32 ~~~~~~~l~~la~~~g~S~~~l~r~f~~~~g~s~~~~~~~~Rl~~A~~lL~ 82 (127)
T COG2207 32 NLAEPLTLEDLARRLGMSRRTLSRLFKKETGTSPSQYLRQLRLEEARRLLR 82 (127)
T ss_pred HhcCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 334457888888888777777777777777777776665554444444443
No 353
>PF11268 DUF3071: Protein of unknown function (DUF3071); InterPro: IPR021421 Some members in this family of proteins are annotated as DNA-binding proteins however this cannot be confirmed. Currently no function is known.
Probab=23.43 E-value=86 Score=29.83 Aligned_cols=24 Identities=17% Similarity=0.202 Sum_probs=21.0
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHH
Q 012638 395 HGKYPEDIEIAKYTGLSLAEIRSA 418 (459)
Q Consensus 395 lgr~PT~eEIAe~LGIS~e~Vk~~ 418 (459)
...+.|.+|||+..|++++.|+..
T Consensus 66 IRaGas~eeVA~~~G~~~~rV~rf 89 (170)
T PF11268_consen 66 IRAGASAEEVAEEAGVPVERVRRF 89 (170)
T ss_pred HHCCCCHHHHHHHhCCCHHHhhhc
Confidence 345889999999999999999864
No 354
>PF06970 RepA_N: Replication initiator protein A (RepA) N-terminus; InterPro: IPR010724 This entry represents the N terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids []. Most proteins in this entry are bacterial, but archaeal and eukaryotic members are also included.
Probab=23.28 E-value=83 Score=25.87 Aligned_cols=22 Identities=14% Similarity=0.003 Sum_probs=19.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHH
Q 012638 399 PEDIEIAKYTGLSLAEIRSASE 420 (459)
Q Consensus 399 PT~eEIAe~LGIS~e~Vk~~l~ 420 (459)
.|++||++.||++..+|..+.+
T Consensus 53 ~s~eel~~~L~~s~~tv~~~~k 74 (76)
T PF06970_consen 53 FSIEELMELLNCSKSTVIKAKK 74 (76)
T ss_pred eeHHHHHHHHCCCHHHHHHHHH
Confidence 5999999999999999988764
No 355
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=23.15 E-value=1.2e+02 Score=27.20 Aligned_cols=28 Identities=18% Similarity=0.217 Sum_probs=23.9
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 396 GKYPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
|..++..|||+.+|||...|+.++....
T Consensus 23 g~~~s~~~ia~~~~is~~~vrk~l~~L~ 50 (141)
T PRK11014 23 GRMTSISEVTEVYGVSRNHMVKIINQLS 50 (141)
T ss_pred CCccCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4567999999999999999999987643
No 356
>PF15545 Toxin_67: Putative toxin 67
Probab=23.04 E-value=86 Score=25.61 Aligned_cols=30 Identities=23% Similarity=0.594 Sum_probs=25.6
Q ss_pred chhhHHHHHHHHHHHHHHHhhccccccccc
Q 012638 347 KFSTYVQYWIRKSISKMVARHARGIKIPCK 376 (459)
Q Consensus 347 rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~ 376 (459)
+-+.|+.-||+|.|...-+.....+|+|..
T Consensus 6 kq~~~vRGwiknEi~~i~~~~r~~iRlPpG 35 (70)
T PF15545_consen 6 KQPSWVRGWIKNEINRIKTGRRKSIRLPPG 35 (70)
T ss_pred cchHHHHHHHHHHHHHHHhCccceecCCCc
Confidence 468899999999999888888888999954
No 357
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=22.98 E-value=2.6e+02 Score=21.15 Aligned_cols=60 Identities=17% Similarity=0.147 Sum_probs=33.5
Q ss_pred CCchHHHHHHcCCCHHHHHHHHHhch-HHHHHHHHHhHHHHHHHHHHhhC-CCCCHHHHHHHHHH
Q 012638 269 AASLNCWAQAAGVSERVLKQHLAFGW-YCREELIKSTRPLVLFLARNYRG-LGIPFSDLLQAGNV 331 (459)
Q Consensus 269 ~pt~~ewa~a~g~deeeL~~~l~~G~-~Are~LI~~nlrLV~sIAkry~g-~g~d~EDLIQEG~I 331 (459)
+++..++|+..|++...|.+.+..-- ......+.. .. +..|..|.. ....++|+.++.-+
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~~~~s~~~~~~~--~r-~~~a~~~l~~~~~~~~~ia~~~g~ 62 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKETGTTPKQYLRD--RR-LERARRLLRDTDLSVTEIALRVGF 62 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHhCcCHHHHHHH--HH-HHHHHHHHHcCCCCHHHHHHHhCC
Confidence 36788999999999988877665321 111122111 11 222333333 34778888776444
No 358
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=22.80 E-value=2e+02 Score=27.43 Aligned_cols=26 Identities=23% Similarity=0.433 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhh
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECL 422 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~a 422 (459)
+-||..|+|+.+|+|..||+.++...
T Consensus 31 ~LPsE~eLa~~~~VSR~TvR~Al~~L 56 (238)
T TIGR02325 31 YLPAEMQLAERFGVNRHTVRRAIAAL 56 (238)
T ss_pred cCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 56899999999999999999997753
No 359
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=22.49 E-value=1.6e+02 Score=22.93 Aligned_cols=26 Identities=15% Similarity=0.178 Sum_probs=22.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 398 YPEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 398 ~PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
..+..|||+.+|++..+|...+....
T Consensus 13 ~~~~~eLa~~l~vS~~tv~~~l~~L~ 38 (69)
T TIGR00122 13 PFSGEKLGEALGMSRTAVNKHIQTLR 38 (69)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45799999999999999999887664
No 360
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=22.37 E-value=87 Score=28.58 Aligned_cols=27 Identities=15% Similarity=0.169 Sum_probs=24.2
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 398 YPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 398 ~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
..+.++||+.|||+...|+.++.....
T Consensus 15 ~~~dedLa~~l~i~~n~vRkiL~~L~e 41 (147)
T smart00531 15 CVTEEDLAELLGIKQKQLRKILYLLYD 41 (147)
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHHHh
Confidence 689999999999999999999887654
No 361
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=22.28 E-value=2.6e+02 Score=27.32 Aligned_cols=29 Identities=24% Similarity=0.078 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHH
Q 012638 383 KIQKARKALTNSHGKYPEDIEIAKYTGLSLAE 414 (459)
Q Consensus 383 kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~ 414 (459)
+|.+|...|. ..+.++.|||..+|.+-..
T Consensus 239 Rl~~A~~lL~---~t~~sI~eIA~~~GF~s~s 267 (287)
T TIGR02297 239 VMQEARRLLL---FTQHSINQIAYDLGYKDPA 267 (287)
T ss_pred HHHHHHHHHH---cCCCCHHHHHHHhCCCCHH
Confidence 3445554443 3457899999999887433
No 362
>PRK12702 mannosyl-3-phosphoglycerate phosphatase; Reviewed
Probab=22.26 E-value=1.7e+02 Score=30.40 Aligned_cols=41 Identities=17% Similarity=0.126 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHHcC------CCCCHHHHHHHhCCCHHHHHHHHHhh
Q 012638 382 SKIQKARKALTNSHG------KYPEDIEIAKYTGLSLAEIRSASECL 422 (459)
Q Consensus 382 ~kI~ka~~~L~~~lg------r~PT~eEIAe~LGIS~e~Vk~~l~~a 422 (459)
..|+....++.++++ -+.|.+|||+.+|++.+..+.+.++.
T Consensus 101 ~~ir~~L~~l~~~~~~~f~gF~d~t~~ei~~~TGL~~~~A~~A~~Re 147 (302)
T PRK12702 101 PCLRHILQQVRQDSHLDLIGFGDWTASELAAATGIPLEEAERAQKRE 147 (302)
T ss_pred HHHHHHHHHHHHHhCCCceehhhCCHHHHHHHhCcCHHHHHHHHhcc
Confidence 344445555555544 45799999999999999999887654
No 363
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=22.18 E-value=1e+02 Score=27.92 Aligned_cols=26 Identities=31% Similarity=0.358 Sum_probs=23.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhh
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECL 422 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~a 422 (459)
+-||..|+|..+|+.+.||..+.+-.
T Consensus 34 kLPSvRelA~~~~VNpnTv~raY~eL 59 (125)
T COG1725 34 KLPSVRELAKDLGVNPNTVQRAYQEL 59 (125)
T ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHH
Confidence 67999999999999999999886643
No 364
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=21.98 E-value=1.9e+02 Score=29.25 Aligned_cols=39 Identities=5% Similarity=-0.079 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHh
Q 012638 383 KIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC 421 (459)
Q Consensus 383 kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ 421 (459)
.+.++...+...+...++.++||+.+|+|+..+..+.+.
T Consensus 192 ~i~~~~~~i~~~~~~~~tl~~lA~~~~~S~~~l~r~Fk~ 230 (302)
T PRK10371 192 YVSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQR 230 (302)
T ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 455566666666677899999999999999988776654
No 365
>PRK09492 treR trehalose repressor; Provisional
Probab=21.95 E-value=70 Score=31.37 Aligned_cols=24 Identities=13% Similarity=0.147 Sum_probs=21.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHh
Q 012638 398 YPEDIEIAKYTGLSLAEIRSASEC 421 (459)
Q Consensus 398 ~PT~eEIAe~LGIS~e~Vk~~l~~ 421 (459)
.+|..+||+..|+|..||..+++.
T Consensus 4 ~~ti~dIA~~agVS~~TVSrvLn~ 27 (315)
T PRK09492 4 KLTIKDIARLSGVGKSTVSRVLNN 27 (315)
T ss_pred CCcHHHHHHHhCCCHHHHhHHhCC
Confidence 479999999999999999999874
No 366
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=21.77 E-value=4.1e+02 Score=27.09 Aligned_cols=56 Identities=5% Similarity=-0.019 Sum_probs=35.1
Q ss_pred HHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHH
Q 012638 308 VLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMV 364 (459)
Q Consensus 308 V~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~L 364 (459)
|..++..........+|+-.+..+.--.=...|... |..|..|+..+--+.....|
T Consensus 147 v~~yI~~~~~~~lsl~~lA~~~g~S~~~L~R~Fk~~-G~S~~~yl~~~Rl~~A~~LL 202 (274)
T PRK09978 147 VCTVINNNIAHEWTLARIASELLMSPSLLKKKLREE-ETSYSQLLTECRMQRALQLI 202 (274)
T ss_pred HHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHhc-CCCHHHHHHHHHHHHHHHHH
Confidence 444444444557889999998877766666667544 77777776654333333333
No 367
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=21.75 E-value=77 Score=31.30 Aligned_cols=23 Identities=13% Similarity=0.170 Sum_probs=20.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHh
Q 012638 399 PEDIEIAKYTGLSLAEIRSASEC 421 (459)
Q Consensus 399 PT~eEIAe~LGIS~e~Vk~~l~~ 421 (459)
+|..+||+..|+|..||..+++.
T Consensus 2 ~ti~dIA~~agVS~sTVSr~Ln~ 24 (311)
T TIGR02405 2 LTIKDIARLAGVGKSTVSRVLNN 24 (311)
T ss_pred CcHHHHHHHhCCCHHHHHHHhCC
Confidence 68999999999999999999864
No 368
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=21.74 E-value=78 Score=31.53 Aligned_cols=23 Identities=17% Similarity=0.196 Sum_probs=21.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHh
Q 012638 399 PEDIEIAKYTGLSLAEIRSASEC 421 (459)
Q Consensus 399 PT~eEIAe~LGIS~e~Vk~~l~~ 421 (459)
+|..+||+..|+|..||..+++-
T Consensus 2 ~Ti~dIA~~agVS~~TVSrvLn~ 24 (341)
T PRK10703 2 ATIKDVAKRAGVSTTTVSHVINK 24 (341)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Confidence 58999999999999999999874
No 369
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=21.60 E-value=2.6e+02 Score=25.20 Aligned_cols=28 Identities=25% Similarity=0.145 Sum_probs=24.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
++.|..+||+.||+|...|..++.--+.
T Consensus 21 eG~Sq~~iA~LLGltqaAVS~Yls~krg 48 (119)
T COG2522 21 EGLSQYRIAKLLGLTQAAVSQYLSGKRG 48 (119)
T ss_pred cCCcHHHHHHHhCCCHHHHHHHHccCCc
Confidence 4889999999999999999998875444
No 370
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=21.52 E-value=78 Score=31.47 Aligned_cols=24 Identities=13% Similarity=0.059 Sum_probs=22.1
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHh
Q 012638 398 YPEDIEIAKYTGLSLAEIRSASEC 421 (459)
Q Consensus 398 ~PT~eEIAe~LGIS~e~Vk~~l~~ 421 (459)
.+|+.+||+..|+|..||..+++.
T Consensus 6 ~~Ti~dIA~~agVS~~TVSr~Ln~ 29 (342)
T PRK10014 6 KITIHDVALAAGVSVSTVSLVLSG 29 (342)
T ss_pred CCcHHHHHHHhCCCHHHHHHHHCC
Confidence 479999999999999999999875
No 371
>PRK13503 transcriptional activator RhaS; Provisional
Probab=21.43 E-value=2.1e+02 Score=27.70 Aligned_cols=38 Identities=13% Similarity=0.046 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHh
Q 012638 384 IQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC 421 (459)
Q Consensus 384 I~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ 421 (459)
+.++..-+........|.++||+.+|++...+....+.
T Consensus 173 i~~~~~~I~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk~ 210 (278)
T PRK13503 173 LNQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQ 210 (278)
T ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 55556666666677889999999999999998876553
No 372
>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=21.32 E-value=72 Score=23.05 Aligned_cols=19 Identities=26% Similarity=0.431 Sum_probs=16.8
Q ss_pred HHHHHhCCCHHHHHHHHHh
Q 012638 403 EIAKYTGLSLAEIRSASEC 421 (459)
Q Consensus 403 EIAe~LGIS~e~Vk~~l~~ 421 (459)
+||+.+|++..+|..+++-
T Consensus 2 ~lA~~~gvs~~tvs~~l~g 20 (52)
T cd01392 2 DIARAAGVSVATVSRVLNG 20 (52)
T ss_pred cHHHHHCcCHHHHHHHHcC
Confidence 7999999999999988763
No 373
>PRK15044 transcriptional regulator SirC; Provisional
Probab=21.25 E-value=6.7e+02 Score=26.01 Aligned_cols=38 Identities=21% Similarity=0.063 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHh
Q 012638 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAF 292 (459)
Q Consensus 255 le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l~~ 292 (459)
.+++..-+.....+.++.+++|+.+|++...|.+.++.
T Consensus 194 ~~kV~~~I~~nl~~~~SLeeLA~~lgmS~~tL~R~Fk~ 231 (295)
T PRK15044 194 KEKVYNIIISDLTRKWSQAEVAGKLFMSVSSLKRKLAA 231 (295)
T ss_pred HHHHHHHHHhCcccCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 55667777778899999999999999999999887765
No 374
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=21.21 E-value=4.2e+02 Score=26.70 Aligned_cols=56 Identities=7% Similarity=-0.019 Sum_probs=35.3
Q ss_pred HHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHH
Q 012638 308 VLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMV 364 (459)
Q Consensus 308 V~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~L 364 (459)
|..++.........++||-++..+.--.=.+.|... |..|..|+..|=-+...+.+
T Consensus 139 v~~~I~~~~~~~~tl~~LA~~~gmS~s~l~R~FK~~-G~T~~eyl~~~Rl~~A~~LL 194 (253)
T PRK09940 139 VRNIVNMKLAHPWKLKDICDCLYISESLLKKKLKQE-QTTFSQILLDARMQHAKNLI 194 (253)
T ss_pred HHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHHc-CCCHHHHHHHHHHHHHHHHH
Confidence 334443334456889999999888776666777655 77777777665433333333
No 375
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=21.13 E-value=1.5e+02 Score=24.03 Aligned_cols=36 Identities=14% Similarity=0.084 Sum_probs=29.2
Q ss_pred HHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 389 KALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 389 ~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
..+...++...+..+.|+.||++...|..-....+.
T Consensus 4 ~~fIrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~ 39 (65)
T PF05344_consen 4 RAFIRLLSQQISVAQAADRLGTDPGTVRRWVRMFRQ 39 (65)
T ss_pred HHHHHHhcccccHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 345556788899999999999999999987766653
No 376
>KOG0917 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.06 E-value=77 Score=32.56 Aligned_cols=82 Identities=29% Similarity=0.368 Sum_probs=58.6
Q ss_pred HHhHHhhhccccccCCcccccccccccchhhccccchhHHhhhhccccccccccccch-HHHHHhhHHHHhhcccchhhh
Q 012638 45 SFLSTISEDSASYFQDPVKAYTCSFVNTQTVENDYSETEEIRQKSTSCIGQDASSRSD-FRLLMENLDVLESTFADSDAL 123 (459)
Q Consensus 45 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~l~~n~~~le~~~~~~~~~ 123 (459)
+.+|.|..--+-..+||+-+|-|-=-|+|+-= |.-++..| .-+ -.-||.-|+.|+..++|.|++
T Consensus 10 si~~~l~~a~e~~k~dpvvayycrlyamq~gm-----------Kid~qT~e----~rk~lsgLm~~lealkkqlaDneai 74 (338)
T KOG0917|consen 10 SIQHHLRTAQEHDKRDPVVAYYCRLYAMQTGM-----------KIDSQTPE----CRKFLSGLMDQLEALKKQLADNEAI 74 (338)
T ss_pred HHHHHHHHHHhhcccccHHHHHHHHHHHHhcc-----------cCCccCHH----HHHHHHHHHHHHHHHHHHhcchhhh
Confidence 66777766666667799998888665555421 11111112 122 356999999999999999999
Q ss_pred HHHHHHHHHhhhhhhhhcc
Q 012638 124 RLEREILQQLGKLGALKLF 142 (459)
Q Consensus 124 rler~il~~~~~lga~~~~ 142 (459)
.+|-+-=-|+|.. |+++|
T Consensus 75 tne~~aqaHiE~f-AlklF 92 (338)
T KOG0917|consen 75 TNEIVAQAHIENF-ALKLF 92 (338)
T ss_pred hhchHHHHHHHHH-HHHHH
Confidence 9998877777765 99999
No 377
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=21.06 E-value=2.4e+02 Score=26.54 Aligned_cols=40 Identities=18% Similarity=0.094 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHHHHHcC-CCCCHHHHHHHhCCCHHHHHHH
Q 012638 379 REISKIQKARKALTNSHG-KYPEDIEIAKYTGLSLAEIRSA 418 (459)
Q Consensus 379 e~i~kI~ka~~~L~~~lg-r~PT~eEIAe~LGIS~e~Vk~~ 418 (459)
+...+|-++...+..+.| ...|..+||+..||+.+.+...
T Consensus 18 ~~r~~IL~AA~~lf~e~Gy~~~s~~dIA~~aGvs~gtiY~h 58 (212)
T PRK15008 18 AKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYY 58 (212)
T ss_pred HHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCcCHHHHHHH
Confidence 445566666666666666 5689999999999999998753
No 378
>PRK09526 lacI lac repressor; Reviewed
Probab=21.01 E-value=88 Score=31.10 Aligned_cols=24 Identities=17% Similarity=0.267 Sum_probs=21.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHh
Q 012638 398 YPEDIEIAKYTGLSLAEIRSASEC 421 (459)
Q Consensus 398 ~PT~eEIAe~LGIS~e~Vk~~l~~ 421 (459)
.+|..+||+..|+|..||..+++-
T Consensus 5 ~~ti~dIA~~aGVS~~TVSrvLn~ 28 (342)
T PRK09526 5 PVTLYDVARYAGVSYQTVSRVLNQ 28 (342)
T ss_pred CCcHHHHHHHhCCCHHHHHHHhcC
Confidence 469999999999999999998874
No 379
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=20.90 E-value=1.1e+02 Score=28.39 Aligned_cols=29 Identities=24% Similarity=0.288 Sum_probs=17.2
Q ss_pred HHHHcCCCCCHHHHHHHhCCCHHHHHHHH
Q 012638 391 LTNSHGKYPEDIEIAKYTGLSLAEIRSAS 419 (459)
Q Consensus 391 L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l 419 (459)
+....+..+|.+|||+.+||+..++-.-.
T Consensus 27 ~~~~~~~r~T~~eiAee~Gis~~tLYrWr 55 (142)
T PF13022_consen 27 LMPENGERRTQAEIAEEVGISRSTLYRWR 55 (142)
T ss_dssp HS------S-HHHHHHHHTS-HHHHHHHH
T ss_pred HhhhccccchHHHHHHHhCCCHHHHHHHH
Confidence 33333566899999999999999986543
No 380
>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=20.82 E-value=1.2e+02 Score=22.36 Aligned_cols=25 Identities=24% Similarity=0.197 Sum_probs=22.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638 399 PEDIEIAKYTGLSLAEIRSASECLR 423 (459)
Q Consensus 399 PT~eEIAe~LGIS~e~Vk~~l~~ar 423 (459)
.+..|||+.+|++..++...+....
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~L~ 45 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKLE 45 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHHHH
Confidence 8999999999999999998877653
No 381
>TIGR03337 phnR transcriptional regulator protein. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.
Probab=20.79 E-value=2.4e+02 Score=26.78 Aligned_cols=26 Identities=23% Similarity=0.327 Sum_probs=23.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhh
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECL 422 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~a 422 (459)
+-|+..|+|+.+|++.-+|+.++...
T Consensus 24 ~lPsE~eLa~~~~Vsr~Tvr~Al~~L 49 (231)
T TIGR03337 24 KLPSERDLGERFNTTRVTIREALQQL 49 (231)
T ss_pred cCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 46899999999999999999987754
No 382
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=20.57 E-value=3.4e+02 Score=21.45 Aligned_cols=19 Identities=26% Similarity=0.412 Sum_probs=13.9
Q ss_pred HHhCCCCchHHHHHHcCCC
Q 012638 264 KESGKAASLNCWAQAAGVS 282 (459)
Q Consensus 264 ~~~gr~pt~~ewa~a~g~d 282 (459)
.+.|.+||..|.|++.|+.
T Consensus 20 ~~~G~~Pt~rEIa~~~g~~ 38 (65)
T PF01726_consen 20 EENGYPPTVREIAEALGLK 38 (65)
T ss_dssp HHHSS---HHHHHHHHTSS
T ss_pred HHcCCCCCHHHHHHHhCCC
Confidence 4569999999999999986
No 383
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=20.37 E-value=1.3e+02 Score=23.62 Aligned_cols=26 Identities=15% Similarity=0.120 Sum_probs=18.4
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHH
Q 012638 395 HGKYPEDIEIAKYTGLSLAEIRSASE 420 (459)
Q Consensus 395 lgr~PT~eEIAe~LGIS~e~Vk~~l~ 420 (459)
..++.|.++||..++|+...++.+-+
T Consensus 7 ~~~glsl~~va~~t~I~~~~l~aiE~ 32 (62)
T PF13413_consen 7 EAKGLSLEDVAEETKISVSYLEAIEN 32 (62)
T ss_dssp HCTT--HHHHHHHCS--HHHHHHHHC
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 36789999999999999999987643
No 384
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=20.17 E-value=5.4e+02 Score=22.76 Aligned_cols=26 Identities=15% Similarity=0.218 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhh
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECL 422 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~a 422 (459)
...+..|||+.+|++..+|-.++...
T Consensus 53 ~~~t~~eLa~~l~i~~~tvsr~l~~L 78 (144)
T PRK11512 53 ACITPVELKKVLSVDLGALTRMLDRL 78 (144)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 35799999999999999998887654
No 385
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=20.07 E-value=3.1e+02 Score=25.95 Aligned_cols=26 Identities=23% Similarity=0.285 Sum_probs=22.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638 399 PEDIEIAKYTGLSLAEIRSASECLRI 424 (459)
Q Consensus 399 PT~eEIAe~LGIS~e~Vk~~l~~ar~ 424 (459)
.+.++||..+|++.++|..+++..+.
T Consensus 174 ~t~~~iA~~lG~tretvsR~l~~L~~ 199 (236)
T PRK09392 174 YEKRVLASYLGMTPENLSRAFAALAS 199 (236)
T ss_pred CCHHHHHHHhCCChhHHHHHHHHHHh
Confidence 47799999999999999998876543
No 386
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=20.01 E-value=1e+02 Score=29.62 Aligned_cols=26 Identities=27% Similarity=0.331 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhh
Q 012638 397 KYPEDIEIAKYTGLSLAEIRSASECL 422 (459)
Q Consensus 397 r~PT~eEIAe~LGIS~e~Vk~~l~~a 422 (459)
+-||..|||+.+|+|..+|+.++...
T Consensus 23 ~LPsE~eLa~~~gVSR~TVR~Al~~L 48 (233)
T TIGR02404 23 YLPSEHELMDQYGASRETVRKALNLL 48 (233)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 56999999999999999999997743
Done!