Query 013472
Match_columns 442
No_of_seqs 316 out of 1686
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 04:12:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013472.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013472hhsearch_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 3.8E-47 8.3E-52 393.2 26.9 221 220-440 57-320 (415)
2 PRK05949 RNA polymerase sigma 100.0 2E-43 4.4E-48 356.8 27.0 217 222-438 17-234 (327)
3 TIGR02997 Sig70-cyanoRpoD RNA 100.0 2.8E-43 6E-48 350.5 26.2 212 226-437 4-216 (298)
4 PRK07406 RNA polymerase sigma 100.0 2.4E-43 5.2E-48 361.6 26.2 216 223-438 63-279 (373)
5 PRK07405 RNA polymerase sigma 100.0 3.2E-42 7E-47 346.5 26.2 216 223-438 8-224 (317)
6 COG0568 RpoD DNA-directed RNA 100.0 8.3E-40 1.8E-44 330.1 20.5 220 221-440 7-247 (342)
7 PRK05901 RNA polymerase sigma 100.0 2.7E-39 5.8E-44 342.1 20.1 205 222-439 210-415 (509)
8 PRK07921 RNA polymerase sigma 100.0 4.5E-38 9.9E-43 317.6 22.3 203 223-438 26-229 (324)
9 PRK09210 RNA polymerase sigma 100.0 1.9E-33 4.1E-38 288.1 21.1 177 222-438 95-272 (367)
10 PRK05658 RNA polymerase sigma 100.0 3.1E-32 6.7E-37 295.6 22.8 164 276-439 354-524 (619)
11 PRK07122 RNA polymerase sigma 100.0 8.9E-31 1.9E-35 257.2 18.0 142 295-436 40-183 (264)
12 TIGR02393 RpoD_Cterm RNA polym 100.0 5.2E-30 1.1E-34 247.0 17.2 143 296-438 1-143 (238)
13 PRK07500 rpoH2 RNA polymerase 100.0 4.2E-29 9E-34 248.4 21.0 176 222-437 5-188 (289)
14 PRK07408 RNA polymerase sigma 100.0 5.9E-29 1.3E-33 242.9 19.1 147 291-437 20-170 (256)
15 TIGR02850 spore_sigG RNA polym 100.0 8E-28 1.7E-32 234.1 20.1 141 295-436 34-174 (254)
16 PRK06596 RNA polymerase factor 100.0 9.8E-28 2.1E-32 238.0 20.9 171 223-435 14-189 (284)
17 TIGR02392 rpoH_proteo alternat 100.0 3.9E-27 8.5E-32 231.6 20.5 141 295-437 35-179 (270)
18 PRK05657 RNA polymerase sigma 100.0 5.5E-27 1.2E-31 237.0 20.7 176 221-437 51-228 (325)
19 PRK08215 sporulation sigma fac 99.9 1.6E-26 3.4E-31 225.4 20.2 142 295-437 37-178 (258)
20 TIGR02885 spore_sigF RNA polym 99.9 4.5E-26 9.7E-31 217.9 18.1 149 288-437 3-152 (231)
21 COG1191 FliA DNA-directed RNA 99.9 5.3E-26 1.1E-30 221.9 17.2 152 284-437 12-167 (247)
22 PRK05911 RNA polymerase sigma 99.9 1E-25 2.2E-30 220.4 18.5 140 292-434 19-164 (257)
23 TIGR02980 SigBFG RNA polymeras 99.9 7.8E-25 1.7E-29 208.6 17.7 140 295-434 3-144 (227)
24 TIGR02941 Sigma_B RNA polymera 99.9 2.8E-24 6.1E-29 208.8 18.5 155 283-437 15-173 (255)
25 PRK06288 RNA polymerase sigma 99.9 6.9E-24 1.5E-28 208.1 19.4 136 295-433 31-171 (268)
26 TIGR02394 rpoS_proteo RNA poly 99.9 1.3E-23 2.8E-28 208.0 20.7 174 222-436 12-187 (285)
27 PRK07670 RNA polymerase sigma 99.9 8.2E-24 1.8E-28 205.5 18.3 153 282-437 7-166 (251)
28 PRK12427 flagellar biosynthesi 99.9 2.3E-23 4.9E-28 201.0 17.1 139 296-438 16-159 (231)
29 PRK05572 sporulation sigma fac 99.9 4.3E-23 9.4E-28 200.6 18.7 152 284-436 20-172 (252)
30 PRK08583 RNA polymerase sigma 99.9 1.7E-22 3.7E-27 196.5 18.5 155 283-437 15-173 (257)
31 TIGR02479 FliA_WhiG RNA polyme 99.9 2.2E-22 4.7E-27 191.9 15.8 132 300-434 1-137 (224)
32 PRK06986 fliA flagellar biosyn 99.9 1.6E-21 3.4E-26 187.6 16.8 142 292-436 5-151 (236)
33 PRK05803 sporulation sigma fac 99.8 7E-18 1.5E-22 162.2 20.3 170 245-424 8-221 (233)
34 TIGR02895 spore_sigI RNA polym 99.8 4.8E-18 1.1E-22 163.5 15.2 129 289-417 3-142 (218)
35 TIGR02846 spore_sigmaK RNA pol 99.8 2.8E-17 6.1E-22 157.6 19.5 143 282-424 34-220 (227)
36 PRK08301 sporulation sigma fac 99.8 1.6E-17 3.5E-22 159.3 15.3 143 282-424 38-224 (234)
37 PRK05602 RNA polymerase sigma 99.8 1.1E-17 2.5E-22 154.2 13.8 144 280-424 4-170 (186)
38 TIGR02859 spore_sigH RNA polym 99.7 3.8E-17 8.2E-22 151.2 15.7 144 281-424 4-191 (198)
39 TIGR02835 spore_sigmaE RNA pol 99.7 4.4E-17 9.6E-22 156.9 16.3 143 282-424 38-224 (234)
40 PRK08295 RNA polymerase factor 99.7 5.5E-17 1.2E-21 151.5 16.4 145 280-424 8-196 (208)
41 PRK12513 RNA polymerase sigma 99.7 9.4E-17 2E-21 149.1 15.4 142 281-424 11-181 (194)
42 PRK09646 RNA polymerase sigma 99.7 8.3E-17 1.8E-21 150.0 14.6 142 282-424 16-184 (194)
43 PRK06811 RNA polymerase factor 99.7 1.1E-16 2.4E-21 148.6 15.3 143 280-423 2-172 (189)
44 PRK09648 RNA polymerase sigma 99.7 2.9E-16 6.2E-21 145.2 15.6 141 283-424 11-181 (189)
45 PRK13919 putative RNA polymera 99.7 2.1E-16 4.7E-21 145.3 14.7 143 281-424 8-177 (186)
46 TIGR02954 Sig70_famx3 RNA poly 99.7 2.5E-16 5.4E-21 143.0 14.9 142 281-424 1-161 (169)
47 PRK09640 RNA polymerase sigma 99.7 3E-16 6.4E-21 145.4 15.6 144 279-424 6-176 (188)
48 PRK12514 RNA polymerase sigma 99.7 2.1E-16 4.6E-21 144.7 14.4 142 282-424 5-171 (179)
49 PRK12537 RNA polymerase sigma 99.7 2.9E-16 6.2E-21 144.8 14.3 143 281-424 8-175 (182)
50 PRK12524 RNA polymerase sigma 99.7 3.7E-16 8.1E-21 145.8 14.8 144 280-424 10-178 (196)
51 PRK09638 RNA polymerase sigma 99.7 4.7E-16 1E-20 141.6 14.8 143 280-424 2-168 (176)
52 TIGR02948 SigW_bacill RNA poly 99.7 4.4E-16 9.4E-21 142.7 14.3 140 283-424 5-178 (187)
53 PRK06759 RNA polymerase factor 99.7 3.9E-16 8.5E-21 139.0 13.6 128 295-424 4-148 (154)
54 PRK09643 RNA polymerase sigma 99.7 5.6E-16 1.2E-20 144.5 14.9 142 281-424 12-176 (192)
55 TIGR02952 Sig70_famx2 RNA poly 99.7 5.4E-16 1.2E-20 139.8 13.9 137 287-424 2-164 (170)
56 PRK09641 RNA polymerase sigma 99.7 5.1E-16 1.1E-20 142.2 13.9 142 281-424 3-178 (187)
57 PRK12534 RNA polymerase sigma 99.7 5.5E-16 1.2E-20 142.9 13.5 142 282-424 11-179 (187)
58 PRK12531 RNA polymerase sigma 99.7 6E-16 1.3E-20 144.3 13.7 141 283-424 14-183 (194)
59 PRK12538 RNA polymerase sigma 99.7 8.8E-16 1.9E-20 148.5 15.2 143 281-424 48-213 (233)
60 TIGR02939 RpoE_Sigma70 RNA pol 99.7 1.6E-15 3.4E-20 139.4 15.3 142 281-424 5-180 (190)
61 PRK12519 RNA polymerase sigma 99.7 1.2E-15 2.7E-20 141.4 14.4 141 282-424 15-183 (194)
62 PRK12526 RNA polymerase sigma 99.7 9.3E-16 2E-20 144.7 13.2 140 284-424 26-195 (206)
63 PRK12536 RNA polymerase sigma 99.7 2.1E-15 4.6E-20 138.9 15.0 140 283-424 8-171 (181)
64 PRK11922 RNA polymerase sigma 99.7 2.4E-15 5.3E-20 144.4 15.8 141 281-423 15-190 (231)
65 PRK12539 RNA polymerase sigma 99.7 2.5E-15 5.4E-20 138.8 14.9 141 282-424 7-173 (184)
66 PRK11923 algU RNA polymerase s 99.6 2.9E-15 6.3E-20 138.8 15.3 141 282-424 6-180 (193)
67 PRK12542 RNA polymerase sigma 99.6 4.1E-16 8.8E-21 144.0 9.0 134 291-424 4-164 (185)
68 PRK09652 RNA polymerase sigma 99.6 1.6E-15 3.4E-20 137.2 12.7 134 289-424 3-170 (182)
69 PRK12515 RNA polymerase sigma 99.6 3.9E-15 8.4E-20 137.9 14.7 143 280-424 6-173 (189)
70 TIGR02999 Sig-70_X6 RNA polyme 99.6 3.4E-15 7.4E-20 136.8 13.7 140 283-424 4-176 (183)
71 TIGR03001 Sig-70_gmx1 RNA poly 99.6 4.2E-15 9.1E-20 145.0 15.0 145 278-424 21-203 (244)
72 PRK09649 RNA polymerase sigma 99.6 4.2E-15 9.1E-20 137.9 14.0 140 283-425 11-173 (185)
73 COG1595 RpoE DNA-directed RNA 99.6 1.1E-14 2.5E-19 134.4 15.3 134 289-424 8-169 (182)
74 PRK12512 RNA polymerase sigma 99.6 1.4E-14 3E-19 133.3 15.4 139 284-424 10-173 (184)
75 TIGR02989 Sig-70_gvs1 RNA poly 99.6 8.4E-15 1.8E-19 130.9 13.2 127 296-424 2-153 (159)
76 PRK12520 RNA polymerase sigma 99.6 1E-14 2.2E-19 135.3 12.7 127 296-424 3-173 (191)
77 PRK11924 RNA polymerase sigma 99.6 2.6E-14 5.7E-19 128.9 14.9 137 286-424 3-167 (179)
78 PRK12522 RNA polymerase sigma 99.6 1.7E-14 3.7E-19 131.6 13.6 127 296-424 4-161 (173)
79 PRK12543 RNA polymerase sigma 99.6 1.6E-14 3.4E-19 132.9 13.0 131 292-424 3-159 (179)
80 TIGR02947 SigH_actino RNA poly 99.6 1.7E-14 3.7E-19 134.0 13.2 128 295-424 11-173 (193)
81 PRK09415 RNA polymerase factor 99.6 3.4E-14 7.4E-19 130.8 13.8 129 294-424 15-169 (179)
82 PRK09645 RNA polymerase sigma 99.6 3E-14 6.5E-19 129.6 13.3 130 294-424 8-160 (173)
83 PRK12518 RNA polymerase sigma 99.6 3.6E-14 7.8E-19 129.1 13.6 135 287-424 2-162 (175)
84 PRK12516 RNA polymerase sigma 99.6 3.9E-14 8.4E-19 132.1 13.8 129 294-424 9-158 (187)
85 TIGR02937 sigma70-ECF RNA poly 99.6 3.8E-14 8.2E-19 122.4 12.4 127 296-424 2-152 (158)
86 PRK08241 RNA polymerase factor 99.6 5.8E-14 1.3E-18 141.5 14.9 139 284-424 7-195 (339)
87 PRK12547 RNA polymerase sigma 99.6 6.3E-14 1.4E-18 127.2 13.7 128 295-424 6-154 (164)
88 TIGR02983 SigE-fam_strep RNA p 99.6 5.3E-14 1.2E-18 126.5 13.0 131 292-424 2-152 (162)
89 PRK12529 RNA polymerase sigma 99.5 3.8E-14 8.3E-19 130.6 12.0 134 291-424 8-169 (178)
90 PRK12541 RNA polymerase sigma 99.5 7.9E-14 1.7E-18 125.7 13.3 127 295-424 5-154 (161)
91 TIGR02984 Sig-70_plancto1 RNA 99.5 7.5E-14 1.6E-18 127.9 13.2 133 292-424 3-182 (189)
92 PRK12535 RNA polymerase sigma 99.5 1.1E-13 2.4E-18 130.1 14.3 138 284-424 13-175 (196)
93 TIGR02985 Sig70_bacteroi1 RNA 99.5 5.8E-14 1.3E-18 124.3 11.5 127 296-424 2-155 (161)
94 PRK12523 RNA polymerase sigma 99.5 4.3E-14 9.4E-19 129.0 10.3 131 291-424 5-161 (172)
95 PRK09644 RNA polymerase sigma 99.5 1.1E-13 2.4E-18 125.4 12.1 125 297-424 3-150 (165)
96 PRK12533 RNA polymerase sigma 99.5 1.8E-13 4E-18 131.1 14.2 130 292-424 15-176 (216)
97 TIGR02960 SigX5 RNA polymerase 99.5 1.3E-13 2.9E-18 137.6 13.4 130 293-424 2-184 (324)
98 PRK09642 RNA polymerase sigma 99.5 9.3E-14 2E-18 124.9 10.6 121 301-424 1-148 (160)
99 PRK12528 RNA polymerase sigma 99.5 1.9E-13 4E-18 123.2 12.2 127 295-424 4-155 (161)
100 PRK12540 RNA polymerase sigma 99.5 4.3E-13 9.4E-18 124.6 13.5 127 296-424 6-153 (182)
101 PRK08311 putative RNA polymera 99.5 6.1E-13 1.3E-17 129.7 15.1 91 282-372 4-97 (237)
102 PRK09639 RNA polymerase sigma 99.5 4.1E-13 8.8E-18 121.0 12.7 126 295-424 3-153 (166)
103 PRK12545 RNA polymerase sigma 99.5 3.4E-13 7.4E-18 126.8 12.3 124 299-424 12-181 (201)
104 PRK12532 RNA polymerase sigma 99.5 4.2E-13 9E-18 124.9 12.6 125 298-424 8-178 (195)
105 PRK12530 RNA polymerase sigma 99.5 4.5E-13 9.7E-18 124.8 12.4 125 298-424 10-176 (189)
106 PRK09647 RNA polymerase sigma 99.5 6E-13 1.3E-17 126.0 13.4 127 295-424 28-180 (203)
107 PRK09637 RNA polymerase sigma 99.5 7.4E-13 1.6E-17 122.8 13.6 125 297-423 3-147 (181)
108 PRK12517 RNA polymerase sigma 99.5 9.7E-13 2.1E-17 122.7 13.7 130 293-424 21-170 (188)
109 TIGR02950 SigM_subfam RNA poly 99.5 4.6E-13 9.9E-18 119.1 11.0 120 302-424 2-147 (154)
110 PRK12544 RNA polymerase sigma 99.4 8.5E-13 1.8E-17 125.3 13.0 126 297-424 20-190 (206)
111 TIGR02943 Sig70_famx1 RNA poly 99.4 8.5E-13 1.8E-17 123.0 11.9 124 299-424 6-173 (188)
112 TIGR02959 SigZ RNA polymerase 99.4 1.1E-12 2.3E-17 120.1 11.9 121 302-424 2-142 (170)
113 PRK12546 RNA polymerase sigma 99.4 1.8E-12 4E-17 121.2 13.6 126 296-424 9-155 (188)
114 PF04542 Sigma70_r2: Sigma-70 99.4 7.5E-13 1.6E-17 102.9 8.2 70 300-369 1-70 (71)
115 PRK12511 RNA polymerase sigma 99.4 2.3E-12 5E-17 119.9 12.5 126 297-424 6-153 (182)
116 PRK09651 RNA polymerase sigma 99.4 2.6E-12 5.5E-17 117.7 12.5 127 295-424 10-161 (172)
117 PRK06704 RNA polymerase factor 99.4 5.9E-12 1.3E-16 122.1 12.6 132 287-424 9-158 (228)
118 PRK07037 extracytoplasmic-func 99.4 7E-12 1.5E-16 112.8 12.0 123 299-424 2-151 (163)
119 PRK12527 RNA polymerase sigma 99.3 6.4E-12 1.4E-16 113.0 11.1 121 301-424 1-147 (159)
120 PRK12525 RNA polymerase sigma 99.3 1.1E-11 2.4E-16 113.0 12.8 128 294-424 8-160 (168)
121 PRK09636 RNA polymerase sigma 99.3 4.8E-11 1E-15 118.6 13.0 125 296-424 5-157 (293)
122 PRK09635 sigI RNA polymerase s 99.2 1.1E-10 2.3E-15 116.8 12.1 126 295-424 5-160 (290)
123 PRK09191 two-component respons 99.2 7.4E-11 1.6E-15 112.6 10.5 121 296-424 2-130 (261)
124 TIGR02957 SigX4 RNA polymerase 99.2 1.5E-10 3.2E-15 114.8 12.6 122 299-424 1-150 (281)
125 TIGR03209 P21_Cbot clostridium 99.2 9.7E-11 2.1E-15 103.6 9.5 113 297-416 1-141 (142)
126 PRK09047 RNA polymerase factor 99.1 4E-10 8.7E-15 100.9 9.6 105 317-424 2-148 (161)
127 PF04539 Sigma70_r3: Sigma-70 98.8 7.8E-09 1.7E-13 83.2 6.7 62 379-440 1-62 (78)
128 PF07638 Sigma70_ECF: ECF sigm 98.8 9.6E-08 2.1E-12 89.2 14.6 141 283-423 4-176 (185)
129 PF00140 Sigma70_r1_2: Sigma-7 97.1 0.00028 6.1E-09 50.0 1.9 34 223-256 2-36 (37)
130 TIGR02393 RpoD_Cterm RNA polym 96.4 0.072 1.6E-06 51.6 13.6 35 254-288 88-122 (238)
131 PRK07670 RNA polymerase sigma 96.2 0.076 1.7E-06 51.9 12.3 36 254-289 110-145 (251)
132 PRK07408 RNA polymerase sigma 96.0 0.027 5.9E-07 55.4 8.5 35 254-288 114-148 (256)
133 PRK09210 RNA polymerase sigma 95.9 0.12 2.6E-06 53.8 13.3 128 254-422 217-349 (367)
134 PRK06288 RNA polymerase sigma 95.8 0.27 5.8E-06 48.6 14.2 35 254-288 119-153 (268)
135 PF12645 HTH_16: Helix-turn-he 95.6 0.046 1E-06 43.5 6.6 57 285-341 2-65 (65)
136 PRK05901 RNA polymerase sigma 95.4 0.46 9.9E-06 51.8 15.4 132 254-422 359-491 (509)
137 PRK05949 RNA polymerase sigma 95.4 0.31 6.8E-06 50.0 13.6 35 254-288 179-213 (327)
138 PRK07122 RNA polymerase sigma 95.4 0.27 5.8E-06 48.8 12.7 34 255-288 129-162 (264)
139 COG1191 FliA DNA-directed RNA 95.3 0.35 7.5E-06 48.1 13.3 126 254-422 111-236 (247)
140 PRK05911 RNA polymerase sigma 95.3 0.28 6.1E-06 48.4 12.6 34 255-288 112-145 (257)
141 PRK07921 RNA polymerase sigma 95.0 0.45 9.7E-06 48.9 13.4 35 254-288 174-208 (324)
142 TIGR02479 FliA_WhiG RNA polyme 94.9 0.58 1.2E-05 44.7 13.1 35 254-288 84-118 (224)
143 PRK07598 RNA polymerase sigma 94.8 0.46 9.9E-06 50.6 13.2 36 254-289 263-298 (415)
144 TIGR02850 spore_sigG RNA polym 94.7 0.33 7.1E-06 47.6 10.9 35 255-289 122-156 (254)
145 TIGR02997 Sig70-cyanoRpoD RNA 94.6 0.7 1.5E-05 46.5 13.4 35 254-288 162-196 (298)
146 TIGR02885 spore_sigF RNA polym 94.4 0.34 7.5E-06 46.4 10.2 34 255-288 99-132 (231)
147 PRK07500 rpoH2 RNA polymerase 94.3 0.47 1E-05 47.7 11.5 28 397-424 244-271 (289)
148 PF04539 Sigma70_r3: Sigma-70 94.1 0.12 2.6E-06 41.3 5.5 38 253-290 4-41 (78)
149 PRK07405 RNA polymerase sigma 93.9 0.75 1.6E-05 47.0 12.1 35 254-288 169-203 (317)
150 PRK06986 fliA flagellar biosyn 93.8 1.3 2.7E-05 42.8 12.8 29 396-424 198-226 (236)
151 PRK07406 RNA polymerase sigma 93.7 1.2 2.5E-05 46.9 13.2 35 254-288 224-258 (373)
152 PF08281 Sigma70_r4_2: Sigma-7 93.6 0.064 1.4E-06 40.0 2.9 30 395-424 23-52 (54)
153 TIGR02941 Sigma_B RNA polymera 93.4 0.49 1.1E-05 46.2 9.5 34 255-288 118-151 (255)
154 TIGR02394 rpoS_proteo RNA poly 93.0 1.5 3.2E-05 43.8 12.2 29 396-424 240-268 (285)
155 PRK08215 sporulation sigma fac 93.0 1.1 2.4E-05 43.9 11.2 34 255-288 125-158 (258)
156 PRK08583 RNA polymerase sigma 92.6 5.2 0.00011 39.1 15.2 28 396-423 219-246 (257)
157 PRK05658 RNA polymerase sigma 92.4 1.5 3.3E-05 48.7 12.6 35 254-288 468-502 (619)
158 TIGR02980 SigBFG RNA polymeras 92.2 0.62 1.3E-05 44.5 8.1 29 396-424 192-220 (227)
159 PHA02547 55 RNA polymerase sig 92.1 0.47 1E-05 44.7 6.8 65 304-368 46-113 (179)
160 PF01726 LexA_DNA_bind: LexA D 92.0 0.51 1.1E-05 37.5 6.0 44 379-422 6-50 (65)
161 PRK12427 flagellar biosynthesi 91.7 1.7 3.6E-05 42.3 10.5 34 255-288 103-136 (231)
162 PRK05572 sporulation sigma fac 91.7 2.1 4.5E-05 41.8 11.3 34 254-287 119-152 (252)
163 PF04545 Sigma70_r4: Sigma-70, 90.9 0.65 1.4E-05 34.2 5.3 30 394-423 16-45 (50)
164 PRK05657 RNA polymerase sigma 89.7 5.1 0.00011 41.1 12.4 29 396-424 280-308 (325)
165 PRK06596 RNA polymerase factor 85.3 10 0.00022 38.1 11.3 27 397-423 247-273 (284)
166 COG0568 RpoD DNA-directed RNA 85.2 23 0.0005 37.1 14.0 36 252-287 188-223 (342)
167 TIGR03879 near_KaiC_dom probab 81.8 1.7 3.7E-05 35.6 3.4 25 397-421 31-55 (73)
168 COG4941 Predicted RNA polymera 80.2 11 0.00025 39.5 9.5 123 299-423 9-161 (415)
169 cd06171 Sigma70_r4 Sigma70, re 78.8 4.4 9.5E-05 28.4 4.5 28 396-423 24-51 (55)
170 PRK00118 putative DNA-binding 78.6 3.6 7.8E-05 35.8 4.6 29 396-424 31-59 (104)
171 PRK06930 positive control sigm 78.5 2.8 6.2E-05 39.2 4.2 30 395-424 127-156 (170)
172 PF13404 HTH_AsnC-type: AsnC-t 78.3 6.4 0.00014 28.6 5.1 24 398-421 17-40 (42)
173 PF13936 HTH_38: Helix-turn-he 75.9 4.9 0.00011 29.2 4.0 27 395-421 17-43 (44)
174 smart00421 HTH_LUXR helix_turn 75.9 5.3 0.00012 28.6 4.3 27 397-423 17-43 (58)
175 PF08279 HTH_11: HTH domain; 75.8 6.5 0.00014 29.1 4.8 36 387-423 5-40 (55)
176 PF10668 Phage_terminase: Phag 75.3 6.4 0.00014 31.1 4.7 30 390-419 14-43 (60)
177 PHA02591 hypothetical protein; 75.2 6.5 0.00014 32.8 4.9 24 397-420 58-81 (83)
178 PF13542 HTH_Tnp_ISL3: Helix-t 75.1 7.4 0.00016 28.5 4.9 26 396-421 25-50 (52)
179 PF00325 Crp: Bacterial regula 74.9 3.4 7.5E-05 28.6 2.7 25 399-423 3-27 (32)
180 PF02796 HTH_7: Helix-turn-hel 74.7 4.7 0.0001 29.3 3.6 23 398-420 21-43 (45)
181 PRK04217 hypothetical protein; 74.0 5.6 0.00012 35.0 4.5 28 397-424 57-84 (110)
182 PF06971 Put_DNA-bind_N: Putat 73.6 6 0.00013 30.1 4.1 46 373-418 3-48 (50)
183 PF14502 HTH_41: Helix-turn-he 73.4 4.4 9.6E-05 30.7 3.2 35 396-430 4-40 (48)
184 cd06170 LuxR_C_like C-terminal 72.7 7.1 0.00015 28.2 4.3 28 397-424 14-41 (57)
185 PF04967 HTH_10: HTH DNA bindi 71.8 5.5 0.00012 30.6 3.5 27 397-423 22-48 (53)
186 PF00196 GerE: Bacterial regul 70.4 4.6 9.9E-05 30.5 2.9 30 394-423 14-43 (58)
187 PF13412 HTH_24: Winged helix- 69.7 15 0.00033 26.5 5.4 27 396-422 15-41 (48)
188 cd00092 HTH_CRP helix_turn_hel 69.3 16 0.00035 27.5 5.7 27 397-423 24-50 (67)
189 PF13384 HTH_23: Homeodomain-l 69.0 5.2 0.00011 29.1 2.8 26 398-423 17-42 (50)
190 PF04297 UPF0122: Putative hel 68.4 9.3 0.0002 33.2 4.6 31 393-423 28-58 (101)
191 COG4367 Uncharacterized protei 68.2 14 0.00031 31.5 5.5 40 385-424 9-49 (97)
192 PF13730 HTH_36: Helix-turn-he 68.2 6.3 0.00014 29.2 3.2 27 396-422 23-49 (55)
193 PF06056 Terminase_5: Putative 68.1 13 0.00029 28.9 5.0 27 397-423 12-38 (58)
194 PF12728 HTH_17: Helix-turn-he 67.0 8 0.00017 28.3 3.5 25 399-423 2-26 (51)
195 TIGR00721 tfx DNA-binding prot 66.4 6.9 0.00015 35.7 3.6 28 396-423 19-46 (137)
196 TIGR02392 rpoH_proteo alternat 65.7 9.3 0.0002 37.9 4.7 26 397-422 235-260 (270)
197 TIGR01764 excise DNA binding d 64.9 9.9 0.00021 26.7 3.5 26 399-424 2-27 (49)
198 PRK03975 tfx putative transcri 61.6 9.7 0.00021 34.9 3.6 28 396-423 19-46 (141)
199 smart00345 HTH_GNTR helix_turn 61.5 11 0.00023 27.6 3.3 26 398-423 20-45 (60)
200 PRK11511 DNA-binding transcrip 61.3 24 0.00052 31.0 6.0 40 381-420 8-47 (127)
201 PF00356 LacI: Bacterial regul 60.5 9.9 0.00021 28.2 2.9 23 400-422 1-23 (46)
202 TIGR03826 YvyF flagellar opero 60.3 31 0.00067 31.6 6.6 49 380-428 28-76 (137)
203 cd04762 HTH_MerR-trunc Helix-T 60.3 14 0.00029 25.7 3.5 25 400-424 2-26 (49)
204 COG2197 CitB Response regulato 57.6 15 0.00031 35.3 4.3 30 393-422 158-187 (211)
205 PRK14082 hypothetical protein; 57.5 42 0.0009 27.1 6.0 54 296-351 10-63 (65)
206 PRK15411 rcsA colanic acid cap 57.2 15 0.00033 34.9 4.3 36 388-423 142-177 (207)
207 PF13744 HTH_37: Helix-turn-he 56.3 29 0.00063 28.1 5.3 36 396-431 29-64 (80)
208 PRK10840 transcriptional regul 55.5 18 0.00039 33.6 4.5 33 390-422 157-189 (216)
209 PRK13870 transcriptional regul 54.9 12 0.00025 36.6 3.2 29 396-424 186-214 (234)
210 TIGR03020 EpsA transcriptional 54.9 23 0.0005 35.2 5.3 28 396-423 203-230 (247)
211 PF03444 HrcA_DNA-bdg: Winged 54.8 44 0.00096 27.8 6.1 43 381-423 6-48 (78)
212 PRK10219 DNA-binding transcrip 54.1 38 0.00083 28.4 5.9 38 383-420 6-43 (107)
213 PF08784 RPA_C: Replication pr 53.7 21 0.00047 30.0 4.3 41 381-422 49-89 (102)
214 PF01325 Fe_dep_repress: Iron 53.6 35 0.00076 26.5 5.1 38 384-422 9-46 (60)
215 COG2771 CsgD DNA-binding HTH d 53.5 30 0.00066 25.7 4.7 27 396-422 17-43 (65)
216 PRK12423 LexA repressor; Provi 53.2 36 0.00078 32.4 6.2 42 381-422 8-50 (202)
217 PRK13719 conjugal transfer tra 53.2 20 0.00044 35.2 4.5 36 388-423 148-183 (217)
218 smart00550 Zalpha Z-DNA-bindin 53.0 43 0.00093 26.4 5.6 30 394-423 17-47 (68)
219 PF04703 FaeA: FaeA-like prote 52.9 20 0.00044 28.3 3.7 28 396-423 13-40 (62)
220 PRK10430 DNA-binding transcrip 52.7 25 0.00055 33.4 5.1 30 394-423 174-203 (239)
221 PRK11161 fumarate/nitrate redu 52.6 55 0.0012 30.9 7.4 26 398-423 184-209 (235)
222 PRK11475 DNA-binding transcrip 51.3 22 0.00048 34.0 4.5 33 390-422 141-173 (207)
223 PF12324 HTH_15: Helix-turn-he 51.2 27 0.00058 29.0 4.2 28 396-423 36-63 (77)
224 TIGR00498 lexA SOS regulatory 51.1 39 0.00084 31.7 6.0 43 381-423 8-51 (199)
225 COG0856 Orotate phosphoribosyl 51.0 27 0.00057 33.6 4.7 29 396-424 16-44 (203)
226 PRK15201 fimbriae regulatory p 50.9 23 0.00051 34.1 4.4 34 390-423 140-173 (198)
227 COG1522 Lrp Transcriptional re 50.5 33 0.00071 30.4 5.2 32 390-422 15-46 (154)
228 TIGR03541 reg_near_HchA LuxR f 49.1 17 0.00037 35.2 3.3 28 397-424 185-212 (232)
229 PF00392 GntR: Bacterial regul 49.0 20 0.00043 27.6 3.1 26 397-422 23-48 (64)
230 PRK10188 DNA-binding transcrip 49.0 17 0.00036 35.6 3.3 29 396-424 192-220 (240)
231 smart00419 HTH_CRP helix_turn_ 48.9 25 0.00054 24.7 3.4 27 398-424 8-34 (48)
232 PRK00423 tfb transcription ini 48.8 2.5E+02 0.0054 28.7 11.8 28 396-423 274-301 (310)
233 PF09339 HTH_IclR: IclR helix- 48.5 20 0.00044 26.5 3.0 27 396-422 16-42 (52)
234 PRK13239 alkylmercury lyase; P 48.2 40 0.00086 32.9 5.6 29 395-423 33-61 (206)
235 COG1318 Predicted transcriptio 47.4 36 0.00077 32.5 5.0 24 398-421 61-84 (182)
236 TIGR03697 NtcA_cyano global ni 47.1 91 0.002 28.2 7.7 26 398-423 143-168 (193)
237 cd00569 HTH_Hin_like Helix-tur 46.6 39 0.00085 20.8 3.8 21 398-418 21-41 (42)
238 cd04761 HTH_MerR-SF Helix-Turn 46.5 29 0.00064 24.6 3.5 25 400-424 2-26 (49)
239 PRK10100 DNA-binding transcrip 46.4 32 0.00069 33.1 4.7 28 396-423 168-195 (216)
240 PRK11179 DNA-binding transcrip 45.4 49 0.0011 29.9 5.6 26 398-423 23-48 (153)
241 PRK10046 dpiA two-component re 45.1 31 0.00068 32.5 4.4 26 398-423 177-202 (225)
242 PF13551 HTH_29: Winged helix- 45.1 61 0.0013 26.7 5.7 42 380-422 62-111 (112)
243 PF04760 IF2_N: Translation in 45.0 21 0.00045 26.7 2.6 37 399-435 4-42 (54)
244 PF04218 CENP-B_N: CENP-B N-te 44.9 22 0.00047 26.9 2.6 27 395-421 19-45 (53)
245 TIGR02531 yecD_yerC TrpR-relat 44.6 53 0.0012 27.7 5.2 25 396-420 48-72 (88)
246 PF10078 DUF2316: Uncharacteri 44.3 51 0.0011 28.1 5.0 33 389-421 13-46 (89)
247 PRK10572 DNA-binding transcrip 43.7 2.8E+02 0.006 27.1 11.0 38 383-420 184-221 (290)
248 COG4977 Transcriptional regula 43.5 50 0.0011 34.4 5.8 71 350-420 186-258 (328)
249 PF01978 TrmB: Sugar-specific 43.3 27 0.00059 27.0 3.1 26 397-422 21-46 (68)
250 PF09012 FeoC: FeoC like trans 43.0 44 0.00096 26.2 4.3 27 396-422 12-38 (69)
251 cd07377 WHTH_GntR Winged helix 43.0 95 0.0021 22.9 6.0 25 399-423 26-50 (66)
252 PRK15369 two component system 42.9 39 0.00084 29.7 4.4 29 396-424 162-190 (211)
253 PRK13918 CRP/FNR family transc 42.6 1E+02 0.0022 28.3 7.3 26 398-423 149-174 (202)
254 PF13545 HTH_Crp_2: Crp-like h 42.5 28 0.00061 27.1 3.1 26 398-423 28-53 (76)
255 COG4566 TtrR Response regulato 42.5 26 0.00056 34.0 3.3 23 396-418 155-177 (202)
256 PRK11169 leucine-responsive tr 42.2 53 0.0012 30.1 5.3 25 399-423 29-53 (164)
257 PRK00215 LexA repressor; Valid 42.1 67 0.0015 30.2 6.1 40 384-423 9-49 (205)
258 PF00376 MerR: MerR family reg 41.9 31 0.00067 24.5 2.9 23 400-422 1-23 (38)
259 PF01381 HTH_3: Helix-turn-hel 41.8 36 0.00078 24.8 3.4 25 397-421 8-32 (55)
260 PF05225 HTH_psq: helix-turn-h 41.3 83 0.0018 23.1 5.2 36 382-420 3-38 (45)
261 PF13518 HTH_28: Helix-turn-he 41.3 45 0.00099 23.9 3.8 24 400-423 14-37 (52)
262 TIGR02844 spore_III_D sporulat 40.5 72 0.0016 26.5 5.3 25 397-421 18-42 (80)
263 PF08280 HTH_Mga: M protein tr 40.4 47 0.001 25.4 3.9 28 396-423 17-44 (59)
264 smart00346 HTH_ICLR helix_turn 40.4 80 0.0017 25.3 5.6 26 397-422 19-44 (91)
265 PRK09464 pdhR transcriptional 39.6 88 0.0019 30.2 6.7 26 397-422 33-58 (254)
266 PRK09483 response regulator; P 38.4 56 0.0012 29.5 4.8 29 396-424 161-189 (217)
267 smart00420 HTH_DEOR helix_turn 38.3 96 0.0021 21.7 5.2 27 397-423 13-39 (53)
268 PF13411 MerR_1: MerR HTH fami 38.0 37 0.00081 26.0 3.1 24 400-423 2-25 (69)
269 smart00354 HTH_LACI helix_turn 37.9 34 0.00074 26.9 2.9 23 399-421 1-23 (70)
270 COG3413 Predicted DNA binding 37.6 63 0.0014 30.9 5.2 27 397-423 177-203 (215)
271 smart00342 HTH_ARAC helix_turn 37.6 1.5E+02 0.0033 22.3 6.6 37 382-421 37-74 (84)
272 PRK10403 transcriptional regul 37.5 47 0.001 29.5 4.1 33 396-428 166-198 (215)
273 PRK09391 fixK transcriptional 37.5 1.5E+02 0.0033 28.2 7.9 26 398-423 179-204 (230)
274 PF02082 Rrf2: Transcriptional 37.1 49 0.0011 26.8 3.8 25 399-423 26-50 (83)
275 PF13443 HTH_26: Cro/C1-type H 37.0 29 0.00063 26.1 2.3 26 397-422 9-34 (63)
276 PRK15418 transcriptional regul 37.0 30 0.00065 35.5 3.1 37 396-432 27-67 (318)
277 PF08220 HTH_DeoR: DeoR-like h 36.8 78 0.0017 24.1 4.6 27 396-422 12-38 (57)
278 PF01710 HTH_Tnp_IS630: Transp 36.5 1.1E+02 0.0025 26.5 6.3 29 396-424 69-97 (119)
279 TIGR03070 couple_hipB transcri 36.4 1E+02 0.0023 22.1 5.2 25 397-421 14-38 (58)
280 COG3769 Predicted hydrolase (H 36.1 77 0.0017 31.8 5.5 41 380-420 102-146 (274)
281 COG1476 Predicted transcriptio 36.1 72 0.0016 25.9 4.4 22 398-419 14-35 (68)
282 PF00440 TetR_N: Bacterial reg 35.7 1.1E+02 0.0025 21.9 5.2 33 386-418 4-36 (47)
283 PRK15044 transcriptional regul 35.4 1.2E+02 0.0026 31.3 7.0 70 350-421 162-231 (295)
284 PRK09935 transcriptional regul 35.2 59 0.0013 29.0 4.4 31 396-426 162-192 (210)
285 PF13022 HTH_Tnp_1_2: Helix-tu 34.8 44 0.00096 30.8 3.4 31 390-420 26-56 (142)
286 COG2524 Predicted transcriptio 34.7 72 0.0016 32.5 5.1 43 381-423 8-50 (294)
287 PRK15320 transcriptional activ 34.2 43 0.00092 33.0 3.4 34 390-423 171-204 (251)
288 PF13551 HTH_29: Winged helix- 34.2 41 0.00088 27.8 2.9 24 400-423 14-37 (112)
289 COG2390 DeoR Transcriptional r 34.0 79 0.0017 32.8 5.5 37 396-432 24-64 (321)
290 PRK13413 mpi multiple promoter 33.3 1.6E+02 0.0035 27.6 7.1 26 396-421 170-195 (200)
291 smart00088 PINT motif in prote 32.7 1.4E+02 0.003 23.9 5.8 37 396-432 22-58 (88)
292 smart00753 PAM PCI/PINT associ 32.7 1.4E+02 0.003 23.9 5.8 37 396-432 22-58 (88)
293 PHA01976 helix-turn-helix prot 32.6 60 0.0013 24.7 3.5 25 397-421 14-38 (67)
294 PF01726 LexA_DNA_bind: LexA D 32.6 1.4E+02 0.0031 23.5 5.6 19 264-282 20-38 (65)
295 PRK10651 transcriptional regul 32.5 69 0.0015 28.5 4.4 31 395-425 167-197 (216)
296 PRK09975 DNA-binding transcrip 32.5 97 0.0021 28.6 5.5 42 377-418 9-51 (213)
297 PF02001 DUF134: Protein of un 32.3 74 0.0016 27.9 4.3 28 397-424 56-83 (106)
298 PRK09390 fixJ response regulat 32.2 91 0.002 27.1 5.0 27 398-424 156-182 (202)
299 PF12802 MarR_2: MarR family; 32.0 74 0.0016 23.6 3.8 25 398-422 21-45 (62)
300 TIGR02297 HpaA 4-hydroxyphenyl 31.6 4.9E+02 0.011 25.2 10.9 39 383-421 187-225 (287)
301 TIGR02147 Fsuc_second hypothet 31.4 3.6E+02 0.0079 27.2 9.7 35 389-423 128-164 (271)
302 cd01104 HTH_MlrA-CarA Helix-Tu 31.1 86 0.0019 23.8 4.1 24 400-423 2-25 (68)
303 PRK11753 DNA-binding transcrip 30.9 2.3E+02 0.005 25.9 7.8 26 398-423 168-193 (211)
304 PRK10079 phosphonate metabolis 30.9 67 0.0015 31.0 4.3 26 396-421 33-58 (241)
305 TIGR02944 suf_reg_Xantho FeS a 30.5 91 0.002 27.2 4.7 28 396-423 23-50 (130)
306 TIGR00373 conserved hypothetic 30.3 57 0.0012 30.2 3.5 26 398-423 28-53 (158)
307 PRK09685 DNA-binding transcrip 29.9 2E+02 0.0044 28.1 7.6 44 310-354 205-248 (302)
308 PF08535 KorB: KorB domain; I 29.8 60 0.0013 26.9 3.3 28 398-425 3-30 (93)
309 smart00342 HTH_ARAC helix_turn 29.8 1.7E+02 0.0038 22.0 5.7 60 269-331 1-62 (84)
310 PF00165 HTH_AraC: Bacterial r 29.6 74 0.0016 22.3 3.2 28 395-422 5-32 (42)
311 PRK11511 DNA-binding transcrip 29.3 83 0.0018 27.6 4.2 39 254-292 10-48 (127)
312 smart00344 HTH_ASNC helix_turn 29.0 1.4E+02 0.0031 24.8 5.5 25 398-422 17-41 (108)
313 COG2207 AraC AraC-type DNA-bin 28.9 2.1E+02 0.0046 23.4 6.5 51 315-365 32-82 (127)
314 cd04764 HTH_MlrA-like_sg1 Heli 28.9 61 0.0013 24.9 2.9 24 400-423 2-25 (67)
315 COG2344 AT-rich DNA-binding pr 28.9 1.2E+02 0.0025 29.7 5.3 52 371-422 5-56 (211)
316 PF13560 HTH_31: Helix-turn-he 28.9 1.2E+02 0.0025 23.1 4.5 26 398-423 14-39 (64)
317 PF01371 Trp_repressor: Trp re 28.6 1.7E+02 0.0037 24.7 5.8 27 396-422 47-73 (87)
318 smart00422 HTH_MERR helix_turn 28.6 69 0.0015 24.4 3.2 24 400-423 2-25 (70)
319 PRK15121 right oriC-binding tr 28.6 1.3E+02 0.0027 29.9 5.8 40 381-420 4-43 (289)
320 PF12840 HTH_20: Helix-turn-he 28.5 1.2E+02 0.0027 22.9 4.6 27 396-422 22-48 (61)
321 smart00418 HTH_ARSR helix_turn 28.4 85 0.0019 22.5 3.6 28 396-423 8-35 (66)
322 TIGR02325 C_P_lyase_phnF phosp 28.4 1.4E+02 0.003 28.4 5.9 25 397-421 31-55 (238)
323 PHA02943 hypothetical protein; 28.4 1.8E+02 0.0038 27.5 6.2 46 374-422 2-48 (165)
324 PRK09726 antitoxin HipB; Provi 28.4 1.6E+02 0.0034 24.2 5.5 24 397-420 24-47 (88)
325 PRK10072 putative transcriptio 28.2 1.1E+02 0.0024 26.2 4.6 28 398-425 46-73 (96)
326 TIGR00180 parB_part ParB-like 28.1 1.1E+02 0.0024 28.6 5.1 35 398-432 120-154 (187)
327 TIGR03826 YvyF flagellar opero 27.8 1.4E+02 0.0031 27.3 5.5 40 255-294 32-71 (137)
328 COG2902 NAD-specific glutamate 27.8 1.3E+03 0.029 29.1 16.3 32 398-429 1466-1497(1592)
329 smart00389 HOX Homeodomain. DN 27.6 1.2E+02 0.0026 22.0 4.2 24 400-423 29-52 (56)
330 TIGR00738 rrf2_super rrf2 fami 27.4 1.1E+02 0.0024 26.4 4.7 26 398-423 25-50 (132)
331 TIGR01610 phage_O_Nterm phage 27.3 1.7E+02 0.0037 24.5 5.6 27 396-422 45-71 (95)
332 smart00351 PAX Paired Box doma 27.2 1.1E+02 0.0025 26.9 4.7 31 398-428 33-63 (125)
333 PRK09393 ftrA transcriptional 27.0 1.2E+02 0.0027 30.4 5.5 40 382-421 218-257 (322)
334 TIGR02404 trehalos_R_Bsub treh 26.8 1.5E+02 0.0032 28.3 5.8 25 397-421 23-47 (233)
335 PRK10402 DNA-binding transcrip 26.7 1.6E+02 0.0036 27.8 6.1 25 399-423 170-194 (226)
336 PRK14999 histidine utilization 26.7 1.5E+02 0.0033 28.5 5.9 25 397-421 35-59 (241)
337 PF10975 DUF2802: Protein of u 26.7 2.2E+02 0.0048 23.0 5.9 25 397-421 43-67 (70)
338 PRK10219 DNA-binding transcrip 26.3 1.5E+02 0.0033 24.6 5.2 38 255-292 7-44 (107)
339 PRK12702 mannosyl-3-phosphogly 26.3 1.3E+02 0.0028 31.1 5.5 42 381-422 100-147 (302)
340 PRK09480 slmA division inhibit 26.0 4.8E+02 0.01 23.3 10.1 76 262-337 23-98 (194)
341 TIGR02337 HpaR homoprotocatech 25.8 2.3E+02 0.0051 24.0 6.3 65 349-422 2-66 (118)
342 smart00530 HTH_XRE Helix-turn- 25.7 90 0.002 20.9 3.1 24 397-420 9-32 (56)
343 PRK09764 DNA-binding transcrip 25.7 1.6E+02 0.0035 28.4 5.9 25 397-421 28-52 (240)
344 PF13309 HTH_22: HTH domain 25.6 1.2E+02 0.0026 23.8 4.1 20 400-419 44-63 (64)
345 PF14394 DUF4423: Domain of un 25.4 1.2E+02 0.0025 28.5 4.7 36 388-423 29-66 (171)
346 TIGR03337 phnR transcriptional 25.4 1.7E+02 0.0036 27.7 5.8 26 397-422 24-49 (231)
347 TIGR03613 RutR pyrimidine util 25.3 1.7E+02 0.0038 26.7 5.8 40 379-418 8-48 (202)
348 PF04255 DUF433: Protein of un 25.2 1.1E+02 0.0023 23.3 3.6 26 396-421 29-55 (56)
349 PF05344 DUF746: Domain of Unk 25.2 1.1E+02 0.0024 24.7 3.7 34 390-423 5-38 (65)
350 PRK09480 slmA division inhibit 25.2 1.5E+02 0.0032 26.7 5.2 41 378-418 9-50 (194)
351 PRK09392 ftrB transcriptional 24.8 2.2E+02 0.0048 26.8 6.6 25 399-423 174-198 (236)
352 PRK09958 DNA-binding transcrip 24.3 1.1E+02 0.0023 27.4 4.1 30 395-424 155-184 (204)
353 PRK11402 DNA-binding transcrip 24.2 1.8E+02 0.0038 28.0 5.8 25 397-421 32-56 (241)
354 cd00131 PAX Paired Box domain 24.2 1.4E+02 0.003 26.6 4.7 33 397-429 32-64 (128)
355 smart00531 TFIIE Transcription 24.1 80 0.0017 28.6 3.3 27 398-424 15-41 (147)
356 COG1725 Predicted transcriptio 24.1 89 0.0019 28.2 3.4 25 397-421 34-58 (125)
357 PRK15044 transcriptional regul 24.1 5.5E+02 0.012 26.5 9.5 70 255-327 194-264 (295)
358 TIGR01321 TrpR trp operon repr 23.9 1.7E+02 0.0036 25.2 4.9 25 397-421 54-78 (94)
359 TIGR02018 his_ut_repres histid 23.9 1.8E+02 0.004 27.6 5.9 25 397-421 24-48 (230)
360 PF04967 HTH_10: HTH DNA bindi 23.9 1.4E+02 0.0031 22.9 4.0 28 267-294 21-48 (53)
361 PRK11014 transcriptional repre 23.8 92 0.002 27.7 3.5 28 396-423 23-50 (141)
362 cd00086 homeodomain Homeodomai 23.7 1.4E+02 0.003 21.7 4.0 23 400-422 29-51 (59)
363 PRK04841 transcriptional regul 23.7 1E+02 0.0023 35.0 4.8 29 395-423 850-878 (903)
364 COG2188 PhnF Transcriptional r 23.6 1.7E+02 0.0038 28.3 5.7 25 397-421 30-54 (236)
365 PF06970 RepA_N: Replication i 23.6 84 0.0018 25.7 2.9 22 399-420 53-74 (76)
366 PF07022 Phage_CI_repr: Bacter 23.6 70 0.0015 25.0 2.4 32 389-421 4-36 (66)
367 PRK13503 transcriptional activ 23.5 1.8E+02 0.0039 28.0 5.8 38 383-420 172-209 (278)
368 PRK10371 DNA-binding transcrip 23.4 1.7E+02 0.0036 29.4 5.7 40 382-421 191-230 (302)
369 PF08765 Mor: Mor transcriptio 23.4 2E+02 0.0044 24.6 5.5 26 398-423 72-97 (108)
370 COG1654 BirA Biotin operon rep 23.3 1.7E+02 0.0037 24.3 4.7 28 396-423 17-44 (79)
371 PRK10360 DNA-binding transcrip 23.2 1.3E+02 0.0029 26.6 4.5 28 397-424 151-178 (196)
372 TIGR02607 antidote_HigA addict 22.9 1.1E+02 0.0024 23.9 3.5 25 397-421 17-41 (78)
373 PRK15008 HTH-type transcriptio 22.6 2E+02 0.0044 26.8 5.8 40 379-418 18-58 (212)
374 cd04763 HTH_MlrA-like Helix-Tu 22.5 88 0.0019 24.1 2.8 22 400-421 2-23 (68)
375 PRK04984 fatty acid metabolism 22.3 89 0.0019 29.8 3.4 26 397-422 30-55 (239)
376 TIGR01636 phage_rinA phage tra 22.0 1.9E+02 0.0041 25.8 5.2 24 399-422 101-124 (134)
377 PF15545 Toxin_67: Putative to 21.9 96 0.0021 25.3 2.8 30 347-376 6-35 (70)
378 PRK10512 selenocysteinyl-tRNA- 21.9 1.2E+03 0.025 26.4 15.5 134 268-422 376-530 (614)
379 TIGR00122 birA_repr_reg BirA b 21.7 1.7E+02 0.0036 22.7 4.2 26 398-423 13-38 (69)
380 COG3415 Transposase and inacti 21.5 2.2E+02 0.0047 26.1 5.4 33 396-428 19-51 (138)
381 PRK13698 plasmid-partitioning 21.4 2.1E+02 0.0046 29.8 6.0 36 391-428 171-206 (323)
382 COG0350 Ada Methylated DNA-pro 21.3 2.5E+02 0.0054 26.3 6.0 46 379-428 88-135 (168)
383 PRK06424 transcription factor; 21.2 2.7E+02 0.0059 25.6 6.1 40 381-422 82-121 (144)
384 PRK15186 AraC family transcrip 21.2 4.4E+02 0.0095 26.7 8.2 69 257-328 185-254 (291)
385 PRK13503 transcriptional activ 21.1 3.7E+02 0.0081 25.8 7.5 27 383-412 224-250 (278)
386 PRK06266 transcription initiat 21.1 1E+02 0.0023 29.1 3.5 26 398-423 36-61 (178)
387 cd01392 HTH_LacI Helix-turn-he 21.1 74 0.0016 22.9 2.0 20 403-422 2-21 (52)
388 cd00090 HTH_ARSR Arsenical Res 21.0 1.2E+02 0.0026 22.3 3.2 24 399-422 21-44 (78)
389 PF10410 DnaB_bind: DnaB-helic 20.9 18 0.00038 27.1 -1.5 41 374-414 18-58 (59)
390 PRK10371 DNA-binding transcrip 20.9 6.5E+02 0.014 25.2 9.3 59 306-365 195-253 (302)
391 PF01022 HTH_5: Bacterial regu 20.8 1.2E+02 0.0025 21.9 3.0 27 397-423 14-40 (47)
392 COG3355 Predicted transcriptio 20.6 1.9E+02 0.0041 26.2 4.8 26 396-421 40-65 (126)
393 PRK00901 methylated-DNA--prote 20.6 2.3E+02 0.0049 26.3 5.5 69 356-428 48-120 (155)
394 PF11268 DUF3071: Protein of u 20.5 1.1E+02 0.0024 29.0 3.4 23 396-418 67-89 (170)
395 PRK15340 transcriptional regul 20.3 5.3E+02 0.011 25.3 8.2 66 352-420 76-147 (216)
396 PRK10130 transcriptional regul 20.3 2.1E+02 0.0045 29.8 5.7 38 383-420 241-278 (350)
397 PF00046 Homeobox: Homeobox do 20.1 1.1E+02 0.0024 22.5 2.8 26 396-421 22-50 (57)
398 PRK03837 transcriptional regul 20.1 1.1E+02 0.0023 29.2 3.4 27 397-423 36-62 (241)
399 TIGR02366 DHAK_reg probable di 20.1 2.2E+02 0.0049 25.4 5.3 37 381-417 5-42 (176)
No 1
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=100.00 E-value=3.8e-47 Score=393.22 Aligned_cols=221 Identities=29% Similarity=0.491 Sum_probs=207.6
Q ss_pred ChhHHHHHHhcccCC-CCCChHHHHHHHHHhHHHHH--------------------HHHHHHHHHHHhCCCCChHHHHH-
Q 013472 220 PTIFSAERALNSRGR-RLTIARNEAEMSKGVQVVAN--------------------LERIKTTLEKESGKAASLNCWAQ- 277 (442)
Q Consensus 220 ~~~~~~~~~~~~~~~-~lLt~eeE~eL~~~iq~~~~--------------------le~~~~~L~~~~gr~pt~~ewA~- 277 (442)
++.|.++-|+..+++ ||||++||++|+++||.++. |++++..|++++|++||..+||.
T Consensus 57 ~~~d~v~~yl~~igr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~~ 136 (415)
T PRK07598 57 RSTDLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKT 136 (415)
T ss_pred CCCChHHHHHHhcccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHHH
Confidence 345667778888887 99999999999999999999 89999999999999999999994
Q ss_pred ---------------------HcCCCHHHHHHHHHhchHHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHh
Q 013472 278 ---------------------AAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQG 336 (442)
Q Consensus 278 ---------------------a~g~deeeL~~~l~~G~~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirA 336 (442)
++||++++|+..++.|..|+++||.+|+++|+++|++|.++|++++||||||++|||+|
T Consensus 137 ~~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~ra 216 (415)
T PRK07598 137 ADISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERA 216 (415)
T ss_pred hCCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHH
Confidence 45566777778888998899999999999999999999999999999999999999999
Q ss_pred HHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHH
Q 013472 337 AERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIR 416 (442)
Q Consensus 337 ieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk 416 (442)
+++|||.+|++|+||+|||||++|.++++++++++++|.|+.+.+++++++...|.+++|+.||.+|||+.|||++++|+
T Consensus 217 vekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr 296 (415)
T PRK07598 217 VEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVR 296 (415)
T ss_pred HHHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhcccCCCCccccCCCCCccc
Q 013472 417 SASECLRIVGSIDQKIGDCLNAKY 440 (442)
Q Consensus 417 ~~l~~ar~~~SLD~~v~~~~d~~~ 440 (442)
.++..++.++|||.++|+++++++
T Consensus 297 ~~l~~~~~~~SLd~~vg~~~d~~l 320 (415)
T PRK07598 297 EVLLRVPRSVSLETKVGKDKDTEL 320 (415)
T ss_pred HHHHHccCCcccccccCCCccccH
Confidence 999999999999999998887653
No 2
>PRK05949 RNA polymerase sigma factor; Validated
Probab=100.00 E-value=2e-43 Score=356.76 Aligned_cols=217 Identities=35% Similarity=0.549 Sum_probs=208.4
Q ss_pred hHHHHHHhcccCC-CCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhchHHHHHH
Q 013472 222 IFSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREEL 300 (442)
Q Consensus 222 ~~~~~~~~~~~~~-~lLt~eeE~eL~~~iq~~~~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~~Are~L 300 (442)
.+.+..|++.+++ ||||++||++|++.|+.++.+++.+..|+..+|+.|+..+||.++++++.+|+..++.|+.|++.|
T Consensus 17 ~d~~~~yl~~i~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~~L 96 (327)
T PRK05949 17 ADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQKM 96 (327)
T ss_pred CCHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHHHH
Confidence 3455677888886 999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccccHHH
Q 013472 301 IKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNRE 380 (442)
Q Consensus 301 I~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v~e~ 380 (442)
|..|+++|+++|++|.+++.+++||+||||+|||+++++|||++|++|+|||+||||++|.++|.++++++|+|.++.+.
T Consensus 97 i~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~~~~~~ 176 (327)
T PRK05949 97 IEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK 176 (327)
T ss_pred HHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccccCCCCCc
Q 013472 381 ISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNA 438 (442)
Q Consensus 381 i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v~~~~d~ 438 (442)
+++++++...+..++|+.||.+|||+.+||++++|..++..++.++|||.|++++++.
T Consensus 177 ~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~ 234 (327)
T PRK05949 177 LNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDT 234 (327)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCc
Confidence 9999999999999999999999999999999999999999999999999999877654
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=2.8e-43 Score=350.51 Aligned_cols=212 Identities=35% Similarity=0.602 Sum_probs=204.1
Q ss_pred HHHhcccCC-CCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhchHHHHHHHHHh
Q 013472 226 ERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKST 304 (442)
Q Consensus 226 ~~~~~~~~~-~lLt~eeE~eL~~~iq~~~~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~~Are~LI~~n 304 (442)
..|++.+++ ||||++||++|++.++.++.+++.+.+|+++.|++|+..+||+++|+++.+|+.+++.|..|+++||.+|
T Consensus 4 ~~yl~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Lv~~~ 83 (298)
T TIGR02997 4 RLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMIKAN 83 (298)
T ss_pred HHHHHHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHHHHHh
Confidence 456777775 9999999999999999999999999999999999999999999999999999999999988999999999
Q ss_pred HHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccccHHHHHHH
Q 013472 305 RPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKI 384 (442)
Q Consensus 305 lrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v~e~i~kI 384 (442)
+++|+++|++|.++|.+++||+||||+|||+|+++|||.+|++|+||++||||++|.+++.++++++++|.++...++++
T Consensus 84 lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~I~r~i~~~~r~vr~p~~~~~~~~~~ 163 (298)
T TIGR02997 84 LRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLNKI 163 (298)
T ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHHHHHHHHhcCCCeeCcHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccccCCCCC
Q 013472 385 QKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLN 437 (442)
Q Consensus 385 ~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v~~~~d 437 (442)
+++...+...+|+.||.+|||+.+|+++++|..++..+..++|||.+++++++
T Consensus 164 rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~ 216 (298)
T TIGR02997 164 KKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEED 216 (298)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCc
Confidence 99999999999999999999999999999999999999999999999876554
No 4
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=2.4e-43 Score=361.64 Aligned_cols=216 Identities=31% Similarity=0.590 Sum_probs=208.2
Q ss_pred HHHHHHhcccCC-CCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhchHHHHHHH
Q 013472 223 FSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELI 301 (442)
Q Consensus 223 ~~~~~~~~~~~~-~lLt~eeE~eL~~~iq~~~~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~~Are~LI 301 (442)
+.+..|++.+++ ||||++||++|+++|+.++.+++.+.+|++..|++|+..+||.++|+++.+|..++..|..|+++||
T Consensus 63 d~l~~Yl~~i~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Li 142 (373)
T PRK07406 63 DSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEKMV 142 (373)
T ss_pred CHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHHHHH
Confidence 446778888886 9999999999999999999999999999999999999999999999999999999999988999999
Q ss_pred HHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccccHHHH
Q 013472 302 KSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREI 381 (442)
Q Consensus 302 ~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v~e~i 381 (442)
.+|+++|+++|++|.+++.+++||+|||+||||+|+++||+.+|++|+|||+||||++|.++|+++++++++|.++.+.+
T Consensus 143 ~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~~~~~ 222 (373)
T PRK07406 143 QSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETI 222 (373)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccccCCCCCc
Q 013472 382 SKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNA 438 (442)
Q Consensus 382 ~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v~~~~d~ 438 (442)
++|+++...|.+.+|+.||.+|||+.||+++++|..++..+..++|||.|++++++.
T Consensus 223 ~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~~ 279 (373)
T PRK07406 223 SRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDS 279 (373)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCcc
Confidence 999999999999999999999999999999999999999889999999999876654
No 5
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=3.2e-42 Score=346.48 Aligned_cols=216 Identities=31% Similarity=0.509 Sum_probs=207.4
Q ss_pred HHHHHHhcccCC-CCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhchHHHHHHH
Q 013472 223 FSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELI 301 (442)
Q Consensus 223 ~~~~~~~~~~~~-~lLt~eeE~eL~~~iq~~~~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~~Are~LI 301 (442)
+.+..|++.+++ ||||++||++|+++|+.++.+++++..|++++|+.|+..+||.++++++.+|+..++.|+.|+++||
T Consensus 8 ~~~~~yl~~i~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~~L~ 87 (317)
T PRK07405 8 DLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRKMV 87 (317)
T ss_pred cHHHHHHHHccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHHHHH
Confidence 345677888886 9999999999999999999999999999999999999999999999999999999999988999999
Q ss_pred HHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccccHHHH
Q 013472 302 KSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREI 381 (442)
Q Consensus 302 ~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v~e~i 381 (442)
..|+++|+++|++|.+++.+++||+||||+|||+++++|||.+|++|+||++||||++|.++|.++++++++|.++.+.+
T Consensus 88 ~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir~p~~~~~~~ 167 (317)
T PRK07405 88 EANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKL 167 (317)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCccCChHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccccCCCCCc
Q 013472 382 SKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNA 438 (442)
Q Consensus 382 ~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v~~~~d~ 438 (442)
++++++...+...+|+.||.+|||+.+|+++++|..++...+.++|||.|++++++.
T Consensus 168 ~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~ 224 (317)
T PRK07405 168 NKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDT 224 (317)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCc
Confidence 999999999999999999999999999999999999999888999999999876654
No 6
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=100.00 E-value=8.3e-40 Score=330.14 Aligned_cols=220 Identities=30% Similarity=0.503 Sum_probs=200.9
Q ss_pred hhHHHHHHhcccCC-CCCChHHHHHHHHHhHHHHHHHHHHHHHHH-HhCCCCChH---------------HHHHHcCCCH
Q 013472 221 TIFSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEK-ESGKAASLN---------------CWAQAAGVSE 283 (442)
Q Consensus 221 ~~~~~~~~~~~~~~-~lLt~eeE~eL~~~iq~~~~le~~~~~L~~-~~gr~pt~~---------------ewA~a~g~de 283 (442)
..+.+..|+...+. ++++.++|.++.++++....+......|.. .++..|+.. +|+.....++
T Consensus 7 ~~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~E 86 (342)
T COG0568 7 SADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEE 86 (342)
T ss_pred chhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHH
Confidence 35667788888886 999999999999999988877777777766 667888886 6665555554
Q ss_pred -HHHHHHHHhch--H-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHH
Q 013472 284 -RVLKQHLAFGW--Y-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (442)
Q Consensus 284 -eeL~~~l~~G~--~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRna 359 (442)
..|..++..|. . |+.+||.+|+++|++||++|.|+|+++.||||||+|||++|++||||++|++|||||+||||++
T Consensus 87 e~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAVekFdp~rG~kFsTYA~wWIrqa 166 (342)
T COG0568 87 EKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQA 166 (342)
T ss_pred HHHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHHHHhcCcccCCcchhHHHHHHHHH
Confidence 67888999995 3 9999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhcCceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccccCCCCCcc
Q 013472 360 ISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAK 439 (442)
Q Consensus 360 I~r~LRkqsr~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v~~~~d~~ 439 (442)
|.++|.++.++|++|.|+.+.++++.++.++|.+++|++|+++|||+.||+++++|+.++..++.|+|||.|+|+++|+.
T Consensus 167 I~raI~~q~rtIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd~~ig~ded~~ 246 (342)
T COG0568 167 ITRAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDDEDSE 246 (342)
T ss_pred HHHHHHHhcchhhHhHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccCCcCCCCcccH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999988764
Q ss_pred c
Q 013472 440 Y 440 (442)
Q Consensus 440 ~ 440 (442)
+
T Consensus 247 l 247 (342)
T COG0568 247 L 247 (342)
T ss_pred H
Confidence 3
No 7
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=100.00 E-value=2.7e-39 Score=342.10 Aligned_cols=205 Identities=30% Similarity=0.476 Sum_probs=184.1
Q ss_pred hHHHHHHhcccCC-CCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhchHHHHHH
Q 013472 222 IFSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREEL 300 (442)
Q Consensus 222 ~~~~~~~~~~~~~-~lLt~eeE~eL~~~iq~~~~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~~Are~L 300 (442)
.+.++.|++.+++ ||||++||++|+++|+.+..++.... ....|+.+ ...+|...+..|..|+++|
T Consensus 210 ~d~l~~YL~~i~~~~lLt~eEE~~La~~i~~g~~~~~~~~----------~~~~~~~~---~~~~l~~~~~~g~~Ar~~L 276 (509)
T PRK05901 210 ADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEELLA----------EGEKLDPE---LRRDLQWIGRDGKRAKNHL 276 (509)
T ss_pred ccHHHHHHHHhccCCCCCHHHHHHHHHHHHhCCchhhhhh----------hcccchhh---hhhhhhhhccchHHHHHHH
Confidence 3556778888886 99999999999999998865554221 11234322 4567888899999999999
Q ss_pred HHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccccHHH
Q 013472 301 IKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNRE 380 (442)
Q Consensus 301 I~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v~e~ 380 (442)
|.+|++||++||++|.++|++++||||||+|||++|+++|||.+|++|+|||+||||++|.++|+++.+.+++|.++.+.
T Consensus 277 I~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP~~~~e~ 356 (509)
T PRK05901 277 LEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVET 356 (509)
T ss_pred HHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecCHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccccCCCCCcc
Q 013472 381 ISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAK 439 (442)
Q Consensus 381 i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v~~~~d~~ 439 (442)
+++|.++...|.+.+|+.||.+|||+.|||++++|..++...+.++|||.+++++++..
T Consensus 357 i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~ 415 (509)
T PRK05901 357 INKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQ 415 (509)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCccc
Confidence 99999999999999999999999999999999999999998899999999998776654
No 8
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=100.00 E-value=4.5e-38 Score=317.57 Aligned_cols=203 Identities=31% Similarity=0.492 Sum_probs=182.0
Q ss_pred HHHHHHhcccCC-CCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhchHHHHHHH
Q 013472 223 FSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELI 301 (442)
Q Consensus 223 ~~~~~~~~~~~~-~lLt~eeE~eL~~~iq~~~~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~~Are~LI 301 (442)
+.+..|++.+++ ||||++||++|+++|+.+..++.. |+..+|+... ...+|...++.|..|+++||
T Consensus 26 ~~~~~Yl~~i~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~~~Lv 92 (324)
T PRK07921 26 DLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAARRHLL 92 (324)
T ss_pred ChHHHHHHHhcccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHHHHHH
Confidence 345677887876 999999999999999988776654 1122232111 35678999999999999999
Q ss_pred HHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccccHHHH
Q 013472 302 KSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREI 381 (442)
Q Consensus 302 ~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v~e~i 381 (442)
..|+++|+++|++|.+++.+++||+|||+||||+|+++|||++|++|+|||+||||++|.++|+++.+.+++|.++.+.+
T Consensus 93 ~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~~~~~~~ 172 (324)
T PRK07921 93 EANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQV 172 (324)
T ss_pred HHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccccCCCCCc
Q 013472 382 SKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNA 438 (442)
Q Consensus 382 ~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v~~~~d~ 438 (442)
++++++...|.+.+|+.||.+|||+.||+++++|..++..+..++|||.|++++++.
T Consensus 173 ~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~ 229 (324)
T PRK07921 173 NKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEA 229 (324)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCc
Confidence 999999999999999999999999999999999999998888999999999876654
No 9
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=1.9e-33 Score=288.10 Aligned_cols=177 Identities=30% Similarity=0.514 Sum_probs=164.9
Q ss_pred hHHHHHHhcccCC-CCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhchHHHHHH
Q 013472 222 IFSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREEL 300 (442)
Q Consensus 222 ~~~~~~~~~~~~~-~lLt~eeE~eL~~~iq~~~~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~~Are~L 300 (442)
.++++.|++.+++ |+||++||.+|++.++.+ +..|++.|
T Consensus 95 ~d~~~~yl~~i~~~~~l~~~ee~~L~~~~~~G----------------------------------------d~~A~~~L 134 (367)
T PRK09210 95 NDPVRMYLKEIGRVPLLTAEEEIELAKRIEEG----------------------------------------DEEAKQRL 134 (367)
T ss_pred CcHHHHHHHHhhccCCCCHHHHHHHHHHHHhh----------------------------------------HHHHHHHH
Confidence 4567888988886 999999999998866532 02389999
Q ss_pred HHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccccHHH
Q 013472 301 IKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNRE 380 (442)
Q Consensus 301 I~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v~e~ 380 (442)
|..|+++|+++|++|.+++.+++||+|||+||||+|+++|||.+|++|+|||+||||++|.++|+++.+.+++|.++.+.
T Consensus 135 i~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~~~~~~ 214 (367)
T PRK09210 135 AEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 214 (367)
T ss_pred HHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccccCCCCCc
Q 013472 381 ISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNA 438 (442)
Q Consensus 381 i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v~~~~d~ 438 (442)
++++.++.+.|..++|+.||.+|||+.|||++++|+.++..++.++|||.|++++++.
T Consensus 215 ~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~ 272 (367)
T PRK09210 215 INKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDS 272 (367)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCCCcc
Confidence 9999999999999999999999999999999999999999988999999999876554
No 10
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=3.1e-32 Score=295.65 Aligned_cols=164 Identities=28% Similarity=0.592 Sum_probs=152.0
Q ss_pred HHHcCCCH---HHHHHHHHhch----HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCCh
Q 013472 276 AQAAGVSE---RVLKQHLAFGW----YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKF 348 (442)
Q Consensus 276 A~a~g~de---eeL~~~l~~G~----~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rF 348 (442)
....+++. ..+.++++.|+ .|+++||.+|++||++||++|.++|++++||||||+|||++|+++|||.+|++|
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 44567778884 489999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhhcCceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCC
Q 013472 349 STYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSI 428 (442)
Q Consensus 349 STYa~~wIRnaI~r~LRkqsr~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SL 428 (442)
+|||+||||++|.++|+++.+++++|.|+.+.++++.++...+.+++|+.||.+|||+.||+|+++|+.++..+..++||
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 ccccCCCCCcc
Q 013472 429 DQKIGDCLNAK 439 (442)
Q Consensus 429 D~~v~~~~d~~ 439 (442)
|.|++++++..
T Consensus 514 d~~i~~~~~~~ 524 (619)
T PRK05658 514 ETPIGDDEDSH 524 (619)
T ss_pred CCCCCCCCCCc
Confidence 99998777653
No 11
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=99.97 E-value=8.9e-31 Score=257.20 Aligned_cols=142 Identities=24% Similarity=0.363 Sum_probs=135.0
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecc
Q 013472 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP 374 (442)
Q Consensus 295 ~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP 374 (442)
.++++||..|++||+++|++|.++|++++||||||+|||++|+++|||++|++|+|||+|||+++|.++++++.+.+++|
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 38999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHh--cccCCCCccccCCCC
Q 013472 375 CKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC--LRIVGSIDQKIGDCL 436 (442)
Q Consensus 375 ~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~--ar~~~SLD~~v~~~~ 436 (442)
.++.+..++++++...|.+++|+.||.+|||+.||+++++|..++.. ...++|||.++++++
T Consensus 120 r~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~ 183 (264)
T PRK07122 120 RRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSGD 183 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccccccCCC
Confidence 99999999999999999999999999999999999999999998764 347899999987543
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=99.97 E-value=5.2e-30 Score=247.04 Aligned_cols=143 Identities=35% Similarity=0.673 Sum_probs=137.4
Q ss_pred HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceeccc
Q 013472 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC 375 (442)
Q Consensus 296 Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~ 375 (442)
|+++||..|+++|+++|++|.+++.+++||+|||+|||++|+++|||.+|++|+|||+||||++|.++++++.+.+++|.
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 ccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccccCCCCCc
Q 013472 376 KLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNA 438 (442)
Q Consensus 376 ~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v~~~~d~ 438 (442)
++.+.++++.++...|..++|+.||.+|||+.||+++++|..++.....++|||.+++++++.
T Consensus 81 ~~~~~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~ 143 (238)
T TIGR02393 81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDS 143 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCCCCCCcc
Confidence 999999999999999999999999999999999999999999988888899999999766553
No 13
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=99.97 E-value=4.2e-29 Score=248.43 Aligned_cols=176 Identities=23% Similarity=0.322 Sum_probs=149.2
Q ss_pred hHHHHHHhcccCC-CCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhch-HHHHH
Q 013472 222 IFSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGW-YCREE 299 (442)
Q Consensus 222 ~~~~~~~~~~~~~-~lLt~eeE~eL~~~iq~~~~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~-~Are~ 299 (442)
++.+..|++.+++ |+||+++|.+|++.++ ..|+ .|+++
T Consensus 5 ~~~~~~y~~~~~~~~~l~~~~e~~L~~~~~----------------------------------------~~gd~~A~~~ 44 (289)
T PRK07500 5 ASADRSMIRSAMKAPYLEREEEHALAYRWK----------------------------------------DHRDEDALHR 44 (289)
T ss_pred hhHHHHHHHHHhcCCCCCHHHHHHHHHHHH----------------------------------------HCCCHHHHHH
Confidence 4556678888876 9999999998888542 1233 49999
Q ss_pred HHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccccHH
Q 013472 300 LIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNR 379 (442)
Q Consensus 300 LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v~e 379 (442)
||..|+++|+++|++|.+++.+++||+||||+|||+++++|||.+|.+|+|||+|||+++|.++|+++.+.+|+|.+..+
T Consensus 45 Lv~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I~~~lr~~~~~iR~p~~~~~ 124 (289)
T PRK07500 45 IISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQ 124 (289)
T ss_pred HHHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHCCCceecCccHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999988655
Q ss_pred --HHHHHHHHHHHHHH---HcCCCCcHHHHHHHhCCCHHHHHHHHH-hcccCCCCccccCCCCC
Q 013472 380 --EISKIQKARKALTN---SHGKYPEDIEIAKYTGLSLAEIRSASE-CLRIVGSIDQKIGDCLN 437 (442)
Q Consensus 380 --~i~kI~ka~~~L~~---elgr~PS~eEIAe~LGIS~etVk~~l~-~ar~~~SLD~~v~~~~d 437 (442)
...+++++...+.. .+|+.||.+|||+.||+++++|..+.. ....++|||.+++++++
T Consensus 125 ~~~~~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~ 188 (289)
T PRK07500 125 KALFFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDE 188 (289)
T ss_pred HHHHHHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCCCCC
Confidence 33455555555544 679999999999999999999987753 34578999999976554
No 14
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=99.96 E-value=5.9e-29 Score=242.90 Aligned_cols=147 Identities=26% Similarity=0.388 Sum_probs=135.8
Q ss_pred HhchH-HHHHHHHHhHHHHHHHHHHhhCC-CCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhc
Q 013472 291 AFGWY-CREELIKSTRPLVLFLARNYRGL-GIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA 368 (442)
Q Consensus 291 ~~G~~-Are~LI~~nlrLV~sIAkrY~g~-g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqs 368 (442)
..|+. |+++||..|+++|+++|++|.+. +.+++||+|||+||||+|+++|||++|++|+|||+|||+|+|.++++++.
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 46654 99999999999999999999876 67799999999999999999999999999999999999999999999999
Q ss_pred CceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHH--hcccCCCCccccCCCCC
Q 013472 369 RGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASE--CLRIVGSIDQKIGDCLN 437 (442)
Q Consensus 369 r~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~--~ar~~~SLD~~v~~~~d 437 (442)
+.+++|.++.+.++++.++...|.+++|+.||.+|||+.||+++++|..++. ....++|||.+++++++
T Consensus 100 ~~vr~pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~~~~ 170 (256)
T PRK07408 100 PTVRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQDED 170 (256)
T ss_pred CeeeeCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCCCCC
Confidence 9999999999999999999999999999999999999999999999999864 34568999999865433
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=99.96 E-value=8e-28 Score=234.13 Aligned_cols=141 Identities=26% Similarity=0.318 Sum_probs=133.8
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecc
Q 013472 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP 374 (442)
Q Consensus 295 ~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP 374 (442)
.|+++||..|.++|+++|++|.+++.+++||+||||+|||+++++||+.+|.+|+||+++||+|.|.++++++ ..+++|
T Consensus 34 ~a~~~L~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~~lr~~-~~ir~p 112 (254)
T TIGR02850 34 TAREKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDN-NPIRVS 112 (254)
T ss_pred HHHHHHHHHhHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHhC-CCccCc
Confidence 3899999999999999999999999999999999999999999999999999999999999999999999987 478999
Q ss_pred cccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccccCCCC
Q 013472 375 CKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCL 436 (442)
Q Consensus 375 ~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v~~~~ 436 (442)
.++.+...++.++...+..++|+.||.+|||+.||+++++|..++.....++|||.++.+++
T Consensus 113 ~~~~~~~~~~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~~ 174 (254)
T TIGR02850 113 RSLRDIAYKALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDG 174 (254)
T ss_pred hHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCCC
Confidence 99999999999999999999999999999999999999999999998888999999986443
No 16
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=99.96 E-value=9.8e-28 Score=237.98 Aligned_cols=171 Identities=26% Similarity=0.412 Sum_probs=141.3
Q ss_pred HHHHHHhcccCC-CCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhch-HHHHHH
Q 013472 223 FSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGW-YCREEL 300 (442)
Q Consensus 223 ~~~~~~~~~~~~-~lLt~eeE~eL~~~iq~~~~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~-~Are~L 300 (442)
+++..|++..++ |+|++++|.+|+...+ ..|+ .|++.|
T Consensus 14 ~~~~~y~~~~~~~~~l~~~~e~~l~~~~~----------------------------------------~~Gd~~a~~~L 53 (284)
T PRK06596 14 GNLDAYIQAVNKIPMLTAEEEYMLAKRLR----------------------------------------EHGDLEAAKQL 53 (284)
T ss_pred cHHHHHHHHHhccCCCCHHHHHHHHHHHH----------------------------------------HcCCHHHHHHH
Confidence 455667776664 8999999988877421 1243 399999
Q ss_pred HHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccccHH-
Q 013472 301 IKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNR- 379 (442)
Q Consensus 301 I~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v~e- 379 (442)
|..|+++|+++|++|.+.+.+++||+|||++||++|+++|||.+|++|+|||+|||+++|.++++++.+.+++|.+...
T Consensus 54 v~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~~~l~~~~~~vr~p~~~~~~ 133 (284)
T PRK06596 54 VLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKAQR 133 (284)
T ss_pred HHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHcCCeeeccchHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999998778899987542
Q ss_pred -HHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhc-ccCCCCccccCCC
Q 013472 380 -EISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL-RIVGSIDQKIGDC 435 (442)
Q Consensus 380 -~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~a-r~~~SLD~~v~~~ 435 (442)
...++.+...++. .++.||.+|||+.|||++++|..++... ..++|||.+++++
T Consensus 134 ~~~~~~~~~~~~l~--~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~ 189 (284)
T PRK06596 134 KLFFNLRKAKKRLG--WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDD 189 (284)
T ss_pred HHHHHHHHHHHHhc--cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCC
Confidence 2334444444442 3489999999999999999999987543 3789999998755
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=99.95 E-value=3.9e-27 Score=231.56 Aligned_cols=141 Identities=30% Similarity=0.480 Sum_probs=119.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecc
Q 013472 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP 374 (442)
Q Consensus 295 ~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP 374 (442)
.|++.||..|+++|+++|++|.+++.+++||+|||++||++|+++|||++|++|+|||+|||+++|.++++++.+.+++|
T Consensus 35 ~a~~~Lv~~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA~~~Ir~~i~~~l~~~~~~ir~p 114 (270)
T TIGR02392 35 DAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVA 114 (270)
T ss_pred HHHHHHHHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhhHHHHHHHHHHHHHHcCCceecC
Confidence 49999999999999999999999999999999999999999999999999999999999999999999999887788999
Q ss_pred cccH--HHHHHHHHHHHHHHHHcCCCC-cHHHHHHHhCCCHHHHHHHHHhcc-cCCCCccccCCCCC
Q 013472 375 CKLN--REISKIQKARKALTNSHGKYP-EDIEIAKYTGLSLAEIRSASECLR-IVGSIDQKIGDCLN 437 (442)
Q Consensus 375 ~~v~--e~i~kI~ka~~~L~~elgr~P-S~eEIAe~LGIS~etVk~~l~~ar-~~~SLD~~v~~~~d 437 (442)
.+.. +...++.++...+. ..+.| +.+|||+.||+++++|..++.... .++|||.+++++++
T Consensus 115 ~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~~~~ 179 (270)
T TIGR02392 115 TTKAQRKLFFNLRKMKKRLQ--GWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDDED 179 (270)
T ss_pred chHHHHHHHHHHHHHHHHHh--cCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCCCCC
Confidence 7643 33445555544442 12455 699999999999999999865443 47999999976543
No 18
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=99.95 E-value=5.5e-27 Score=237.00 Aligned_cols=176 Identities=26% Similarity=0.493 Sum_probs=159.9
Q ss_pred hhHHHHHHhcccCC-CCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhchH-HHH
Q 013472 221 TIFSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWY-CRE 298 (442)
Q Consensus 221 ~~~~~~~~~~~~~~-~lLt~eeE~eL~~~iq~~~~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~~-Are 298 (442)
..+.+..|++.++. |+||+++|.+|...+ +.|+. |++
T Consensus 51 ~~~~~~~y~~~~~~~~~l~~~ee~~li~~~-----------------------------------------~~Gd~~A~~ 89 (325)
T PRK05657 51 VLDATQLYLNEIGYSPLLTAEEEVYFARRA-----------------------------------------LRGDFAARQ 89 (325)
T ss_pred cccHHHHHHHHHhcCCCCCHHHHHHHHHHH-----------------------------------------HcCCHHHHH
Confidence 45667889988886 999999998777643 23433 999
Q ss_pred HHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccccH
Q 013472 299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLN 378 (442)
Q Consensus 299 ~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v~ 378 (442)
.||..|.++|+++|++|.+++.+++||+||||||+|+++++||+.+|++|+||++||||++|.++++++.+.+++|.++.
T Consensus 90 ~Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~~i~~~~r~ir~p~~~~ 169 (325)
T PRK05657 90 RMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVV 169 (325)
T ss_pred HHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHcCCccccCHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred HHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccccCCCCC
Q 013472 379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLN 437 (442)
Q Consensus 379 e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v~~~~d 437 (442)
..++.+.++...|...+|+.|+.+|||+.||+++++|..++.....+.|||.+++++..
T Consensus 170 ~~l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~~~~~~ 228 (325)
T PRK05657 170 KELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPE 228 (325)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCCCCCCC
Confidence 88888889999999999999999999999999999999999877788999999876554
No 19
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=99.95 E-value=1.6e-26 Score=225.36 Aligned_cols=142 Identities=27% Similarity=0.322 Sum_probs=134.1
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecc
Q 013472 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP 374 (442)
Q Consensus 295 ~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP 374 (442)
.|+++||..|.++|+.+|++|.+++.+++||+|||++|||+++++||+.+|.+|+||+++||+|+|.++++++ +.+++|
T Consensus 37 ~a~~~l~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~~~lr~~-~~vrip 115 (258)
T PRK08215 37 EAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDN-NPIRVS 115 (258)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhC-CceEec
Confidence 3899999999999999999999999999999999999999999999999999999999999999999999988 488999
Q ss_pred cccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccccCCCCC
Q 013472 375 CKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLN 437 (442)
Q Consensus 375 ~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v~~~~d 437 (442)
.++.....++.++...+..++|+.|+.+|||+.|||++++|...+.....+.|||.++.++++
T Consensus 116 ~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~~~ 178 (258)
T PRK08215 116 RSLRDIAYKALQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGG 178 (258)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCCCC
Confidence 999999999999999999999999999999999999999999998888888999999865443
No 20
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=99.94 E-value=4.5e-26 Score=217.91 Aligned_cols=149 Identities=26% Similarity=0.328 Sum_probs=139.1
Q ss_pred HHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHh
Q 013472 288 QHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVAR 366 (442)
Q Consensus 288 ~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRk 366 (442)
.+++.|+. |+++||..|.++|+++|++|.+++.+++||+|||++|||+++++||+.+|.+|+||+++||+|.|.+++|+
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 44566755 99999999999999999999999999999999999999999999999989999999999999999999999
Q ss_pred hcCceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccccCCCCC
Q 013472 367 HARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLN 437 (442)
Q Consensus 367 qsr~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v~~~~d 437 (442)
+. .+++|.++.+...++.++...|..++|+.||.+|||+.||+++++|..++..+..+.|||.+++++++
T Consensus 83 ~~-~i~~p~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~ 152 (231)
T TIGR02885 83 DG-IIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDG 152 (231)
T ss_pred CC-CeECCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCCCC
Confidence 85 78999999999999999999999999999999999999999999999999888889999999876543
No 21
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=99.94 E-value=5.3e-26 Score=221.89 Aligned_cols=152 Identities=30% Similarity=0.425 Sum_probs=140.2
Q ss_pred HHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCC-CHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHH
Q 013472 284 RVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGI-PFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS 361 (442)
Q Consensus 284 eeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~-d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~ 361 (442)
+.+....+.|+. ++ .||+.|+|||.++|++|.+++. +.|||+|.|+|||++|+++|||++|.+|+|||...|+++|+
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 456677777866 88 9999999999999999998877 99999999999999999999999999999999999999999
Q ss_pred HHHHhhcCceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcc--cCCCCccccCCCCC
Q 013472 362 KMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR--IVGSIDQKIGDCLN 437 (442)
Q Consensus 362 r~LRkqsr~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar--~~~SLD~~v~~~~d 437 (442)
+++|++. .+++|+.+++..+++..+...|..++|++||++|||+.|||+.+.|..++.... ..+|+|..+..++|
T Consensus 91 d~LR~~~-~v~vpR~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~d 167 (247)
T COG1191 91 DYLRKND-SVKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDD 167 (247)
T ss_pred HHHHhCC-CccCcHHHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhccccc
Confidence 9999997 899999999999999999999999999999999999999999999999987664 77899887764444
No 22
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=99.94 E-value=1e-25 Score=220.41 Aligned_cols=140 Identities=24% Similarity=0.363 Sum_probs=127.7
Q ss_pred hch-HHHHHHHHHhHHHHHHHHHHhhC---CCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhh
Q 013472 292 FGW-YCREELIKSTRPLVLFLARNYRG---LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARH 367 (442)
Q Consensus 292 ~G~-~Are~LI~~nlrLV~sIAkrY~g---~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkq 367 (442)
.|+ .|+++||..|+++|+.+|++|.+ .+++++||+|||+||||+|+++|||++|++|+||++|||+++|.+++|++
T Consensus 19 ~~~~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~ 98 (257)
T PRK05911 19 TQEIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQ 98 (257)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhc
Confidence 454 49999999999999999999862 35689999999999999999999999999999999999999999999987
Q ss_pred cCceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcc--cCCCCccccCC
Q 013472 368 ARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR--IVGSIDQKIGD 434 (442)
Q Consensus 368 sr~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar--~~~SLD~~v~~ 434 (442)
. ++|.++.+.++++.++...|.+.+|+.||.+|||+.|||++++|..++..++ .++|||.++.+
T Consensus 99 ~---~~pr~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~Sld~~~~~ 164 (257)
T PRK05911 99 D---WVPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPC 164 (257)
T ss_pred C---CCCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHHhhccceeeccccCCC
Confidence 4 5899999999999999999999999999999999999999999999987665 46899988643
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=99.93 E-value=7.8e-25 Score=208.60 Aligned_cols=140 Identities=34% Similarity=0.487 Sum_probs=133.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecc
Q 013472 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP 374 (442)
Q Consensus 295 ~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP 374 (442)
.|+++||..|.++|+++|++|.+++.+++||+|||++||++|+++||+.+|.+|+||+++||+|.|.++++++.+.+++|
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 48999999999999999999999999999999999999999999999999999999999999999999999998899999
Q ss_pred cccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhccc--CCCCccccCC
Q 013472 375 CKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRI--VGSIDQKIGD 434 (442)
Q Consensus 375 ~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~--~~SLD~~v~~ 434 (442)
.++.+...+++++...+...+|+.|+.+|+|+.||+++++|..++..... +.|||.++++
T Consensus 83 ~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~ 144 (227)
T TIGR02980 83 RRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIED 144 (227)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCC
Confidence 99999999999999999999999999999999999999999998876664 8999999873
No 24
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=99.92 E-value=2.8e-24 Score=208.84 Aligned_cols=155 Identities=25% Similarity=0.271 Sum_probs=142.0
Q ss_pred HHHHHHHHHh-chH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHH
Q 013472 283 ERVLKQHLAF-GWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (442)
Q Consensus 283 eeeL~~~l~~-G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI 360 (442)
+.+|+.+++. |+. |+++|+..|.++|+.+|++|.+++.+++||+||||+|||+++++||++.|.+|.||+++||+|.|
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 4567777777 554 99999999999999999999999999999999999999999999999989999999999999999
Q ss_pred HHHHHhhcCceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhc--ccCCCCccccCCCCC
Q 013472 361 SKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL--RIVGSIDQKIGDCLN 437 (442)
Q Consensus 361 ~r~LRkqsr~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~a--r~~~SLD~~v~~~~d 437 (442)
.++++++...+++|.++.+..+++..+...+...+|+.|+.+|||+.+|++.+.+..++... ..+.|||.+++++.+
T Consensus 95 ~~~lr~~~~~iri~~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~~~ 173 (255)
T TIGR02941 95 KRYLRDKTWSVHVPRRIKELGPKIKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSD 173 (255)
T ss_pred HHHHHHcCCCcCCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCCCC
Confidence 99999998889999999999999999999999999999999999999999999999887654 367899998865443
No 25
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=99.92 E-value=6.9e-24 Score=208.05 Aligned_cols=136 Identities=32% Similarity=0.408 Sum_probs=124.6
Q ss_pred HHHHHHHHHhHHHHHHHHHHhh-C--CCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCce
Q 013472 295 YCREELIKSTRPLVLFLARNYR-G--LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGI 371 (442)
Q Consensus 295 ~Are~LI~~nlrLV~sIAkrY~-g--~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~i 371 (442)
.|++.++..|.++|+.+|++|. + .+.+++||+||||+|||+++++||+.+|++|+||++|||+|.|.+++|+. +
T Consensus 31 ~a~~~l~~~y~~lv~~~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i~d~~R~~---~ 107 (268)
T PRK06288 31 KIREYLILKYSPLVKYVAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSI---D 107 (268)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhc---C
Confidence 3899999999999999999986 3 46789999999999999999999999889999999999999999999965 5
Q ss_pred ecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhc--ccCCCCccccC
Q 013472 372 KIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL--RIVGSIDQKIG 433 (442)
Q Consensus 372 rlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~a--r~~~SLD~~v~ 433 (442)
++|.++.....++.++...|...+++.||.+|||+.+|++++.|..++... ..++|||.++.
T Consensus 108 ~~p~~~~~~~~~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~ 171 (268)
T PRK06288 108 WIPRSVRQKARQIERAIAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWF 171 (268)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhc
Confidence 689999999999999999999999999999999999999999999998654 36789998864
No 26
>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=1.3e-23 Score=208.01 Aligned_cols=174 Identities=28% Similarity=0.500 Sum_probs=155.7
Q ss_pred hHHHHHHhcccCC-CCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhchH-HHHH
Q 013472 222 IFSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWY-CREE 299 (442)
Q Consensus 222 ~~~~~~~~~~~~~-~lLt~eeE~eL~~~iq~~~~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~~-Are~ 299 (442)
.++++.|+..+.. |.|+.++|.+|...+ +.|+. |++.
T Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~~li~~~-----------------------------------------~~gd~~a~~~ 50 (285)
T TIGR02394 12 ADVTQLYLREIGFKPLLTAEEEIAYARRA-----------------------------------------LAGDFEARKV 50 (285)
T ss_pred chHHHHHHHHHhccCCCCHHHHHHHHHHH-----------------------------------------HcCCHHHHHH
Confidence 4677778877775 788888877666533 34433 9999
Q ss_pred HHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccccHH
Q 013472 300 LIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNR 379 (442)
Q Consensus 300 LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v~e 379 (442)
||..|.++|+++|++|.+++.+++||+|||+||||+|+++||+.+|++|+||+.|||+.++.++++++.+.+++|.++.+
T Consensus 51 L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ain~~i~~~~~~~~~p~~~~~ 130 (285)
T TIGR02394 51 MIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHVIK 130 (285)
T ss_pred HHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHHHHHHHHcCCceeCcHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccccCCCC
Q 013472 380 EISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCL 436 (442)
Q Consensus 380 ~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v~~~~ 436 (442)
..+.+.+..+.+...+|+.|+.+|+|+.+|+++..|..++..+...+|||.++.++.
T Consensus 131 ~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~~~~~ 187 (285)
T TIGR02394 131 ELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDS 187 (285)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCCCCCC
Confidence 999888888888888899999999999999999999999988888899998876544
No 27
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=99.92 E-value=8.2e-24 Score=205.50 Aligned_cols=153 Identities=24% Similarity=0.309 Sum_probs=136.8
Q ss_pred CHHHHHHHHHh-chH-HHHHHHHHhHHHHHHHHHHhhC---CCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHH
Q 013472 282 SERVLKQHLAF-GWY-CREELIKSTRPLVLFLARNYRG---LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI 356 (442)
Q Consensus 282 deeeL~~~l~~-G~~-Are~LI~~nlrLV~sIAkrY~g---~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wI 356 (442)
++.+|+++.+. |+. |++.||..|.++|+.+|++|.+ ++.+++||+||||+|||+++++||+.+|.+|+||+++||
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 45667777444 555 9999999999999999999976 689999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhcCceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHH--hcccCCCCccccCC
Q 013472 357 RKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASE--CLRIVGSIDQKIGD 434 (442)
Q Consensus 357 RnaI~r~LRkqsr~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~--~ar~~~SLD~~v~~ 434 (442)
+|.|++++|++. ++|..+.+.+.+++++...+.+.+|+.|+.+|||+.||+++++|..++. ....++|||.++.+
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 999999999874 6899999999999999999999999999999999999999999999976 34578999999865
Q ss_pred CCC
Q 013472 435 CLN 437 (442)
Q Consensus 435 ~~d 437 (442)
+++
T Consensus 164 ~~~ 166 (251)
T PRK07670 164 QDD 166 (251)
T ss_pred CCC
Confidence 544
No 28
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=99.91 E-value=2.3e-23 Score=201.03 Aligned_cols=139 Identities=20% Similarity=0.213 Sum_probs=124.2
Q ss_pred HHHHHHHHhHHHHHHHHHHhhC---CCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCcee
Q 013472 296 CREELIKSTRPLVLFLARNYRG---LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIK 372 (442)
Q Consensus 296 Are~LI~~nlrLV~sIAkrY~g---~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~ir 372 (442)
....|+..|+++|+++|++|.. .+.+++||+|||+||||+|+++||+.+| +|+||++|||+|+|.+++++. .+
T Consensus 16 ~~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~il~~lr~~---~~ 91 (231)
T PRK12427 16 EEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELREL---DW 91 (231)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHHHHhc---CC
Confidence 3558899999999999999875 4689999999999999999999998666 899999999999999999975 35
Q ss_pred cccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHh--cccCCCCccccCCCCCc
Q 013472 373 IPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC--LRIVGSIDQKIGDCLNA 438 (442)
Q Consensus 373 lP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~--ar~~~SLD~~v~~~~d~ 438 (442)
.|..+....++++++...|.+++|+.||.+|||+.||+++++|..++.. +..++|||.+++++++.
T Consensus 92 ~~r~vr~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~ 159 (231)
T PRK12427 92 RPRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALEAHN 159 (231)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccCCCcc
Confidence 7888899999999999999999999999999999999999999998764 45789999998766543
No 29
>PRK05572 sporulation sigma factor SigF; Validated
Probab=99.91 E-value=4.3e-23 Score=200.56 Aligned_cols=152 Identities=26% Similarity=0.385 Sum_probs=140.6
Q ss_pred HHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHH
Q 013472 284 RVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISK 362 (442)
Q Consensus 284 eeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r 362 (442)
.+|+..+..|+. |+++||..|.++|+.+|++|.+++.+++||+||||+++|+++++||+.+|.+|.||+++||++.|.+
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 446666777765 9999999999999999999999999999999999999999999999988889999999999999999
Q ss_pred HHHhhcCceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccccCCCC
Q 013472 363 MVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCL 436 (442)
Q Consensus 363 ~LRkqsr~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v~~~~ 436 (442)
++++. ..+++|..+.+...++.++...+..++|+.|+..|||+.+|++++.|..++.....+.||+.++.+++
T Consensus 100 ~lr~~-~~~r~~~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~ 172 (252)
T PRK05572 100 FLRDD-GTVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHEND 172 (252)
T ss_pred HHHhC-CCCCCCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCcccCC
Confidence 99987 47899999999999999999999999999999999999999999999999888888999999886544
No 30
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=99.90 E-value=1.7e-22 Score=196.52 Aligned_cols=155 Identities=26% Similarity=0.272 Sum_probs=140.7
Q ss_pred HHHHHHHHHh-chH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHH
Q 013472 283 ERVLKQHLAF-GWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (442)
Q Consensus 283 eeeL~~~l~~-G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI 360 (442)
+.+|+..++. |+. |+++||..|.++|+++|++|.+++.+++||+||||++||+++++||+..|.+|+||+++||+|.|
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 4567777764 655 99999999999999999999999999999999999999999999999988899999999999999
Q ss_pred HHHHHhhcCceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcc--cCCCCccccCCCCC
Q 013472 361 SKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR--IVGSIDQKIGDCLN 437 (442)
Q Consensus 361 ~r~LRkqsr~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar--~~~SLD~~v~~~~d 437 (442)
.++++++...+++|.++.+..+++..+...+...+++.|+.+|+|+.+|++.+.|..++.... .++|+|.+++++.+
T Consensus 95 ~~~lr~~~~~~~i~r~~~~~~~~~~~~~~~~~~~~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~~~ 173 (257)
T PRK08583 95 KRYLRDKTWSVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSD 173 (257)
T ss_pred HHHHHhcCCCcCCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCCCC
Confidence 999999989999999999999999999999999999999999999999999999988876543 67899998865443
No 31
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=99.89 E-value=2.2e-22 Score=191.89 Aligned_cols=132 Identities=32% Similarity=0.475 Sum_probs=121.6
Q ss_pred HHHHhHHHHHHHHHHhhC---CCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccc
Q 013472 300 LIKSTRPLVLFLARNYRG---LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCK 376 (442)
Q Consensus 300 LI~~nlrLV~sIAkrY~g---~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~ 376 (442)
|+..|.++|+.+|++|.+ ++.+++||+|||++|||+++++|||.+|++|+||+++||+|.+++++|+.. ++|..
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 588999999999999986 789999999999999999999999999999999999999999999999763 68999
Q ss_pred cHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcc--cCCCCccccCC
Q 013472 377 LNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR--IVGSIDQKIGD 434 (442)
Q Consensus 377 v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar--~~~SLD~~v~~ 434 (442)
+...++++.++..+|...+|+.|+.+|||+.||++++.|..++..+. .++|+|.++.+
T Consensus 78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~~ 137 (224)
T TIGR02479 78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLES 137 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcccC
Confidence 99999999999999999999999999999999999999999986443 57889887654
No 32
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=99.87 E-value=1.6e-21 Score=187.60 Aligned_cols=142 Identities=30% Similarity=0.416 Sum_probs=127.1
Q ss_pred hchHHHHHHHHHhHHHHHHHHHHhh---CCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhc
Q 013472 292 FGWYCREELIKSTRPLVLFLARNYR---GLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA 368 (442)
Q Consensus 292 ~G~~Are~LI~~nlrLV~sIAkrY~---g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqs 368 (442)
.|.-++++|+..|.++|+.+|++|. +++.+++||+||||+|||+++++||+..|.+|+||+++||+|.|.+++|++.
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 6789999999999999999999999998899999999999999999999875
Q ss_pred CceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhc--ccCCCCccccCCCC
Q 013472 369 RGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL--RIVGSIDQKIGDCL 436 (442)
Q Consensus 369 r~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~a--r~~~SLD~~v~~~~ 436 (442)
++|..+.....++.++...+.+.+++.||.+|||+.||+++++|..++... ..++|+|.++++++
T Consensus 85 ---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~ 151 (236)
T PRK06986 85 ---WVPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHG 151 (236)
T ss_pred ---CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccccCCC
Confidence 368777777788899999999999999999999999999999999987743 35678998865543
No 33
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=99.79 E-value=7e-18 Score=162.17 Aligned_cols=170 Identities=22% Similarity=0.252 Sum_probs=127.7
Q ss_pred HHHHhHHHHHHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHH
Q 013472 245 MSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFS 323 (442)
Q Consensus 245 L~~~iq~~~~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~E 323 (442)
|.--++..++|.+....+ ++.|.+.. .++..|+..+..|+. |++.|+..|.++|+++|.+|.+++.+++
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 344456667776666554 44443322 124567888888866 9999999999999999999999999999
Q ss_pred hHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCce---ec-------------------cc---ccH
Q 013472 324 DLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGI---KI-------------------PC---KLN 378 (442)
Q Consensus 324 DLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~i---rl-------------------P~---~v~ 378 (442)
|++|||+|++|+++++||+++|.+|.||+++|++|.+++++|+..+.. .+ +. ...
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------------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 379 ------REISKIQKARKALTNSH------------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 379 ------e~i~kI~ka~~~L~~el------------gr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
+....+.++...|+... ..+.|++|||+.+|+|.++|+..+++++.
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 12223555555554432 24579999999999999999999877653
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=99.77 E-value=4.8e-18 Score=163.52 Aligned_cols=129 Identities=18% Similarity=0.301 Sum_probs=114.0
Q ss_pred HHHhchHHHHHHHHHhHHHHHHHHHHhhCCC--CCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHh
Q 013472 289 HLAFGWYCREELIKSTRPLVLFLARNYRGLG--IPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVAR 366 (442)
Q Consensus 289 ~l~~G~~Are~LI~~nlrLV~sIAkrY~g~g--~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRk 366 (442)
.++.|+..+++||..|.|+|.++|.+|.++. .+.+|++|+|+||||+|+++||+++|.+|.|||.++|++.|++++|+
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 5678887899999999999999999998775 58999999999999999999999999999999999999999999998
Q ss_pred hc---CceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHH------hCCCHHHHHH
Q 013472 367 HA---RGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKY------TGLSLAEIRS 417 (442)
Q Consensus 367 qs---r~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~------LGIS~etVk~ 417 (442)
.. ..+++|....+....+..+..++..+.++.|+.+||+.. .||+.+.+-+
T Consensus 83 ~~k~~~~v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~~~~~L~~~gi~~~dLv~ 142 (218)
T TIGR02895 83 NQKYQNLLYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILEYKKLLKQFGIEFVELVK 142 (218)
T ss_pred cccccCeeeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcCCcHHHHhh
Confidence 87 456888766666778888888999999999999999954 4888877643
No 35
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=99.77 E-value=2.8e-17 Score=157.57 Aligned_cols=143 Identities=24% Similarity=0.354 Sum_probs=115.7
Q ss_pred CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHH
Q 013472 282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (442)
Q Consensus 282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI 360 (442)
.+..|+..++.|+. |++.|+..|.+.|+++|.+|.++..+++|++||+|+++|+++++|+++.+.+|.||+++|++|.|
T Consensus 34 ~~~~li~~~~~gd~~af~~l~~~y~~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~ 113 (227)
T TIGR02846 34 EEKKYLDRLKEGDEEARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEI 113 (227)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHH
Confidence 35778888999976 99999999999999999999999999999999999999999999999888889999999999999
Q ss_pred HHHHHhhcCcee-c---------------------cc---c------cHHHHHHHHHHHHHHHHHc--------C----C
Q 013472 361 SKMVARHARGIK-I---------------------PC---K------LNREISKIQKARKALTNSH--------G----K 397 (442)
Q Consensus 361 ~r~LRkqsr~ir-l---------------------P~---~------v~e~i~kI~ka~~~L~~el--------g----r 397 (442)
++++|+..+... . +. . ..+....|.+++..|+... - .
T Consensus 114 ~d~~Rk~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~il~l~y~~~~~e 193 (227)
T TIGR02846 114 LMHLRALKKTKGEVSLQDPIGVDKEGNEISLIDILGSDGDSVIEQVELNLEIKKLYKKLSVLDGREREVIEMRYGLGDGR 193 (227)
T ss_pred HHHHHHHhccccceeccccccCCcccCcccHHHHhcCCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHcCCCCC
Confidence 999998754211 0 00 0 0012233555566555443 1 5
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 398 YPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
+.|.+|||++||+|+++|+..+++++.
T Consensus 194 ~~S~~EIAe~lgis~~tV~~~~~rAl~ 220 (227)
T TIGR02846 194 RKTQREIAKILGISRSYVSRIEKRALM 220 (227)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 679999999999999999999887764
No 36
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=99.75 E-value=1.6e-17 Score=159.27 Aligned_cols=143 Identities=24% Similarity=0.387 Sum_probs=116.8
Q ss_pred CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHH
Q 013472 282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (442)
Q Consensus 282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI 360 (442)
.+..|+..++.|+. |++.++..|.++|+.+|++|.+++.+++|++||+|+++|+++++|++..+++|.||++++++|.|
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 46778888999976 99999999999999999999999999999999999999999999999877889999999999999
Q ss_pred HHHHHhhcCcee---c--c-----------------c--cc----H---HHHHHHHHHHHHHHHHc------------CC
Q 013472 361 SKMVARHARGIK---I--P-----------------C--KL----N---REISKIQKARKALTNSH------------GK 397 (442)
Q Consensus 361 ~r~LRkqsr~ir---l--P-----------------~--~v----~---e~i~kI~ka~~~L~~el------------gr 397 (442)
++++|++.+... + + . .. . .....+.+++.+|+.+. ..
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 01224666776665543 25
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 398 YPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
+.|++|||+.||||+++|+..+++++.
T Consensus 198 g~s~~EIA~~lgis~~tVk~~~~rA~~ 224 (234)
T PRK08301 198 EKTQKEVADMLGISQSYISRLEKRIIK 224 (234)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 789999999999999999999887763
No 37
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=99.75 E-value=1.1e-17 Score=154.19 Aligned_cols=144 Identities=17% Similarity=0.129 Sum_probs=117.9
Q ss_pred CCCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHH
Q 013472 280 GVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK 358 (442)
Q Consensus 280 g~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRn 358 (442)
.++++.|+..++.|+. |++.|+..|.++|+.+|++|.+++.+++|++||+|+++|+++.+|++. +.+|.||++.+++|
T Consensus 4 ~~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n 82 (186)
T PRK05602 4 ADPDEELLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLN 82 (186)
T ss_pred cccHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHH
Confidence 3567889999999976 999999999999999999999999999999999999999999999975 35799999999999
Q ss_pred HHHHHHHhhcCcee--ccc---------c---cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHH
Q 013472 359 SISKMVARHARGIK--IPC---------K---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIR 416 (442)
Q Consensus 359 aI~r~LRkqsr~ir--lP~---------~---v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk 416 (442)
.+.+++|+++.... ++. . ..+....+.++...|+.+. -.+.+++|||+.||+|..+|+
T Consensus 83 ~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~ 162 (186)
T PRK05602 83 LCYDRLRRRREVPVEDAPDVPDPAPGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALE 162 (186)
T ss_pred HHHHHHHhcCCCCcccccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHhcCCCHHHHHHHhCcCHHHHH
Confidence 99999997754211 110 0 0122334666666665443 267799999999999999999
Q ss_pred HHHHhccc
Q 013472 417 SASECLRI 424 (442)
Q Consensus 417 ~~l~~ar~ 424 (442)
..+++++.
T Consensus 163 ~~l~Rar~ 170 (186)
T PRK05602 163 SLLARGRR 170 (186)
T ss_pred HHHHHHHH
Confidence 99998875
No 38
>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=3.8e-17 Score=151.24 Aligned_cols=144 Identities=18% Similarity=0.200 Sum_probs=114.1
Q ss_pred CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHH
Q 013472 281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (442)
Q Consensus 281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRna 359 (442)
|++.+|+..++.|+. |++.|+..|.+.|+.+|+++.++..+++|++||+|+++|+++.+|++..+..|.||++.+|++.
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 567889999999976 9999999999999999999999999999999999999999999999977778999999999999
Q ss_pred HHHHHHhhcCceec----------------------------cccc-------HHHHHHHHHHHHHHHHHc--------C
Q 013472 360 ISKMVARHARGIKI----------------------------PCKL-------NREISKIQKARKALTNSH--------G 396 (442)
Q Consensus 360 I~r~LRkqsr~irl----------------------------P~~v-------~e~i~kI~ka~~~L~~el--------g 396 (442)
+.+++++..+..+. +... .+....+.++...|+... -
T Consensus 84 ~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~~~~~ 163 (198)
T TIGR02859 84 IITAIKTATRQKHIPLNSYVSLNKPIYDEESDRTLLDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVLQSYL 163 (198)
T ss_pred HHHHHHHHHHhcccchhhhcCcccccccccccchHHHHhhccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence 98888743111000 0000 111233555555542221 2
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
.+.|++|||+.||+|+++|+.++++++.
T Consensus 164 ~~~s~~eIA~~l~~s~~tV~~~l~r~r~ 191 (198)
T TIGR02859 164 DGKSYQEIACDLNRHVKSIDNALQRVKR 191 (198)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6779999999999999999999998874
No 39
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=99.74 E-value=4.4e-17 Score=156.88 Aligned_cols=143 Identities=24% Similarity=0.385 Sum_probs=116.3
Q ss_pred CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHH
Q 013472 282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (442)
Q Consensus 282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI 360 (442)
.++.|+..+..|+. |++.++..|.+.|+.+|++|.+++.+++|++||+|+++|+++++|++..+++|.||++++++|.+
T Consensus 38 ~~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~ 117 (234)
T TIGR02835 38 EEEALLQKLTQGDESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEI 117 (234)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHH
Confidence 35678888888866 99999999999999999999999999999999999999999999998877789999999999999
Q ss_pred HHHHHhhcCce-ecc----------------------c-----cc---HHHHHHHHHHHHHHHHHc------------CC
Q 013472 361 SKMVARHARGI-KIP----------------------C-----KL---NREISKIQKARKALTNSH------------GK 397 (442)
Q Consensus 361 ~r~LRkqsr~i-rlP----------------------~-----~v---~e~i~kI~ka~~~L~~el------------gr 397 (442)
++++|++.+.. ..+ . .. ......+.+++..|+... ..
T Consensus 118 ~d~~Rk~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~e 197 (234)
T TIGR02835 118 LMYLRRNNKTRSEVSFDEPLNVDWDGNELLLSDVLGTDSDIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGT 197 (234)
T ss_pred HHHHHHhccccCcccccccccCCCCCCcchHHHhcCCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCC
Confidence 99999865421 100 0 00 011234667777665543 14
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 398 YPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
+.|++|||+.||+|+++|+..+++++.
T Consensus 198 g~s~~EIA~~Lgis~~tV~~~l~ra~~ 224 (234)
T TIGR02835 198 EKTQKEVADMLGISQSYISRLEKRILK 224 (234)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 689999999999999999999887763
No 40
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=99.74 E-value=5.5e-17 Score=151.48 Aligned_cols=145 Identities=21% Similarity=0.254 Sum_probs=113.1
Q ss_pred CCCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHH
Q 013472 280 GVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK 358 (442)
Q Consensus 280 g~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRn 358 (442)
.++++.|+..++.|+. |++.|+..|.++|+.+|.+|.++..+++|++||+++++|+++++||+.++.+|.||++.+++|
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 4567788888988976 999999999999999999999999999999999999999999999998777999999999999
Q ss_pred HHHHHHHhhcCceeccc-----------------------------ccH------HHHHHH-HHHHHHHHHH-------c
Q 013472 359 SISKMVARHARGIKIPC-----------------------------KLN------REISKI-QKARKALTNS-------H 395 (442)
Q Consensus 359 aI~r~LRkqsr~irlP~-----------------------------~v~------e~i~kI-~ka~~~L~~e-------l 395 (442)
.+.+++++..+..+.+. ... +....+ ..+...|+.. +
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 99999986433211110 000 011111 1222222222 2
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
-.+.|++|||+.||+|+++|+.++++++.
T Consensus 168 ~e~~s~~EIA~~lgis~~tV~~~l~rar~ 196 (208)
T PRK08295 168 LDGKSYQEIAEELNRHVKSIDNALQRVKR 196 (208)
T ss_pred HccCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 36789999999999999999999988874
No 41
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=99.72 E-value=9.4e-17 Score=149.07 Aligned_cols=142 Identities=18% Similarity=0.143 Sum_probs=116.7
Q ss_pred CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHH
Q 013472 281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (442)
Q Consensus 281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRna 359 (442)
++++.|+..+..|+. |++.|+..|.+.|+++|.++.++..+++|++||+|+++|+++++|++. ..|.+|++++++|.
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 457889999999976 999999999999999999999999999999999999999999999974 36999999999999
Q ss_pred HHHHHHhhcCceeccc------------c--------cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCC
Q 013472 360 ISKMVARHARGIKIPC------------K--------LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLS 411 (442)
Q Consensus 360 I~r~LRkqsr~irlP~------------~--------v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS 411 (442)
+++++|++.+....+. . ..+....+..+...|+.... .+.|++|||+.||||
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 01122346666666665542 567999999999999
Q ss_pred HHHHHHHHHhccc
Q 013472 412 LAEIRSASECLRI 424 (442)
Q Consensus 412 ~etVk~~l~~ar~ 424 (442)
+++|+..+++++.
T Consensus 169 ~~tV~~~l~ra~~ 181 (194)
T PRK12513 169 EETVKSRLRYALQ 181 (194)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999888774
No 42
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=99.72 E-value=8.3e-17 Score=150.03 Aligned_cols=142 Identities=18% Similarity=0.098 Sum_probs=115.4
Q ss_pred CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHH
Q 013472 282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (442)
Q Consensus 282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI 360 (442)
++..|+..+..|+. |+++|+..|.++|+.+|.+|.++..+++|++||+|+++|+++++||+.+| .|.+|++.+++|.+
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 45778888898976 99999999999999999999999999999999999999999999998655 79999999999999
Q ss_pred HHHHHhhcCceec---------cc---cc------HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHH
Q 013472 361 SKMVARHARGIKI---------PC---KL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAE 414 (442)
Q Consensus 361 ~r~LRkqsr~irl---------P~---~v------~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~et 414 (442)
+++++++.+..+. +. .. .+....+..++..|+... ..+.|++|||+.||+|+.+
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 112234556666555443 2678999999999999999
Q ss_pred HHHHHHhccc
Q 013472 415 IRSASECLRI 424 (442)
Q Consensus 415 Vk~~l~~ar~ 424 (442)
|+..+++++.
T Consensus 175 Vk~~l~ra~~ 184 (194)
T PRK09646 175 VKTRMRDGLI 184 (194)
T ss_pred HHHHHHHHHH
Confidence 9999988874
No 43
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=99.72 E-value=1.1e-16 Score=148.65 Aligned_cols=143 Identities=16% Similarity=0.127 Sum_probs=115.5
Q ss_pred CCCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCC---CCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHH
Q 013472 280 GVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLG---IPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYW 355 (442)
Q Consensus 280 g~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g---~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~w 355 (442)
.++++.|+..+..|+. |+++|+..|.+.|+.++.++.+++ .+++|++||+++++|+++++|++..+ .|.||++.+
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 4678889999999976 999999999999999999998853 57999999999999999999997544 799999999
Q ss_pred HHHHHHHHHHhhcCceecc---c-------c------cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCC
Q 013472 356 IRKSISKMVARHARGIKIP---C-------K------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLS 411 (442)
Q Consensus 356 IRnaI~r~LRkqsr~irlP---~-------~------v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS 411 (442)
++|.+++++|++.+..... . . ..+....+.++...|+.+. -.+.|++|||+.||+|
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 9999999999876432211 0 0 0112233556666665543 2678999999999999
Q ss_pred HHHHHHHHHhcc
Q 013472 412 LAEIRSASECLR 423 (442)
Q Consensus 412 ~etVk~~l~~ar 423 (442)
..+|+..+++++
T Consensus 161 ~~~V~~~l~Ra~ 172 (189)
T PRK06811 161 RSAIDNRLSRGR 172 (189)
T ss_pred HHHHHHHHHHHH
Confidence 999999998886
No 44
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=99.70 E-value=2.9e-16 Score=145.25 Aligned_cols=141 Identities=18% Similarity=0.187 Sum_probs=112.6
Q ss_pred HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCC----CCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHH
Q 013472 283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGL----GIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIR 357 (442)
Q Consensus 283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~----g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIR 357 (442)
...|+..+..|+. |+++|+..|.+.|+.+|.++.++ ..+++|++||+|+++|+++.+|++. +..|.||++.+++
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 3567888899966 99999999999999999998765 4689999999999999999999864 4579999999999
Q ss_pred HHHHHHHHhhcCceec-----cc------cc------HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCH
Q 013472 358 KSISKMVARHARGIKI-----PC------KL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSL 412 (442)
Q Consensus 358 naI~r~LRkqsr~irl-----P~------~v------~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~ 412 (442)
|.++++++++.+.... +. .. .+....+.+++..|+... ..+.|++|||+.||+|+
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 9999999987653221 10 00 112234566666665543 26789999999999999
Q ss_pred HHHHHHHHhccc
Q 013472 413 AEIRSASECLRI 424 (442)
Q Consensus 413 etVk~~l~~ar~ 424 (442)
.+|+..+++++.
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=99.70 E-value=2.1e-16 Score=145.30 Aligned_cols=143 Identities=21% Similarity=0.195 Sum_probs=115.4
Q ss_pred CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHH
Q 013472 281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (442)
Q Consensus 281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRna 359 (442)
+++.+|+..++.|+. |++.++..|.+.|+.+|++|.+++.+++|++||+|+++|+++++|++.. ..|.+|++++++|.
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 467888888988976 9999999999999999999999999999999999999999999998754 36999999999999
Q ss_pred HHHHHHhhcCcee-c------c------cc--c---HHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHH
Q 013472 360 ISKMVARHARGIK-I------P------CK--L---NREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLA 413 (442)
Q Consensus 360 I~r~LRkqsr~ir-l------P------~~--v---~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~e 413 (442)
+++++|++.+... + + .. . ......+.++...|+.... .+.+++|||+.||||+.
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 0112336666666655432 67799999999999999
Q ss_pred HHHHHHHhccc
Q 013472 414 EIRSASECLRI 424 (442)
Q Consensus 414 tVk~~l~~ar~ 424 (442)
+|+..+++++.
T Consensus 167 ~V~~~l~ra~~ 177 (186)
T PRK13919 167 TLKTRARRALS 177 (186)
T ss_pred HHHHHHHHHHH
Confidence 99999988874
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=99.70 E-value=2.5e-16 Score=143.00 Aligned_cols=142 Identities=14% Similarity=0.080 Sum_probs=115.7
Q ss_pred CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHH
Q 013472 281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (442)
Q Consensus 281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRna 359 (442)
|+++.|+..+..|+. |++.++..|.+.|+.+|.++.++..+++|++||+++.+|+++++|++.. +|.||++.+++|.
T Consensus 1 ~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~~--~~~~wl~~i~~n~ 78 (169)
T TIGR02954 1 MNDEELVKKAKRGNKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPK--YFNTWLTRILINE 78 (169)
T ss_pred CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCcc--ccHHHHHHHHHHH
Confidence 457788888999966 9999999999999999999999999999999999999999999999753 6999999999999
Q ss_pred HHHHHHhhcCceecccc----------cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHh
Q 013472 360 ISKMVARHARGIKIPCK----------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASEC 421 (442)
Q Consensus 360 I~r~LRkqsr~irlP~~----------v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ 421 (442)
+++++|+..+...++.. ..+....+..+...|+... -.+.|++|||+.||+|+++|+..+.+
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 0111224555555555443 26789999999999999999999988
Q ss_pred ccc
Q 013472 422 LRI 424 (442)
Q Consensus 422 ar~ 424 (442)
++.
T Consensus 159 a~~ 161 (169)
T TIGR02954 159 ALK 161 (169)
T ss_pred HHH
Confidence 874
No 47
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=99.70 E-value=3e-16 Score=145.44 Aligned_cols=144 Identities=15% Similarity=0.109 Sum_probs=117.2
Q ss_pred cCCCHHHHHHHHHh---chH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHH
Q 013472 279 AGVSERVLKQHLAF---GWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQY 354 (442)
Q Consensus 279 ~g~deeeL~~~l~~---G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~ 354 (442)
..++++.|+..++. |+. |++.|+..|.+.|+.+|.+|.++..+++|++||+|+++|+++++|++. .+|.||+++
T Consensus 6 ~~~~~~~li~~~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~~~~~~~~~--~~~~~wl~~ 83 (188)
T PRK09640 6 RELNDEELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGK--SKFKTWLYS 83 (188)
T ss_pred CCCCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHHHhcCC--CcchHHHHH
Confidence 35677888888885 455 999999999999999999999999999999999999999999999963 479999999
Q ss_pred HHHHHHHHHHHhhcCceecc---------c---c---cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCC
Q 013472 355 WIRKSISKMVARHARGIKIP---------C---K---LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLS 411 (442)
Q Consensus 355 wIRnaI~r~LRkqsr~irlP---------~---~---v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS 411 (442)
+++|.+++++|+..+..... . . ..+....+.++...|+.... .+.|++|||+.||||
T Consensus 84 ia~n~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~lgis 163 (188)
T PRK09640 84 ITYNECITQYRKERRKRRLMDALSLDPLEEASEEKAPKPEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMG 163 (188)
T ss_pred HHHHHHHHHHHHhcccccCcchhhhcccccccccccccHHHHHHHHHHHHhcChhheeeeeeHHhcCCCHHHHHHHHCCC
Confidence 99999999999764322111 0 0 11233457777777766542 567999999999999
Q ss_pred HHHHHHHHHhccc
Q 013472 412 LAEIRSASECLRI 424 (442)
Q Consensus 412 ~etVk~~l~~ar~ 424 (442)
+++|+..+.+++.
T Consensus 164 ~~tV~~~l~Ra~~ 176 (188)
T PRK09640 164 LSATKMRYKRALD 176 (188)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999988874
No 48
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=99.70 E-value=2.1e-16 Score=144.70 Aligned_cols=142 Identities=14% Similarity=0.054 Sum_probs=114.4
Q ss_pred CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHH
Q 013472 282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (442)
Q Consensus 282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI 360 (442)
+...|+..+..|+. |++.|+..|.+.|+.+|.++.++..+++|++||+|+++|+++++|++.. ..|.||++.+++|.+
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 45678888888866 9999999999999999999999999999999999999999999999654 369999999999999
Q ss_pred HHHHHhhcCce-ec------cc------cc---HHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHH
Q 013472 361 SKMVARHARGI-KI------PC------KL---NREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIR 416 (442)
Q Consensus 361 ~r~LRkqsr~i-rl------P~------~v---~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk 416 (442)
++++|++.+.. .+ +. .. .+....+..+...|+.... .+.|++|||+.||||+.+|+
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 99999865421 00 00 00 1122345566666654432 67899999999999999999
Q ss_pred HHHHhccc
Q 013472 417 SASECLRI 424 (442)
Q Consensus 417 ~~l~~ar~ 424 (442)
..+++++.
T Consensus 164 ~~l~Rar~ 171 (179)
T PRK12514 164 TWLRRSLL 171 (179)
T ss_pred HHHHHHHH
Confidence 99998874
No 49
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=99.69 E-value=2.9e-16 Score=144.81 Aligned_cols=143 Identities=16% Similarity=0.103 Sum_probs=116.3
Q ss_pred CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHH
Q 013472 281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (442)
Q Consensus 281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRna 359 (442)
++..+|+..+..|+. |++.|+..|.+.|+.++.++.++..+++|++||+|+.+|+.+++|++.. ..|.+|++.+++|.
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 355678999999966 9999999999999999999999999999999999999999999998643 37999999999999
Q ss_pred HHHHHHhhcCceeccc----------c------cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHH
Q 013472 360 ISKMVARHARGIKIPC----------K------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEI 415 (442)
Q Consensus 360 I~r~LRkqsr~irlP~----------~------v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etV 415 (442)
++++++++.+...... . ..+....+.++...|+... -.+.+++|||+.||||+++|
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 0112334666666655543 26789999999999999999
Q ss_pred HHHHHhccc
Q 013472 416 RSASECLRI 424 (442)
Q Consensus 416 k~~l~~ar~ 424 (442)
+..+++++.
T Consensus 167 ~~~l~ra~~ 175 (182)
T PRK12537 167 KAWIKRSLK 175 (182)
T ss_pred HHHHHHHHH
Confidence 999998874
No 50
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=99.69 E-value=3.7e-16 Score=145.83 Aligned_cols=144 Identities=17% Similarity=0.137 Sum_probs=116.8
Q ss_pred CCCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHH
Q 013472 280 GVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK 358 (442)
Q Consensus 280 g~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRn 358 (442)
.+++..|+.++..|+. |++.|+..|.+.|+.+|.++.++..+++|++||+++++|+.+.+|++.. ..|.||++.+++|
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 4567889999999966 9999999999999999999999999999999999999999999998533 4799999999999
Q ss_pred HHHHHHHhhcCce-ec---c------c---c---cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHH
Q 013472 359 SISKMVARHARGI-KI---P------C---K---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAE 414 (442)
Q Consensus 359 aI~r~LRkqsr~i-rl---P------~---~---v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~et 414 (442)
.+++++|++.+.. .+ + . . ..+....+.++...|+... -.+.+++|||+.||+|+.+
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 9999999764421 11 0 0 0 0112234666666665543 3678999999999999999
Q ss_pred HHHHHHhccc
Q 013472 415 IRSASECLRI 424 (442)
Q Consensus 415 Vk~~l~~ar~ 424 (442)
|+..+++++.
T Consensus 169 V~~~l~Ra~~ 178 (196)
T PRK12524 169 VESLTARGKR 178 (196)
T ss_pred HHHHHHHHHH
Confidence 9999998874
No 51
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=99.69 E-value=4.7e-16 Score=141.62 Aligned_cols=143 Identities=16% Similarity=0.048 Sum_probs=116.6
Q ss_pred CCCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHH
Q 013472 280 GVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK 358 (442)
Q Consensus 280 g~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRn 358 (442)
.|++..++..+..|+. |++.|+..|.+.|+.+|++|.++..+++|++||+|+++|++++.|++. .+|.+|++.+++|
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 4567888899999976 999999999999999999999999999999999999999999999874 4799999999999
Q ss_pred HHHHHHHhhcCceeccc-------c-c-------HHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHH
Q 013472 359 SISKMVARHARGIKIPC-------K-L-------NREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEI 415 (442)
Q Consensus 359 aI~r~LRkqsr~irlP~-------~-v-------~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etV 415 (442)
.+++++++.++...... . . ......+.++...|+.... .+.+++|||+.||+|+.+|
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 1123345556666655442 5679999999999999999
Q ss_pred HHHHHhccc
Q 013472 416 RSASECLRI 424 (442)
Q Consensus 416 k~~l~~ar~ 424 (442)
+..+.+++.
T Consensus 160 ~~~l~ra~~ 168 (176)
T PRK09638 160 KSRVHHGIK 168 (176)
T ss_pred HHHHHHHHH
Confidence 999988874
No 52
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=99.69 E-value=4.4e-16 Score=142.70 Aligned_cols=140 Identities=14% Similarity=0.069 Sum_probs=112.3
Q ss_pred HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHH
Q 013472 283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS 361 (442)
Q Consensus 283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~ 361 (442)
++.|+..++.|+. |+++|+..|.+.|+.+|.+|.+++.+++|++||+|+++|+++.+|++.. .|.||++.+++|.+.
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 4567888999976 9999999999999999999999999999999999999999999999865 599999999999999
Q ss_pred HHHHhhcCceeccc-------------------cc------HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHh
Q 013472 362 KMVARHARGIKIPC-------------------KL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYT 408 (442)
Q Consensus 362 r~LRkqsr~irlP~-------------------~v------~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~L 408 (442)
+++|+..+...... .. .+....+.++...|+... -.+.|++|||+.|
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 99998654211000 00 011223555555554433 2567999999999
Q ss_pred CCCHHHHHHHHHhccc
Q 013472 409 GLSLAEIRSASECLRI 424 (442)
Q Consensus 409 GIS~etVk~~l~~ar~ 424 (442)
|+|+.+|+..+++++.
T Consensus 163 gis~~~v~~~l~Rar~ 178 (187)
T TIGR02948 163 DLPVGTVKTRIHRGRE 178 (187)
T ss_pred CCCHHHHHHHHHHHHH
Confidence 9999999999998874
No 53
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=99.69 E-value=3.9e-16 Score=139.00 Aligned_cols=128 Identities=16% Similarity=0.146 Sum_probs=103.4
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCc----
Q 013472 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG---- 370 (442)
Q Consensus 295 ~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~---- 370 (442)
.|+++|+..|.++|+.+++++ +...++||++|||++++|+++++|++..| .|.+|++.+++|.+++++|++.+.
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 799999999999999999987431
Q ss_pred --eecccc---cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 371 --IKIPCK---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 371 --irlP~~---v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
...|.. ..+....+..+...|+... ..+.|++|||+.||+|+++|+..+.+++.
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 1223345666666665443 37789999999999999999999988764
No 54
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=99.68 E-value=5.6e-16 Score=144.55 Aligned_cols=142 Identities=16% Similarity=0.117 Sum_probs=117.4
Q ss_pred CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHH
Q 013472 281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (442)
Q Consensus 281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRna 359 (442)
+++..++..+..|+. +++.++..|.+.|++++.++.++..++||++||+|+.+|+++++|++.. .|.+|++.+++|.
T Consensus 12 ~~~~~l~~~~~~gd~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~~--~f~~wL~~i~rn~ 89 (192)
T PRK09643 12 RSDAELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDA--AVSSWLHRIVVNA 89 (192)
T ss_pred cCHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCCC--ccHHHHHHHHHHH
Confidence 467888999999976 9999999999999999999999999999999999999999999999753 6999999999999
Q ss_pred HHHHHHhhcCceecc-----------cc---cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHH
Q 013472 360 ISKMVARHARGIKIP-----------CK---LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRS 417 (442)
Q Consensus 360 I~r~LRkqsr~irlP-----------~~---v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~ 417 (442)
+++++|+.++....+ .. ..+....+..+...|+.... .+.+++|||+.||+|+.+|+.
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 11233456677777665442 678999999999999999999
Q ss_pred HHHhccc
Q 013472 418 ASECLRI 424 (442)
Q Consensus 418 ~l~~ar~ 424 (442)
.+.+++.
T Consensus 170 rl~rar~ 176 (192)
T PRK09643 170 RCARGRA 176 (192)
T ss_pred HHHHHHH
Confidence 9988874
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=99.68 E-value=5.4e-16 Score=139.78 Aligned_cols=137 Identities=15% Similarity=0.067 Sum_probs=109.7
Q ss_pred HHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHH
Q 013472 287 KQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVA 365 (442)
Q Consensus 287 ~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LR 365 (442)
+..+.+|+. |++.|+..|.+.++.++.++.++..+++|++||+|+++|+++++|+...+ .|.+|++.+++|.+++++|
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 456777866 99999999999999999999999999999999999999999999997544 7999999999999999999
Q ss_pred hhcCceeccc-----------cc------HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHH
Q 013472 366 RHARGIKIPC-----------KL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASE 420 (442)
Q Consensus 366 kqsr~irlP~-----------~v------~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~ 420 (442)
++.+....+. .. .+....+.++...|+... -.+.+++|||+.||||+.+|+..++
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 8754322110 00 112234555555555433 3678999999999999999999998
Q ss_pred hccc
Q 013472 421 CLRI 424 (442)
Q Consensus 421 ~ar~ 424 (442)
+++.
T Consensus 161 ra~~ 164 (170)
T TIGR02952 161 RAIK 164 (170)
T ss_pred HHHH
Confidence 8764
No 56
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=99.68 E-value=5.1e-16 Score=142.23 Aligned_cols=142 Identities=15% Similarity=0.086 Sum_probs=114.3
Q ss_pred CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHH
Q 013472 281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (442)
Q Consensus 281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRna 359 (442)
...+.|+..++.|+. |++.++..|.++|+.+|+++.++..+++|++||++++||+++++|++.. +|.+|++.+++|.
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 345678888999976 9999999999999999999999999999999999999999999999753 6999999999999
Q ss_pred HHHHHHhhcCceec----------------ccc---c------HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHH
Q 013472 360 ISKMVARHARGIKI----------------PCK---L------NREISKIQKARKALTNSH--------GKYPEDIEIAK 406 (442)
Q Consensus 360 I~r~LRkqsr~irl----------------P~~---v------~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe 406 (442)
+++++|++++...+ +.. . .+....+.++...|+... -.+.+++|||+
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 99999987543211 000 0 111223555555554433 26779999999
Q ss_pred HhCCCHHHHHHHHHhccc
Q 013472 407 YTGLSLAEIRSASECLRI 424 (442)
Q Consensus 407 ~LGIS~etVk~~l~~ar~ 424 (442)
.||||+++|+..+++++.
T Consensus 161 ~lgis~~~v~~~l~Rar~ 178 (187)
T PRK09641 161 ILDLPVGTVKTRIHRGRE 178 (187)
T ss_pred HHCCCHHHHHHHHHHHHH
Confidence 999999999999988874
No 57
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=99.67 E-value=5.5e-16 Score=142.93 Aligned_cols=142 Identities=15% Similarity=0.034 Sum_probs=114.3
Q ss_pred CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHH
Q 013472 282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (442)
Q Consensus 282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI 360 (442)
+...++..+..|+. +++.|+..|.+.|+.+|+++.++..++||++||+|+++|+++++|++.++ .|.||++.+++|.+
T Consensus 11 ~~~~l~~~~~~~~~~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~~n~~ 89 (187)
T PRK12534 11 ETGRLLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIARNKA 89 (187)
T ss_pred hHHHHHHHHHcCCHHHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHH
Confidence 34567777778865 99999999999999999999999999999999999999999999998654 68999999999999
Q ss_pred HHHHHhhcCce-e-----ccc---------c---cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHH
Q 013472 361 SKMVARHARGI-K-----IPC---------K---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAE 414 (442)
Q Consensus 361 ~r~LRkqsr~i-r-----lP~---------~---v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~et 414 (442)
++++|++.+.. . .+. . ..+....+..++..|+... -.+.+++|||+.||||+++
T Consensus 90 ~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~~ 169 (187)
T PRK12534 90 IDHLRANAPQRRNVALDDAGELRAADASPLERTERASTRRRIDHCLAELEPPRSELIRTAFFEGITYEELAARTDTPIGT 169 (187)
T ss_pred HHHHHhcccccccccccchhhhccccCChhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCChhH
Confidence 99999865321 0 110 0 1122345666666665543 2678999999999999999
Q ss_pred HHHHHHhccc
Q 013472 415 IRSASECLRI 424 (442)
Q Consensus 415 Vk~~l~~ar~ 424 (442)
|+..+++++.
T Consensus 170 v~~~l~Rar~ 179 (187)
T PRK12534 170 VKSWIRRGLA 179 (187)
T ss_pred HHHHHHHHHH
Confidence 9999998874
No 58
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=99.67 E-value=6e-16 Score=144.25 Aligned_cols=141 Identities=14% Similarity=0.058 Sum_probs=112.9
Q ss_pred HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHH
Q 013472 283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS 361 (442)
Q Consensus 283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~ 361 (442)
..+|+..+..|+. |++.|+..|.+.|+.+|.++.++..+++|++||+|+.+|+...+|++..+ .|.||++.+++|.++
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 3457888888976 99999999999999999999999999999999999999999999997544 699999999999999
Q ss_pred HHHHhhcCcee-c------cc---------c-cH---HHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHH
Q 013472 362 KMVARHARGIK-I------PC---------K-LN---REISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLA 413 (442)
Q Consensus 362 r~LRkqsr~ir-l------P~---------~-v~---e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~e 413 (442)
+++|++++... . +. . .. .....+.++...|+.+.. .+.+++|||+.||||++
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 112345556666555432 57799999999999999
Q ss_pred HHHHHHHhccc
Q 013472 414 EIRSASECLRI 424 (442)
Q Consensus 414 tVk~~l~~ar~ 424 (442)
+|+..+++++.
T Consensus 173 tVk~rl~ra~~ 183 (194)
T PRK12531 173 TVKSRLRLAVE 183 (194)
T ss_pred HHHHHHHHHHH
Confidence 99999988874
No 59
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=99.67 E-value=8.8e-16 Score=148.55 Aligned_cols=143 Identities=18% Similarity=0.133 Sum_probs=115.7
Q ss_pred CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHH
Q 013472 281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (442)
Q Consensus 281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRna 359 (442)
.++.+|+..++.|+. |++.|+..|.+.|+.+++++.++..++||++||+|+++|+.+++|++..+ .|.+|++.+++|.
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 456788888999976 99999999999999999999999999999999999999999999986544 7999999999999
Q ss_pred HHHHHHhhcCce--ec-------ccc-----cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHH
Q 013472 360 ISKMVARHARGI--KI-------PCK-----LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRS 417 (442)
Q Consensus 360 I~r~LRkqsr~i--rl-------P~~-----v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~ 417 (442)
+++++|++.+.. .. |.. ..+....+..+...|+.... .+.|++|||+.||+|+++|+.
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 999999764321 11 110 01122346666666655432 677999999999999999999
Q ss_pred HHHhccc
Q 013472 418 ASECLRI 424 (442)
Q Consensus 418 ~l~~ar~ 424 (442)
.+++++.
T Consensus 207 ~l~RAr~ 213 (233)
T PRK12538 207 LLKRGRQ 213 (233)
T ss_pred HHHHHHH
Confidence 9988874
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=99.67 E-value=1.6e-15 Score=139.38 Aligned_cols=142 Identities=15% Similarity=0.087 Sum_probs=114.0
Q ss_pred CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHH
Q 013472 281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (442)
Q Consensus 281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRna 359 (442)
.++..|+..+..|+. |++.|+..|.+.|+.+|+++.++..+++|++||+|+++|+++.+|++. .+|.+|++.+++|.
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 356778889999976 999999999999999999999999999999999999999999999975 36999999999999
Q ss_pred HHHHHHhhcCceecc----------------------cc---cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHH
Q 013472 360 ISKMVARHARGIKIP----------------------CK---LNREISKIQKARKALTNSHG--------KYPEDIEIAK 406 (442)
Q Consensus 360 I~r~LRkqsr~irlP----------------------~~---v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe 406 (442)
++++++++.+..... .. ..+....+..+...|+.... .+.+++|||+
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 999998654422110 00 00112235556666655432 5679999999
Q ss_pred HhCCCHHHHHHHHHhccc
Q 013472 407 YTGLSLAEIRSASECLRI 424 (442)
Q Consensus 407 ~LGIS~etVk~~l~~ar~ 424 (442)
.||||+.+|+..+++++.
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=99.66 E-value=1.2e-15 Score=141.36 Aligned_cols=141 Identities=21% Similarity=0.193 Sum_probs=112.8
Q ss_pred CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHH
Q 013472 282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (442)
Q Consensus 282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI 360 (442)
++.+|+..+..|+. |++.|+..|.+.|+.+++++.++..+++|++||+|+++|+. ..|++..+ .|.||++.+++|.+
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 56788888999976 99999999999999999999999999999999999999976 67887554 79999999999999
Q ss_pred HHHHHhhcCceecc------------c-c------cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHH
Q 013472 361 SKMVARHARGIKIP------------C-K------LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLA 413 (442)
Q Consensus 361 ~r~LRkqsr~irlP------------~-~------v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~e 413 (442)
++++|++.+..... . . ..+....+..+...|+.+.. .+.++.|||+.||+|+.
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 99999865421110 0 0 01122345666666655442 57799999999999999
Q ss_pred HHHHHHHhccc
Q 013472 414 EIRSASECLRI 424 (442)
Q Consensus 414 tVk~~l~~ar~ 424 (442)
+|+..+++++.
T Consensus 173 tV~~~l~Ra~~ 183 (194)
T PRK12519 173 TVKARARQGLL 183 (194)
T ss_pred HHHHHHHHHHH
Confidence 99999888764
No 62
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=99.66 E-value=9.3e-16 Score=144.75 Aligned_cols=140 Identities=14% Similarity=0.073 Sum_probs=111.0
Q ss_pred HHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHH
Q 013472 284 RVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISK 362 (442)
Q Consensus 284 eeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r 362 (442)
..|...+..|+. |+++|+..|.+.|+.++.++.++..+++|++||+|+.+|+++.+|++.++ .|.||++.+++|.+++
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 345666777866 99999999999999999999999999999999999999999999997655 5999999999999999
Q ss_pred HHHhhcCceec-------cc-------c-c-HH-----HHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHH
Q 013472 363 MVARHARGIKI-------PC-------K-L-NR-----EISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLA 413 (442)
Q Consensus 363 ~LRkqsr~irl-------P~-------~-v-~e-----~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~e 413 (442)
++|++.+.... |. . . .+ ....+.+++..|+.+. ..+.|++|||+.||+|+.
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 99986532110 10 0 0 00 1123555555555443 367899999999999999
Q ss_pred HHHHHHHhccc
Q 013472 414 EIRSASECLRI 424 (442)
Q Consensus 414 tVk~~l~~ar~ 424 (442)
+|+..+++++.
T Consensus 185 tV~~~l~Ra~~ 195 (206)
T PRK12526 185 TVKSRLRLALA 195 (206)
T ss_pred HHHHHHHHHHH
Confidence 99999998875
No 63
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=99.66 E-value=2.1e-15 Score=138.93 Aligned_cols=140 Identities=15% Similarity=0.075 Sum_probs=111.9
Q ss_pred HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhC-CCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHH
Q 013472 283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRG-LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (442)
Q Consensus 283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g-~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI 360 (442)
...++..+..|+. |++.++..|.+.|+.++.++.+ ...+++|++||+|+++|+.++.|++. ..|.+|++.+++|.+
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 4567788888876 9999999999999999998764 57899999999999999999999974 369999999999999
Q ss_pred HHHHHhhcCceecc--------------cccHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHH
Q 013472 361 SKMVARHARGIKIP--------------CKLNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSA 418 (442)
Q Consensus 361 ~r~LRkqsr~irlP--------------~~v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~ 418 (442)
++++|++.+..... ....+....+.+++..|+.... .+.|++|||+.||||+++|+..
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 0112233346666666655332 6779999999999999999999
Q ss_pred HHhccc
Q 013472 419 SECLRI 424 (442)
Q Consensus 419 l~~ar~ 424 (442)
+++++.
T Consensus 166 l~rar~ 171 (181)
T PRK12536 166 IHRGLK 171 (181)
T ss_pred HHHHHH
Confidence 998874
No 64
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=99.65 E-value=2.4e-15 Score=144.40 Aligned_cols=141 Identities=16% Similarity=0.136 Sum_probs=115.8
Q ss_pred CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHH
Q 013472 281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (442)
Q Consensus 281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRna 359 (442)
++++.|+..+..|+. |++.|+..|.+.|+.+|.++.+.+.+++|++||+|+++|+++++|++. ..|.||++.+++|.
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 456778888888866 999999999999999999999999999999999999999999999985 37999999999999
Q ss_pred HHHHHHhhcCceeccc------------------c--------cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHH
Q 013472 360 ISKMVARHARGIKIPC------------------K--------LNREISKIQKARKALTNSHG--------KYPEDIEIA 405 (442)
Q Consensus 360 I~r~LRkqsr~irlP~------------------~--------v~e~i~kI~ka~~~L~~elg--------r~PS~eEIA 405 (442)
+++++|+..+...++. . ..+....+.+++..|+.... .+.|++|||
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 9999998765322210 0 01122346666666665542 567999999
Q ss_pred HHhCCCHHHHHHHHHhcc
Q 013472 406 KYTGLSLAEIRSASECLR 423 (442)
Q Consensus 406 e~LGIS~etVk~~l~~ar 423 (442)
+.||+|+++|+..+++++
T Consensus 173 e~lgis~~tVk~~l~Rar 190 (231)
T PRK11922 173 QALGLPEETVKTRLHRAR 190 (231)
T ss_pred HHHCcCHHHHHHHHHHHH
Confidence 999999999999988876
No 65
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=99.65 E-value=2.5e-15 Score=138.81 Aligned_cols=141 Identities=11% Similarity=0.059 Sum_probs=113.5
Q ss_pred CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHH----HhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHH
Q 013472 282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLAR----NYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI 356 (442)
Q Consensus 282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAk----rY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wI 356 (442)
+...|+..++.|+. |++.|+..|.+.|+.+|+ ++.++..+++|++||+++.+|++++.|++.. .|.+|++.++
T Consensus 7 ~~~~l~~~~~~gd~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~--~f~~wl~~i~ 84 (184)
T PRK12539 7 ELKALMLASLDGDAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTPWVYAIA 84 (184)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCCC--ChHHHHHHHH
Confidence 35678888888976 999999999999999987 5557889999999999999999999999753 6999999999
Q ss_pred HHHHHHHHHhhcCc-eecc---------c---ccHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHH
Q 013472 357 RKSISKMVARHARG-IKIP---------C---KLNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEI 415 (442)
Q Consensus 357 RnaI~r~LRkqsr~-irlP---------~---~v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etV 415 (442)
+|.+++++|+..+. ...+ . ...+....+..+...|++... .+.+++|||+.||+|+++|
T Consensus 85 ~n~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV 164 (184)
T PRK12539 85 RYKLIDHLRRTRASLADVPIDDADELVAHDDHAAVESTLDLGRLLARLPEKMRLAIQAVKLEGLSVAEAATRSGMSESAV 164 (184)
T ss_pred HHHHHHHHHHHhccccccChhhhccccCCcHHhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCcHHHHHHHHCcCHHHH
Confidence 99999999986542 1111 0 012334456777776665542 6789999999999999999
Q ss_pred HHHHHhccc
Q 013472 416 RSASECLRI 424 (442)
Q Consensus 416 k~~l~~ar~ 424 (442)
+..+++++.
T Consensus 165 ~~~l~ra~~ 173 (184)
T PRK12539 165 KVSVHRGLK 173 (184)
T ss_pred HHHHHHHHH
Confidence 999988874
No 66
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=99.65 E-value=2.9e-15 Score=138.78 Aligned_cols=141 Identities=12% Similarity=0.073 Sum_probs=112.5
Q ss_pred CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHH
Q 013472 282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (442)
Q Consensus 282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI 360 (442)
+++.|+..++.|+. |++.|+..|.+.|+.+++++.++..+++|++||+|+++|+++.+|++.. .|.+|++.+++|.+
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 45678888899976 9999999999999999999999999999999999999999999999864 59999999999999
Q ss_pred HHHHHhhcCcee---ccc-------------c---------cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHH
Q 013472 361 SKMVARHARGIK---IPC-------------K---------LNREISKIQKARKALTNSHG--------KYPEDIEIAKY 407 (442)
Q Consensus 361 ~r~LRkqsr~ir---lP~-------------~---------v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~ 407 (442)
+++++++.+... .+. . ..+....+..+...|+.+.. .+.+++|||+.
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 999987644211 000 0 00112235555555554432 56799999999
Q ss_pred hCCCHHHHHHHHHhccc
Q 013472 408 TGLSLAEIRSASECLRI 424 (442)
Q Consensus 408 LGIS~etVk~~l~~ar~ 424 (442)
||+|+.+|+..+.+++.
T Consensus 164 lgis~~tv~~~l~Rar~ 180 (193)
T PRK11923 164 MQCPVGTVRSRIFRARE 180 (193)
T ss_pred HCCCHHHHHHHHHHHHH
Confidence 99999999999988874
No 67
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=99.65 E-value=4.1e-16 Score=143.96 Aligned_cols=134 Identities=16% Similarity=0.108 Sum_probs=107.4
Q ss_pred HhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcC
Q 013472 291 AFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (442)
Q Consensus 291 ~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr 369 (442)
..|+. |++.|+..|.+.|+.+|.+++++..+++|++||+|+.+|+++++|+...+..|.||++.+++|.+++++|++.+
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 35654 99999999999999999999999999999999999999999999986544579999999999999999998754
Q ss_pred ceecc------------ccc------HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 370 GIKIP------------CKL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 370 ~irlP------------~~v------~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
..... ... .+....+.+++..|+... -.+.|++|||+.||+|+++|+..+.+++
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 32110 000 011234666666665543 2678999999999999999999999887
Q ss_pred c
Q 013472 424 I 424 (442)
Q Consensus 424 ~ 424 (442)
.
T Consensus 164 ~ 164 (185)
T PRK12542 164 K 164 (185)
T ss_pred H
Confidence 5
No 68
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=99.64 E-value=1.6e-15 Score=137.19 Aligned_cols=134 Identities=17% Similarity=0.118 Sum_probs=106.3
Q ss_pred HHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhh
Q 013472 289 HLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARH 367 (442)
Q Consensus 289 ~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkq 367 (442)
+++.|+. |+++|+..|.++|+.++++|.+++.+++|++||++++||+++++|+ .+.+|.||++.++++.+.+++++.
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 4677866 9999999999999999999999999999999999999999999999 345899999999999999999976
Q ss_pred cCceecc-------c---------c---c------HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHH
Q 013472 368 ARGIKIP-------C---------K---L------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAE 414 (442)
Q Consensus 368 sr~irlP-------~---------~---v------~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~et 414 (442)
.+....+ . . . .+....+..+...|+... ..+.+++|||+.||||+.+
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~t 160 (182)
T PRK09652 81 GRRPPASDVDAEEAEDFDLADALRDISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGT 160 (182)
T ss_pred cCCCCccccccccccccccccccccccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHH
Confidence 5432211 0 0 0 012334455555444332 2677999999999999999
Q ss_pred HHHHHHhccc
Q 013472 415 IRSASECLRI 424 (442)
Q Consensus 415 Vk~~l~~ar~ 424 (442)
|+..+++++.
T Consensus 161 V~~~l~ra~~ 170 (182)
T PRK09652 161 VRSRIFRARE 170 (182)
T ss_pred HHHHHHHHHH
Confidence 9999887764
No 69
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=99.64 E-value=3.9e-15 Score=137.88 Aligned_cols=143 Identities=13% Similarity=0.073 Sum_probs=115.4
Q ss_pred CCCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHH
Q 013472 280 GVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK 358 (442)
Q Consensus 280 g~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRn 358 (442)
.+++.+|+..+..|+. |++.|+..|.+.|+.++.++.++..+++|++||+|+.+|++.++|++. ..|.||++.+++|
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 3577889999999976 999999999999999999999999999999999999999999999974 3799999999999
Q ss_pred HHHHHHHhhcCceec-------ccc---c------HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHH
Q 013472 359 SISKMVARHARGIKI-------PCK---L------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAE 414 (442)
Q Consensus 359 aI~r~LRkqsr~irl-------P~~---v------~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~et 414 (442)
.++++++++.+.... +.. . .+....+.++...|+.+. -.+.+++|||+.||+|+.+
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 000 0 011223555555555443 2678999999999999999
Q ss_pred HHHHHHhccc
Q 013472 415 IRSASECLRI 424 (442)
Q Consensus 415 Vk~~l~~ar~ 424 (442)
|+..+.+++.
T Consensus 164 V~~~l~Rar~ 173 (189)
T PRK12515 164 VKTRMFYARK 173 (189)
T ss_pred HHHHHHHHHH
Confidence 9999998874
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=99.63 E-value=3.4e-15 Score=136.76 Aligned_cols=140 Identities=16% Similarity=0.145 Sum_probs=109.0
Q ss_pred HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCC-----CHHhHHHHHHHHHHH-hHHhcCCCCCCChHHHHHHH
Q 013472 283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGI-----PFSDLLQAGNVGVLQ-GAERFDHTRGYKFSTYVQYW 355 (442)
Q Consensus 283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~-----d~EDLIQEG~IGLir-AieKFDp~kG~rFSTYa~~w 355 (442)
...|+..+..|+. |++.|+..|.+.|+.+|++|.++.. +++|++||+|+.+|+ ...+|++. ..|.||++.+
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 4567888888976 9999999999999999999999877 899999999999998 78889764 3699999999
Q ss_pred HHHHHHHHHHhhcCcee------c------cc---ccHHHHHHHHHHHHH---HHHHc--------CCCCcHHHHHHHhC
Q 013472 356 IRKSISKMVARHARGIK------I------PC---KLNREISKIQKARKA---LTNSH--------GKYPEDIEIAKYTG 409 (442)
Q Consensus 356 IRnaI~r~LRkqsr~ir------l------P~---~v~e~i~kI~ka~~~---L~~el--------gr~PS~eEIAe~LG 409 (442)
++|.+++++|++.+..+ . |. ...+....+..+... |+... -.+.|++|||+.||
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 99999999997543211 0 11 011222223333333 44443 26789999999999
Q ss_pred CCHHHHHHHHHhccc
Q 013472 410 LSLAEIRSASECLRI 424 (442)
Q Consensus 410 IS~etVk~~l~~ar~ 424 (442)
||+++|+..+++++.
T Consensus 162 is~~tVk~~l~Rar~ 176 (183)
T TIGR02999 162 VSVRTVERDWRFARA 176 (183)
T ss_pred CCHHHHHHHHHHHHH
Confidence 999999999998874
No 71
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=99.63 E-value=4.2e-15 Score=145.00 Aligned_cols=145 Identities=12% Similarity=-0.019 Sum_probs=116.9
Q ss_pred HcCCCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHH-------hHHhcCCCCCCChH
Q 013472 278 AAGVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQ-------GAERFDHTRGYKFS 349 (442)
Q Consensus 278 a~g~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLir-------AieKFDp~kG~rFS 349 (442)
.++.++..|+..++.|+. |++.|+..|.+.|+.++.++.++..++||++||+|+.+|. .+.+|++. ..|.
T Consensus 21 ~~~~~d~~Li~~~~~gd~~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~--~~~~ 98 (244)
T TIGR03001 21 QLHAADLYLACACAQGEPAALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGR--GPLL 98 (244)
T ss_pred cccccHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccchhhhhhccCCC--CchH
Confidence 345678889999999976 9999999999999999999999999999999999999994 78889864 3699
Q ss_pred HHHHHHHHHHHHHHHHhhcCceeccc---------c--c-H----------HHHHHHHHHHHHHHHHcC--------CCC
Q 013472 350 TYVQYWIRKSISKMVARHARGIKIPC---------K--L-N----------REISKIQKARKALTNSHG--------KYP 399 (442)
Q Consensus 350 TYa~~wIRnaI~r~LRkqsr~irlP~---------~--v-~----------e~i~kI~ka~~~L~~elg--------r~P 399 (442)
||++.+++|.++++++++.+...+.. . . . +....|.+++.+|+.... .+.
T Consensus 99 tWL~~Ia~N~~id~lRk~~r~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~e~~~~l~~aL~~Lp~~~R~v~~L~~~eg~ 178 (244)
T TIGR03001 99 SWVRIVATRIALELQAQERRHSPVEEPTELAALPAPGSDPELDLLRERYRQDFRQALREALAALSERERHLLRLHFVDGL 178 (244)
T ss_pred hHHHHHHHHHHHHHHHHhcccCccccccccccccCCCCCHHHHHHHHhhHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC
Confidence 99999999999999997654322110 0 0 0 122346677777766542 678
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 400 EDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 400 S~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
|++|||+.||||+++|+..+++++.
T Consensus 179 S~~EIA~~Lgis~~TVk~rl~RAr~ 203 (244)
T TIGR03001 179 SMDRIGAMYQVHRSTVSRWVAQARE 203 (244)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 9999999999999999999887763
No 72
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=99.63 E-value=4.2e-15 Score=137.92 Aligned_cols=140 Identities=18% Similarity=0.102 Sum_probs=113.2
Q ss_pred HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHH
Q 013472 283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS 361 (442)
Q Consensus 283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~ 361 (442)
...|+.++..|+. |++.|+..|.+.|+.++. +.++..+++|++||.|+.+|+..++|++. ..|.+|++.+++|.++
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 3567888888976 999999999999999995 67888999999999999999999999964 3699999999999999
Q ss_pred HHHHhhcCceec-----ccc---------cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHH
Q 013472 362 KMVARHARGIKI-----PCK---------LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSAS 419 (442)
Q Consensus 362 r~LRkqsr~irl-----P~~---------v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l 419 (442)
+++|++.+.... +.. ..+....+.+++..|+.... .+.|++|||+.||+|+++|+..+
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 01223456677777766543 67799999999999999999999
Q ss_pred HhcccC
Q 013472 420 ECLRIV 425 (442)
Q Consensus 420 ~~ar~~ 425 (442)
++++..
T Consensus 168 ~Rar~~ 173 (185)
T PRK09649 168 ARARDA 173 (185)
T ss_pred HHHHHH
Confidence 998863
No 73
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=99.62 E-value=1.1e-14 Score=134.37 Aligned_cols=134 Identities=20% Similarity=0.199 Sum_probs=110.9
Q ss_pred HHHhc-hHHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhh
Q 013472 289 HLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARH 367 (442)
Q Consensus 289 ~l~~G-~~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkq 367 (442)
....| ..+++.++..|.+.++.+|++++++..++|||+||+|+.+|+++..| .. +..|.||++.+++|.++|++|+.
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~-~~~~~~wl~~Ia~n~~iD~~R~~ 85 (182)
T COG1595 8 EALRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RG-RSSFKAWLYRIARNLAIDRLRKR 85 (182)
T ss_pred HHHhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CC-CCchHHHHHHHHHHHHHHHHHHh
Confidence 33344 45999999999999999999999998899999999999999999999 33 34799999999999999999987
Q ss_pred cCceec-c-------------ccc-----HHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHH
Q 013472 368 ARGIKI-P-------------CKL-----NREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASE 420 (442)
Q Consensus 368 sr~irl-P-------------~~v-----~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~ 420 (442)
++.... + ... .+....+.++...|+.... .+.|++|||+.||||+++|+..++
T Consensus 86 ~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~~~gls~~EIA~~l~i~~~tVks~l~ 165 (182)
T COG1595 86 KRRRARVEEADLLPEEADPAPDLAELLLAEEELERLRRALARLPPRQREAFLLRYLEGLSYEEIAEILGISVGTVKSRLH 165 (182)
T ss_pred cccccccccccccccccCcccccchHHHHHHHHHHHHHHHHhCCHHHhHHhhhHhhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 653321 0 101 2344568888888877764 678999999999999999999999
Q ss_pred hccc
Q 013472 421 CLRI 424 (442)
Q Consensus 421 ~ar~ 424 (442)
+++.
T Consensus 166 ra~~ 169 (182)
T COG1595 166 RARK 169 (182)
T ss_pred HHHH
Confidence 8874
No 74
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=99.61 E-value=1.4e-14 Score=133.28 Aligned_cols=139 Identities=15% Similarity=0.094 Sum_probs=110.6
Q ss_pred HHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhC----CCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHH
Q 013472 284 RVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRG----LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK 358 (442)
Q Consensus 284 eeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g----~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRn 358 (442)
..|+..+..|+. |+++|+..|.+.|+.+|+++++ ...+++|++||+++.+|...++|+.. ..|.+|++.+++|
T Consensus 10 ~~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~--~~~~~wl~~i~rn 87 (184)
T PRK12512 10 TDLMRSANAGDAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWLFAIARN 87 (184)
T ss_pred HHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCcc--ccHHHHHHHHHHH
Confidence 346777777866 9999999999999999999876 34799999999999999999999873 4699999999999
Q ss_pred HHHHHHHhhcCceecc---------cc---cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHH
Q 013472 359 SISKMVARHARGIKIP---------CK---LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSA 418 (442)
Q Consensus 359 aI~r~LRkqsr~irlP---------~~---v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~ 418 (442)
.+.++++++.+....+ .. .......+.++...|+.... .+.|++|||+.||+|+.+|+..
T Consensus 88 ~~~d~~Rr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l~is~~tV~~~ 167 (184)
T PRK12512 88 KLIDALRRRGRRVFVDIDDFAETLPAEPATETLPAGDVGRHLETLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVRVA 167 (184)
T ss_pred HHHHHHHhhcccccCCchhccccccccchhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Confidence 9999999875432221 11 11223456666666655442 6779999999999999999999
Q ss_pred HHhccc
Q 013472 419 SECLRI 424 (442)
Q Consensus 419 l~~ar~ 424 (442)
+++++.
T Consensus 168 l~ra~~ 173 (184)
T PRK12512 168 LHRGLA 173 (184)
T ss_pred HHHHHH
Confidence 988875
No 75
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=99.61 E-value=8.4e-15 Score=130.88 Aligned_cols=127 Identities=14% Similarity=0.136 Sum_probs=103.3
Q ss_pred HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceeccc
Q 013472 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC 375 (442)
Q Consensus 296 Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~ 375 (442)
|++.++..|.+.|+.+|+++.++..++||++||+++.+|+++++|++.. .|.+|++.+++|.++++++++.+......
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 7899999999999999999999999999999999999999999999754 59999999999999999998755322100
Q ss_pred c-----------------cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 376 K-----------------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 376 ~-----------------v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
. ..+....+.+++..|+... -.+.+++|||+.||||+.+|+..+++++.
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~v~~l~~~~g~~~~eIA~~l~is~~tv~~~l~Rar~ 153 (159)
T TIGR02989 80 DELLEALAAEAEATEADRSEDELQALEGCLEKLPERQRELLQLRYQRGVSLTALAEQLGRTVNAVYKALSRLRV 153 (159)
T ss_pred HHHHHHHHhhcccchHhhHHHHHHHHHHHHHHCCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 0 0111233555565555443 26789999999999999999999998875
No 76
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=99.59 E-value=1e-14 Score=135.31 Aligned_cols=127 Identities=17% Similarity=0.160 Sum_probs=103.8
Q ss_pred HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceeccc
Q 013472 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC 375 (442)
Q Consensus 296 Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~ 375 (442)
+|+.|+..|.+.|+.+|.+++++..+++|++||.|+.+|+.+++|++.. +|.||++.+++|.+++++|++++....+.
T Consensus 3 ~~~~l~~~~~~~l~~~a~~~~~~~~~AeDivQevfl~~~~~~~~~~~~~--~~~~WL~~ia~n~~~d~~Rk~~r~~~~~~ 80 (191)
T PRK12520 3 IAPAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQS--SLKTYLVGILKHKIIDAIRSGRREVRLSL 80 (191)
T ss_pred chHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhcccc--cHHHHHHHHHHHHHHHHHHhhcCcCcccc
Confidence 6899999999999999999999999999999999999999999998643 69999999999999999998754322111
Q ss_pred ------------------------------cc------HHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCC
Q 013472 376 ------------------------------KL------NREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLS 411 (442)
Q Consensus 376 ------------------------------~v------~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS 411 (442)
.. .+....+..++..|+.... .+.|++|||+.||+|
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 0112346666666665543 567999999999999
Q ss_pred HHHHHHHHHhccc
Q 013472 412 LAEIRSASECLRI 424 (442)
Q Consensus 412 ~etVk~~l~~ar~ 424 (442)
+++|+..+++++.
T Consensus 161 ~~tV~~~l~Rar~ 173 (191)
T PRK12520 161 ATNAWVLLYRARM 173 (191)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999998874
No 77
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=99.59 E-value=2.6e-14 Score=128.87 Aligned_cols=137 Identities=20% Similarity=0.165 Sum_probs=108.8
Q ss_pred HHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHH
Q 013472 286 LKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMV 364 (442)
Q Consensus 286 L~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~L 364 (442)
|...+..|+. |++.++..|.+.|+.+|+++.++..+++|++||++++||.+.++|+ .+..|.+|++.++++.+++++
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 5566778865 9999999999999999999999999999999999999999999998 345899999999999999999
Q ss_pred HhhcCceeccc-----c--------------cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHH
Q 013472 365 ARHARGIKIPC-----K--------------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRS 417 (442)
Q Consensus 365 Rkqsr~irlP~-----~--------------v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~ 417 (442)
++..+...... . ..+....+..+...|+... ..+.+.+|||+.||||+.+|+.
T Consensus 81 r~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~~~~~~eIA~~lgis~~tv~~ 160 (179)
T PRK11924 81 RRRRREKAVLSDDALEPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKS 160 (179)
T ss_pred HhcccccccCcccccccccCCccCCHHHHHhhHHHHHHHHHHHHhCCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHH
Confidence 97654322110 0 0112233455555444432 3577999999999999999999
Q ss_pred HHHhccc
Q 013472 418 ASECLRI 424 (442)
Q Consensus 418 ~l~~ar~ 424 (442)
.+++++.
T Consensus 161 ~~~ra~~ 167 (179)
T PRK11924 161 RLRRARQ 167 (179)
T ss_pred HHHHHHH
Confidence 9888764
No 78
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=99.59 E-value=1.7e-14 Score=131.65 Aligned_cols=127 Identities=10% Similarity=0.109 Sum_probs=103.5
Q ss_pred HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceec--
Q 013472 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI-- 373 (442)
Q Consensus 296 Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irl-- 373 (442)
.+++|+..|.++|+.+|++|.++..+++|++||+++.+|++.++|++.. +|.+|++.+++|.+++++|++++....
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 799999999999999999986543110
Q ss_pred -------------cc--cc------HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 374 -------------PC--KL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 374 -------------P~--~v------~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
+. .. .+....+.++...|+... -.+.+++|||+.||||+++|+..+.+++.
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 00 00 112234666666665543 26779999999999999999999988874
No 79
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=99.58 E-value=1.6e-14 Score=132.92 Aligned_cols=131 Identities=12% Similarity=0.084 Sum_probs=105.0
Q ss_pred hchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCc
Q 013472 292 FGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG 370 (442)
Q Consensus 292 ~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~ 370 (442)
.|+. |++.|+..|.+.|+.++++|.++..+++|++||+|+.+|+++.+|++.. .|.+|++.+++|.+.+++++..+.
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 4544 9999999999999999999999999999999999999999999999864 699999999999999999865421
Q ss_pred ee---------------ccccc--HHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 371 IK---------------IPCKL--NREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 371 ir---------------lP~~v--~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
.+ .|.++ .+....+.++...|+.... .+.|++|||+.||||+++|+..+++++.
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 01110 1223456666666655442 6779999999999999999999888764
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=99.58 E-value=1.7e-14 Score=134.01 Aligned_cols=128 Identities=13% Similarity=0.012 Sum_probs=105.0
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecc
Q 013472 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP 374 (442)
Q Consensus 295 ~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP 374 (442)
.+|++|+..|.+.|+.+|++++++..+++|++||+|+.+|+++.+|++. ..|.+|++.+++|.+++++|++.+.....
T Consensus 11 ~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~~~~~~~~~--~~~~~wL~~iarN~~~d~~Rk~~~~~~~~ 88 (193)
T TIGR02947 11 QRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPG--TNLKAWLYRILTNTYINSYRKAQRRPQQS 88 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcccCCC--CcchHHHHHHHHHHHHHHHHHhcCCcccc
Confidence 4899999999999999999999999999999999999999999999864 36999999999999999999765432110
Q ss_pred --------------cc------cH-------HHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHH
Q 013472 375 --------------CK------LN-------REISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSAS 419 (442)
Q Consensus 375 --------------~~------v~-------e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l 419 (442)
.+ .. .....+..++..|+.... .+.|++|||+.||||+++|+..+
T Consensus 89 ~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~r~i~~L~~~~g~s~~EIA~~lgis~~tVk~~l 168 (193)
T TIGR02947 89 DDDDIEDWQLAKAASHTSNGLRSAELEALDGLPDQDIKDALQGLPEEFRQAVYLADVEGFAYKEIAEIMGTPIGTVMSRL 168 (193)
T ss_pred cchhhhhhhhccccccccccccchhHHHHhhhhHHHHHHHHHhCCHHHhhheeehhhcCCCHHHHHHHHCCCHHHHHHHH
Confidence 00 00 112456677777766553 56799999999999999999999
Q ss_pred Hhccc
Q 013472 420 ECLRI 424 (442)
Q Consensus 420 ~~ar~ 424 (442)
++++.
T Consensus 169 ~Rar~ 173 (193)
T TIGR02947 169 HRGRK 173 (193)
T ss_pred HHHHH
Confidence 98874
No 81
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=99.57 E-value=3.4e-14 Score=130.85 Aligned_cols=129 Identities=16% Similarity=0.058 Sum_probs=103.9
Q ss_pred hHHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceec
Q 013472 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI 373 (442)
Q Consensus 294 ~~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irl 373 (442)
..|+++|+..|.+.|+.+|.++.++..+++|++||+|+.+|+++.+|++. ..|.+|++.+++|.+++++|+..+....
T Consensus 15 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~--~~~~awl~~ia~n~~~d~~Rk~~~~~~~ 92 (179)
T PRK09415 15 EDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGK--SSLKTWLYRIAINHCKDYLKSWHNKKVI 92 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--cccHHHHHHHHHHHHHHHHHhhcccccc
Confidence 34999999999999999999999999999999999999999999999874 3699999999999999999975321111
Q ss_pred c---------c---c------cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 374 P---------C---K------LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 374 P---------~---~------v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
+ . . ..+....+.++...|+.... .+.|++|||+.||||+++|+..+++++.
T Consensus 93 ~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tv~~~l~Ra~~ 169 (179)
T PRK09415 93 VTEDIFTYMESQKESVEEEVIQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKE 169 (179)
T ss_pred ccccccccccccccCcHHHHHHHHHHHHHHHHHHhCCHHHhhHhHhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 0 0 0 11223446666666655442 5679999999999999999999998875
No 82
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=99.57 E-value=3e-14 Score=129.63 Aligned_cols=130 Identities=13% Similarity=0.022 Sum_probs=104.1
Q ss_pred hHHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCcee-
Q 013472 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIK- 372 (442)
Q Consensus 294 ~~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~ir- 372 (442)
..|++.|+..|.+.|+.+|.++.++..++||++||.|+.+|+..++|++.. ..|.+|++.+++|.+++++|++++...
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 479999999999999999997643211
Q ss_pred -------cccc-----c--HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 373 -------IPCK-----L--NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 373 -------lP~~-----v--~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
.|.. . ......+..++..|+... -.+.|++|||+.||+|+++|+..+++++.
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 1100 1 111224666666665554 26789999999999999999999988875
No 83
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=99.57 E-value=3.6e-14 Score=129.14 Aligned_cols=135 Identities=16% Similarity=0.093 Sum_probs=105.0
Q ss_pred HHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHH
Q 013472 287 KQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVA 365 (442)
Q Consensus 287 ~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LR 365 (442)
+..++.|+. |++.++..|.+.|+.+++++.+ ..+++|++||+|+.+|+.++.|++. ..|.+|++.+++|.+++++|
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 455677866 9999999999999999999875 4789999999999999999999974 46999999999999999999
Q ss_pred hhcCce----ecc--------cc---c--HHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHH
Q 013472 366 RHARGI----KIP--------CK---L--NREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASE 420 (442)
Q Consensus 366 kqsr~i----rlP--------~~---v--~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~ 420 (442)
+..+.. ..+ .. . .+....+..+...|+.... .+.|++|||+.||+|+++|+..++
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 764321 110 00 0 0111235555555555432 566999999999999999999999
Q ss_pred hccc
Q 013472 421 CLRI 424 (442)
Q Consensus 421 ~ar~ 424 (442)
+++.
T Consensus 159 Rar~ 162 (175)
T PRK12518 159 YARR 162 (175)
T ss_pred HHHH
Confidence 8875
No 84
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=99.56 E-value=3.9e-14 Score=132.13 Aligned_cols=129 Identities=13% Similarity=0.099 Sum_probs=105.5
Q ss_pred hHHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceec
Q 013472 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI 373 (442)
Q Consensus 294 ~~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irl 373 (442)
..++++|+..|.+.|+.+|++++++..++||++||.|+.+|+..++|+... .|.+|++.+++|.+++++|++++....
T Consensus 9 ~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~~--~~~awL~~Ia~n~~~d~~R~~~~~~~~ 86 (187)
T PRK12516 9 TPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGT--NMKAWLFTILRNEFYSQMRKRGREVQD 86 (187)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCcc--cHHHHHHHHHHHHHHHHHHhhcCCccc
Confidence 349999999999999999999999999999999999999999999998643 699999999999999999987653211
Q ss_pred cc---------c----cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 374 PC---------K----LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 374 P~---------~----v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
.. . .......+..++..|+.... .+.+++|||+.||||+++|+..+.+++.
T Consensus 87 ~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~i~~L~~~~g~s~~EIA~~Lgis~~tVk~~l~Rar~ 158 (187)
T PRK12516 87 TDGMFTEQLAVHPSQYGTLDLQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQ 158 (187)
T ss_pred cccccccccCCCcchhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 00 0 11123456677777766542 6789999999999999999999988874
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=99.56 E-value=3.8e-14 Score=122.37 Aligned_cols=127 Identities=24% Similarity=0.288 Sum_probs=101.1
Q ss_pred HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcC------
Q 013472 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR------ 369 (442)
Q Consensus 296 Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr------ 369 (442)
|++.++..|.++|+++++++.+++.+.+|++|||+++++++++.|++. .+|.+|+++++++.+.++++++.+
T Consensus 2 a~~~l~~~~~~~v~~~~~~~~~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~rk~~~~~~~~~ 79 (158)
T TIGR02937 2 AFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRRLRRELD 79 (158)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHHHHHHHHhccCCcchh
Confidence 789999999999999999999999999999999999999999999997 589999999999999999998764
Q ss_pred c-eec------ccc---cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 370 G-IKI------PCK---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 370 ~-irl------P~~---v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
. ... |.. .......+.++...|+... ..+.+..|||+.+|+|+.+|+..+..++.
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~ii~~~~~~g~s~~eIA~~l~~s~~~v~~~~~~~~~ 152 (158)
T TIGR02937 80 LLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARK 152 (158)
T ss_pred hhhhcccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 0 000 000 1122233445544443322 36779999999999999999999887653
No 86
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=99.55 E-value=5.8e-14 Score=141.51 Aligned_cols=139 Identities=18% Similarity=0.104 Sum_probs=112.4
Q ss_pred HHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHH
Q 013472 284 RVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISK 362 (442)
Q Consensus 284 eeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r 362 (442)
.+|+..++.|+. |+++|+..|.+.|+.+|++++++..+++|++||.|+.+|+.+++|++. ..|.+|++.+++|.+++
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 578889999976 999999999999999999999999999999999999999999999853 36999999999999999
Q ss_pred HHHhhcCcee---c-----------------------cc-----------cc---HHH-HHHHHHHHHHHHHHcC-----
Q 013472 363 MVARHARGIK---I-----------------------PC-----------KL---NRE-ISKIQKARKALTNSHG----- 396 (442)
Q Consensus 363 ~LRkqsr~ir---l-----------------------P~-----------~v---~e~-i~kI~ka~~~L~~elg----- 396 (442)
++|++++... . +. .. .+. ...+..++..|+....
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 9997653210 0 00 00 011 1235566666665543
Q ss_pred ---CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 397 ---KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 397 ---r~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
.+.|++|||+.||+|+++|+..+++++.
T Consensus 165 ~~~~g~s~~EIA~~lgis~~tVk~~l~RAr~ 195 (339)
T PRK08241 165 RDVLGWSAAEVAELLDTSVAAVNSALQRARA 195 (339)
T ss_pred HHhhCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 5679999999999999999999988874
No 87
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=99.55 E-value=6.3e-14 Score=127.20 Aligned_cols=128 Identities=13% Similarity=0.107 Sum_probs=104.1
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecc
Q 013472 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP 374 (442)
Q Consensus 295 ~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP 374 (442)
..|.+++..|.+.|+.+|+++.++..++||++||+|+.+|+..++|+... .|.+|++.+++|.+++++|++++.....
T Consensus 6 ~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~~~~~~ 83 (164)
T PRK12547 6 KNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGT--NLKAWLFTILRNEFYSQMRKRGREVQDS 83 (164)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCcc--cHHHHHHHHHHHHHHHHHHhhccccccc
Confidence 47899999999999999999999999999999999999999999998643 5999999999999999999765432110
Q ss_pred ---------cc----cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 375 ---------CK----LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 375 ---------~~----v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
.. .......+..++..|+.... .+.|++|||+.||||+++|+..+++++.
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 01122346666666655432 6789999999999999999999998875
No 88
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=99.55 E-value=5.3e-14 Score=126.48 Aligned_cols=131 Identities=15% Similarity=0.030 Sum_probs=104.5
Q ss_pred hch-HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCc
Q 013472 292 FGW-YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG 370 (442)
Q Consensus 292 ~G~-~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~ 370 (442)
.|+ .+++.++..|.+.|+.+|.+++++..+++|++||+|+.+|++.++|+. ...|.+|++.+++|.++++++++.+.
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 354 499999999999999999999999999999999999999999999964 34799999999999999999977541
Q ss_pred eec----cc----c---cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 371 IKI----PC----K---LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 371 irl----P~----~---v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
... |. . .......+..+...|+.... .+.+++|||+.||+|+++|+..+.+++.
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 110 10 0 11233445566665555432 5679999999999999999999988874
No 89
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=99.55 E-value=3.8e-14 Score=130.57 Aligned_cols=134 Identities=9% Similarity=-0.013 Sum_probs=104.9
Q ss_pred HhchH-HHHHHHHHhHHHHHHHHHHhhC--CCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhh
Q 013472 291 AFGWY-CREELIKSTRPLVLFLARNYRG--LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARH 367 (442)
Q Consensus 291 ~~G~~-Are~LI~~nlrLV~sIAkrY~g--~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkq 367 (442)
..|+. ||+.|+..|.+.|+.++.++.+ +..+++|++||.|+.+|+..++|+......|.||++.+++|.+++++|++
T Consensus 8 ~~~d~~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~~Rk~ 87 (178)
T PRK12529 8 LSADRDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSWRRRQ 87 (178)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHHHHHH
Confidence 34544 9999999999999998766665 46889999999999999999999754345799999999999999999976
Q ss_pred cCce-------ecc-------cc---cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 368 ARGI-------KIP-------CK---LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 368 sr~i-------rlP-------~~---v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
.+.. ..+ .. ..+....|.+++.+|+.+.. .+.|++|||+.||+|+++|+..++++
T Consensus 88 ~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~rA 167 (178)
T PRK12529 88 SLELAWLEALATLPEPLHPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQA 167 (178)
T ss_pred HHHhhhhhHhhhccCcCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 4311 011 10 11234457777777777653 57899999999999999999998877
Q ss_pred cc
Q 013472 423 RI 424 (442)
Q Consensus 423 r~ 424 (442)
..
T Consensus 168 l~ 169 (178)
T PRK12529 168 YV 169 (178)
T ss_pred HH
Confidence 63
No 90
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=99.54 E-value=7.9e-14 Score=125.65 Aligned_cols=127 Identities=17% Similarity=0.101 Sum_probs=101.5
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceec-
Q 013472 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI- 373 (442)
Q Consensus 295 ~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irl- 373 (442)
.|+++++..|.+.|+.+|.+++++..+++|++||+|+.+|+..++|++. .|.||++.+++|.+++++|++.+....
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 599999999999999999986542111
Q ss_pred ---------ccc-----cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 374 ---------PCK-----LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 374 ---------P~~-----v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
|.. ..+....+..+...|+... -.+.+++|||+.||+|+++|+..+++++.
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 0112223344555555433 26779999999999999999999998874
No 91
>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=99.54 E-value=7.5e-14 Score=127.89 Aligned_cols=133 Identities=17% Similarity=0.098 Sum_probs=102.1
Q ss_pred hchH-HHHHHHHHhHHHHHHHHHHhh----CCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHh
Q 013472 292 FGWY-CREELIKSTRPLVLFLARNYR----GLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVAR 366 (442)
Q Consensus 292 ~G~~-Are~LI~~nlrLV~sIAkrY~----g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRk 366 (442)
.|+. |++.|+..|.+.|+.+|++|. ++..+++|++||+++.+|+++.+|+...+.+|.+|++.+++|.+++++++
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 4554 999999999999999999875 35689999999999999999999987655689999999999999999986
Q ss_pred hc----Cce--ecc-------------------------cc---cHHHHHHHHHHHHHHHHHc--------CCCCcHHHH
Q 013472 367 HA----RGI--KIP-------------------------CK---LNREISKIQKARKALTNSH--------GKYPEDIEI 404 (442)
Q Consensus 367 qs----r~i--rlP-------------------------~~---v~e~i~kI~ka~~~L~~el--------gr~PS~eEI 404 (442)
+. +.. ..+ .. ..+....+.++...|+... ..+.+.+||
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 0112234555555554432 367899999
Q ss_pred HHHhCCCHHHHHHHHHhccc
Q 013472 405 AKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 405 Ae~LGIS~etVk~~l~~ar~ 424 (442)
|+.||||+++|+..+++++.
T Consensus 163 A~~lgis~~~v~~~l~Ra~~ 182 (189)
T TIGR02984 163 AERMDRSEGAVSMLWVRGLA 182 (189)
T ss_pred HHHHCcCHHHHHHHHHHHHH
Confidence 99999999999999988764
No 92
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=99.54 E-value=1.1e-13 Score=130.11 Aligned_cols=138 Identities=19% Similarity=0.058 Sum_probs=109.9
Q ss_pred HHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHH
Q 013472 284 RVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISK 362 (442)
Q Consensus 284 eeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r 362 (442)
.+|+..+..|+. |++.++..|.+.++.++. +.++..+++|++||.|+.+|+..++|++. ..|.+|++.+++|.+++
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 567778888876 999999999999999975 67888999999999999999999999864 36999999999999999
Q ss_pred HHHhhcCceec--------------ccc--cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHH
Q 013472 363 MVARHARGIKI--------------PCK--LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSA 418 (442)
Q Consensus 363 ~LRkqsr~irl--------------P~~--v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~ 418 (442)
++|++.+.... |.. ..+....+.+++..|+.... .+.|++|||+.||+|+++|+..
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 99976432110 000 11222346666666665442 5679999999999999999999
Q ss_pred HHhccc
Q 013472 419 SECLRI 424 (442)
Q Consensus 419 l~~ar~ 424 (442)
+++++.
T Consensus 170 l~Rar~ 175 (196)
T PRK12535 170 VARARA 175 (196)
T ss_pred HHHHHH
Confidence 988774
No 93
>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=99.53 E-value=5.8e-14 Score=124.30 Aligned_cols=127 Identities=17% Similarity=0.082 Sum_probs=99.9
Q ss_pred HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceec--
Q 013472 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI-- 373 (442)
Q Consensus 296 Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irl-- 373 (442)
|+++|+..|.+.|+.+++++.++..+++|++||+++++|+++.+|++. .+|.+|++.++++.+.+++++..+....
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 3799999999999999999977532111
Q ss_pred ------cc--------c---cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 374 ------PC--------K---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 374 ------P~--------~---v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
+. . ..+....+..+...|+... ..+.|..|||+.+|+|+.+|+..+++++.
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 00 0 0112223444444433322 35779999999999999999999988764
No 94
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=99.53 E-value=4.3e-14 Score=129.02 Aligned_cols=131 Identities=15% Similarity=0.070 Sum_probs=102.4
Q ss_pred HhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcC
Q 013472 291 AFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (442)
Q Consensus 291 ~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr 369 (442)
+.|+. |+..|+..|.+.|+.+|.++.++..+++|++||+|+.+|+. ..|+.. ..|.+|++.+++|.+++++|++.+
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 45654 99999999999999999999999999999999999999986 446543 369999999999999999998643
Q ss_pred cee-------cc-------cc---cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 370 GIK-------IP-------CK---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 370 ~ir-------lP-------~~---v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
... .+ .. ..+....+..++..|+.+. -.+.+++|||+.||||+++|+..+.+++.
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~ 161 (172)
T PRK12523 82 EQAYLAELALVPEAEQPSPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGLR 161 (172)
T ss_pred HHHHHHHHhhcccccCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 110 00 00 0122234666666665543 26789999999999999999999988764
No 95
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=99.52 E-value=1.1e-13 Score=125.38 Aligned_cols=125 Identities=16% Similarity=0.008 Sum_probs=100.4
Q ss_pred HHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecc--
Q 013472 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP-- 374 (442)
Q Consensus 297 re~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP-- 374 (442)
++.|+..|.+.|+.+|++|.++..+++|++||+|+.+|++++.|++. .|.+|++.+++|.+++++|+.++.....
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 5999999999999999999876432111
Q ss_pred ----------ccc---HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 375 ----------CKL---NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 375 ----------~~v---~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
... .+....+..+...|+... -.+.+++|||+.||+|+++|+..+++++.
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 000 112234555555554443 25679999999999999999999998874
No 96
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=99.52 E-value=1.8e-13 Score=131.08 Aligned_cols=130 Identities=15% Similarity=0.056 Sum_probs=104.9
Q ss_pred hchHHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCce
Q 013472 292 FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGI 371 (442)
Q Consensus 292 ~G~~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~i 371 (442)
....+++.|+..|.+.|+.+++++.++..++||++||+|+.+|+.+++|++. .|.+|++++++|.++++++++++..
T Consensus 15 ~~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~~---~~~aWL~~IarN~~~d~~Rk~~~~~ 91 (216)
T PRK12533 15 ARGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRGD---NARPWLLAIVRHTWYSEWRRRANAH 91 (216)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCcc---chHhHHHHHHHHHHHHHHHhhcccc
Confidence 3355999999999999999999999999999999999999999999999852 4999999999999999999765321
Q ss_pred ec------cc------------c------cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHH
Q 013472 372 KI------PC------------K------LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSAS 419 (442)
Q Consensus 372 rl------P~------------~------v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l 419 (442)
.. +. . ..+....+.+++..|+.... .+.|++|||+.||||+++|+..+
T Consensus 92 ~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y~eg~s~~EIAe~LgiS~~tVk~~L 171 (216)
T PRK12533 92 EVAAPDTLDDADSLDDWQPAGEDPLALLLRAEDVRLVNAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRL 171 (216)
T ss_pred cccccccccccccccccccCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHhHhhhHHhcCCCHHHHHHHHCCCHHHHHHHH
Confidence 10 00 0 01233456666666665442 67899999999999999999999
Q ss_pred Hhccc
Q 013472 420 ECLRI 424 (442)
Q Consensus 420 ~~ar~ 424 (442)
++++.
T Consensus 172 ~RAr~ 176 (216)
T PRK12533 172 ARARR 176 (216)
T ss_pred HHHHH
Confidence 88874
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=99.51 E-value=1.3e-13 Score=137.56 Aligned_cols=130 Identities=17% Similarity=0.075 Sum_probs=103.6
Q ss_pred chH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCce
Q 013472 293 GWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGI 371 (442)
Q Consensus 293 G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~i 371 (442)
|+. |+++|+..|.+.|+.+|++++++..++||++||.|+.+|+.+++|+.. ..|.||++.+++|.+++++|++++..
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 444 999999999999999999999999999999999999999999999864 36999999999999999999764321
Q ss_pred e--------------------------ccc-----------c---c---HHH-HHHHHHHHHHHHHHcC--------CCC
Q 013472 372 K--------------------------IPC-----------K---L---NRE-ISKIQKARKALTNSHG--------KYP 399 (442)
Q Consensus 372 r--------------------------lP~-----------~---v---~e~-i~kI~ka~~~L~~elg--------r~P 399 (442)
. ++. . . .+. ...+..++.+|+.... .+.
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 1235556666655442 567
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 400 EDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 400 S~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
+++|||+.||+|+++|+..+++++.
T Consensus 160 s~~EIA~~lgis~~tV~~~l~Rar~ 184 (324)
T TIGR02960 160 RAAETAELLGTSTASVNSALQRARA 184 (324)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 9999999999999999999988874
No 98
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=99.51 E-value=9.3e-14 Score=124.87 Aligned_cols=121 Identities=11% Similarity=0.060 Sum_probs=96.5
Q ss_pred HHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCcee-cc-----
Q 013472 301 IKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIK-IP----- 374 (442)
Q Consensus 301 I~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~ir-lP----- 374 (442)
++.|.+.|+.+|++++++..+++|++||+|+.+|+++++|++. .|.||++.+++|.+++++|++.+... ..
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 49999999999999999998654211 00
Q ss_pred -----c--cc------HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 375 -----C--KL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 375 -----~--~v------~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
. .. .+....+..++..|+... -.+.|++|||+.||+|+++|+..+++++.
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 112234666666666553 26789999999999999999999998875
No 99
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=99.50 E-value=1.9e-13 Score=123.22 Aligned_cols=127 Identities=17% Similarity=0.096 Sum_probs=101.3
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCce---
Q 013472 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGI--- 371 (442)
Q Consensus 295 ~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~i--- 371 (442)
.|+++|+..|.+.|+.+|.++.++..++||++||+|+.+|+..+.|++ ..|.+|++++++|.+++++|++.+..
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 26999999999999999999764211
Q ss_pred ----eccc----c------cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 372 ----KIPC----K------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 372 ----rlP~----~------v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
..|. . ..+....+.+++.+|+... -.+.+++|||+.||+|+++|+..+++++.
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 0122234556666665543 26789999999999999999999988753
No 100
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=99.48 E-value=4.3e-13 Score=124.59 Aligned_cols=127 Identities=16% Similarity=0.156 Sum_probs=103.3
Q ss_pred HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceec--
Q 013472 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI-- 373 (442)
Q Consensus 296 Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irl-- 373 (442)
++..++..|.+.|+.+|.+++++..+++|++||+|+.+|+..++|++.. .|.+|++.+++|.++++++++.+....
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---cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 374 --------PCK---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 374 --------P~~---v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
+.. .......+..++.+|+... -.+.|++|||+.||||+.+|+..+++++.
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 0112234666677665554 26789999999999999999999988874
No 101
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=99.48 E-value=6.1e-13 Score=129.71 Aligned_cols=91 Identities=19% Similarity=0.293 Sum_probs=82.1
Q ss_pred CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCC--CHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHH
Q 013472 282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGI--PFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK 358 (442)
Q Consensus 282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~--d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRn 358 (442)
+.++|+..++.|+. |++.|+..|.++|+++|.+++++.. +++|++|||++++|+++++|++.+|.+|.+|++++|+|
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 45678888899966 9999999999999999999998875 59999999999999999999999888899999999999
Q ss_pred HHHHHHHhhcCcee
Q 013472 359 SISKMVARHARGIK 372 (442)
Q Consensus 359 aI~r~LRkqsr~ir 372 (442)
.+++++|++.+...
T Consensus 84 ~~iDylRk~~~~~~ 97 (237)
T PRK08311 84 RLIDYFRKESKHNL 97 (237)
T ss_pred HHHHHHHHhhcccc
Confidence 99999998766433
No 102
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=99.48 E-value=4.1e-13 Score=121.00 Aligned_cols=126 Identities=15% Similarity=0.035 Sum_probs=99.5
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecc
Q 013472 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP 374 (442)
Q Consensus 295 ~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP 374 (442)
.|++.++..|.+.|+.+|.++.++..+++|++||+|+.+|++ .|+. +..|.||++.+++|.+++++|+..+.....
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 347999999999999999999875432111
Q ss_pred ---------------cc---cHHHHHHHHHHHHHHHHHcC-------CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 375 ---------------CK---LNREISKIQKARKALTNSHG-------KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 375 ---------------~~---v~e~i~kI~ka~~~L~~elg-------r~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
.. ..+....+.++...|+.... .+.+++|||+.||+|+.+|+..+.+++.
T Consensus 79 ~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~~g~s~~eIA~~lgis~~tV~~~i~ra~~ 153 (166)
T PRK09639 79 LGEFQWQEVDNEPSPEEIWIRKEEITKVQEVLAKMTERDRTVLLLRFSGYSYKEIAEALGIKESSVGTTLARAKK 153 (166)
T ss_pred cchhhhhhccCCCChHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 00 01222345555555543321 6789999999999999999999988764
No 103
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=99.47 E-value=3.4e-13 Score=126.85 Aligned_cols=124 Identities=15% Similarity=0.046 Sum_probs=98.7
Q ss_pred HHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecc---c
Q 013472 299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP---C 375 (442)
Q Consensus 299 ~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP---~ 375 (442)
.++..|.+.|+.+|++++++..+++|++||+|+.+|+.+++|++.. .|.||++.+++|.+++++|++.+...++ .
T Consensus 12 ~~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~~--~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~~~ 89 (201)
T PRK12545 12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQS--AHKTWVFGILRNKLIDTLRARQRTVNLSALDA 89 (201)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhccccc--hHHHHHHHHHHHHHHHHHHhhccccccccccc
Confidence 4488999999999999999999999999999999999999999753 6999999999999999999876432211 0
Q ss_pred -----------------------------ccH------HHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCH
Q 013472 376 -----------------------------KLN------REISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSL 412 (442)
Q Consensus 376 -----------------------------~v~------e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~ 412 (442)
... +....+.+++..|+... ..+.+++|||+.||+|+
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 11123555666665543 36789999999999999
Q ss_pred HHHHHHHHhccc
Q 013472 413 AEIRSASECLRI 424 (442)
Q Consensus 413 etVk~~l~~ar~ 424 (442)
++|+..+.+++.
T Consensus 170 ~tVk~~l~RAr~ 181 (201)
T PRK12545 170 NHCSVLLYRART 181 (201)
T ss_pred HHHHHHHHHHHH
Confidence 999999888874
No 104
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=99.47 E-value=4.2e-13 Score=124.92 Aligned_cols=125 Identities=16% Similarity=0.102 Sum_probs=98.7
Q ss_pred HHHHHHhHHHHHHHHHHhhCCCCC-HHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecc--
Q 013472 298 EELIKSTRPLVLFLARNYRGLGIP-FSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP-- 374 (442)
Q Consensus 298 e~LI~~nlrLV~sIAkrY~g~g~d-~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP-- 374 (442)
+..+..|.+.|+.+|++++++..+ ++|++||+|+.+|++.++|++. .+|.||++.+++|.+++++|++++.....
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 456788999999999999999888 9999999999999999999864 37999999999999999999875422110
Q ss_pred ----------------------c----c---------cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCC
Q 013472 375 ----------------------C----K---------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLS 411 (442)
Q Consensus 375 ----------------------~----~---------v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS 411 (442)
. . ..+....+.++...|+... -.+.|++|||+.||+|
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 0112233566666665543 2577999999999999
Q ss_pred HHHHHHHHHhccc
Q 013472 412 LAEIRSASECLRI 424 (442)
Q Consensus 412 ~etVk~~l~~ar~ 424 (442)
+++|+..+++++.
T Consensus 166 ~~tVk~~l~Rar~ 178 (195)
T PRK12532 166 TSNYHTIMHRARE 178 (195)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999988874
No 105
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=99.47 E-value=4.5e-13 Score=124.77 Aligned_cols=125 Identities=13% Similarity=0.079 Sum_probs=99.2
Q ss_pred HHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecc---
Q 013472 298 EELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP--- 374 (442)
Q Consensus 298 e~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP--- 374 (442)
+..|..|.+.|+.+|.+++++..+++|++||+|+.+|+..++|++.. +|.||++++++|.+++++|++++.....
T Consensus 10 ~~~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~~--~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~~~~ 87 (189)
T PRK12530 10 SLEIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQS--ALKTWIFAILKNKIIDLIRYRKRFVNESELI 87 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCCc--cHHHHHHHHHHHHHHHHHHhhccCCCccccc
Confidence 35578889999999999999999999999999999999999998753 6999999999999999999875432110
Q ss_pred ----------------------cc--c-------HHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHH
Q 013472 375 ----------------------CK--L-------NREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEI 415 (442)
Q Consensus 375 ----------------------~~--v-------~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etV 415 (442)
.. . .+....+..++.+|+.... .+.|++|||+.||+|+++|
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 0111235666666665542 5789999999999999999
Q ss_pred HHHHHhccc
Q 013472 416 RSASECLRI 424 (442)
Q Consensus 416 k~~l~~ar~ 424 (442)
+..+++++.
T Consensus 168 k~~l~RAr~ 176 (189)
T PRK12530 168 HVLLYRARL 176 (189)
T ss_pred HHHHHHHHH
Confidence 999998874
No 106
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=99.47 E-value=6e-13 Score=126.04 Aligned_cols=127 Identities=24% Similarity=0.212 Sum_probs=102.3
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCc--ee
Q 013472 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG--IK 372 (442)
Q Consensus 295 ~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~--ir 372 (442)
.++++|+..|.+.|+.++.++.++..+++|++||+|+.+|++..+|++ + +|.+|++.+++|.+++++|+..+. ..
T Consensus 28 ~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~~~d~~Rk~~~~~~~~ 104 (203)
T PRK09647 28 PSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNLFLDMVRRRARIRMEA 104 (203)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHHHHHHHHhcccCcccc
Confidence 399999999999999999999999999999999999999999999985 3 699999999999999999987531 10
Q ss_pred cc-------cc---------cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 373 IP-------CK---------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 373 lP-------~~---------v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
++ .. ..+....+..++..|+... ..+.+++|||+.||||+++|+..+.+++.
T Consensus 105 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~L~~~~r~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RArk 180 (203)
T PRK09647 105 LPEDYDRVPGDEPNPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQ 180 (203)
T ss_pred ccccccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 10 00 0112334555555555443 26789999999999999999999988874
No 107
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=99.46 E-value=7.4e-13 Score=122.78 Aligned_cols=125 Identities=15% Similarity=0.107 Sum_probs=99.7
Q ss_pred HHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccc
Q 013472 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCK 376 (442)
Q Consensus 297 re~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~ 376 (442)
++.|+..|.+.|+.+|.++.++..+++|++||.++.+|+.+..|++. .+|.+|++.+++|.+++++|++++...++..
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 4799999999999999999987543322110
Q ss_pred ------------cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 377 ------------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 377 ------------v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
..+....+..+...|+... -.+.+.+|||+.||+|+++|+..+.+++
T Consensus 81 ~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~~~~EIA~~lgis~~tV~~~l~Rar 147 (181)
T PRK09637 81 LLFEDEEREENAKKELAPCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGR 147 (181)
T ss_pred hhccCCChhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 0112223444444444332 2677999999999999999999988776
No 108
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=99.46 E-value=9.7e-13 Score=122.69 Aligned_cols=130 Identities=13% Similarity=0.012 Sum_probs=104.0
Q ss_pred chHHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCce-
Q 013472 293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGI- 371 (442)
Q Consensus 293 G~~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~i- 371 (442)
...+++.++..|.+.|+.+|.++.++..+++|++||+|+.+|+.++.|++. ..|.+|++.+++|.+.+..+++.+..
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 455999999999999999999999999999999999999999999999864 36999999999999988877643211
Q ss_pred e-----ccc---c---cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 372 K-----IPC---K---LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 372 r-----lP~---~---v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
. .+. . .......+..++..|+.... .+.+++|||+.||||+.+|+..+++++.
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 0 010 0 01112346677777766543 6779999999999999999999988874
No 109
>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=99.45 E-value=4.6e-13 Score=119.05 Aligned_cols=120 Identities=18% Similarity=0.052 Sum_probs=96.6
Q ss_pred HHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceec-----c--
Q 013472 302 KSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI-----P-- 374 (442)
Q Consensus 302 ~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irl-----P-- 374 (442)
..|.+.|+.+|.++.++..+++|++||+++.+|+.+++|++ .+|.||++.++++.++++++++.+.... +
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~~~d~~r~~~~~~~~~~~~~~~~ 78 (154)
T TIGR02950 2 REYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNAFIDWYRKDKKIQTIDDDAIGDL 78 (154)
T ss_pred chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHHHHHHHHHhhhhccccHhhhhhc
Confidence 57899999999999999999999999999999999999997 3799999999999999999976532211 0
Q ss_pred --------ccc---HHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 375 --------CKL---NREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 375 --------~~v---~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
... .+....+.++...|+.... .+.+++|||+.||+|+.+|+..+++++.
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~ 147 (154)
T TIGR02950 79 EQHPVESPEHHLLIKIEQEEITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARK 147 (154)
T ss_pred cccccCChhHHHHHHHHHHHHHHHHHhCCHhheeeeeehhhccCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 000 1122446677777765442 5679999999999999999999998864
No 110
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=99.45 E-value=8.5e-13 Score=125.25 Aligned_cols=126 Identities=16% Similarity=0.136 Sum_probs=99.9
Q ss_pred HHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceeccc-
Q 013472 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC- 375 (442)
Q Consensus 297 re~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~- 375 (442)
-..++..|.+.|+.+|+++.++..+++|++||+|+.+|+.+.+|+.. .+|.+|++++++|.+++++|++++....+.
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 35788999999999999999999999999999999999999999864 369999999999999999997654321110
Q ss_pred ------------------------------c---c---HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCC
Q 013472 376 ------------------------------K---L---NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLS 411 (442)
Q Consensus 376 ------------------------------~---v---~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS 411 (442)
. . .+....+..++..|+.+. -.+.+++|||+.||+|
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 0 0 011123455555555443 2677999999999999
Q ss_pred HHHHHHHHHhccc
Q 013472 412 LAEIRSASECLRI 424 (442)
Q Consensus 412 ~etVk~~l~~ar~ 424 (442)
+++|+..+++++.
T Consensus 178 ~~tV~~~l~RAr~ 190 (206)
T PRK12544 178 VSNLNVLLYRARL 190 (206)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999998875
No 111
>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=99.44 E-value=8.5e-13 Score=122.96 Aligned_cols=124 Identities=15% Similarity=0.059 Sum_probs=98.9
Q ss_pred HHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceeccc---
Q 013472 299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC--- 375 (442)
Q Consensus 299 ~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~--- 375 (442)
+.+..|.+.|+.+|++++++..+++|++||+|+.+|+..++|++. .+|.+|++.+++|.+++++|++.+....+.
T Consensus 6 ~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R~~~r~~~~~~~~~ 83 (188)
T TIGR02943 6 QELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKNKIIDALRAKGREVKVSDLDD 83 (188)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHHHHHHHHHhhcccCCcccccc
Confidence 678889999999999999999999999999999999999999964 479999999999999999998754322110
Q ss_pred c--------------------------c-------HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHH
Q 013472 376 K--------------------------L-------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAE 414 (442)
Q Consensus 376 ~--------------------------v-------~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~et 414 (442)
. . .+....+.+++..|+... -.+.+++|||+.||+|+++
T Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~lgis~~t 163 (188)
T TIGR02943 84 ELDDEAFNALFTQNGHWAQHGQPQHWNTPEKQLENKEFWEVFEACLYHLPEQTARVFMMREVLGFESDEICQELEISTSN 163 (188)
T ss_pred ccccchhhhhhccccchhccccccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHhCCCHHH
Confidence 0 0 011233555655555433 2678999999999999999
Q ss_pred HHHHHHhccc
Q 013472 415 IRSASECLRI 424 (442)
Q Consensus 415 Vk~~l~~ar~ 424 (442)
|+..+.+++.
T Consensus 164 vk~rl~Rar~ 173 (188)
T TIGR02943 164 CHVLLYRARL 173 (188)
T ss_pred HHHHHHHHHH
Confidence 9999988874
No 112
>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=99.43 E-value=1.1e-12 Score=120.14 Aligned_cols=121 Identities=19% Similarity=0.168 Sum_probs=96.0
Q ss_pred HHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceeccccc----
Q 013472 302 KSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKL---- 377 (442)
Q Consensus 302 ~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v---- 377 (442)
..|.+.|+.+++++.++..+++|++||+|+.+|+++++|+.. .+|.+|++.+++|.+++++|+..+...++...
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 47999999999999999999876543332111
Q ss_pred --------HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 378 --------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 378 --------~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
.+....+.+++..|+... -.+.+++|||+.||||+.+|+..+++++.
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 112223455555554432 26789999999999999999999888763
No 113
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=99.43 E-value=1.8e-12 Score=121.20 Aligned_cols=126 Identities=17% Similarity=0.198 Sum_probs=100.1
Q ss_pred HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecc-
Q 013472 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP- 374 (442)
Q Consensus 296 Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP- 374 (442)
+++.|+. |.+.|+.+|+++.++..+++|++||.|+.+|+.+..|+.. ..|.+|++.+++|.+++++|++.+.....
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 7799999999999999999999999999999999999864 36999999999999999999875422110
Q ss_pred -----------cc-cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 375 -----------CK-LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 375 -----------~~-v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
.. .......+..++..|+.... .+.+.+|||+.||||+.+|+..+++++.
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 01112346667776665543 6779999999999999999999988874
No 114
>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=99.41 E-value=7.5e-13 Score=102.85 Aligned_cols=70 Identities=24% Similarity=0.375 Sum_probs=67.0
Q ss_pred HHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcC
Q 013472 300 LIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (442)
Q Consensus 300 LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr 369 (442)
|++.|.++|+.+|.+|.+++.+++|++||++++||+++++||+..+..|.+|++.++++.++++++++++
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 6899999999999999999999999999999999999999999998899999999999999999998754
No 115
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=99.41 E-value=2.3e-12 Score=119.87 Aligned_cols=126 Identities=13% Similarity=0.083 Sum_probs=100.0
Q ss_pred HHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecc--
Q 013472 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP-- 374 (442)
Q Consensus 297 re~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP-- 374 (442)
.+..+..+.+.|+.+|.++.++..+++|++||.|+.+|+....|+.. .+|.||++.+++|.+++++|++++.....
T Consensus 6 ~~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~Rk~~~~~~~~~~ 83 (182)
T PRK12511 6 KRFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSG--GNLRTWLMSILHNAFIDELRRRRVEARRADE 83 (182)
T ss_pred hhhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCc--cchHHHHHHHHHHHHHHHHHhhccccccccc
Confidence 45568889999999999999999999999999999999999999864 36999999999999999999865421110
Q ss_pred ----------cc--cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 375 ----------CK--LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 375 ----------~~--v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
.. .......+.+++..|+.... .+.|++|||+.||||+++|+..+++++.
T Consensus 84 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~eg~s~~EIA~~lgis~~tV~~~l~Rar~ 153 (182)
T PRK12511 84 LAVLADASLPAAQEHAVRLAQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARA 153 (182)
T ss_pred hhhccccCCCcchHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 00 11122345666666655542 6789999999999999999999888763
No 116
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=99.40 E-value=2.6e-12 Score=117.68 Aligned_cols=127 Identities=13% Similarity=0.076 Sum_probs=99.8
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCce---
Q 013472 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGI--- 371 (442)
Q Consensus 295 ~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~i--- 371 (442)
.|++.++..|.+.|+.++.++.++..++||++||.|+.+|+. ..|++-. .|.+|++.+++|.+++++|++.+..
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 ----eccc----c---c---HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 372 ----KIPC----K---L---NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 372 ----rlP~----~---v---~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
.++. . . .+....+..++..|+.+. ..+.+++|||+.||+|+++|+..+++++.
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 1110 0 0 122334566666666544 26779999999999999999999988763
No 117
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=99.36 E-value=5.9e-12 Score=122.13 Aligned_cols=132 Identities=15% Similarity=-0.041 Sum_probs=100.1
Q ss_pred HHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHH
Q 013472 287 KQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVA 365 (442)
Q Consensus 287 ~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LR 365 (442)
.++...|+. +++.+++.| +.|+.+|.++.++..++|||+||.|+.+|+. |+.. ..|.+|++.+++|.+++++|
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 344445544 888888777 7899999999999999999999999999986 6543 25999999999999999999
Q ss_pred hhcCceecccc---------cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 366 RHARGIKIPCK---------LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 366 kqsr~irlP~~---------v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
++++...+... ..+....+..+...|+.... .+.|++|||+.||+|+++|+..+++++.
T Consensus 83 k~k~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~R~v~lL~~~eg~S~~EIAe~LgiS~~tVksrL~Rark 158 (228)
T PRK06704 83 SKSVHEKIRDQITFEEPHEKIADLHEMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRN 158 (228)
T ss_pred ccccccccccccccCChHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHhhCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 87543221110 11222345666666665432 5679999999999999999999998874
No 118
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=99.36 E-value=7e-12 Score=112.85 Aligned_cols=123 Identities=15% Similarity=0.142 Sum_probs=95.1
Q ss_pred HHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCcee------
Q 013472 299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIK------ 372 (442)
Q Consensus 299 ~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~ir------ 372 (442)
.++..|.+.|+.+|.++.++..+++|++||+++++|+....|++. .|.+|++.+++|.+++++|++++...
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 467888999999999999999999999999999999998888753 48999999999999999997653211
Q ss_pred ----ccc---c------cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 373 ----IPC---K------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 373 ----lP~---~------v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
.+. . ..+....+.++...|+.+. -.+.|++|||+.||+|+.+|+..+.+++.
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 0112233455555554433 26779999999999999999999887764
No 119
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=99.35 E-value=6.4e-12 Score=112.99 Aligned_cols=121 Identities=12% Similarity=0.030 Sum_probs=94.9
Q ss_pred HHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceec-------
Q 013472 301 IKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI------- 373 (442)
Q Consensus 301 I~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irl------- 373 (442)
+..|.+.++.++.+++++..+++|++||+|+.+|+..+.|++ + +|.||++.+++|.+++++|++......
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--ccc---HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 374 ------P--CKL---NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 374 ------P--~~v---~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
| ... .+....+..+...|+.+. ..+.|++|||+.||+|+++|+..+.+++.
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 112234666666665553 26779999999999999999999988874
No 120
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=99.35 E-value=1.1e-11 Score=112.95 Aligned_cols=128 Identities=12% Similarity=0.009 Sum_probs=98.8
Q ss_pred hHHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCce--
Q 013472 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGI-- 371 (442)
Q Consensus 294 ~~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~i-- 371 (442)
+.++.+++..|.+.++.+|.++.++..+++|++||.|+.+|+..+.++. ..|.+|++++++|.+++++|+.....
T Consensus 8 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~~---~~~~~wl~~Iarn~~~d~~Rr~~~~~~~ 84 (168)
T PRK12525 8 NTLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEGWRRQDLERAY 84 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCcccc---cCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3489999999999999999999999999999999999999986665542 36999999999999999998753210
Q ss_pred -----eccc----c------cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 372 -----KIPC----K------LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 372 -----rlP~----~------v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
..|. . ..+....+.+++..|+.... .+.|++|||+.||+|+++|+..+.+++.
T Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~eg~s~~EIA~~l~is~~tV~~~l~ra~~ 160 (168)
T PRK12525 85 LQSLAEAPEAVQPSPEEQWMVIETLLAIDRLLDGLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAFK 160 (168)
T ss_pred HHHHhcccccccCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 0110 0 11123345566666655432 6779999999999999999999887763
No 121
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=99.26 E-value=4.8e-11 Score=118.61 Aligned_cols=125 Identities=16% Similarity=0.060 Sum_probs=96.4
Q ss_pred HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCc--e--
Q 013472 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG--I-- 371 (442)
Q Consensus 296 Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~--i-- 371 (442)
...+++..|.+.++.+|++++++..++||++||.|+. |.....|+. ..|.||++++++|.|++++|++++. .
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 4668999999999999999999999999999999999 556677762 4799999999999999999975421 1
Q ss_pred --eccccc-------------HHH-HHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 372 --KIPCKL-------------NRE-ISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 372 --rlP~~v-------------~e~-i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
.+|... .+. ...+..+...|+.... .+.+++|||+.||+|+.+|+..+++++.
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 1234555565555432 5779999999999999999999998874
No 122
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=99.20 E-value=1.1e-10 Score=116.85 Aligned_cols=126 Identities=10% Similarity=-0.103 Sum_probs=96.4
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCc--e-
Q 013472 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG--I- 371 (442)
Q Consensus 295 ~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~--i- 371 (442)
..+..++..|.+.++.+|+++.++..++||++||.|+.+|++...+. ..|.+|++.+++|.|++++|+..+. .
T Consensus 5 ~~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~~----~~~~aWL~~Ia~n~~id~lRk~~~rr~~~ 80 (290)
T PRK09635 5 DPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGDI----DDERGWLIVVTSRLCLDHIKSASTRRERP 80 (290)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCcccc----ccHHHHHHHHHHHHHHHHHhhhhccCcCc
Confidence 36889999999999999999999999999999999999999875431 3699999999999999999974321 0
Q ss_pred -----ecccc-------c------H-HHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 372 -----KIPCK-------L------N-REISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 372 -----rlP~~-------v------~-e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
+.|.. - . +....+..+...|+... -.+.+++|||+.||+|+.+|+..+++++.
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 01123445555554433 25679999999999999999999998875
No 123
>PRK09191 two-component response regulator; Provisional
Probab=99.20 E-value=7.4e-11 Score=112.59 Aligned_cols=121 Identities=16% Similarity=0.037 Sum_probs=95.8
Q ss_pred HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceeccc
Q 013472 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC 375 (442)
Q Consensus 296 Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~ 375 (442)
|+.+++..|.+.|+.+|.++.++..+++|++||+|+.+|+...+|++. ..|.||+++++++...+..... ..+.
T Consensus 2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~--~~~~~wl~~~~~~~~~~~~~~~----~~~~ 75 (261)
T PRK09191 2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEA--SSPRVGLYRLFHRLWSSAGAND----PEPG 75 (261)
T ss_pred chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCC--cchhhHHHHHHHHHhccccccC----CCCC
Confidence 578999999999999999999999999999999999999999999874 3699999999988764432211 0111
Q ss_pred ccHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 376 KLNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 376 ~v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
......+.+++.+|+.... .+.|++|||+.||+|+++|+..+.+++.
T Consensus 76 --~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~l~~s~~tV~~~l~ra~~ 130 (261)
T PRK09191 76 --SPFEARAERRLAGLTPLPRQAFLLTALEGFSVEEAAEILGVDPAEAEALLDDARA 130 (261)
T ss_pred --CCchHHHHHHHHhCCHHHhHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 1111256667777665543 5779999999999999999999888774
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=99.20 E-value=1.5e-10 Score=114.78 Aligned_cols=122 Identities=17% Similarity=0.070 Sum_probs=91.3
Q ss_pred HHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCc------ee
Q 013472 299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG------IK 372 (442)
Q Consensus 299 ~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~------ir 372 (442)
+++..|.+.++.+|++++++..++||++||+|+.+++. .|+.. ..|.+|++++++|.+++++|++++. .+
T Consensus 1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~~--~~~~awL~~Ia~n~~ld~lR~~~~~~~~~~~~~ 76 (281)
T TIGR02957 1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQI--ENPKAYLTKVVTRRCIDVLRSARARREVYVGPW 76 (281)
T ss_pred ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Ccccc--cCHHHHHHHHHHHHHHHHHHHhhhcccccCCCC
Confidence 47899999999999999999999999999999998775 55532 3699999999999999999976421 12
Q ss_pred ccccc----------HH---HH-HHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 373 IPCKL----------NR---EI-SKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 373 lP~~v----------~e---~i-~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
+|... .. .+ ..+..+...|+... -.+.+++|||+.||+|+.+|+..+++++.
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 01 11 12333444444332 25779999999999999999999998874
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=99.18 E-value=9.7e-11 Score=103.59 Aligned_cols=113 Identities=16% Similarity=0.152 Sum_probs=84.9
Q ss_pred HHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHh-----cCCCCCCChHHHHHHHHHHHHHHHHHhhcCce
Q 013472 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAER-----FDHTRGYKFSTYVQYWIRKSISKMVARHARGI 371 (442)
Q Consensus 297 re~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieK-----FDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~i 371 (442)
++.++..|.+.++.+|++|... +| +||.++.+|....+ |++. ..|.||++.+++|.+++++|++.+..
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 4689999999999999999662 34 49999999999865 5543 46999999999999999999765421
Q ss_pred ecc-------------cc--cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHH
Q 013472 372 KIP-------------CK--LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIR 416 (442)
Q Consensus 372 rlP-------------~~--v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk 416 (442)
... .. ..+....+.+++..|+.... .+.|++|||+.||||+++|+
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 01123346677777766543 67899999999999999996
No 126
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=99.10 E-value=4e-10 Score=100.86 Aligned_cols=105 Identities=11% Similarity=0.042 Sum_probs=78.4
Q ss_pred CCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecc----------------------
Q 013472 317 GLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP---------------------- 374 (442)
Q Consensus 317 g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP---------------------- 374 (442)
++..+++|++||+|+.+|+..+. ++ +..|.+|++.+++|.+++++|++.+.....
T Consensus 2 ~~~~~AeDivQe~fl~~~~~~~~-~~--~~~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 78 (161)
T PRK09047 2 RDDDAALDIVQDAMIKLAEKYGD-RP--AAEWPPLFQRILQNRIHDWFRRQKVRNTWVSLFSSFSDDDDDDDFDPLETLD 78 (161)
T ss_pred CCHHHHHHHHHHHHHHHHHHHhh-cc--cCchHHHHHHHHHHHHHHHHHhhcccccccccccccccccccccccHHHHhc
Confidence 45568999999999999999886 33 347999999999999999999865321110
Q ss_pred ------ccc------HHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 375 ------CKL------NREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 375 ------~~v------~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
... .+....+.+++..|+.... .+.|++|||+.||||+++|+..+++++.
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 1123346666666655542 6779999999999999999999988874
No 127
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=98.83 E-value=7.8e-09 Score=83.24 Aligned_cols=62 Identities=32% Similarity=0.480 Sum_probs=54.8
Q ss_pred HHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccccCCCCCccc
Q 013472 379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKY 440 (442)
Q Consensus 379 e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v~~~~d~~~ 440 (442)
+.+++|.++..+|.+++||.||.+|||+.|||++++|+.++.+++.++|||.+++.+++.++
T Consensus 1 E~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~~~~l 62 (78)
T PF04539_consen 1 EKLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDEDDSTL 62 (78)
T ss_dssp HHHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSSSEEG
T ss_pred ChHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCCCCch
Confidence 46789999999999999999999999999999999999999999999999999998877654
No 128
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=98.82 E-value=9.6e-08 Score=89.23 Aligned_cols=141 Identities=16% Similarity=0.125 Sum_probs=100.3
Q ss_pred HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCC---CCCHHh--HHHHHHHHHHHhHHhcCCCCCCChHHHHHHHH
Q 013472 283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGL---GIPFSD--LLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI 356 (442)
Q Consensus 283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~---g~d~ED--LIQEG~IGLirAieKFDp~kG~rFSTYa~~wI 356 (442)
-.+|+.+++.|+. |.++|+..|.+-++.+|+++... +.+.+| |++|.|+.+++.-...+.+.-..|-.|+..++
T Consensus 4 it~ll~~~~~GD~~A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~~lv~ea~lrl~~~~~~~~~~~~~~f~~~~~~~~ 83 (185)
T PF07638_consen 4 ITELLDRWRQGDEAALDQLFERYYPELRRLARRRLRRERRGHDLQDTALVHEAFLRLARRGRFVQFSDRRHFWALLARIM 83 (185)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHhccccCCchhHHHHHHHHHHHHhccccccCCCCHHHHHHHHHHHH
Confidence 3578899999987 99999999999999999987643 345555 57788888877333223332246999999999
Q ss_pred HHHHHHHHHhhcCcee------cc---------cccHHHHHHHHHHHHHHHH-----------HcCCCCcHHHHHHHhCC
Q 013472 357 RKSISKMVARHARGIK------IP---------CKLNREISKIQKARKALTN-----------SHGKYPEDIEIAKYTGL 410 (442)
Q Consensus 357 RnaI~r~LRkqsr~ir------lP---------~~v~e~i~kI~ka~~~L~~-----------elgr~PS~eEIAe~LGI 410 (442)
++.+++++|++....+ .+ ....+..-.+.++...|.. ..-.+.|.+|||+.|||
T Consensus 84 rr~lid~~R~~~a~KRg~~~~~~~l~~~~~~~~~~~~~~~~~l~e~l~~L~~l~~~~~~~v~l~~~~Gls~~EIA~~lgi 163 (185)
T PF07638_consen 84 RRKLIDHARRRQAQKRGGDQVRVELDERADSGDEPSPEELLELEEALERLLALDPRQRRVVELRFFEGLSVEEIAERLGI 163 (185)
T ss_pred HHHHHHHHHHHHHHhcCCCCcccchhhhhccccCCCHHHHHHHHHHHHHHHccCHHHHHHHHHHHHCCCCHHHHHHHHCc
Confidence 9999999997654322 11 1122233344444444432 11256799999999999
Q ss_pred CHHHHHHHHHhcc
Q 013472 411 SLAEIRSASECLR 423 (442)
Q Consensus 411 S~etVk~~l~~ar 423 (442)
|+.+|+..+..++
T Consensus 164 S~~tV~r~l~~aR 176 (185)
T PF07638_consen 164 SERTVRRRLRRAR 176 (185)
T ss_pred CHHHHHHHHHHHH
Confidence 9999999998876
No 129
>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPro: IPR009042 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1SMY_F 1IW7_P 1SIG_A 3IYD_F 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P 3DXJ_P ....
Probab=97.09 E-value=0.00028 Score=50.03 Aligned_cols=34 Identities=24% Similarity=0.220 Sum_probs=27.3
Q ss_pred HHHHHHhcccCC-CCCChHHHHHHHHHhHHHHHHH
Q 013472 223 FSAERALNSRGR-RLTIARNEAEMSKGVQVVANLE 256 (442)
Q Consensus 223 ~~~~~~~~~~~~-~lLt~eeE~eL~~~iq~~~~le 256 (442)
+.++.|++.+++ ||||++||++|+++|+.+...+
T Consensus 2 D~l~~Yl~ei~~~~LLt~eeE~~LA~~i~~g~~~a 36 (37)
T PF00140_consen 2 DSLRLYLKEIGRYPLLTAEEEIELARRIRKGDEAA 36 (37)
T ss_dssp HHHHHHHHHHHHS-EETTHHHHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhHHhc
Confidence 456778887875 9999999999999999886643
No 130
>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=96.42 E-value=0.072 Score=51.61 Aligned_cols=35 Identities=17% Similarity=0.311 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHH
Q 013472 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (442)
Q Consensus 254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~ 288 (442)
.+.+....+...+|++||.++.|+.+|++.+.+..
T Consensus 88 ~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~ 122 (238)
T TIGR02393 88 KLIKAERQLTQELGREPTDEELAERMGMPAEKVRE 122 (238)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 34556677888899999999999999999887654
No 131
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=96.17 E-value=0.076 Score=51.86 Aligned_cols=36 Identities=17% Similarity=0.178 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHH
Q 013472 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQH 289 (442)
Q Consensus 254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~ 289 (442)
.+.+....+...+|+.|+..++|+..|++.+++...
T Consensus 110 ~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~ 145 (251)
T PRK07670 110 KVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEAT 145 (251)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHH
Confidence 344556667778899999999999999998887653
No 132
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=96.03 E-value=0.027 Score=55.39 Aligned_cols=35 Identities=20% Similarity=0.280 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHH
Q 013472 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (442)
Q Consensus 254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~ 288 (442)
++.+.+.+|...+|++|+.++.|+.+|++.+++..
T Consensus 114 ~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~ 148 (256)
T PRK07408 114 QAKKVRQELRQELGRQPTDQEIAQALDISLEEWQE 148 (256)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHH
Confidence 45567778888999999999999999999887654
No 133
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=95.95 E-value=0.12 Score=53.76 Aligned_cols=128 Identities=13% Similarity=0.157 Sum_probs=72.2
Q ss_pred HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhchHHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHH-HHH
Q 013472 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAG-NVG 332 (442)
Q Consensus 254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG-~IG 332 (442)
++.+...+|...+|+.||.++.|+.+|++.+.+...+... . ...++++.+.++ -..
T Consensus 217 ~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~-------------------~----~~~SLd~~~~~~~~~~ 273 (367)
T PRK09210 217 KLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIA-------------------Q----EPVSLETPIGEEDDSH 273 (367)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHh-------------------c----CCCCcCCCCCCCCcch
Confidence 3455677788889999999999999999998865532211 1 111111111110 011
Q ss_pred HHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccccHHHHHHHHHHHHHHHHHc----CCCCcHHHHHHHh
Q 013472 333 VLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSH----GKYPEDIEIAKYT 408 (442)
Q Consensus 333 LirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v~e~i~kI~ka~~~L~~el----gr~PS~eEIAe~L 408 (442)
+...+. |..............++..+.++|. .+|..- ..| |...+ |.+.|.+|||+.|
T Consensus 274 l~d~i~--d~~~~~p~~~~~~~~~~~~l~~~l~------~L~~rE----r~V------l~lrygl~~~~~~tl~EIa~~l 335 (367)
T PRK09210 274 LGDFIE--DQDATSPADHAAYELLKEQLEDVLD------TLTDRE----ENV------LRLRFGLDDGRTRTLEEVGKVF 335 (367)
T ss_pred hhhhcc--CCCCCCHHHHHHHHHHHHHHHHHHH------hCCHHH----HHH------HHHHhccCCCCCccHHHHHHHH
Confidence 111111 1111223444555566666666653 234321 111 11122 3678999999999
Q ss_pred CCCHHHHHHHHHhc
Q 013472 409 GLSLAEIRSASECL 422 (442)
Q Consensus 409 GIS~etVk~~l~~a 422 (442)
|+|.++|+.+...|
T Consensus 336 gvs~erVrQi~~~A 349 (367)
T PRK09210 336 GVTRERIRQIEAKA 349 (367)
T ss_pred CCCHHHHHHHHHHH
Confidence 99999999885544
No 134
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=95.76 E-value=0.27 Score=48.60 Aligned_cols=35 Identities=26% Similarity=0.284 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHH
Q 013472 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (442)
Q Consensus 254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~ 288 (442)
.+.+.+..|+..+|++||.++.|...|++.+.+..
T Consensus 119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~ 153 (268)
T PRK06288 119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYNS 153 (268)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHH
Confidence 45566777888899999999999999999877654
No 135
>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=95.61 E-value=0.046 Score=43.52 Aligned_cols=57 Identities=21% Similarity=0.243 Sum_probs=47.9
Q ss_pred HHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhh----C--CCCCHHhHHHHHHHHHHHhHHhcC
Q 013472 285 VLKQHLAFGWY-CREELIKSTRPLVLFLARNYR----G--LGIPFSDLLQAGNVGVLQGAERFD 341 (442)
Q Consensus 285 eL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~----g--~g~d~EDLIQEG~IGLirAieKFD 341 (442)
+++.++.+|+. |.++++..|.++|.+++.|-. + .+.-=+|+-|+--..|++++-+|+
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 35677888977 999999999999999998732 2 245569999999999999999996
No 136
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=95.38 E-value=0.46 Score=51.84 Aligned_cols=132 Identities=16% Similarity=0.199 Sum_probs=70.2
Q ss_pred HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhchHHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHH-HHHH
Q 013472 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQA-GNVG 332 (442)
Q Consensus 254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQE-G~IG 332 (442)
++.+...+|...+|+.||.++.|+.+|++.+.+....+ +....+.+++.+.+ +-..
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 45566778888899999999999999999887655221 11122233332221 1111
Q ss_pred HHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCH
Q 013472 333 VLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSL 412 (442)
Q Consensus 333 LirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~ 412 (442)
+...+. |+..............+..+..++. .+|.. -..|-....-| ..+...|.+|||+.||||.
T Consensus 416 l~d~l~--D~~~~~p~~~~~~~~l~~~L~~aL~------~L~eR----Er~VI~lRyGL--~~~e~~TL~EIa~~lGVSr 481 (509)
T PRK05901 416 FGDFIE--DSEAVSPVDAVSFTLLQDQLQEVLE------TLSER----EAGVIRMRFGL--TDGQPKTLDEIGQVYGVTR 481 (509)
T ss_pred HHHhcc--CCCCCCHHHHHHHHHHHHHHHHHHh------hCCHH----HHHHHHHHhhc--cCCCCCCHHHHHHHHCCCH
Confidence 111111 1111112333334444444444443 12321 11111111111 0136789999999999999
Q ss_pred HHHHHHHHhc
Q 013472 413 AEIRSASECL 422 (442)
Q Consensus 413 etVk~~l~~a 422 (442)
++|+++...+
T Consensus 482 ERVRQIe~kA 491 (509)
T PRK05901 482 ERIRQIESKT 491 (509)
T ss_pred HHHHHHHHHH
Confidence 9999885544
No 137
>PRK05949 RNA polymerase sigma factor; Validated
Probab=95.38 E-value=0.31 Score=50.04 Aligned_cols=35 Identities=11% Similarity=0.275 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHH
Q 013472 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (442)
Q Consensus 254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~ 288 (442)
.+.+...++...+|++|+.++.|+.+|++.+.+..
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 34455667777889999999999999999877654
No 138
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=95.37 E-value=0.27 Score=48.80 Aligned_cols=34 Identities=21% Similarity=0.311 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHH
Q 013472 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (442)
Q Consensus 255 le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~ 288 (442)
+.+....|...+|+.||.++.|+.+|++.+++..
T Consensus 129 i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~ 162 (264)
T PRK07122 129 LGRATAELSQRLGRAPTASELAAELGMDREEVVE 162 (264)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 4456667778889999999999999999988765
No 139
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=95.35 E-value=0.35 Score=48.13 Aligned_cols=126 Identities=15% Similarity=0.079 Sum_probs=73.3
Q ss_pred HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhchHHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHH
Q 013472 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGV 333 (442)
Q Consensus 254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGL 333 (442)
.++++..+|+.++|++||.++.|+..|++.+++...+..+. -....++--.....+.. +
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 45567888999999999999999999999988776443332 11111111111111100 0
Q ss_pred HHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHH
Q 013472 334 LQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLA 413 (442)
Q Consensus 334 irAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~e 413 (442)
+ +...+..+..+-.+...+.+...+. .+|.. .+.+-. -.+..+.|..|||+.||||+.
T Consensus 170 ---~---~~~~~~~~~~~~~~~~~~~l~~ai~------~L~ER--------Ek~Vl~--l~y~eelt~kEI~~~LgISes 227 (247)
T COG1191 170 ---V---DDQIENPDDGVEKEELLEILKEAIE------PLPER--------EKLVLV--LRYKEELTQKEIAEVLGISES 227 (247)
T ss_pred ---h---hhccccchhHHHHHHHHHHHHHHHH------ccCHH--------HHHHHH--HHHHhccCHHHHHHHhCccHH
Confidence 0 1112234555556666666666664 12321 111111 123456799999999999999
Q ss_pred HHHHHHHhc
Q 013472 414 EIRSASECL 422 (442)
Q Consensus 414 tVk~~l~~a 422 (442)
+|-.+...+
T Consensus 228 ~VSql~kka 236 (247)
T COG1191 228 RVSRLHKKA 236 (247)
T ss_pred HHHHHHHHH
Confidence 998775443
No 140
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=95.31 E-value=0.28 Score=48.37 Aligned_cols=34 Identities=18% Similarity=0.200 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHH
Q 013472 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (442)
Q Consensus 255 le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~ 288 (442)
+.+....|...+|++|+.++.|+.+|++.+++..
T Consensus 112 l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~ 145 (257)
T PRK05911 112 LADAMDSLRQSLGKEPTDGELCEYLNISQQELSG 145 (257)
T ss_pred HHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHH
Confidence 3445556777889999999999999999887644
No 141
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=95.02 E-value=0.45 Score=48.91 Aligned_cols=35 Identities=29% Similarity=0.470 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHH
Q 013472 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (442)
Q Consensus 254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~ 288 (442)
++.++...|...+|++||.++.|+.+|++.+.+..
T Consensus 174 ~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~ 208 (324)
T PRK07921 174 KLARIKRELHQQLGREATDEELAEESGIPEEKIAD 208 (324)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHH
Confidence 45567778888899999999999999999887654
No 142
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=94.90 E-value=0.58 Score=44.74 Aligned_cols=35 Identities=26% Similarity=0.333 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHH
Q 013472 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (442)
Q Consensus 254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~ 288 (442)
.+.+...+|...+|+.|+.++.|+.+|++.+.+..
T Consensus 84 ~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~ 118 (224)
T TIGR02479 84 KLERAIRELEARLGREPTEEEIAEELGMDLKEYRQ 118 (224)
T ss_pred HHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHH
Confidence 45566677888889999999999999999877654
No 143
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=94.83 E-value=0.46 Score=50.61 Aligned_cols=36 Identities=11% Similarity=0.325 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHH
Q 013472 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQH 289 (442)
Q Consensus 254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~ 289 (442)
.+.+.+..|...+|+.|+.++.|+.+|++.+.+...
T Consensus 263 ~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~ 298 (415)
T PRK07598 263 KIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREV 298 (415)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 466677788888999999999999999999887653
No 144
>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=94.66 E-value=0.33 Score=47.60 Aligned_cols=35 Identities=14% Similarity=0.144 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHH
Q 013472 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQH 289 (442)
Q Consensus 255 le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~ 289 (442)
+.+...++..++|++||.++.|+.+|++.+++...
T Consensus 122 ~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~ 156 (254)
T TIGR02850 122 ALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFA 156 (254)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHH
Confidence 44556677788899999999999999999887654
No 145
>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=94.61 E-value=0.7 Score=46.50 Aligned_cols=35 Identities=14% Similarity=0.308 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHH
Q 013472 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (442)
Q Consensus 254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~ 288 (442)
.+.+.+..+...+|+.|+.++.|+.+|++.+.+..
T Consensus 162 ~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~ 196 (298)
T TIGR02997 162 KIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRE 196 (298)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 34455667777889999999999999999887654
No 146
>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=94.38 E-value=0.34 Score=46.42 Aligned_cols=34 Identities=32% Similarity=0.446 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHH
Q 013472 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (442)
Q Consensus 255 le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~ 288 (442)
+.+....+...+|+.||.++.|+.+|++.+++..
T Consensus 99 ~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~ 132 (231)
T TIGR02885 99 IRYMKEELSKELGREPTINELAEALGVSPEEIVM 132 (231)
T ss_pred HHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHH
Confidence 3345567777889999999999999999887654
No 147
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=94.33 E-value=0.47 Score=47.72 Aligned_cols=28 Identities=11% Similarity=-0.003 Sum_probs=24.8
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
.+.|.+|||+.||||.++|+.+.+.+..
T Consensus 244 ~~~t~~EIa~~lgvs~~~V~q~~~~Al~ 271 (289)
T PRK07500 244 DGATLEALGEELGISKERVRQIEARALE 271 (289)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5779999999999999999999877653
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=94.10 E-value=0.12 Score=41.27 Aligned_cols=38 Identities=26% Similarity=0.408 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHH
Q 013472 253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL 290 (442)
Q Consensus 253 ~~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l 290 (442)
.++.+++.+|+..+||.||.++.|+.+|++.+++...+
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 45778899999999999999999999999998876543
No 149
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=93.92 E-value=0.75 Score=46.97 Aligned_cols=35 Identities=14% Similarity=0.389 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHH
Q 013472 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (442)
Q Consensus 254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~ 288 (442)
.+.+....+...+|+.||.++.|+.+|++.+.+..
T Consensus 169 ~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~ 203 (317)
T PRK07405 169 KIKKAQRQLSQQLGRAATIGELAEELELTPKQVRE 203 (317)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHH
Confidence 45566777788889999999999999999877654
No 150
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=93.78 E-value=1.3 Score=42.82 Aligned_cols=29 Identities=14% Similarity=-0.011 Sum_probs=25.4
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
..+.|++|||+.||||+++|+..+++++.
T Consensus 198 ~~g~s~~EIA~~lgis~~tV~~~~~ra~~ 226 (236)
T PRK06986 198 QEELNLKEIGAVLGVSESRVSQIHSQAIK 226 (236)
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45779999999999999999999887763
No 151
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=93.66 E-value=1.2 Score=46.88 Aligned_cols=35 Identities=14% Similarity=0.230 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHH
Q 013472 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (442)
Q Consensus 254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~ 288 (442)
++.+....|...+|+.||.++.|+.+|++.+.+..
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 152
>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=93.64 E-value=0.064 Score=39.98 Aligned_cols=30 Identities=20% Similarity=0.067 Sum_probs=22.8
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 395 HGKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 395 lgr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
+..+.|++|||+.+|+|+.+|+..+++++.
T Consensus 23 ~~~g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 23 YFQGMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp HTS---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred HHHCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 457789999999999999999999988753
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=93.45 E-value=0.49 Score=46.21 Aligned_cols=34 Identities=15% Similarity=0.200 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHH
Q 013472 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (442)
Q Consensus 255 le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~ 288 (442)
+.+....+...+|+.|+.++.|...|++.+++..
T Consensus 118 ~~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~ 151 (255)
T TIGR02941 118 IKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLE 151 (255)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 4445666777789999999999999999877654
No 154
>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=93.00 E-value=1.5 Score=43.82 Aligned_cols=29 Identities=17% Similarity=0.013 Sum_probs=25.7
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
..+.|+.|||+.||+|+++|+.++++++.
T Consensus 240 ~e~~s~~EIA~~Lgis~~tVk~~l~rAlk 268 (285)
T TIGR02394 240 YEPATLEEVAAEVGLTRERVRQIQVEALK 268 (285)
T ss_pred CCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 35679999999999999999999888763
No 155
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=92.95 E-value=1.1 Score=43.89 Aligned_cols=34 Identities=15% Similarity=0.152 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHH
Q 013472 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (442)
Q Consensus 255 le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~ 288 (442)
+.+...++...+|+.|+..+.|..+|++.+++..
T Consensus 125 ~~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~ 158 (258)
T PRK08215 125 ALQVREKLINENSKEPTVEEIAKELEVPREEVVF 158 (258)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHH
Confidence 3445667777889999999999999999988654
No 156
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=92.57 E-value=5.2 Score=39.08 Aligned_cols=28 Identities=11% Similarity=-0.005 Sum_probs=25.1
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
..+.|.+|||+.||||+++|+..+++++
T Consensus 219 ~~g~s~~eIA~~l~is~~tV~~~~~ra~ 246 (257)
T PRK08583 219 IENLSQKETGERLGISQMHVSRLQRQAI 246 (257)
T ss_pred hCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4778999999999999999999988765
No 157
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=92.41 E-value=1.5 Score=48.70 Aligned_cols=35 Identities=23% Similarity=0.402 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHH
Q 013472 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (442)
Q Consensus 254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~ 288 (442)
++.+....+...+|++||.++.|+.+|++.+.+..
T Consensus 468 k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~ 502 (619)
T PRK05658 468 KLNRISRQMLQEIGREPTPEELAERLGMPEDKVRK 502 (619)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 45566777888899999999999999999887654
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=92.21 E-value=0.62 Score=44.48 Aligned_cols=29 Identities=17% Similarity=0.020 Sum_probs=25.2
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
..+.|++|||+.+|+|..+|...++++..
T Consensus 192 ~~~~s~~eIA~~lgis~~~v~~~~~ra~~ 220 (227)
T TIGR02980 192 FEDKTQSEIAERLGISQMHVSRLLRRALK 220 (227)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 35779999999999999999999887653
No 159
>PHA02547 55 RNA polymerase sigma factor; Provisional
Probab=92.08 E-value=0.47 Score=44.73 Aligned_cols=65 Identities=15% Similarity=0.179 Sum_probs=53.1
Q ss_pred hHHHHHHHHHHhhCCCCC---HHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhc
Q 013472 304 TRPLVLFLARNYRGLGIP---FSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA 368 (442)
Q Consensus 304 nlrLV~sIAkrY~g~g~d---~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqs 368 (442)
-+..+-.++++|.-++.. -+|.|.+|.-.+++.+..||+++...+-+|++.++-++..+.|.+.+
T Consensus 46 imkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~kEk 113 (179)
T PHA02547 46 IMKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIKKEK 113 (179)
T ss_pred HHHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHHHHH
Confidence 345555566666444444 68999999999999999999999999999999999999999887654
No 160
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=92.01 E-value=0.51 Score=37.49 Aligned_cols=44 Identities=18% Similarity=0.240 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCC-HHHHHHHHHhc
Q 013472 379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLS-LAEIRSASECL 422 (442)
Q Consensus 379 e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS-~etVk~~l~~a 422 (442)
+...+|-.++.+...+.|..||..|||+.+|++ ..+|...+...
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 344567778888888899999999999999997 99999887654
No 161
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=91.73 E-value=1.7 Score=42.31 Aligned_cols=34 Identities=6% Similarity=0.120 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHH
Q 013472 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (442)
Q Consensus 255 le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~ 288 (442)
+.+....+...+|+.|+.++.|+.+|++.+++..
T Consensus 103 i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~ 136 (231)
T PRK12427 103 TNDAIREIAKRLGHEPNFEEISAELNLTAEEYQE 136 (231)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHH
Confidence 4456677778889999999999999999887654
No 162
>PRK05572 sporulation sigma factor SigF; Validated
Probab=91.72 E-value=2.1 Score=41.84 Aligned_cols=34 Identities=24% Similarity=0.357 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHH
Q 013472 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLK 287 (442)
Q Consensus 254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~ 287 (442)
++.+....+..++|+.|+..+.|+..|++.+.+.
T Consensus 119 ~~~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v~ 152 (252)
T PRK05572 119 KIRKDKDELSKELGREPTIEELAEYLGVTPEEVV 152 (252)
T ss_pred HHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHH
Confidence 3455566777778999999999999999887654
No 163
>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=90.87 E-value=0.65 Score=34.18 Aligned_cols=30 Identities=20% Similarity=-0.005 Sum_probs=25.0
Q ss_pred HcCCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 394 SHGKYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 394 elgr~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
.+..+.|.+|||+.||+|.++|+.+...+.
T Consensus 16 ~y~~~~t~~eIa~~lg~s~~~V~~~~~~al 45 (50)
T PF04545_consen 16 RYFEGLTLEEIAERLGISRSTVRRILKRAL 45 (50)
T ss_dssp HHTST-SHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred HhcCCCCHHHHHHHHCCcHHHHHHHHHHHH
Confidence 347788999999999999999999887653
No 164
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=89.73 E-value=5.1 Score=41.14 Aligned_cols=29 Identities=14% Similarity=0.038 Sum_probs=25.7
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
..+.|.+|||+.||+|+++|+.++++++.
T Consensus 280 ~e~~s~~EIA~~Lgis~~tV~~~~~rAl~ 308 (325)
T PRK05657 280 YEAATLEDVAREIGLTRERVRQIQVEALR 308 (325)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 35789999999999999999999887764
No 165
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=85.30 E-value=10 Score=38.10 Aligned_cols=27 Identities=19% Similarity=0.129 Sum_probs=23.7
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
.+.|.+|||+.||||.++|+.+.+.+.
T Consensus 247 ~~~Tl~EIA~~lgvS~~rVrqi~~~Al 273 (284)
T PRK06596 247 DKSTLQELAAEYGVSAERVRQIEKNAM 273 (284)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 578999999999999999999876553
No 166
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=85.22 E-value=23 Score=37.07 Aligned_cols=36 Identities=28% Similarity=0.417 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHH
Q 013472 252 VANLERIKTTLEKESGKAASLNCWAQAAGVSERVLK 287 (442)
Q Consensus 252 ~~~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~ 287 (442)
.-++.+++.+|...+|++|+.++.|+.+|++..+..
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 345667788888889999999999999999987543
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=81.77 E-value=1.7 Score=35.57 Aligned_cols=25 Identities=20% Similarity=0.106 Sum_probs=22.6
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHh
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASEC 421 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~ 421 (442)
.+.|+.|||+.||+|+.+|+..+..
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 5779999999999999999998863
No 168
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=80.22 E-value=11 Score=39.45 Aligned_cols=123 Identities=20% Similarity=0.056 Sum_probs=78.6
Q ss_pred HHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccccH
Q 013472 299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLN 378 (442)
Q Consensus 299 ~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v~ 378 (442)
..+..-.+.++.---+|+++-..+||.+||.|+...+.--+=-+-+ .-..|++-..|+.-+|.+|++.+....|.+..
T Consensus 9 ~~~r~~~~r~~a~L~r~~rd~dlAEEa~~dA~~~Ale~WPr~G~P~--~PaAWL~~v~R~~aiD~~Rr~~~~~~~~~el~ 86 (415)
T COG4941 9 AAARIERPRAMAALARYLRDLDLAEEALQDAFAAALERWPRAGPPR--NPAAWLIAVGRNRAIDRVRRRARRDAAPPELL 86 (415)
T ss_pred HHHHHhhhHHHHHHHHHhcccchHHHHHHHHHHHHHHhCcccCCCC--ChHHHHHHHHhhhHHHHHHHHHHhccCChhhc
Confidence 3344445555555556777778899999999876544433333333 47899999999999999999877655544322
Q ss_pred HHH--HHHHHH----------------------------HHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 379 REI--SKIQKA----------------------------RKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 379 e~i--~kI~ka----------------------------~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
... ..+..+ .-.|.-..--+.|.+|||...=+++.++.+.+-+++
T Consensus 87 ~~~e~~e~~~a~~~~d~~i~Dd~LRLiFvccHPal~~~~riALtLR~v~GLs~~eIArAFLv~e~am~QRivRAK 161 (415)
T COG4941 87 LSDEDEEMEEAEALDDEHIRDDRLRLIFVCCHPALPPEQRIALTLRLVGGLSTAEIARAFLVPEAAMAQRIVRAK 161 (415)
T ss_pred ccccchhhhccccccccccchhhHHhhhhhcCCCCChhhHHHHHHHHHcCCcHHHHHHHHcCCcHHHHHHHHHHH
Confidence 111 111111 011111112456889999999999999988877766
No 169
>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=78.83 E-value=4.4 Score=28.40 Aligned_cols=28 Identities=25% Similarity=0.191 Sum_probs=24.4
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
..+.+..+||+.+|++..+|...++.++
T Consensus 24 ~~~~~~~~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 24 GEGLSYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3577999999999999999999887664
No 170
>PRK00118 putative DNA-binding protein; Validated
Probab=78.55 E-value=3.6 Score=35.84 Aligned_cols=29 Identities=14% Similarity=-0.159 Sum_probs=25.5
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
..+.|+.|||+.+|+|..+|...+.+++.
T Consensus 31 ~eg~S~~EIAe~lGIS~~TV~r~L~RArk 59 (104)
T PRK00118 31 LDDYSLGEIAEEFNVSRQAVYDNIKRTEK 59 (104)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 45789999999999999999999887763
No 171
>PRK06930 positive control sigma-like factor; Validated
Probab=78.47 E-value=2.8 Score=39.19 Aligned_cols=30 Identities=23% Similarity=0.184 Sum_probs=26.2
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 395 HGKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 395 lgr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
+..+.|+.|||+.||+|+.+|+..+.+++.
T Consensus 127 ~~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~ 156 (170)
T PRK06930 127 RGYGLSYSEIADYLNIKKSTVQSMIERAEK 156 (170)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 346789999999999999999999887764
No 172
>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=78.28 E-value=6.4 Score=28.56 Aligned_cols=24 Identities=25% Similarity=0.201 Sum_probs=19.4
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHh
Q 013472 398 YPEDIEIAKYTGLSLAEIRSASEC 421 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~l~~ 421 (442)
..++.|||+.+|+|..+|...++.
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 358899999999999999998765
No 173
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=75.95 E-value=4.9 Score=29.21 Aligned_cols=27 Identities=22% Similarity=0.021 Sum_probs=18.6
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHh
Q 013472 395 HGKYPEDIEIAKYTGLSLAEIRSASEC 421 (442)
Q Consensus 395 lgr~PS~eEIAe~LGIS~etVk~~l~~ 421 (442)
+..+.|..|||+.||.+..+|...+++
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 346789999999999999999887754
No 174
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=75.88 E-value=5.3 Score=28.63 Aligned_cols=27 Identities=19% Similarity=0.190 Sum_probs=23.6
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
.+.+..|||+.+|+|..+|...+..+.
T Consensus 17 ~g~s~~eia~~l~is~~tv~~~~~~~~ 43 (58)
T smart00421 17 EGLTNKEIAERLGISEKTVKTHLSNIM 43 (58)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 356999999999999999999988765
No 175
>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=75.81 E-value=6.5 Score=29.15 Aligned_cols=36 Identities=31% Similarity=0.218 Sum_probs=25.9
Q ss_pred HHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 387 ARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 387 a~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
....|....+ ..|.+|||+.||+|..+|...+...+
T Consensus 5 il~~L~~~~~-~it~~eLa~~l~vS~rTi~~~i~~L~ 40 (55)
T PF08279_consen 5 ILKLLLESKE-PITAKELAEELGVSRRTIRRDIKELR 40 (55)
T ss_dssp HHHHHHHTTT-SBEHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHHHHHcCC-CcCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 3344434333 38999999999999999999877554
No 176
>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=75.26 E-value=6.4 Score=31.12 Aligned_cols=30 Identities=20% Similarity=0.140 Sum_probs=24.8
Q ss_pred HHHHHcCCCCcHHHHHHHhCCCHHHHHHHH
Q 013472 390 ALTNSHGKYPEDIEIAKYTGLSLAEIRSAS 419 (442)
Q Consensus 390 ~L~~elgr~PS~eEIAe~LGIS~etVk~~l 419 (442)
++..+.+...+..+||+.||++..+|+..-
T Consensus 14 e~y~~~~g~i~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 14 EIYKESNGKIKLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred HHHHHhCCCccHHHHHHHHCCCHHHHHHHh
Confidence 444556778899999999999999998754
No 177
>PHA02591 hypothetical protein; Provisional
Probab=75.22 E-value=6.5 Score=32.79 Aligned_cols=24 Identities=29% Similarity=0.224 Sum_probs=22.0
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHH
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASE 420 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~ 420 (442)
++.|.++||+.||++..+|+..++
T Consensus 58 qGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 58 KGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHh
Confidence 478999999999999999999875
No 178
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=75.13 E-value=7.4 Score=28.47 Aligned_cols=26 Identities=15% Similarity=0.173 Sum_probs=22.4
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHh
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASEC 421 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ 421 (442)
...+|..+||+.+|++..+|..++..
T Consensus 25 ~~~~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 25 RESRSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred hhcCCHHHHHHHHCCCHHHHHHHHHh
Confidence 34479999999999999999998764
No 179
>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=74.86 E-value=3.4 Score=28.63 Aligned_cols=25 Identities=24% Similarity=0.319 Sum_probs=19.3
Q ss_pred CcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 399 PEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 399 PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
.|.+|||+.+|++.++|-.++...+
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 4789999999999999998876543
No 180
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=74.68 E-value=4.7 Score=29.33 Aligned_cols=23 Identities=26% Similarity=0.083 Sum_probs=17.8
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHH
Q 013472 398 YPEDIEIAKYTGLSLAEIRSASE 420 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~l~ 420 (442)
+.|..+||+.+||+..+|..++.
T Consensus 21 G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 21 GMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp T--HHHHHHHTTS-HHHHHHHHC
T ss_pred CCCHHHHHHHHCcCHHHHHHHHh
Confidence 47999999999999999988763
No 181
>PRK04217 hypothetical protein; Provisional
Probab=73.96 E-value=5.6 Score=35.00 Aligned_cols=28 Identities=21% Similarity=0.108 Sum_probs=24.8
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
.+.|++|||+.+|||..+|...++.++.
T Consensus 57 eGlS~~EIAk~LGIS~sTV~r~L~RArk 84 (110)
T PRK04217 57 EGLTQEEAGKRMGVSRGTVWRALTSARK 84 (110)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4679999999999999999999887764
No 182
>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=73.57 E-value=6 Score=30.06 Aligned_cols=46 Identities=20% Similarity=0.228 Sum_probs=31.4
Q ss_pred cccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHH
Q 013472 373 IPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSA 418 (442)
Q Consensus 373 lP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~ 418 (442)
+|....+.+...-+....|..+--...+-.|||+.+|++..+|+.=
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 4555555556666677777665446679999999999999999864
No 183
>PF14502 HTH_41: Helix-turn-helix domain
Probab=73.39 E-value=4.4 Score=30.70 Aligned_cols=35 Identities=20% Similarity=0.212 Sum_probs=28.5
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhcc--cCCCCcc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLR--IVGSIDQ 430 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar--~~~SLD~ 430 (442)
.|-||+.|.++.++++.++|+.++.... ..++|+.
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 4779999999999999999999988654 3455553
No 184
>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=72.70 E-value=7.1 Score=28.16 Aligned_cols=28 Identities=18% Similarity=0.182 Sum_probs=24.2
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
.+.+..|||+.+|++..+|+..++.++.
T Consensus 14 ~~~s~~eia~~l~~s~~tv~~~~~~~~~ 41 (57)
T cd06170 14 EGKTNKEIADILGISEKTVKTHLRNIMR 41 (57)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3569999999999999999999887653
No 185
>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=5.5 Score=30.60 Aligned_cols=27 Identities=15% Similarity=0.071 Sum_probs=24.1
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
|..|..|||+.|||+..++...++.+-
T Consensus 22 R~~tl~elA~~lgis~st~~~~LRrae 48 (53)
T PF04967_consen 22 RRITLEELAEELGISKSTVSEHLRRAE 48 (53)
T ss_pred CcCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 667999999999999999999888764
No 186
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=70.38 E-value=4.6 Score=30.54 Aligned_cols=30 Identities=20% Similarity=0.154 Sum_probs=24.0
Q ss_pred HcCCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 394 SHGKYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 394 elgr~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
-+..+.+..|||+.+|+++.+|+.......
T Consensus 14 ~l~~G~~~~eIA~~l~is~~tV~~~~~~i~ 43 (58)
T PF00196_consen 14 LLAQGMSNKEIAEELGISEKTVKSHRRRIM 43 (58)
T ss_dssp HHHTTS-HHHHHHHHTSHHHHHHHHHHHHH
T ss_pred HHHhcCCcchhHHhcCcchhhHHHHHHHHH
Confidence 345677999999999999999998876554
No 187
>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=69.71 E-value=15 Score=26.49 Aligned_cols=27 Identities=19% Similarity=0.155 Sum_probs=21.0
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
....|..|||+.+|+|..+|...++..
T Consensus 15 ~~~~t~~ela~~~~is~~tv~~~l~~L 41 (48)
T PF13412_consen 15 NPRITQKELAEKLGISRSTVNRYLKKL 41 (48)
T ss_dssp CTTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred cCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 334899999999999999999987643
No 188
>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=69.27 E-value=16 Score=27.55 Aligned_cols=27 Identities=26% Similarity=0.258 Sum_probs=23.3
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
...+..|||+.+|++..+|..++....
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~ 50 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELE 50 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 356999999999999999999887554
No 189
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=69.04 E-value=5.2 Score=29.06 Aligned_cols=26 Identities=27% Similarity=0.052 Sum_probs=19.0
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 398 YPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
+.|..+||+.+|+|..+|...++..+
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 66999999999999999999987654
No 190
>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=68.39 E-value=9.3 Score=33.22 Aligned_cols=31 Identities=16% Similarity=-0.016 Sum_probs=23.4
Q ss_pred HHcCCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 393 NSHGKYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 393 ~elgr~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
.-+..+.|..|||+.+|||.+.|.+.++++.
T Consensus 28 lyy~eDlSlsEIAe~~~iSRqaV~d~ikr~~ 58 (101)
T PF04297_consen 28 LYYEEDLSLSEIAEELGISRQAVYDSIKRAE 58 (101)
T ss_dssp HHCTS---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHccCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3456889999999999999999999988776
No 191
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=68.25 E-value=14 Score=31.50 Aligned_cols=40 Identities=15% Similarity=0.120 Sum_probs=28.9
Q ss_pred HHHHHHHHHHcC-CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 385 QKARKALTNSHG-KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 385 ~ka~~~L~~elg-r~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
+....+|...+. ...|++|||+.||+++.+++.+++...+
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 334444544333 4569999999999999999999865543
No 192
>PF13730 HTH_36: Helix-turn-helix domain
Probab=68.22 E-value=6.3 Score=29.20 Aligned_cols=27 Identities=30% Similarity=0.421 Sum_probs=23.4
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
+--||.+.||+.+|++..+|..++...
T Consensus 23 ~~~pS~~~la~~~g~s~~Tv~~~i~~L 49 (55)
T PF13730_consen 23 GCFPSQETLAKDLGVSRRTVQRAIKEL 49 (55)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 356899999999999999999987643
No 193
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=68.11 E-value=13 Score=28.86 Aligned_cols=27 Identities=19% Similarity=0.062 Sum_probs=23.5
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
.+.++.|||+.||++..+|.....+..
T Consensus 12 ~G~~~~eIA~~Lg~~~~TV~~W~~r~~ 38 (58)
T PF06056_consen 12 QGWSIKEIAEELGVPRSTVYSWKDRYK 38 (58)
T ss_pred cCCCHHHHHHHHCCChHHHHHHHHhhC
Confidence 477999999999999999999877654
No 194
>PF12728 HTH_17: Helix-turn-helix domain
Probab=66.98 E-value=8 Score=28.29 Aligned_cols=25 Identities=16% Similarity=0.004 Sum_probs=21.8
Q ss_pred CcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 399 PEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 399 PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
.|.+|+|+.|||+..+|...++...
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
>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=66.39 E-value=6.9 Score=35.72 Aligned_cols=28 Identities=21% Similarity=0.050 Sum_probs=24.2
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
..+.|++|||+.||+|..+|....+.++
T Consensus 19 ~~GlTq~EIAe~LgiS~stV~~~e~ra~ 46 (137)
T TIGR00721 19 EKGLSQKEIAKELKTTRANVSAIEKRAM 46 (137)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHhHH
Confidence 3578999999999999999998876654
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=65.72 E-value=9.3 Score=37.85 Aligned_cols=26 Identities=23% Similarity=0.133 Sum_probs=22.6
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
.+.|..|||+.||||.++|+.+...+
T Consensus 235 ~~~t~~eIA~~lgvS~~~V~q~~~~A 260 (270)
T TIGR02392 235 DKLTLQELAAEYGVSAERIRQIEKNA 260 (270)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 46799999999999999999876654
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=64.85 E-value=9.9 Score=26.69 Aligned_cols=26 Identities=19% Similarity=0.096 Sum_probs=22.4
Q ss_pred CcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 399 PEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 399 PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
.|.+|+|+.+|++..+|....+...-
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g~i 27 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEGEL 27 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcCCC
Confidence 47899999999999999999876553
No 198
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=61.56 E-value=9.7 Score=34.93 Aligned_cols=28 Identities=29% Similarity=0.223 Sum_probs=23.5
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
..+.|.+|||+.||+|..+|....+.++
T Consensus 19 ~~GlTq~EIAe~LGiS~~tVs~ie~ra~ 46 (141)
T PRK03975 19 ERGLTQQEIADILGTSRANVSSIEKRAR 46 (141)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3578999999999999999988866543
No 199
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=61.48 E-value=11 Score=27.56 Aligned_cols=26 Identities=31% Similarity=0.425 Sum_probs=22.9
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 398 YPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
-||..|||+.+|+|..+|..++....
T Consensus 20 l~s~~~la~~~~vs~~tv~~~l~~L~ 45 (60)
T smart00345 20 LPSERELAAQLGVSRTTVREALSRLE 45 (60)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45999999999999999999987654
No 200
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=61.31 E-value=24 Score=31.01 Aligned_cols=40 Identities=8% Similarity=-0.001 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHH
Q 013472 381 ISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASE 420 (442)
Q Consensus 381 i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~ 420 (442)
...+.++...+...+...++.++||+.+|+++..+....+
T Consensus 8 ~~~i~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk 47 (127)
T PRK11511 8 AITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFK 47 (127)
T ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3456677777777778889999999999999999987754
No 201
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=60.47 E-value=9.9 Score=28.23 Aligned_cols=23 Identities=17% Similarity=0.154 Sum_probs=20.7
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhc
Q 013472 400 EDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 400 S~eEIAe~LGIS~etVk~~l~~a 422 (442)
|..+||+.+|+|..+|-.+++..
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 57899999999999999998755
No 202
>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=60.29 E-value=31 Score=31.56 Aligned_cols=49 Identities=22% Similarity=0.086 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCC
Q 013472 380 EISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSI 428 (442)
Q Consensus 380 ~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SL 428 (442)
......++..-|...-++..|..||++.+|+++..|...++-.|-.++=
T Consensus 28 ~e~~f~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~IreGRL~~~~ 76 (137)
T TIGR03826 28 EEREFEKVYKFLRKHENRQATVSEIVEETGVSEKLILKFIREGRLQLKH 76 (137)
T ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCCeeccC
Confidence 3344444444454444566899999999999999999999888854443
No 203
>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=60.29 E-value=14 Score=25.75 Aligned_cols=25 Identities=20% Similarity=0.191 Sum_probs=21.7
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 400 EDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 400 S~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
|..|+|+.+|++..+|.........
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcCCC
Confidence 6789999999999999998876553
No 204
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=57.59 E-value=15 Score=35.25 Aligned_cols=30 Identities=17% Similarity=0.104 Sum_probs=24.9
Q ss_pred HHcCCCCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 393 NSHGKYPEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 393 ~elgr~PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
..+.++.|..|||+.|++|+.||+......
T Consensus 158 ~lla~G~snkeIA~~L~iS~~TVk~h~~~i 187 (211)
T COG2197 158 RLLAEGLSNKEIAEELNLSEKTVKTHVSNI 187 (211)
T ss_pred HHHHCCCCHHHHHHHHCCCHhHHHHHHHHH
Confidence 334678899999999999999999876544
No 205
>PRK14082 hypothetical protein; Provisional
Probab=57.52 E-value=42 Score=27.06 Aligned_cols=54 Identities=17% Similarity=0.087 Sum_probs=41.0
Q ss_pred HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHH
Q 013472 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTY 351 (442)
Q Consensus 296 Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTY 351 (442)
..+.+|..+.+.|.+-.. .....+-+||.||--|.+++-+..++...+.-|--|
T Consensus 10 e~e~ii~~FepkIkKsL~--~T~yqeREDLeQElk~Ki~eK~~~~~~~e~PGF~ef 63 (65)
T PRK14082 10 EIEHLIENFSPMIKKKLS--NTSYQEREDLEQELKIKIIEKADMLLCQEVPGFWEF 63 (65)
T ss_pred HHHHHHHHccHHHHHHHh--cCChhhHHHHHHHHHHHHHHHHHHhhcccCCcHHHh
Confidence 567788888888776443 234577899999999999999999987665556444
No 206
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=57.24 E-value=15 Score=34.90 Aligned_cols=36 Identities=8% Similarity=0.097 Sum_probs=27.8
Q ss_pred HHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 388 RKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 388 ~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
..+.......+.|.+|||+.||+|+.+|+.......
T Consensus 142 E~eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~I~ 177 (207)
T PRK15411 142 ESSMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIK 177 (207)
T ss_pred HHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHH
Confidence 334444456788999999999999999999876443
No 207
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=56.30 E-value=29 Score=28.11 Aligned_cols=36 Identities=17% Similarity=0.049 Sum_probs=23.6
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQK 431 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~ 431 (442)
.++.|..|+|+.||++..+|-.+++--....|+|.-
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 467899999999999999999887533444576653
No 208
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=55.54 E-value=18 Score=33.64 Aligned_cols=33 Identities=21% Similarity=0.050 Sum_probs=26.0
Q ss_pred HHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 390 ALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 390 ~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
+....+..+.|..|||+.|+||..||+......
T Consensus 157 evl~~~~~G~s~~eIA~~l~iS~~TV~~h~~~i 189 (216)
T PRK10840 157 EVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSA 189 (216)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 333344568899999999999999999886544
No 209
>PRK13870 transcriptional regulator TraR; Provisional
Probab=54.93 E-value=12 Score=36.63 Aligned_cols=29 Identities=17% Similarity=0.035 Sum_probs=25.3
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
..+.|..|||.+||||+.+|+..++.++.
T Consensus 186 A~GKT~~EIa~ILgISe~TV~~Hl~na~~ 214 (234)
T PRK13870 186 AVGKTMEEIADVEGVKYNSVRVKLREAMK 214 (234)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 34679999999999999999999887764
No 210
>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=54.88 E-value=23 Score=35.19 Aligned_cols=28 Identities=18% Similarity=0.167 Sum_probs=24.7
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
..+.|..|||+.||||+.+|+..++.+.
T Consensus 203 a~G~s~~eIA~~L~IS~~TVk~hl~~i~ 230 (247)
T TIGR03020 203 RDGKTNEEIAAILGISSLTVKNHLQHIF 230 (247)
T ss_pred HCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3578999999999999999999987665
No 211
>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=54.81 E-value=44 Score=27.84 Aligned_cols=43 Identities=30% Similarity=0.176 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 381 ISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 381 i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
...|-+++-++..+.++...-++||+.+|++..+|++.|....
T Consensus 6 q~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le 48 (78)
T PF03444_consen 6 QREILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADLE 48 (78)
T ss_pred HHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHH
Confidence 3455666666667778889999999999999999999887554
No 212
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=54.07 E-value=38 Score=28.36 Aligned_cols=38 Identities=16% Similarity=-0.037 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHH
Q 013472 383 KIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASE 420 (442)
Q Consensus 383 kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~ 420 (442)
.+.++...+...+...++.++||+.+|+|...+....+
T Consensus 6 ~~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~ 43 (107)
T PRK10219 6 IIQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFR 43 (107)
T ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 35566666666777889999999999999999877654
No 213
>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=53.67 E-value=21 Score=29.97 Aligned_cols=41 Identities=27% Similarity=0.207 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 381 ISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 381 i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
..+|-.+++. ........+..+||+.|++++.+|+.++...
T Consensus 49 ~~~Vl~~i~~-~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L 89 (102)
T PF08784_consen 49 QDKVLNFIKQ-QPNSEEGVHVDEIAQQLGMSENEVRKALDFL 89 (102)
T ss_dssp HHHHHHHHHC-----TTTEEHHHHHHHSTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHh-cCCCCCcccHHHHHHHhCcCHHHHHHHHHHH
Confidence 3344444444 2223457899999999999999999998754
No 214
>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=53.60 E-value=35 Score=26.48 Aligned_cols=38 Identities=24% Similarity=0.208 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 384 IQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 384 I~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
.-+++-.|.. .+..++..+||+.||++..+|-..++..
T Consensus 9 YL~~Iy~l~~-~~~~v~~~~iA~~L~vs~~tvt~ml~~L 46 (60)
T PF01325_consen 9 YLKAIYELSE-EGGPVRTKDIAERLGVSPPTVTEMLKRL 46 (60)
T ss_dssp HHHHHHHHHH-CTSSBBHHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHc-CCCCccHHHHHHHHCCChHHHHHHHHHH
Confidence 3445556655 4678899999999999999999887754
No 215
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=53.54 E-value=30 Score=25.68 Aligned_cols=27 Identities=19% Similarity=0.284 Sum_probs=23.1
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
..+.+..|||..+|+++.+|...+...
T Consensus 17 ~~G~s~~eia~~l~is~~tV~~h~~~i 43 (65)
T COG2771 17 AQGKSNKEIARILGISEETVKTHLRNI 43 (65)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 445799999999999999999887654
No 216
>PRK12423 LexA repressor; Provisional
Probab=53.21 E-value=36 Score=32.37 Aligned_cols=42 Identities=24% Similarity=0.182 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHHcCCCCcHHHHHHHhC-CCHHHHHHHHHhc
Q 013472 381 ISKIQKARKALTNSHGKYPEDIEIAKYTG-LSLAEIRSASECL 422 (442)
Q Consensus 381 i~kI~ka~~~L~~elgr~PS~eEIAe~LG-IS~etVk~~l~~a 422 (442)
...|-..+.....+.|..||..|||+.+| .+...|+..+...
T Consensus 8 q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L 50 (202)
T PRK12423 8 RAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQAL 50 (202)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHH
Confidence 34455555555556688899999999999 4899998776543
No 217
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=53.19 E-value=20 Score=35.17 Aligned_cols=36 Identities=6% Similarity=-0.088 Sum_probs=27.9
Q ss_pred HHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 388 RKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 388 ~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
..++...+.++.|.+|||+.|+|++.+|+.......
T Consensus 148 E~eVL~Lia~G~SnkEIA~~L~IS~~TVk~hvs~I~ 183 (217)
T PRK13719 148 QNDVFILYSFGFSHEYIAQLLNITVGSSKNKISEIL 183 (217)
T ss_pred HHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 334444456789999999999999999998866543
No 218
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=53.05 E-value=43 Score=26.44 Aligned_cols=30 Identities=23% Similarity=0.348 Sum_probs=24.5
Q ss_pred HcCC-CCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 394 SHGK-YPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 394 elgr-~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
..|. ..+..|||+.|||+..+|...+....
T Consensus 17 ~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~ 47 (68)
T smart00550 17 NSGDETSTALQLAKNLGLPKKEVNRVLYSLE 47 (68)
T ss_pred HCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3444 48999999999999999999987543
No 219
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=52.85 E-value=20 Score=28.35 Aligned_cols=28 Identities=32% Similarity=0.213 Sum_probs=22.3
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
...++..|||+.+||+..+++..|....
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 5567999999999999999999977543
No 220
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=52.68 E-value=25 Score=33.39 Aligned_cols=30 Identities=17% Similarity=-0.025 Sum_probs=25.8
Q ss_pred HcCCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 394 SHGKYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 394 elgr~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
....+.|.+|||+.||+|..+|+..+....
T Consensus 174 ~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~ 203 (239)
T PRK10430 174 HQDYEFSTDELANAVNISRVSCRKYLIWLV 203 (239)
T ss_pred CCCCCcCHHHHHHHhCchHHHHHHHHHHHH
Confidence 346788999999999999999999987653
No 221
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=52.58 E-value=55 Score=30.92 Aligned_cols=26 Identities=19% Similarity=0.257 Sum_probs=22.6
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 398 YPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
..|.++||+.+|++.++|-.+++..+
T Consensus 184 ~lt~~~iA~~lG~sr~tvsR~l~~l~ 209 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETISRLLGRFQ 209 (235)
T ss_pred cccHHHHHHHhCCcHHHHHHHHHHHH
Confidence 46899999999999999999887554
No 222
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=51.29 E-value=22 Score=34.02 Aligned_cols=33 Identities=12% Similarity=0.002 Sum_probs=26.0
Q ss_pred HHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 390 ALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 390 ~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
+.......+.|..|||+.|+||+.||+......
T Consensus 141 eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~I 173 (207)
T PRK11475 141 EILRFMSRGYSMPQIAEQLERNIKTIRAHKFNV 173 (207)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 333344568899999999999999999876544
No 223
>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=51.16 E-value=27 Score=29.04 Aligned_cols=28 Identities=21% Similarity=0.285 Sum_probs=21.4
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
|+..|.+++|..+|+++++|+.++..+.
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 8899999999999999999999997664
No 224
>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=51.11 E-value=39 Score=31.66 Aligned_cols=43 Identities=23% Similarity=0.227 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHHHcCCCCcHHHHHHHhCCC-HHHHHHHHHhcc
Q 013472 381 ISKIQKARKALTNSHGKYPEDIEIAKYTGLS-LAEIRSASECLR 423 (442)
Q Consensus 381 i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS-~etVk~~l~~ar 423 (442)
..+|-..+.+...+.+..||..|||+.+|++ ..+|...+....
T Consensus 8 q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~ 51 (199)
T TIGR00498 8 QQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALE 51 (199)
T ss_pred HHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHH
Confidence 3445555555555667889999999999998 999998876543
No 225
>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]
Probab=51.02 E-value=27 Score=33.62 Aligned_cols=29 Identities=17% Similarity=-0.170 Sum_probs=25.6
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
.++.|..|||++|++|.+++..++.++..
T Consensus 16 ~~Glt~gEIAdELNvSreTa~WL~~r~~~ 44 (203)
T COG0856 16 SKGLTTGEIADELNVSRETATWLLTRAFK 44 (203)
T ss_pred HCCCcHHHhhhhhhhhHHHHHHHHhhhhh
Confidence 46889999999999999999999887654
No 226
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=50.90 E-value=23 Score=34.09 Aligned_cols=34 Identities=18% Similarity=0.005 Sum_probs=26.5
Q ss_pred HHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 390 ALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 390 ~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
++..-...+.|..|||+.|++|+.+|+.......
T Consensus 140 EVLrLLAqGkTnKEIAe~L~IS~rTVkth~srIm 173 (198)
T PRK15201 140 HLLKLIASGYHLSETAALLSLSEEQTKSLRRSIM 173 (198)
T ss_pred HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 3333445688999999999999999998866543
No 227
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=50.47 E-value=33 Score=30.37 Aligned_cols=32 Identities=22% Similarity=0.279 Sum_probs=25.2
Q ss_pred HHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 390 ALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 390 ~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
.+.++.++ .++.|||+.+|+|..+|..+++..
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 33344455 799999999999999999987654
No 228
>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=49.08 E-value=17 Score=35.22 Aligned_cols=28 Identities=18% Similarity=0.138 Sum_probs=24.8
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
.+.|..|||++||||+.+|+..+..++.
T Consensus 185 ~G~t~~eIa~~l~is~~Tv~~~l~~~~~ 212 (232)
T TIGR03541 185 LGRRQADIAAILGISERTVENHLRSARR 212 (232)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4679999999999999999999887753
No 229
>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=49.02 E-value=20 Score=27.56 Aligned_cols=26 Identities=31% Similarity=0.469 Sum_probs=20.2
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
+-|+..+||+.+|+|..+|+.++...
T Consensus 23 ~lps~~~la~~~~vsr~tvr~al~~L 48 (64)
T PF00392_consen 23 RLPSERELAERYGVSRTTVREALRRL 48 (64)
T ss_dssp BE--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred EeCCHHHHHHHhccCCcHHHHHHHHH
Confidence 44699999999999999999998754
No 230
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=49.00 E-value=17 Score=35.61 Aligned_cols=29 Identities=14% Similarity=0.084 Sum_probs=25.1
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
..+.|..|||++||||+.+|+..+..++.
T Consensus 192 a~G~t~~eIa~~l~is~~TV~~h~~~~~~ 220 (240)
T PRK10188 192 AEGKTSAEIAMILSISENTVNFHQKNMQK 220 (240)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 34679999999999999999999887664
No 231
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=48.86 E-value=25 Score=24.66 Aligned_cols=27 Identities=22% Similarity=0.181 Sum_probs=23.1
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 398 YPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
.++..|||+.+|++..+|..++.....
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~ 34 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEK 34 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 468899999999999999998876553
No 232
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=48.83 E-value=2.5e+02 Score=28.65 Aligned_cols=28 Identities=21% Similarity=0.337 Sum_probs=22.8
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
|...|.+|||...|++..+|+...+...
T Consensus 274 g~~~t~keIa~v~~Vs~~tI~~~ykel~ 301 (310)
T PRK00423 274 GERRTQREVAEVAGVTEVTVRNRYKELA 301 (310)
T ss_pred CCCCCHHHHHHHcCCCHHHHHHHHHHHH
Confidence 4555999999999999999998765443
No 233
>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=48.47 E-value=20 Score=26.48 Aligned_cols=27 Identities=26% Similarity=0.233 Sum_probs=22.0
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
+...+..|||+.+|++..++..++...
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 445699999999999999999988643
No 234
>PRK13239 alkylmercury lyase; Provisional
Probab=48.24 E-value=40 Score=32.90 Aligned_cols=29 Identities=17% Similarity=0.268 Sum_probs=26.9
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 395 HGKYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 395 lgr~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
.|+.||..+||+.+|+++++|+.+|+...
T Consensus 33 ~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 33 KGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 59999999999999999999999998765
No 235
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=47.42 E-value=36 Score=32.53 Aligned_cols=24 Identities=21% Similarity=0.043 Sum_probs=21.4
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHh
Q 013472 398 YPEDIEIAKYTGLSLAEIRSASEC 421 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~l~~ 421 (442)
+.|+.|||+.+|.++++|++.++-
T Consensus 61 g~Ti~EIAeelG~TeqTir~hlkg 84 (182)
T COG1318 61 GMTISEIAEELGRTEQTVRNHLKG 84 (182)
T ss_pred cCcHHHHHHHhCCCHHHHHHHHhc
Confidence 569999999999999999998763
No 236
>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=47.12 E-value=91 Score=28.17 Aligned_cols=26 Identities=23% Similarity=0.107 Sum_probs=23.1
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 398 YPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
..|.+|||..+|++.++|-.+++..+
T Consensus 143 ~~t~~~iA~~lG~tretvsR~l~~l~ 168 (193)
T TIGR03697 143 RLSHQAIAEAIGSTRVTITRLLGDLR 168 (193)
T ss_pred CCCHHHHHHHhCCcHHHHHHHHHHHH
Confidence 46999999999999999999987665
No 237
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=46.65 E-value=39 Score=20.77 Aligned_cols=21 Identities=24% Similarity=0.154 Sum_probs=18.1
Q ss_pred CCcHHHHHHHhCCCHHHHHHH
Q 013472 398 YPEDIEIAKYTGLSLAEIRSA 418 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~ 418 (442)
+.+..+||+.+|++..+|...
T Consensus 21 ~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 21 GESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCCHHHHHHHHCCCHHHHHHh
Confidence 349999999999999998764
No 238
>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=46.48 E-value=29 Score=24.59 Aligned_cols=25 Identities=28% Similarity=0.195 Sum_probs=21.4
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 400 EDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 400 S~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
+..|+|+.+|++..+|+........
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~~g~l 26 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYERIGLL 26 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 6789999999999999988766553
No 239
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=46.35 E-value=32 Score=33.13 Aligned_cols=28 Identities=18% Similarity=-0.002 Sum_probs=24.1
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
..+.|..|||+.|++|+.+|+..+....
T Consensus 168 ~~G~s~~eIA~~L~iS~~TVk~~~~~i~ 195 (216)
T PRK10100 168 RIGASNNEIARSLFISENTVKTHLYNLF 195 (216)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 4477999999999999999999877554
No 240
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=45.42 E-value=49 Score=29.92 Aligned_cols=26 Identities=27% Similarity=0.249 Sum_probs=22.5
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 398 YPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
..++.|||+.+|+|+.+|..+++...
T Consensus 23 R~s~~eiA~~lglS~~tV~~Ri~rL~ 48 (153)
T PRK11179 23 RTPYAELAKQFGVSPGTIHVRVEKMK 48 (153)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 35889999999999999999987654
No 241
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=45.13 E-value=31 Score=32.46 Aligned_cols=26 Identities=15% Similarity=0.004 Sum_probs=22.8
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 398 YPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
+.|.+|||+.||||+.||+..+....
T Consensus 177 g~s~~eIa~~l~iS~~Tv~~~~~~~~ 202 (225)
T PRK10046 177 QHTAETVAQALTISRTTARRYLEYCA 202 (225)
T ss_pred CcCHHHHHHHhCccHHHHHHHHHHHH
Confidence 57999999999999999999876543
No 242
>PF13551 HTH_29: Winged helix-turn helix
Probab=45.10 E-value=61 Score=26.70 Aligned_cols=42 Identities=14% Similarity=0.096 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHHHHcC-CCCcHHHHHHHh-------CCCHHHHHHHHHhc
Q 013472 380 EISKIQKARKALTNSHG-KYPEDIEIAKYT-------GLSLAEIRSASECL 422 (442)
Q Consensus 380 ~i~kI~ka~~~L~~elg-r~PS~eEIAe~L-------GIS~etVk~~l~~a 422 (442)
....|.+...+-+.. | ...+..+|++.| .++..+|..+++..
T Consensus 62 ~~~~l~~~~~~~p~~-g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~~~ 111 (112)
T PF13551_consen 62 QRAQLIELLRENPPE-GRSRWTLEELAEWLIEEEFGIDVSPSTIRRILKRA 111 (112)
T ss_pred HHHHHHHHHHHCCCC-CCCcccHHHHHHHHHHhccCccCCHHHHHHHHHHC
Confidence 333444444443333 3 246788998865 78999999988753
No 243
>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=45.00 E-value=21 Score=26.74 Aligned_cols=37 Identities=30% Similarity=0.219 Sum_probs=24.4
Q ss_pred CcHHHHHHHhCCCHHHHHHHHHh-ccc-CCCCccccCCC
Q 013472 399 PEDIEIAKYTGLSLAEIRSASEC-LRI-VGSIDQKIGDC 435 (442)
Q Consensus 399 PS~eEIAe~LGIS~etVk~~l~~-ar~-~~SLD~~v~~~ 435 (442)
.+..|+|+.+|++...|-..+.. ... ..+..+.+.++
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 36689999999999999998833 443 36666666543
No 244
>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=44.87 E-value=22 Score=26.94 Aligned_cols=27 Identities=15% Similarity=0.119 Sum_probs=20.2
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHh
Q 013472 395 HGKYPEDIEIAKYTGLSLAEIRSASEC 421 (442)
Q Consensus 395 lgr~PS~eEIAe~LGIS~etVk~~l~~ 421 (442)
+..+++..+||..+||+..+|..++..
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 345679999999999999999998764
No 245
>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=44.59 E-value=53 Score=27.72 Aligned_cols=25 Identities=24% Similarity=0.135 Sum_probs=21.6
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHH
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASE 420 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~ 420 (442)
..+.|..|||+.+|+|..+|..+.+
T Consensus 48 ~~G~S~~eIA~~LgISrsTIyRi~R 72 (88)
T TIGR02531 48 KQGKTYSDIEAETGASTATISRVKR 72 (88)
T ss_pred HCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3457999999999999999998665
No 246
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=44.25 E-value=51 Score=28.10 Aligned_cols=33 Identities=15% Similarity=0.028 Sum_probs=25.3
Q ss_pred HHHHHHcC-CCCcHHHHHHHhCCCHHHHHHHHHh
Q 013472 389 KALTNSHG-KYPEDIEIAKYTGLSLAEIRSASEC 421 (442)
Q Consensus 389 ~~L~~elg-r~PS~eEIAe~LGIS~etVk~~l~~ 421 (442)
.+|.+.+. -+.|.++||+.||+|++.|..++..
T Consensus 13 ~ELq~nf~~~~ls~~~ia~dL~~s~~~le~vL~l 46 (89)
T PF10078_consen 13 QELQANFELSGLSLEQIAADLGTSPEHLEQVLNL 46 (89)
T ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 34443332 4679999999999999999998753
No 247
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=43.71 E-value=2.8e+02 Score=27.14 Aligned_cols=38 Identities=11% Similarity=0.086 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHH
Q 013472 383 KIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASE 420 (442)
Q Consensus 383 kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~ 420 (442)
.+.++...+........+.+++|+.+|+|...+..+.+
T Consensus 184 ~i~~~~~~i~~~~~~~isl~~lA~~~~lS~~~l~r~Fk 221 (290)
T PRK10572 184 RVREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFR 221 (290)
T ss_pred HHHHHHHHHHhcccCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 46666667767777899999999999999998877644
No 248
>COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]
Probab=43.54 E-value=50 Score=34.40 Aligned_cols=71 Identities=13% Similarity=0.124 Sum_probs=49.8
Q ss_pred HHHHHHHHHHHHHHHHhhcCceecccc--cHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHH
Q 013472 350 TYVQYWIRKSISKMVARHARGIKIPCK--LNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASE 420 (442)
Q Consensus 350 TYa~~wIRnaI~r~LRkqsr~irlP~~--v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~ 420 (442)
+.+....++-+.+.+|.-...-++|.. ....-.+|.+++..+.+.+.+..+.+|||+.+|||..++..+.+
T Consensus 186 ~~a~~va~~lv~~~~R~~~~~Q~~~~~~~~~~~~~~l~~~i~~me~nle~plsl~~LA~~~~~S~R~leRlF~ 258 (328)
T COG4977 186 ALANRVARQLVVDPIRSGGDRQRLPLLGRLGHRDPRLLRAIELMEANLEEPLSLEELADRAGLSRRQLERLFR 258 (328)
T ss_pred HHHHHHHHHhhhccccCCCccccccccccCCCCCHHHHHHHHHHHHhhcCCcCHHHHHHHhCCCHHHHHHHHH
Confidence 445566666666666653222223322 22344678888888888889999999999999999999987644
No 249
>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=43.32 E-value=27 Score=27.04 Aligned_cols=26 Identities=27% Similarity=0.224 Sum_probs=22.5
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
...|..|||+.+|++..+|..+++..
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 35699999999999999999988744
No 250
>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=43.05 E-value=44 Score=26.22 Aligned_cols=27 Identities=22% Similarity=0.158 Sum_probs=20.9
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
+...|..|||..+|++++.|+..+..-
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 456799999999999999999987654
No 251
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=43.02 E-value=95 Score=22.86 Aligned_cols=25 Identities=32% Similarity=0.442 Sum_probs=22.1
Q ss_pred CcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 399 PEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 399 PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
++..+||+.+|++..+|..++....
T Consensus 26 ~~~~~la~~~~is~~~v~~~l~~L~ 50 (66)
T cd07377 26 PSERELAEELGVSRTTVREALRELE 50 (66)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 5799999999999999999887654
No 252
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=42.94 E-value=39 Score=29.67 Aligned_cols=29 Identities=10% Similarity=0.069 Sum_probs=24.6
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
..+.+.+|||+.++++..+|+..+...+.
T Consensus 162 ~~g~~~~~Ia~~l~~s~~tv~~~~~~~~~ 190 (211)
T PRK15369 162 TEGYTNRDIAEQLSISIKTVETHRLNMMR 190 (211)
T ss_pred HCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 34668999999999999999998876654
No 253
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=42.65 E-value=1e+02 Score=28.25 Aligned_cols=26 Identities=19% Similarity=0.173 Sum_probs=22.8
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 398 YPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
..|.++||..+|++.++|-..+...+
T Consensus 149 ~~t~~~iA~~lG~tretvsR~l~~l~ 174 (202)
T PRK13918 149 YATHDELAAAVGSVRETVTKVIGELS 174 (202)
T ss_pred cCCHHHHHHHhCccHHHHHHHHHHHH
Confidence 45899999999999999999887655
No 254
>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=42.51 E-value=28 Score=27.07 Aligned_cols=26 Identities=23% Similarity=0.201 Sum_probs=22.9
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 398 YPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
..|.++||..+|++..+|...++..+
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~ 53 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLK 53 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 35899999999999999999987665
No 255
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=42.49 E-value=26 Score=34.02 Aligned_cols=23 Identities=17% Similarity=0.011 Sum_probs=20.2
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHH
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSA 418 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~ 418 (442)
-++...++||..||||+.||+..
T Consensus 155 V~G~~NKqIA~dLgiS~rTVe~H 177 (202)
T COG4566 155 VRGLMNKQIAFDLGISERTVELH 177 (202)
T ss_pred HcCcccHHHHHHcCCchhhHHHH
Confidence 36778899999999999999865
No 256
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=42.16 E-value=53 Score=30.10 Aligned_cols=25 Identities=24% Similarity=0.272 Sum_probs=21.9
Q ss_pred CcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 399 PEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 399 PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
.|..|||+.+|+|..+|..+++...
T Consensus 29 ~s~~eiA~~lglS~~tv~~Ri~rL~ 53 (164)
T PRK11169 29 ISNVELSKRVGLSPTPCLERVRRLE 53 (164)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 5889999999999999999877553
No 257
>PRK00215 LexA repressor; Validated
Probab=42.15 E-value=67 Score=30.21 Aligned_cols=40 Identities=25% Similarity=0.261 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHcCCCCcHHHHHHHhCC-CHHHHHHHHHhcc
Q 013472 384 IQKARKALTNSHGKYPEDIEIAKYTGL-SLAEIRSASECLR 423 (442)
Q Consensus 384 I~ka~~~L~~elgr~PS~eEIAe~LGI-S~etVk~~l~~ar 423 (442)
+-+.+.+.....+..||..|||+.+|+ +..+|..++....
T Consensus 9 il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~ 49 (205)
T PRK00215 9 ILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALE 49 (205)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 334444444566888999999999999 9999998876543
No 258
>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=41.87 E-value=31 Score=24.46 Aligned_cols=23 Identities=26% Similarity=0.101 Sum_probs=18.8
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhc
Q 013472 400 EDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 400 S~eEIAe~LGIS~etVk~~l~~a 422 (442)
|+.|+|+.+|++..+++..-...
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 46799999999999999887654
No 259
>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=41.83 E-value=36 Score=24.82 Aligned_cols=25 Identities=24% Similarity=0.199 Sum_probs=20.0
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHh
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASEC 421 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~ 421 (442)
.+.|..|+|+.+|++..+|..+..-
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 4668999999999999999988765
No 260
>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=41.28 E-value=83 Score=23.05 Aligned_cols=36 Identities=28% Similarity=0.299 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHH
Q 013472 382 SKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASE 420 (442)
Q Consensus 382 ~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~ 420 (442)
..|..|+..+. .|. .|..+.|+..|||..++...++
T Consensus 3 e~l~~Ai~~v~--~g~-~S~r~AA~~ygVp~sTL~~r~~ 38 (45)
T PF05225_consen 3 EDLQKAIEAVK--NGK-MSIRKAAKKYGVPRSTLRRRLR 38 (45)
T ss_dssp HHHHHHHHHHH--TTS-S-HHHHHHHHT--HHHHHHHHH
T ss_pred HHHHHHHHHHH--hCC-CCHHHHHHHHCcCHHHHHHHHc
Confidence 34666776665 344 8999999999999999997664
No 261
>PF13518 HTH_28: Helix-turn-helix domain
Probab=41.26 E-value=45 Score=23.89 Aligned_cols=24 Identities=25% Similarity=0.176 Sum_probs=21.9
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 400 EDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 400 S~eEIAe~LGIS~etVk~~l~~ar 423 (442)
|..+||..+||+..+|...+....
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHH
Confidence 999999999999999999887665
No 262
>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=40.54 E-value=72 Score=26.52 Aligned_cols=25 Identities=20% Similarity=0.097 Sum_probs=22.2
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHh
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASEC 421 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~ 421 (442)
..++..+||+.+|+|..+|...+..
T Consensus 18 ~~~ti~dvA~~~gvS~~TVsr~L~~ 42 (80)
T TIGR02844 18 TKATVRETAKVFGVSKSTVHKDVTE 42 (80)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHhcC
Confidence 4679999999999999999998864
No 263
>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=40.45 E-value=47 Score=25.44 Aligned_cols=28 Identities=25% Similarity=0.205 Sum_probs=23.4
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
....+..|||+.+|+|..+++..+....
T Consensus 17 ~~~~~~~ela~~l~~S~rti~~~i~~L~ 44 (59)
T PF08280_consen 17 NKWITLKELAKKLNISERTIKNDINELN 44 (59)
T ss_dssp HTSBBHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCCCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4578999999999999999999887655
No 264
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=40.37 E-value=80 Score=25.26 Aligned_cols=26 Identities=23% Similarity=0.092 Sum_probs=23.1
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
...+..|||+.+|++..+|...+...
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l~~L 44 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLNTL 44 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 46899999999999999999987754
No 265
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=39.61 E-value=88 Score=30.22 Aligned_cols=26 Identities=35% Similarity=0.423 Sum_probs=22.7
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
+-|+..|||+.+|+|...|+.++...
T Consensus 33 ~LpsE~eLa~~lgVSRtpVREAL~~L 58 (254)
T PRK09464 33 KLPPERELAKQFDVSRPSLREAIQRL 58 (254)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 34699999999999999999998754
No 266
>PRK09483 response regulator; Provisional
Probab=38.44 E-value=56 Score=29.54 Aligned_cols=29 Identities=21% Similarity=0.005 Sum_probs=24.5
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
..+.+..|||+.|++++.+|+...+....
T Consensus 161 ~~G~~~~~Ia~~l~is~~TV~~~~~~i~~ 189 (217)
T PRK09483 161 TKGQKVNEISEQLNLSPKTVNSYRYRMFS 189 (217)
T ss_pred HCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 45679999999999999999998776553
No 267
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=38.33 E-value=96 Score=21.71 Aligned_cols=27 Identities=26% Similarity=0.174 Sum_probs=23.5
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
..++..+||+.+|++..+|...+....
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~L~ 39 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNKLE 39 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 358999999999999999999887654
No 268
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=38.03 E-value=37 Score=25.97 Aligned_cols=24 Identities=25% Similarity=0.123 Sum_probs=21.1
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 400 EDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 400 S~eEIAe~LGIS~etVk~~l~~ar 423 (442)
|..|+|+.+|+|..+|+...+..-
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 678999999999999999887555
No 269
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=37.89 E-value=34 Score=26.92 Aligned_cols=23 Identities=17% Similarity=0.237 Sum_probs=19.7
Q ss_pred CcHHHHHHHhCCCHHHHHHHHHh
Q 013472 399 PEDIEIAKYTGLSLAEIRSASEC 421 (442)
Q Consensus 399 PS~eEIAe~LGIS~etVk~~l~~ 421 (442)
++..|||+.+|++..+|-.+++-
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln~ 23 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLNG 23 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCC
Confidence 46789999999999999888754
No 270
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=37.62 E-value=63 Score=30.89 Aligned_cols=27 Identities=15% Similarity=0.102 Sum_probs=24.7
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
|..+..|||+.|||+..++...|++|.
T Consensus 177 R~~~l~dLA~~lGISkst~~ehLRrAe 203 (215)
T COG3413 177 RRVSLKDLAKELGISKSTLSEHLRRAE 203 (215)
T ss_pred ccCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 667999999999999999999998875
No 271
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=37.62 E-value=1.5e+02 Score=22.34 Aligned_cols=37 Identities=24% Similarity=0.269 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHHcCCCCcHHHHHHHhCC-CHHHHHHHHHh
Q 013472 382 SKIQKARKALTNSHGKYPEDIEIAKYTGL-SLAEIRSASEC 421 (442)
Q Consensus 382 ~kI~ka~~~L~~elgr~PS~eEIAe~LGI-S~etVk~~l~~ 421 (442)
.++..+...+... ..+.+|||..+|+ +........+.
T Consensus 37 ~r~~~a~~~l~~~---~~~~~~ia~~~g~~s~~~f~r~Fk~ 74 (84)
T smart00342 37 RRLERARRLLRDT---DLSVTEIALRVGFSSQSYFSRAFKK 74 (84)
T ss_pred HHHHHHHHHHHcC---CCCHHHHHHHhCCCChHHHHHHHHH
Confidence 3466666666432 6799999999999 98888776543
No 272
>PRK10403 transcriptional regulator NarP; Provisional
Probab=37.54 E-value=47 Score=29.49 Aligned_cols=33 Identities=12% Similarity=0.025 Sum_probs=26.7
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCC
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLRIVGSI 428 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SL 428 (442)
..+.|.+|||+.+|++..+|+..+.+.+..+.+
T Consensus 166 ~~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~ 198 (215)
T PRK10403 166 AQGLSNKQIASVLNISEQTVKVHIRNLLRKLNV 198 (215)
T ss_pred HCCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 346899999999999999999988877654433
No 273
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=37.46 E-value=1.5e+02 Score=28.23 Aligned_cols=26 Identities=27% Similarity=0.376 Sum_probs=22.8
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 398 YPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
..|.++||..+|++.++|-.+++..+
T Consensus 179 ~lt~~~IA~~lGisretlsR~L~~L~ 204 (230)
T PRK09391 179 PMSRRDIADYLGLTIETVSRALSQLQ 204 (230)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 35899999999999999999887665
No 274
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=37.07 E-value=49 Score=26.77 Aligned_cols=25 Identities=28% Similarity=0.307 Sum_probs=21.4
Q ss_pred CcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 399 PEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 399 PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
.|.+|||+.+|+|...|+.+++...
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 7999999999999999999977554
No 275
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=37.01 E-value=29 Score=26.14 Aligned_cols=26 Identities=15% Similarity=0.162 Sum_probs=18.3
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
++.|..++|+.+||+..++..+++.-
T Consensus 9 ~~it~~~La~~~gis~~tl~~~~~~~ 34 (63)
T PF13443_consen 9 RGITQKDLARKTGISRSTLSRILNGK 34 (63)
T ss_dssp TT--HHHHHHHHT--HHHHHHHHTTT
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcc
Confidence 34589999999999999999888744
No 276
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=36.99 E-value=30 Score=35.48 Aligned_cols=37 Identities=19% Similarity=0.106 Sum_probs=29.9
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhccc----CCCCcccc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLRI----VGSIDQKI 432 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar~----~~SLD~~v 432 (442)
..+.|..|||+.||+|.-+|-.++..||. -+.++.|.
T Consensus 27 ~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~I~I~~~~ 67 (318)
T PRK15418 27 HDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQINSRF 67 (318)
T ss_pred hcCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEEEEEeCCC
Confidence 45789999999999999999999999883 24455443
No 277
>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=36.76 E-value=78 Score=24.06 Aligned_cols=27 Identities=26% Similarity=0.118 Sum_probs=22.6
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
....+.+|||+.+|+|..+|+.-+...
T Consensus 12 ~~~~s~~ela~~~~VS~~TiRRDl~~L 38 (57)
T PF08220_consen 12 KGKVSVKELAEEFGVSEMTIRRDLNKL 38 (57)
T ss_pred cCCEEHHHHHHHHCcCHHHHHHHHHHH
Confidence 346799999999999999999876543
No 278
>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=36.54 E-value=1.1e+02 Score=26.53 Aligned_cols=29 Identities=28% Similarity=0.180 Sum_probs=24.9
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
..+.|..|||+.+||+..+|-.+++....
T Consensus 69 ~pd~tl~Ela~~l~Vs~~ti~~~Lkrlg~ 97 (119)
T PF01710_consen 69 NPDATLRELAERLGVSPSTIWRALKRLGI 97 (119)
T ss_pred CCCcCHHHHHHHcCCCHHHHHHHHHHcCc
Confidence 45668899999999999999999987654
No 279
>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=36.40 E-value=1e+02 Score=22.06 Aligned_cols=25 Identities=20% Similarity=0.232 Sum_probs=21.8
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHh
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASEC 421 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~ 421 (442)
.+.|.+++|+.+|++..+|..+.+-
T Consensus 14 ~gltq~~lA~~~gvs~~~vs~~e~g 38 (58)
T TIGR03070 14 LGLTQADLADLAGVGLRFIRDVENG 38 (58)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 4679999999999999999988753
No 280
>COG3769 Predicted hydrolase (HAD superfamily) [General function prediction only]
Probab=36.12 E-value=77 Score=31.76 Aligned_cols=41 Identities=29% Similarity=0.353 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHHHHcC----CCCcHHHHHHHhCCCHHHHHHHHH
Q 013472 380 EISKIQKARKALTNSHG----KYPEDIEIAKYTGLSLAEIRSASE 420 (442)
Q Consensus 380 ~i~kI~ka~~~L~~elg----r~PS~eEIAe~LGIS~etVk~~l~ 420 (442)
.+.+|++..++|.+.+| .+.+.+||++.+|+|.+.+.-++.
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 45677777777777776 577999999999999999876643
No 281
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=36.07 E-value=72 Score=25.91 Aligned_cols=22 Identities=27% Similarity=0.214 Sum_probs=19.4
Q ss_pred CCcHHHHHHHhCCCHHHHHHHH
Q 013472 398 YPEDIEIAKYTGLSLAEIRSAS 419 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~l 419 (442)
+.|.+|+|+.+|++.+++-.+-
T Consensus 14 ~ltQ~elA~~vgVsRQTi~~iE 35 (68)
T COG1476 14 GLTQEELAKLVGVSRQTIIAIE 35 (68)
T ss_pred CcCHHHHHHHcCcCHHHHHHHH
Confidence 5699999999999999998763
No 282
>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=35.71 E-value=1.1e+02 Score=21.88 Aligned_cols=33 Identities=15% Similarity=0.061 Sum_probs=24.3
Q ss_pred HHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHH
Q 013472 386 KARKALTNSHGKYPEDIEIAKYTGLSLAEIRSA 418 (442)
Q Consensus 386 ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~ 418 (442)
.+...+.+.--...|..+||+.+|++...+...
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 344444444447889999999999999998653
No 283
>PRK15044 transcriptional regulator SirC; Provisional
Probab=35.36 E-value=1.2e+02 Score=31.25 Aligned_cols=70 Identities=13% Similarity=0.076 Sum_probs=44.4
Q ss_pred HHHHHHHHHHHHHHHHhhcCceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHh
Q 013472 350 TYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC 421 (442)
Q Consensus 350 TYa~~wIRnaI~r~LRkqsr~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ 421 (442)
.|....+.--+..+++++....-+.. ...+....++...+.....+.++.++||+.+|+|..++....+.
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 34444445555555554332221111 11233456677777777888999999999999999999987653
No 284
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=35.16 E-value=59 Score=28.95 Aligned_cols=31 Identities=16% Similarity=-0.119 Sum_probs=26.3
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhcccCC
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLRIVG 426 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar~~~ 426 (442)
..+.+.+|||+.|+++..+|+..+.+.+.-+
T Consensus 162 ~~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl 192 (210)
T PRK09935 162 VSGLSNKEIADQLLLSNKTVSAHKSNIYGKL 192 (210)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 3458999999999999999999988776543
No 285
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=34.84 E-value=44 Score=30.82 Aligned_cols=31 Identities=23% Similarity=0.288 Sum_probs=19.1
Q ss_pred HHHHHcCCCCcHHHHHHHhCCCHHHHHHHHH
Q 013472 390 ALTNSHGKYPEDIEIAKYTGLSLAEIRSASE 420 (442)
Q Consensus 390 ~L~~elgr~PS~eEIAe~LGIS~etVk~~l~ 420 (442)
.+....+..+|.+|||+.+||+..++-...+
T Consensus 26 e~~~~~~~r~T~~eiAee~Gis~~tLYrWr~ 56 (142)
T PF13022_consen 26 ELMPENGERRTQAEIAEEVGISRSTLYRWRQ 56 (142)
T ss_dssp HHS------S-HHHHHHHHTS-HHHHHHHHH
T ss_pred HHhhhccccchHHHHHHHhCCCHHHHHHHHh
Confidence 4444445678999999999999999877654
No 286
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=34.66 E-value=72 Score=32.52 Aligned_cols=43 Identities=19% Similarity=0.157 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 381 ISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 381 i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
...+-.+.-.|..+.++...-+|||+.+|..+++|++.++..+
T Consensus 8 QkeIL~aLi~LY~~~~r~IKgeeIA~~l~rnpGTVRNqmq~Lk 50 (294)
T COG2524 8 QKEILQALINLYRRKKRPIKGEEIAEVLNRNPGTVRNQMQSLK 50 (294)
T ss_pred HHHHHHHHHHHHHhcCCCcchHHHHHHHccCcchHHHHHHHHH
Confidence 3456667777777778888889999999999999999987655
No 287
>PRK15320 transcriptional activator SprB; Provisional
Probab=34.23 E-value=43 Score=33.00 Aligned_cols=34 Identities=24% Similarity=0.110 Sum_probs=26.9
Q ss_pred HHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 390 ALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 390 ~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
++...+..+.|..|||+.|++|.++|.....+..
T Consensus 171 EVL~LLAkG~SNKEIAekL~LS~KTVSTYKnRLL 204 (251)
T PRK15320 171 ALLILLSSGHPAIELAKKFGLGTKTVSIYRKKVM 204 (251)
T ss_pred HHHHHHHcCCCHHHHHHHhccchhhHHHHHHHHH
Confidence 4444456688999999999999999998866544
No 288
>PF13551 HTH_29: Winged helix-turn helix
Probab=34.15 E-value=41 Score=27.80 Aligned_cols=24 Identities=25% Similarity=0.178 Sum_probs=21.9
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 400 EDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 400 S~eEIAe~LGIS~etVk~~l~~ar 423 (442)
+..+||+.+|++..+|...++...
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~ 37 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYR 37 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHH
Confidence 699999999999999999988765
No 289
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=34.03 E-value=79 Score=32.79 Aligned_cols=37 Identities=24% Similarity=0.117 Sum_probs=29.7
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhccc----CCCCcccc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLRI----VGSIDQKI 432 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar~----~~SLD~~v 432 (442)
-.+.|..|||+.||||..+|...+..++. .++++.++
T Consensus 24 ~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I~i~~~~ 64 (321)
T COG2390 24 VEGLTQSEIAERLGISRATVSRLLAKAREEGIVKISINSPV 64 (321)
T ss_pred hcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEEEeCCCC
Confidence 45779999999999999999999998873 34555444
No 290
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=33.26 E-value=1.6e+02 Score=27.64 Aligned_cols=26 Identities=23% Similarity=0.192 Sum_probs=22.6
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHh
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASEC 421 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ 421 (442)
..+.|..+||+.||||..+|..++..
T Consensus 170 ~~g~s~~~iak~lgis~~Tv~r~~k~ 195 (200)
T PRK13413 170 DKGTSKSEIARKLGVSRTTLARFLKT 195 (200)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 34579999999999999999998864
No 291
>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=32.66 E-value=1.4e+02 Score=23.94 Aligned_cols=37 Identities=27% Similarity=0.205 Sum_probs=26.7
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCcccc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKI 432 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v 432 (442)
....+.++||+.++++.+.|+..+..+-..-.|+..+
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 3457999999999999999998876554333344433
No 292
>smart00753 PAM PCI/PINT associated module.
Probab=32.66 E-value=1.4e+02 Score=23.94 Aligned_cols=37 Identities=27% Similarity=0.205 Sum_probs=26.7
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCcccc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKI 432 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v 432 (442)
....+.++||+.++++.+.|+..+..+-..-.|+..+
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 3457999999999999999998876554333344433
No 293
>PHA01976 helix-turn-helix protein
Probab=32.62 E-value=60 Score=24.70 Aligned_cols=25 Identities=12% Similarity=0.053 Sum_probs=20.6
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHh
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASEC 421 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~ 421 (442)
++.|..|+|+.+|++..+|..+...
T Consensus 14 ~glt~~~lA~~~gvs~~~v~~~e~g 38 (67)
T PHA01976 14 RAWSAPELSRRAGVRHSLIYDFEAD 38 (67)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 4578999999999999999887653
No 294
>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=32.61 E-value=1.4e+02 Score=23.54 Aligned_cols=19 Identities=26% Similarity=0.412 Sum_probs=13.8
Q ss_pred HHhCCCCChHHHHHHcCCC
Q 013472 264 KESGKAASLNCWAQAAGVS 282 (442)
Q Consensus 264 ~~~gr~pt~~ewA~a~g~d 282 (442)
...|.+||..|.|+++|+.
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 3459999999999999986
No 295
>PRK10651 transcriptional regulator NarL; Provisional
Probab=32.51 E-value=69 Score=28.51 Aligned_cols=31 Identities=6% Similarity=-0.004 Sum_probs=25.6
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHhcccC
Q 013472 395 HGKYPEDIEIAKYTGLSLAEIRSASECLRIV 425 (442)
Q Consensus 395 lgr~PS~eEIAe~LGIS~etVk~~l~~ar~~ 425 (442)
+..+.+.+|||..++++..+|+..+...+.-
T Consensus 167 l~~g~~~~~ia~~l~is~~tV~~~~~~l~~K 197 (216)
T PRK10651 167 IAQGLPNKMIARRLDITESTVKVHVKHMLKK 197 (216)
T ss_pred HHcCCCHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 3456789999999999999999988766543
No 296
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=32.48 E-value=97 Score=28.59 Aligned_cols=42 Identities=12% Similarity=0.009 Sum_probs=34.2
Q ss_pred cHHHHHHHHHHHHHHHHHcC-CCCcHHHHHHHhCCCHHHHHHH
Q 013472 377 LNREISKIQKARKALTNSHG-KYPEDIEIAKYTGLSLAEIRSA 418 (442)
Q Consensus 377 v~e~i~kI~ka~~~L~~elg-r~PS~eEIAe~LGIS~etVk~~ 418 (442)
..+...+|.++..++..+.| ...|.++||+..|++.+++...
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 44556778888888888878 5789999999999999998654
No 297
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=32.27 E-value=74 Score=27.92 Aligned_cols=28 Identities=21% Similarity=0.126 Sum_probs=25.6
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
.+.+.+|-|+.||||..|+..++..||.
T Consensus 56 egl~QeeaA~~MgVSR~T~~ril~~ARk 83 (106)
T PF02001_consen 56 EGLSQEEAAERMGVSRPTFQRILESARK 83 (106)
T ss_pred cCCCHHHHHHHcCCcHHHHHHHHHHHHH
Confidence 4689999999999999999999998884
No 298
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=32.24 E-value=91 Score=27.14 Aligned_cols=27 Identities=11% Similarity=-0.034 Sum_probs=23.0
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 398 YPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
+.+.++||+.+|++..+|+..+...+.
T Consensus 156 ~~~~~~ia~~l~~s~~tv~~~~~~~~~ 182 (202)
T PRK09390 156 GLSNKVIARDLDISPRTVEVYRANVMT 182 (202)
T ss_pred cCchHHHHHHcCCCHHHHHHHHHHHHH
Confidence 457899999999999999988776653
No 299
>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=31.95 E-value=74 Score=23.60 Aligned_cols=25 Identities=20% Similarity=0.206 Sum_probs=20.8
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 398 YPEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
..+..|||+.+|++..+|..++...
T Consensus 21 ~~t~~~la~~l~~~~~~vs~~v~~L 45 (62)
T PF12802_consen 21 ELTQSELAERLGISKSTVSRIVKRL 45 (62)
T ss_dssp GEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3699999999999999999887654
No 300
>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=31.60 E-value=4.9e+02 Score=25.20 Aligned_cols=39 Identities=10% Similarity=0.019 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHh
Q 013472 383 KIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC 421 (442)
Q Consensus 383 kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ 421 (442)
.+.++...+.+......|.++||+.+|+|...+..+.+.
T Consensus 187 ~~~~~~~~I~~~~~~~~sl~~lA~~~~~S~~~l~r~Fk~ 225 (287)
T TIGR02297 187 LFNRFNFLIEENYKQHLRLPEYADRLGISESRLNDICRR 225 (287)
T ss_pred HHHHHHHHHHHhhccCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 345555555566677889999999999999998766543
No 301
>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=31.43 E-value=3.6e+02 Score=27.24 Aligned_cols=35 Identities=17% Similarity=0.151 Sum_probs=25.4
Q ss_pred HHHHHHcCCCCcHHHHHHHhC--CCHHHHHHHHHhcc
Q 013472 389 KALTNSHGKYPEDIEIAKYTG--LSLAEIRSASECLR 423 (442)
Q Consensus 389 ~~L~~elgr~PS~eEIAe~LG--IS~etVk~~l~~ar 423 (442)
++|..-.+-.+++++||+.++ ||.++|++.+....
T Consensus 128 rel~~~~~~~~~~~~ia~~l~p~is~~ev~~sL~~L~ 164 (271)
T TIGR02147 128 RELLGVMPFADDPEELAKRCFPKISAEQVKESLDLLE 164 (271)
T ss_pred HHHhhcCCCCCCHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence 333333344567889999999 99999999877543
No 302
>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=31.10 E-value=86 Score=23.84 Aligned_cols=24 Identities=21% Similarity=0.177 Sum_probs=20.5
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 400 EDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 400 S~eEIAe~LGIS~etVk~~l~~ar 423 (442)
+..|+|+.+||+..+++...+...
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~~g 25 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERRYG 25 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHhCC
Confidence 678999999999999998876543
No 303
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=30.88 E-value=2.3e+02 Score=25.94 Aligned_cols=26 Identities=19% Similarity=0.141 Sum_probs=22.7
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 398 YPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
..|.+|||..+|++.++|-.+++..+
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR~l~~l~ 193 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRVLKMLE 193 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 46889999999999999999887655
No 304
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=30.86 E-value=67 Score=30.95 Aligned_cols=26 Identities=15% Similarity=0.210 Sum_probs=23.3
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHh
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASEC 421 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ 421 (442)
.+-||..|||+.+|+|..||+.++..
T Consensus 33 ~~LPsE~eLa~~~~VSR~TVR~Al~~ 58 (241)
T PRK10079 33 DYLPAEQQLAARYEVNRHTLRRAIDQ 58 (241)
T ss_pred CcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 36799999999999999999999763
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=30.51 E-value=91 Score=27.17 Aligned_cols=28 Identities=25% Similarity=0.240 Sum_probs=23.6
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
+...+..|||+.+|+|...|..+++..+
T Consensus 23 ~~~~s~~eia~~l~is~~~v~~~l~~L~ 50 (130)
T TIGR02944 23 SQPYSAAEIAEQTGLNAPTVSKILKQLS 50 (130)
T ss_pred CCCccHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4557999999999999999999876544
No 306
>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=30.28 E-value=57 Score=30.18 Aligned_cols=26 Identities=35% Similarity=0.296 Sum_probs=23.2
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 398 YPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
..|.+|||+.|||+...|+.++....
T Consensus 28 ~~tdEeLa~~Lgi~~~~VRk~L~~L~ 53 (158)
T TIGR00373 28 EFTDEEISLELGIKLNEVRKALYALY 53 (158)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 67999999999999999999977554
No 307
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=29.91 E-value=2e+02 Score=28.15 Aligned_cols=44 Identities=9% Similarity=0.078 Sum_probs=28.9
Q ss_pred HHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHH
Q 013472 310 FLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQY 354 (442)
Q Consensus 310 sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~ 354 (442)
.|...|....+..+++.+...|..-.-...|... |..|..|+..
T Consensus 205 ~I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk~~-G~T~~~yi~~ 248 (302)
T PRK09685 205 LIDQSIQEEILRPEWIAGELGISVRSLYRLFAEQ-GLVVAQYIRN 248 (302)
T ss_pred HHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHc-CCCHHHHHHH
Confidence 3344444445889999998887776666667644 6667666654
No 308
>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=29.81 E-value=60 Score=26.93 Aligned_cols=28 Identities=25% Similarity=0.057 Sum_probs=19.5
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHhcccC
Q 013472 398 YPEDIEIAKYTGLSLAEIRSASECLRIV 425 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~l~~ar~~ 425 (442)
+.|.+|||+.+|.|...|...+.....|
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 4688999999999999999998766544
No 309
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=29.79 E-value=1.7e+02 Score=22.03 Aligned_cols=60 Identities=17% Similarity=0.141 Sum_probs=34.1
Q ss_pred CCChHHHHHHcCCCHHHHHHHHHhch-HHHHHHHHHhHHHHHHHHHHhhC-CCCCHHhHHHHHHH
Q 013472 269 AASLNCWAQAAGVSERVLKQHLAFGW-YCREELIKSTRPLVLFLARNYRG-LGIPFSDLLQAGNV 331 (442)
Q Consensus 269 ~pt~~ewA~a~g~deeeL~~~l~~G~-~Are~LI~~nlrLV~sIAkrY~g-~g~d~EDLIQEG~I 331 (442)
+++..++|+.+|++...|.+.+..-. ......+.. .-+..|..|.. .....+|+.++.-+
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~~~~s~~~~~~~---~r~~~a~~~l~~~~~~~~~ia~~~g~ 62 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKETGTTPKQYLRD---RRLERARRLLRDTDLSVTEIALRVGF 62 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHhCcCHHHHHHH---HHHHHHHHHHHcCCCCHHHHHHHhCC
Confidence 36788999999999988877665321 111111111 11222333333 35788888776444
No 310
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=29.56 E-value=74 Score=22.26 Aligned_cols=28 Identities=14% Similarity=-0.048 Sum_probs=19.6
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 395 HGKYPEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 395 lgr~PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
+....+.++||+.+|++......+.+..
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 3456799999999999999988876543
No 311
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=29.31 E-value=83 Score=27.56 Aligned_cols=39 Identities=18% Similarity=0.176 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHh
Q 013472 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAF 292 (442)
Q Consensus 254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~ 292 (442)
.+.++..-+...+...++.+++|+.+|++...|.+.++.
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 445566667777788899999999999999888776553
No 312
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=29.02 E-value=1.4e+02 Score=24.77 Aligned_cols=25 Identities=28% Similarity=0.247 Sum_probs=21.8
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 398 YPEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
..+..|||+.+|++..+|...+...
T Consensus 17 ~~~~~~la~~l~~s~~tv~~~l~~L 41 (108)
T smart00344 17 RISLAELAKKVGLSPSTVHNRVKRL 41 (108)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4689999999999999999887654
No 313
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=28.95 E-value=2.1e+02 Score=23.41 Aligned_cols=51 Identities=12% Similarity=0.113 Sum_probs=35.4
Q ss_pred hhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHH
Q 013472 315 YRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVA 365 (442)
Q Consensus 315 Y~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LR 365 (442)
....+...+++.++.-+.-..-...|....|..|..|+..+-.+.....+.
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 344558889999888777777777787777777776666655555555554
No 314
>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=28.93 E-value=61 Score=24.91 Aligned_cols=24 Identities=13% Similarity=0.156 Sum_probs=20.3
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 400 EDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 400 S~eEIAe~LGIS~etVk~~l~~ar 423 (442)
+..|+|+.+||+..+++.......
T Consensus 2 ~i~evA~~~gvs~~tlR~~~~~g~ 25 (67)
T cd04764 2 TIKEVSEIIGVKPHTLRYYEKEFN 25 (67)
T ss_pred CHHHHHHHHCcCHHHHHHHHHhcC
Confidence 678999999999999998866543
No 315
>COG2344 AT-rich DNA-binding protein [General function prediction only]
Probab=28.87 E-value=1.2e+02 Score=29.72 Aligned_cols=52 Identities=19% Similarity=0.190 Sum_probs=41.9
Q ss_pred eecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 371 IKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 371 irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
..+|......+....+....|..+.-...|-+|||+.+|++..+|+.-+.+.
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 3678777777777788888887776677899999999999999999765543
No 316
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=28.85 E-value=1.2e+02 Score=23.15 Aligned_cols=26 Identities=15% Similarity=0.147 Sum_probs=19.8
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 398 YPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
+.|.+++|+.+|++..+|..+..--+
T Consensus 14 gls~~~lA~~~g~s~s~v~~iE~G~~ 39 (64)
T PF13560_consen 14 GLSQAQLADRLGVSQSTVSRIERGRR 39 (64)
T ss_dssp TS-HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred CCCHHHHHHHHCcCHHHHHHHHCCCC
Confidence 57999999999999999998875333
No 317
>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=28.64 E-value=1.7e+02 Score=24.70 Aligned_cols=27 Identities=41% Similarity=0.497 Sum_probs=22.0
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
..+.|+.|||+.+|+|..+|-..-++.
T Consensus 47 ~~g~syreIa~~tgvS~aTItRvsr~L 73 (87)
T PF01371_consen 47 DEGKSYREIAEETGVSIATITRVSRCL 73 (87)
T ss_dssp HTTSSHHHHHHHHTSTHHHHHHHHHHH
T ss_pred HCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 457899999999999999987665443
No 318
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=28.61 E-value=69 Score=24.39 Aligned_cols=24 Identities=25% Similarity=0.176 Sum_probs=20.3
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 400 EDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 400 S~eEIAe~LGIS~etVk~~l~~ar 423 (442)
|..|+|+.+|++..+++.......
T Consensus 2 s~~eva~~~gvs~~tlr~~~~~gl 25 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYERIGL 25 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCCC
Confidence 678999999999999998876443
No 319
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=28.56 E-value=1.3e+02 Score=29.92 Aligned_cols=40 Identities=13% Similarity=-0.039 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHH
Q 013472 381 ISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASE 420 (442)
Q Consensus 381 i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~ 420 (442)
...|.++...+...+...++.++||+.+|+|...+..+.+
T Consensus 4 ~~~i~~~~~~i~~~~~~~~~l~~lA~~~~~S~~~l~r~F~ 43 (289)
T PRK15121 4 AGIIRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFK 43 (289)
T ss_pred HHHHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3567778888888888889999999999999999887654
No 320
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=28.52 E-value=1.2e+02 Score=22.87 Aligned_cols=27 Identities=19% Similarity=0.082 Sum_probs=22.2
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
+...|..|||+.+|++..++..-+...
T Consensus 22 ~~~~t~~ela~~l~~~~~t~s~hL~~L 48 (61)
T PF12840_consen 22 NGPMTVSELAEELGISQSTVSYHLKKL 48 (61)
T ss_dssp CSTBEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 667799999999999999998876644
No 321
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=28.45 E-value=85 Score=22.48 Aligned_cols=28 Identities=25% Similarity=0.159 Sum_probs=23.3
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
....+..+|++.+|++..+|..+++...
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~ 35 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLR 35 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3456899999999999999999877543
No 322
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=28.41 E-value=1.4e+02 Score=28.38 Aligned_cols=25 Identities=20% Similarity=0.397 Sum_probs=22.8
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHh
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASEC 421 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~ 421 (442)
+-||..|+|+.+|+|..||+.++..
T Consensus 31 ~LPsE~eLa~~~~VSR~TvR~Al~~ 55 (238)
T TIGR02325 31 YLPAEMQLAERFGVNRHTVRRAIAA 55 (238)
T ss_pred cCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 6789999999999999999999764
No 323
>PHA02943 hypothetical protein; Provisional
Probab=28.41 E-value=1.8e+02 Score=27.52 Aligned_cols=46 Identities=24% Similarity=0.318 Sum_probs=29.4
Q ss_pred ccccHHHH-HHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 374 PCKLNREI-SKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 374 P~~v~e~i-~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
|..+.+.+ .++.+...-+ ..| ..|..|||+.||+|-+.|+.++...
T Consensus 2 Pr~~sd~v~~R~~eILE~L--k~G-~~TtseIAkaLGlS~~qa~~~LyvL 48 (165)
T PHA02943 2 PRGMSDTVHTRMIKTLRLL--ADG-CKTTSRIANKLGVSHSMARNALYQL 48 (165)
T ss_pred CcchhHHHHHHHHHHHHHH--hcC-CccHHHHHHHHCCCHHHHHHHHHHH
Confidence 44444333 2344444444 223 3468899999999999999987643
No 324
>PRK09726 antitoxin HipB; Provisional
Probab=28.38 E-value=1.6e+02 Score=24.16 Aligned_cols=24 Identities=25% Similarity=0.194 Sum_probs=20.5
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHH
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASE 420 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~ 420 (442)
++.|.+|+|+.+|++..+|..+.+
T Consensus 24 ~gltq~elA~~~gvs~~tis~~e~ 47 (88)
T PRK09726 24 NGWTQSELAKKIGIKQATISNFEN 47 (88)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHC
Confidence 367899999999999999988765
No 325
>PRK10072 putative transcriptional regulator; Provisional
Probab=28.25 E-value=1.1e+02 Score=26.22 Aligned_cols=28 Identities=14% Similarity=-0.009 Sum_probs=23.2
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHhcccC
Q 013472 398 YPEDIEIAKYTGLSLAEIRSASECLRIV 425 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~l~~ar~~ 425 (442)
+.|..|+|+.+|++..+|.....--+.|
T Consensus 46 glTQ~elA~~lGvS~~TVs~WE~G~r~P 73 (96)
T PRK10072 46 GLKIDDFARVLGVSVAMVKEWESRRVKP 73 (96)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHcCCCCC
Confidence 6689999999999999999987644433
No 326
>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=28.10 E-value=1.1e+02 Score=28.59 Aligned_cols=35 Identities=26% Similarity=0.257 Sum_probs=27.8
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHhcccCCCCcccc
Q 013472 398 YPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKI 432 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v 432 (442)
+.|.+|||+.+|++...|..++..+..+-.+...+
T Consensus 120 g~s~~~iA~~lg~s~~~V~r~l~l~~lp~~v~~~~ 154 (187)
T TIGR00180 120 SMTQEDLAKKIGKSRAHITNLLRLLKLPSEIQSAI 154 (187)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHcCCHHHHHHH
Confidence 45889999999999999999998877554444433
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=27.81 E-value=1.4e+02 Score=27.32 Aligned_cols=40 Identities=23% Similarity=0.403 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhch
Q 013472 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGW 294 (442)
Q Consensus 255 le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~ 294 (442)
.++++.-|.+..++..|..+.+++.|++++.+..-++.|+
T Consensus 32 f~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~IreGR 71 (137)
T TIGR03826 32 FEKVYKFLRKHENRQATVSEIVEETGVSEKLILKFIREGR 71 (137)
T ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 3445555666667888999999999999999999999884
No 328
>COG2902 NAD-specific glutamate dehydrogenase [Amino acid transport and metabolism]
Probab=27.80 E-value=1.3e+03 Score=29.08 Aligned_cols=32 Identities=28% Similarity=0.311 Sum_probs=24.5
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHhcccCCCCc
Q 013472 398 YPEDIEIAKYTGLSLAEIRSASECLRIVGSID 429 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD 429 (442)
-|.+-+||+..|+++.+|..+..+....+++|
T Consensus 1466 ~~dii~ia~~~~~~~~~~Ak~yf~v~~~~~~~ 1497 (1592)
T COG2902 1466 VLDIIDIADITGIDVAEVAKAYFAVSDALGLD 1497 (1592)
T ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHHHhCch
Confidence 34778899999999999998876665555554
No 329
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=27.62 E-value=1.2e+02 Score=22.03 Aligned_cols=24 Identities=29% Similarity=0.245 Sum_probs=19.3
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 400 EDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 400 S~eEIAe~LGIS~etVk~~l~~ar 423 (442)
..++||+.+|++..+|.......|
T Consensus 29 ~~~~la~~~~l~~~qV~~WF~nrR 52 (56)
T smart00389 29 EREELAAKLGLSERQVKVWFQNRR 52 (56)
T ss_pred HHHHHHHHHCcCHHHHHHhHHHHh
Confidence 456899999999999998765443
No 330
>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=27.43 E-value=1.1e+02 Score=26.42 Aligned_cols=26 Identities=27% Similarity=0.213 Sum_probs=22.7
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 398 YPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
.++.+|||+.+|+|...|..++....
T Consensus 25 ~~s~~eia~~~~i~~~~v~~il~~L~ 50 (132)
T TIGR00738 25 PVSVKEIAERQGISRSYLEKILRTLR 50 (132)
T ss_pred cCcHHHHHHHHCcCHHHHHHHHHHHH
Confidence 67999999999999999999976543
No 331
>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=27.34 E-value=1.7e+02 Score=24.50 Aligned_cols=27 Identities=30% Similarity=0.298 Sum_probs=23.1
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
...+|..|||+.+|++..+|..++...
T Consensus 45 ~~~is~~eLa~~~g~sr~tVsr~L~~L 71 (95)
T TIGR01610 45 QDRVTATVIAELTGLSRTHVSDAIKSL 71 (95)
T ss_pred CCccCHHHHHHHHCcCHHHHHHHHHHH
Confidence 457799999999999999999986643
No 332
>smart00351 PAX Paired Box domain.
Probab=27.24 E-value=1.1e+02 Score=26.88 Aligned_cols=31 Identities=16% Similarity=0.038 Sum_probs=25.7
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHhcccCCCC
Q 013472 398 YPEDIEIAKYTGLSLAEIRSASECLRIVGSI 428 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~l~~ar~~~SL 428 (442)
+.+..+||+.+||+..+|...++..+..-++
T Consensus 33 G~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~ 63 (125)
T smart00351 33 GVRPCDISRQLCVSHGCVSKILGRYYETGSI 63 (125)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHcCCc
Confidence 5588999999999999999999887644333
No 333
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=26.99 E-value=1.2e+02 Score=30.38 Aligned_cols=40 Identities=8% Similarity=-0.021 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHh
Q 013472 382 SKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC 421 (442)
Q Consensus 382 ~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ 421 (442)
..+.++...+...+...++.++||+.+|||+.++....+.
T Consensus 218 ~~~~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~ 257 (322)
T PRK09393 218 DRLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEA 257 (322)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 4567777777777788899999999999999999887553
No 334
>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=26.82 E-value=1.5e+02 Score=28.31 Aligned_cols=25 Identities=24% Similarity=0.291 Sum_probs=22.8
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHh
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASEC 421 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~ 421 (442)
+-||..|||+.+|+|..||+.++..
T Consensus 23 ~LPsE~eLa~~~gVSR~TVR~Al~~ 47 (233)
T TIGR02404 23 YLPSEHELMDQYGASRETVRKALNL 47 (233)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 6789999999999999999999763
No 335
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=26.73 E-value=1.6e+02 Score=27.80 Aligned_cols=25 Identities=16% Similarity=0.212 Sum_probs=21.9
Q ss_pred CcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 399 PEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 399 PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
.|.+|||+.+|++.++|-..+...+
T Consensus 170 ~t~~~lA~~lG~sretvsR~L~~L~ 194 (226)
T PRK10402 170 EKHTQAAEYLGVSYRHLLYVLAQFI 194 (226)
T ss_pred chHHHHHHHHCCcHHHHHHHHHHHH
Confidence 3789999999999999999887655
No 336
>PRK14999 histidine utilization repressor; Provisional
Probab=26.68 E-value=1.5e+02 Score=28.53 Aligned_cols=25 Identities=24% Similarity=0.319 Sum_probs=22.8
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHh
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASEC 421 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~ 421 (442)
+-||..|||+.+|+|..+|+.++..
T Consensus 35 ~LPsE~eLa~~~gVSR~TVR~Al~~ 59 (241)
T PRK14999 35 RIPSEAELVAQYGFSRMTINRALRE 59 (241)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 5789999999999999999999764
No 337
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=26.66 E-value=2.2e+02 Score=22.95 Aligned_cols=25 Identities=24% Similarity=0.077 Sum_probs=20.9
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHh
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASEC 421 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~ 421 (442)
.+.+.+||++.+|+|..++.-++..
T Consensus 43 ~Ga~~~el~~~CgL~~aEAeLl~~L 67 (70)
T PF10975_consen 43 QGASVEELMEECGLSRAEAELLLSL 67 (70)
T ss_pred cCCCHHHHHHHcCCCHHHHHHHHHH
Confidence 4568999999999999999877653
No 338
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=26.33 E-value=1.5e+02 Score=24.65 Aligned_cols=38 Identities=11% Similarity=0.239 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHh
Q 013472 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAF 292 (442)
Q Consensus 255 le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~ 292 (442)
++++..-+...+...++.+++|+.+|++...|.+.++.
T Consensus 7 ~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~ 44 (107)
T PRK10219 7 IQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRT 44 (107)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 45556666777788899999999999999888776654
No 339
>PRK12702 mannosyl-3-phosphoglycerate phosphatase; Reviewed
Probab=26.30 E-value=1.3e+02 Score=31.11 Aligned_cols=42 Identities=17% Similarity=0.117 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHHcC------CCCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 381 ISKIQKARKALTNSHG------KYPEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 381 i~kI~ka~~~L~~elg------r~PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
...|+....++.++++ -+.|.+|||+.+|++.+..+.+.++.
T Consensus 100 y~~ir~~L~~l~~~~~~~f~gF~d~t~~ei~~~TGL~~~~A~~A~~Re 147 (302)
T PRK12702 100 YPCLRHILQQVRQDSHLDLIGFGDWTASELAAATGIPLEEAERAQKRE 147 (302)
T ss_pred HHHHHHHHHHHHHHhCCCceehhhCCHHHHHHHhCcCHHHHHHHHhcc
Confidence 3455556666666654 46799999999999999999887643
No 340
>PRK09480 slmA division inhibitor protein; Provisional
Probab=26.03 E-value=4.8e+02 Score=23.34 Aligned_cols=76 Identities=20% Similarity=0.019 Sum_probs=48.5
Q ss_pred HHHHhCCCCChHHHHHHcCCCHHHHHHHHHhchHHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhH
Q 013472 262 LEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGA 337 (442)
Q Consensus 262 L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAi 337 (442)
+.+.-|...|..+.|+.+|++...+-.-....+.-+..++..+..-+............+..+.++..+-.++.-+
T Consensus 23 ~~~~~G~~~ti~~Ia~~agvs~gt~Y~~F~~K~~L~~~v~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~ 98 (194)
T PRK09480 23 LESPPGERITTAKLAARVGVSEAALYRHFPSKARMFEGLIEFIEESLFSRINQILKDEKDTLARARLILLLLLGFA 98 (194)
T ss_pred HHhcCCCccCHHHHHHHhCCCHhHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHH
Confidence 3344368889999999999999888877766555556666665554444444333333456666666555555433
No 341
>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=25.78 E-value=2.3e+02 Score=24.01 Aligned_cols=65 Identities=8% Similarity=-0.027 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHHHHHHHhhcCceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 349 STYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 349 STYa~~wIRnaI~r~LRkqsr~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
..|...++.+.+.+.+...-....+. ..... ....|.. ....+..|||+.+|++..+|-..+...
T Consensus 2 ~~~~l~~~~~~~~~~~~~~l~~~~lt----~~q~~---iL~~l~~--~~~~t~~ela~~~~~~~~tvs~~l~~L 66 (118)
T TIGR02337 2 LPLALLQAREAAMSFFRPILAQHGLT----EQQWR---ILRILAE--QGSMEFTQLANQACILRPSLTGILARL 66 (118)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHcCCC----HHHHH---HHHHHHH--cCCcCHHHHHHHhCCCchhHHHHHHHH
Confidence 45666777777777666442211121 11111 2222222 335789999999999999998876644
No 342
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=25.74 E-value=90 Score=20.88 Aligned_cols=24 Identities=21% Similarity=0.192 Sum_probs=20.8
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHH
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASE 420 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~ 420 (442)
...|..++|+.+|++..+|.....
T Consensus 9 ~~~s~~~la~~~~i~~~~i~~~~~ 32 (56)
T smart00530 9 KGLTQEELAEKLGVSRSTLSRIEN 32 (56)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHC
Confidence 456899999999999999988765
No 343
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=25.68 E-value=1.6e+02 Score=28.36 Aligned_cols=25 Identities=20% Similarity=0.275 Sum_probs=22.7
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHh
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASEC 421 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~ 421 (442)
+-||..|||+.+|+|..+|+.++..
T Consensus 28 ~LPsE~eL~~~~~VSR~TvR~Al~~ 52 (240)
T PRK09764 28 ALPTESALQTEFGVSRVTVRQALRQ 52 (240)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 5789999999999999999999764
No 344
>PF13309 HTH_22: HTH domain
Probab=25.64 E-value=1.2e+02 Score=23.76 Aligned_cols=20 Identities=20% Similarity=0.061 Sum_probs=18.2
Q ss_pred cHHHHHHHhCCCHHHHHHHH
Q 013472 400 EDIEIAKYTGLSLAEIRSAS 419 (442)
Q Consensus 400 S~eEIAe~LGIS~etVk~~l 419 (442)
+.+.+|+.||||..+|-..+
T Consensus 44 av~~vA~~L~iS~~TVY~YL 63 (64)
T PF13309_consen 44 AVEYVAEKLGISRATVYRYL 63 (64)
T ss_pred HHHHHHHHHCCCHHHHHHHc
Confidence 88999999999999998765
No 345
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=25.44 E-value=1.2e+02 Score=28.49 Aligned_cols=36 Identities=28% Similarity=0.201 Sum_probs=26.6
Q ss_pred HHHHHHHcCCCCcHHHHHHHh--CCCHHHHHHHHHhcc
Q 013472 388 RKALTNSHGKYPEDIEIAKYT--GLSLAEIRSASECLR 423 (442)
Q Consensus 388 ~~~L~~elgr~PS~eEIAe~L--GIS~etVk~~l~~ar 423 (442)
+++|..-.+-.+++.+||+.+ +||.++|++.+....
T Consensus 29 ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~ 66 (171)
T PF14394_consen 29 IRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLE 66 (171)
T ss_pred HHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHH
Confidence 333333345566999999999 999999999876543
No 346
>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=25.41 E-value=1.7e+02 Score=27.71 Aligned_cols=26 Identities=23% Similarity=0.327 Sum_probs=22.9
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
+-|+..|+|+.+|++.-+|+.++...
T Consensus 24 ~lPsE~eLa~~~~Vsr~Tvr~Al~~L 49 (231)
T TIGR03337 24 KLPSERDLGERFNTTRVTIREALQQL 49 (231)
T ss_pred cCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 47899999999999999999997643
No 347
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=25.31 E-value=1.7e+02 Score=26.66 Aligned_cols=40 Identities=18% Similarity=0.086 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHcC-CCCcHHHHHHHhCCCHHHHHHH
Q 013472 379 REISKIQKARKALTNSHG-KYPEDIEIAKYTGLSLAEIRSA 418 (442)
Q Consensus 379 e~i~kI~ka~~~L~~elg-r~PS~eEIAe~LGIS~etVk~~ 418 (442)
+...+|-.+..++..+.| ...|..+||+..|+|.+.+...
T Consensus 8 ~~r~~Il~aA~~lf~e~G~~~~s~~~IA~~agvs~~~lY~h 48 (202)
T TIGR03613 8 AKRKAILSAALDTFSRFGFHGTSLEQIAELAGVSKTNLLYY 48 (202)
T ss_pred HHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCCCHHHHHHH
No 348
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=25.19 E-value=1.1e+02 Score=23.32 Aligned_cols=26 Identities=31% Similarity=0.247 Sum_probs=18.8
Q ss_pred CCCCcHHHHHHHhC-CCHHHHHHHHHh
Q 013472 396 GKYPEDIEIAKYTG-LSLAEIRSASEC 421 (442)
Q Consensus 396 gr~PS~eEIAe~LG-IS~etVk~~l~~ 421 (442)
..+.|.+||++... ++.+.|+.++..
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 34679999999998 999999998864
No 349
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=25.18 E-value=1.1e+02 Score=24.74 Aligned_cols=34 Identities=15% Similarity=0.081 Sum_probs=28.4
Q ss_pred HHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 390 ALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 390 ~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
.+...++...+..+.|+.||+++..|.......|
T Consensus 5 ~fIrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR 38 (65)
T PF05344_consen 5 AFIRLLSQQISVAQAADRLGTDPGTVRRWVRMFR 38 (65)
T ss_pred HHHHHhcccccHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4445568888999999999999999999877665
No 350
>PRK09480 slmA division inhibitor protein; Provisional
Probab=25.17 E-value=1.5e+02 Score=26.75 Aligned_cols=41 Identities=17% Similarity=0.186 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHHHH-HHcCCCCcHHHHHHHhCCCHHHHHHH
Q 013472 378 NREISKIQKARKALT-NSHGKYPEDIEIAKYTGLSLAEIRSA 418 (442)
Q Consensus 378 ~e~i~kI~ka~~~L~-~elgr~PS~eEIAe~LGIS~etVk~~ 418 (442)
.+...+|-.+...+. .+.|...|.++||+..||+.+++...
T Consensus 9 ~~~r~~Il~aa~~l~~~~~G~~~ti~~Ia~~agvs~gt~Y~~ 50 (194)
T PRK09480 9 GERREQILQALAQMLESPPGERITTAKLAARVGVSEAALYRH 50 (194)
T ss_pred hhHHHHHHHHHHHHHHhcCCCccCHHHHHHHhCCCHhHHHHH
Confidence 344456666665654 44368899999999999999998653
No 351
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=24.81 E-value=2.2e+02 Score=26.83 Aligned_cols=25 Identities=24% Similarity=0.320 Sum_probs=21.7
Q ss_pred CcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 399 PEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 399 PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
.+.++||..+|++.++|-.+++..+
T Consensus 174 ~t~~~iA~~lG~tretvsR~l~~L~ 198 (236)
T PRK09392 174 YEKRVLASYLGMTPENLSRAFAALA 198 (236)
T ss_pred CCHHHHHHHhCCChhHHHHHHHHHH
Confidence 4679999999999999999887654
No 352
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=24.26 E-value=1.1e+02 Score=27.40 Aligned_cols=30 Identities=13% Similarity=-0.051 Sum_probs=25.1
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 395 HGKYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 395 lgr~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
+..+.+.+|||+.++++..+|+....+.+.
T Consensus 155 l~~g~~~~~I~~~l~~s~~tv~~~~~~l~~ 184 (204)
T PRK09958 155 ILDGKDNNDIAEKMFISNKTVSTYKSRLME 184 (204)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 345679999999999999999998876654
No 353
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=24.22 E-value=1.8e+02 Score=27.99 Aligned_cols=25 Identities=24% Similarity=0.259 Sum_probs=22.7
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHh
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASEC 421 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~ 421 (442)
+-||..|||+.+|+|..||+.++..
T Consensus 32 kLPsE~eLa~~~~VSR~TvR~Al~~ 56 (241)
T PRK11402 32 QIPTENELCTQYNVSRITIRKAISD 56 (241)
T ss_pred cCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 6799999999999999999999763
No 354
>cd00131 PAX Paired Box domain
Probab=24.19 E-value=1.4e+02 Score=26.60 Aligned_cols=33 Identities=15% Similarity=0.053 Sum_probs=27.5
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCc
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASECLRIVGSID 429 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD 429 (442)
.+.+..+||+.+|++..+|..+++..+..-++.
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 356999999999999999999998877554553
No 355
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=24.14 E-value=80 Score=28.64 Aligned_cols=27 Identities=15% Similarity=0.169 Sum_probs=23.7
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 398 YPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
..+.++||+.|||+...|+.++.....
T Consensus 15 ~~~dedLa~~l~i~~n~vRkiL~~L~e 41 (147)
T smart00531 15 CVTEEDLAELLGIKQKQLRKILYLLYD 41 (147)
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHHHh
Confidence 579999999999999999999876553
No 356
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=24.09 E-value=89 Score=28.19 Aligned_cols=25 Identities=28% Similarity=0.319 Sum_probs=22.5
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHh
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASEC 421 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~ 421 (442)
+-||..|+|..+|+.+.||..+.+-
T Consensus 34 kLPSvRelA~~~~VNpnTv~raY~e 58 (125)
T COG1725 34 KLPSVRELAKDLGVNPNTVQRAYQE 58 (125)
T ss_pred CCCcHHHHHHHhCCCHHHHHHHHHH
Confidence 6799999999999999999998653
No 357
>PRK15044 transcriptional regulator SirC; Provisional
Probab=24.06 E-value=5.5e+02 Score=26.53 Aligned_cols=70 Identities=14% Similarity=-0.029 Sum_probs=44.5
Q ss_pred HHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhchHHHHHHHHHhHHHHHHHHHHhhCC-CCCHHhHHH
Q 013472 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGL-GIPFSDLLQ 327 (442)
Q Consensus 255 le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~~Are~LI~~nlrLV~sIAkrY~g~-g~d~EDLIQ 327 (442)
.+++..-+.....++++.++||+.+|++...|.+.++.-...+.+.+. ..-...|++.... .....|+..
T Consensus 194 ~~kV~~~I~~nl~~~~SLeeLA~~lgmS~~tL~R~Fk~eg~T~~~y~~---~~RL~~A~~LL~~t~~sIseIA~ 264 (295)
T PRK15044 194 KEKVYNIIISDLTRKWSQAEVAGKLFMSVSSLKRKLAAEEVSFSKIYL---DARMNQAIKLLRMGAGNISQVAT 264 (295)
T ss_pred HHHHHHHHHhCcccCCCHHHHHHHhCCCHHHHHHHHHHcCCCHHHHHH---HHHHHHHHHHHHcCCCCHHHHHH
Confidence 456667777788999999999999999999998877653222333332 2222445544432 345555444
No 358
>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=23.95 E-value=1.7e+02 Score=25.24 Aligned_cols=25 Identities=32% Similarity=0.290 Sum_probs=21.0
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHh
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASEC 421 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~ 421 (442)
.+.|+.|||+.+|||..+|-..-+.
T Consensus 54 ~~~tQrEIa~~lGiS~atIsR~sn~ 78 (94)
T TIGR01321 54 GNMSQREIASKLGVSIATITRGSNN 78 (94)
T ss_pred CCCCHHHHHHHhCCChhhhhHHHhh
Confidence 5689999999999999999765543
No 359
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=23.95 E-value=1.8e+02 Score=27.64 Aligned_cols=25 Identities=20% Similarity=0.242 Sum_probs=22.7
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHh
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASEC 421 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~ 421 (442)
+-||..|+|+.+|+|..+|+.++..
T Consensus 24 ~LPsE~eLa~~~~VSR~TVR~Al~~ 48 (230)
T TIGR02018 24 RIPSEHELVAQYGCSRMTVNRALRE 48 (230)
T ss_pred cCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 5789999999999999999999764
No 360
>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=23.86 E-value=1.4e+02 Score=22.88 Aligned_cols=28 Identities=21% Similarity=0.290 Sum_probs=23.3
Q ss_pred CCCCChHHHHHHcCCCHHHHHHHHHhch
Q 013472 267 GKAASLNCWAQAAGVSERVLKQHLAFGW 294 (442)
Q Consensus 267 gr~pt~~ewA~a~g~deeeL~~~l~~G~ 294 (442)
.|..+..+.|+..|++...+-..++.+.
T Consensus 21 PR~~tl~elA~~lgis~st~~~~LRrae 48 (53)
T PF04967_consen 21 PRRITLEELAEELGISKSTVSEHLRRAE 48 (53)
T ss_pred CCcCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 5788999999999999988877777653
No 361
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=23.84 E-value=92 Score=27.74 Aligned_cols=28 Identities=18% Similarity=0.217 Sum_probs=23.9
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
|..++..|||+.+|+|...|+.++....
T Consensus 23 g~~~s~~~ia~~~~is~~~vrk~l~~L~ 50 (141)
T PRK11014 23 GRMTSISEVTEVYGVSRNHMVKIINQLS 50 (141)
T ss_pred CCccCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4567999999999999999999977544
No 362
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=23.73 E-value=1.4e+02 Score=21.69 Aligned_cols=23 Identities=26% Similarity=0.209 Sum_probs=18.5
Q ss_pred cHHHHHHHhCCCHHHHHHHHHhc
Q 013472 400 EDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 400 S~eEIAe~LGIS~etVk~~l~~a 422 (442)
..++||..+|++...|......-
T Consensus 29 ~~~~la~~~~l~~~qV~~WF~nr 51 (59)
T cd00086 29 EREELAKELGLTERQVKIWFQNR 51 (59)
T ss_pred HHHHHHHHHCcCHHHHHHHHHHH
Confidence 35679999999999999876543
No 363
>PRK04841 transcriptional regulator MalT; Provisional
Probab=23.68 E-value=1e+02 Score=35.04 Aligned_cols=29 Identities=14% Similarity=-0.018 Sum_probs=24.6
Q ss_pred cCCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 395 HGKYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 395 lgr~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
...+.|.+|||+.|+||+.||+..++...
T Consensus 850 ~~~g~~~~~ia~~l~~s~~tv~~h~~~~~ 878 (903)
T PRK04841 850 IYSGYSNEQIAGELDVAATTIKTHIRNLY 878 (903)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 34678999999999999999999877543
No 364
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=23.65 E-value=1.7e+02 Score=28.33 Aligned_cols=25 Identities=32% Similarity=0.440 Sum_probs=22.9
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHh
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASEC 421 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~ 421 (442)
+-||..|+|+.+|+|.-||+.++..
T Consensus 30 ~LPsE~eLa~~f~VSR~TvRkAL~~ 54 (236)
T COG2188 30 KLPSERELAEQFGVSRMTVRKALDE 54 (236)
T ss_pred CCCCHHHHHHHHCCcHHHHHHHHHH
Confidence 6799999999999999999999763
No 365
>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=23.64 E-value=84 Score=25.75 Aligned_cols=22 Identities=14% Similarity=0.003 Sum_probs=19.8
Q ss_pred CcHHHHHHHhCCCHHHHHHHHH
Q 013472 399 PEDIEIAKYTGLSLAEIRSASE 420 (442)
Q Consensus 399 PS~eEIAe~LGIS~etVk~~l~ 420 (442)
.|.+||++.||++..+|..+.+
T Consensus 53 ~s~eel~~~L~~s~~tv~~~~k 74 (76)
T PF06970_consen 53 FSIEELMELLNCSKSTVIKAKK 74 (76)
T ss_pred eeHHHHHHHHCCCHHHHHHHHH
Confidence 4999999999999999988764
No 366
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=23.61 E-value=70 Score=24.97 Aligned_cols=32 Identities=22% Similarity=0.296 Sum_probs=20.5
Q ss_pred HHHHHHcCCCCcHHHHHHHhCCCHHHHH-HHHHh
Q 013472 389 KALTNSHGKYPEDIEIAKYTGLSLAEIR-SASEC 421 (442)
Q Consensus 389 ~~L~~elgr~PS~eEIAe~LGIS~etVk-~~l~~ 421 (442)
+++.+.+|- .+..|+|+.|||+..+|. ....+
T Consensus 4 ~rl~~~~g~-~~~~~lA~~lgis~st~s~~~~~r 36 (66)
T PF07022_consen 4 ERLKEALGV-KSDKELAERLGISKSTLSNNWKKR 36 (66)
T ss_dssp HHHHHHHT--SSCHHHHCCTT--HHHHH-HHHHS
T ss_pred HHHHHHhCC-CCHHHHHHHhCcCHHHhhHHHHhC
Confidence 344444453 367899999999999999 66553
No 367
>PRK13503 transcriptional activator RhaS; Provisional
Probab=23.45 E-value=1.8e+02 Score=27.99 Aligned_cols=38 Identities=13% Similarity=0.091 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHH
Q 013472 383 KIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASE 420 (442)
Q Consensus 383 kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~ 420 (442)
.+.++..-+.+......|.++||+.+|+++..+....+
T Consensus 172 ~i~~~~~~I~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk 209 (278)
T PRK13503 172 RLNQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLK 209 (278)
T ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 36666666777777788999999999999999877654
No 368
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=23.41 E-value=1.7e+02 Score=29.40 Aligned_cols=40 Identities=5% Similarity=-0.100 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHh
Q 013472 382 SKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC 421 (442)
Q Consensus 382 ~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ 421 (442)
..++++...+...+...+|.++||+.+|+|+..+....+.
T Consensus 191 ~~i~~~~~~i~~~~~~~~tl~~lA~~~~~S~~~l~r~Fk~ 230 (302)
T PRK10371 191 FYVSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQR 230 (302)
T ss_pred HHHHHHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3566777777777777899999999999999988776553
No 369
>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=23.41 E-value=2e+02 Score=24.60 Aligned_cols=26 Identities=27% Similarity=0.165 Sum_probs=20.2
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 398 YPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
+.+..|||...|+|+..|..+++..+
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 55899999999999999999987665
No 370
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=23.27 E-value=1.7e+02 Score=24.27 Aligned_cols=28 Identities=21% Similarity=0.346 Sum_probs=24.1
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
+...|-++||+.||||...|-..++..+
T Consensus 17 ~~~~SGe~La~~LgiSRtaVwK~Iq~Lr 44 (79)
T COG1654 17 GNFVSGEKLAEELGISRTAVWKHIQQLR 44 (79)
T ss_pred CCcccHHHHHHHHCccHHHHHHHHHHHH
Confidence 4567999999999999999998877665
No 371
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=23.23 E-value=1.3e+02 Score=26.56 Aligned_cols=28 Identities=25% Similarity=0.064 Sum_probs=23.7
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASECLRI 424 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~ar~ 424 (442)
.+.+.++||+.++++..+|+......+.
T Consensus 151 ~g~~~~~Ia~~l~~s~~tv~~~~~~l~~ 178 (196)
T PRK10360 151 QGMAVKEIAAELGLSPKTVHVHRANLME 178 (196)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4579999999999999999988776553
No 372
>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=22.93 E-value=1.1e+02 Score=23.86 Aligned_cols=25 Identities=16% Similarity=-0.005 Sum_probs=20.5
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHh
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASEC 421 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~ 421 (442)
.+.|.+++|+.+|++..+|..++.-
T Consensus 17 ~~~t~~~lA~~~gis~~tis~~~~g 41 (78)
T TIGR02607 17 LGLSIRALAKALGVSRSTLSRIVNG 41 (78)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 4568889999999999999888763
No 373
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=22.63 E-value=2e+02 Score=26.84 Aligned_cols=40 Identities=18% Similarity=0.094 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHHHHHcC-CCCcHHHHHHHhCCCHHHHHHH
Q 013472 379 REISKIQKARKALTNSHG-KYPEDIEIAKYTGLSLAEIRSA 418 (442)
Q Consensus 379 e~i~kI~ka~~~L~~elg-r~PS~eEIAe~LGIS~etVk~~ 418 (442)
+...+|-++...+..+.| ...|..+||+..|++.+.+...
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 455667777777777777 5689999999999999998654
No 374
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=22.55 E-value=88 Score=24.12 Aligned_cols=22 Identities=23% Similarity=0.126 Sum_probs=19.3
Q ss_pred cHHHHHHHhCCCHHHHHHHHHh
Q 013472 400 EDIEIAKYTGLSLAEIRSASEC 421 (442)
Q Consensus 400 S~eEIAe~LGIS~etVk~~l~~ 421 (442)
+..|+|+.+|++..+++.....
T Consensus 2 ~i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 2 TIGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh
Confidence 6789999999999999987654
No 375
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=22.32 E-value=89 Score=29.83 Aligned_cols=26 Identities=19% Similarity=0.402 Sum_probs=22.8
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
+-|+..|||+.+|+|..+|+.++...
T Consensus 30 ~LPsE~eLae~~gVSRt~VReAL~~L 55 (239)
T PRK04984 30 ILPAERELSELIGVTRTTLREVLQRL 55 (239)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 45699999999999999999997754
No 376
>TIGR01636 phage_rinA phage transcriptional activator, RinA family. This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.
Probab=21.98 E-value=1.9e+02 Score=25.80 Aligned_cols=24 Identities=8% Similarity=-0.046 Sum_probs=20.5
Q ss_pred CcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 399 PEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 399 PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
.|..+||..+|||..++......+
T Consensus 101 ~t~~~Ia~~l~iS~~t~~r~r~~~ 124 (134)
T TIGR01636 101 LTLVGLAQQLFISKSTAYRLRNHI 124 (134)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Confidence 499999999999999998775543
No 377
>PF15545 Toxin_67: Putative toxin 67
Probab=21.95 E-value=96 Score=25.26 Aligned_cols=30 Identities=23% Similarity=0.594 Sum_probs=25.8
Q ss_pred ChHHHHHHHHHHHHHHHHHhhcCceecccc
Q 013472 347 KFSTYVQYWIRKSISKMVARHARGIKIPCK 376 (442)
Q Consensus 347 rFSTYa~~wIRnaI~r~LRkqsr~irlP~~ 376 (442)
+-+.|+.-||+|.|...-+.+...+|+|..
T Consensus 6 kq~~~vRGwiknEi~~i~~~~r~~iRlPpG 35 (70)
T PF15545_consen 6 KQPSWVRGWIKNEINRIKTGRRKSIRLPPG 35 (70)
T ss_pred cchHHHHHHHHHHHHHHHhCccceecCCCc
Confidence 468899999999999888877788999965
No 378
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=21.95 E-value=1.2e+03 Score=26.37 Aligned_cols=134 Identities=12% Similarity=-0.016 Sum_probs=70.0
Q ss_pred CCCChHHHHHHcCCCHHHHHHHHHhc-----------hHHHHHHHHHhHHHHHHHHHHhhC-CCCCHHhHHHHHHHHHHH
Q 013472 268 KAASLNCWAQAAGVSERVLKQHLAFG-----------WYCREELIKSTRPLVLFLARNYRG-LGIPFSDLLQAGNVGVLQ 335 (442)
Q Consensus 268 r~pt~~ewA~a~g~deeeL~~~l~~G-----------~~Are~LI~~nlrLV~sIAkrY~g-~g~d~EDLIQEG~IGLir 335 (442)
...+..+.+...+++.+++...+..| ..+++++.+.-...+-.+-.+|-. .|++.++|.+-
T Consensus 376 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~h~~~p~~~g~~~~~l~~~------- 448 (614)
T PRK10512 376 GAVNLADFAWARQLNGEGMRALLQQPGYIQAGDSLLSAPVAARWQRKLLDTLATYHEQHRDEPGPGRERLRRM------- 448 (614)
T ss_pred cCCCHHHHHHHhcCCHHHHHHHhccCCeEEEccEEECHHHHHHHHHHHHHHHHHHHHHCCcccCCCHHHHHhh-------
Confidence 45566666666677776666554443 113344444444444333333322 35666655421
Q ss_pred hHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhc------CceecccccH---HHHHHHHHHHHHHHHHcCCCCcHHHHHH
Q 013472 336 GAERFDHTRGYKFSTYVQYWIRKSISKMVARHA------RGIKIPCKLN---REISKIQKARKALTNSHGKYPEDIEIAK 406 (442)
Q Consensus 336 AieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqs------r~irlP~~v~---e~i~kI~ka~~~L~~elgr~PS~eEIAe 406 (442)
+..|+-..+-+.+++.+.+.. ..+++|.+.. .....+.+.+..+.. -..|+.+|+++
T Consensus 449 ------------~~~~~~~~~~~~~l~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~--~~p~~~~~~~~ 514 (614)
T PRK10512 449 ------------ALPMEDEALVLLLIEKMRESGDIHSHHGWLHLPDHKAGFSEEQQALWQKAEPLFG--DEPWWVRDLAK 514 (614)
T ss_pred ------------cccCCCHHHHHHHHHHHHhCCCEEEeCCEEECCCCCCCCCHHHHHHHHHHHHHHh--cCCCCHHHHHH
Confidence 111222333444445444332 3456666532 222233222222222 35789999999
Q ss_pred HhCCCHHHHHHHHHhc
Q 013472 407 YTGLSLAEIRSASECL 422 (442)
Q Consensus 407 ~LGIS~etVk~~l~~a 422 (442)
.+|++...++.++...
T Consensus 515 ~l~~~~~~~~~~l~~l 530 (614)
T PRK10512 515 ETGTDEQAMRLTLRQA 530 (614)
T ss_pred HhCCCHHHHHHHHHHH
Confidence 9999999988887654
No 379
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=21.66 E-value=1.7e+02 Score=22.65 Aligned_cols=26 Identities=15% Similarity=0.178 Sum_probs=22.4
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 398 YPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
..+..|||+.+|++..+|...+....
T Consensus 13 ~~~~~eLa~~l~vS~~tv~~~l~~L~ 38 (69)
T TIGR00122 13 PFSGEKLGEALGMSRTAVNKHIQTLR 38 (69)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45799999999999999999877654
No 380
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=21.47 E-value=2.2e+02 Score=26.13 Aligned_cols=33 Identities=24% Similarity=0.126 Sum_probs=28.5
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCC
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASECLRIVGSI 428 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SL 428 (442)
..+.|..|||+.+|++..+|...+++.+..-++
T Consensus 19 ~~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~~ 51 (138)
T COG3415 19 GEGLSCREAAKRFGVSISTVYRWVRRYRETGLD 51 (138)
T ss_pred HcCccHHHHHHHhCccHHHHHHHHHHhcccccc
Confidence 567899999999999999999999988865444
No 381
>PRK13698 plasmid-partitioning protein; Provisional
Probab=21.43 E-value=2.1e+02 Score=29.82 Aligned_cols=36 Identities=17% Similarity=0.141 Sum_probs=28.5
Q ss_pred HHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCC
Q 013472 391 LTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSI 428 (442)
Q Consensus 391 L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SL 428 (442)
|...++ .|.+|||+.+|+|...|-++++.+.-|..+
T Consensus 171 L~~~~~--~tQeeLA~~lG~SRs~Vsn~Lrla~LP~~v 206 (323)
T PRK13698 171 LQNEFA--GNISALADAENISRKIITRCINTAKLPKSV 206 (323)
T ss_pred HHHhcC--CCHHHHHHHHCCCHHHHHHHHHHHcCCHHH
Confidence 443433 699999999999999999999887755444
No 382
>COG0350 Ada Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=21.27 E-value=2.5e+02 Score=26.30 Aligned_cols=46 Identities=17% Similarity=0.039 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCH--HHHHHHHHhcccCCCC
Q 013472 379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLSL--AEIRSASECLRIVGSI 428 (442)
Q Consensus 379 e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~--etVk~~l~~ar~~~SL 428 (442)
....++-++..+++ +|...|+.|||+.+|-+. ..|-.+ +.++|++|
T Consensus 88 ~Fq~~Vw~aL~~IP--~Get~TY~eiA~~ig~p~a~rAVG~A--~~~NPl~I 135 (168)
T COG0350 88 GFQGRVWQALREIP--YGETVTYGEIARRLGRPTAVRAVGNA--NGANPLPI 135 (168)
T ss_pred hHHHHHHHHHhcCC--CCCcEeHHHHHHHhCCCcHHHHHHHH--hccCCceE
Confidence 45556666665554 688889999999999933 224443 45666665
No 383
>PRK06424 transcription factor; Provisional
Probab=21.24 E-value=2.7e+02 Score=25.57 Aligned_cols=40 Identities=10% Similarity=-0.091 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 381 ISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 381 i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
...+...++.+..+ ++.|.+|+|+.+|++..+|..+.+--
T Consensus 82 ~~~~g~~Ir~lRe~--~GLSQ~eLA~~iGvs~stIskiE~G~ 121 (144)
T PRK06424 82 VEDYAELVKNARER--LSMSQADLAAKIFERKNVIASIERGD 121 (144)
T ss_pred HHHHHHHHHHHHHH--cCCCHHHHHHHhCCCHHHHHHHHCCC
Confidence 34444444544443 56799999999999999999887533
No 384
>PRK15186 AraC family transcriptional regulator; Provisional
Probab=21.18 E-value=4.4e+02 Score=26.75 Aligned_cols=69 Identities=12% Similarity=-0.011 Sum_probs=42.9
Q ss_pred HHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhchHHHHHHHHHhHHHHHHHHHHhhCC-CCCHHhHHHH
Q 013472 257 RIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGL-GIPFSDLLQA 328 (442)
Q Consensus 257 ~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~~Are~LI~~nlrLV~sIAkrY~g~-g~d~EDLIQE 328 (442)
++...+........+.++||+.+||+...|.+.++.-.-.+...+.. .|+ ..|+++... +....|+..+
T Consensus 185 ~i~~~I~~~~~~~~sl~~lA~~~gmS~stl~R~Fk~~g~s~~~~~~~-~Rl--~~A~~lL~~~~~sI~~IA~~ 254 (291)
T PRK15186 185 NIYNIIISDISRKWALKDISDSLYMSCSTLKRKLKQENTSFSEVYLN-ARM--NKATKLLRNSEYNITRVAYM 254 (291)
T ss_pred HHHHHHHhCccCCCCHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHH-HHH--HHHHHHHHcCCCCHHHHHHH
Confidence 34445666678899999999999999999988877521233333332 233 335555433 3555555443
No 385
>PRK13503 transcriptional activator RhaS; Provisional
Probab=21.15 E-value=3.7e+02 Score=25.80 Aligned_cols=27 Identities=26% Similarity=0.249 Sum_probs=15.6
Q ss_pred HHHHHHHHHHHHcCCCCcHHHHHHHhCCCH
Q 013472 383 KIQKARKALTNSHGKYPEDIEIAKYTGLSL 412 (442)
Q Consensus 383 kI~ka~~~L~~elgr~PS~eEIAe~LGIS~ 412 (442)
+|.+|.+.|. ....++.|||..+|.+-
T Consensus 224 Rl~~A~~LL~---~~~~sI~eIA~~~GF~~ 250 (278)
T PRK13503 224 RLLKARHLLR---HSDASVTDIAYRCGFGD 250 (278)
T ss_pred HHHHHHHHHH---cCCCCHHHHHHHhCCCC
Confidence 4555555543 22457788887776543
No 386
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=21.12 E-value=1e+02 Score=29.09 Aligned_cols=26 Identities=35% Similarity=0.312 Sum_probs=23.0
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 398 YPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 398 ~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
..|.+|||+.|||+...|+..+....
T Consensus 36 ~~tdeeLA~~Lgi~~~~VRk~L~~L~ 61 (178)
T PRK06266 36 EVTDEEIAEQTGIKLNTVRKILYKLY 61 (178)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 57999999999999999999977543
No 387
>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=21.06 E-value=74 Score=22.86 Aligned_cols=20 Identities=25% Similarity=0.375 Sum_probs=17.2
Q ss_pred HHHHHhCCCHHHHHHHHHhc
Q 013472 403 EIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 403 EIAe~LGIS~etVk~~l~~a 422 (442)
+||+.+|++..+|..+++-.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~ 21 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGK 21 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCC
Confidence 79999999999999887643
No 388
>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=20.96 E-value=1.2e+02 Score=22.25 Aligned_cols=24 Identities=25% Similarity=0.199 Sum_probs=21.6
Q ss_pred CcHHHHHHHhCCCHHHHHHHHHhc
Q 013472 399 PEDIEIAKYTGLSLAEIRSASECL 422 (442)
Q Consensus 399 PS~eEIAe~LGIS~etVk~~l~~a 422 (442)
.+..|||+.+|++..++...+...
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~L 44 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKL 44 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHHH
Confidence 899999999999999998887654
No 389
>PF10410 DnaB_bind: DnaB-helicase binding domain of primase; InterPro: IPR019475 This entry represents the C-terminal region three-helical domain of DNA primase []. Primases synthesise short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases. Primases are recruited to single-stranded DNA by helicases - this domain binds DnaB-helicase []. It is associated with the Toprim domain IPR006171 from INTERPRO, which is the central catalytic core. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=20.91 E-value=18 Score=27.09 Aligned_cols=41 Identities=12% Similarity=0.055 Sum_probs=25.7
Q ss_pred ccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHH
Q 013472 374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAE 414 (442)
Q Consensus 374 P~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~et 414 (442)
|....+.++++...+..++...-++.-..++|+.+|+++++
T Consensus 18 ~egk~~~~~~~~~~i~~i~~~i~r~~y~~~la~~~~i~~~~ 58 (59)
T PF10410_consen 18 PEGKAEAVREAAPLIAQIPDPIERELYIRELAERLGISEDA 58 (59)
T ss_dssp HHHHHHHHHHHHHHHTT--SHHHHHHHHHHHHHHCT-SSTT
T ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhCcCccc
Confidence 44455566666666666655555556678999999998764
No 390
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=20.86 E-value=6.5e+02 Score=25.18 Aligned_cols=59 Identities=12% Similarity=0.255 Sum_probs=37.8
Q ss_pred HHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHH
Q 013472 306 PLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVA 365 (442)
Q Consensus 306 rLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LR 365 (442)
+++..|...|. ...+.+||.....+..-.-...|...-|..|..|+...-.+...+.|.
T Consensus 195 ~~~~~i~~~~~-~~~tl~~lA~~~~~S~~~l~r~Fk~~~G~t~~~~l~~~Rl~~A~~lL~ 253 (302)
T PRK10371 195 QMLGFIAENYD-QALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRALLS 253 (302)
T ss_pred HHHHHHHHhhc-CCCCHHHHHHHHCcCHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHh
Confidence 33444445554 568999999888777666666666555777777776655444444444
No 391
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=20.81 E-value=1.2e+02 Score=21.93 Aligned_cols=27 Identities=26% Similarity=0.172 Sum_probs=21.4
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
...+..|||+.+|++..+|..-+...+
T Consensus 14 ~~~~~~el~~~l~~s~~~vs~hL~~L~ 40 (47)
T PF01022_consen 14 GPLTVSELAEELGLSQSTVSHHLKKLR 40 (47)
T ss_dssp SSEEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCchhhHHHhccccchHHHHHHHHHH
Confidence 456899999999999999988776543
No 392
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=20.57 E-value=1.9e+02 Score=26.18 Aligned_cols=26 Identities=12% Similarity=-0.070 Sum_probs=22.6
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHHHHh
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSASEC 421 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~l~~ 421 (442)
....|.+|||+.||++..+|..+++.
T Consensus 40 ~~~~tvdelae~lnr~rStv~rsl~~ 65 (126)
T COG3355 40 NGPLTVDELAEILNRSRSTVYRSLQN 65 (126)
T ss_pred cCCcCHHHHHHHHCccHHHHHHHHHH
Confidence 44679999999999999999988764
No 393
>PRK00901 methylated-DNA--protein-cysteine methyltransferase; Provisional
Probab=20.56 E-value=2.3e+02 Score=26.32 Aligned_cols=69 Identities=17% Similarity=0.146 Sum_probs=42.8
Q ss_pred HHHHHHHHHHhhcCceeccccc--HHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCH--HHHHHHHHhcccCCCC
Q 013472 356 IRKSISKMVARHARGIKIPCKL--NREISKIQKARKALTNSHGKYPEDIEIAKYTGLSL--AEIRSASECLRIVGSI 428 (442)
Q Consensus 356 IRnaI~r~LRkqsr~irlP~~v--~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~--etVk~~l~~ar~~~SL 428 (442)
+...+..|+..+.....+|.+. .....+|-++..+++ .|...|+.|||+.+|-+. ..|-.++. ++|+.+
T Consensus 48 ~~~~l~~Yf~G~~~~f~lpl~~~gt~fq~~Vw~~l~~Ip--~G~t~tY~~lA~~~g~p~a~RAVg~A~~--~NP~~i 120 (155)
T PRK00901 48 ANKQLEEYFEGKRKKFDLPLAPQGTEFQKKVWKALQEIP--YGETRSYKEIAVNIGNPKACRAVGLANN--KNPIPI 120 (155)
T ss_pred HHHHHHHHHcCCCcCCceeecCCCChHHHHHHHHHccCC--CCCcCCHHHHHHHHCCCchHHHHHHHHH--hCCCCC
Confidence 3455566666554444455543 244556666665554 588899999999999865 55555554 344443
No 394
>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=20.47 E-value=1.1e+02 Score=28.98 Aligned_cols=23 Identities=17% Similarity=0.242 Sum_probs=20.3
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHH
Q 013472 396 GKYPEDIEIAKYTGLSLAEIRSA 418 (442)
Q Consensus 396 gr~PS~eEIAe~LGIS~etVk~~ 418 (442)
.-+.|.+|||+..|++++.|+..
T Consensus 67 RaGas~eeVA~~~G~~~~rV~rf 89 (170)
T PF11268_consen 67 RAGASAEEVAEEAGVPVERVRRF 89 (170)
T ss_pred HCCCCHHHHHHHhCCCHHHhhhc
Confidence 44789999999999999999864
No 395
>PRK15340 transcriptional regulator InvF; Provisional
Probab=20.29 E-value=5.3e+02 Score=25.32 Aligned_cols=66 Identities=12% Similarity=0.055 Sum_probs=38.3
Q ss_pred HHHHHHHHHHHHHHhhcCceecccccHHHHHHHHHH------HHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHH
Q 013472 352 VQYWIRKSISKMVARHARGIKIPCKLNREISKIQKA------RKALTNSHGKYPEDIEIAKYTGLSLAEIRSASE 420 (442)
Q Consensus 352 a~~wIRnaI~r~LRkqsr~irlP~~v~e~i~kI~ka------~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~ 420 (442)
+.|--+.++-.++... +.-|....+.+..+-+. ...|........+.++||+.+|+|+..+....+
T Consensus 76 ~~~~~~~~~e~~l~~~---~~~~d~~~~~~~~~~r~~e~y~l~~~Ll~~~~~~~sleeLA~~~gvS~r~f~RlFk 147 (216)
T PRK15340 76 AIWQDRKRCEYWFLQQ---IITPSPAFNKVLALLRKSESYWLVGYLLAQSTSGNTMRMLGEDYGVSYTHFRRLCS 147 (216)
T ss_pred hhhhhHHHHHHHHHhc---cCCCChhHHHHHHHHHHHHHHHHHHHHHhCccCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3444555555555432 12233333333332222 234445556778999999999999999887744
No 396
>PRK10130 transcriptional regulator EutR; Provisional
Probab=20.27 E-value=2.1e+02 Score=29.84 Aligned_cols=38 Identities=11% Similarity=0.141 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHH
Q 013472 383 KIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASE 420 (442)
Q Consensus 383 kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~ 420 (442)
.|+++..-+.+......|.++||+.+|||..++....+
T Consensus 241 ~v~~~~~~i~~~~~~~ltv~~lA~~~gvS~r~L~r~Fk 278 (350)
T PRK10130 241 LLSRAREYVLENMSEPVTVLDLCNQLHVSRRTLQNAFH 278 (350)
T ss_pred HHHHHHHHHHhhhcCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 35555555555667778999999999999999987654
No 397
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=20.13 E-value=1.1e+02 Score=22.45 Aligned_cols=26 Identities=31% Similarity=0.442 Sum_probs=20.0
Q ss_pred CCCC---cHHHHHHHhCCCHHHHHHHHHh
Q 013472 396 GKYP---EDIEIAKYTGLSLAEIRSASEC 421 (442)
Q Consensus 396 gr~P---S~eEIAe~LGIS~etVk~~l~~ 421 (442)
...| ..++||..|||+...|......
T Consensus 22 ~~~p~~~~~~~la~~l~l~~~~V~~WF~n 50 (57)
T PF00046_consen 22 NPYPSKEEREELAKELGLTERQVKNWFQN 50 (57)
T ss_dssp SSSCHHHHHHHHHHHHTSSHHHHHHHHHH
T ss_pred hccccccccccccccccccccccccCHHH
Confidence 4455 4467999999999999887543
No 398
>PRK03837 transcriptional regulator NanR; Provisional
Probab=20.09 E-value=1.1e+02 Score=29.23 Aligned_cols=27 Identities=22% Similarity=0.518 Sum_probs=23.2
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472 397 KYPEDIEIAKYTGLSLAEIRSASECLR 423 (442)
Q Consensus 397 r~PS~eEIAe~LGIS~etVk~~l~~ar 423 (442)
+-|+..+||+.+|+|...|+.++....
T Consensus 36 ~Lp~E~~Lae~~gVSRt~VREAL~~L~ 62 (241)
T PRK03837 36 QLPSERELMAFFGVGRPAVREALQALK 62 (241)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 456999999999999999999987543
No 399
>TIGR02366 DHAK_reg probable dihydroxyacetone kinase regulator. The seed alignment for this family was built from a set of closely related uncharacterized proteins associated with operons for the type of bacterial dihydroxyacetone kinase that transfers PEP-derived phosphate from a phosphoprotein, as in phosphotransferase system transport, rather than from ATP. Members have a TetR transcriptional regulator domain (pfam00440) at the N-terminus and sequence homology throughout.
Probab=20.05 E-value=2.2e+02 Score=25.40 Aligned_cols=37 Identities=19% Similarity=0.094 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHHHHcC-CCCcHHHHHHHhCCCHHHHHH
Q 013472 381 ISKIQKARKALTNSHG-KYPEDIEIAKYTGLSLAEIRS 417 (442)
Q Consensus 381 i~kI~ka~~~L~~elg-r~PS~eEIAe~LGIS~etVk~ 417 (442)
..+|.++..+|..+.| ...|..|||+..||+.++.-.
T Consensus 5 k~~I~~a~~~Ll~~k~~~~ITV~~I~~~AgvsR~TFY~ 42 (176)
T TIGR02366 5 KKKIAKAFKDLMEVQAFSKISVSDIMSTAQIRRQTFYN 42 (176)
T ss_pred HHHHHHHHHHHHHHCCCccCCHHHHHHHhCCCHHHHHH
Confidence 4567777777777766 668999999999999988753
Done!